TY - JOUR A1 - Roy, Sutapa A1 - Höfling, Felix T1 - Critical surface adsorption of confined binary liquids with locally conserved mass and composition JF - Molecular Physics N2 - Close to a solid surface, the properties of a fluid deviate significantly from their bulk values. In this context, we study the surface adsorption profiles of a symmetric binary liquid confined to a slit pore by means of molecular dynamics simulations; the latter naturally entails that mass and concentration are locally conserved. Near a bulk consolute point, where the liquid exhibits a demixing transition with the local concentration as the order parameter, we determine the order parameter profiles and characterise the relevant critical scaling behaviour, in the regime of strong surface attraction, for a range of pore widths and temperatures. The obtained order parameter profiles decay monotonically near the surfaces, also in the presence of a pronounced layering in the number density. Overall, our results agree qualitatively with recent theoretical predictions from a mesoscopic field-theoretical approach for the canonical ensemble. Y1 - 2024 U6 - https://doi.org/10.1080/00268976.2024.2391998 SP - e2391998 ER - TY - JOUR A1 - Fischbach, Jan David A1 - Betz, Fridtjof A1 - Asadova, Nigar A1 - Tassan, Pietro A1 - Urbonas, Darius A1 - Stöferle, Thilo A1 - Mahrt, Rainer F. A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Binkowski, Felix A1 - Sturges, Thomas Jebb T1 - A framework to compute resonances arising from multiple scattering JF - arXiv Y1 - 2024 U6 - https://doi.org/10.48550/arXiv.2409.05563 SP - arXiv:2409.05563 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Achterberg, Tobias T1 - Efficient separation of RLT cuts for implicit and explicit bilinear terms JF - Mathematical Programming Y1 - 2024 U6 - https://doi.org/10.1007/s10107-024-02104-0 ER - TY - JOUR A1 - Stengl, Steven-Marian A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Pokutta, Sebastian T1 - Existence and uniqueness of solutions of the Koopman--von Neumann equation on bounded domains JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2024 U6 - https://doi.org/10.1088/1751-8121/ad6f7d VL - 57 IS - 39 ER - TY - JOUR A1 - Eifler, Leon A1 - Nicolas-Thouvenin, Jules A1 - Gleixner, Ambros T1 - Combining precision boosting with LP iterative refinement for exact linear optimization JF - INFORMS Journal on Computing Y1 - 2024 U6 - https://doi.org/10.1287/ijoc.2023.0409 ER - TY - JOUR A1 - Böttcher, Julia A1 - Parczyk, Olaf A1 - Sgueglia, Amedeo A1 - Skokan, Jozef T1 - The square of a Hamilton cycle in randomly perturbed graphs JF - Random Structures & Algorithms Y1 - 2024 U6 - https://doi.org/10.1002/rsa.21215 VL - 65 IS - 2 SP - 342 EP - 386 ER - TY - JOUR A1 - Deza, Antoine A1 - Onn, Shmuel A1 - Pokutta, Sebastian A1 - Pournin, Lionel T1 - Kissing polytopes JF - SIAM Journal on Discrete Mathematics Y1 - 2024 ER - TY - GEN A1 - Kiessling, David A1 - Leyffer, Sven A1 - Vanaret, Charlie T1 - A Unified Funnel Restoration SQP Algorithm N2 - We consider nonlinearly constrained optimization problems and discuss a generic double-loop framework consisting of four algorithmic ingredients that unifies a broad range of nonlinear optimization solvers. This framework has been implemented in the open-source solver Uno, a Swiss-army knife-like C++ optimization framework that unifies many nonlinearly constrained nonconvex optimization solvers. We illustrate the framework with a sequential quadratic programming (SQP) algorithm that maintain an acceptable upper bound on the constraint violation , called a funnel, that is monotonically decreased to control the feasibility of the iterates. Infeasible quadratic subproblems are handled by a feasibility restoration strategy. Globalization is controlled by a line search or a trust-region method. We prove global convergence of the trust-region funnel SQP method, building upon known results from filter methods. We implement the algorithm in Uno, and we provide extensive test results for the trust-region line-search funnel SQP on small CUTEst instances. Y1 - 2024 ER - TY - CHAP A1 - Siqueira Rodrigues, Lucas A1 - Kosch, Thomas A1 - Nyakatura, John A1 - Zachow, Stefan A1 - Israel, Johann Habakuk T1 - MorphoHaptics: An Open-Source Tool for Visuohaptic Exploration of Morphological Image Datasets T2 - Proceedings of the 21st International Conference on Culture and Computer Science N2 - Although digital methods have significantly advanced morphology, practitioners are still challenged to understand and process tomographic data of specimens. As automated processing of fossil data is still insufficient, morphologists still engage in intensive manual work to digitally prepare fossils for research objectives. We present an open-source tool that enables morphologists to explore tomographic data similarly to the physical workflows that traditional fossil preparators experience in the field. Using questionnaires, we assessed the usability of our prototype for virtual fossil preparation and related common tasks in the digital preparation workflow. Our findings indicate that integrating haptics into the virtual preparation workflow enhances the understanding of the morphology and material properties of working specimens and that the visuohaptic sculpting of fossil volumes is straightforward and is an improvement over current digital specimen processing methods. Y1 - 2024 ER - TY - JOUR A1 - Zimper, Sebastian A1 - Cornalba, Federico A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana T1 - On reduced inertial PDE models for Cucker-Smale flocking dynamics JF - arxiv N2 - In particle systems, flocking refers to the phenomenon where particles’ individual velocities eventually align. The Cucker-Smale model is a well-known mathematical framework that describes this behaviour. Many continuous descriptions of the Cucker-Smale model use PDEs with both particle position and velocity as independent variables, thus providing a full description of the particles mean-field limit (MFL) dynamics. In this paper, we introduce a novel reduced inertial PDE model consisting of two equations that depend solely on particle position. In contrast to other reduced models, ours is not derived from the MFL, but directly includes the model reduction at the level of the empirical densities, thus allowing for a straightforward connection to the underlying particle dynamics. We present a thorough analytical investigation of our reduced model, showing that: firstly, our reduced PDE satisfies a natural and interpretable continuous definition of flocking; secondly, in specific cases, we can fully quantify the discrepancy between PDE solution and particle system. Our theoretical results are supported by numerical simulations. Y1 - 2024 ER - TY - JOUR A1 - Gossing, Anne A1 - Beckert, Andreas A1 - Fischer, Christoph A1 - Klenert, Nicolas A1 - Natarajan, Vijay A1 - Pacey, George A1 - Vogt, Thorwin A1 - Rautenhaus, Marc A1 - Baum, Daniel T1 - A Ridge-based Approach for Extraction and Visualization of 3D Atmospheric Fronts JF - 2024 IEEE Visualization and Visual Analytics (VIS) N2 - An atmospheric front is an imaginary surface that separates two distinct air masses and is commonly defined as the warm-air side of a frontal zone with high gradients of atmospheric temperature and humidity. These fronts are a widely used conceptual model in meteorology, which are often encountered in the literature as two-dimensional (2D) front lines on surface analysis charts. This paper presents a method for computing three-dimensional (3D) atmospheric fronts as surfaces that is capable of extracting continuous and well-confined features suitable for 3D visual analysis, spatio-temporal tracking, and statistical analyses. Recently developed contour-based methods for 3D front extraction rely on computing the third derivative of a moist potential temperature field. Additionally, they require the field to be smoothed to obtain continuous large-scale structures. This paper demonstrates the feasibility of an alternative method to front extraction using ridge surface computation. The proposed method requires only the sec- ond derivative of the input field and produces accurate structures even from unsmoothed data. An application of the ridge-based method to a data set corresponding to Cyclone Friederike demonstrates its benefits and utility towards visual analysis of the full 3D structure of fronts. Y1 - 2024 ER - TY - GEN A1 - Sikorski, Alexander T1 - ISOKANN.jl N2 - Julia pacarkge implementing the ISOKANN algorithm for the computation of invariant subspaces of Koopman operators Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.11519359 ER - TY - JOUR A1 - Weimann, Kuba A1 - Conrad, Tim T1 - FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems JF - International Journal of Data Science and Analytics Y1 - 2024 ER - TY - JOUR A1 - Binkowski, Felix A1 - Burger, Sven A1 - Kewes, Günter T1 - A tiny Drude scatterer can accurately model a coherent emitter in nanophotonics JF - Nanophotonics Y1 - 2024 U6 - https://doi.org/10.1515/nanoph-2024-0170 ER - TY - JOUR A1 - Roche, Léo J. A1 - Betz, Fridtjof A1 - Yang, Yuhui A1 - Limame, Imad A1 - Shih, Ching-Wen A1 - Burger, Sven A1 - Reitzenstein, Stephan T1 - Numerical Investigation of a Coupled Micropillar - Waveguide System for Integrated Quantum Photonic Circuits JF - Adv Quantum Technol. Y1 - 2024 U6 - https://doi.org/10.1002/qute.202400195 SP - 2400195 ER - TY - JOUR A1 - Asadova, Nigar A1 - Achouri, Karim A1 - Arjas, Kristian A1 - Ajuguié, Baptiste A1 - Aydin, Roland A1 - Baron, Alexandre A1 - Beutel, Dominik A1 - Bodermann, Bernd A1 - Boussaoud, Kaoutar A1 - Burger, Sven A1 - Choi, Minseok A1 - Czajkowski, Krzysztof A1 - Evlyukhin, Andrey B. A1 - Fazel-Najafabadi, Atefeh A1 - Fernandez-Corbaton, Ivan A1 - Garg, Puneet A1 - Globosits, David A1 - Hohenester, Ulrich A1 - Kim, Hongyoon A1 - Kim, Seokwoo A1 - Lalanne, Philippe A1 - Le Ru, Eric C. A1 - Meyer, Jörg A1 - Mun, Jungho A1 - Patelli, Lorenzo A1 - Pflug, Lukas A1 - Rockstuhl, Carsten A1 - Rho, Junsuk A1 - Rotter, Stefan A1 - Stout, Brian A1 - Törmä, Päivi A1 - Trigo, Jorge Olmos A1 - Tristram, Frank A1 - Tsitsas, Nikolaos L. A1 - Vallée, Renaud A1 - Vynck, Kevin A1 - Weiss, Thomas A1 - Wiecha, Peter A1 - Wriedt, Thomas A1 - Yannopapas, Vassilios A1 - Yurkin, Maxim A. A1 - Zouros, Grigorios P. T1 - T-matrix representation of optical scattering response: Suggestion for a data format JF - arXiv Y1 - 2024 U6 - https://doi.org/10.48550/arXiv.2408.10727 SP - 2408.10727 ER - TY - JOUR A1 - Kameda, Takeru A1 - Saha, Daniel K. A1 - Ray, Sourav A1 - Togashi, Yuichi A1 - Asano, Katsura T1 - Protocol for calculating binding free energy of RNA:RNA interactions through molecular dynamics simulations using adaptive biasing force technique JF - STAR Protocols Y1 - 2024 U6 - https://doi.org/10.1016/j.xpro.2024.103223 VL - 5 IS - 3 PB - Elsevier BV ER - TY - CHAP A1 - Winkler, Ludwig A1 - Richter, Lorenz A1 - Opper, Manfred T1 - Bridging discrete and continuous state spaces: Exploring the Ehrenfest process in time-continuous diffusion models T2 - Proceedings of the 41st International Conference on Machine Learning N2 - Generative modeling via stochastic processes has led to remarkable empirical results as well as to recent advances in their theoretical understanding. In principle, both space and time of the processes can be discrete or continuous. In this work, we study time-continuous Markov jump processes on discrete state spaces and investigate their correspondence to state-continuous diffusion processes given by SDEs. In particular, we revisit the Ehrenfest process, which converges to an Ornstein-Uhlenbeck process in the infinite state space limit. Likewise, we can show that the time-reversal of the Ehrenfest process converges to the time-reversed Ornstein-Uhlenbeck process. This observation bridges discrete and continuous state spaces and allows to carry over methods from one to the respective other setting. Additionally, we suggest an algorithm for training the time-reversal of Markov jump processes which relies on conditional expectations and can thus be directly related to denoising score matching. We demonstrate our methods in multiple convincing numerical experiments. Y1 - 2024 UR - https://raw.githubusercontent.com/mlresearch/v235/main/assets/winkler24a/winkler24a.pdf VL - 235 SP - 53017 EP - 53038 ER - TY - JOUR A1 - Sun, Jingtong A1 - Berner, Julius A1 - Richter, Lorenz A1 - Zeinhofer, Marius A1 - Müller, Johannes A1 - Azizzadenesheli, Kamyar A1 - Anandkumar, Anima T1 - Dynamical Measure Transport and Neural PDE Solvers for Sampling JF - arxiv N2 - The task of sampling from a probability density can be approached as transporting a tractable density function to the target, known as dynamical measure transport. In this work, we tackle it through a principled unified framework using deterministic or stochastic evolutions described by partial differential equations (PDEs). This framework incorporates prior trajectory-based sampling methods, such as diffusion models or Schrödinger bridges, without relying on the concept of time-reversals. Moreover, it allows us to propose novel numerical methods for solving the transport task and thus sampling from complicated targets without the need for the normalization constant or data samples. We employ physics-informed neural networks (PINNs) to approximate the respective PDE solutions, implying both conceptional and computational advantages. In particular, PINNs allow for simulation- and discretization-free optimization and can be trained very efficiently, leading to significantly better mode coverage in the sampling task compared to alternative methods. Moreover, they can readily be fine-tuned with Gauss-Newton methods to achieve high accuracy in sampling. Y1 - 2024 SP - arXiv:2407.07873 ER - TY - CHAP A1 - Vaitl, Lorenz A1 - Winkler, Ludwig A1 - Richter, Lorenz A1 - Kessel, Pan T1 - Fast and unified path gradient estimators for normalizing flows T2 - International Conference on Learning Representations 2024 N2 - Recent work shows that path gradient estimators for normalizing flows have lower variance compared to standard estimators for variational inference, resulting in improved training. However, they are often prohibitively more expensive from a computational point of view and cannot be applied to maximum likelihood train- ing in a scalable manner, which severely hinders their widespread adoption. In this work, we overcome these crucial limitations. Specifically, we propose a fast path gradient estimator which improves computational efficiency significantly and works for all normalizing flow architectures of practical relevance. We then show that this estimator can also be applied to maximum likelihood training for which it has a regularizing effect as it can take the form of a given target energy func- tion into account. We empirically establish its superior performance and reduced variance for several natural sciences applications. Y1 - 2024 UR - https://openreview.net/pdf?id=zlkXLb3wpF ER - TY - JOUR A1 - Richter, Lorenz A1 - Sallandt, Leon A1 - Nüsken, Nikolas T1 - From continuous-time formulations to discretization schemes: tensor trains and robust regression for BSDEs and parabolic PDEs JF - Journal of Machine Learning Research N2 - The numerical approximation of partial differential equations (PDEs) poses formidable challenges in high dimensions since classical grid-based methods suffer from the so-called curse of dimensionality. Recent attempts rely on a combination of Monte Carlo methods and variational formulations, using neural networks for function approximation. Extending previous work (Richter et al., 2021), we argue that tensor trains provide an appealing framework for parabolic PDEs: The combination of reformulations in terms of backward stochastic differential equations and regression-type methods holds the romise of leveraging latent low-rank structures, enabling both compression and efficient computation. Emphasizing a continuous-time viewpoint, we develop iterative schemes, which differ in terms of computational efficiency and robustness. We demonstrate both theoretically and numerically that our methods can achieve a favorable trade-off between accuracy and computational efficiency. While previous methods have been either accurate or fast, we have identified a novel numerical strategy that can often combine both of these aspects. Y1 - 2024 ER - TY - JOUR A1 - Schmitt, Kira A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - CoDA: Interactive Segmentation and Morphological Analysis of Dendroid Structures Exemplified on Stony Cold-Water Corals N2 - Dendroid stony corals build highly complex colonies that develop from a single coral polyp sitting in a cup-like skeleton, called corallite, by asexual reproduction, resulting in a tree-like branching pattern of its skeleton. Despite their beauty and ecological importance as reef builders in tropical shallow-water reefs as well as in cold-water coral mounds in the deep ocean, systematic studies investigating the ontogenetic morphological development of such coral colonies are largely missing. One reason for this is the sheer number of corallites – up to several thousands in a single coral colony. Another limiting factor, especially for the analysis of dendroid cold-water corals, is the existence of many secondary joints in the ideally tree-like structure that make a reconstruction of the skeleton tree extremely tedious. Herein, we present CoDA, the Coral Dendroid structure Analyzer, a visual analytics suite that allows for the first time to investigate the ontogenetic morphological development of complex dendroid coral colonies, exemplified on three important framework-forming dendroid cold-water corals: Lophelia pertusa (Linnaeus, 1758), Madrepora oculata (Linnaeus, 1758), and Goniocorella dumosa (Alcock, 1902). Input to CoDA is an initial instance segmentation of the coral polyp cavities (calices), from which it estimates the skeleton tree of the colony and extracts classical morphological measurements and advanced shape features of the individual corallites. CoDA also works as a proofreading and error correction tool by helping to identify wrong parts in the skeleton tree and providing tools to quickly correct these errors. The final skeleton tree enables the derivation of additional information about the calices/corallite instances that otherwise could not be obtained, including their ontogenetic generation and branching patterns – the basis of a fully quantitative statistical analysis of the coral colony morphology. Part of CoDA is CoDA.Graph, a feature-rich link-and-brush user interface for visualizing the extracted features and 2D graph layouts of the skeleton tree, enabling the real-time exploration of complex coral colonies and their building blocks, the individual corallites and branches. In the future, we expect CoDA to greatly facilitate the analysis of large stony corals of different species and morphotypes, as well as other dendroid structures, enabling new insights into the influence of genetic and environmental factors on their ontogenetic morphological development. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.48550/arXiv.2406.18236 ER - TY - GEN A1 - Villani, Paolo A1 - Weiser, Martin T1 - Adaptive Gaussian process regression for inverse problems. ALGORITMY 2024 N2 - This submission contains the code used for the proceedings paper for ALGORITMY 2024, concerning surrogate model-based inverse problems. Version 2 modified plot appearances and fixed some minor typos. Y1 - 2024 ER - TY - THES A1 - Danecker, Fabian T1 - A Discrete-Continuous Algorithm for Globally Optimal Free Flight Trajectory Optimization N2 - This thesis introduces the novel hybrid algorithm DisCOptER for globally optimal flight planning. DisCOptER (Discrete-Continuous Optimization for Enhanced Resolution) com- bines discrete and continuous optimization in a two-stage approach to find optimal trajectories up to arbitrary precision in finite time. In the discrete phase, a directed auxiliary graph is created in order to define a set of candidate paths that densely covers the relevant part of the trajectory space. Then, Yen’s algorithm is employed to identify a set of promising candidate paths. These are used as starting points for the subsequent stage in which they are refined with a locally convergent optimal control method. The correctness, accuracy, and complexity of DisCOptER are intricately linked to the choice of the switch-over point, defined by the discretization coarseness. Only a sufficiently dense graph enables the algorithm to find a path within the convex domain surrounding the global minimizer. Initialized with such a path, the second stage rapidly converges to the optimum. Conversely, an excessively dense graph poses the risk of overly costly and redundant computations. The determination of the optimal switch-over point necessitates a profound understanding of the local behavior of the problem, the approximation properties of the graph, and the convergence characteristics of the employed optimal control method. These topics are explored extensively in this thesis. Crucially, the density of the auxiliary graph is solely dependent on the en- vironmental conditions, yet independent of the desired solution accuracy. As a consequence, the algorithm inherits the superior asymptotic convergence properties of the optimal control stage. The practical implications of this computational efficiency are demonstrated in realistic environments, where the DisCOptER algorithm consistently delivers highly accurate globally optimal trajectories with exceptional computational efficiency. This notable improvement upon existing approaches underscores the algorithm’s significance. Beyond its technical prowess, the DisCOptER algorithm stands as a valuable tool contributing to the reduction of costs and the overall enhancement of flight operations efficiency. Y1 - 2023 UR - http://dx.doi.org/10.17169/refubium-43526 ER - TY - JOUR A1 - Mako, Sato A1 - Shimada, Naoki A1 - Yaegashi, Yuta A1 - Koch, Thorsten A1 - Le, Thi Thai T1 - Estimation of Volume-of-Fluid Method with Level Set Function under Stable and Unstable Interface Conditions JF - Journal of Chemical Engineering of Japan N2 - It is necessary to consider the nonlinear effects such as inertia force, gravity, viscosity, and surface tension on interface stability to understand the instability mechanism of an interface between two fluid layers comprehensively. Our study thus focuses on the viscosity’s impact on the interface stability of viscosity fluids by comparing the linear stability theory to the modified S-CLSVOF method. Our results show that when the relative velocity (U) between the two fluid layers is below a particular critical value determined by the Kelvin-Helmholtz instability (KHI) theory, the waves at the interface do not exhibit divergence, i.e., the shape of waves remain stable and undistorted. Conversely, when U significantly exceeds the critical value established by the KHI theory, the waves become highly distorted and unstable. In addition, U has non-linear advection effects in the momentum equation and could distort the waves. Y1 - 2024 ER - TY - JOUR A1 - Boniface, Dolachai A1 - Straube, Arthur A1 - Tierno, Pietro T1 - Photocatalytic magnetic microgyroscopes with activity-tunable precessional dynamics N2 - Magnetic nano/microrotors are passive elements that spin around an axis due to an external rotating field while remaining confined to a close plane. They have been used to date in different applications related to fluid mixing, drug delivery or biomedicine. Here we realize an active version of a magnetic microgyroscope which is simultaneously driven by a photo-activated catalytic reaction and a rotating magnetic field. We investigate the uplift dynamics of this colloidal spinner when it stands up and precesses around its long axis while self-propelling due to the light induced decomposition of hydrogen peroxide in water. By combining experiments with theory, we show that activity emerging from the cooperative action of phoretic and osmotic forces effectively increase the gravitational torque which counteracts the magnetic and viscous ones, and carefully measure its contribution. Y1 - 2024 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Memory effects in colloidal motion under confinement and driving JF - J. Phys. A: Math. Theor. N2 - The transport of individual particles in inhomogeneous environments is complex and exhibits non-Markovian responses. The latter may be quantified by a memory function within the framework of the linear generalised Langevin equation (GLE). Here, we exemplify the implications of steady driving on the memory function of a colloidal model system for Brownian motion in a corrugated potential landscape, specifically, for one-dimensional motion in a sinusoidal potential. To this end, we consider the overdamped limit of the GLE, which is facilitated by separating the memory function into a singular (Markovian) and a regular (non-Markovian) part. Relying on exact solutions for the investigated model, we show that the random force entering the GLE must display a bias far from equilibrium, which corroborates a recent general prediction. Based on data for the mean-square displacement (MSD) obtained from Brownian dynamics simulations, we estimate the memory function for different driving strengths and show that already moderate driving accelerates the decay of the memory function by several orders of magnitude in time. We find that the memory may persist on much longer timescales than expected from the convergence of the MSD to its long-time asymptote. Furthermore, the functional form of the memory function changes from a monotonic decay to a non-monotonic, damped oscillatory behaviour, which can be understood from a competition of confined motion and depinning. Our analysis of the simulation data further reveals a pronounced non-Gaussianity, which questions the Gaussian approximation of the random force entering the GLE. Y1 - 2024 U6 - https://doi.org/10.1088/1751-8121/ad5b2d SN - 1751-8113 VL - 57 SP - 295003 PB - IOP Publishing ER - TY - JOUR A1 - Trower, Maia A1 - Djurdjevac Conrad, Natasa A1 - Klus, Stefan T1 - Clustering Time-Evolving Networks Using the Dynamic Graph Laplacian N2 - Time-evolving graphs arise frequently when modeling complex dynamical systems such as social networks, traffic flow, and biological processes. Developing techniques to identify and analyze communities in these time-varying graph structures is an important challenge. In this work, we generalize existing spectral clustering algorithms from static to dynamic graphs using canonical correlation analysis (CCA) to capture the temporal evolution of clusters. Based on this extended canonical correlation framework, we define the dynamic graph Laplacian and investigate its spectral properties. We connect these concepts to dynamical systems theory via transfer operators, and illustrate the advantages of our method on benchmark graphs by comparison with existing methods. We show that the dynamic graph Laplacian allows for a clear interpretation of cluster structure evolution over time for directed and undirected graphs. Y1 - 2024 ER - TY - JOUR A1 - Wehlitz, Nathalie A1 - Sadeghi, Mohsen A1 - Montefusco, Alberto A1 - Schütte, Christof A1 - Pavliotis, Grigorios A. A1 - Winkelmann, Stefanie T1 - Approximating particle-based clustering dynamics by stochastic PDEs N2 - This work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane mediated receptor dynamics on cell surfaces, we formulate a stochastic particle-based model for diffusion and pairwise interaction of particles, leading to intriguing clustering phenomena. Employing numerical simulation and cluster detection methods, we explore the approximation of the particle-based clustering dynamics through mean-field approaches. We find that SPDEs successfully reproduce spatiotemporal clustering dynamics, not only in the initial cluster formation period, but also on longer time scales where the successive merging of clusters cannot be tracked by deterministic mean-field models. The computational efficiency of the SPDE approach allows us to generate extensive statistical data for parameter estimation in a simpler model that uses a Markov jump process to capture the temporal evolution of the cluster number. Y1 - 2024 ER - TY - JOUR A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - Model bias identification for Bayesian calibration of stochastic digital twins of bridges N2 - Simulation-based digital twins must provide accurate, robust and reliable digital representations of their physical counterparts. Quantifying the uncertainty in their predictions plays, therefore, a key role in making better-informed decisions that impact the actual system. The update of the simulation model based on data must be then carefully implemented. When applied to complex standing structures such as bridges, discrepancies between the computational model and the real system appear as model bias, which hinders the trustworthiness of the digital twin and increases its uncertainty. Classical Bayesian updating approaches aiming to infer the model parameters often fail at compensating for such model bias, leading to overconfident and unreliable predictions. In this paper, two alternative model bias identification approaches are evaluated in the context of their applicability to digital twins of bridges. A modularized version of Kennedy and O'Hagan's approach and another one based on Orthogonal Gaussian Processes are compared with the classical Bayesian inference framework in a set of representative benchmarks. Additionally, two novel extensions are proposed for such models: the inclusion of noise-aware kernels and the introduction of additional variables not present in the computational model through the bias term. The integration of such approaches in the digital twin corrects the predictions, quantifies their uncertainty, estimates noise from unknown physical sources of error and provides further insight into the system by including additional pre-existing information without modifying the computational model. Y1 - 2023 ER - TY - JOUR A1 - Maier, Kristina A1 - Weiser, Martin A1 - Conrad, Tim T1 - Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology N2 - This paper introduces a novel hybrid mathematical modeling approach that effectively couples Partial Differential Equations (PDEs) with Ordinary Differential Equations (ODEs), exemplified through the simulation of epidemiological processes. The hybrid model aims to integrate the spatially detailed representation of disease dynamics provided by PDEs with the computational efficiency of ODEs. In the presented epidemiological use-case, this integration allows for the rapid assessment of public health interventions and the potential impact of infectious diseases across large populations. We discuss the theoretical formulation of the hybrid PDE-ODE model, including the governing equations and boundary conditions. The model's capabilities are demonstrated through detailed simulations of disease spread in synthetic environments and real-world scenarios, specifically focusing on the regions of Lombardy, Italy, and Berlin, Germany. Results indicate that the hybrid model achieves a balance between computational speed and accuracy, making it a valuable tool for policymakers in real-time decision-making and scenario analysis in epidemiology and potentially in other fields requiring similar modeling approaches. Y1 - 2024 ER - TY - CHAP A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - Evaluation of Model Bias Identification Approaches Based on Bayesian Inference and Applications to Digital Twins T2 - 5th ECCOMAS Thematic Conference on Uncertainty Quantification in Computational Sciences and Engineering N2 - In recent years, the use of simulation-based digital twins for monitoring and assessment of complex mechanical systems has greatly expanded. Their potential to increase the information obtained from limited data makes them an invaluable tool for a broad range of real-world applications. Nonetheless, there usually exists a discrepancy between the predicted response and the measurements of the system once built. One of the main contributors to this difference in addition to miscalibrated model parameters is the model error. Quantifying this socalled model bias (as well as proper values for the model parameters) is critical for the reliable performance of digital twins. Model bias identification is ultimately an inverse problem where information from measurements is used to update the original model. Bayesian formulations can tackle this task. Including the model bias as a parameter to be inferred enables the use of a Bayesian framework to obtain a probability distribution that represents the uncertainty between the measurements and the model. Simultaneously, this procedure can be combined with a classic parameter updating scheme to account for the trainable parameters in the original model. This study evaluates the effectiveness of different model bias identification approaches based on Bayesian inference methods. This includes more classical approaches such as direct parameter estimation using MCMC in a Bayesian setup, as well as more recent proposals such as stat-FEM or orthogonal Gaussian Processes. Their potential use in digital twins, generalization capabilities, and computational cost is extensively analyzed. Y1 - 2023 UR - https://2023.uncecomp.org/proceedings/pdf/19795.pdf SP - 1 EP - 15 ER - TY - JOUR A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Faidon-Stelios A1 - Unger, Jörg F. T1 - A Bayesian Framework for Simulation-based Digital Twins of Bridges JF - EUROSTRUCT 2023:European Association on Quality Control of Bridges and Structures: Digital Transformation in Sustainability N2 - Simulation-based digital twins have emerged as a powerful tool for evaluating the mechanical response of bridges. As virtual representations of physical systems, digital twins can provide a wealth of information that complements traditional inspection and monitoring data. By incorporating virtual sensors and predictive maintenance strategies, they have the potential to improve our understanding of the behavior and performance of bridges over time. However, as bridges age and undergo regular loading and extreme events, their structural characteristics change, often differing from the predictions of their initial design. Digital twins must be continuously adapted to reflect these changes. In this article, we present a Bayesian framework for updating simulation-based digital twins in the context of bridges. Our approach integrates information from measurements to account for inaccuracies in the simulation model and quantify uncertainties. Through its implementation and assessment, this work demonstrates the potential for digital twins to provide a reliable and up-to-date representation of bridge behavior, helping to inform decision-making for maintenance and management. Y1 - 2023 U6 - https://doi.org/10.1002/cepa.2177 VL - 6 IS - 5 SP - 734 EP - 740 ER - TY - CHAP A1 - Villani, Paolo A1 - Unger, Jörg F. A1 - Weiser, Martin T1 - Adaptive Gaussian Process Regression for Bayesian inverse problems T2 - ALGORITMY 2024 Proceedings N2 - We introduce a novel adaptive Gaussian Process Regression (GPR) methodology for efficient construction of surrogate models for Bayesian inverse problems with expensive forward model evaluations. An adaptive design strategy focuses on optimizing both the positioning and simulation accuracy of training data in order to reduce the computational cost of simulating training data without compromising the fidelity of the posterior distributions of parameters. The method interleaves a goal-oriented active learning algorithm selecting evaluation points and tolerances based on the expected impact on the Kullback-Leibler divergence of surrogated and true posterior with a Markov Chain Monte Carlo sampling of the posterior. The performance benefit of the adaptive approach is demonstrated for two simple test problems. Y1 - 2024 ER - TY - CHAP A1 - Ghannam, Mohammed A1 - Mexi, Gioni A1 - Lam, Edward A1 - Gleixner, Ambros T1 - Branch and price for the length-constrained cycle partition problem T2 - Proceedings of INFORMS Optimization Society Conference Y1 - 2024 ER - TY - JOUR A1 - Bolusani, Suresh A1 - Besançon, Mathieu A1 - Gleixner, Ambros A1 - Berthold, Timo A1 - D'Ambrosio, Claudia A1 - Muñoz, Gonzalo A1 - Paat, Joseph A1 - Thomopulos, Dimitri T1 - The MIP workshop 2023 computational competition on reoptimization JF - Mathematical Programming Computation N2 - This paper describes the computational challenge developed for a computational competition held in 2023 for the 20th anniversary of the Mixed Integer Programming Workshop. The topic of this competition was reoptimization, also known as warm starting, of mixed integer linear optimization problems after slight changes to the input data for a common formulation. The challenge was to accelerate the proof of optimality of the modified instances by leveraging the information from the solving processes of previously solved instances, all while creating high-quality primal solutions. Specifically, we discuss the competition’s format, the creation of public and hidden datasets, and the evaluation criteria. Our goal is to establish a methodology for the generation of benchmark instances and an evaluation framework, along with benchmark datasets, to foster future research on reoptimization of mixed integer linear optimization problems. Y1 - 2024 U6 - https://doi.org/10.1007/s12532-024-00256-w VL - 16 SP - 255 EP - 266 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Scalable Frank-Wolfe on generalized self-concordant functions via simple steps JF - SIAM Journal on Optimization Y1 - 2024 U6 - https://doi.org/10.1137/23M1616789 VL - 34 IS - 3 ER - TY - CHAP A1 - Eifler, Leon A1 - Witzig, Jakob A1 - Gleixner, Ambros T1 - Branch and cut for partitioning a graph into a cycle of clusters T2 - Combinatorial Optimization. ISCO 2024 N2 - In this paper we study formulations and algorithms for the cycle clustering problem, a partitioning problem over the vertex set of a directed graph with nonnegative arc weights that is used to identify cyclic behavior in simulation data generated from nonreversible Markov state models. Here, in addition to partitioning the vertices into a set of coherent clusters, the resulting clusters must be ordered into a cycle such as to maximize the total net flow in the forward direction of the cycle. We provide a problem-specific binary programming formulation and compare it to a formulation based on the reformulation-linearization technique (RLT). We present theoretical results on the polytope associated with our custom formulation and develop primal heuristics and separation routines for both formulations. In computational experiments on simulation data from biology we find that branch and cut based on the problem-specific formulation outperforms the one based on RLT. Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-60924-4_8 VL - 14594 ER - TY - JOUR A1 - Gupta, Pranshu A1 - Hamann, Fabian A1 - Müyesser, Alp A1 - Sgueglia, Amedeo A1 - Parczyk, Olaf T1 - A general approach to transversal versions of Dirac-type theorems JF - Bulletin of the London Mathematical Society Y1 - 2023 ER - TY - JOUR A1 - Barros, Gabriel F. A1 - Cavalar, Bruno P. A1 - Mota, Guilherme O. A1 - Parczyk, Olaf T1 - Anti-Ramsey threshold of cycles for sparse graphs JF - Discrete Applied Mathematics Y1 - 2022 ER - TY - JOUR A1 - Kohayakawa, Yoshiharu A1 - Mota, Guilherme O. A1 - Schnitzer, Jakob A1 - Parczyk, Olaf T1 - Anti-Ramsey threshold of complete graphs for sparse graphs JF - Discrete Mathematics Y1 - 2023 ER - TY - CHAP A1 - Pauls, Jan A1 - Zimmer, Max A1 - Kelly, Una M A1 - Schwartz, Martin A1 - Saatchi, Sassan A1 - Ciais, Philippe A1 - Pokutta, Sebastian A1 - Brandt, Martin A1 - Gieseke, Fabian T1 - Estimating canopy height at scale T2 - Proceedings of the 41st International Conference on Machine Learning N2 - We propose a framework for global-scale canopy height estimation based on satellite data. Our model leverages advanced data preprocessing techniques, resorts to a novel loss function designed to counter geolocation inaccuracies inherent in the ground-truth height measurements, and employs data from the Shuttle Radar Topography Mission to effectively filter out erroneous labels in mountainous regions, enhancing the reliability of our predictions in those areas. A comparison between predictions and ground-truth labels yields an MAE/RMSE of 2.43 / 4.73 (meters) overall and 4.45 / 6.72 (meters) for trees taller than five meters, which depicts a substantial improvement compared to existing global-scale products. The resulting height map as well as the underlying framework will facilitate and enhance ecological analyses at a global scale, including, but not limited to, large-scale forest and biomass monitoring. Y1 - 2024 UR - https://raw.githubusercontent.com/mlresearch/v235/main/assets/pauls24a/pauls24a.pdf VL - 235 SP - 39972 EP - 39988 ER - TY - CHAP A1 - Hendrych, Deborah A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Solving the optimal experiment design problem with mixed-integer convex methods T2 - 22nd International Symposium on Experimental Algorithms (SEA 2024) N2 - We tackle the Optimal Experiment Design Problem, which consists of choosing experiments to run or observations to select from a finite set to estimate the parameters of a system. The objective is to maximize some measure of information gained about the system from the observations, leading to a convex integer optimization problem. We leverage Boscia.jl, a recent algorithmic framework, which is based on a nonlinear branch-and-bound algorithm with node relaxations solved to approximate optimality using Frank-Wolfe algorithms. One particular advantage of the method is its efficient utilization of the polytope formed by the original constraints which is preserved by the method, unlike alternative methods relying on epigraph-based formulations. We assess our method against both generic and specialized convex mixed-integer approaches. Computational results highlight the performance of our proposed method, especially on large and challenging instances. Y1 - 2024 U6 - https://doi.org/10.4230/LIPIcs.SEA.2024.16 VL - 301 SP - 16:1 EP - 16:22 ER - TY - CHAP A1 - Kiem, Aldo A1 - Pokutta, Sebastian A1 - Spiegel, Christoph T1 - Categorification of Flag Algebras T2 - Proceedings of Discrete Mathematics Days Y1 - 2024 ER - TY - CHAP A1 - Kiem, Aldo A1 - Pokutta, Sebastian A1 - Spiegel, Christoph T1 - The 4-color Ramsey multiplicity of triangles T2 - Proceedings of Discrete Mathematics Days Y1 - 2024 ER - TY - JOUR A1 - Hahn-Klimroth, Max A1 - Person, Yury A1 - Parczyk, Olaf T1 - Minimum degree conditions for containing an r-regular r-connected subgraph JF - European Journal of Combinatorics Y1 - 2024 ER - TY - JOUR A1 - Mundinger, Konrad A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Extending the Continuum of Six-Colorings JF - Geombinatorics Quarterly Y1 - 2024 VL - 34 IS - 1 SP - 20 EP - 29 ER - TY - CHAP A1 - Mundinger, Konrad A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Extending the Continuum of Six-Colorings T2 - Proceedings of Discrete Mathematics Days Y1 - 2024 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Roux, Christophe A1 - Pokutta, Sebastian T1 - Convergence and Trade-Offs in Riemannian Gradient Descent and Riemannian Proximal Point T2 - Proceedings of the 41st International Conference on Machine Learning N2 - In this work, we analyze two of the most fundamental algorithms in geodesically convex optimization: Riemannian gradient descent and (possibly inexact) Riemannian proximal point. We quantify their rates of convergence and produce different variants with several trade-offs. Crucially, we show the iterates naturally stay in a ball around an optimizer, of radius depending on the initial distance and, in some cases, on the curvature. Previous works simply assumed bounded iterates, resulting in rates that were not fully quantified. We also provide an implementable inexact proximal point algorithm and prove several new useful properties of Riemannian proximal methods: they work when positive curvature is present, the proximal operator does not move points away from any optimizer, and we quantify the smoothness of its induced Moreau envelope. Further, we explore beyond our theory with empirical tests. Y1 - 2024 UR - https://raw.githubusercontent.com/mlresearch/v235/main/assets/marti-nez-rubio24a/marti-nez-rubio24a.pdf VL - 235 SP - 34920 EP - 34948 ER - TY - JOUR A1 - Gebhard, Oliver A1 - Hahn-Klimroth, Max A1 - Penschuck, Manuel A1 - Rolvien, Maurice A1 - Scarlett, Jonathan A1 - Tan, Nelvin A1 - Parczyk, Olaf T1 - Near optimal sparsity-constrained group testing: improved bounds JF - IEEE Transactions on Information Theory Y1 - 2022 ER - TY - JOUR A1 - Parczyk, Olaf A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Szabó, Tibor T1 - New Ramsey multiplicity bounds and search heuristics JF - Foundations of Computational Mathematics Y1 - 2024 ER - TY - JOUR A1 - Allen, Peter A1 - Pfenninger, Vincent A1 - Parczyk, Olaf T1 - Resilience for tight Hamiltonicity JF - Combinatorial Theory Y1 - 2024 U6 - https://doi.org/10.5070/C64163846 VL - 4 IS - 1 ER - TY - JOUR A1 - Böttcher, Julia A1 - Sgueglia, Amedeo A1 - Skokan, Jozef A1 - Parczyk, Olaf T1 - Triangles in randomly perturbed graphs JF - Combinatorics, Probability and Computing Y1 - 2022 ER - TY - JOUR A1 - Vu-Han, Tu-Lan A1 - Schettino, Rodrigo Bermudez A1 - Weiß, Claudia A1 - Perka, Carsten A1 - Winkler, Tobias A1 - Sunkara, Vikram A1 - Pumberger, Matthias T1 - An interpretable data-driven prediction model to anticipate scoliosis in spinal muscular atrophy in the era of (gene-) therapies JF - Scientific Reports N2 - 5q-spinal muscular atrophy (SMA) is a neuromuscular disorder (NMD) that has become one of the first 5% treatable rare diseases. The efficacy of new SMA therapies is creating a dynamic SMA patient landscape, where disease progression and scoliosis development play a central role, however, remain difficult to anticipate. New approaches to anticipate disease progression and associated sequelae will be needed to continuously provide these patients the best standard of care. Here we developed an interpretable machine learning (ML) model that can function as an assistive tool in the anticipation of SMA-associated scoliosis based on disease progression markers. We collected longitudinal data from 86 genetically confirmed SMA patients. We selected six features routinely assessed over time to train a random forest classifier. The model achieved a mean accuracy of 0.77 (SD 0.2) and an average ROC AUC of 0.85 (SD 0.17). For class 1 ‘scoliosis’ the average precision was 0.84 (SD 0.11), recall 0.89 (SD 0.22), F1-score of 0.85 (SD 0.17), respectively. Our trained model could predict scoliosis using selected disease progression markers and was consistent with the radiological measurements. During post validation, the model could predict scoliosis in patients who were unseen during training. We also demonstrate that rare disease data sets can be wrangled to build predictive ML models. Interpretable ML models can function as assistive tools in a changing disease landscape and have the potential to democratize expertise that is otherwise clustered at specialized centers. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s41598-024-62720-w VL - 14 IS - 11838 ER - TY - GEN A1 - Hajarolasvadi, Noushin A1 - Baum, Daniel T1 - Data for Training the DeepOrientation Model: Simulated cryo-ET tomogram patches N2 - A major restriction to applying deep learning methods in cryo-electron tomography is the lack of annotated data. Many large learning-based models cannot be applied to these images due to the lack of adequate experimental ground truth. One appealing alternative solution to the time-consuming and expensive experimental data acquisition and annotation is the generation of simulated cryo-ET images. In this context, we exploit a public cryo-ET simulator called PolNet to generate three datasets of two macromolecular structures, namely the ribosomal complex 4v4r and Thermoplasma acidophilum 20S proteasome, 3j9i. We select these two specific particles to test whether our models work for macromolecular structures with and without rotational symmetry. The three datasets contain 50, 150, and 450 tomograms with a voxel size of 10 ̊A, respectively. Here, we publish patches of size 40 × 40 × 40 extracted from the medium-sized dataset with 26,703 samples of 4v4r and 40,671 samples of 3j9i. The original tomograms from which the samples were extracted are of size 500 × 500 × 250. Finally, it should be noted that the currently published test dataset is employed for reporting the results of our paper titled ”DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography” paper. Y1 - 2024 U6 - https://doi.org/10.12752/9686 ER - TY - JOUR A1 - Siqueira Rodrigues, Lucas A1 - Schmidt, Timo Torsten A1 - Israel, Johann Habakuk A1 - Nyakatura, John A1 - Zachow, Stefan A1 - Kosch, Thomas T1 - Comparing the Effects of Visual, Haptic, and Visuohaptic Encoding on Memory Retention of Digital Objects in Virtual Reality N2 - Although Virtual Reality (VR) has undoubtedly improved human interaction with 3D data, users still face difficulties retaining important details of complex digital objects in preparation for physical tasks. To address this issue, we evaluated the potential of visuohaptic integration to improve the memorability of virtual objects in immersive visualizations. In a user study (N=20), participants performed a delayed match-to-sample task where they memorized stimuli of visual, haptic, or visuohaptic encoding conditions. We assessed performance differences between the conditions through error rates and response time. We found that visuohaptic encoding significantly improved memorization accuracy compared to unimodal visual and haptic conditions. Our analysis indicates that integrating haptics into immersive visualizations enhances the memorability of digital objects. We discuss its implications for the optimal encoding design in VR applications that assist professionals who need to memorize and recall virtual objects in their daily work. Y1 - 2024 ER - TY - JOUR A1 - Veldhuijzen, Ben A1 - Veltkamp, Remco C. A1 - Ikne, Omar A1 - Allaert, Benjamin A1 - Wannous, Hazem A1 - Emporio, Marco A1 - Giachetti, Andrea A1 - LaViola Jr, Joseph J. A1 - He, Ruiwen A1 - Benhabiles, Halim A1 - Cabani, Adnane A1 - Fleury, Anthony A1 - Hammoudi, Karim A1 - Gavalas, Konstantinos A1 - Vlachos, Christoforos A1 - Papanikolaou, Athanasios A1 - Romanelis, Ioannis A1 - Fotis, Vlassis A1 - Arvanitis, Gerasimos A1 - Moustakas, Konstantinos A1 - Hanik, Martin A1 - Nava-Yazdani, Esfandiar A1 - von Tycowicz, Christoph T1 - SHREC 2024: Recognition Of Dynamic Hand Motions Molding Clay JF - Computers & Graphics N2 - Gesture recognition is a tool to enable novel interactions with different techniques and applications, like Mixed Reality and Virtual Reality environments. With all the recent advancements in gesture recognition from skeletal data, it is still unclear how well state-of- the-art techniques perform in a scenario using precise motions with two hands. This paper presents the results of the SHREC 2024 contest organized to evaluate methods for their recognition of highly similar hand motions using the skeletal spatial coordinate data of both hands. The task is the recognition of 7 motion classes given their spatial coordinates in a frame-by-frame motion. The skeletal data has been captured using a Vicon system and pre-processed into a coordinate system using Blender and Vicon Shogun Post. We created a small, novel dataset with a high variety of durations in frames. This paper shows the results of the contest, showing the techniques created by the 5 research groups on this challenging task and comparing them to our baseline method. Y1 - 2024 U6 - https://doi.org/10.1016/j.cag.2024.104012 VL - 123 SP - 104012 ER - TY - JOUR A1 - Weimann, Kuba A1 - Tim, Conrad T1 - Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification JF - IEEE Journal of Biomedical and Health Informatics Y1 - 2024 U6 - https://doi.org/10.1109/JBHI.2024.3427787 ER - TY - GEN A1 - Winkler, Alexander T1 - URIs im GLAM-Bereich – was sie sind und wie man sie verwendet N2 - Das Papier gibt Hinweise zu URIs (Uniform Resource Identifiers) im GLAM-Sektor. Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.11608433 ER - TY - JOUR A1 - Das, Somenath A1 - Sridharamurthy, Raghavendra A1 - Natarajan, Vijay T1 - Time-varying Extremum Graphs JF - Computer Graphics Forum N2 - We introduce time-varying extremum graph (TVEG), a topological structure to support visualization and analysis of a time- varying scalar field. The extremum graph is a substructure of the Morse-Smale complex. It captures the adjacency relationship between cells in the Morse decomposition of a scalar field. We define the TVEG as a time-varying extension of the extremum graph and demonstrate how it captures salient feature tracks within a dynamic scalar field. We formulate the construction of the TVEG as an optimization problem and describe an algorithm for computing the graph. We also demonstrate the capabilities of TVEG towards identification and exploration of topological events such as deletion, generation, split, and merge within a dynamic scalar field via comprehensive case studies including a viscous fingers and a 3D von Kármán vortex street dataset. Y1 - 2024 U6 - https://doi.org/10.1111/cgf.15162 SP - e15162 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Quang Vu, Nhu A1 - Nagel, Soeren T1 - Co-evolving networks for opinion and social dynamics in agent-based models JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - The rise of digital social media has strengthened the coevolution of public opinions and social interactions, that shape social structures and collective outcomes in increasingly complex ways. Existing literature often explores this interplay as a one-directional influence, focusing on how opinions determine social ties within adaptive networks. However, this perspective overlooks the intrinsic dynamics driving social interactions, which can significantly influence how opinions form and evolve. In this work, we address this gap, by introducing the co-evolving opinion and social dynamics using stochastic agent-based models. Agents' mobility in a social space is governed by both their social and opinion similarity with others. Similarly, the dynamics of opinion formation is driven by the opinions of agents in their social vicinity. We analyze the underlying social and opinion interaction networks and explore the mechanisms influencing the appearance of emerging phenomena, like echo chambers and opinion consensus. To illustrate the model's potential for real-world analysis, we apply it to General Social Survey data on political identity and public opinion regarding governmental issues. Our findings highlight the model's strength in capturing the coevolution of social connections and individual opinions over time. Y1 - 2024 U6 - https://doi.org/10.1063/5.0226054 SN - 1054-1500 VL - 34 IS - 9 ER - TY - CHAP A1 - Semler, Phillip A1 - Weiser, Martin T1 - Adaptive Gradient Enhanced Gaussian Process Surrogates for Inverse Problems T2 - Proceedings of the MATH+ Thematic Einstein Semester on Mathematical Optimization for Machine Learning N2 - Generating simulated training data needed for constructing sufficiently accurate surrogate models to be used for efficient optimization or parameter identification can incur a huge computational effort in the offline phase. We consider a fully adaptive greedy approach to the computational design of experiments problem using gradient-enhanced Gaussian process regression as surrogates. Designs are incrementally defined by solving an optimization problem for accuracy given a certain computational budget. We address not only the choice of evaluation points but also of required simulation accuracy, both of values and gradients of the forward model. Numerical results show a significant reduction of the computational effort compared to just position-adaptive and static designs as well as a clear benefit of including gradient information into the surrogate training. Y1 - 2024 ER - TY - JOUR A1 - Fürst, Steffen A1 - Conrad, Tim A1 - Jaeger, Carlo A1 - Wolf, Sarah T1 - Vahana.jl - A framework (not only) for large-scale agent-based models JF - Proceedings of Social Simulation Conference 2024 (SSC24) Y1 - 2024 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Obermeier, Patrick A1 - Ma, Xiaolin A1 - Schweiger, Brunhilde A1 - Opota, Onya A1 - Rath, Barbara T1 - Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study JF - Viruses N2 - Respiratory viral infections (RVIs) are common reasons for healthcare consultations. The inpatient management of RVIs consumes significant resources. From 2009 to 2014, we assessed the costs of RVI management in 4776 hospitalized children aged 0–18 years participating in a quality improvement program, where all ILI patients underwent virologic testing at the National Reference Centre followed by detailed recording of their clinical course. The direct (medical or non-medical) and indirect costs of inpatient management outside the ICU (‘non-ICU’) versus management requiring ICU care (‘ICU’) added up to EUR 2767.14 (non-ICU) vs. EUR 29,941.71 (ICU) for influenza, EUR 2713.14 (non-ICU) vs. EUR 16,951.06 (ICU) for RSV infections, and EUR 2767.33 (non-ICU) vs. EUR 14,394.02 (ICU) for human rhinovirus (hRV) infections, respectively. Non-ICU inpatient costs were similar for all eight RVIs studied: influenza, RSV, hRV, adenovirus (hAdV), metapneumovirus (hMPV), parainfluenza virus (hPIV), bocavirus (hBoV), and seasonal coronavirus (hCoV) infections. ICU costs for influenza, however, exceeded all other RVIs. At the time of the study, influenza was the only RVI with antiviral treatment options available for children, but only 9.8% of influenza patients (non-ICU) and 1.5% of ICU patients with influenza received antivirals; only 2.9% were vaccinated. Future studies should investigate the economic impact of treatment and prevention of influenza, COVID-19, and RSV post vaccine introduction. Y1 - 2024 U6 - https://doi.org/10.3390/v16040507 VL - 16 IS - 4 ER - TY - CHAP A1 - Becker, Christiane A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Ehrler, Bruno A1 - Gordon, Ivan A1 - Isabella, Olindo A1 - Jaeger, Klaus A1 - Jost, Marko A1 - Manley, Phillip A1 - Muñoz, Delfina A1 - Paetzold, Ulrich W. A1 - Sai, Hitoshi A1 - Yablonovitch, Eli T1 - Optical challenges for terawatt-scale photovoltaics T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3016415 VL - PC13014 SP - PC1301401 PB - SPIE ER - TY - CHAP A1 - Schaible, Jonas A1 - Yoo, Danbi A1 - Winarto, Hanifa A1 - Miaskiewicz, Alexandra A1 - Albrecht, Steve A1 - Wessels, Andreas A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Jaeger, Klaus A1 - Becker, Christiane T1 - On aesthetical appearance of colored perovskite solar modules T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3017427 VL - PC13014 SP - PC1301406 PB - SPIE ER - TY - GEN A1 - Vanaret, Charlie A1 - Leyffer, Sven T1 - Unifying nonlinearly constrained nonconvex optimization N2 - Derivative-based iterative methods for nonlinearly constrained non-convex optimization usually share common algorithmic components, such as strategies for computing a descent direction and mechanisms that promote global convergence. Based on this observation, we introduce an abstract framework based on four common ingredients that describes most derivative-based iterative methods and unifies their workflows. We then present Uno, a modular C++ solver that implements our abstract framework and allows the automatic generation of various strategy combinations with no programming effort from the user. Uno is meant to (1) organize mathematical optimization strategies into a coherent hierarchy; (2) offer a wide range of efficient and robust methods that can be compared for a given instance; (3) enable researchers to experiment with novel optimization strategies; and (4) reduce the cost of development and maintenance of multiple optimization solvers. Uno's software design allows user to compose new customized solvers for emerging optimization areas such as robust optimization or optimization problems with complementarity constraints, while building on reliable nonlinear optimization techniques. We demonstrate that Uno is highly competitive against state-of-the-art solvers filterSQP, IPOPT, SNOPT, MINOS, LANCELOT, LOQO, and CONOPT on a subset of 429 small problems from the CUTEst collection. Uno is available as open-source software under the MIT license at https://github.com/cvanaret/Uno . Y1 - 2024 ER - TY - THES A1 - Bena, Noor-Cella T1 - Finding Rules and Patterns in Egyptological Research Objects using Boolean Polynomial Rings Y1 - 2023 ER - TY - JOUR A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Burger, Sven T1 - Modelling luminescent coupling in multi-junction solar cells: perovskite silicon tandem case study JF - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3023941 VL - 13014 SP - 1301404 ER - TY - JOUR A1 - Raharinirina, Nomenjanahary Alexia A1 - Sunkara, Vikram A1 - von Kleist, Max A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables JF - PLOS ONE Y1 - 2024 U6 - https://doi.org/10.1371/journal.pone.0302425 VL - 19 IS - 5 PB - Public Library of Science ER - TY - GEN A1 - Sekuliĉ, Ivan A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - Machine-learning driven design of metasurfaces: learn the physics and not the objective function T2 - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3022119 VL - PC13017 SP - PC130170X ER - TY - CHAP A1 - Lücke, Marvin A1 - Koltai, Peter A1 - Winkelmann, Stefanie A1 - Molkethin, Nora A1 - Heitzig, Jobst T1 - Discovering collective variable dynamics of agent-based models T2 - 25th International Symposium on Mathematical Theory of Networks and Systems MTNS 2022 N2 - Analytical approximations of the macroscopic behavior of agent-based models (e.g. via mean-field theory) often introduce a significant error, especially in the transient phase. For an example model called continuous-time noisy voter model, we use two data-driven approaches to learn the evolution of collective variables instead. The first approach utilizes the SINDy method to approximate the macroscopic dynamics without prior knowledge, but has proven itself to be not particularly robust. The second approach employs an informed learning strategy which includes knowledge about the agent-based model. Both approaches exhibit a considerably smaller error than the conventional analytical approximation. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.15495/EPub_UBT_00006809 ER - TY - JOUR A1 - Pfeuffer, Julianus A1 - Bielow, Chris A1 - Wein, Samuel A1 - Jeong, Kyowon A1 - Netz, Eugen A1 - Walter, Axel A1 - Alka, Oliver A1 - Nilse, Lars A1 - Colaianni, Pasquale Domenico A1 - McCloskey, Douglas A1 - Kim, Jihyung A1 - Rosenberger, George A1 - Bichmann, Leon A1 - Walzer, Mathias A1 - Veit, Johannes A1 - Boudaud, Bertrand A1 - Bernt, Matthias A1 - Patikas, Nikolaos A1 - Pilz, Matteo A1 - Startek, Michał Piotr A1 - Kutuzova, Svetlana A1 - Heumos, Lukas A1 - Charkow, Joshua A1 - Sing, Justin Cyril A1 - Feroz, Ayesha A1 - Siraj, Arslan A1 - Weisser, Hendrik A1 - Dijkstra, Tjeerd M. H. A1 - Perez-Riverol, Yasset A1 - Röst, Hannes A1 - Kohlbacher, Oliver A1 - Sachsenberg, Timo T1 - OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data JF - Nature Methods Y1 - 2024 U6 - https://doi.org/10.1038/s41592-024-02197-7 SN - 1548-7091 VL - 21 IS - 3 SP - 365 EP - 367 PB - Springer Science and Business Media LLC ER - TY - THES A1 - Kunt, Tim T1 - The n-Queens Problem in Higher Dimensions N2 - How many mutually non-attacking queens can be placed on a d-dimensional chessboard of size n? The n-queens problem in higher dimensions is a generalization of the well-known n-queens problem. We provide a comprehensive overview of theoretical results, bounds, solution methods, and the interconnectivity of the problem within topics of discrete optimization and combinatorics. We present an integer programming formulation of the n-queens problem in higher dimensions and several strengthenings through additional valid inequalities. Compared to recent benchmarks, we achieve a speedup in computational time between 15-70x over all instances of the integer programs. Our computational results prove optimality of certificates for several large instances. Breaking additional, previously unsolved instances with the proposed methods is likely possible. On the primal side, we further discuss heuristic approaches to constructing solutions that turn out to be optimal when compared to the IP. We conclude with preliminary results on the number and density of the solutions. T3 - ZIB-Report - 24-05 KW - Integer Programming KW - Maximum Independent Set KW - n-Queens Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96468 ER - TY - JOUR A1 - Ernst, Marco A1 - Asselineau, Charles-Alexis A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Becker, Christiane T1 - Modelling bifacial irradiance – Step-by-step comparison and validation of view factor and ray tracing models JF - Appl. Energy Y1 - 2024 U6 - https://doi.org/10.1016/j.apenergy.2024.123574 SN - 0306-2619 VL - 369 SP - 123574 PB - Elsevier BV ER - TY - JOUR A1 - Van Bulck, David A1 - Goossens, Dries A1 - Clarner, Jan-Patrick A1 - Dimitsas, Angelos A1 - Fonseca, Georg H. G. A1 - Lamas-Fernandez, Carlos A1 - Lester, Martin Mariusz A1 - Pedersen, Jaap A1 - Phillips, Antony E. A1 - Rosati, Roberto Maria T1 - Which algorithm to select in sports timetabling? JF - European Journal of Operational Research N2 - Any sports competition needs a timetable, specifying when and where teams meet each other. The recent International Timetabling Competition (ITC2021) on sports timetabling showed that, although it is possible to develop general algorithms, the performance of each algorithm varies considerably over the problem instances. This paper provides a problem type analysis for sports timetabling, resulting in powerful insights into the strengths and weaknesses of eight state-of-the-art algorithms. Based on machine learning techniques, we propose an algorithm selection system that predicts which algorithm is likely to perform best based on the type of competition and constraints being used (i.e., the problem type) in a given sports timetabling problem instance. Furthermore, we visualize how the problem type relates to algorithm performance, providing insights and possibilities to further enhance several algorithms. Finally, we assess the empirical hardness of the instances. Our results are based on large computational experiments involving about 50 years of CPU time on more than 500 newly generated problem instances. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.06.005 VL - 318 IS - 2 SP - 575 EP - 591 ER - TY - JOUR A1 - Paltra, Sydney A1 - Bostanci, Inan A1 - Nagel, Kai T1 - The effect of mobility reductions on infection growth is quadratic in many cases JF - Scientific Reports Y1 - 2024 U6 - https://doi.org/10.1038/s41598-024-64230-1 VL - 14 ER - TY - JOUR A1 - Conrad, Tim A1 - Ferrer, Eloi A1 - Mietchen, Daniel A1 - Pusch, Larissa A1 - Stegmuller, Johannes A1 - Schubotz, Moritz T1 - Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing JF - Scientific Data Y1 - 2024 U6 - https://doi.org/10.1038/s41597-024-03480-0 VL - 11 ER - TY - JOUR A1 - Meduri, Dhruv A1 - Sharma, Mohit A1 - Natarajan, Vijay T1 - Jacobi Set Simplification for Tracking Topological Features in Time-Varying Scalar Fields JF - Vis Comput N2 - The Jacobi set of a bivariate scalar field is the set of points where the gradients of the two constituent scalar fields align with each other. It captures the regions of topological changes in the bivariate field. The Jacobi set is a bivariate analog of critical points, and may correspond to features of interest. In the specific case of time-varying fields and when one of the scalar fields is time, the Jacobi set corresponds to temporal tracks of critical points, and serves as a feature-tracking graph. The Jacobi set of a bivariate field or a time-varying scalar field is complex, resulting in cluttered visualizations that are difficult to analyze. This paper addresses the problem of Jacobi set simplification. Specifically, we use the time-varying scalar field scenario to introduce a method that computes a reduced Jacobi set. The method is based on a stability measure called robustness that was originally developed for vector fields and helps capture the structural stability of critical points. We also present a mathematical analysis for the method, and describe an implementation for 2D time-varying scalar fields. Applications to both synthetic and real-world datasets demonstrate the effectiveness of the method for tracking features. Y1 - 2024 U6 - https://doi.org/10.1007/s00371-024-03484-2 VL - 40 SP - 4843 EP - 4855 ER - TY - JOUR A1 - Dhar, Amritendu A1 - Natarajan, Vijay A1 - Rathod, Abhishek T1 - Geometric localization of homology cycles JF - CCCG 2024: Proc. 36th Canadian Conference on Computational Geometry N2 - Computing an optimal cycle in a given homology class, also referred to as the homology localization problem, is known to be an NP-hard problem in general. Furthermore, there is currently no known optimality criterion that localizes classes geometrically and admits a stability property under the setting of persistent homology. We present a geometric optimization of the cycles that is computable in polynomial time and is stable in an approximate sense. Tailoring our search criterion to different settings, we obtain various optimization problems like optimal homologous cycle, minimum homology basis, and minimum persistent homology basis. In practice, the (trivial) exact algorithm is computationally expensive despite having a worst case polynomial runtime. Therefore, we design approximation algorithms for the above problems and study their performance experimentally. These algorithms have reasonable runtimes for moderate sized datasets and the cycles computed by these algorithms are consistently of high quality as demonstrated via experiments on multiple datasets. Y1 - 2024 SP - 1 EP - 8 ER - TY - JOUR A1 - Singh, Upkar A1 - Vinayachandran, P. N. A1 - Natarajan, Vijay T1 - Advection-Based Tracking and Analysis of Salinity Movement in the Indian Ocean JF - Computers & Geosciences N2 - The Bay of Bengal (BoB) has maintained its salinity distribution over the years despite a continuous flow of fresh water entering it through rivers on the northern coast, which is capable of diluting the salinity. This can be attributed to the cyclic flow of high salinity water (>= 35 psu), coming from Arabian sea and entering BoB from the south, which moves northward and mixes with this fresh water. The movement of this high salinity water has been studied and analyzed in previous work (Singh et al., 2022). This paper extends the computational methods and analysis of salinity movement. Specifically, we introduce an advection based feature definition that represents the movement of high salinity water, and describe algorithms to track their evolution over time. This method allows us to trace the movement of high salinity water caused due to ocean currents. The method is validated via comparison with established observations on the flow of high salinity water in the BoB, including its entry from the Arabian Sea and its movement near Sri Lanka. Further, the visual analysis and tracking framework enables us to compare it with previous work and analyze the contribution of advection to salinity transport. Y1 - 2024 U6 - https://doi.org/10.1016/j.cageo.2023.105493 VL - 182 IS - 105493 SP - 1 EP - 10 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Herrera, Kristian A1 - Tavhelidse-Suck, Tinatini A1 - Knoblich, Simon A1 - Seleit, Ali A1 - Boulanger-Weill, Jonathan A1 - Chambule, Sydney A1 - Aspiras, Ariel A1 - Santoriello, Cristina A1 - Randlett, Owen A1 - Wittbrodt, Joachim A1 - Aulehla, Alexander A1 - Lichtman, Jeff W. A1 - Fishman, Mark A1 - Hege, Hans-Christian A1 - Baum, Daniel A1 - Engert, Florian A1 - Isoe, Yasuko T1 - Multi-species community platform for comparative neuroscience in teleost fish N2 - Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community’s research and its easy extensibility will encourage contributions to its continuous expansion. Y1 - 2024 U6 - https://doi.org/10.1101/2024.02.14.580400 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Le, Thi Thai A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Optimal discrete pipe sizing for tree-shaped CO2 networks JF - OR Spectrum N2 - For industries like the cement industry, switching to a carbon-neutral production process is impossible. They must rely on carbon capture, utilization and storage (CCUS) technologies to reduce their production processes’ inevitable carbon dioxide (CO2) emissions. For transporting continuously large amounts of CO2, utilizing a pipeline network is the most effective solution; however, building such a network is expensive. Therefore minimizing the cost of the pipelines to be built is extremely important to make the operation financially feasible. In this context, we investigate the problem of finding optimal pipeline diameters from a discrete set of diameters for a tree-shaped network transporting captured CO2 from multiple sources to a single sink. The general problem of optimizing arc capacities in potential-based fluid networks is already a challenging mixed-integer nonlinear optimization problem. The problem becomes even more complex when adding the highly sensitive nonlinear behavior of CO2 regarding temperature and pressure changes. We propose an iterative algorithm splitting the problem into two parts: a) the pipe-sizing problem under a fixed supply scenario and temperature distribution and b) the thermophysical modeling, including mixing effects, the Joule-Thomson effect, and heat exchange with the surrounding environment. We demonstrate the effectiveness of our approach by applying our algorithm to a real-world network planning problem for a CO2 network in Western Germany. Further, we show the robustness of the algorithm by solving a large artificially created set of network instances. Y1 - 2024 U6 - https://doi.org/10.1007/s00291-024-00773-z ER - TY - JOUR A1 - Euler, Ricardo A1 - Maristany de las Casas, Pedro T1 - Labeling methods for partially ordered paths JF - European Journal of Operational Research N2 - The landscape of applications and subroutines relying on shortest path computations continues to grow steadily. This growth is driven by the undeniable success of shortest path algorithms in theory and practice. It also introduces new challenges as the models and assessing the optimality of paths become more complicated. Hence, multiple recent publications in the field adapt existing labeling methods in an ad hoc fashion to their specific problem variant without considering the underlying general structure: they always deal with multi-criteria scenarios, and those criteria define different partial orders on the paths. In this paper, we introduce the partial order shortest path problem (POSP), a generalization of the multi-objective shortest path problem (MOSP) and in turn also of the classical shortest path problem. POSP captures the particular structure of many shortest path applications as special cases. In this generality, we study optimality conditions or the lack of them, depending on the objective functions’ properties. Our final contribution is a big lookup table summarizing our findings and providing the reader with an easy way to choose among the most recent multi-criteria shortest path algorithms depending on their problems’ weight structure. Examples range from time-dependent shortest path and bottleneck path problems to the electric vehicle shortest path problem with recharging and complex financial weight functions studied in the public transportation community. Our results hold for general digraphs and, therefore, surpass previous generalizations that were limited to acyclic graphs. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.05.002 VL - 318 IS - 1 SP - 19 EP - 30 PB - Elsevier BV ET - 1 ER - TY - CHAP A1 - Muschner, Christoph A1 - Yüksel-Ergün, Inci A1 - Gehring, Marie-Claire A1 - Bartoszuk, Karolina A1 - Haas, Sabine A1 - Zittel, Janina T1 - Sensitivity analysis of the energy transition path in the Berlin-Brandenburg area to uncertainties in operational and investment costs of diverse energy production technologies. T2 - Proceedings of the 37th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems – ECOS 2024 N2 - The investigation of energy transition paths toward a sustainable and decarbonized future under uncertainty is a critical aspect of contemporary energy planning and policy development. There are numerous methods for analysing uncertainties and sensitivities and many studies on sustainable transformation paths, but there is a lack of combined application to relevant use-cases. In this study, we investigate the sensitivity of energy transition paths to uncertainties in operational and investment costs of power plants in the metropolitan area of Berlin and its rural surroundings. By employing the linear programming energy system model oemof-B3, we extensively focus on the system's energy technologies, such as wind turbines, photovoltaics, hydro and combustion plants, and energy storages. Greenhouse gas reduction and electrification rates per commodity are realized by selected constraints. Our research aims to discern how investments in energy production capacities are influenced by uncertainties of other energy technologies' investment and operational costs in the system. We apply a quantitative approach to investigate such interdependencies of cost variations and their impact on long-term energy planning. Thus, the analysis sheds light on the robustness of energy transition paths in the face of these uncertainties. The region Berlin-Brandenburg serves as a case study and thus reflects on the present space conflicts to meet energy demands in urban and suburban areas and their rural surroundings. An electricity-intensive scenario is selected that assumes a 100 % reduction in greenhouse gas emissions by 2050. With the results of the case study, we show how our approach enables rural and metropolitan decision-makers to collaborate in achieving sustainable energy. Decision-making in long-term energy planning can be made more robust and flexible by acknowledging the identified sensitivities and enable such regions better to navigate challenges and uncertainties associated with sustainable energy planning. Y1 - 2024 ER - TY - GEN A1 - Le, Thi Thai T1 - Effect of viscous forces on the interface stability of a tangential-velocity discontinuity in compressible fluids T2 - Journal N2 - Compressible flows are prevalent in natural and technological processes, particularly in the energy transition to renewable energy systems. Consequently, extensive research has focused on understanding the stability of tangential--velocity discontinuity in compressible media. Despite recent advancements that address industrial challenges more realistically, many studies have ignored viscous stress tensors' impact, leading to inaccuracies in predicting interface stability. This omission becomes critical, especially in high Reynolds or low Mach number flows, where viscous forces dissipate kinetic energy across interfaces, affect total energy dissipation, and dampen flow instabilities. Our work is thus motivated to analyze the viscosity force effect by including the viscous stress tensor terms in the motion equations. Our results show that by considering the effect of viscous forces, the tangential-velocity discontinuity interface is constantly destabilized for the entire range of the Mach number. T3 - ZIB-Report - 24-04 Y1 - 2024 ER - TY - CHAP A1 - Euler, Ricardo A1 - Borndörfer, Ralf A1 - Puchert, Christian A1 - Takkula, Tuomo T1 - ULD Build-Up Scheduling with Logic-Based Benders Decomposition T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research N2 - We study a complex planning and scheduling problem arising from the build-up process of air cargo pallets and containers, collectively referred to as unit load devices (ULD), in which ULDs must be assigned to workstations for loading. Since air freight usually becomes available gradually along the planning horizon, ULD build-ups must be scheduled neither too early to avoid underutilizing ULD capacity, nor too late to avoid resource conflicts with other flights. Whenever possible, ULDs should be built up in batches, thereby giving ground handlers more freedom to rearrange cargo and utilize the ULD's capacity efficiently. The resulting scheduling problem has an intricate cost function and produces large time-expanded models, especially for longer planning horizons. We propose a logic-based Benders decomposition approach that assigns batches to time intervals and workstations in the master problem, while the actual schedule is decided in a subproblem. By choosing appropriate intervals, the subproblem becomes a feasibility problem that decomposes over the workstations. Additionally, the similarity of many batches is exploited by a strengthening procedure for no-good cuts. We benchmark our approach against a time-expanded MIP formulation from the literature on a publicly available data set. It solves 15% more instances to optimality and decreases run times by more than 50% in the geometric mean. This improvement is especially pronounced for longer planning horizons of up to one week, where the Benders approach solves over 50% instances more than the baseline Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1007/978-3-031-60597-0_17 VL - 14742 SP - 259 EP - 276 ER - TY - CHAP A1 - Zittel, Janina A1 - Clarner, Jan-Patrick A1 - Tawfik, Christine A1 - Dykes, Maxwell A1 - Rivetta, Fabian A1 - Riedmüller, Stephanie T1 - A multi-objective optimization strategy for district heating production portfolio planning. T2 - Proceedings of the 37th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems – ECOS 2024 N2 - The imperative to decarbonize energy systems has intensified the need for efficient transformations within the heating sector, with a particular focus on district heating networks. This study addresses this challenge by proposing a comprehensive optimization approach evaluated on the district heating network of the Märkisches Viertel of Berlin. Our objective is to simultaneously optimize heat production with three targets: minimizing costs, minimizing CO2-emissions, and maximizing heat generation from Combined Heat and Power (CHP) plants for enhanced efficiency. To tackle this optimization problem, we employed a Mixed-Integer Linear Program (MILP) that encompasses the conversion of various fuels into heat and power, integration with relevant markets, and considerations for technical constraints on power plant operation. These constraints include startup and minimum downtime, activation costs, and storage limits. The ultimate goal is to delineate the Pareto front, representing the optimal trade-offs between the three targets. We evaluate variants of the 𝜖-constraint algorithm for their effectiveness in coordinating these objectives, with a simultaneous focus on the quality of the estimated Pareto front and computational efficiency. One algorithm explores solutions on an evenly spaced grid in the objective space, while another dynamically adjusts the grid based on identified solutions. Initial findings highlight the strengths and limitations of each algorithm, providing guidance on algorithm selection depending on desired outcomes and computational constraints. Our study emphasizes that the optimal choice of algorithm hinges on the density and distribution of solutions in the feasible space. Whether solutions are clustered or evenly distributed significantly influences algorithm performance. These insights contribute to a nuanced understanding of algorithm selection for multi-objective multi-energy system optimization, offering valuable guidance for future research and practical applications for planning sustainable district heating networks. Y1 - 2024 ER - TY - CHAP A1 - Reidelbach, Marco A1 - Schembera, Björn A1 - Weber, Marcus T1 - Towards a FAIR Documentation of Workflows and Models in Applied Mathematics T2 - Mathematical Software – ICMS 2024 N2 - Modeling-Simulation-Optimization workflows play a fundamental role in applied mathematics. The Mathematical Research Data Initiative, MaRDI, responded to this by developing a FAIR and machine-interpretable template for a comprehensive documentation of such workflows. MaRDMO, a Plugin for the Research Data Management Organiser, enables scientists from diverse fields to document and publish their workflows on the MaRDI Portal seamlessly using the MaRDI template. Central to these workflows are mathematical models. MaRDI addresses them with the MathModDB ontology, offering a structured formal model description. Here, we showcase the interaction between MaRDMO and the MathModDB Knowledge Graph through an algebraic modeling workflow from the Digital Humanities. This demonstration underscores the versatility of both services beyond their original numerical domain. Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-64529-7_27 VL - 14749 SP - 254 EP - 262 PB - Springer Nature Switzerland CY - Cham ET - Lecture Notes in Computer Science ER - TY - JOUR A1 - Diederichs, Katja A1 - Krause, Celia A1 - Lemaire, Marina A1 - Reidelbach, Marco A1 - Windeck, Jürgen T1 - A Vision for Data Management Plans in the NFDI N2 - At present, data management plans (DMPs) are still often perceived as mere documents for funding agencies providing clarity on how research data will be handled during a funded project, but are not usually actively involved in the processes. However, they contain a great deal of information that can be shared automatically to facilitate active research data management (RDM) by providing metadata to research infrastructures and supporting communication between all involved stakeholders. This position paper brings together a number of ideas developed and collected during interdisciplinary workshops of the Data Management Planning Working Group (infra-dmp), which is part of the section Common Infrastructures of the National Research Data Infrastructure (NFDI) in Germany. We present our vision of a possible future role of DMPs, templates, and tools in the upcoming NFDI service architecture. Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10570653 ER - TY - CHAP A1 - Schembera, Björn A1 - Wübbeling, Frank A1 - Kleikamp, Hendrik A1 - Biedinger, Christine A1 - Fiedler, Jochen A1 - Reidelbach, Marco A1 - Shehu, Aurela A1 - Schmidt, Burkhard A1 - Koprucki, Thomas A1 - Iglezakis, Dotothea A1 - Göddeke, Dominik T1 - Ontologies for Models and Algorithms in Applied Mathematics and Related Disciplines T2 - Metadata and Semantic Research - MTSR 2023 N2 - In applied mathematics and related disciplines, the modeling-simulation-optimization workflow is a prominent scheme, with mathematical models and numerical algorithms playing a crucial role. For these types of mathematical research data, the Mathematical Research Data Initiative has developed, merged and implemented ontologies and knowledge graphs. This contributes to making mathematical research data FAIR by introducing semantic technology and documenting the mathematical foundations accordingly. Using the concrete example of microfracture analysis of porous media, it is shown how the knowledge of the underlying mathematical model and the corresponding numerical algorithms for its solution can be represented by the ontologies. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-65990-4_14 SP - 161 EP - 168 PB - Springer Nature Switzerland CY - Cham ET - Communications in Computer and Information Science ER - TY - JOUR A1 - Schembera, Björn A1 - Wübbeling, Frank A1 - Koprucki, Thomas A1 - Biedinger, Christine A1 - Reidelbach, Marco A1 - Schmidt, Burkhard A1 - Göddeke, Dominik A1 - Fiedler, Jochen T1 - Building Ontologies and Knowledge Graphs for Mathematics and its Applications JF - Proceedings of the Conference on Research Data Infrastructure N2 - Ontologies and knowledge graphs for mathematical algorithms and models are presented, that have been developed by the Mathematical Research Data Initiative. This enables FAIR data handling in mathematics and the applied disciplines. Moreover, challenges of harmonization during the ontology development are discussed. Y1 - 2023 U6 - https://doi.org/10.52825/cordi.v1i.255 SN - 2941-296X VL - 1 PB - TIB Open Publishing ER - TY - JOUR A1 - Reidelbach, Marco A1 - Ferrer, Eloi A1 - Weber, Marcus T1 - MaRDMO Plugin BT - Document and Retrieve Workflows Using the MaRDI Portal JF - Proceedings of the Conference on Research Data Infrastructure N2 - MaRDMO, a plugin for the Research Data Management Organiser, was developed in the Mathematical Research Data Initiative to document interdisciplinary workflows using a standardised scheme. Interdisciplinary workflows recorded this way are published directly on the MaRDI portal. In addition, central information is integrated into the MaRDI knowledge graph. Next to the documentation, MaRDMO offers the possibility to retrieve existing interdisciplinary workflows from the MaRDI Knowledge Graph to allow the reproduction of the initial work and to provide scientists with new researchimpulses. Thus, MaRDMO creates a community-driven knowledge loop that could help to overcome the replication crisis. Y1 - 2023 U6 - https://doi.org/10.52825/cordi.v1i.254 SN - 2941-296X VL - 1 PB - TIB Open Publishing ER - TY - JOUR A1 - Benner, Peter A1 - Danabalan, Renita A1 - Gödekke, Dominik A1 - Kastner, Lars A1 - Krause, Tabea A1 - Mietchen, Daniel A1 - Reidelbach, Marco A1 - Schembera, Björn A1 - Schubotz, Moritz A1 - Sinn, Rainer A1 - Tabelow, Karsten T1 - Research Data Management Planning in Mathematics N2 - Research data are crucial in mathematics and all scientific disciplines, as they form the foundation for empirical evidence, by enabling the validation and reproducibility of scientific findings. Mathematical research data (MathRD) have become vast and complex, and their interdisciplinary potential and abstract nature make them ubiquitous in various scientific fields. The volume of data and the velocity of its creation are rapidly increasing due to advancements in data science and computing power. This complexity extends to other disciplines, resulting in diverse research data and computational models. Thus, proper handling of research data is crucial both within mathematics and for its manifold connections and exchange with other disciplines. The National Research Data Infrastructure (NFDI), funded by the federal and state governments of Germany, consists of discipline-oriented consortia, including the Mathematical Research Data Initiative (MaRDI). MaRDI has been established to develop services, guidelines and outreach measures for all aspects of MathRD, and thus support the mathematical research community. Research data management (RDM) should be an integral component of every scientific project, and is becoming a mandatory component of grants with funding bodies such as the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). At the core of RDM are the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This document aims to guide mathematicians and researchers from related disciplines who create RDM plans. It highlights the benefits and opportunities of RDM in mathematics and interdisciplinary studies, showcases examples of diverse MathRD, and suggests technical solutions that meet the requirements of funding agencies with specific examples. The document is regularly updated to reflect the latest developments within the mathematical community represented by MaRDI. Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.10018245 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Heida, Martin T1 - Voronoi Graph - Improved raycasting and integration schemes for high dimensional Voronoi diagrams N2 - The computation of Voronoi Diagrams, or their dual Delauney triangulations is difficult in high dimensions. In a recent publication Polianskii and Pokorny propose an iterative randomized algorithm facilitating the approximation of Voronoi tesselations in high dimensions. In this paper, we provide an improved vertex search method that is not only exact but even faster than the bisection method that was previously recommended. Building on this we also provide a depth-first graph-traversal algorithm which allows us to compute the entire Voronoi diagram. This enables us to compare the outcomes with those of classical algorithms like qHull, which we either match or marginally beat in terms of computation time. We furthermore show how the raycasting algorithm naturally lends to a Monte Carlo approximation for the volume and boundary integrals of the Voronoi cells, both of which are of importance for finite Volume methods. We compare the Monte-Carlo methods to the exact polygonal integration, as well as a hybrid approximation scheme. Y1 - 2024 ER - TY - JOUR A1 - Schaible, Jonas A1 - Nouri, Bijan A1 - Höpken, Lars A1 - Kotzab, Tim A1 - Loevenich, Matthias A1 - Blum, Niklas A1 - Hammer, Annette A1 - Stührenberg, Jonas A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Wilbert, Stefan T1 - Application of nowcasting to reduce the impact of irradiance ramps on PV power plants JF - EPJ Photovolt. Y1 - 2024 U6 - https://doi.org/10.1051/epjpv/2024009 VL - 15 SP - 15 ER - TY - JOUR A1 - Krüger, Jan A1 - Manley, Phillip A1 - Bergmann, Detlef A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Eder, Christian A1 - Heinrich, Andreas A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Manske, Eberhard T1 - Introduction and application of a new approach for model-based optical bidirectional measurements JF - Meas. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6501/ad4b53 VL - 35 IS - 8 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Dynamical systems and complex networks: A Koopman operator perspective N2 - The Koopman operator has entered and transformed many research areas over the last years. Although the underlying concept–representing highly nonlinear dynamical systems by infinite-dimensional linear operators–has been known for a long time, the availability of large data sets and efficient machine learning algorithms for estimating the Koopman operator from data make this framework extremely powerful and popular. Koopman operator theory allows us to gain insights into the characteristic global properties of a system without requiring detailed mathematical models. We will show how these methods can also be used to analyze complex networks and highlight relationships between Koopman operators and graph Laplacians. Y1 - 2024 ER - TY - GEN A1 - Secker, Christopher T1 - Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists (Dataset) N2 - Virtual Screening Dataset for the paper "Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists" by Secker et al. (https://doi.org/10.1186/s13321-023-00746-4) Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96220 ER - TY - GEN A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - ‘Sawfish’ Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications (Advanced Optical Materials 13/2024) T2 - Adv. Optical Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202470046 VL - 12 SP - 2470046 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics N2 - This paper is concerned with collective variables, or reaction coordinates, that map a discrete-in-time Markov process X_n in R^d to a (much) smaller dimension k≪d. We define the effective dynamics under a given collective variable map ξ as the best Markovian representation of X_n under ξ. The novelty of the paper is that it gives strict criteria for selecting optimal collective variables via the properties of the effective dynamics. In particular, we show that the transition density of the effective dynamics of the optimal collective variable solves a relative entropy minimization problem from certain family of densities to the transition density of X_n. We also show that many transfer operator-based data-driven numerical approaches essentially learn quantities of the effective dynamics. Furthermore, we obtain various error estimates for the effective dynamics in approximating dominant timescales / eigenvalues and transition rates of the original process X_n and how optimal collective variables minimize these errors. Our results contribute to the development of theoretical tools for the understanding of complex dynamical systems, e.g. molecular kinetics, on large timescales. These results shed light on the relations among existing data-driven numerical approaches for identifying good collective variables, and they also motivate the development of new methods. Y1 - 2024 ER - TY - JOUR A1 - Erban, Radek A1 - Winkelmann, Stefanie T1 - Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling N2 - The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem. Y1 - 2024 ER - TY - JOUR A1 - Müller, Gabriel A1 - Martínez-Lahuerta, V. J. A1 - Sekuliĉ, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Gaaloul, Naceur T1 - Bayesian optimization for state engineering of quantum gases JF - arXiv Y1 - 2024 SP - arXiv:2404.18234 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Weinand, Jann Michael A1 - Syranidou, Chloi A1 - Rehfeldt, Daniel T1 - An efficient solver for large-scale onshore wind farm siting including cable routing JF - European Journal of Operational Research N2 - Existing planning approaches for onshore wind farm siting and grid integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an exact approach for the integrated layout and cable routing problem of onshore wind farm planning using the Quota Steiner tree problem. Applying a novel transformation on a known directed cut formulation, reduction techniques, and heuristics, we design an exact solver that makes large problem instances solvable and outperforms generic MIP solvers. In selected regions of Germany, the trade-offs between minimizing costs and landscape impact of onshore wind farm siting are investigated. Although our case studies show large trade-offs between the objective criteria of cost and landscape impact, small burdens on one criterion can significantly improve the other criteria. In addition, we demonstrate that contrary to many approaches for exclusive turbine siting, grid integration must be simultaneously optimized to avoid excessive costs or landscape impacts in the course of a wind farm project. Our novel problem formulation and the developed solver can assist planners in decision-making and help optimize wind farms in large regions in the future. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.04.026 VL - 317 IS - 2 SP - 616 EP - 630 ER - TY - GEN A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Source Code and Simulation Results: Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10598255 SP - doi: 10.5281/zenodo.10598255 ER - TY - CHAP A1 - Pedersen, Jaap A1 - Ljubić, Ivana ED - Pardalos, Panos M. ED - Prokopyev, Oleg A. T1 - Prize Collecting Steiner Tree Problem and its Variants T2 - Encyclopedia of Optimization Y1 - 2024 PB - Springer International Publishing CY - Cham ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Speeding up all-electron real-time TDDFT demonstrated by the exciting package JF - Comput. Phys. Commun. Y1 - 2024 U6 - https://doi.org/10.1016/j.cpc.2024.109292 VL - 304 SP - 109292 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Olivet, Julien A1 - Blavier, Jeremy A1 - Kostova, Simona A1 - Maseko, Sibusiso B A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A A1 - Hill, David E A1 - Landthaler, Markus A1 - Choi, Soon Gang A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E T1 - AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - Molecular Systems Biology N2 - Protein–protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways. KW - Applied Mathematics KW - Computational Theory and Mathematics KW - General Agricultural and Biological Sciences KW - General Immunology and Microbiology KW - General Biochemistry, Genetics and Molecular Biology KW - Information Systems Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s44320-024-00019-8 SN - 1744-4292 VL - 20 IS - 4 SP - 428 EP - 457 PB - Springer Science and Business Media LLC ER - TY - CHAP A1 - Prause, Felix T1 - A Multi-Swap Heuristic for Rolling Stock Rotation Planning with Predictive Maintenance T2 - Proceedings of the 11th International Network Optimization Conference (INOC), Dublin, Ireland, March 11-23, 2024 N2 - We present a heuristic solution approach for the rolling stock rotation problem with predictive maintenance (RSRP-PdM). The task of this problem is to assign a sequence of trips to each of the vehicles and to schedule their maintenance such that all trips can be operated. Here, the health states of the vehicles are considered to be random variables distributed by a family of probability distribution functions, and the maintenance services should be scheduled based on the failure probability of the vehicles. The proposed algorithm first generates a solution by solving an integer linear program and then heuristically improves this solution by applying a local search procedure. For this purpose, the trips assigned to the vehicles are split up and recombined, whereby additional deadhead trips can be inserted between the partial assignments. Subsequently, the maintenance is scheduled by solving a shortest path problem in a state-expanded version of a space-time graph restricted to the trips of the individual vehicles. The solution approach is tested and evaluated on a set of test instances based on real-world timetables. Y1 - 2024 U6 - https://doi.org/10.48786/inoc.2024.11 SP - 58 EP - 63 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf T1 - An Iterative Refinement Approach for the Rolling Stock Rotation Problem with Predictive Maintenance N2 - The rolling stock rotation problem with predictive maintenance (RSRP-PdM) involves the assignment of trips to a fleet of vehicles with integrated maintenance scheduling based on the predicted failure probability of the vehicles. These probabilities are determined by the health states of the vehicles, which are considered to be random variables distributed by a parameterized family of probability distribution functions. During the operation of the trips, the corresponding parameters get updated. In this article, we present a dual solution approach for RSRP-PdM and generalize a linear programming based lower bound for this problem to families of probability distribution functions with more than one parameter. For this purpose, we define a rounding function that allows for a consistent underestimation of the parameters and model the problem by a state-expanded event-graph in which the possible states are restricted to a discrete set. This induces a flow problem that is solved by an integer linear program. We show that the iterative refinement of the underlying discretization leads to solutions that converge from below to an optimal solution of the original instance. Thus, the linear relaxation of the considered integer linear program results in a lower bound for RSRP-PdM. Finally, we report on the results of computational experiments conducted on a library of test instances. Y1 - 2024 ER - TY - GEN A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Source code and simulation results: Efficient rational approximation of optical response functions with the AAA algorithm T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10853692 SP - doi: 10.5281/zenodo.10853692 ER - TY - JOUR A1 - Winkler, Alexander T1 - Berliner Kulturerbe digital: Ein quantitativer Blick auf die Metadatenqualität JF - EVA BERLIN 2023. Elektronische Medien & Kunst, Kultur und Historie. 27. Berliner Veranstaltung der internationalen EVA-Serie (29. November 2023 – 01. Dezember 2023) N2 - Die Metadatenqualität bestimmt wesentlich den Nutzen und Wert von Kulturerbedaten. ‚Gute‘ Metadaten erhöhen die Auffindbarkeit, Interoperabilität und Nutzbarkeit von Daten signifikant. Mit Blick auf Retrieval bzw. Discovery, Vernetzung im Kontext von Linked Open Data und wissenschaftliches Data Mining hängt die Qualität dabei wesentlich von der Verwendung von maschinenlesbaren kontrollierten Vokabularen ab. Diese wird in der vorliegenden Arbeit quantitativ untersucht. Als Datengrundlage dienen die in der Deutschen Digitalen Bibliothek aggregierten Metadaten aus Berliner Museen (ca. 1,2 Millionen Metadatenobjekte im LIDO-Format) Y1 - 2023 SP - 101 EP - 108 ER - TY - JOUR A1 - Sherratt, Katharine A1 - Srivastava, Ajitesh A1 - Ainslie, Kylie A1 - Singh, David E. A1 - Cublier, Aymar A1 - Marinescu, Maria Cristina A1 - Carretero, Jesus A1 - Garcia, Alberto Cascajo A1 - Franco, Nicolas A1 - Willem, Lander A1 - Abrams, Steven A1 - Faes, Christel A1 - Beutels, Philippe A1 - Hens, Niel A1 - Müller, Sebastian A1 - Charlton, Billy A1 - Ewert, Ricardo A1 - Paltra, Sydney A1 - Rakow, Christian A1 - Rehmann, Jakob A1 - Conrad, Tim A1 - Schütte, Christof A1 - Nagel, Kai A1 - Abbott, Sam A1 - Grah, Rok A1 - Niehus, Rene A1 - Prasse, Bastian A1 - Sandmann, Frank A1 - Funk, Sebastian T1 - Characterising information gains and losses when collecting multiple epidemic model outputs JF - Epidemics N2 - Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results. Methods We compared July 2022 projections from the European COVID-19 Scenario Modelling Hub. Five modelling teams projected incidence in Belgium, the Netherlands, and Spain. We compared projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model’s quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data. Results. By collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models’ quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes. Conclusions. We observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort’s aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts. Data availability All code and data available on Github: https://github.com/covid19-forecast-hub-europe/aggregation-info-loss KW - Virology KW - Infectious Diseases KW - Public Health, Environmental and Occupational Health KW - Microbiology KW - Parasitology KW - Epidemiology Y1 - 2024 U6 - https://doi.org/10.1016/j.epidem.2024.100765 SN - 1755-4365 VL - 47 PB - Elsevier BV ER - TY - JOUR A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Efficient rational approximation of optical response functions with the AAA algorithm JF - Laser Photonics Rev. Y1 - 2024 U6 - https://doi.org/10.1002/lpor.202400584 SP - 2400584 ER - TY - CHAP A1 - Kiessling, David A1 - Vanaret, Charlie A1 - Astudillo, Alejandro A1 - Decré, Wilm A1 - Swevers, Jan T1 - An Almost Feasible Sequential Linear Programming Algorithm T2 - 2024 European Control Conference (ECC), Stockholm, Sweden N2 - This paper proposes an almost feasible Sequential Linear Programming (afSLP) algorithm. In the first part, the practical limitations of previously proposed Feasible Sequential Linear Programming (FSLP) methods are discussed along with illustrative examples. Then, we present a generalization of FSLP based on a tolerance-tube method that addresses the shortcomings of FSLP. The proposed algorithm afSLP consists of two phases. Phase I starts from random infeasible points and iterates towards a relaxation of the feasible set. Once the tolerance-tube around the feasible set is reached, phase II is started and all future iterates are kept within the tolerance-tube. The novel method includes enhancements to the originally proposed tolerance-tube method that are necessary for global convergence. afSLP is shown to outperform FSLP and the state-of-the-art solver IPOPT on a SCARA robot optimization problem. Y1 - 2024 U6 - https://doi.org/10.23919/ECC64448.2024.10590864 SP - 2328 EP - 2335 ER - TY - JOUR A1 - Schintke, Florian A1 - Belhajjame, Khalid A1 - De Mecquenem, Ninon A1 - Frantz, David A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Missier, Paolo A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel T. A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity constraints for data analysis workflows JF - Future Generation Computer Systems Y1 - 2024 U6 - https://doi.org/10.1016/j.future.2024.03.037 VL - 157 SP - 82 EP - 97 ER - TY - GEN A1 - Yueksel-Erguen, Inci A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Mathematical optimization based flow scenario generation for operational analysis of European gas transport networks based on open data N2 - The decarbonization of the European energy system demands a rapid and comprehensive transformation while securing energy supplies at all times. Still, natural gas plays a crucial role in this process. Recent unexpected events forced drastic changes in gas routes throughout Europe. Therefore, operational-level analysis of the gas transport networks and technical capacities to cope with these transitions using unconventional scenarios has become essential. Unfortunately, data limitations often hinder such analyses. To overcome this challenge, we propose a mathematical model-based scenario generator that enables operational analysis of the European gas network using open data. Our approach focuses on the consistent analysis of specific partitions of the gas transport network, whose network topology data is readily available. We generate reproducible and consistent node-based gas in/out-flow scenarios for these defined network partitions to enable feasibility analysis and data quality assessment. Our proposed method is demonstrated through several applications that address the feasibility analysis and data quality assessment of the German gas transport network. By using open data and a mathematical modeling approach, our method allows for a more comprehensive understanding of the gas transport network's behavior and assists in decision-making during the transition to decarbonization. T3 - ZIB-Report - 24-03 Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-95789 SN - 1438-0064 ER - TY - GEN A1 - Cao, Karl-Kien A1 - Anderson, Lovis A1 - Böhme, Aileen A1 - Breuer, Thomas A1 - Buschmann, Jan A1 - Fiand, Frederick A1 - Frey, Ulrich A1 - Fuchs, Benjamin A1 - Kempe, Nils-Christian A1 - von Krbek, Kai A1 - Medjroubi, Wided A1 - Riehm, Judith A1 - Sasanpour, Shima A1 - Simon, Sonja A1 - Vanaret, Charlie A1 - Wetzel, Manuel A1 - Xiao, Mengzhu A1 - Zittel, Janina T1 - Evaluation of Uncertainties in Linear-Optimizing Energy System Models - Compendium T2 - DLR-Forschungsbericht N2 - Für die Energiesystemforschung sind Software-Modelle ein Kernelement zur Analyse von Szenarien. Das Forschungsprojekt UNSEEN hatte das Ziel eine bisher unerreichte Anzahl an modellbasierten Energieszenarien zu berechnen, um Unsicherheiten – vor allem unter Nutzung linear optimierender Energiesystem-Modelle - besser bewerten zu können. Hierfür wurden umfangreiche Parametervariationen auf Energieszenarien angewendet und das wesentliche methodische Hindernis in diesem Zusammenhang adressiert: die rechnerische Beherrschbarkeit der zu lösenden mathematischen Optimierungsprobleme. Im Vorläuferprojekt BEAM-ME wurde mit der Entwicklung und Anwendung des Open-Source-Lösers PIPS-IPM++ die Grundlage für den Einsatz von High-Performance-Computing (HPC) zur Lösung dieser Modelle gelegt. In UNSEEN war dieser Löser die zentrale Komponente eines Workflows, welcher zur Generierung, Lösung und multi-kriteriellen Bewertung von Energieszenarien auf dem Hochleistungscomputer JUWELS am Forschungszentrum Jülich implementiert wurde. Zur effizienten Generierung und Kommunikation von Modellinstanzen für Methoden der mathematischen Optimierung auf HPC wurde eine weitere Workflow-Komponente von der GAMS Software GmbH entwickelt: der Szenariogenerator. Bei der Weiterentwicklung von Lösungsalgorithmen für linear optimierende Energie-Systemmodelle standen gemischt-ganzzahlige Optimierungsprobleme im Fokus, welche für die Modellierung konkreter Infrastrukturen und Maßnahmen zur Umsetzung der Energiewende gelöst werden müssen. Die in diesem Zusammenhang stehenden Arbeiten zur Entwicklung von Algorithmen wurden von der Technischen Universität Berlin verantwortet. Bei Design und Implementierung dieser Methoden wurde sie vom Zuse Instituts Berlin unterstützt. Y1 - 2023 U6 - https://doi.org/10.57676/w2rq-bj85 IS - DLR-FB-2023-15 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Kuen, Lilli A1 - Burger, Sven T1 - Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2024 U6 - https://doi.org/10.1016/j.softx.2024.101694 VL - 26 SP - 101694 ER - TY - JOUR A1 - Mukherjee, Deshabrato A1 - Kertész, Krisztián A1 - Zolnai, Zsolt A1 - Kovács, Zoltán A1 - Deák, András A1 - Pálinkás, András A1 - Osváth, Zoltán A1 - Olasz, Dániel A1 - Romanenko, Alekszej A1 - Fried, Miklós A1 - Burger, Sven A1 - Sáfrán, György A1 - Petrik, Peter T1 - Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing Y1 - 2024 U6 - https://doi.org/10.2139/ssrn.4752470 ER - TY - JOUR A1 - Kofler, Andreas A1 - Wald, Christian A1 - Kolbitsch, Christoph A1 - von Tycowicz, Christoph A1 - Ambellan, Felix T1 - Joint Reconstruction and Segmentation in Undersampled 3D Knee MRI combining Shape Knowledge and Deep Learning JF - Physics in Medicine and Biology N2 - Task-adapted image reconstruction methods using end-to-end trainable neural networks (NNs) have been proposed to optimize reconstruction for subsequent processing tasks, such as segmentation. However, their training typically requires considerable hardware resources and thus, only relatively simple building blocks, e.g. U-Nets, are typically used, which, albeit powerful, do not integrate model-specific knowledge. In this work, we extend an end-to-end trainable task-adapted image reconstruction method for a clinically realistic reconstruction and segmentation problem of bone and cartilage in 3D knee MRI by incorporating statistical shape models (SSMs). The SSMs model the prior information and help to regularize the segmentation maps as a final post-processing step. We compare the proposed method to a state-of-the-art (SOTA) simultaneous multitask learning approach for image reconstruction and segmentation (MTL) and to a complex SSMs-informed segmentation pipeline (SIS). Our experiments show that the combination of joint end-to-end training and SSMs to further regularize the segmentation maps obtained by MTL highly improves the results, especially in terms of mean and maximal surface errors. In particular, we achieve the segmentation quality of SIS and, at the same time, a substantial model reduction that yields a five-fold decimation in model parameters and a computational speedup of an order of magnitude. Remarkably, even for undersampling factors of up to R=8, the obtained segmentation maps are of comparable quality to those obtained by SIS from ground-truth images. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6560/ad3797 VL - 69 IS - 9 ER - TY - GEN A1 - Bolusani, Suresh A1 - Besançon, Mathieu A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Dionísio, João A1 - Donkiewicz, Tim A1 - van Doornmalen, Jasper A1 - Eifler, Leon A1 - Ghannam, Mohammed A1 - Gleixner, Ambros A1 - Graczyk, Christoph A1 - Halbig, Katrin A1 - Hedtke, Ivo A1 - Hoen, Alexander A1 - Hojny, Christopher A1 - van der Hulst, Rolf A1 - Kamp, Dominik A1 - Koch, Thorsten A1 - Kofler, Kevin A1 - Lentz, Jurgen A1 - Manns, Julian A1 - Mexi, Gioni A1 - Mühmer, Erik A1 - E. Pfetsch, Marc A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Turner, Mark A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Xu, Liding T1 - The SCIP Optimization Suite 9.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization, centered around the constraint integer programming framework SCIP. This report discusses the enhancements and extensions included in the SCIP Optimization Suite 9.0. The updates in SCIP 9.0 include improved symmetry handling, additions and improvements of nonlinear handlers and primal heuristics, a new cut generator and two new cut selection schemes, a new branching rule, a new LP interface, and several bug fixes. The SCIP Optimization Suite 9.0 also features new Rust and C++ interfaces for SCIP, new Python interface for SoPlex, along with enhancements to existing interfaces. The SCIP Optimization Suite 9.0 also includes new and improved features in the LP solver SoPlex, the presolving library PaPILO, the parallel framework UG, the decomposition framework GCG, and the SCIP extension SCIP-SDP. These additions and enhancements have resulted in an overall performance improvement of SCIP in terms of solving time, number of nodes in the branch-and-bound tree, as well as the reliability of the solver. T3 - ZIB-Report - 24-02-29 KW - Constraint integer programming KW - Linear programming KW - Mixed-integer linear programming KW - Mixed-integer nonlinear programming KW - Optimization solver KW - Branch-and-cut KW - Branch-and-price KW - Column generation KW - Parallelization KW - Mixed-integer semidefinite programming Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-95528 SN - 1438-0064 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Tesch, Alexander T1 - Approximating rolling stock rotations with integrated predictive maintenance JF - Journal of Rail Transport Planning & Management N2 - We study the solution of the rolling stock rotation problem with predictive maintenance (RSRP-PdM) by an iterative refinement approach that is based on a state-expanded event-graph. In this graph, the states are parameters of a failure distribution, and paths correspond to vehicle rotations with associated health state approximations. An optimal set of paths including maintenance can be computed by solving an integer linear program. Afterwards, the graph is refined and the procedure repeated. An associated linear program gives rise to a lower bound that can be used to determine the solution quality. Computational results for six instances derived from real-world timetables of a German railway company are presented. The results show the effectiveness of the approach and the quality of the solutions. Y1 - 2024 U6 - https://doi.org/10.1016/j.jrtpm.2024.100434 VL - 30 SP - 100434 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Rabben, Robert Julian A1 - Chewle, Surahit A1 - Weber, Marcus T1 - Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions N2 - Markov processes serve as foundational models in many scientific disciplines, such as molecular dynamics, and their simulation forms a common basis for analysis. While simulations produce useful trajectories, obtaining macroscopic information directly from microstate data presents significant challenges. This paper addresses this gap by introducing the concept of membership functions being the macrostates themselves. We derive equations for the holding times of these macrostates and demonstrate their consistency with the classical definition. Furthermore, we discuss the application of the ISOKANN method for learning these quantities from simulation data. In addition, we present a novel method for extracting transition paths based on the ISOKANN results and demonstrate its efficacy by applying it to simulations of the 𝜇-opioid receptor. With this approach we provide a new perspective on analyzing the macroscopic behaviour of Markov systems. Y1 - 2024 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Niknejad, Amir A1 - Weber, Marcus A1 - Donati, Luca T1 - Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies JF - Journal of Chemical Physics N2 - Estimating the rate of rare conformational changes in molecular systems is one of the goals of molecular dynamics simulations. In the past few decades, a lot of progress has been done in data-based approaches toward this problem. In contrast, model-based methods, such as the Square Root Approximation (SqRA), directly derive these quantities from the potential energy functions. In this article, we demonstrate how the SqRA formalism naturally blends with the tensor structure obtained by coupling multiple systems, resulting in the tensor-based Square Root Approximation (tSqRA). It enables efficient treatment of high-dimensional systems using the SqRA and provides an algebraic expression of the impact of coupling energies between molecular subsystems. Based on the tSqRA, we also develop the projected rate estimation, a hybrid data-model-based algorithm that efficiently estimates the slowest rates for coupled systems. In addition, we investigate the possibility of integrating low-rank approximations within this framework to maximize the potential of the tSqRA. Y1 - 2024 U6 - https://doi.org/10.1063/5.0187792 VL - 160 SP - 104112 ER - TY - CHAP A1 - Mexi, Gioni A1 - Shamsi, Somayeh A1 - Besançon, Mathieu A1 - Bodic, Pierre T1 - Probabilistic Lookahead Strong Branching via a Stochastic Abstract Branching Model T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research. CPAIOR 2024 N2 - Strong Branching (SB) is a cornerstone of all modern branching rules used in the Branch-and-Bound (BnB) algorithm, which is at the center of Mixed-Integer Programming solvers. In its full form, SB evaluates all variables to branch on and then selects the one producing the best relaxation, leading to small trees, but high runtimes. State-of-the-art branching rules therefore use SB with working limits to achieve both small enough trees and short run times. So far, these working limits have been established empirically. In this paper, we introduce a theoretical approach to guide how much SB to use at each node within the BnB. We first define an abstract stochastic tree model of the BnB algorithm where the geometric mean dual gains of all variables follow a given probability distribution. This model allows us to relate expected dual gains to tree sizes and explicitly compare the cost of sampling an additional SB candidate with the reward in expected tree size reduction. We then leverage the insight from the abstract model to design a new stopping criterion for SB, which fits a distribution to the dual gains and, at each node, dynamically continues or interrupts SB. This algorithm, which we refer to as Probabilistic Lookahead Strong Branching, improves both the tree size and runtime over MIPLIB instances, providing evidence that the method not only changes the amount of SB, but allocates it better. Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-60599-4_4 VL - 14743 ER - TY - JOUR A1 - Tjusila, Gennesaret A1 - Besançon, Mathieu A1 - Turner, Mark A1 - Koch, Thorsten T1 - How Many Clues To Give? A Bilevel Formulation For The Minimum Sudoku Clue Problem JF - Operations Research Letters N2 - It has been shown that any 9 by 9 Sudoku puzzle must contain at least 17 clues to have a unique solution. This paper investigates the more specific question: given a particular completed Sudoku grid, what is the minimum number of clues in any puzzle whose unique solution is the given grid? We call this problem the Minimum Sudoku Clue Problem (MSCP). We formulate MSCP as a binary bilevel linear program, present a class of globally valid inequalities, and provide a computational study on 50 MSCP instances of 9 by 9 Sudoku grids. Using a general bilevel solver, we solve 95% of instances to optimality, and show that the solution process benefits from the addition of a moderate amount of inequalities. Finally, we extend the proposed model to other combinatorial problems in which uniqueness of the solution is of interest. Y1 - 2024 U6 - https://doi.org/10.1016/j.orl.2024.107105 VL - 54 SP - 107105 ER - TY - CHAP A1 - Sharma, Kartikey A1 - Hendrych, Deborah A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Network Design for the Traffic Assignment Problem with Mixed-Integer Frank-Wolfe T2 - Proceedings of INFORMS Optimization Society Conference Y1 - 2024 ER - TY - JOUR A1 - Breugem, Thomas A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Borndörfer, Ralf T1 - A three-phase heuristic for the Fairness-Oriented Crew Rostering Problem JF - Computers & Operations Research N2 - The Fairness-Oriented Crew Rostering Problem (FCRP) considers the joint optimization of attractiveness and fairness in cyclic crew rostering. Like many problems in scheduling and logistics, the combinatorial complexity of cyclic rostering causes exact methods to fail for large-scale practical instances. In case of the FCRP, this is accentuated by the additionally imposed fairness requirements. Hence, heuristic methods are necessary. We present a three-phase heuristic for the FCRP combining column generation techniques with variable-depth neighborhood search. The heuristic exploits different mathematical formulations to find feasible solutions and to search for improvements. We apply our methodology to practical instances from Netherlands Railways (NS), the main passenger railway operator in the Netherlands Our results show the three-phase heuristic finds good solutions for most instances and outperforms a state-of-the-art commercial solver. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1016/j.cor.2023.106186 VL - 154 ER - TY - GEN A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Source code and simulation results: Computing eigenfrequency sensitivities near exceptional points T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10715639 SP - doi: 10.5281/zenodo.10715639 ER - TY - JOUR A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Computing eigenfrequency sensitivities near exceptional points JF - Phys. Rev. Research Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.023148 VL - 6 SP - 023148 ER - TY - GEN A1 - Iommazzo, Gabriele A1 - D'Ambrosio, Claudia A1 - Frangioni, Antonio A1 - Liberti, Leo T1 - Algorithm configuration problem T2 - Encyclopedia of Optimization Y1 - 2022 ER - TY - GEN A1 - Gahururu, Deborah A1 - Hintermüller, Michael A1 - Stengl, Steven-Marian A1 - Surowiec, Thomas M. T1 - Generalized Nash equilibrium problems with partial differential operators: theory, algorithms, and risk aversion T2 - Non-smooth and Complementarity-based Distributed Parameter Systems: Simulation and Hierarchical Optimization Y1 - 2022 ER - TY - JOUR A1 - Kreimeier, Timo A1 - Pokutta, Sebastian A1 - Walther, Andrea A1 - Woodstock, Zev T1 - On a Frank-Wolfe approach for abs-smooth functions JF - Optimization Methods and Software Y1 - U6 - https://doi.org/10.1080/10556788.2023.2296985 ER - TY - JOUR A1 - Hunkenschröder, Christoph A1 - Pokutta, Sebastian A1 - Weismantel, Robert T1 - Optimizing a low-dimensional convex function over a high-dimensional cube JF - SIAM Journal on Optimization Y1 - 2022 ER - TY - CHAP A1 - Thuerck, Daniel A1 - Sofranac, Boro A1 - Pfetsch, Marc A1 - Pokutta, Sebastian T1 - Learning cuts via enumeration oracles T2 - Proceedings of Conference on Neural Information Processing Systems Y1 - 2023 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Pokutta, Sebastian T1 - Accelerated Riemannian optimization: Handling constraints with a prox to bound geometric penalties T2 - Proceedings of Optimization for Machine Learning (NeurIPS Workshop OPT 2022) Y1 - 2022 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Roux, Christophe A1 - Criscitiello, Christopher A1 - Pokutta, Sebastian T1 - Accelerated Riemannian Min-Max Optimization Ensuring Bounded Geometric Penalties T2 - Proceedings of Optimization for Machine Learning (NeurIPS Workshop OPT 2023) Y1 - 2023 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Vértesi, Tamás A1 - Pokutta, Sebastian T1 - Symmetric multipartite Bell inequalities via Frank-Wolfe algorithms JF - Physics Review A N2 - In multipartite Bell scenarios, we study the nonlocality robustness of the Greenberger-Horne-Zeilinger (GHZ) state. When each party performs planar measurements forming a regular polygon, we exploit the symmetry of the resulting correlation tensor to drastically accelerate the computation of (i) a Bell inequality via Frank-Wolfe algorithms and (ii) the corresponding local bound. The Bell inequalities obtained are facets of the symmetrized local polytope and they give the best-known upper bounds on the nonlocality robustness of the GHZ state for three to ten parties. Moreover, for four measurements per party, we generalize our facets and hence show, for any number of parties, an improvement on Mermin's inequality in terms of noise robustness. We also compute the detection efficiency of our inequalities and show that some give rise to the activation of nonlocality in star networks, a property that was only shown with an infinite number of measurements. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevA.109.022205 VL - 109 IS - 2 ER - TY - CHAP A1 - Ghannam, Mohammed A1 - Gleixner, Ambros T1 - Hybrid genetic search for dynamic vehicle routing with time windows T2 - Proceedings of Conference of the Society for Operations Research in Germany Y1 - 2023 ER - TY - CHAP A1 - Hoen, Alexander A1 - Oertel, Andy A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Certifying MIP-based presolve reductions for 0-1 integer linear programs T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research. CPAIOR 2024 N2 - It is well known that reformulating the original problem can be crucial for the performance of mixed-integer programming (MIP) solvers. To ensure correctness, all transformations must preserve the feasibility status and optimal value of the problem, but there is currently no established methodology to express and verify the equivalence of two mixed-integer programs. In this work, we take a first step in this direction by showing how the correctness of MIP presolve reductions on – integer linear programs can be certified by using (and suitably extending) the VeriPB tool for pseudo-Boolean proof logging. Our experimental evaluation on both decision and optimization instances demonstrates the computational viability of the approach and leads to suggestions for future revisions of the proof format that will help to reduce the verbosity of the certificates and to accelerate the certification and verification process further. Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-60597-0_20 VL - 14742 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and verified Gomory mixed integer cuts in a rational MIP framework JF - SIAM Journal on Optimization N2 - This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009 [INFORMS J. Comput., 21 (2009), pp. 641–649]. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5% more instances to exact optimality and reduce solving times by 26.8% on the MIPLIB 2017 benchmark test set. Y1 - 2024 U6 - https://doi.org/10.1137/23M156046X VL - 34 IS - 1 ER - TY - GEN A1 - Musial, Anna A1 - Sek, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Reitzenstein, Stephan T1 - Fiber-coupled solid-state-based single-photon sources T2 - Specialty Optical Fibers Y1 - 2024 U6 - https://doi.org/10.1016/B978-0-443-18495-6.00004-4 SP - 345 EP - 384 PB - Woodhead Publishing ER - TY - GEN A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Research data for "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes" T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.8131611 SP - doi: 10.5281/zenodo.8131611 ER - TY - JOUR A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes JF - J. Opt. Soc. Am. B Y1 - 2024 U6 - https://doi.org/10.1364/JOSAB.505767 VL - 41 SP - 850 ER - TY - JOUR A1 - Zhao, Yue A1 - Zhang, Wei A1 - Li, Tiejun T1 - EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation JF - National Science Review N2 - We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice mathematical fact that the desired negative potential gradient is simply the orthogonal projection of the driving force of the underlying dynamics in a weighted inner-product space. Remarkably, our loss function has an intimate connection with the steady entropy production rate (EPR), enabling simultaneous landscape construction and EPR estimation. We introduce an enhanced learning strategy for systems with small noise, and extend our framework to include dimensionality reduction and state-dependent diffusion coefficient case in a unified fashion. Comparative evaluations on benchmark problems demonstrate the superior accuracy, effectiveness, and robustness of EPR-Net compared to existing methods. We apply our approach to challenging biophysical problems, such as an 8D limit cycle and a 52D multi-stability problem, which provide accurate solutions and interesting insights on constructed landscapes. With its versatility and power, EPR-Net offers a promising solution for diverse landscape construction problems in biophysics. Y1 - 2024 U6 - https://doi.org/10.1093/nsr/nwae052 VL - 11 IS - 7 ER - TY - JOUR A1 - Euler, Ricardo A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - Price optimal routing in public transportation JF - EURO Journal on Transportation and Logistics KW - Management Science and Operations Research KW - Transportation KW - Modeling and Simulation Y1 - 2024 U6 - https://doi.org/10.1016/j.ejtl.2024.100128 SN - 2192-4376 VL - 13 SP - 1 EP - 15 PB - Elsevier BV ER - TY - CHAP A1 - Steyer, Joshua A1 - Chegini, Fatemeh A1 - Potse, Mark A1 - Loewe, Axel A1 - Weiser, Martin T1 - Continuity of Microscopic Cardiac Conduction in a Computational Cell-by-Cell Model T2 - 2023 Computing in Cardiology Conference (CinC) N2 - Conduction velocity in cardiac tissue is a crucial electrophysiological parameter for arrhythmia vulnerability. Pathologically reduced conduction velocity facilitates arrhythmogenesis because such conduction velocities decrease the wavelength with which re-entry may occur. Computational studies on CV and how it changes regionally in models at spatial scales multiple times larger than actual cardiac cells exist. However, microscopic conduction within cells and between them have been studied less in simulations. In this work, we study the relation of microscopic conduction patterns and clinically observable macroscopic conduction using an extracellular-membrane-intracellular model which represents cardiac tissue with these subdomains at subcellular resolution. By considering cell arrangement and non-uniform gap junction distribution, it yields anisotropic excitation propagation. This novel kind of model can for example be used to understand how discontinuous conduction on the microscopic level affects fractionation of electrograms in healthy and fibrotic tissue. Along the membrane of a cell, we observed a continuously propagating activation wavefront. When transitioning from one cell to the neighbouring one, jumps in local activation times occurred, which led to lower global conduction velocities than locally within each cell. Y1 - 2023 U6 - https://doi.org/10.22489/CinC.2023.385 SN - 2325-887X VL - 50 PB - Computing in Cardiology ER - TY - JOUR A1 - Hennings, Felix A1 - Hoppmann-Baum, Kai A1 - Zittel, Janina T1 - Optimizing transient gas network control for challenging real-world instances using MIP-based heuristics JF - Open Journal of Mathematical Optimization Y1 - 2024 U6 - https://doi.org/10.5802/ojmo.29 VL - 5 ER - TY - JOUR A1 - Hanik, Martin A1 - Navayazdani, Esfandiar A1 - von Tycowicz, Christoph T1 - De Casteljau's Algorithm in Geometric Data Analysis: Theory and Application JF - Computer Aided Geometric Design N2 - For decades, de Casteljau's algorithm has been used as a fundamental building block in curve and surface design and has found a wide range of applications in fields such as scientific computing, and discrete geometry to name but a few. With increasing interest in nonlinear data science, its constructive approach has been shown to provide a principled way to generalize parametric smooth curves to manifolds. These curves have found remarkable new applications in the analysis of parameter-dependent, geometric data. This article provides a survey of the recent theoretical developments in this exciting area as well as its applications in fields such as geometric morphometrics and longitudinal data analysis in medicine, archaeology, and meteorology. Y1 - 2024 U6 - https://doi.org/10.1016/j.cagd.2024.102288 VL - 110 SP - 102288 ER - TY - JOUR A1 - Navayazdani, Esfandiar T1 - On Geodesics in the Spaces of Constrained Curves JF - Journal of Differential Geometry and its Applications N2 - In this work, we study the geodesics of the space of certain geometrically and physically motivated subspaces of the space of immersed curves endowed with a first order Sobolev metric. This includes elastic curves and also an extension of some results on planar concentric circles to surfaces. The work focuses on intrinsic and constructive approaches. Y1 - 2024 ER - TY - JOUR A1 - Amiranashvili, Tamaz A1 - Lüdke, David A1 - Li, Hongwei Bran A1 - Zachow, Stefan A1 - Menze, Bjoern T1 - Learning continuous shape priors from sparse data with neural implicit functions JF - Medical Image Analysis N2 - Statistical shape models are an essential tool for various tasks in medical image analysis, including shape generation, reconstruction and classification. Shape models are learned from a population of example shapes, which are typically obtained through segmentation of volumetric medical images. In clinical practice, highly anisotropic volumetric scans with large slice distances are prevalent, e.g., to reduce radiation exposure in CT or image acquisition time in MR imaging. For existing shape modeling approaches, the resolution of the emerging model is limited to the resolution of the training shapes. Therefore, any missing information between slices prohibits existing methods from learning a high-resolution shape prior. We propose a novel shape modeling approach that can be trained on sparse, binary segmentation masks with large slice distances. This is achieved through employing continuous shape representations based on neural implicit functions. After training, our model can reconstruct shapes from various sparse inputs at high target resolutions beyond the resolution of individual training examples. We successfully reconstruct high-resolution shapes from as few as three orthogonal slices. Furthermore, our shape model allows us to embed various sparse segmentation masks into a common, low-dimensional latent space — independent of the acquisition direction, resolution, spacing, and field of view. We show that the emerging latent representation discriminates between healthy and pathological shapes, even when provided with sparse segmentation masks. Lastly, we qualitatively demonstrate that the emerging latent space is smooth and captures characteristic modes of shape variation. We evaluate our shape model on two anatomical structures: the lumbar vertebra and the distal femur, both from publicly available datasets. Y1 - 2024 U6 - https://doi.org/10.1016/j.media.2024.103099 VL - 94 SP - 103099 ER - TY - GEN A1 - Lindner, Niels A1 - Masing, Berenike T1 - SAT-Generated Initial Solutions for Integrated Line Planning and Turn-Sensitive Periodic Timetabling with Track Choice N2 - Periodic timetabling is a challenging planning task in public transport. As safety requirements are crucial, track allocation is indispensable for validating the practical feasibility of a railway timetable. For busy stations with limited capacities, this requires a detailed planning of turnarounds. It is therefore desirable to integrate timetabling not only with track allocation, but also with vehicle scheduling and line planning. This is captured by the Integrated Line Planning and Turn-Sensitive Periodic Timetabling Problem with Track Choice, whose MIP formulation has been demonstrated to be effective for construction site railway rescheduling, as long as a good quality initial solution is available. In this paper, we discuss how to generate such a solution by extending the SAT formulation of the Periodic Event Scheduling Problem with track choice, track occupation, and minimum service frequency components. The SAT approach is superior to pure MIP on real-world instances of the S-Bahn Berlin network. T3 - ZIB-Report - 24-01 KW - Periodic Timetabling KW - Railway Timetabling KW - Railway Track Allocation KW - Boolean Satisfiability Problem KW - Rescheduling KW - Line Planning Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-94644 SN - 1438-0064 ER - TY - JOUR A1 - Gaskin, Thomas A1 - Conrad, Tim A1 - Pavliotis, Grigorios A. A1 - Schütte, Christof T1 - Neural parameter calibration and uncertainty quantification for epidemic forecasting JF - PLOS ONE N2 - The recent COVID-19 pandemic has thrown the importance of accurately forecasting contagion dynamics and learning infection parameters into sharp focus. At the same time, effective policy-making requires knowledge of the uncertainty on such predictions, in order, for instance, to be able to ready hospitals and intensive care units for a worst-case scenario without needlessly wasting resources. In this work, we apply a novel and powerful computational method to the problem of learning probability densities on contagion parameters and providing uncertainty quantification for pandemic projections. Using a neural network, we calibrate an ODE model to data of the spread of COVID-19 in Berlin in 2020, achieving both a significantly more accurate calibration and prediction than Markov-Chain Monte Carlo (MCMC)-based sampling schemes. The uncertainties on our predictions provide meaningful confidence intervals e.g. on infection figures and hospitalisation rates, while training and running the neural scheme takes minutes where MCMC takes hours. We show convergence of our method to the true posterior on a simplified SIR model of epidemics, and also demonstrate our method's learning capabilities on a reduced dataset, where a complex model is learned from a small number of compartments for which data is available. Y1 - 2024 ER - TY - JOUR A1 - Donati, Luca A1 - Schütte, Christof A1 - Weber, Marcus T1 - The Kramers turnover in terms of a macro-state projection on phase space JF - Molecular Physics N2 - We have investigated how Langevin dynamics is affected by the friction coefficient using the novel algorithm ISOKANN, which combines the transfer operator approach with modern machine learning techniques. ISOKANN describes the dynamics in terms of an invariant subspace projection of the Koopman operator defined in the entire state space, avoiding approximations due to dimensionality reduction and discretization. Our results are consistent with the Kramers turnover and show that in the low and moderate friction regimes, metastable macro-states and transition rates are defined in phase space, not only in position space. Y1 - 2024 U6 - https://doi.org/10.1080/00268976.2024.2356748 IS - Ciccotti Special Issue (by invitation only) SP - e2356748 PB - Taylor & Francis ER - TY - JOUR A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna JF - Appl. Phys. Lett. Y1 - 2024 U6 - https://doi.org/10.1063/5.0201748 VL - 124 SP - 231102 ER - TY - JOUR A1 - Grimm, Boris A1 - Hoogervorst, Rowan A1 - Borndörfer, Ralf T1 - A Comparison of Models for Rolling Stock Scheduling N2 - A major step in the planning process of passenger railway operators is the assignment of rolling stock, i.e., train units, to the trips of the timetable. A wide variety of mathematical optimization models have been proposed to support this task, which we discuss and argue to be justified in order to deal with operational differences between railway operators, and hence different planning requirements, in the best possible way. Our investigation focuses on two commonly used models, the Composition model and the Hypergraph model, that were developed for Netherlands Railways (NS) and DB Fernverkehr AG (DB), respectively. We compare these models in a rolling stock scheduling setting similar to that of NS, which we show to be strongly NP-hard, and propose different variants of the Hypergraph model to tune the model to the NS setting. We prove that, in this setting, the linear programming bounds of both models are equally strong as long as a Hypergraph model variant is chosen that is sufficiently expressive. However, through a numerical evaluation on NS instances, we show that the Composition model is generally more compact in practice and can find optimal solutions in the shortest running time. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2312.09697 ER - TY - JOUR A1 - Combettes, P. L. A1 - Woodstock, Zev T1 - a variational inequality model for the construction of signals from inconsistent nonlinear equations JF - SIAM Journal on Imaging Sciences Y1 - 2022 ER - TY - CHAP A1 - Combettes, P. L. A1 - Woodstock, Zev T1 - signal recovery from inconsistent nonlinear observations T2 - Proceedings of ICASSP 2022 - 2022 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) Y1 - 2022 ER - TY - JOUR A1 - Wilken, St. Elmo A1 - Besançon, Mathieu A1 - Kratochvíl, Miroslav A1 - Kuate, Chilperic Armel Foko A1 - Trefois, Christophe A1 - Gu, Wei A1 - Ebenhöh, Oliver T1 - Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models JF - Metabolic Engineering Y1 - 2022 ER - TY - CHAP A1 - Gasse, Maxime A1 - Bowly, Simon A1 - Cappart, Quentin A1 - Charfreitag, Jonas A1 - Charlin, Laurent A1 - Chételat, Didier A1 - Chmiela, Antonia A1 - Dumouchelle, Justin A1 - Gleixner, Ambros A1 - Kazachkov, Aleksandr M. A1 - Khalil, Elias A1 - Lichocki, Pawel A1 - Lodi, Andrea A1 - Lubin, Miles A1 - Maddison, Chris J. A1 - Christopher, Morris A1 - Papageorgiou, Dimitri J. A1 - Parjadis, Augustin A1 - Pokutta, Sebastian A1 - Prouvost, Antoine A1 - Scavuzzo, Lara A1 - Zarpellon, Giulia A1 - Yang, Linxin A1 - Lai, Sha A1 - Wang, Akang A1 - Luo, Xiaodong A1 - Zhou, Xiang A1 - Huang, Haohan A1 - Shao, Shengcheng A1 - Zhu, Yuanming A1 - Zhang, Dong A1 - Quan, Tao A1 - Cao, Zixuan A1 - Xu, Yang A1 - Huang, Zhewei A1 - Zhou, Shuchang A1 - Binbin, Chen A1 - Minggui, He A1 - Hao, Hao A1 - Zhiyu, Zhang A1 - Zhiwu, An A1 - Kun, Mao T1 - The Machine Learning for Combinatorial Optimization Competition (ML4CO): results and insights T2 - Proceedings of Conference on Neural Information Processing Systems Y1 - 2022 ER - TY - CHAP A1 - Búi, M. N. A1 - Combettes, P. L. A1 - Woodstock, Zev T1 - block-activated algorithms for multicomponent fully nonsmooth minimization T2 - Proceedings of ICASSP 2022 - 2022 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) Y1 - 2022 ER - TY - JOUR A1 - Bolusani, Suresh A1 - Ralphs, Ted K. T1 - a framework for generalized Benders' decomposition and its applications to multilevel optimization JF - Mathematical Programming Y1 - 2022 ER - TY - JOUR A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs JF - Mathematical Programming B Y1 - 2023 U6 - https://doi.org/10.1007/s10107-022-01808-5 VL - 197 SP - 549 EP - 586 ER - TY - GEN A1 - Schlechte, Thomas A1 - Blome, Christian A1 - Gerber, Stefan A1 - Hauser, Stefan A1 - Kasten, Jens A1 - Müller, Gilbert A1 - Schulz, Christof A1 - Thüring, Michel A1 - Weider, Steffen T1 - The Bouquet of Features in Rolling Stock Rotation Planning T2 - Conference Proceedings RailBelgrade 2023 N2 - Rolling stock is one of the major assets for a railway transportation company. Hence, their utilization should be as efficiently and effectively as possible. Railway undertakings are facing rolling stock scheduling challenges in different forms - from rather idealized weekly strategic problems to very concrete operational ones. Thus, a vast of optimization models with different features and objectives exist. Thorlacius et al. (2015) provides a comprehensive and valuable collection on technical requirements, models, and methods considered in the scientific literature. We contribute with an update including recent works. The main focus of the paper is to present a classification and elaboration of the major features which our solver R-OPT is able to handle. Moreover, the basic optimization model and algorithmic ingredients of R-OPT are discussed. Finally, we present computational results for a cargo application at SBB CARGO AG and other railway undertakings for passenger traffic in Europe to show the capabilities of R-OPT. Y1 - 2023 UR - https://easychair.org/publications/preprint/Nms6 ER - TY - CHAP A1 - Zimmer, Max A1 - Spiegel, Christoph A1 - Pokutta, Sebastian T1 - Sparse Model Soups T2 - Proceedings of International Conference on Learning Representations Y1 - 2024 ER - TY - CHAP A1 - Wäldchen, Stephan A1 - Sharma, Kartikey A1 - Turan, Berkant A1 - Zimmer, Max A1 - Pokutta, Sebastian T1 - Interpretability Guarantees with Merlin-Arthur Classifiers T2 - Proceedings of The 27th International Conference on Artificial Intelligence and Statistics N2 - We propose an interactive multi-agent classifier that provides provable interpretability guarantees even for complex agents such as neural networks. These guarantees consist of lower bounds on the mutual information between selected features and the classification decision. Our results are inspired by the Merlin-Arthur protocol from Interactive Proof Systems and express these bounds in terms of measurable metrics such as soundness and completeness. Compared to existing interactive setups, we rely neither on optimal agents nor on the assumption that features are distributed independently. Instead, we use the relative strength of the agents as well as the new concept of Asymmetric Feature Correlation which captures the precise kind of correlations that make interpretability guarantees difficult. We evaluate our results on two small-scale datasets where high mutual information can be verified explicitly. Y1 - 2024 UR - https://proceedings.mlr.press/v238/waldchen24a/waldchen24a.pdf VL - 238 SP - 1963 EP - 1971 ER - TY - JOUR A1 - Pokutta, Sebastian T1 - The Frank-Wolfe algorithm: a short introduction JF - Jahresbericht der Deutschen Mathematiker-Vereinigung Y1 - 2023 ER - TY - JOUR A1 - Deza, Antoine A1 - Pokutta, Sebastian A1 - Pournin, Lionel T1 - The complexity of geometric scaling JF - Operations Research Letters Y1 - 2024 U6 - https://doi.org/10.1016/j.orl.2023.11.010 VL - 52 SP - 107057 ER - TY - JOUR A1 - Besançon, Mathieu A1 - Garcia, Joaquim Dias A1 - Legat, Benoît A1 - Sharma, Akshay T1 - Flexible Differentiable Optimization via Model Transformations JF - INFORMS Journal on Computing N2 - We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus leveraging the rich ecosystem of solvers and composing well with modeling languages like JuMP. DiffOpt offers both forward and reverse differentiation modes, enabling multiple use cases from hyperparameter optimization to backpropagation and sensitivity analysis, bridging constrained optimization with end-to-end differentiable programming. DiffOpt is built on two known rules for differentiating quadratic programming and conic programming standard forms. However, thanks to its ability to differentiate through model transformations, the user is not limited to these forms and can differentiate with respect to the parameters of any model that can be reformulated into these standard forms. This notably includes programs mixing affine conic constraints and convex quadratic constraints or objective function. Y1 - 2023 U6 - https://doi.org/10.1287/ijoc.2022.0283 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Iommazzo, Gabriele A1 - Besançon, Mathieu A1 - Knebel, Sebastian A1 - Gelß, Patrick A1 - Pokutta, Sebastian T1 - Improved local models and new Bell inequalities via Frank-Wolfe algorithms JF - Physical Review Research N2 - In Bell scenarios with two outcomes per party, we algorithmically consider the two sides of the membership problem for the local polytope: Constructing local models and deriving separating hyperplanes, that is, Bell inequalities. We take advantage of the recent developments in so-called Frank-Wolfe algorithms to significantly increase the convergence rate of existing methods. First, we study the threshold value for the nonlocality of two-qubit Werner states under projective measurements. Here, we improve on both the upper and lower bounds present in the literature. Importantly, our bounds are entirely analytical; moreover, they yield refined bounds on the value of the Grothendieck constant of order three: 1.4367⩽KG(3)⩽1.4546. Second, we demonstrate the efficiency of our approach in multipartite Bell scenarios, and present local models for all projective measurements with visibilities noticeably higher than the entanglement threshold. We make our entire code accessible as a julia library called BellPolytopes.jl. Y1 - 2023 U6 - https://doi.org/10.1103/PhysRevResearch.5.043059 VL - 5 SP - 043059 ER - TY - CHAP A1 - Criscitiello, Christopher A1 - Martínez-Rubio, David A1 - Boumal, Nicolas T1 - Open problem: polynomial linearly-convergent method for g-convex optimization? T2 - Proceedings of Thirty Sixth Conference on Learning Theory, PMLR Y1 - 2023 UR - https://proceedings.mlr.press/v195/criscitiello23b.html VL - 195 SP - 5950 EP - 5956 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A computational status update for exact rational mixed integer programming JF - Mathematical Programming N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours. Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01749-5 VL - 197 SP - 793 EP - 812 ER - TY - JOUR A1 - Liberti, Leo A1 - Iommazzo, Gabriele A1 - Lavor, Carlile A1 - Maculan, Nelson T1 - Cycle-based formulations in distance geometry JF - Open Journal of Mathematical Optimization N2 - The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension , where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, the formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation and on the existing edge-based formulation. While edge-based formulations take less time to reach termination, cycle-based formulations are generally better on solution quality measures. Y1 - 2023 U6 - https://doi.org/10.5802/ojmo.18 VL - 4 ER - TY - JOUR A1 - Braun, Gábor A1 - Guzmán, Cristóbal A1 - Pokutta, Sebastian T1 - Corrections to “Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization via Information Theory” JF - IEEE Transactions on Information Theory N2 - This note closes a gap in the proof of Theorem VI.3 from the article “Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization via Information Theory” (2017). Y1 - 2024 U6 - https://doi.org/10.1109/TIT.2024.3357200 VL - 70 IS - 7 SP - 5408 EP - 5409 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Besançon, Mathieu A1 - Chen, Wei-Kun A1 - Chmiela, Antonia A1 - Donkiewicz, Tim A1 - Doornmalen, Jasper A1 - Eifler, Leon A1 - Gaul, Oliver A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Graczyk, Christoph A1 - Halbig, Katrin A1 - Hoen, Alexander A1 - Hojny, Christopher A1 - Hulst, Rolf A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Matter, Frederic A1 - Mühmer, Erik A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Rehfeldt, Daniel A1 - Schlein, Steffan A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Sofranac, Boro A1 - Turner, Mark A1 - Vigerske, Stefan A1 - Wegscheider, Fabian A1 - Wellner, Philipp A1 - Weninger, Dieter A1 - Witzig, Jakob T1 - Enabling research through the SCIP optimization suite 8.0 JF - ACM Transactions on Mathematical Software N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. The focus of this article is on the role of the SCIP Optimization Suite in supporting research. SCIP’s main design principles are discussed, followed by a presentation of the latest performance improvements and developments in version 8.0, which serve both as examples of SCIP’s application as a research tool and as a platform for further developments. Furthermore, this article gives an overview of interfaces to other programming and modeling languages, new features that expand the possibilities for user interaction with the framework, and the latest developments in several extensions built upon SCIP. Y1 - 2023 U6 - https://doi.org/10.1145/3585516 VL - 49 IS - 2 SP - 1 EP - 21 ER - TY - JOUR A1 - Hanik, Martin A1 - Steidl, Gabriele A1 - von Tycowicz, Christoph T1 - Manifold GCN: Diffusion-based Convolutional Neural Network for Manifold-valued Graphs N2 - We propose two graph neural network layers for graphs with features in a Riemannian manifold. First, based on a manifold-valued graph diffusion equation, we construct a diffusion layer that can be applied to an arbitrary number of nodes and graph connectivity patterns. Second, we model a tangent multilayer perceptron by transferring ideas from the vector neuron framework to our general setting. Both layers are equivariant with respect to node permutations and isometries of the feature manifold. These properties have been shown to lead to a beneficial inductive bias in many deep learning tasks. Numerical examples on synthetic data as well as on triangle meshes of the right hippocampus to classify Alzheimer's disease demonstrate the very good performance of our layers. Y1 - 2024 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Kostova, Simona A1 - Maseko, Sibusiso B. A1 - Gang Choi, Soon A1 - Blavier, Jeremy A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J. A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A. A1 - Hill, David E. A1 - Landthaler, Markus A1 - Olivet, Julien A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E. T1 - AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - bioRxiv Y1 - 2023 U6 - https://doi.org/10.1101/2023.06.14.544560 ER - TY - JOUR A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties JF - Journal of Geophysical Research: Planets N2 - The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes. Y1 - 2024 U6 - https://doi.org/10.1029/2023JE008152 VL - 129 IS - 3 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Non-gravitational acceleration and torque on comet 67P/Churyumov-Gerasimenko T2 - Bulletin of the AAS N2 - From August 2014 to September 2016, the ESA operated the Rosetta spacecraft mission alongside with comet 67P/Churyumov-Gerasimenko (67P). The mission provided valuable long-term data on the comet’s nucleus, including its volume, mass, tensor of inertia, spatial position of the orbital trajectory, and rotational state. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i218p02 VL - 55 IS - 8 ER - TY - JOUR A1 - Majewski, Maciej A1 - Pérez, Adrià A1 - Thölke, Philipp A1 - Doerr, Stefan A1 - Charron, Nicholas A1 - Giorgino, Toni A1 - Husic, Brooke A1 - Clementi, Cecilia A1 - Noé, Frank A1 - De Fabritiis, Gianni T1 - Machine learning coarse-grained potentials of protein thermodynamics JF - Nature Communications N2 - A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-41343-1 VL - 14 ER - TY - CHAP A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - Investigating the Latitudinal Dependence of Lunar Regolith Properties Using LRO/Diviner Data and a Microphysical Thermal Model T2 - Bulletin of the AAS N2 - Regolith is formed through weathering of the local rock by meteorite bombardment, space weathering (Pieters & Noble, 2016) and thermal erosion (Delbo et al., 2014). In the case of the Moon, the space weathering effects and diurnal temperature variations are reduced towards the poles. The aim of this study is to investigate whether the lunar regolith properties derived from the comparison of regolith temperatures measured by the Diviner radiometer (Paige et al., 2010) on board the Lunar Reconnaissance Orbiter (LRO) with simulated temperatures derived from a microphysical thermal model show a latitudinal dependence. The developed microphysical thermal model expands upon previous models by more directly simulating regolith properties, such as grain radius and volume filling factor. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i207p02 VL - 55 IS - 8 ER - TY - JOUR A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Templeton, Clark A1 - Musil, Félix A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Chen, Yaoyi A1 - Kelkar, Atharva A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Machine learned coarse-grained protein force-fields: Are we there yet? JF - Current Opinion in Structural Biology N2 - The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning of force-fields at coarser resolutions is rapidly gaining relevance as an efficient way to represent the higher-body interactions needed in coarse-grained force-fields to compensate for the omitted degrees of freedom. Coarse-grained models are important for the study of systems at time and length scales exceeding those of atomistic simulations. However, the development of transferable coarse-grained models via machine learning still presents significant challenges. Here, we discuss recent developments in this field and current efforts to address the remaining challenges. Y1 - 2023 U6 - https://doi.org/10.1016/j.sbi.2023.102533 VL - 79 ER - TY - JOUR A1 - Krämer, Andreas A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Chen, Yaoyi A1 - Clementi, Cecilia A1 - Noé, Frank T1 - Statistically optimal force aggregation for coarse-graining molecular dynamics JF - The Journal of Physical Chemistry Letters N2 - Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used methodology for learning bottom-up CG force fields maps forces from all-atom molecular dynamics to the CG representation and matches them with a CG force field on average. We show that there is flexibility in how to map all-atom forces to the CG representation and that the most commonly used mapping methods are statistically inefficient and potentially even incorrect in the presence of constraints in the all-atom simulation. We define an optimization statement for force mappings and demonstrate that substantially improved CG force fields can be learned from the same simulation data when using optimized force maps. The method is demonstrated on the miniproteins chignolin and tryptophan cage and published as open-source code. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpclett.3c00444 VL - 14 IS - 17 SP - 3970 EP - 3979 ER - TY - JOUR A1 - Koyanagi, Gregory K. A1 - Lambo, Ricardo Lewis A1 - Ragyanszki, Anita A1 - Fournier, Rene A. A1 - Horbatsch, Marko W. A1 - Hessels, Eric A. T1 - Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment JF - Journal of Molecular Spectroscopy Y1 - 2023 U6 - https://doi.org/10.1016/j.jms.2023.111736 VL - 391 SP - 111736 ER - TY - JOUR A1 - Lambo, Ricardo Lewis A1 - Koyanagi, Gregory K. A1 - Ragyanszki, Anita A1 - Horbatsch, Marko A1 - Fournier, Rene A1 - Hessels, Eric A. T1 - Calculation of the local environment of a barium monofluoride molecule in an argon matrix: a step towards using matrix-isolated BaF for determining the electron electric dipole moment JF - Molecular Physics Y1 - 2023 U6 - https://doi.org/10.1080/00268976.2023.2198044 VL - 121 IS - 6 ER - TY - THES A1 - Chewle, Surahit T1 - Probing effects of organic solvents on paracetamol crystallization using in silico and orthogonal in situ methods N2 - Polymorphism is the property exhibited by many inorganic and organic molecules to crystallize in more than one crystal structure. There is a strong need for understanding the influencing factors on polymorphism, as it is responsible for differences in many physicochemical properties such as stability and solubility. Nearly 80 % of marketed drugs exhibit polymorphism. In this work, we took the model system of paracetamol to investigate the influence of solvent choice on its polymorphism. Different methods were developed and employed to understand the influence of small organic solvents on the crystallization of paracetamol. Non-equilibrium molecular dynamics simulations with periodic simulated annealing were used as a tool to probe the nature of precursors of the metastable intermediates occurring in the crystallization process. Using this method, it was found that the structures of the building blocks of crystals of paracetamol is governed by solvent-solute interactions. In situ Raman spectroscopy was used with a custom-made acoustic levitator to follow crystallization. This set-up is a reliable method for investigating solvent influence, attenuating heterogeneous nucleation and stabilizing other environmental factors. It was established that as a solvent, ethanol is much stronger than methanol in its effect of driving paracetamol solutions to their crystal form. The time-resolved Raman spectroscopy crystallization data was processed using a newly developed objective function based non-negative matrix factorization method (NMF). An orthogonal time-lapse photography was used in conjunction with NMF to get unique and accurate factors that pertain to the spectra and concentrations of different moieties of paracetamol crystallization existing as latent components in the untreated data. Y1 - 2023 UR - https://edoc.hu-berlin.de/handle/18452/27957 ER - TY - CHAP A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - On the state of QUBO solving T2 - Operations Research Proceedings 2023 N2 - It is regularly claimed that quantum computers will bring breakthrough progress in solving challenging combinatorial optimization problems relevant in practice. In particular, Quadratic Unconstrained Binary Optimization (QUBO) problems are said to be the model of choice for use in (adiabatic) quantum systems during the noisy intermediate- scale quantum (NISQ) era. Even the first commercial quantum-based systems are advertised to solve such problems. Theoretically, any Integer Program can be converted into a QUBO. In practice, however, there are some caveats, as even for problems that can be nicely modeled as a QUBO, this might not be the most effective way to solve them. We review the state of QUBO solving on digital and quantum computers and provide insights regarding current benchmark instances and modeling. Y1 - 2023 ER - TY - JOUR A1 - Steudle, Gesine A1 - Winkelmann, Stefanie A1 - Fürst, Steffen A1 - Wolf, Sarah T1 - Understanding Memory Mechanisms in Socio-Technical Systems: the Case of an Agent-based Mobility Model JF - Advances in Complex Systems N2 - This paper explores memory mechanisms in complex socio-technical systems, using a mobility demand model as an example case. We simplified a large-scale agent-based mobility model into a Markov process and discover that the mobility decision process is non-Markovian. This is due to its dependence on the system’s history, including social structure and local infrastructure, which evolve based on prior mobility decisions. To make the process Markovian, we extend the state space by incorporating two history-dependent components. Although our model is a very much reduced version of the original one, it remains too complex for the application of usual analytic methods. Instead, we employ simulations to examine the functionalities of the two history-dependent components. We think that the structure of the analyzed stochastic process is exemplary for many socio-technical, -economic, -ecological systems. Additionally, it exhibits analogies with the framework of extended evolution, which has previously been used to study cultural evolution. Y1 - 2024 U6 - https://doi.org/10.1142/S0219525924400034 VL - 27 ER - TY - CHAP A1 - Steyer, Joshua A1 - Chegini, Fatemeh A1 - Starý, Tomas A1 - Potse, Mark A1 - Weiser, Martin A1 - Loewe, Axel T1 - Electrograms in a Cardiac Cell-by-Cell Model N2 - Cardiac electrograms are an important tool to study the spread of excitation waves inside the heart, which in turn underlie muscle contraction. Electrograms can be used to analyse the dynamics of these waves, e.g. in fibrotic tissue. In computational models, these analyses can be done with greater detail than during minimally invasive in vivo procedures. Whilst homogenised models have been used to study electrogram genesis, such analyses have not yet been done in cellularly resolved models. Such high resolution may be required to develop a thorough understanding of the mechanisms behind abnormal excitation patterns leading to arrhythmias. In this study, we derived electrograms from an excitation propagation simulation in the Extracellular, Membrane, Intracellular (EMI) model, which represents these three domains explicitly in the mesh. We studied the effects of the microstructural excitation dynamics on electrogram genesis and morphology. We found that electrograms are sensitive to the myocyte alignment and connectivity, which translates into micro-fractionations in the electrograms. Y1 - 2024 ER - TY - CHAP A1 - Witzke, Joel A1 - Schintke, Florian A1 - Lößer, Ansgar A1 - Scheuermann, Björn T1 - Proactive Resource Management to Optimize Distributed Workflow Executions T2 - IEEE International Conference on Big Data, BigData 2023, Sorrento, Italy, December 15-18, 2023 Y1 - 2023 U6 - https://doi.org/10.1109/BigData59044.2023.10386493 SP - 6305 EP - 6307 PB - IEEE ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Froehly, Algiane A1 - Huynh, Ngoc Mai Monica A1 - Pavarino, Luca A1 - Potse, Mark A1 - Scacchi, Simone A1 - Weiser, Martin T1 - Efficient numerical methods for simulating cardiac electrophysiology with cellular resolution T2 - 10th Int. Conf. Computational Methods for Coupled Problems in Science and Engineering 2023 N2 - The cardiac extracellular-membrane-intracellular (EMI) model enables the precise geometrical representation and resolution of aggregates of individual myocytes. As a result, it not only yields more accurate simulations of cardiac excitation compared to homogenized models but also presents the challenge of solving much larger problems. In this paper, we introduce recent advancements in three key areas: (i) the creation of artificial, yet realistic grids, (ii) efficient higher-order time stepping achieved by combining low-overhead spatial adaptivity on the algebraic level with progressive spectral deferred correction methods, and (iii) substructuring domain decomposition preconditioners tailored to address the complexities of heterogeneous problem structures. The efficiency gains of these proposed methods are demonstrated through numerical results on cardiac meshes of different sizes. Y1 - 2023 UR - https://www.scipedia.com/public/2023f U6 - https://doi.org/10.23967/c.coupled.2023.004 ER - TY - THES A1 - Tack, Alexander T1 - Machine Learning-based Assessment of Multiple Anatomical Structures in Medical Image Data for Diagnosis and Prediction of Knee Osteoarthritis N2 - Knee osteoarthritis (KOA) is a degenerative disease that leads to pain and loss of function. It is estimated to affect over 500 million humans world-wide and is one of the most common reasons for disability. KOA is usually diagnosed by radiologists or clinical experts by anamnesis, physical examination, and by assessing medical image data. The latter is typically acquired using X-Ray or magnetic resonance imaging. Since manual image reading is subjective, tedious and time-consuming, automated methods are required for a fast and objective decision support and for a better understanding of the pathogenesis of KOA. This thesis sets a foundation towards automated computation of image-based KOA biomarkers for holistic assessment of the knee. This involves the assessment of multiple knee bones and soft tissues. An assessment of particular structures requires localization of these tissues. In order to automate a faithful localization of anatomical structures, deep learning-based methods are investigated and utilized. Additionally, convolutional neural networks (CNNs) are used for classification of medical image data, i.e., for a direct determination of the disease status and to detect anatomical structures and landmarks. The automatically computed anatomical volumes, locations, and other measurements are finally compared to values acquired by clinical experts and evaluated for clustering of KOA groups, classification of KOA severity, prediction of KOA progression, and prediction of total knee replacement. In various experiments it is shown that CNN-based methods are suitable for accurate medical image segmentation, object detection, landmark detection, and direct classification of disease stages from the image data. Computed features related to the menisci are found to be most expressive in terms of clustering of KOA groups and predicting of future disease states, thus allowing diagnosis of current KOA conditions and prediction of future conditions. The conclusion of this thesis is that machine learning-based, fully automated processing of medical image data shows potential for diagnosis and prediction of KOA grades. Future studies could investigate additional features in order to achieve an assessment of the whole knee or validate the findings of this work in clinical studies. KW - Deep learning KW - cartilage KW - meniscus KW - segmentation KW - classification KW - prediction KW - incident osteoarthritis KW - total knee replacement KW - landmark detection KW - hip-knee-ankle angle Y1 - 2024 U6 - https://doi.org/10.14279/depositonce-19738 ER - TY - THES A1 - Peter, Clea T1 - Improving the Realism of Synthetic Cryogenic Electron Micrographs Using Generative Adversarial Networks N2 - This thesis addresses the problem of synthetic-to-real image refinement applied to tilt series of cryogenic electron micrographs. It explores the possibility of improving the realism of synthesized micrographs using generative adversarial networks, which could help to improve the automatic segmentation of cellular structures based on deep learning methods. For image refinement, three image-to-image translation networks were used to transfer the appearance of real micrographs to synthetic micrographs while preserving their original content, including the location and shape of particles. The first model, called SimGAN, was unable to produce any meaningful refinement. Instead, the content of the synthetic micrographs was corrupted by the addition of extensive noise, making SimGAN unsuitable for the problem of this thesis. As a result, CycleGAN was introduced and its refinement of synthetic micrographs matches the appearance of real micrographs very well. However, structural changes in the position and shape of particles were observed after translation. To avoid this behavior, CUT was used as a third model on an exploratory basis but its performance was inferior to that of CycleGAN. In conclusion, CycleGAN proved to be the most promising image-to-image translation model for the images presented, although it does not solve the main problem of this thesis. In order to do so, further modifications, such as the addition of a structural constraint during translation, are required. Y1 - 2023 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven A1 - Kuen, Lilli T1 - RPExpand (Version 2.0) T2 - Zenodo Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.10371002 SP - doi: 10.5281/zenodo.10371002 ER - TY - THES A1 - Turner, Mark T1 - Cutting Plane Selection for Mixed-Integer Linear Programming N2 - Mixed-Integer Linear Programming (MILP) is a ubiquitous and practical modelling paradigm that is essential for optimising a broad range of real-world systems. The backbone of all modern MILP solvers is the branch-and-cut algorithm, which is a hybrid of the branch-and-bound and cutting planes algorithms. Cutting planes (cuts) are linear inequalities that tighten the relaxation of a MILP. While a lot of research has gone into deriving valid cuts for MILPs, less emphasis has been put on determining which cuts to select. Cuts in general are generated in rounds, and a subset of the generated cuts must be added to the relaxation. The decision on which subset of cuts to add is called cut selection. This is a crucial task since adding too many cuts makes the relaxation large and slow to optimise over. Conversely, adding too few cuts results in an insufficiently tightened relaxation, and more relaxations need to be enumerated. To further emphasise the difficulty, the effectiveness of an applied cut is both dependent on the other applied cuts, and the state of the MILP solver. In this thesis, we present theoretical results on the importance and difficulty of cut selection, as well as practical results that use cut selection to improve general MILP solver performance. Improving general MILP solver performance is of great importance for practitioners and has many runoff effects. Reducing the solve time of currently solved systems can directly improve efficiency within the application area. In addition, improved performance enables larger systems to be modelled and optimised, and MILP to be used in areas where it was previously impractical due to time restrictions. Each chapter of this thesis corresponds to a publication on cut selection, where the contributions of this thesis can naturally be divided into four components. The first two components are motivated by instance-dependent performance. In practice, for each subroutine, including cut selection, MILP solvers have adjustable parameters with hard-coded default values. It is ultimately unrealistic to expect these default values to perform well for every instance. Rather, it would be ideal if the parameters were dependent on the given instance. To show this motivation is well founded, we first introduce a family of parametric MILP instances and cuts to showcase worst-case performance of cut selection for any fixed parameter value. We then introduce a graph neural network architecture and reinforcement learning framework for learning instance-dependent cut scoring parameters. In the following component, we formalise language for determining if a cut has theoretical usefulness from a polyhedral point of view in relation to other cuts. In addition, to overcome issues of infeasible projections and dual degeneracy, we introduce analytic center based distance measures. We then construct a lightweight multi-output regression model that predicts relative solver performance of an instance for a set of distance measures. The final two components are motivated by general MILP solver improvement via cut selection. Such improvement was shown to be possible, albeit difficult to achieve, by the first half of this thesis. We relate branch-and-bound and cuts through their underlying disjunctions. Using a history of previously computed Gomory mixed-integer cuts, we reduce the solve time of SCIP over the 67% of affected MIPLIB 2017 instances by 4%. In the final component, we introduce new cut scoring measures and filtering methods based on information from other MILP solving processes. The new cut selection techniques reduce the solve time of SCIP over the 97% of affected MIPLIB 2017 instances by 5%. KW - Mixed-Integer Programming KW - Cutting Planes KW - Cut Selection KW - Machine Learning Y1 - 2024 ER - TY - CHAP A1 - Petkovic, Milena A1 - Zittel, Janina T1 - Resilient Forecasting of High-Dimensional Network Time Series in the Energy Domain: A Hybrid Approach T2 - Operations Research Proceedings 2023 N2 - Energy systems are complex networks consisting of various interconnected components. Accurate energy demand and supply forecasts are crucial for efficient system operation and decision-making. However, high-dimensional data, complex network structures, and dynamic changes and disruptions in energy networks pose significant challenges for forecasting models. To address this, we propose a hybrid approach for resilient forecasting of network time series (HRF-NTS) in the energy domain. Our approach combines mathematical optimization methods with state-of-the-art machine learning techniques to achieve accurate and robust forecasts for high-dimensional energy network time series. We incorporate an optimization framework to account for uncertainties and disruptive changes in the energy system. The effectiveness of the proposed approach is demonstrated through a case study of forecasting energy demand and supply in a complex, large-scale natural gas transmission network. The results show that the hybrid approach outperforms alternative prediction models in terms of accuracy and resilience to structural changes and disruptions, providing stable, multi-step ahead forecasts for different short to mid-term forecasting horizons. Y1 - 2023 ER - TY - CHAP A1 - Navayazdani, Esfandiar T1 - Elastic Analysis of Augmented Curves and Constrained Surfaces T2 - Proc. of IAPR Third International Conference on Discrete Geometry and Mathematical Morphology Y1 - 2024 U6 - https://doi.org/10.1007/978-3-031-57793-2_27 SP - 353 EP - 363 PB - Springer ER - TY - JOUR A1 - Anton, Oliver A1 - Henderson, Victoria A. A1 - Da Ros, Elisa A1 - Sekuliĉ, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Krutzik, Markus T1 - Review and experimental benchmarking of machine learning algorithms for efficient optimization of cold atom experiments JF - Mach. Learn. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/2632-2153/ad3cb6 VL - 5 SP - 025022 ER - TY - JOUR A1 - Nagel, Soeren A1 - Heitzig, Jobst A1 - Schoell, Eckehard T1 - Capital Inequality Induced Business Cycles N2 - In this letter we present a stochastic dynamic model which can explain economic cycles. We show that the macroscopic description yields a complex dynamical landscape consisting of multiple stable fixed points, each corresponding to a split of the population into a large low and a small high income group. The stochastic fluctuations induce switching between the resulting metastable states, and excitation oscillations just below a deterministic bifurcation. The shocks are caused by the decisions of a few agents who have a disproportionate influence over the macroscopic state of the economy due to the unequal distribution of wealth among the population. The fluctuations have a long-term effect on the growth of economic output and lead to business cycle oscillations exhibiting coherence resonance, where the correlation time is controlled by the population size which is inversely proportional to the noise intensity. Y1 - 2023 SP - 1 EP - 6 ER - TY - JOUR A1 - Vanaret, Charlie T1 - Interval constraint programming for globally solving catalog-based categorical optimization JF - Journal of Global Optimization N2 - In this article, we propose an interval constraint programming method for globally solving catalog-based categorical optimization problems. It supports catalogs of arbitrary size and properties of arbitrary dimension, and does not require any modeling effort from the user. A novel catalog-based contractor (or filtering operator) guarantees consistency between the categorical properties and the existing catalog items. This results in an intuitive and generic approach that is exact, rigorous (robust to roundoff errors) and can be easily implemented in an off-the-shelf interval-based continuous solver that interleaves branching and constraint propagation. We demonstrate the validity of the approach on a numerical problem in which a categorical variable is described by a two-dimensional property space. A Julia prototype is available as open-source software under the MIT license. Y1 - 2024 U6 - https://doi.org/10.1007/s10898-023-01362-0 VL - 89 SP - 457 EP - 476 ER - TY - JOUR A1 - Cereceda-López, Eric A1 - Ostinato, Mattia A1 - Ortiz-Ambriz, Antonio A1 - Straube, Arthur A1 - Palassini, Matteo A1 - Tierno, Pietro T1 - Excluded volume induces buckling in optically driven colloidal rings JF - Phys. Rev. Research N2 - In our combined experimental, theoretical and numerical work, we study the out of equilibrium deformations in a shrinking ring of optically trapped, interacting colloidal particles. Steerable optical tweezers are used to confine dielectric microparticles along a circle of discrete harmonic potential wells, and to reduce the ring radius at a controlled quench speed. We show that excluded-volume interactions are enough to induce particle sliding from their equilibrium positions and nonequilibrium zigzag roughening of the colloidal structure. Our work unveils the underlying mechanism of interfacial deformation in radially driven microscopic discrete rings. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.L012044 VL - 6 SP - L012044 ER - TY - JOUR A1 - Ghysbrecht, Simon A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal JF - Submitted to The Journal of Physical Chemistry A N2 - Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit disparities of up to four orders of magnitude. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models. Y1 - 2023 ER - TY - GEN A1 - Prause, Felix T1 - A Multi-Swap Heuristic for Rolling Stock Rotation Planning with Predictive Maintenance N2 - We present a heuristic solution approach for the rolling stock rotation problem with predictive maintenance (RSRP-PdM). The task of this problem is to assign a sequence of trips to each of the vehicles and to schedule their maintenance such that all trips can be operated. Here, the health states of the vehicles are considered to be random variables distributed by a family of probability distribution functions, and the maintenance services should be scheduled based on the failure probability of the vehicles. The proposed algorithm first generates a solution by solving an integer linear program and then heuristically improves this solution by applying a local search procedure. For this purpose, the trips assigned to the vehicles are split up and recombined, whereby additional deadhead trips can be inserted between the partial assignments. Subse- quently, the maintenance is scheduled by solving a shortest path problem in a state-expanded version of a space-time graph restricted to the trips of the individual vehicles. The solution approach is tested and evaluated on a set of test instances based on real-world timetables. T3 - ZIB-Report - 23-29 KW - Rolling stock rotation planning KW - Predictive maintenance KW - Heuristic KW - State-expanded graph model KW - Integer linear program Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93133 SN - 1438-0064 ER - TY - GEN A1 - Zakiyeva, Nazgul A1 - Petkovic, Milena T1 - High-dimensional high-frequency time series prediction with a mixed integer optimisation method T2 - Operations Research Proceedings T3 - ZIB-Report - 23-30 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93114 SN - 1438-0064 ER - TY - CHAP A1 - Turner, Mark A1 - Chmiela, Antonia A1 - Koch, Thorsten A1 - Winkler, Michael T1 - PySCIPOpt-ML: Embedding Trained Machine Learning Models into Mixed-Integer Programs N2 - A standard tool for modelling real-world optimisation problems is mixed-integer programming (MIP). However, for many of these problems there is either incomplete information describing variable relations, or the relations between variables are highly complex. To overcome both these hurdles, machine learning (ML) models are often used and embedded in the MIP as surrogate models to represent these relations. Due to the large amount of available ML frameworks, formulating ML models into MIPs is highly non-trivial. In this paper we propose a tool for the automatic MIP formulation of trained ML models, allowing easy integration of ML constraints into MIPs. In addition, we introduce a library of MIP instances with embedded ML constraints. The project is available at https://github.com/Opt-Mucca/PySCIPOpt-ML. Y1 - 2023 ER - TY - GEN A1 - Turner, Mark A1 - Chmiela, Antonia A1 - Koch, Thorsten A1 - Winkler, Michael T1 - PySCIPOpt-ML: Embedding Trained Machine Learning Models into Mixed-Integer Programs N2 - A standard tool for modelling real-world optimisation problems is mixed-integer programming (MIP). However, for many of these problems there is either incomplete information describing variable relations, or the relations between variables are highly complex. To overcome both these hurdles, machine learning (ML) models are often used and embedded in the MIP as surrogate models to represent these relations. Due to the large amount of available ML frameworks, formulating ML models into MIPs is highly non-trivial. In this paper we propose a tool for the automatic MIP formulation of trained ML models, allowing easy integration of ML constraints into MIPs. In addition, we introduce a library of MIP instances with embedded ML constraints. The project is available at https://github.com/Opt-Mucca/PySCIPOpt-ML. T3 - ZIB-Report - 23-28 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93095 SN - 1438-0064 ER - TY - GEN A1 - Fujii, Koichi A1 - Kim, Sunyoung A1 - Kojima, Masakazu A1 - Mittelmann, Hans D. A1 - Shinano, Yuji T1 - An Exceptionally Difficult Binary Quadratic Optimization Problem with Symmetry: a Challenge for The Largest Unsolved QAP Instance Tai256c N2 - Tai256c is the largest unsolved quadratic assignment problem (QAP) instance in QAPLIB. It is known that QAP tai256c can be converted into a 256 dimensional binary quadratic optimization problem (BQOP) with a single cardinality constraint which requires the sum of the binary variables to be 92. As the BQOP is much simpler than the original QAP, the conversion increases the possibility to solve the QAP. Solving exactly the BQOP, however, is still very difficult. Indeed, a 1.48% gap remains between the best known upper bound (UB) and lower bound (LB) of the unknown optimal value. This paper shows that the BQOP admits a nontrivial symmetry, a property that makes the BQOP very hard to solve. The symmetry induces equivalent subproblems in branch and bound (BB) methods. To effectively improve the LB, we propose an efficient BB method that incorporates a doubly nonnegative relaxation, the standard orbit branching and a technique to prune equivalent subproblems. With this BB method, a new LB with 1.25% gap is successfully obtained, and computing an LB with 1.0% gap is shown to be still quite difficult. T3 - ZIB-Report - 23-27 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93072 SN - 1438-0064 ER - TY - JOUR A1 - Zakiyeva, Nazgul A1 - Petkovic, Milena T1 - High-dimensional high-frequency time series prediction with a mixed integer optimisation method JF - Operations Research Proceedings N2 - We study a functional autoregressive model for high-frequency time series. We approach the estimation of the proposed model using a Mixed Integer Optimisation method. The proposed model captures serial dependence in the functional time series by including high-dimensional curves. We illustrate our methodology on large-scale natural gas network data. Our model provides more accurate day-ahead hourly out-of-sample forecast of the gas in and out-flows compared to alternative prediction models. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93068 SN - 1438-0064 ER - TY - JOUR A1 - Schimunek, Johannes A1 - Seidl, Philipp A1 - Elez, Katarina A1 - Hempel, Tim A1 - Le, Tuan A1 - Noé, Frank A1 - Olsson, Simon A1 - Raich, Lluís A1 - Winter, Robin A1 - Gokcan, Hatice A1 - Gusev, Filipp A1 - Gutkin, Evgeny M. A1 - Isayev, Olexandr A1 - Kurnikova, Maria G. A1 - Narangoda, Chamali H. A1 - Zubatyuk, Roman A1 - Bosko, Ivan P. A1 - Furs, Konstantin V. A1 - Karpenko, Anna D. A1 - Kornoushenko, Yury V. A1 - Shuldau, Mikita A1 - Yushkevich, Artsemi A1 - Benabderrahmane, Mohammed B. A1 - Bousquet-Melou, Patrick A1 - Bureau, Ronan A1 - Charton, Beatrice A1 - Cirou, Bertrand C. A1 - Gil, Gérard A1 - Allen, William J. A1 - Sirimulla, Suman A1 - Watowich, Stanley A1 - Antonopoulos, Nick A1 - Epitropakis, Nikolaos A1 - Krasoulis, Agamemnon A1 - Itsikalis, Vassilis A1 - Theodorakis, Stavros A1 - Kozlovskii, Igor A1 - Maliutin, Anton A1 - Medvedev, Alexander A1 - Popov, Petr A1 - Zaretckii, Mark A1 - Eghbal-Zadeh, Hamid A1 - Halmich, Christina A1 - Hochreiter, Sepp A1 - Mayr, Andreas A1 - Ruch, Peter A1 - Widrich, Michael A1 - Berenger, Francois A1 - Kumar, Ashutosh A1 - Yamanishi, Yoshihiro A1 - Zhang, Kam Y. J. A1 - Bengio, Emmanuel A1 - Bengio, Yoshua A1 - Jain, Moksh J. A1 - Korablyov, Maksym A1 - Liu, Cheng-Hao A1 - Marcou, Gilles A1 - Glaab, Enrico A1 - Barnsley, Kelly A1 - Iyengar, Suhasini M. A1 - Ondrechen, Mary Jo A1 - Haupt, V. Joachim A1 - Kaiser, Florian A1 - Schroeder, Michael A1 - Pugliese, Luisa A1 - Albani, Simone A1 - Athanasiou, Christina A1 - Beccari, Andrea A1 - Carloni, Paolo A1 - D’Arrigo, Giulia A1 - Gianquinto, Eleonora A1 - Goßen, Jonas A1 - Hanke, Anton A1 - Joseph, Benjamin P. A1 - Kokh, Daria B. A1 - Kovachka, Sandra A1 - Manelfi, Candida A1 - Mukherjee, Goutam A1 - Muñiz-Chicharro, Abraham A1 - Musiani, Francesco A1 - Nunes-Alves, Ariane A1 - Paiardi, Giulia A1 - Rossetti, Giulia A1 - Sadiq, S. Kashif A1 - Spyrakis, Francesca A1 - Talarico, Carmine A1 - Tsengenes, Alexandros A1 - Wade, Rebecca C. A1 - Copeland, Conner A1 - Gaiser, Jeremiah A1 - Olson, Daniel R. A1 - Roy, Amitava A1 - Venkatraman, Vishwesh A1 - Wheeler, Travis J. A1 - Arthanari, Haribabu A1 - Blaschitz, Klara A1 - Cespugli, Marco A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Fischer, Patrick D. A1 - Gorgulla, Christoph A1 - Gruber, Christian A1 - Gruber, Karl A1 - Hetmann, Michael A1 - Kinney, Jamie E. A1 - Padmanabha Das, Krishna M. A1 - Pandita, Shreya A1 - Singh, Amit A1 - Steinkellner, Georg A1 - Tesseyre, Guilhem A1 - Wagner, Gerhard A1 - Wang, Zi-Fu A1 - Yust, Ryan J. A1 - Druzhilovskiy, Dmitry S. A1 - Filimonov, Dmitry A. A1 - Pogodin, Pavel V. A1 - Poroikov, Vladimir A1 - Rudik, Anastassia V. A1 - Stolbov, Leonid A. A1 - Veselovsky, Alexander V. A1 - De Rosa, Maria A1 - De Simone, Giada A1 - Gulotta, Maria R. A1 - Lombino, Jessica A1 - Mekni, Nedra A1 - Perricone, Ugo A1 - Casini, Arturo A1 - Embree, Amanda A1 - Gordon, D. Benjamin A1 - Lei, David A1 - Pratt, Katelin A1 - Voigt, Christopher A. A1 - Chen, Kuang-Yu A1 - Jacob, Yves A1 - Krischuns, Tim A1 - Lafaye, Pierre A1 - Zettor, Agnès A1 - Rodríguez, M. Luis A1 - White, Kris M. A1 - Fearon, Daren A1 - Von Delft, Frank A1 - Walsh, Martin A. A1 - Horvath, Dragos A1 - Brooks III, Charles L. A1 - Falsafi, Babak A1 - Ford, Bryan A1 - García-Sastre, Adolfo A1 - Yup Lee, Sang A1 - Naffakh, Nadia A1 - Varnek, Alexandre A1 - Klambauer, Günter A1 - Hermans, Thomas M. T1 - A community effort in SARS-CoV-2 drug discovery JF - Molecular Informatics KW - COVID-19 KW - drug discovery KW - machine learning KW - SARS-CoV-2 Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1002/minf.202300262 VL - 43 IS - 1 SP - e202300262 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Nigam, AkshatKumar A1 - Koop, Matt A1 - Selim Çınaroğlu, Süleyman A1 - Secker, Christopher A1 - Haddadnia, Mohammad A1 - Kumar, Abhishek A1 - Malets, Yehor A1 - Hasson, Alexander A1 - Li, Minkai A1 - Tang, Ming A1 - Levin-Konigsberg, Roni A1 - Radchenko, Dmitry A1 - Kumar, Aditya A1 - Gehev, Minko A1 - Aquilanti, Pierre-Yves A1 - Gabb, Henry A1 - Alhossary, Amr A1 - Wagner, Gerhard A1 - Aspuru-Guzik, Alán A1 - Moroz, Yurii S. A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules JF - bioRxiv KW - preprint Y1 - 2023 U6 - https://doi.org/10.1101/2023.04.25.537981 ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Hsiao, Ching-Lien A1 - Hultman, Lars A1 - Birch, Jens A1 - Gueorguiev, Gueorgui Kostov T1 - Electronic and optical properties of core-shell InAlN nanorods: a comparative study via LDA, LDA-1/2, mBJ, HSE06, G0W0 and BSE methods JF - Physical Chemistry Chemical Physics Y1 - 2024 U6 - https://doi.org/10.1039/D3CP05295H VL - 26 SP - 7504 EP - 7514 PB - Royal Society of Chemistry ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Vona, Cecilia A1 - Lubeck, Sven A1 - Alex, Ben A1 - Gonzalez Oliva, Ignacio A1 - Draxl, Claudia T1 - Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2 JF - npj Comput. Mater. Y1 - 2024 U6 - https://doi.org/10.1038/s41524-024-01253-2 VL - 10 SP - 77 ER - TY - THES A1 - Zonker, Johannes T1 - Coarse Graining of Agent-Based Models and Spatio-Temporal Modeling of Spreading Processes Y1 - 2023 UR - http://dx.doi.org/10.17169/refubium-41220 ER - TY - CHAP A1 - Weimann, Kuba A1 - Conrad, Tim T1 - Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks T2 - Computing in Cardiology (CinC) 2023 N2 - Aims: Interpretation of continuous EEG is a demanding task that requires the expertise of trained neurologists. However, these experts are not always available in many medical centers. As part of the 2023 George B. Moody PhysioNet Challenge, we developed a deep learning based method for analyzing EEG data of comatose patients and predicting prognosis following cardiac arrest. Methods: Our approach is a two-step pipeline that consists of a prediction model and a decision-making strategy. The prediction model is a residual neural network (ResNet-18) that extracts features and makes a prediction based on a short 5-minute EEG recording. In the second step, a majority vote over multiple predictions made for several EEG recordings of a patient determines the final prognosis. Results: Based on 10-fold cross-validation on the training set, we achieved a true positive rate (TPR) of 0.41 for predicting poor outcome while keeping the false positive rate below 0.05 at 72 hours after recovery of spontaneous circulation. On the official challenge leaderboard, our team ZIB_Visual scored 0.426 TPR. Conclusion: Our approach, while simple to implement and execute, faced overfitting challenges during the official competition phase. In this paper, we discuss our implementation and potential improvements to address these issues. Y1 - 2023 U6 - https://doi.org/10.22489/CinC.2023.093 VL - 50 PB - IEEE ER - TY - CHAP A1 - Yueksel-Erguen, Inci A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Consistent flow scenario generation based on open data for operational analysis of European gas transport networks T2 - Operations Research Proceedings 2023 N2 - In recent years, European gas transport has been affected by major disruptive events like political issues such as, most recently, the Russian war on Ukraine. To incorporate the impacts of such events into decision-making during the energy transition, more complex models for gas network analysis are required. However, the limited availability of consistent data presents a significant obstacle in this endeavor. We use a mathematical-modeling-based scenario generator to deal with this obstacle. The scenario generator consists of capacitated network flow models representing the gas network at different aggregation levels. In this study, we present the coarse-to-fine approach utilized in this scenario generator. Y1 - 2023 ER - TY - CHAP A1 - Clausecker, Robert A1 - Kaiser, Benjamin T1 - Sliding Tile Puzzles T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 57 ER - TY - JOUR A1 - Le, Thi Thai A1 - Tran, Van Cuc A1 - Phung, Dang Hieu T1 - Numerical simulation of tidal flow in Danang Bay Based on non-hydrostatic shallow water equations JF - Pacific Journal of Mathematics for Industry N2 - This paper presents a numerical simulation of the tidal flow in Danang Bay (Vietnam) based on the non-hydrostatic shallow water equations. First, to test the simulation capability of the non-hydrostatic model, we have made a test simulation comparing it with the experiment by Beji and Battjes 1993. Simulation results for this case are compared with both the experimental data and calculations obtained from the traditional hydrostatic model. It is shown that the non-hydrostatic model is better than the hydrostatic model when the seabed topography variation is complex. The usefulness of the non-hydrostatic model is father shown by successfully simulating the tidal flow of Danang Bay. Y1 - 2016 U6 - https://doi.org/10.1186/s40736-015-0020-6 VL - 8 IS - 1 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Schade, Stanley T1 - A Robustness Analysis of Long Distance Train Crew Schedules in Germany T2 - Proceedings Of The Fifth Iinternational Conference On Railway Technology: Research, Development and Maintenance N2 - Nowadays railway networks are highly complex and often very fragile systems. A wide variety of individual operations that influence each other have to go hand in hand to end up with a smoothly and efficiently running system. Many of these operations suffer from uncertainty as trains could be delayed, the signaling system be disrupted or scheduled crews could be ill. Usually these opartions could be organized hierarchically from long term strategical decisions to real time decision management. Each stage in the hierarchy defines a different mathematical optimization problem, which is solved sequentially. At every stage the knowledge about preceding or succeeding planning stages may vary and also the interaction between two stages in this chain of problems may vary from almost no interaction to highly dependent situations. This paper deals with a topic that is an example for the latter case, namely the interaction between vehicle schedules, vehicle punctuality, and crew schedules. To reduce the number of potential rescheduling actions we developed a software tool in cooperation with our practical partner DB Fernverkehr AG (DBF) to predict a certain set of critical crew schedules. This tool evaluates, predicts, and determines "bottlenecks" in the crew schedule in the sense of potentially required rescheduling actions due to likely delays. The approach was tested on real life crew and train timetable data of DBF and can be regarded as the computation of key performance indicators, which is often desired. For our experiments we had access to the operated timetable and crew schedule of DBF for periods of two and six weeks in 2019. Y1 - 2023 U6 - https://doi.org/10.4203/ccc.1.23.17 SN - 2753-3239 VL - CCC 1 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Bushe, Julian T1 - Assignment Based Resource Constrained Path Generation for Railway Rolling Stock Optimization T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - The fundamental task of every passenger railway operator is to offer an attractive railway timetable to the passengers while operating it as cost efficiently as possible. The available rolling stock has to be assigned to trips so that all trips are operated, operational requirements are satisfied, and the operating costs are minimum. This so-called Rolling Stock Rotation Problem (RSRP) is well studied in the literature. In this paper we consider an acyclic version of the RSRP that includes vehicle maintenance. As the latter is an important aspect, maintenance services have to be planned simultaneously to ensure the rotation’s feasibility in practice. Indeed, regular maintenance is important for the safety and reliability of the rolling stock as well as enforced by law in many countries. We present a new integer programming formulation that links a hyperflow to model vehicle compositions and their coupling decisions to a set of path variables that take care of the resource consumption of the individual vehicles. To solve the model we developed different column generation algorithms which are compared to each other as well as to the MILP flow formulation of [Ralf Borndörfer et al., 2016] on a test set of real world instances. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.4230/OASIcs.ATMOS.2023.13 VL - 115 SP - 13:1 EP - 13:15 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - JOUR A1 - Charron, Nicholas A1 - Musil, Félix A1 - Guljas, Andrea A1 - Chen, Yaoyi A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Jacopo, Venturin A1 - Daria, Gusew A1 - Zaporozhets, Iryna A1 - Krämer, Andreas A1 - Templeton, Clark A1 - Atharva, Kelkar A1 - Durumeric, Aleksander A1 - Olsson, Simon A1 - Pérez, Adrià A1 - Majewski, Maciej A1 - Husic, Brooke A1 - Patel, Ankit A1 - De Fabritiis, Gianni A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Navigating protein landscapes with a machine-learned transferable coarse-grained model JF - Arxiv N2 - The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.48550/arXiv.2310.18278 ER - TY - CHAP A1 - Şahin, Güvenç A1 - Lindner, Niels A1 - Schlechte, Thomas ED - Pardalos, P. M. ED - Prokopyev, O. A. T1 - Line Planning Problem T2 - Encyclopedia of Optimization Y1 - 2023 SN - 978-3-030-54621-2 U6 - https://doi.org/10.1007/978-3-030-54621-2_782-1 SP - 1 EP - 6 PB - Springer International Publishing CY - Cham ER - TY - CHAP A1 - Wirth, Elias A1 - Kerdreux, Thomas A1 - Pokutta, Sebastian T1 - Acceleration of Frank-Wolfe Algorithms with Open Loop Step-sizes T2 - Proceedings of International Conference on Artificial Intelligence and Statistics Y1 - 2023 ER - TY - CHAP A1 - Wirth, Elias A1 - Kera, A1 - Pokutta, Sebastian T1 - Approximate Vanishing Ideal Computations at Scale T2 - Proceedings of International Conference on Learning Representations Y1 - 2023 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Besançon, Mathieu A1 - Iommazzo, Gabriele A1 - Knebel, Sebastian A1 - Gelß, Patrick A1 - Pokutta, Sebastian T1 - Improved Local Models and New Bell Inequalities Via Frank-Wolfe Algorithms JF - Physical Review Research N2 - In Bell scenarios with two outcomes per party, we algorithmically consider the two sides of the membership problem for the local polytope: Constructing local models and deriving separating hyperplanes, that is, Bell inequalities. We take advantage of the recent developments in so-called Frank-Wolfe algorithms to significantly increase the convergence rate of existing methods. First, we study the threshold value for the nonlocality of two-qubit Werner states under projective measurements. Here, we improve on both the upper and lower bounds present in the literature. Importantly, our bounds are entirely analytical; moreover, they yield refined bounds on the value of the Grothendieck constant of order three: 1.4367⩽KG(3)⩽1.4546. Second, we demonstrate the efficiency of our approach in multipartite Bell scenarios, and present local models for all projective measurements with visibilities noticeably higher than the entanglement threshold. We make our entire code accessible as a julia library called BellPolytopes.jl. Y1 - 2023 U6 - https://doi.org/10.1103/PhysRevResearch.5.043059 VL - 5 SP - 043059 ER - TY - JOUR A1 - Kruser, Jacqueline M. A1 - Sharma, Kartikey A1 - Holl, Jane L. A1 - Nohadani, Omid T1 - Identifying Patterns of Medical Intervention in Acute Respiratory Failure: A Retrospective Observational Study JF - Critical Care Explorations Y1 - 2023 U6 - https://doi.org/10.1097/CCE.0000000000000984 VL - 5 IS - 10 SP - p e0984 ER - TY - JOUR A1 - Bienstock, Daniel A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - Principled Deep Neural Network Training Through Linear Programming JF - Discrete Optimization N2 - Deep learning has received much attention lately due to the impressive empirical performance achieved by training algorithms. Consequently, a need for a better theoretical understanding of these problems has become more evident and multiple works in recent years have focused on this task. In this work, using a unified framework, we show that there exists a polyhedron that simultaneously encodes, in its facial structure, all possible deep neural network training problems that can arise from a given architecture, activation functions, loss function, and sample size. Notably, the size of the polyhedral representation depends only linearly on the sample size, and a better dependency on several other network parameters is unlikely. Using this general result, we compute the size of the polyhedral encoding for commonly used neural network architectures. Our results provide a new perspective on training problems through the lens of polyhedral theory and reveal strong structure arising from these problems. Y1 - 2023 U6 - https://doi.org/10.1016/j.disopt.2023.100795 VL - 49 ER - TY - CHAP A1 - Mexi, Gioni A1 - Besançon, Mathieu A1 - Bolusani, Suresh A1 - Chmiela, Antonia A1 - Hoen, Alexander A1 - Gleixner, Ambros T1 - Scylla: a matrix-free fix-propagate-and-project heuristic for mixed-integer optimization T2 - Proceedings of Conference of the Society for Operations Research in Germany Y1 - 2023 ER - TY - CHAP A1 - Zimmer, Max A1 - Spiegel, Christoph A1 - Pokutta, Sebastian T1 - How I Learned to Stop Worrying and Love Retraining T2 - Proceedings of International Conference on Learning Representations Y1 - 2023 ER - TY - THES A1 - Binkowski, Felix T1 - Riesz-projection-based methods for the numerical simulation of resonance phenomena in nanophotonics Y1 - 2023 U6 - https://doi.org/10.17169/refubium-41230 ER - TY - GEN A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Supplementary code for the paper Modelling opinion dynamics under the impact of influencer and media strategies N2 - This repository contains the Julia code accompanying the paper "Modelling opinion dynamics under the impact of influencer and media strategies", Scientific Reports, Vol.13, p. 19375, 2023. Y1 - 2023 U6 - https://doi.org/10.12752/9267 ER - TY - JOUR A1 - Policht, Veronica R. A1 - Mittenzwey, Henry A1 - Dogadov, Oleg A1 - Katzer, Manuel A1 - Villa, Andrea A1 - Li, Qiuyang A1 - Kaiser, Benjamin A1 - Ross, Aaron M. A1 - Scotognella, Francesco A1 - Zhu, Xiaoyang A1 - Knorr, Andreas A1 - Selig, Malte A1 - Cerullo, Giulio A1 - Dal Conte, Stefano T1 - Time-domain observation of interlayer exciton formation and thermalization in a MoSe2/WSe2 heterostructure JF - Nature Communications N2 - Vertical heterostructures of transition metal dichalcogenides (TMDs) host interlayer excitons with electrons and holes residing in different layers. With respect to their intralayer counterparts, interlayer excitons feature longer lifetimes and diffusion lengths, paving the way for room temperature excitonic optoelectronic devices. The interlayer exciton formation process and its underlying physical mechanisms are largely unexplored. Here we use ultrafast transient absorption spectroscopy with a broadband white-light probe to simultaneously resolve interlayer charge transfer and interlayer exciton formation dynamics in a MoSe2/WSe2 heterostructure. We observe an interlayer exciton formation timescale nearly an order of magnitude (~1 ps) longer than the interlayer charge transfer time (~100 fs). Microscopic calculations attribute this relative delay to an interplay of a phonon-assisted interlayer exciton cascade and thermalization, and excitonic wave-function overlap. Our results may explain the efficient photocurrent generation observed in optoelectronic devices based on TMD heterostructures, as the interlayer excitons are able to dissociate during thermalization. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-42915-x VL - 14 SP - 1 EP - 9 PB - Springer Nature ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert A1 - Mavroskoufis, Michael T1 - Prioritised Unit Propagation by Partitioning the Watch Lists T2 - Proceedings of the 14th International Workshop on Pragmatics of SAT co-located with the 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023) N2 - Conflict Driven Clause Learning (CDCL) SAT solvers spend most of their execution time iterating through clauses in unit propagation. Efficient implementations of unit propagation mostly rely on the two watched literals (TWL) scheme, a specialised data structure watching two literals per clause to prevent as many clause lookups as possible. In this paper, we present Priority Propagation (PriPro)—a minimally invasive method to adapt unit propagation in existing SAT solvers. With PriPro the traditional TWL scheme is partitioned to allow for rearranging the order in which clauses are examined. This is used to achieve a prioritisation of certain clauses. Using PriPro in combination with a dynamic heuristic to prioritise resolvents from recent conflicts, the effectiveness of unit propagation can be increased. In the state-of-the-art CDCL SAT solver CaDiCaL modified to use PriPro, we obtained a 5–10 % speedup on the SAT Competition 2021 benchmark set in a fair comparison with the unmodified CaDiCaL. Y1 - 2023 UR - https://ceur-ws.org/Vol-3545/paper2.pdf VL - 3545 SP - 14 EP - 34 PB - CEUR Workshop Proceedings ER - TY - GEN A1 - Eifler, Leon A1 - Nicolas-Thouvenin, Jules A1 - Gleixner, Ambros T1 - Combining Precision Boosting with LP Iterative Refinement for Exact Linear Optimization N2 - This article studies a combination of the two state-of-the-art algorithms for the exact solution of linear programs (LPs) over the rational numbers, i.e., without any roundoff errors or numerical tolerances. By integrating the method of precision boosting inside an LP iterative refinement loop, the combined algorithm is able to leverage the strengths of both methods: the speed of LP iterative refinement, in particular in the majority of cases when a double-precision floating-point solver is able to compute approximate solutions with small errors, and the robustness of precision boosting whenever extended levels of precision become necessary. We compare the practical performance of the resulting algorithm with both puremethods on a large set of LPs and mixed-integer programs (MIPs). The results show that the combined algorithm solves more instances than a pure LP iterative refinement approach, while being faster than pure precision boosting. When embedded in an exact branch-and-cut framework for MIPs, the combined algorithm is able to reduce the number of failed calls to the exact LP solver to zero, while maintaining the speed of the pure LP iterative refinement approach. T3 - ZIB-Report - 23-26 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-92573 SN - 1438-0064 ER - TY - JOUR A1 - Eifler, Leon A1 - Nicolas-Thouvenin, Jules A1 - Gleixner, Ambros T1 - Combining Precision Boosting with LP Iterative Refinement for Exact Linear Optimization N2 - This article studies a combination of the two state-of-the-art algorithms for the exact solution of linear programs (LPs) over the rational numbers, i.e., without any roundoff errors or numerical tolerances. By integrating the method of precision boosting inside an LP iterative refinement loop, the combined algorithm is able to leverage the strengths of both methods: the speed of LP iterative refinement, in particular in the majority of cases when a double-precision floating-point solver is able to compute approximate solutions with small errors, and the robustness of precision boosting whenever extended levels of precision become necessary. We compare the practical performance of the resulting algorithm with both puremethods on a large set of LPs and mixed-integer programs (MIPs). The results show that the combined algorithm solves more instances than a pure LP iterative refinement approach, while being faster than pure precision boosting. When embedded in an exact branch-and-cut framework for MIPs, the combined algorithm is able to reduce the number of failed calls to the exact LP solver to zero, while maintaining the speed of the pure LP iterative refinement approach. Y1 - 2023 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Structure of liquid–vapor interfaces: perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence X-ray diffraction JF - J Chem Phys. N2 - Grazing-incidence X-ray diffraction (GIXRD) is a scattering technique which allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of the surface tension and of the interface roughness. However, the corresponding standard data analysis at non-zero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here we overcome this ambiguity by proposing a physically consistent model of the bulk contribution which is based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the X-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid--vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid--vapor coexistence line. A sensitivity analysis demonstrates the robustness of our findings concerning the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments. Y1 - 2024 U6 - https://doi.org/10.1063/5.0186955 VL - 160 SP - 104107 ER - TY - GEN A1 - Zonker, Johannes A1 - Padilla-Iglesias, Cecilia A1 - Djurdjevac Conrad, Natasa T1 - Supplementary code and data for Royal Society Open Science Manuscript rsos.230495 N2 - In this repository are all files necessary to run the agent-based model of the paper "Insights into drivers of mobility and cultural dynamics of African hunter–gatherers over the past 120 000 years", Royal Society Open Science, 10(11), 2023. Y1 - 2023 U6 - https://doi.org/10.12752/9254 ER - TY - CHAP A1 - Sekuliĉ, Ivan A1 - Schneider, Philipp-Immanuel A1 - Anton, Oliver A1 - Da Ros, Elisa A1 - Henderson, Victoria A1 - Krutzik, Markus T1 - Efficient machine-learning approach to optimize trapped cold atom ensembles for quantum memory applications T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2684406 VL - 12740 SP - 127400F ER - TY - JOUR A1 - Yueksel-Erguen, Inci A1 - Most, Dieter A1 - Wyrwoll, Lothar A1 - Schmitt, Carlo A1 - Zittel, Janina T1 - Modeling the transition of the multimodal pan-European energy system including an integrated analysis of electricity and gas transport JF - Energy Systems N2 - Most recently, the European energy system has undergone a fundamental transformation to meet decarbonization targets without compromising the security of the energy supply. The transition involves several energy-generating and consuming sectors emphasizing sector coupling. The increase in the share of renewable energy sources has revealed the need for flexibility in supporting the electricity grid to cope with the resulting high degree of uncertainty. The new technologies accompanying the energy system transition and the recent political crisis in Europe threatening the security of the energy supply have invalidated the experience from the past by drastically changing the conventional scenarios. Hence, supporting strategic planning tools with detailed operational energy network models with appropriate mathematical precision has become more important than ever to understand the impacts of these disruptive changes. In this paper, we propose a workflow to investigate optimal energy transition pathways considering sector coupling. This workflow involves an integrated operational analysis of the electricity market, its transmission grid, and the gas grid in high spatio-temporal resolution. Thus, the workflow enables decision-makers to evaluate the reliability of high-level models even in case of disruptive events. We demonstrate the capabilities of the proposed workflow using results from a pan-European case study. The case study, spanning 2020-2050, illustrates that feasible potential pathways to carbon neutrality are heavily influenced by political and technological constraints. Through integrated operational analysis, we identify scenarios where strategic decisions become costly or infeasible given the existing electricity and gas networks. Y1 - 2023 U6 - https://doi.org/10.1007/s12667-023-00637-5 ER - TY - JOUR A1 - Anteghini, Marco A1 - Martins dos Santos, Vitor AP A1 - Saccenti, Edoardo T1 - PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates JF - Journal of Cellular Biochemistry N2 - The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importance of transporter proteins is unquestionable. The prediction and study of previously unknown transporters can lead to the discovery of new biological pathways, drugs and treatments. Here we present PortPred, a tool to accurately identify transporter proteins and their substrate starting from the protein amino acid sequence. PortPred successfully combines pre-trained deep learning-based protein embeddings and machine learning classification approaches and outperforms other state-of-the-art methods. In addition, we present a comparison of the most promising protein sequence embeddings (Unirep, SeqVec, ProteinBERT, ESM-1b) and their performances for this specific task. Y1 - 2023 U6 - https://doi.org/10.1002/jcb.30490 VL - 124 IS - 11 SP - 1665 EP - 1885 ER - TY - GEN A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang A1 - Schlösser, Franziska T1 - Software Management Plan developed in HPO-Navi N2 - This publication comprises the Software Management Plan (SMP) developed in the HPO-Navi project. The project was funded in the Literature and Information System (LIS) track of the DFG with the aim of increasing the maturity level of scientific software under development, developing improved measures for the quality assurance of this software and for long-term availability. The Ubiquity Generator Framework (UG) software developed in the project provides a software infrastructure to make existing sequential implementations HPC-capable. The UG framework is of interest to developers of specialized optimization algorithms and can be used directly to solve specific problem classes in the field of scientific computing. Due to the naturally high software technology hurdles on HPC systems, UG was initially a highly specialized tool and could only be used to a limited extent without the involvement of the main developer. The central challenge of the project was to create a mechanism for the sustainable development and permanent provision and archiving of the research software. The aim was for UG to achieve the status of a "software product" with implementation of the following project content: - Documentation of the software: a description of the API and the simple connection of further basic solvers, installation instructions for various target platforms and a description of the structure and documentation of the source code as a basis for the distributed sustainable development of UG. - Development of missing user functions of UG: increased platform independence for shared memory parallelization and better logging function for the analysis and verification of results. - Development of a sample data management plan for future research projects that want to use UG and document their research results according to DFG standards for good scientific practice. - Quality assurance: by defining code guidelines, uniform concepts and criteria for the qualitative evaluation of new functions and implementing standards for code review and processes for continuous integration. A complementary goal was to improve the provision, accessibility and long-term reusability of the research software. - Use of an open Git server as a distributed development platform, provision of a download server for releases and sustainable storage of the software code and the associated meta-information. - Improved presentation and visibility through publication in publicly accessible repositories. This includes the prototypical extension of the OPUS 4 repository software widely used in Germany as a means of publishing software with a landing page that can be resolved via a DOI, and improved linking and presentation of UG in swMATH. - Digital long-term archiving: experimental inclusion of software code in an OAIS-compliant digital archiving system and evaluation of the approach in the areas of digital archiving and research data management. Y1 - 2023 U6 - https://doi.org/10.12752/9250 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Periodic timetabling with integrated track choice for railway construction sites JF - Journal of Rail Transport Planning & Management N2 - We propose a mixed-integer linear programming model to generate and optimize periodic timetables with integrated track choice in the context of railway construction sites. When a section of a railway network becomes unavailable, the nearby areas are typically operated close to their capacity limits, and hence carefully modeling headways and allowing flexible routings becomes vital. We therefore discuss first how to integrate headway constraints into the Periodic Event Scheduling Problem (PESP) that do not only prevent overtaking, but also guarantee conflict-free timetables in general and particularly inside stations. Secondly, we introduce a turn-sensitive event-activity network, which is able to integrate routing alternatives for turnarounds at stations, e.g., turning at a platform vs. at a pocket track for metro-like systems. We propose several model formulations to include track choice, and finally evaluate them on six real construction site scenarios on the S-Bahn Berlin network. Y1 - 2023 U6 - https://doi.org/10.1016/j.jrtpm.2023.100416 VL - 28 SP - 100416 ER - TY - JOUR A1 - Lelièvre, Tony A1 - Pigeon, Thomas A1 - Stoltz, Gabriel A1 - Zhang, Wei T1 - Analyzing multimodal probability measures with autoencoders JF - J. Phys. Chem. B N2 - Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively used to complement and possibly bypass expert knowledge in order to construct collective variables. Our focus here is on neural network approaches based on autoencoders. We study some relevant mathematical properties of the loss function considered for training autoencoders, and provide physical interpretations based on conditional variances and minimum energy paths. We also consider various extensions in order to better describe physical systems, by incorporating more information on transition states at saddle points, and/or allowing for multiple decoders in order to describe several transition paths. Our results are illustrated on toy two dimensional systems and on alanine dipeptide. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpcb.3c07075 VL - 128 IS - 11 SP - 2607 EP - 2631 ER - TY - JOUR A1 - Bleich, Amnon A1 - Linnemann, Antje A1 - Jaidi, Benjamin A1 - Diem, Bjoern H A1 - Conrad, Tim T1 - Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification JF - Machine Learning and Knowledge Extraction N2 - Implantable Cardiac Monitor (ICM) devices are demonstrating as of today, the fastest-growing market for implantable cardiac devices. As such, they are becoming increasingly common in patients for measuring heart electrical activity. ICMs constantly monitor and record a patient's heart rhythm and when triggered - send it to a secure server where health care professionals (denote HCPs from here on) can review it. These devices employ a relatively simplistic rule-based algorithm (due to energy consumption constraints) to alert for abnormal heart rhythms. This algorithm is usually parameterized to an over-sensitive mode in order to not miss a case (resulting in a relatively high false-positive rate) and this, combined with the device's nature of constantly monitoring the heart rhythm and its growing popularity, results in HCPs having to analyze and diagnose an increasingly growing amount of data. In order to reduce the load on the latter, automated methods for ECG analysis are nowadays becoming a great tool to assist HCPs in their analysis. While state-of-the-art algorithms are data-driven rather than rule-based, training data for ICMs often consist of specific characteristics that make its analysis unique and particularly challenging. This study presents the challenges and solutions in automatically analyzing ICM data and introduces a method for its classification that outperforms existing methods on such data. It does so by combining high-frequency noise detection (which often occurs in ICM data) with a semi-supervised learning pipeline that allows for re-labeling of training episodes, and by using segmentation and dimension reduction techniques that are robust to morphology variations of the sECG signal (which are typical to ICM data). As a result, it performs better than state-of-the-art techniques on such data with e.g. F1 score of 0.51 vs. 0.38 of our baseline state-of-the-art technique in correctly calling Atrial Fibrilation in ICM data. As such, it could be used in numerous ways such as aiding HCPs in the analysis of ECGs originating from ICMs by, e.g., suggesting a rhythm type. Y1 - 2023 U6 - https://doi.org/10.3390/make5040077 VL - 5 IS - 4 PB - MDPI ER - TY - JOUR A1 - Chewle, Surahit A1 - Weber, Marcus A1 - Emmerling, Franziska T1 - Revealing Kinetics of Paracetamol Crystallization Using Time-Resolved Raman Spectroscopy, Orthogonal Time-Lapse Photography, and Non-Negative Matrix Factorization (OSANO) JF - Crystal Growth & Design N2 - Crystallization is a complex phenomenon with far-reaching implications for the production and formulation of active pharmaceutical ingredients. Understanding this process is critical for achieving control over key physicochemical properties that can affect, for example, the bioavailability and stability of a drug. In this study, we were able to reveal intricate and diverse dynamics of the formation of metastable intermediates of paracetamol crystallization varying with the choice of solvent. We demonstrate the efficacy of our novel approach utilizing an objective function-based non-negative matrix factorization technique for the analysis of time-resolved Raman spectroscopy data, in conjunction with time-lapse photography. Furthermore, we emphasize the crucial importance of integrating Raman spectroscopy with supplementary experimental instrumentation for the mathematical analysis of the obtained spectra. Y1 - 2023 U6 - https://doi.org/10.1021/acs.cgd.3c00617 VL - 23 IS - 9 SP - 6737 EP - 6746 PB - American Chemical Society ET - Crystal Growth & Design ER - TY - GEN A1 - Löbel, Fabian A1 - Borndörfer, Ralf A1 - Weider, Steffen T1 - Non-Linear Battery Behavior in Electric Vehicle Scheduling Problems N2 - The currently most popular approach to handle non-linear battery behavior for electric vehicle scheduling is to use a linear spline interpolation of the charge curve. We show that this can lead to approximate models that underestimate the charge duration and overestimate the state of charge, which is not desirable. While the error is of second order with respect to the interpolation step size, the associated mixed-integer linear programs do not scale well with the number of spline segments. It is therefore recommendable to use coarse interpolation grids adapted to the curvature of the charge curve, and to include sufficient safety margins to ensure solutions of approximate models remain feasible subjected to the exact charge curve. T3 - ZIB-Report - 23-24 KW - Electric Vehicle Scheduling KW - Non-Linear Charging Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-92441 SN - 1438-0064 ER - TY - JOUR A1 - Oehme, Stephan A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Bartek, Benjamin A1 - von Tycowicz, Christoph A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Jung, Tobias T1 - Altered knee kinematics after posterior cruciate single-bundle reconstruction - a comprehensive prospective biomechanical in vivo analysis JF - Frontiers in Bioengineering and Biotechnology Y1 - 2024 U6 - https://doi.org/10.3389/fbioe.2024.1322136 VL - 12 ER - TY - CHAP A1 - Christgau, Steffen A1 - Everingham, Dylan A1 - Mikolajczak, Florian A1 - Schelten, Niklas A1 - Schnor, Bettina A1 - Schroetter, Max A1 - Stabernack, Benno A1 - Steinert, Fritjof T1 - Enabling Communication with FPGA-based Network-attached Accelerators for HPC Workloads T2 - Proceedings of the SC'23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, SC-W 2023, Denver, CO, USA, November 12-17, 2023 N2 - The use of stand-alone, network-coupled Field Programmable Gate Array (FPGA) accelerators is intended to significantly increase the energy efficiency of HPC applications and thus also of HPC data centers. A loose coupling between the nodes of the HPC data center and the FPGAs is established through the high-speed network of the data center. This allows greater flexibility in combining different nodes and accelerators. Both the resulting energy savings and the increased flexibility through the network connection, enable the economical use of FPGAs. This work presents a communication stack to integrate the so-called Network-attached Accelerator (NAA) into the HPC data center. A low-level Remote Direct Memory Access (RDMA) Application Programming Interface (API) and a high-level Remote Procedure Call (RPC) API is designed on top of the RDMA over Converged Ethernet v2 (RoCEv2) communication stack. The experimental results over 100 Gbps RoCEv2 show that our design and implementation deliver performance close to the theoretical maximum. Y1 - 2023 U6 - https://doi.org/10.1145/3624062.3624540 SP - 530 EP - 538 PB - ACM ER - TY - JOUR A1 - Ji, Hongchen A1 - Ragyanszki, Anita A1 - Fournier, Rene A. T1 - Machine learning estimation of reaction energy barriers JF - Computational and Theoretical Chemistry N2 - We describe a machine learning approach to approximate reaction energy barriers (E), requiring as input only estimates of geometry and energies of reactants and products. Using the dataset of Grambow, Pattanaik, and Green [Sci. Data 7 (1 3 7) (2020)] for reactions involving seven or fewer non-hydrogen atoms, 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel to a subset of Density Functional Theory reaction barriers. Our main interest is small energy barriers with the goal of modeling reactions in the interstellar medium and circumstellar envelope. We omitted reactions with E > 40 kcal mol−1 to obtain a subset of 5,276 reactions for 5-fold cross-validation. For this set, the KRR model predicts E with a mean absolute error of 4.13 kcal mol−1 and a root-mean square error of 6.02 kcal mol−1. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114332 VL - 1229 SP - 114332 ER - TY - JOUR A1 - Juhasz, Anett A1 - Serra, Uneri Haymana A1 - Lakatos, Csilla A1 - Vadkerti, Bence A1 - Ragyanszki, Anita A1 - Farkas, Odon A1 - Keki, Sandor A1 - Nagy, Lajos T1 - The kinetics of uncatalyzed and catalyzed urethane forming reactions of aliphatic diisocyanates with butan-1-ol JF - New J. Chem. N2 - The kinetics of the urethane forming reactions of hexamethylene diisocyanate (HDI), 4,4′-dicyclohexyl-methane-diisocyanate (HMDI) and isophorone diisocyanate (IPDI) with butan-1-ol were systematically studied by electrospray ionization mass spectrometry (ESI-MS) in the off-line mode. The reactions were performed in toluene solution in the temperature range of 50–80 °C and perdeuterated butan-1-ol was used for quenching the reaction. The butan-1-ol was employed in high excess to diisocyanates to obtain pseudo first-order rate coefficients. For rendering the kinetics, a simple A → B → C consecutive model was applied and found to adequately describe the observed kinetic behaviors. The corresponding rate coefficients were determined and reactivities of the diisocyanates were found to decrease in the order HDI > IPDI > HMDI. Furthermore, it was observed that the second isocyanate group in HDI, due to the ring formation by intramolecular hydrogen bonds, reacted faster with butan-1-ol after the first isocyanate moiety had reacted. The formation of hydrogen bonding rings was also confirmed by DFT calculations. However, the reactivity of the second isocyanate moiety (after the first one has reacted) did not change significantly in the case of HMDI. From the temperature dependences the apparent activation parameters such as the pre-exponential factors and activation energies were determined. In addition, the reactions were also studied at 80 °C in the presence of tin(II)-2-ethylhexanoate at different concentrations and a mechanism was proposed for the catalytic process. Y1 - 2023 U6 - https://doi.org/10.1039/d3nj02747c VL - 47 SP - 16096 EP - 16107 ER - TY - CHAP A1 - Schubotz, Moritz A1 - Ferrer, Eloi A1 - Stegmüller, Johannes A1 - Mietchen, Daniel A1 - Teschke, Olaf A1 - Pusch, Larissa A1 - Conrad, Tim T1 - Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics T2 - Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023) N2 - Mathematical world knowledge is a fundamental component of Wikidata. However, to date, no expertly curated knowledge graph has focused specifically on contemporary mathematics. Addressing this gap, the Mathematical Research Data Initiative (MaRDI) has developed a comprehensive knowledge graph that links multimodal research data in mathematics. This encompasses traditional research data items like datasets, software, and publications and includes semantically advanced objects such as mathematical formulae and hypotheses. This paper details the abilities of the MaRDI knowledge graph, which is based on Wikibase, leading up to its inaugural public release, codenamed Bravo, available on https://portal.mardi4nfdi.de. Y1 - 2023 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeño-Noda, Antonio A1 - Borndörfer, Ralf A1 - Huneshagen, Max T1 - K-Shortest Simple Paths Using Biobjective Path Search JF - Arxiv Preprint N2 - In this paper we introduce a new algorithm for the k-Shortest Simple Paths (K-SSP) problem with an asymptotic running time matching the state of the art from the literature. It is based on a black-box algorithm due to Roditty and Zwick (2012) that solves at most 2k instances of the Second Shortest Simple Path (2-SSP) problem without specifying how this is done. We fill this gap using a novel approach: we turn the scalar 2-SSP into instances of the Biobjective Shortest Path problem. Our experiments on grid graphs and on road networks show that the new algorithm is very efficient in practice. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2309.10377 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeño-Noda, Antonio A1 - Borndörfer, Ralf T1 - New Dynamic Programming Algorithm for the Multiobjective Minimum Spanning Tree Problem JF - Arxiv Preprint N2 - The Multiobjective Minimum Spanning Tree (MO-MST) problem is a variant of the Minimum Spanning Tree problem, in which the costs associated with every edge of the input graph are vectors. In this paper, we design a new dynamic programming MO-MST algorithm. Dynamic programming for a MO-MST instance leads to the definition of an instance of the One-to-One Multiobjective Shortest Path (MOSP) problem and both instances have equivalent solution sets. The arising MOSP instance is defined on a so called transition graph. We study the original size of this graph in detail and reduce its size using cost dependent arc pruning criteria. To solve the MOSP instance on the reduced transition graph, we design the Implicit Graph Multiobjective Dijkstra Algorithm (IG-MDA), exploiting recent improvements on MOSP algorithms from the literature. All in all, the new IG-MDA outperforms the current state of the art on a big set of instances from the literature. Our code and results are publicly available. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2306.16203 ER - TY - GEN A1 - Bortoletto, Enrico A1 - Lindner, Niels T1 - Scaling and Rounding Periodic Event Scheduling Instances to Different Period Times N2 - The Periodic Event Scheduling Problem (PESP) is a notoriously hard combinatorial optimization problem, essential for the design of periodic timetables in public transportation. The coefficients of the integer variables in the standard mixed integer linear programming formulations of PESP are the period time, e.g., 60 for a horizon of one hour with a resolution of one minute. In many application scenarios, lines with different frequencies have to be scheduled, leading to period times with many divisors. It then seems natural to consider derived instances, where the period time is a divisor of the original one, thereby smaller, and bounds are scaled and rounded accordingly. To this end, we identify two rounding schemes: wide and tight. We then discuss the approximation performance of both strategies, in theory and practice. T3 - ZIB-Report - 23-23 KW - Timetabling KW - Mixed-Integer Programming KW - Public Transport Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-92315 SN - 1438-0064 ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Incremental Heuristics for Periodic Timetabling N2 - We present incremental heuristics for the Periodic Event Scheduling Problem (PESP), the standard mathematical tool to optimize periodic timetables in public transport. The core of our method is to solve successively larger subinstances making use of previously found solutions. Introducing the technical notion of free stratifications, we formulate a general scheme for incremental heuristics for PESP. More practically, we use line and station information to create heuristics that add lines or stations one by one, and we evaluate these heuristics on instances of the benchmarking library PESPlib. This approach is indeed viable, and leads to new incumbent solutions for six PESPlib instances. T3 - ZIB-Report - 23-22 KW - Timetabling KW - Mixed-Integer Programming KW - Public Transport Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-92309 SN - 1438-0064 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Understanding recent deep-learning techniques for identifying collective variables of molecular dynamics BT - Special Issue: 93rd Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM) JF - Proceedings in Applied Mathematics and Mechanics N2 - High-dimensional metastable molecular dynamics (MD) can often be characterised by a few features of the system, that is, collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep learning-based CV identification techniques have been developed in recent years, allowing accurate modelling and efficient simulation of complex molecular systems. In this paper, we look at two different categories of deep learning-based approaches for finding CVs, either by computing leading eigenfunctions of transfer operator associated to the underlying dynamics, or by learning an autoencoder via minimisation of reconstruction error. We present a concise overview of the mathematics behind these two approaches and conduct a comparative numerical study of these two approaches on illustrative examples. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300189 VL - 23 IS - 4 ER - TY - CHAP A1 - Jäger, Klaus A1 - Berwig, Sebastian A1 - Kurpiers, Jona A1 - Yang, Fengjiu A1 - Tockhorn, Philipp A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Optical Simulations of Perovskite/Perovskite Tandem Solar Cells T2 - Integrated Photonics Research, Silicon and Nanophotonics Y1 - 2023 U6 - https://doi.org/10.1364/IPRSN.2023.JM4D.3 SP - JM4D.3 ER - TY - CHAP A1 - Anteghini, Marco A1 - Martins Dos Santos, Vitor T1 - Computational Approaches for Peroxisomal Protein Localization T2 - Peroxisomes N2 - Computational approaches are practical when investigating putative peroxisomal proteins and for sub-peroxisomal protein localization in unknown protein sequences. Nowadays, advancements in computational methods and Machine Learning (ML) can be used to hasten the discovery of novel peroxisomal proteins and can be combined with more established computational methodologies. Here, we explain and list some of the most used tools and methodologies for novel peroxisomal protein detection and localization. Y1 - 2023 SN - 978-1-0716-3047-1 U6 - https://doi.org/10.1007/978-1-0716-3048-8_29 VL - 2643 SP - 405 EP - 411 PB - Humana, New York ER - TY - JOUR A1 - Schintke, Florian A1 - De Mecquenem, Ninon A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity Constraints for Data Analysis Workflows JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2305.08409 SP - 1 EP - 28 ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - CAWL: A Cache-aware Write Performance Model of Linux Systems JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2306.05701 SP - 1 EP - 22 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel T1 - Transcoding unicode characters with AVX-512 instructions JF - Software: Practice and Experience N2 - Intel includes in its recent processors a powerful set of instructions capable of processing 512-bit registers with a single instruction (AVX-512). Some of these instructions have no equivalent in earlier instruction sets. We leverage these instructions to efficiently transcode strings between the most common formats: UTF-8 and UTF-16. With our novel algorithms, we are often twice as fast as the previous best solutions. For example, we transcode Chinese text from UTF-8 to UTF-16 at more than 5 GiB s−1 using fewer than 2 CPU instructions per character. To ensure reproducibility, we make our software freely available as an open-source library. Our library is part of the popular Node.js JavaScript runtime. Y1 - 2023 U6 - https://doi.org/10.1002/spe.3261 VL - 53 IS - 12 SP - 2430 EP - 2462 PB - John Wiley & Sons Ltd. ER - TY - GEN A1 - Colom, Rémi A1 - Mikheeva, Elena A1 - Achouri, Karim A1 - Zuniga-Perez, Jesus A1 - Bonod, Nicolas A1 - Martin, Olivier J.F. A1 - Burger, Sven A1 - Genevet, Patrice T1 - Crossing of the Branch Cut: The Topological Origin of a Universal 2π-Phase Retardation in Non-Hermitian Metasurfaces (Laser Photonics Rev. 17(6)/2023) T2 - Laser Photonics Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202370029 VL - 17 SP - 2370029 ER - TY - JOUR A1 - Ernst, Ariane A1 - Falkenhagen, Undine A1 - Winkelmann, Stefanie T1 - Model reduction for calcium-induced vesicle fusion dynamics JF - Proceedings in Applied Mathematics & Mechanics N2 - In this work, we adapt an established model for the Ca2+-induced fusion dynamics of synaptic vesicles and employ a lumping method to reduce its complexity. In the reduced system, sequential Ca2+-binding steps are merged to a single releasable state, while keeping the important dependence of the reaction rates on the local Ca2+ concentration. We examine the feasibility of this model reduction for a representative stimulus train over the physiologically relevant site-channel distances. Our findings show that the approximation error is generally small and exhibits an interesting nonlinear and non-monotonic behavior where it vanishes for very low distances and is insignificant at intermediary distances. Furthermore, we give expressions for the reduced model’s reaction rates and suggest that our approach may be used to directly compute effective fusion rates for assessing the validity of a fusion model, thereby circumventing expensive simulations. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300184 VL - 23 IS - 4 ER - TY - CHAP A1 - Löbel, Fabian A1 - Borndörfer, Ralf A1 - Weider, Steffen T1 - Non-Linear Charge Functions for Electric Vehicle Scheduling with Dynamic Recharge Rates T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - The ongoing electrification of logistics systems and vehicle fleets increases the complexity of associated vehicle routing or scheduling problems. Battery-powered vehicles have to be scheduled to recharge in-service, and the relationship between charging time and replenished driving range is non-linear. In order to access the powerful toolkit offered by mixed-integer and linear programming techniques, this battery behavior has to be linearized. Moreover, as electric fleets grow, power draw peaks have to be avoided to save on electricity costs or to adhere to hard grid capacity limits, such that it becomes desirable to keep recharge rates dynamic. We suggest a novel linearization approach of battery charging behavior for vehicle scheduling problems, in which the recharge rates are optimization variables and not model parameters. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0030-drops-187765 VL - 115 SP - 15:1 EP - 15:6 ER - TY - JOUR A1 - Kiewisz, Robert A1 - Baum, Daniel A1 - Müller-Reichert, Thomas A1 - Fabig, Gunar T1 - Serial-section electron tomography and quantitative analysis of the microtubule organization in 3D-reconstructed mitotic spindles JF - Bio-protocol Y1 - 2023 U6 - https://doi.org/10.21769/BioProtoc.4849 VL - 13 IS - 20 ER - TY - CHAP A1 - Masing, Berenike A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Integrating Line Planning for Construction Sites into Periodic Timetabling via Track Choice T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - We consider maintenance sites for urban rail systems, where unavailable tracks typically require changes to the regular timetable, and often even to the line plan. In this paper, we present an integrated mixed-integer linear optimization model to compute an optimal line plan that makes best use of the available tracks, together with a periodic timetable, including its detailed routing on the tracks within the stations. The key component is a flexible, turn-sensitive event-activity network that allows to integrate line planning and train routing using a track choice extension of the Periodic Event Scheduling Problem (PESP). Major goals are to maintain as much of the regular service as possible, and to keep the necessary changes rather local. Moreover, we present computational results on real construction site scenarios on the S-Bahn Berlin network. We demonstrate that this integrated problem is indeed solvable on practically relevant instances. Y1 - 2023 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2023.5 VL - 115 SP - 5:1 EP - 5:15 ER - TY - CHAP A1 - Bortoletto, Enrico A1 - Lindner, Niels A1 - Masing, Berenike T1 - Periodic Timetabling with Cyclic Order Constraints T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - Periodic timetabling for highly utilized railway networks is a demanding challenge. We formulate an infrastructure-aware extension of the Periodic Event Scheduling Problem (PESP) by requiring that not only events, but also activities using the same infrastructure must be separated by a minimum headway time. This extended problem can be modeled as a mixed-integer program by adding constraints on the sum of periodic tensions along certain cycles, so that it shares some structural properties with standard PESP. We further refine this problem by fixing cyclic orders at each infrastructure element. Although the computational complexity remains unchanged, the mixed-integer programming model then becomes much smaller. Furthermore, we also discuss how to find a minimal subset of infrastructure elements whose cyclic order already prescribes the order for the remaining parts of the network, and how cyclic order information can be modeled in a mixed-integer programming context. In practice, we evaluate the impact of cyclic orders on a real-world instance on the S-Bahn Berlin network, which turns out to be computationally fruitful. Y1 - 2023 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2023.7 VL - 115 SP - 7:1 EP - 7:18 ER - TY - JOUR A1 - Schiewe, Philine A1 - Goerigk, Marc A1 - Lindner, Niels T1 - Introducing TimPassLib – A Library for Integrated Periodic Timetabling and Passenger Routing JF - Operations Research Forum N2 - Classic models to derive a timetable for public transport often face a chicken-and-egg situation: A good timetable should offer passengers routes with small travel times, but the route choice of passengers depends on the timetable. While models that fix passenger routes were frequently considered in the literature, integrated models that simultaneously optimize timetables and passenger routes have seen increasing attention lately. This creates a growing need for a set of instances that allows to test and compare new algorithmic developments for the integrated problem. Our paper addresses this requirement by presenting TimPassLib, a new benchmark library of instances for integrated periodic timetabling and passenger routing. Y1 - 2023 U6 - https://doi.org/10.1007/s43069-023-00244-1 VL - 4 IS - 3 SP - 64 ER - TY - JOUR A1 - Longren, Luke L. A1 - Eigen, Lennart A1 - Shubitidze, Ani A1 - Lieschnegg, Oliver A1 - Baum, Daniel A1 - Nyakatura, John A. A1 - Hildebrandt, Thomas A1 - Brecht, Michael T1 - Dense Reconstruction of Elephant Trunk Musculature JF - Current Biology N2 - The elephant trunk operates as a muscular hydrostat and is actuated by the most complex musculature known in animals. Because the number of trunk muscles is unclear, we performed dense reconstructions of trunk muscle fascicles, elementary muscle units, from microCT scans of an Asian baby elephant trunk. Muscle architecture changes markedly across the trunk. Trunk tip and finger consist of about 8,000 extraordinarily filigree fascicles. The dexterous finger consists exclusively of microscopic radial fascicles pointing to a role of muscle miniaturization in elephant dexterity. Radial fascicles also predominate (at 82% volume) the remainder of the trunk tip and we wonder if radial muscle fascicles are of particular significance for fine motor control of the dexterous trunk tip. By volume, trunk-shaft muscles comprise one-third of the numerous, small radial muscle fascicles, two-thirds of the three subtypes of large longitudinal fascicles (dorsal longitudinals, ventral outer obliques, and ventral inner obliques), and a small fraction of transversal fascicles. Shaft musculature is laterally, but not radially, symmetric. A predominance of dorsal over ventral radial muscles and of ventral over dorsal longitudinal muscles may result in a larger ability of the shaft to extend dorsally than ventrally and to bend inward rather than outward. There are around 90,000 trunk muscle fascicles. While primate hand control is based on fine control of contraction by the convergence of many motor neurons on a small set of relatively large muscles, evolution of elephant grasping has led to thousands of microscopic fascicles, which probably outnumber facial motor neurons. Y1 - 2023 U6 - https://doi.org/10.1016/j.cub.2023.09.007 VL - 33 SP - 1 EP - 8 ER - TY - JOUR A1 - Wagendorf, Oliver A1 - Nahles, Susanne A1 - Vach, Kirstin A1 - Kernen, Florian A1 - Zachow, Stefan A1 - Heiland, Max A1 - Flügge, Tabea T1 - The impact of teeth and dental restorations on gray value distribution in cone-beam computer tomography - a pilot study JF - International Journal of Implant Dentistry N2 - Purpose: To investigate the influence of teeth and dental restorations on the facial skeleton's gray value distributions in cone-beam computed tomography (CBCT). Methods: Gray value selection for the upper and lower jaw segmentation was performed in 40 patients. In total, CBCT data of 20 maxillae and 20 mandibles, ten partial edentulous and ten fully edentulous in each jaw, respectively, were evaluated using two different gray value selection procedures: manual lower threshold selection and automated lower threshold selection. Two sample t tests, linear regression models, linear mixed models, and Pearson's correlation coefficients were computed to evaluate the influence of teeth, dental restorations, and threshold selection procedures on gray value distributions. Results: Manual threshold selection resulted in significantly different gray values in the fully and partially edentulous mandible. (p = 0.015, difference 123). In automated threshold selection, only tendencies to different gray values in fully edentulous compared to partially edentulous jaws were observed (difference: 58–75). Significantly different gray values were evaluated for threshold selection approaches, independent of the dental situation of the analyzed jaw. No significant correlation between the number of teeth and gray values was assessed, but a trend towards higher gray values in patients with more teeth was noted. Conclusions: Standard gray values derived from CT imaging do not apply for threshold-based bone segmentation in CBCT. Teeth influence gray values and segmentation results. Inaccurate bone segmentation may result in ill-fitting surgical guides produced on CBCT data and misinterpreting bone density, which is crucial for selecting surgical protocols. Y1 - 2023 U6 - https://doi.org/10.1186/s40729-023-00493-z VL - 9 IS - 27 ER - TY - CHAP A1 - Skoblin, Viktor A1 - Höfling, Felix A1 - Christgau, Steffen T1 - Gaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL T2 - 29. PARS-Workshop 2023 N2 - Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of HAL’s MD package that has been successfully migrated from CUDA to SYCL. We describe the different strategies that we followed in the process of porting the code. Following these strategies, we achieved code portability across major GPU vendors. Depending on the actual kernels, both significant performance improvements and regressions are observed. As a side effect of the migration process, we obtained impressing speedups also for execution on CPUs. Y1 - 2023 SN - 0177-0454 VL - 36 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Convergence Properties of Newton’s Method for Globally Optimal Free Flight Trajectory Optimization T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - The algorithmic efficiency of Newton-based methods for Free Flight Trajectory Optimization is heavily influenced by the size of the domain of convergence. We provide numerical evidence that the convergence radius is much larger in practice than what the theoretical worst case bounds suggest. The algorithm can be further improved by a convergence-enhancing domain decomposition. Y1 - 2023 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2023.3 VL - 115 SP - 3:1 EP - 3:6 ER - TY - CHAP A1 - Siqueira Rodrigues, Lucas A1 - Nyakatura, John A1 - Zachow, Stefan A1 - Israel, Johann Habakuk T1 - Design Challenges and Opportunities of Fossil Preparation Tools and Methods T2 - Proceedings of the 20th International Conference on Culture and Computer Science: Code and Materiality N2 - Fossil preparation is the activity of processing paleontological specimens for research and exhibition purposes. In addition to traditional mechanical extraction of fossils, preparation presently comprises non-destructive digital methods that are part of a relatively new field, namely virtual paleontology. Despite significant technological advances, both traditional and digital preparation remain cumbersome and time-consuming endeavors. However, this field has received scarce attention from a human-computer interaction perspective. The present study aims to elucidate the state-of-the-art for paleontological fossil preparation in order to determine its main challenges and start a conversation regarding opportunities for creating novel designs that tackle the field's current issues. We conducted a qualitative study involving both technical preparators and virtual paleontologists. The study was divided into two parts: First, we assembled technical preparators and paleontology researchers in a focus group session to discuss their workflows, obtain a preliminary understanding of their issues, and ideate solutions based on their counterparts' workflows. Next, we conducted a series of contextual inquiries involving direct observation and semi-structured in-depth interviews. We transcribed our recordings and examined the data through theoretical and inductive thematic analysis, clustering emerging themes and applying concepts from human-computer interaction and related fields. Our findings report on challenges faced by traditional and digital fossil preparators and potential opportunities to improve their tools and workflows. We contribute with a novel analysis of fossil preparation from an HCI perspective. Y1 - 2023 U6 - https://doi.org/10.1145/3623462.3623470 PB - Association for Computing Machinery CY - New York, NY, USA ER - TY - CHAP A1 - Siqueira Rodrigues, Lucas A1 - Riehm, Felix A1 - Zachow, Stefan A1 - Israel, Johann Habakuk T1 - VoxSculpt: An Open-Source Voxel Library for Tomographic Volume Sculpting in Virtual Reality T2 - 2023 9th International Conference on Virtual Reality (ICVR), Xianyang, China, 2023 N2 - Manual processing of tomographic data volumes, such as interactive image segmentation in medicine or paleontology, is considered a time-consuming and cumbersome endeavor. Immersive volume sculpting stands as a potential solution to improve its efficiency and intuitiveness. However, current open-source software solutions do not yield the required performance and functionalities. We address this issue by contributing a novel open-source game engine voxel library that supports real-time immersive volume sculpting. Our design leverages GPU instancing, parallel computing, and a chunk-based data structure to optimize collision detection and rendering. We have implemented features that enable fast voxel interaction and improve precision. Our benchmark evaluation indicates that our implementation offers a significant improvement over the state-of-the-art and can render and modify millions of visible voxels while maintaining stable performance for real-time interaction in virtual reality. Y1 - 2023 U6 - https://doi.org/10.1109/ICVR57957.2023.10169420 SP - 515 EP - 523 ER - TY - CHAP A1 - Harth, Philipp A1 - Bast, Arco A1 - Troidl, Jakob A1 - Meulemeester, Bjorge A1 - Pfister, Hanspeter A1 - Beyer, Johanna A1 - Oberlaender, Marcel A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - Rapid Prototyping for Coordinated Views of Multi-scale Spatial and Abstract Data: A Grammar-based Approach T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - Visualization grammars are gaining popularity as they allow visualization specialists and experienced users to quickly create static and interactive views. Existing grammars, however, mostly focus on abstract views, ignoring three-dimensional (3D) views, which are very important in fields such as natural sciences. We propose a generalized interaction grammar for the problem of coordinating heterogeneous view types, such as standard charts (e.g., based on Vega-Lite) and 3D anatomical views. An important aspect of our web-based framework is that user interactions with data items at various levels of detail can be systematically integrated and used to control the overall layout of the application workspace. With the help of a concise JSON-based specification of the intended workflow, we can handle complex interactive visual analysis scenarios. This enables rapid prototyping and iterative refinement of the visual analysis tool in collaboration with domain experts. We illustrate the usefulness of our framework in two real-world case studies from the field of neuroscience. Since the logic of the presented grammar-based approach for handling interactions between heterogeneous web-based views is free of any application specifics, it can also serve as a template for applications beyond biological research. Y1 - 2023 U6 - https://doi.org/10.2312/vcbm.20231218 ER - TY - CHAP A1 - Manley, Phillip A1 - Krüger, Jan A1 - Bodermann, Bernd A1 - Köning, Rainer A1 - Heinrich, Andreas A1 - Eder, Christian A1 - Goehnermeier, Aksel A1 - Zeiser, Ulrike A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Schneider, Philipp-Immanuel T1 - Efficient simulation of microscopic imaging for reconstruction of nanostructures T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2673077 VL - PC12619 SP - PC126190B ER - TY - CHAP A1 - Krüger, Jan A1 - Bodermann, Bernd A1 - Köning, Rainer A1 - Manley, Phillip A1 - Zschiedrich, Lin A1 - Schneider, Philipp-Immanuel A1 - Heinrich, Andreas A1 - Eder, Christian A1 - Zeiser, Ulrike A1 - Goehnermeier, Aksel T1 - On aberration retrieval for optical microscopes in length metrology T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2672294 VL - PC12619 SP - PC126190A ER - TY - JOUR A1 - Toulkeridou, Evropi A1 - Gutierrez, Carlos Enrique A1 - Baum, Daniel A1 - Doya, Kenji A1 - Economo, Evan P. T1 - Automated segmentation of insect anatomy from micro-CT images using deep learning JF - Natural Sciences N2 - Three-dimensional (3D) imaging, such as micro-computed tomography (micro-CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully-automated segmentation of anatomical structures in micro-CT images utilizing state-of-the-art deep learning methods, selecting the ant brain as a test case. We implemented the U-Net architecture for 2D image segmentation for our convolutional neural network (CNN), combined with pixel-island detection. For training and validation of the network, we assembled a dataset of semi-manually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full-body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large datasets, a step toward a big data approach to organismal anatomy. Y1 - 2023 U6 - https://doi.org/10.1002/ntls.20230010 VL - 3 IS - 4 ER - TY - JOUR A1 - Le, Thi Thai A1 - Petkovic, Milena T1 - Predicting Fluid Interface Instability in Energy Systems for Sustainable Energy Transition JF - Operations Research Proceedings N2 - Due to the coexistence of different gases in underground storage, this work explores the interface stability's impact on energy storage, specifically during the injection and withdrawal of gases such as hydrogen and natural gas. A new approach of combing simulation and time series analysis is used to accurately predict instability modes in energy systems. Our simulation is based on the 2D Euler equations, solved using a second-order finite volume method with a staggered grid. The solution is validated by comparing them to experimental data and analytical solutions, accurately predicting the instability's behavior. We use time series analysis and state-of-the-art regime-switching methods to identify critical features of the interface dynamics, providing crucial insights into system optimization and design. Y1 - 2023 ER - TY - JOUR A1 - Yoo, Danbi A1 - Tillmann, Peter A1 - Krauss, Tobias A1 - Sutter, Johannes A1 - Harter, Angelika A1 - Trofimov, Sergei A1 - Naydenov, Boris A1 - Jäger, Klaus A1 - Hauser, Hubert A1 - Becker, Christiane T1 - Comparative Optical Analysis of Imprinted Nano-, Micro- and Biotextures on Solar Glasses for Increased Energy Yield JF - Solar RRL Y1 - 2023 U6 - https://doi.org/10.1002/solr.202300071 VL - 7 SP - 2300071 ER - TY - CHAP A1 - Plock, Matthias A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Efficient reconstruction of model parameters using Bayesian target-vector optimization T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2673590 VL - PC12619 SP - PC1261905 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Siaudinyté, Lauryna A1 - Manley, Phillip A1 - Schneider, Philipp-Immanuel A1 - Burger, Sven T1 - Forward simulation of coherent beams on grating structures for coherent scatterometry T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2673231 VL - PC12619 SP - PC1261907 ER - TY - JOUR A1 - Müller, Sebastian A1 - Paltra, Sydney A1 - Rehmann, Jakob A1 - Nagel, Kai A1 - Conrad, Tim T1 - Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2 JF - iScience N2 - Measurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibody levels are dynamic: due to waning, antibody levels will drop over time. During the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to support the planning of public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects. This paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. The model was developed in response to the complexity of different immunization sequences and types and is based on neutralization titer studies. This approach allows complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases. Y1 - 2023 U6 - https://doi.org/10.1016/j.isci.2023.107554 VL - 26 IS - 9 ER - TY - JOUR A1 - Arndt, Thomas A1 - Boltze, Julia A1 - Hoffmann, Katrin A1 - Kaden, Ben A1 - Seeliger, Frank T1 - Open Access in Berlin und Brandenburg – Klappe, die zweite JF - b.i.t.online Y1 - 2023 UR - https://www.b-i-t-online.de/heft/2023-01-reportage-arndt.pdf VL - 26 IS - 1 SP - 58 EP - 64 ER - TY - JOUR A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide A1 - Koch, Thorsten T1 - Linear stability of a simple shear layer between two parallel streams in a shallow water flow JF - Physics Letters A N2 - The stability of shear layers in fluid flows is a crucial factor in forming vortices and jets and plays a fundamental role in the development of turbulence. Such shear layer instabilities are ubiquitous in natural phenomena, such as atmospheric and oceanic flows, contributing to the formation of weather systems and predicting tsunamis. This study specifically focuses on the stability of a shear layer sandwiched between two semi-infinite layers within a two-dimensional flow. The velocity profile of the shear layer is assumed to be linearly dependent on the vertical coordinate, while the velocity of the other layers remains uniform with differing strengths. The effect of viscosity and surface tension is ignored to simplify the analysis. The shallow water equations are used to analyze the interface stability of the shear layer, and the resulting dispersion relation between wave frequency and other wave characteristics is obtained. This relation incorporates Whittaker functions and their first derivatives and is used to derive appropriate limits corresponding to various physical conditions. Our study thus contributes to a deeper understanding of the stability of shear layers and their implications for natural phenomena. Y1 - 2024 U6 - https://doi.org/10.1016/j.physleta.2023.129264 VL - 493 PB - Elservier ER - TY - CHAP A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - ‘Sawfish’ Spin-Photon Interface for Near-Unity Emitter-to-Waveguide Coupling T2 - Conference on Lasers and Electro-Optics (CLEO) Y1 - 2023 U6 - https://doi.org/10.1364/CLEO_SI.2023.SF1O.6 SP - SF1O.6 ER - TY - THES A1 - Miltenberger, Matthias T1 - Linear Programming in MILP Solving - A Computational Perspective N2 - Mixed-integer linear programming (MILP) plays a crucial role in the field of mathematical optimization and is especially relevant for practical applications due to the broad range of problems that can be modeled in that fashion. The vast majority of MILP solvers employ the LP-based branch-and-cut approach. As the name suggests, the linear programming (LP) subproblems that need to be solved therein influence their behavior and performance significantly. This thesis explores the impact of various LP solvers as well as LP solving techniques on the constraint integer programming framework SCIP Optimization Suite. SCIP allows for comparisons between academic and open-source LP solvers like Clp and SoPlex, as well as commercially developed, high-end codes like CPLEX, Gurobi, and Xpress. We investigate how the overall performance and stability of an MILP solver can be improved by new algorithmic enhancements like LP solution polishing and persistent scaling that we have implemented in the LP solver SoPlex. The former decreases the fractionality of LP solutions by selecting another vertex on the optimal hyperplane of the LP relaxation, exploiting degeneracy. The latter provides better numerical properties for the LP solver throughout the MILP solving process by preserving and extending the initial scaling factors, effectively also improving the overall performance of SCIP. Both enhancement techniques are activated by default in the SCIP Optimization Suite. Additionally, we provide an analysis of numerical conditions in SCIP through the lens of the LP solver by comparing different measures and how these evolve during the different stages of the solving process. A side effect of our work on this topic was the development of TreeD: a new and convenient way of presenting the search tree interactively and animated in the three-dimensional space. This visualization technique facilitates a better understanding of the MILP solving process of SCIP. Furthermore, this thesis presents the various algorithmic techniques like the row representation and iterative refinement that are implemented in SoPlex and that distinguish the solver from other simplex-based codes. Although it is often not as performant as its competitors, SoPlex demonstrates the ongoing research efforts in the field of linear programming with the simplex method. Aside from that, we demonstrate the rapid prototyping of algorithmic ideas and modeling approaches via PySCIPOpt, the Python interface to the SCIP Optimization Suite. This tool allows for convenient access to SCIP's internal data structures from the user-friendly Python programming language to implement custom algorithms and extensions without any prior knowledge of SCIP's programming language C. TreeD is one such example, demonstrating the use of several Python libraries on top of SCIP. PySCIPOpt also provides an intuitive modeling layer to formulate problems directly in the code without having to utilize another modeling language or framework. All contributions presented in this thesis are readily accessible in source code in SCIP Optimization Suite or as separate projects on the public code-sharing platform GitHub. KW - linear programming KW - mixed-integer programming KW - optimization KW - simplex KW - SCIP Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91873 UR - https://www.dr.hut-verlag.de/9783843953238.html SN - 9783843953238 PB - Verlag Dr. Hut GmbH ER - TY - THES A1 - Pfeuffer, Julianus T1 - Computational Methods for Protein Inference in Shotgun Proteomics Experiments N2 - Since the beginning of this millennium, the advent of high-throughput methods in numerous fields of the life sciences led to a shift in paradigms. A broad variety of technologies emerged that allow comprehensive quantification of molecules involved in biological processes. Simultaneously, a major increase in data volume has been recorded with these techniques through enhanced instrumentation and other technical advances. By supplying computational methods that automatically process raw data to obtain biological information, the field of bioinformatics plays an increasingly important role in the analysis of the ever-growing mass of data. Computational mass spectrometry in particular, is a bioinformatics field of research which provides means to gather, analyze and visualize data from high-throughput mass spectrometric experiments. For the study of the entirety of proteins in a cell or an environmental sample, even current techniques reach limitations that need to be circumvented by simplifying the samples subjected to the mass spectrometer. These pre-digested (so-called bottom-up) proteomics experiments then pose an even bigger computational burden during analysis since complex ambiguities need to be resolved during protein inference, grouping and quantification. In this thesis, we present several developments in the pursuit of our goal to provide means for a fully automated analysis of complex and large-scale bottom-up proteomics experiments. Firstly, due to prohibitive computational complexities in state-of-the-art Bayesian protein inference techniques, a refined, more stable technique for performing inference on sums of random variables was developed to enable a variation of standard Bayesian inference for the problem. nextflow and part of a set of standardized, well-tested, and community-maintained workflows by the nf-core collective. Our workflow runs on large-scale data with complex experimental designs and allows a one-command analysis of local and publicly available data sets with state-of-the-art accuracy on various high-performance computing environments or the cloud. Y1 - 2023 UR - http://hdl.handle.net/10900/142644 ER - TY - JOUR A1 - Klenert, Nicolas A1 - Lepper, Verena A1 - Baum, Daniel T1 - A Local Iterative Approach for the Extraction of 2D Manifolds from Strongly Curved and Folded Thin-Layer Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - Ridge surfaces represent important features for the analysis of 3-dimensional (3D) datasets in diverse applications and are often derived from varying underlying data including flow fields, geological fault data, and point data, but they can also be present in the original scalar images acquired using a plethora of imaging techniques. Our work is motivated by the analysis of image data acquired using micro-computed tomography (μCT) of ancient, rolled and folded thin-layer structures such as papyrus, parchment, and paper as well as silver and lead sheets. From these documents we know that they are 2-dimensional (2D) in nature. Hence, we are particularly interested in reconstructing 2D manifolds that approximate the document’s structure. The image data from which we want to reconstruct the 2D manifolds are often very noisy and represent folded, densely-layered structures with many artifacts, such as ruptures or layer splitting and merging. Previous ridge-surface extraction methods fail to extract the desired 2D manifold for such challenging data. We have therefore developed a novel method to extract 2D manifolds. The proposed method uses a local fast marching scheme in combination with a separation of the region covered by fast marching into two sub-regions. The 2D manifold of interest is then extracted as the surface separating the two sub-regions. The local scheme can be applied for both automatic propagation as well as interactive analysis. We demonstrate the applicability and robustness of our method on both artificial data as well as real-world data including folded silver and papyrus sheets. Y1 - 2023 U6 - https://doi.org/10.1109/TVCG.2023.3327403 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Newton's Method for Global Free Flight Trajectory Optimization JF - Operations Research Forum N2 - Globally optimal free flight trajectory optimization can be achieved with a combination of discrete and continuous optimization. A key requirement is that Newton's method for continuous optimization converges in a sufficiently large neighborhood around a minimizer. We show in this paper that, under certain assumptions, this is the case. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91846 VL - 4 ER - TY - CHAP A1 - Türkseven, Doğa A1 - Rekik, Islem A1 - von Tycowicz, Christoph A1 - Hanik, Martin T1 - Predicting Shape Development: A Riemannian Method T2 - Shape in Medical Imaging N2 - Predicting the future development of an anatomical shape from a single baseline observation is a challenging task. But it can be essential for clinical decision-making. Research has shown that it should be tackled in curved shape spaces, as (e.g., disease-related) shape changes frequently expose nonlinear characteristics. We thus propose a novel prediction method that encodes the whole shape in a Riemannian shape space. It then learns a simple prediction technique founded on hierarchical statistical modeling of longitudinal training data. When applied to predict the future development of the shape of the right hippocampus under Alzheimer's disease and to human body motion, it outperforms deep learning-supported variants as well as state-of-the-art. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-46914-5_17 SP - 211 EP - 222 PB - Springer Nature ER - TY - JOUR A1 - Fogalli, Giovani Bressan A1 - Peres Line, Sérgio Roberto A1 - Baum, Daniel T1 - Segmentation of tooth enamel microstructure images using classical image processing and U-Net approaches JF - Frontiers in Imaging N2 - Tooth enamel is the hardest tissue in human organism, formed by prism layers in regularly alternating directions. These prisms form the Hunter-Schreger Bands (HSB) pattern when under side illumination, which is composed of light and dark stripes resembling fingerprints. We have shown in previous works that HSB pattern is highly variable, seems to be unique for each tooth and can be used as a biometric method for human identification. Since this pattern cannot be acquired with sensors, the HSB region in the digital photograph must be identified and correctly segmented from the rest of the tooth and background. Although these areas can be manually removed, this process is not reliable as excluded areas can vary according to the individual‘s subjective impression. Therefore, the aim of this work was to develop an algorithm that automatically selects the region of interest (ROI), thus, making the entire biometric process straightforward. We used two different approaches: a classical image processing method which we called anisotropy-based segmentation (ABS) and a machine learning method known as U-Net, a fully convolutional neural network. Both approaches were applied to a set of extracted tooth images. U-Net with some post processing outperformed ABS in the segmentation task with an Intersection Over Union (IOU) of 0.837 against 0.766. Even with a small dataset, U-Net proved to be a potential candidate for fully automated in-mouth application. However, the ABS technique has several parameters which allow a more flexible segmentation with interactive adjustments specific to image properties. Y1 - 2023 U6 - https://doi.org/10.3389/fimag.2023.1215764 VL - 2 ER - TY - THES A1 - Hanik, Martin T1 - Geometric Data Analysis: Advancements of the Statistical Methodology and Applications N2 - Data analysis has become fundamental to our society and comes in multiple facets and approaches. Nevertheless, in research and applications, the focus was primarily on data from Euclidean vector spaces. Consequently, the majority of methods that are applied today are not suited for more general data types. Driven by needs from fields like image processing, (medical) shape analysis, and network analysis, more and more attention has recently been given to data from non-Euclidean spaces---particularly (curved) manifolds. It has led to the field of geometric data analysis whose methods explicitly take the structure (for example, the topology and geometry) of the underlying space into account. This thesis contributes to the methodology of geometric data analysis by generalizing several fundamental notions from multivariate statistics to manifolds. We thereby focus on two different viewpoints. First, we use Riemannian structures to derive a novel regression scheme for general manifolds that relies on splines of generalized Bézier curves. It can accurately model non-geodesic relationships, for example, time-dependent trends with saturation effects or cyclic trends. Since Bézier curves can be evaluated with the constructive de Casteljau algorithm, working with data from manifolds of high dimensions (for example, a hundred thousand or more) is feasible. Relying on the regression, we further develop a hierarchical statistical model for an adequate analysis of longitudinal data in manifolds, and a method to control for confounding variables. We secondly focus on data that is not only manifold- but even Lie group-valued, which is frequently the case in applications. We can only achieve this by endowing the group with an affine connection structure that is generally not Riemannian. Utilizing it, we derive generalizations of several well-known dissimilarity measures between data distributions that can be used for various tasks, including hypothesis testing. Invariance under data translations is proven, and a connection to continuous distributions is given for one measure. A further central contribution of this thesis is that it shows use cases for all notions in real-world applications, particularly in problems from shape analysis in medical imaging and archaeology. We can replicate or further quantify several known findings for shape changes of the femur and the right hippocampus under osteoarthritis and Alzheimer's, respectively. Furthermore, in an archaeological application, we obtain new insights into the construction principles of ancient sundials. Last but not least, we use the geometric structure underlying human brain connectomes to predict cognitive scores. Utilizing a sample selection procedure, we obtain state-of-the-art results. KW - Regression in Riemannian manifolds KW - Bi-invariant statistics KW - Bézier splines KW - Shape analysis KW - Brain connectomes KW - Ancient sundials Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-refubium-40087-8 PB - Refubium ER - TY - JOUR A1 - Boelts, Jan A1 - Harth, Philipp A1 - Gao, Richard A1 - Udvary, Daniel A1 - Yanez, Felipe A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel A1 - Macke, Jakob H. T1 - Simulation-based inference for efficient identification of generative models in computational connectomics JF - PLOS Computational Biology N2 - Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pcbi.1011406 VL - 19 IS - 9 ER - TY - GEN A1 - Prause, Felix A1 - Borndörfer, Ralf T1 - Construction of a Test Library for the Rolling Stock Rotation Problem with Predictive Maintenance N2 - We describe the development of a test library for the rolling stock rotation problem with predictive maintenance (RSRP-PdM). Our approach involves the utilization of genuine timetables from a private German railroad company. The generated instances incorporate probability distribution functions for modeling the health states of the vehicles and the considered trips possess varying degradation functions. RSRP-PdM involves assigning trips to a fleet of vehicles and scheduling their maintenance based on their individual health states. The goal is to minimize the total costs consisting of operational costs and the expected costs associated with vehicle failures. The failure probability is dependent on the health states of the vehicles, which are assumed to be random variables distributed by a family of probability distributions. Each distribution is represented by the parameters characterizing it and during the operation of the trips, these parameters get altered. Our approach incorporates non-linear degradation functions to describe the inference of the parameters but also linear ones could be applied. The resulting instances consist of the timetables of the individual lines that use the same vehicle type. Overall, we employ these assumptions and utilize open-source data to create a library of instances with varying difficulty. Our approach is vital for evaluating and comparing algorithms designed to solve the RSRP-PdM. T3 - ZIB-Report - 23-20 KW - Rolling Stock Rotation Planning KW - Predictive Maintenance KW - Test Library Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91734 SN - 1438-0064 ER - TY - CHAP A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu T1 - A Context-Aware Cutting Plane Selection Algorithm for Mixed-Integer Programming N2 - The current cut selection algorithm used in mixed-integer programming solvers has remained largely unchanged since its creation. In this paper, we propose a set of new cut scoring measures, cut filtering techniques, and stopping criteria, extending the current state-of-the-art algorithm and obtaining a 5\% performance improvement for SCIP over the MIPLIB 2017 benchmark set. Y1 - 2023 ER - TY - GEN A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu T1 - A Context-Aware Cutting Plane Selection Algorithm for Mixed-Integer Programming N2 - The current cut selection algorithm used in mixed-integer programming solvers has remained largely unchanged since its creation. In this paper, we propose a set of new cut scoring measures, cut filtering techniques, and stopping criteria, extending the current state-of-the-art algorithm and obtaining a 5\% performance improvement for SCIP over the MIPLIB 2017 benchmark set. T3 - ZIB-Report - 23-21 KW - cutting plane selection KW - mixed-integer programming Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91691 SN - 1438-0064 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Chemnitz, Robin A1 - Kostre, Margarita A1 - Schweigart, Fleur A1 - Fless, Friederike A1 - Schütte, Christof A1 - Ducke, Benjamin T1 - A Mathematical perspective on Romanisation: Modelling the Roman road activation process in ancient Tunisia Y1 - 2023 ER - TY - JOUR A1 - Zonker, Johannes A1 - Padilla-Iglesias, Cecilia A1 - Djurdjevac Conrad, Natasa T1 - Insights into drivers of mobility and cultural dynamics of African hunter-gatherers over the past 120 000 years JF - Royal Society Open Science N2 - Humans have a unique capacity to innovate, transmit and rely on complex, cumulative culture for survival. While an important body of work has attempted to explore the role of changes in the size and interconnectedness of populations in determining the persistence, diversity and complexity of material culture, results have achieved limited success in explaining the emergence and spatial distribution of cumulative culture over our evolutionary trajectory. Here, we develop a spatio-temporally explicit agent-based model to explore the role of environmentally driven changes in the population dynamics of hunter–gatherer communities in allowing the development, transmission and accumulation of complex culture. By modelling separately demography- and mobility-driven changes in interaction networks, we can assess the extent to which cultural change is driven by different types of population dynamics. We create and validate our model using empirical data from Central Africa spanning 120 000 years. We find that populations would have been able to maintain diverse and elaborate cultural repertoires despite abrupt environmental changes and demographic collapses by preventing isolation through mobility. However, we also reveal that the function of cultural features was also an essential determinant of the effects of environmental or demographic changes on their dynamics. Our work can therefore offer important insights into the role of a foraging lifestyle on the evolution of cumulative culture. Y1 - 2023 U6 - https://doi.org/10.1098/rsos.230495 VL - 10 IS - 11 ER - TY - JOUR A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Branching via Cutting Plane Selection: Improving Hybrid Branching N2 - Cutting planes and branching are two of the most important algorithms for solving mixed-integer linear programs. For both algorithms, disjunctions play an important role, being used both as branching candidates and as the foundation for some cutting planes. We relate branching decisions and cutting planes to each other through the underlying disjunctions that they are based on, with a focus on Gomory mixed-integer cuts and their corresponding split disjunctions. We show that selecting branching decisions based on quality measures of Gomory mixed-integer cuts leads to relatively small branch-and-bound trees, and that the result improves when using cuts that more accurately represent the branching decisions. Finally, we show how the history of previously computed Gomory mixed-integer cuts can be used to improve the performance of the state-of-the-art hybrid branching rule of SCIP. Our results show a $4\%$ decrease in solve time, and an $8\%$ decrease in number of nodes over affected instances of MIPLIB 2017. Y1 - 2023 PB - Springer ER - TY - JOUR A1 - Ragyanszki, Anita A1 - Fiser, Bela A1 - Lee-Ruff, Edward A1 - Liebman, Joel F. T1 - Strained Small Nitrogen Heterocycles-Azabicyclobutanes and Azirines JF - ChemistrySelect N2 - Small ring nitrogen heterocycles, azabicyclobutanes and azirines, were investigated by computational methods in order to address the discrepancy between their regioisomers 1- and 2-azabicyclobutane and 1H- and 2H-azirines. Both 1-azabicyclobutane and 2H-azirine are well known synthetic starting points to larger nitrogen heterocycles whereas 2-azabicyclobutane and 1H-azirine and their derivatives have yet to be reported as isolable compounds. Calculated parameters such as structure, base strength (proton affinities), NICS values and enthalpies of formation from which strain energies are derived are reported. The destabilization of the less stable regioisomers is attributed to homoantiaromaticity in 2-azabicyclobutane and antiaromaticity in 1H-azirine. Two stereoisomers exist for 2-azabicyclobutane with the endo- stereoisomer being more stable. This phenomenon is indicative of the hydrogen bond acceptor properties of the neighboring cyclpropane and the π-bond character of the central bond in 2-azabicyclobutane. Y1 - 2023 U6 - https://doi.org/10.1002/slct.202301405 VL - 8 IS - 26 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Genevet, Patrice A1 - Burger, Sven T1 - Poles and zeros in non-Hermitian systems: Application to photonics JF - Phys. Rev. B Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevB.109.045414 VL - 109 SP - 045414 ER - TY - GEN A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Genevet, Patrice A1 - Burger, Sven T1 - Source code and simulation results: Poles and zeros of electromagnetic quantities in photonic systems T2 - Zenodo Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.8063931 SP - 8063931 ER - TY - JOUR A1 - Rozsa, Zsofia Borbala A1 - Ragyanszki, Anita A1 - Viskolcz, Bela A1 - Szori, Milan T1 - Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties JF - Computational and Theoretical Chemistry N2 - The goal of this study was to explore and define the thermodynamic properties of one of the subspaces of ‘chemical space’ using a mixture of graph theory and theoretical chemistry tools. Therefore, all possible mo- lecular structures with C4H8O2 stoichiometry were generated, considering constitutional isomers and molecular complexes. The thermodynamic properties of the obtained isomers have been obtained by G3MP2B3 protocol. The classification of the obtained isomers was simplified by using thermodynamic maps, which is an effective method for the comparison of thermodynamic stability for entities of complex molecular systems. Modern computational methods can be used to understand larger systems, which has made it possible to characterize a chemical subspace not only by selecting individual entities, but also as a whole. With this pro- cedure one can catch a glimpse into the diversity of a molecular system and predict further uses of newly discovered molecules or design molecules with predefined properties. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114162 VL - 1225 SP - 114162 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus T1 - Efficient Estimation of Transition Rates as Functions of pH JF - Proceedings in Applied Mathematics & Mechanics N2 - Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ensemble. As an alternative, we present a novel strategy that requires simulating only the most recurrent Canonical Ensembles that compose the Grand Canonical Ensemble. The simulations are used to estimate the Gran Canonical distribution for a specific pH value by reweighting and to construct the transition rate matrix by discretizing the Fokker-Planck equation by Square Root Approximation and robust Perron Cluster Cluster Analysis. As an application, we have studied the tripeptide Ala-Asp-Ala. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300264 VL - 23 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - An effective approach for deriving and evaluating approximate optimal design solutions of energy supply systems by time series aggregation JF - Frontiers in Energy Research N2 - It is important to design multi-energy supply systems optimally in consideration of their operations for variations in energy demands. An approach for efficiently solving such an optimal design problem with a large number of periods for variations in energy demands is to derive an approximate optimal design solution by time series aggregation. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. In this paper, an effective approach for time series aggregation is proposed to derive an approximate optimal design solution and evaluate a proper gap between the upper and lower bounds for the optimal value of the objective function based on a mixed-integer linear model. In accordance with aggregation, energy demands are relaxed to uncertain parameters and the problem for deriving an approximate optimal design solution and evaluating it is transformed to a three-level optimization problem, and it is solved by applying both the robust and hierarchical optimization methods. A case study is conducted on a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to derive much smaller gaps as compared with those obtained by a conventional approach. Y1 - 2023 U6 - https://doi.org/10.3389/fenrg.2023.1128681 VL - 11 SP - 1 EP - 14 ER - TY - JOUR A1 - Lücke, Marvin A1 - Winkelmann, Stefanie A1 - Heitzig, Jobst A1 - Molkenthin, Nora A1 - Koltai, Péter T1 - Learning interpretable collective variables for spreading processes on networks JF - Physical Review E N2 - Collective variables (CVs) are low-dimensional projections of high-dimensional system states. They are used to gain insights into complex emergent dynamical behaviors of processes on networks. The relation between CVs and network measures is not well understood and its derivation typically requires detailed knowledge of both the dynamical system and the network topology. In this Letter, we present a data-driven method for algorithmically learning and understanding CVs for binary-state spreading processes on networks of arbitrary topology. We demonstrate our method using four example networks: the stochastic block model, a ring-shaped graph, a random regular graph, and a scale-free network generated by the Albert-Barabási model. Our results deliver evidence for the existence of low-dimensional CVs even in cases that are not yet understood theoretically. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevE.109.L022301 VL - 109 IS - 2 SP - L022301 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Depinning transition of self-propelled particles N2 - A depinning transition is observed in a variety of contexts when a certain threshold force must be applied to drive a system out of an immobile state. A well-studied example is the depinning of colloidal particles from a corrugated landscape, whereas its active-matter analogue has remained unexplored. We discuss how active noise due to self-propulsion impacts the nature of the transition: it causes a change of the critical exponent from 1/2 for quickly reorienting particles to 3/2 for slowly reorienting ones. In between these analytically tractable limits, the drift velocity exhibits a superexponential behavior as is corroborated by high-precision data. Giant diffusion phenomena occur in the two different regimes. Our predictions appear amenable to experimental tests, lay foundations for insight into the depinning of collective variables in active matter, and are relevant for any system with a saddle-node bifurcation in the presence of a bounded noise. Y1 - 2023 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Klus, Stefan A1 - Conrad, Natasa Djurdjevac A1 - Schütte, Christof T1 - Koopman-Based Surrogate Models for Multi-Objective Optimization of Agent-Based Systems JF - Physica D: Nonlinear Phenomena N2 - Agent-based models (ABMs) provide an intuitive and powerful framework for studying social dynamics by modeling the interactions of individuals from the perspective of each individual. In addition to simulating and forecasting the dynamics of ABMs, the demand to solve optimization problems to support, for example, decision-making processes naturally arises. Most ABMs, however, are non-deterministic, high-dimensional dynamical systems, so objectives defined in terms of their behavior are computationally expensive. In particular, if the number of agents is large, evaluating the objective functions often becomes prohibitively time-consuming. We consider data-driven reduced models based on the Koopman generator to enable the efficient solution of multi-objective optimization problems involving ABMs. In a first step, we show how to obtain data-driven reduced models of non-deterministic dynamical systems (such as ABMs) that depend on potentially nonlinear control inputs. We then use them in the second step as surrogate models to solve multi-objective optimal control problems. We first illustrate our approach using the example of a voter model, where we compute optimal controls to steer the agents to a predetermined majority, and then using the example of an epidemic ABM, where we compute optimal containment strategies in a prototypical situation. We demonstrate that the surrogate models effectively approximate the Pareto-optimal points of the ABM dynamics by comparing the surrogate-based results with test points, where the objectives are evaluated using the ABM. Our results show that when objectives are defined by the dynamic behavior of ABMs, data-driven surrogate models support or even enable the solution of multi-objective optimization problems. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1016/j.physd.2024.134052 VL - 460 SP - 134052 ER - TY - JOUR A1 - Combettes, Cyrille A1 - Pokutta, Sebastian T1 - Revisiting the Approximate Carathéodory Problem via the Frank-Wolfe Algorithm JF - Mathematical Programming Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01735-x VL - 197 SP - 191 EP - 214 ER - TY - JOUR A1 - Riedel, Jerome A1 - Gelß, Patrick A1 - Klein, Rupert A1 - Schmidt, Burkhard T1 - WaveTrain: a Python Package for Numerical Quantum Mechanics of Chain-like Systems Based on Tensor Trains JF - The Journal of Chemical Physics N2 - WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only. The Python package is centered around tensor train (TT, or matrix product) format representations of Hamiltonian operators and (stationary or time-evolving) state vectors. It builds on the Python tensor train toolbox Scikit_tt, which provides efficient construction methods and storage schemes for the TT format. Its solvers for eigenvalue problems and linear differential equations are used in WaveTrain for the time-independent and time-dependent Schrödinger equations, respectively. Employing efficient decompositions to construct low-rank representations, the tensor-train ranks of state vectors are often found to depend only marginally on the chain length N. This results in the computational effort growing only slightly more than linearly with N, thus mitigating the curse of dimensionality. As a complement to the classes for full quantum mechanics, WaveTrain also contains classes for fully classical and mixed quantum–classical (Ehrenfest or mean field) dynamics of bipartite systems. The graphical capabilities allow visualization of quantum dynamics “on the fly,” with a choice of several different representations based on reduced density matrices. Even though developed for treating quasi-one-dimensional excitonic energy transport in molecular solids or conjugated organic polymers, including coupling to phonons, WaveTrain can be used for any kind of chain-like quantum systems, with or without periodic boundary conditions and with NN interactions only. The present work describes version 1.0 of our WaveTrain software, based on version 1.2 of scikit_tt, both of which are freely available from the GitHub platform where they will also be further developed. Moreover, WaveTrain is mirrored at SourceForge, within the framework of the WavePacket project for numerical quantum dynamics. Worked-out demonstration examples with complete input and output, including animated graphics, are available. Y1 - 2023 U6 - https://doi.org/10.1063/5.0147314 VL - 158 IS - 16 SP - 164801 ER - TY - JOUR A1 - Kevin-Martin, Aigner A1 - Bärmann, Andreas A1 - Braun, Kristin A1 - Liers, Frauke A1 - Pokutta, Sebastian A1 - Schneider, Oskar A1 - Sharma, Kartikey A1 - Tschuppik, Sebastian T1 - Data-driven Distributionally Robust Optimization over Time JF - INFORMS Journal on Optimization N2 - Stochastic optimization (SO) is a classical approach for optimization under uncertainty that typically requires knowledge about the probability distribution of uncertain parameters. Because the latter is often unknown, distributionally robust optimization (DRO) provides a strong alternative that determines the best guaranteed solution over a set of distributions (ambiguity set). In this work, we present an approach for DRO over time that uses online learning and scenario observations arriving as a data stream to learn more about the uncertainty. Our robust solutions adapt over time and reduce the cost of protection with shrinking ambiguity. For various kinds of ambiguity sets, the robust solutions converge to the SO solution. Our algorithm achieves the optimization and learning goals without solving the DRO problem exactly at any step. We also provide a regret bound for the quality of the online strategy that converges at a rate of O(log T/T−−√), where T is the number of iterations. Furthermore, we illustrate the effectiveness of our procedure by numerical experiments on mixed-integer optimization instances from popular benchmark libraries and give practical examples stemming from telecommunications and routing. Our algorithm is able to solve the DRO over time problem significantly faster than standard reformulations. Y1 - 2023 U6 - https://doi.org/10.1287/ijoo.2023.0091 VL - 5 IS - 4 SP - 376 EP - 394 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Vigerske, Stefan T1 - A Computational Study of Perspective Cuts JF - Mathematical Programming Computation N2 - The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to nonconvex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time. Y1 - 2023 U6 - https://doi.org/10.1007/s12532-023-00246-4 VL - 15 SP - 703 EP - 731 ER - TY - CHAP A1 - Rué Perna, Juanjo A1 - Spiegel, Christoph T1 - The Rado Multiplicity Problem in Vector Spaces Over Finite Fields T2 - Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, EUROCOMB’23 Y1 - 2023 U6 - https://doi.org/10.5817/CZ.MUNI.EUROCOMB23-108 SP - 784 EP - 789 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Wirth, Elias A1 - Pokutta, Sebastian T1 - Accelerated and Sparse Algorithms for Approximate Personalized PageRank and Beyond T2 - Proceedings of Machine Learning Research N2 - It has recently been shown that ISTA, an unaccelerated optimization method, presents sparse updates for the ℓ1-regularized undirected personalized PageRank problem (Fountoulakis et al., 2019), leading to cheap iteration complexity and providing the same guarantees as the approximate personalized PageRank algorithm (APPR) (Andersen et al., 2006). In this work, we design an accelerated optimization algorithm for this problem that also performs sparse updates, providing an affirmative answer to the COLT 2022 open question of Fountoulakis and Yang (2022). Acceleration provides a reduced dependence on the condition number, while the dependence on the sparsity in our updates differs from the ISTA approach. Further, we design another algorithm by using conjugate directions to achieve an exact solution while exploiting sparsity. Both algorithms lead to faster convergence for certain parameter regimes. Our findings apply beyond PageRank and work for any quadratic objective whose Hessian is a positive-definite 푀-matrix. Y1 - 2023 UR - https://proceedings.mlr.press/v195/martinez-rubio23a/martinez-rubio23a.pdf VL - 195 SP - 1 EP - 35 ER - TY - CHAP A1 - Mexi, Gioni A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Improving Conflict Analysis in MIP Solvers by Pseudo-Boolean Reasoning T2 - 29th International Conference on Principles and Practice of Constraint Programming (CP 2023) N2 - Conflict analysis has been successfully generalized from Boolean satisfiability (SAT) solving to mixed integer programming (MIP) solvers, but although MIP solvers operate with general linear inequalities, the conflict analysis in MIP has been limited to reasoning with the more restricted class of clausal constraint. This is in contrast to how conflict analysis is performed in so-called pseudo-Boolean solving, where solvers can reason directly with 0-1 integer linear inequalities rather than with clausal constraints extracted from such inequalities. In this work, we investigate how pseudo-Boolean conflict analysis can be integrated in MIP solving, focusing on 0-1 integer linear programs (0-1 ILPs). Phrased in MIP terminology, conflict analysis can be understood as a sequence of linear combinations and cuts. We leverage this perspective to design a new conflict analysis algorithm based on mixed integer rounding (MIR) cuts, which theoretically dominates the state-of-the-art division-based method in pseudo-Boolean solving. We also report results from a first proof-of-concept implementation of different pseudo-Boolean conflict analysis methods in the open-source MIP solver SCIP. When evaluated on a large and diverse set of 0-1 ILP instances from MIPLIB2017, our new MIR-based conflict analysis outperforms both previous pseudo-Boolean methods and the clause-based method used in MIP. Our conclusion is that pseudo-Boolean conflict analysis in MIP is a promising research direction that merits further study, and that it might also make sense to investigate the use of such conflict analysis to generate stronger no-goods in constraint programming. Y1 - 2023 U6 - https://doi.org/10.4230/LIPIcs.CP.2023.27 VL - 280 SP - 27:1 EP - 27:19 PB - Schloss Dagstuhl - Leibniz-Zentrum für Informatik ER - TY - CHAP A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Achterberg, Tobias T1 - Efficient Separation of RLT Cuts for Implicit and Explicit Bilinear Products T2 - Integer Programming and Combinatorial Optimization. IPCO 2023. N2 - The reformulation-linearization technique (RLT) is a prominent approach to constructing tight linear relaxations of non-convex continuous and mixed-integer optimization problems. The goal of this paper is to extend the applicability and improve the performance of RLT for bilinear product relations. First, a method for detecting bilinear product relations implicitly contained in mixed-integer linear programs is developed based on analyzing linear constraints with binary variables, thus enabling the application of bilinear RLT to a new class of problems. Our second contribution addresses the high computational cost of RLT cut separation, which presents one of the major difficulties in applying RLT efficiently in practice. We propose a new RLT cutting plane separation algorithm which identifies combinations of linear constraints and bound factors that are expected to yield an inequality that is violated by the current relaxation solution. A detailed computational study based on implementations in two solvers evaluates the performance impact of the proposed methods. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-32726-1_2 VL - 13904 SP - 14 EP - 28 PB - Springer, Cham ER - TY - JOUR A1 - Montefusco, Alberto A1 - Helfmann, Luzie A1 - Okunola, Toluwani A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Partial mean-field model for neurotransmission dynamics JF - Mathematical Biosciences N2 - This article addresses reaction networks in which spatial and stochastic effects are of crucial importance. For such systems, particle-based models allow us to describe all microscopic details with high accuracy. However, they suffer from computational inefficiency if particle numbers and density get too large. Alternative coarse-grained-resolution models reduce computational effort tremendously, e.g., by replacing the particle distribution by a continuous concentration field governed by reaction-diffusion PDEs. We demonstrate how models on the different resolution levels can be combined into hybrid models that seamlessly combine the best of both worlds, describing molecular species with large copy numbers by macroscopic equations with spatial resolution while keeping the stochastic-spatial particle-based resolution level for the species with low copy numbers. To this end, we introduce a simple particle-based model for the binding dynamics of ions and vesicles at the heart of the neurotransmission process. Within this framework, we derive a novel hybrid model and present results from numerical experiments which demonstrate that the hybrid model allows for an accurate approximation of the full particle-based model in realistic scenarios. Y1 - 2024 U6 - https://doi.org/10.1016/j.mbs.2024.109143 VL - 369 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Convergence Properties of Newton's Method for Globally Optimal Free Flight Trajectory Optimization N2 - The algorithmic efficiency of Newton-based methods for Free Flight Trajectory Optimization is heavily influenced by the size of the domain of convergence. We provide numerical evidence that the convergence radius is much larger in practice than what the theoretical worst case bounds suggest. The algorithm can be further improved by a convergence-enhancing domain decomposition. T3 - ZIB-Report - 23-19 KW - shortest path KW - flight planning KW - free flight KW - optimal control KW - global optimization KW - Newton's method Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91309 SN - 1438-0064 ER - TY - CHAP A1 - Hartmann, Carsten A1 - Richter, Lorenz ED - Klimczak, Peter ED - Petersen, Christer T1 - Transgressing the Boundaries: Towards a Rigorous Understanding of Deep Learning and Its (Non )Robustness T2 - AI - Limits and Prospects of Artificial Intelligence N2 - The recent advances in machine learning in various fields of applications can be largely attributed to the rise of deep learning (DL) methods and architectures. Despite being a key technology behind autonomous cars, image processing, speech recognition, etc., a notorious problem remains the lack of theoretical understanding of DL and related interpretability and (adversarial) robustness issues. Understanding the specifics of DL, as compared to, say, other forms of nonlinear regression methods or statistical learning, is interesting from a mathematical perspective, but at the same time it is of crucial importance in practice: treating neural networks as mere black boxes might be sufficient in certain cases, but many applications require waterproof performance guarantees and a deeper understanding of what could go wrong and why it could go wrong. It is probably fair to say that, despite being mathematically well founded as a method to approximate complicated functions, DL is mostly still more like modern alchemy that is firmly in the hands of engineers and computer scientists. Nevertheless, it is evident that certain specifics of DL that could explain its success in applications demands systematic mathematical approaches. In this work, we review robustness issues of DL and particularly bridge concerns and attempts from approximation theory to statistical learning theory. Further, we review Bayesian Deep Learning as a means for uncertainty quantification and rigorous explainability. Y1 - 2023 U6 - https://doi.org/10.1515/9783839457320 VL - 4 SP - 43 EP - 82 PB - transcript Verlag ER - TY - CHAP A1 - Richter, Lorenz A1 - Berner, Julius T1 - Improved sampling via learned diffusions T2 - International Conference on Learning Representations 2024 N2 - Recently, a series of papers proposed deep learning-based approaches to sample from unnormalized target densities using controlled diffusion processes. In this work, we identify these approaches as special cases of the Schrödinger bridge problem, seeking the most likely stochastic evolution between a given prior distribution and the specified target. We further generalize this framework by introducing a variational formulation based on divergences between path space measures of time-reversed diffusion processes. This abstract perspective leads to practical losses that can be optimized by gradient-based algorithms and includes previous objectives as special cases. At the same time, it allows us to consider divergences other than the reverse Kullback-Leibler divergence that is known to suffer from mode collapse. In particular, we propose the so-called log-variance loss, which exhibits favorable numerical properties and leads to significantly improved performance across all considered approaches. Y1 - 2024 UR - https://openreview.net/pdf?id=h4pNROsO06 ER - TY - CHAP A1 - Zink, Christof A1 - Ekterai, Michael A1 - Martin, Dominik A1 - Clemens, William A1 - Maennel, Angela A1 - Mundinger, Konrad A1 - Richter, Lorenz A1 - Crump, Paul A1 - Knigge, Andrea T1 - Deep-learning-based visual inspection of facets and p-sides for efficient quality control of diode lasers T2 - High-Power Diode Laser Technology XXI N2 - The optical inspection of the surfaces of diode lasers, especially the p-sides and facets, is an essential part of the quality control in the laser fabrication procedure. With reliable, fast, and flexible optical inspection processes, it is possible to identify and eliminate defects, accelerate device selection, reduce production costs, and shorten the cycle time for product development. Due to a vast range of rapidly changing designs, structures, and coatings, however, it is impossible to realize a practical inspection with conventional software. In this work, we therefore suggest a deep learning based defect detection algorithm that builds on a Faster Regional Convolutional Neural Network (Faster R-CNN) as a core component. While for related, more general object detection problems, the application of such models is straightforward, it turns out that our task exhibits some additional challenges. On the one hand, a sophisticated pre- and postprocessing of the data has to be deployed to make the application of the deep learning model feasible. On the other hand, we find that creating labeled training data is not a trivial task in our scenario, and one has to be extra careful with model evaluation. We can demonstrate in multiple empirical assessments that our algorithm can detect defects in diode lasers accurately and reliably in most cases. We analyze the results of our production-ready pipeline in detail, discuss its limitations and provide some proposals for further improvements. Y1 - 2023 U6 - https://doi.org/10.1117/12.2648691 VL - 12403 SP - 94 EP - 112 PB - SPIE ER - TY - JOUR A1 - Weilandt, Frank A1 - Behling, Robert A1 - Goncalves, Romulo A1 - Madadi, Arash A1 - Richter, Lorenz A1 - Sanona, Tiago A1 - Spengler, Daniel A1 - Welsch, Jona T1 - Early Crop Classification via Multi-Modal Satellite Data Fusion and Temporal Attention JF - Remote Sensing N2 - In this article, we propose a deep learning-based algorithm for the classification of crop types from Sentinel-1 and Sentinel-2 time series data which is based on the celebrated transformer architecture. Crucially, we enable our algorithm to do early classification, i.e., predict crop types at arbitrary time points early in the year with a single trained model (progressive intra-season classification). Such early season predictions are of practical relevance for instance for yield forecasts or the modeling of agricultural water balances, therefore being important for the public as well as the private sector. Furthermore, we improve the mechanism of combining different data sources for the prediction task, allowing for both optical and radar data as inputs (multi-modal data fusion) without the need for temporal interpolation. We can demonstrate the effectiveness of our approach on an extensive data set from three federal states of Germany reaching an average F1 score of 0.92 using data of a complete growing season to predict the eight most important crop types and an F1 score above 0.8 when doing early classification at least one month before harvest time. In carefully chosen experiments, we can show that our model generalizes well in time and space. Y1 - 2023 U6 - https://doi.org/10.3390/rs15030799 VL - 15 IS - 3 SP - 799 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Ebert, Patricia T1 - Forward and Line-Based Cycle Bases for Periodic Timetabling JF - Operations Research Forum N2 - The optimization of periodic timetables is an indispensable planning task in public transport. Although the periodic event scheduling problem (PESP) provides an elegant mathematical formulation of the periodic timetabling problem that led to many insights for primal heuristics, it is notoriously hard to solve to optimality. One reason is that for the standard mixed-integer linear programming formulations, linear programming relaxations are weak, and the integer variables are of pure technical nature and in general do not correlate with the objective value. While the first problem has been addressed by developing several families of cutting planes, we focus on the second aspect. We discuss integral forward cycle bases as a concept to compute improved dual bounds for PESP instances. To this end, we develop the theory of forward cycle bases on general digraphs. Specifically for the application of timetabling, we devise a generic procedure to construct line-based event-activity networks and give a simple recipe for an integral forward cycle basis on such networks. Finally, we analyze the 16 railway instances of the benchmark library PESPlib, match them to the line-based structure, and use forward cycle bases to compute better dual bounds for 14 out of the 16 instances. Y1 - 2023 U6 - https://doi.org/10.1007/s43069-023-00229-0 VL - 4 IS - 3 SP - 53 ER - TY - GEN A1 - Sikorski, Alexander A1 - Sechi, Renata A1 - Helfmann, Luzie T1 - cmdtools N2 - Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.5281/zenodo.4749331 ER - TY - GEN A1 - Peters-Kottig, Wolfgang A1 - Brandtner, Andreas A1 - Christof, Jürgen A1 - Hauffe, Yves A1 - Koch, Thorsten A1 - Kuo, Leslie A1 - Krause, Katja A1 - Müller, Anja A1 - Seeliger, Frank A1 - Stanek, Ursula A1 - Stöhr, Elena A1 - Vetter, Danilo A1 - Winkler, Alexander A1 - Zeyns, Andrea A1 - Rusch, Beate T1 - KOBV Jahresbericht 2021-2022 T3 - KOBV-Jahresbericht - 2021-2022 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91162 SN - 0934-5892 VL - 2021-2022 CY - Berlin ER - TY - THES A1 - Şirin, Ege T1 - Probabilistic Image Segmentation With Continuous Shape Representations Y1 - 2023 ER - TY - GEN A1 - Lindner, Niels A1 - Masing, Berenike T1 - On the Split Closure of the Periodic Timetabling Polytope N2 - The Periodic Event Scheduling Problem (PESP) is the central mathematical tool for periodic timetable optimization in public transport. PESP can be formulated in several ways as a mixed-integer linear program with typically general integer variables. We investigate the split closure of these formulations and show that split inequalities are identical with the recently introduced flip inequalities. While split inequalities are a general mixed-integer programming technique, flip inequalities are defined in purely combinatorial terms, namely cycles and arc sets of the digraph underlying the PESP instance. It is known that flip inequalities can be separated in pseudo-polynomial time. We prove that this is best possible unless P $=$ NP, but also observe that the complexity becomes linear-time if the cycle defining the flip inequality is fixed. Moreover, introducing mixed-integer-compatible maps, we compare the split closures of different formulations, and show that reformulation or binarization by subdivision do not lead to stronger split closures. Finally, we estimate computationally how much of the optimality gap of the instances of the benchmark library PESPlib can be closed exclusively by split cuts, and provide better dual bounds for five instances. T3 - ZIB-Report - 23-16 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Split Closure KW - Mixed-Integer Programming Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91156 SN - 1438-0064 ER - TY - GEN A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Branching via Cutting Plane Selection: Improving Hybrid Branching N2 - Cutting planes and branching are two of the most important algorithms for solving mixed-integer linear programs. For both algorithms, disjunctions play an important role, being used both as branching candidates and as the foundation for some cutting planes. We relate branching decisions and cutting planes to each other through the underlying disjunctions that they are based on, with a focus on Gomory mixed-integer cuts and their corresponding split disjunctions. We show that selecting branching decisions based on quality measures of Gomory mixed-integer cuts leads to relatively small branch-and-bound trees, and that the result improves when using cuts that more accurately represent the branching decisions. Finally, we show how the history of previously computed Gomory mixed-integer cuts can be used to improve the performance of the state-of-the-art hybrid branching rule of SCIP. Our results show a 4% decrease in solve time, and an 8% decrease in number of nodes over affected instances of MIPLIB 2017. T3 - ZIB-Report - 23-17 KW - cutting plane selection KW - variable selection KW - mixed-integer programming Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91120 SN - 1438-0064 ER - TY - CHAP A1 - Petkovic, Milena A1 - Zittel, Janina T1 - Forecasting and modeling the dynamics of large-scale energy networks under the supply and demand balance constraint T2 - AIRO Springer Series: International Conference on Optimization and Decision Science N2 - With the emergence of ”Big Data” the analysis of large data sets of high-dimensional energy time series in network structures have become feasible. However, building large-scale data-driven and computationally efficient models to accurately capture the underlying spatial and temporal dynamics and forecast the multivariate time series data remains a great challenge. Additional constraints make the problem more challenging to solve with conventional methods. For example, to ensure the security of supply, energy networks require the demand and supply to be balanced. This paper introduces a novel large-scale Hierarchical Network Regression model with Relaxed Balance constraint (HNR-RB) to investigate the network dynamics and predict multistep-ahead flows in the natural gas transmission network, where the total in- and out-flows of the network have to be balanced over a period of time. We concurrently address three main challenges: high dimensionality of networks with more than 100 nodes, unknown network dynamics, and constraint of balanced supply and demand in the network. The effectiveness of the proposed model is demonstrated through a real-world case study of forecasting demand and supply in a large-scale natural gas transmission network. The results demonstrate that HNR-RB outperforms alternative models for short- and mid-term horizons. Y1 - 2023 ER - TY - THES A1 - Hennings, Felix T1 - Modeling and solving real-world transient gas network transport problems using mathematical programming N2 - This thesis considers the transient gas network control optimization problem for on-shore pipeline-based transmission networks with numerous gas routing options. As input, the problem is given the network's topology, its initial state, and future demands at the boundaries of the network, which prescribe the gas flow exchange and potentially the pressure values. The task is to find a set of future control measures for all the active, i.e., controllable, elements in the network that minimizes a combination of different penalty functions. The problem is examined in the context of a decision support tool for gas network dispatchers. This results in detailed models featuring a diverse set of constraints, large and challenging real-world instances, and demanding time limit requirements. All these factors further complicate the problem, which is already difficult to solve in theory due to the inherent combination of non-linear and combinatorial aspects. Our contributions concern different steps of the process of solving the problem. Regarding the model formulation, we investigate the validity of two common approximations of the gas flow description in transport pipes: neglecting the inertia term and assuming a friction term that linearly depends on the gas flow and the pressure. For both, we examine if they can be applied under real-world conditions by evaluating a large amount of historical state data of the network of our project partner, the gas network operator Open Grid Europe. While we can confirm that it is reasonable to ignore the influence of the inertia term, the friction term linearization leads to significant errors and, as a consequence, cannot be used for describing the general gas flow behavior in transport pipes. As another topic of this thesis, we introduce the target value concept as a more realistic approach to express control actions of dispatchers regarding regulators and compressor stations. Here, we derive the mechanisms defined for target values based on the gas flow principles in pipes and develop a mixed-integer programming model capturing their behavior. The accuracy of this model is demonstrated in comparison to a target-value-based industry-standard simulator. Furthermore, we present two heuristics for the transient gas network control optimization problem featuring target values that are based on approximative models for the target-value-based control and determine the final decisions in a post-processing step. To compare the performance of the two heuristics with the approach of directly solving the corresponding model, we evaluate them on a set of artificially created test instances. Finally, we develop problem-specific algorithms for two variants of the described problem. One considers the control optimization for a single network station, which represents a local operation site featuring a large number of active elements. The used transient model is very detailed and includes a sophisticated representation of the compressor stations. Based on the shortness of the pipes in the station, the corresponding algorithm finds valid solutions by solving a series of stationary model variants as well as a transient rolling horizon approach. As the second variant, we consider the problem on the entire network but assume an approximative model representing the control capabilities of network stations. Aside from a new description of the compression capabilities, we introduce an algorithm that uses a combination of sequential mixed-integer programming, two heuristics based on reduced time horizons, and a specialized dynamic branch-and-bound node limit to determine promising values for the binary variables of the model. Complete solutions for the problem are obtained by fixing the binary values and solving the remaining non-linear program. Both algorithms are investigated in extensive empirical studies based on real-world instances of the corresponding model variants. N2 - Diese Arbeit behandelt das Optimierungsproblem der transienten Gasnetzwerksteuerung von Fernleitungsnetzen auf dem Festland mit einer großen Anzahl möglicher Gastransportrouten. Die Eingabedaten bestehen aus der Netzwerktopologie, dem Anfangszustand des Netzes und zukünftigen Vorgaben an den Randknoten des Netzes, welche den Gaseinfluss und Gasausfluss sowie eine potenzielle Vorgabe von Druckwerten umfassen. Gegeben diese Daten besteht die Aufgabe besteht darin, eine Menge an zukünftigen Steuerungsentscheidungen für alle aktiven, also steuerbaren, Elemente des Netzes zu finden, sodass eine Kombination von Straffunktionen minimiert wird. Das Problem wird in dieser Arbeit im Rahmen der Erstellung eines entscheidungsunterstützenden Systems für Dispatcher betrachtet, welche das Gasnetz steuern. Dies resultiert in einer detaillierten Modellierung mit einer Vielzahl von Nebenbedingungen, großen und herausfordernden realistischen Instanzen sowie anspruchsvollen Vorgaben zur maximalen Laufzeit. Diese Eigenschaften erhöhen die Komplexität des Problems, welches bereits in der Theorie auf Grund der inhärenten Kombination von nichtlinearen und kombinatorischen Aspekten schwierig zu lösen ist. Die Beiträge dieser Arbeit betreffen verschiedene Schritte des Prozesses zur Lösung des Problems. Bezüglich der Modellformulierung werden zwei übliche Approximationen der Gasflussbeschreibung in Fernleitungsrohren auf Validität überprüft: die Vernachlässigung des Trägheitsterms und die Annahme einer linearisierten Beschreibung des Reibungsterms. Für beide Approximationen wird untersucht, ob sie für reale Gasflussbedingungen zulässig sind. Dazu wird eine große Anzahl historischer Netzzustandsdaten des Gasnetzbetreibers Open Grid Europe ausgewertet. Während bestätigt werden kann, dass eine Vernachlässigung des Trägheitsterms unter Realbedingungen angemessen ist, führt die Linearisierung des Reibungsterms zu signifikanten Fehlern und kann daher nicht für die allgemeine Beschreibung des Gasflusses in Fernleitungsrohren verwendet werden. In einem weiteren Teil dieser Arbeit wird das Konzept der Sollwerte eingeführt. Mit diesen ist eine realistischere Beschreibung der Steuerungsbefehle möglich, welche den Dispatchern für Regler und Verdichterstationen zur Verfügung stehen. Der Sollwertmechanismus wird basierend auf den Gasflussprinzipien in Rohrleitungen hergeleitet, um anschließend ein gemischt-ganzzahliges Programm zu entwickeln, welches das entsprechende Verhalten erzeugt. Die Präzision dieses Modells wird durch einen Vergleich mit einem Simulator von Industriestandard sichergestellt, welcher auf Sollwerten basiert. Außerdem werden zwei Heuristiken für das Optimierungsproblem der transienten Gasnetzwerksteuerung mit Sollwertmodellierung vorgestellt. Diese basieren auf approximativen Modellen für die Sollwertsteuerung und ermitteln die letztendlichen Steuerungsentscheidungen in einer nachgelagerten Routine. Basierend auf künstlich erzeugten Testinstanzen werden die Heuristiken schließlich mit dem direkten Lösen des entsprechenden Modells verglichen. Zudem werden in dieser Arbeit problemspezifische Algorithmen für zwei Varianten des beschriebenen Optimierungsproblems entwickelt. Die erste Variante betrachtet das Gasnetzwerksteuerungsproblem beschränkt auf eine einzelne Netzstation, die lokale Betriebsstellen darstellen und über eine Vielzahl an aktiven Steuerungselementen verfügen. Das entsprechende transiente Modell ist sehr detailliert und beinhaltet eine differenzierte Beschreibung der Verdichterstationen. Der problemspezifische Algorithmus basiert auf der Kürze der Rohre innerhalb der Station und findet zulässige Lösungen durch das Lösen von stationären Varianten des Modells sowie der Nutzung eines transienten Rolling-Horizon Ansatzes. In der zweiten Problemvariante wird das gesamte Gasnetz betrachtet, wobei eine vereinfachte Modellierung der Steuerungsmöglichkeiten innerhalb von Netzstationen angenommen wird. Neben einer neuen Beschreibung der Verdichtungsmöglichkeiten einer Station wird ebenfalls ein problemspezifischer Algorithmus entwickelt. Dieser erstellt aussichtsreiche Werte für die Binärvariablen und nutzt dafür eine Kombination aus sequenzieller gemischt-ganzzahliger Programmierung, zwei auf verkürzten Zeithorizonten basierenden Heuristiken und eine spezialisierte dynamische Obergrenze für die Anzahl der Branch-and-Bound-Knoten. Diese Teillösungen werden durch eine Fixierung der binären Variablen und das anschließende Lösen des restlichen nichtlinearen Programms komplettiert. Die Güte beider Algorithmen wird in umfangreichen empirischen Experimenten untersucht, welche reale Instanzen der jeweiligen Problemvarianten betrachten. Y1 - 2023 ER - TY - JOUR A1 - Hennings, Felix A1 - Petkovic, Milena A1 - Streubel, Tom T1 - On the Numerical Treatment of Interlaced Target Values - Modeling, Optimization and Simulation of Regulating Valves in Gas Networks JF - Optimization and Engineering N2 - Due to the current and foreseeable shifts towards carbon dioxide neutral energy production, which will likely result in balancing fluctuating renewable energy generation by transforming power-to-gas-to-power as well as building a large-scale hydrogen transport infrastructure, the trading and transport operations of gas will become more dynamic, volatile, and hence also less predictable. Therefore, computer-aided support in terms of rapid simulation and control optimization will further broaden its importance for gas network dispatching. In this paper, we aim to contribute and openly publish two new mathematical models for regulators, also referred to as control valves, which together with compressors make up the most complex and involved types of active elements in gas network infrastructures. They provide direct control over gas networks but are in turn controlled via target values, also known as set-point values, themselves. Our models incorporate up to six dynamical target values to define desired transient states for the elements' local vicinity within the network. That is, each pair of every two target values defines a bounding box for the inlet pressure, outlet pressure as well as the passing mass flow of gas. In the proposed models, those target values are prioritized differently and are constantly in competition with each other, which can only be resolved dynamically at run-time of either a simulation or optimization process. Besides careful derivation, we compare simulation and optimization results with predictions of the widely adopted commercial simulation tool SIMONE, serving as our substitute for actual real-world transport operations. Y1 - 2023 U6 - https://doi.org/10.1007/s11081-023-09812-0 PB - Springer Nature ER - TY - JOUR A1 - Sterzik, Anna A1 - Lichtenberg, Nils A1 - Krone, Michael A1 - Baum, Daniel A1 - Cunningham, Douglas W. A1 - Lawonn, Kai T1 - Enhancing molecular visualization: Perceptual evaluation of line variables with application to uncertainty visualization JF - Computers & Graphics N2 - Data are often subject to some degree of uncertainty, whether aleatory or epistemic. This applies both to experimental data acquired with sensors as well as to simulation data. Displaying these data and their uncertainty faithfully is crucial for gaining knowledge. Specifically, the effective communication of the uncertainty can influence the interpretation of the data and the user’s trust in the visualization. However, uncertainty-aware visualization has gotten little attention in molecular visualization. When using the established molecular representations, the physicochemical attributes of the molecular data usually already occupy the common visual channels like shape, size, and color. Consequently, to encode uncertainty information, we need to open up another channel by using feature lines. Even though various line variables have been proposed for uncertainty visualizations, they have so far been primarily used for two-dimensional data and there has been little perceptual evaluation. Thus, we conducted two perceptual studies to determine the suitability of the line variables blur, dashing, grayscale, sketchiness, and width for distinguishing several values in molecular visualizations. While our work was motivated by uncertainty visualization, our techniques and study results also apply to other types of scalar data. Y1 - 2023 U6 - https://doi.org/10.1016/j.cag.2023.06.006 VL - 114 SP - 401 EP - 413 ER - TY - THES A1 - Bautz, Lisa T1 - Unsupervised Shape Correspondence Estimation for Anatomical Shapes N2 - The concept of shape correspondence describes a relation between two or more shapes of the same class. It often consists of a mapping between points on semantically similar locations of all shapes. One possible application for shape correspondence in medicine is the automatic location of anatomical landmarks. Another popular application is the construction of statistical shape models. These models are an established way to represent geometric variation of anatomical shapes in a compact way. Possible applications range from the generation of shapes and reconstruction tasks to disease classification. This thesis aims to investigate unsupervised methods that can be used to estimate such a correspondence on anatomical shapes. While most methods used in the medical domain focus on classical optimization algorithms to establish correspondence, the broader computer vision domain developed a versatile field of data-driven methods. Recently, the new shape model FlowSSM was introduced, which does not require predefined correspondences for training as it generates them itself. As the performance of the shape model is quite competitive, it is natural to assume that the generated correspondences are of high quality as well. For this reason, we evaluate the quality of the correspondences generated by FlowSSM within this thesis. Furthermore, we modify the method by adding a second loss term that minimizes geodesic distortions. This is done to favor isometric deformations which can lead to better correspondences. We compare the results with two established methods from the medical domain, LDDMM and Meshmonk. Furthermore, we investigate the performance of a fourth method called Neuromoph. This data-driven method comes from the wider computer vision field and was not tested on anatomical data yet. All methods are evaluated with a set of different metrics. This includes metrics to assess the quality of the resulting meshes, a sparse correspondence error on anatomical landmarks, and metrics to measure the quality of the resulting shape models. Furthermore, we test all methods on three datasets with different degrees of geometric variation, namely liver, distal femur and face. We show that FlowSSM produces correspondences with state-of-the-art quality. Moreover, our modification further improved the quality of correspondences at a global level. Nevertheless, there is no clear ranking between all methods, as the results differ between metrics and datasets. Thereby, we can show that there are different qualities to a proper correspondence which are reflected in the different metrics. It is therefore strongly recommendable to choose a correspondence estimation method specifically for the problem at hand. N2 - Das Konzept der Formkorrespondenz zwischen 3D-Objekten einer Klasse beschreibt eine Beziehung zwischen den Instanzen (oft Punkten) der unterschiedlichen Objekten. Hierbei werden Punkte, die an semantisch gleichwertigen Orten liegen, miteinander in Verbindung gebracht. Eine mögliche Anwednung der Formkorrespondenz im medizinischen Bereich ist daher die automatisierte Lokalisierung von anatomischen Landmarken. Eine weitere Anwendung ist das Erstellen von statistischen Formmodellen. Mit diesen kann die geometrische Variation anatomischer Formen kompakt abgebildet werden. Medizinische Anwendungen reichen dabei von der einfachen Formgenerierung zu komplexeren Rekonstruktionsaufgaben und der Klassifizierung von gesunden und pathologischen Formen. In dieser Arbeit werden unterschiedliche Methoden zur Erzeugung von Formkorrespondenzen untersucht. Die entsprechende Literatur im medizinischen Bereich verwendet hierzu meist Methoden, die das klassische Optimierungsproblem einer nichtrigiden Transformation lösen. Im Computer Vision Bereich wurden in den letzten Jahren auch einige datengetriebene Methoden zur Korrespondenzgenerierung veröffentlicht. Im letzten Jahr wurde außerdem die Methode FlowSSM zur Erstellung statistischer Formmodelle vorgestellt, die nicht auf korrespondierenden Oberflächen basiert, sondern diese selbst erzeugt. Da FlowSSM trotzdem konkurenzfähige Ergebnisse erzielt, ist naheliegend, dass auch die zugrundeliegenden, selbst generierten Korrespondenzen von hoher Qualität sind. Innerhalb dieser Arbeit wird daher die Qualität der von FlowSSM erzeugten Korrespondenzen evaluiert. Außerdem wird die Methode um eine zusätzliche Kostenfunktion erweitert, die geod#tische Verzerrungen verhindern soll. Dadurch sollen nichtisometrische Deformationen vermieden werden, wodurch die Qualität der resultierenden Korrenspondenzen gesteigert werden kann. Die Ergebnisse von FlowSSM werden mit zwei etablierten Methoden aus dem medizinischen Bereich, LDDMM und Meshmonk, verglichen. Außerdem wird NeuroMorph, eine aktuelle, datengetriebene Methode aus dem Bereich des maschinellen Sehens getestet. Letztere wurde bisher noch nicht auf medizinischen Daten evaluiert. Die Bewertung aller generierten Korrespondenzen basiert auf ausgewählten indirekten Metriken. Hierzu gehört auch die Performance bei konkreten Anwendungsfällen wie der Lokalisierung von Landmarken und dem Erstellen von statistischen Formmodellen. Im Rahmen der Arbeit wird gezeigt, dass FlowSSM Korrespondenzen produziert, deren Qualität dem aktuellen State-of-the-art entspricht. Durch das Hinzufügen der zweiten Kostenfunktion wird die Qualität der Korrespondenzen auf einem globalen Level noch weiter gesteigert. Prinzipiell lässt sich jedoch keine Hierarchie zwischen den Methoden ableiten, da die Performance stark innerhalb der untersuchten Metriken und Datensätzen schwankt. Die Auswahl einer passenden Methode sollte sich daher vor allem am Anwendungsfall orientieren. Y1 - 2023 ER - TY - CHAP A1 - Kuen, Lilli A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Heermeier, Niels A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - Applying a Riesz-projection-based contour integral eigenvalue solver to compute resonance modes of a VCSEL T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2665490 VL - 12575 SP - 125750J ER - TY - BOOK A1 - Ternes, Thomas A1 - Bauer, Karl-Heinz A1 - Brauer, Frank A1 - Drewes, Jörg A1 - Joss, Adriano A1 - Hiller, Georg A1 - Jewell, Kevin A1 - Oehlmann, Jörg A1 - Radke, Michael A1 - Schulte-Oehlmann, Ulrike A1 - Schwartz, Thomas A1 - Seel, Peter A1 - Völker, Jeanette A1 - Weber, Lilo A1 - Weber, Marcus ED - Wilhelm, Christian T1 - Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen N2 - Das vorliegende Statuspapier beschreibt ein Konzept zur weitergehenden Abwasserbehandlung für die Bewertung von Aufbereitungsverfahren, sowohl in einer Pilotphase zur Auswahl von Verfah- rensoptionen als auch für die Bewertung großtechnischer Anlagen. Y1 - 2023 SN - 978-3-96862-563-8 VL - T1/2023 PB - DWA / GDCh ER - TY - JOUR A1 - Bai, Mingze A1 - Deng, Jingwen A1 - Dai, Chengxin A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Perez-Riverol, Yasset T1 - LFQ-Based Peptide and Protein Intensity Differential Expression Analysis JF - J. Proteome Res. N2 - Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jproteome.2c00812 VL - 22 IS - 6 SP - 2114 EP - 2123 PB - American Chemical Society ER - TY - JOUR A1 - Paltra, Sydney A1 - Conrad, Tim T1 - Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review JF - Advances in Respiratory Medicine N2 - Nirmatrelvir/Ritonavir is an oral treatment for mild to moderate COVID-19 cases with a high risk for a severe course of the disease. For this paper, a comprehensive literature review was performed, leading to a summary of currently available data on Nirmatrelvir/Ritonavir’s ability to reduce the risk of progressing to a severe disease state. Herein, the focus lies on publications that include comparisons between patients receiving Nirmatrelvir/Ritonavir and a control group. The findings can be summarized as follows: Data from the time when the Delta-variant was dominant show that Nirmatrelvir/Ritonavir reduced the risk of hospitalization or death by 88.9% for unvaccinated, non-hospitalized high-risk individuals. Data from the time when the Omicron variant was dominant found decreased relative risk reductions for various vaccination statuses: between 26% and 65% for hospitalization. The presented papers that differentiate between unvaccinated and vaccinated individuals agree that unvaccinated patients benefit more from treatment with Nirmatrelvir/Ritonavir. However, when it comes to the dependency of potential on age and comorbidities, further studies are necessary. From the available data, one can conclude that Nirmatrelvir/Ritonavir cannot substitute vaccinations; however, its low manufacturing cost and easy administration make it a valuable tool in fighting COVID-19, especially for countries with low vaccination rates. Y1 - 2024 U6 - https://doi.org/10.3390/arm92010009 VL - 92 IS - 1 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Spreckelsen, Klaus A1 - Gotzes, Uwe A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Beimischung von Wasserstoff zum Erdgas: Eine Kapazitätsstudie des deutschen Gasnetzes JF - 3R – Fachzeitschrift für Rohrleitungssystem N2 - Die europäische Gasinfrastruktur wird disruptiv in ein zukünftiges dekarbonisiertes Energiesystem verändert; ein Prozess, der angesichts der jüngsten politischen Situation beschleunigt werden muss. Mit einem wachsenden Wasserstoffmarkt wird der pipelinebasierte Transport unter Nutzung der bestehenden Erdgasinfrastruktur wirtschaftlich sinnvoll, trägt zur Erhöhung der öffentlichen Akzeptanz bei und beschleunigt den Umstellungsprozess. In diesem Fachbeitrag wird die maximal technisch machbare Einspeisung von Wasserstoff in das bestehende deutsche Erdgastransportnetz hinsichtlich regulatorischer Grenzwerte der Gasqualität analysiert. Die Analyse erfolgt auf Basis eines transienten Tracking-Modells, das auf dem allgemeinen Pooling-Problem einschließlich Linepack aufbaut. Es zeigt sich, dass das Gasnetz auch bei strengen Grenzwerten genügend Kapazität bietet, um für einen großen Teil der bis 2030 geplanten Erzeugungskapazität für grünen Wasserstoff als garantierter Abnehmer zu dienen. Y1 - 2023 IS - 06/2023 SP - 70 EP - 75 ER - TY - JOUR A1 - Mikheeva, Elena A1 - Colom, Rémi A1 - Achouri, Karim A1 - Overvig, Adam A1 - Binkowski, Felix A1 - Duboz, Jean-Yves A1 - Cueff, Sébastien A1 - Fan, Shanhui A1 - Burger, Sven A1 - Alù, Andrea A1 - Genevet, Patrice T1 - Asymmetric phase modulation with light with parity-symmetry broken metasurfaces JF - Optica Y1 - 2023 U6 - https://doi.org/10.1364/OPTICA.495681 VL - 10 SP - 1287 ER - TY - JOUR A1 - Kontou, Eftychia E. A1 - Walter, Axel A1 - Alka, Oliver A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Mohite, Omkar A1 - Nuhamunanda, Matin A1 - Kohlbacher, Oliver A1 - Weber, Tilmann T1 - UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis JF - Journal of Cheminformatics N2 - Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC–MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. Y1 - 2023 U6 - https://doi.org/10.1186/s13321-023-00724-w VL - 15 ER - TY - JOUR A1 - Hanik, Martin A1 - Ducke, Benjamin A1 - Hege, Hans-Christian A1 - Fless, Friederike A1 - von Tycowicz, Christoph T1 - Intrinsic shape analysis in archaeology: A case study on ancient sundials JF - Journal on Computing and Cultural Heritage N2 - The fact that the physical shapes of man-made objects are subject to overlapping influences—such as technological, economic, geographic, and stylistic progressions—holds great information potential. On the other hand, it is also a major analytical challenge to uncover these overlapping trends and to disentagle them in an unbiased way. This paper explores a novel mathematical approach to extract archaeological insights from ensembles of similar artifact shapes. We show that by considering all shape information in a find collection, it is possible to identify shape patterns that would be difficult to discern by considering the artifacts individually or by classifying shapes into predefined archaeological types and analyzing the associated distinguishing characteristics. Recently, series of high-resolution digital representations of artifacts have become available. Such data sets enable the application of extremely sensitive and flexible methods of shape analysis. We explore this potential on a set of 3D models of ancient Greek and Roman sundials, with the aim of providing alternatives to the traditional archaeological method of “trend extraction by ordination” (typology). In the proposed approach, each 3D shape is represented as a point in a shape space—a high-dimensional, curved, non-Euclidean space. Proper consideration of its mathematical properties reduces bias in data analysis and thus improves analytical power. By performing regression in shape space, we find that for Roman sundials, the bend of the shadow-receiving surface of the sundials changes with the latitude of the location. This suggests that, apart from the inscribed hour lines, also a sundial’s shape was adjusted to the place of installation. As an example of more advanced inference, we use the identified trend to infer the latitude at which a sundial, whose location of installation is unknown, was placed. We also derive a novel method for differentiated morphological trend assertion, building upon and extending the theory of geometric statistics and shape analysis. Specifically, we present a regression-based method for statistical normalization of shapes that serves as a means of disentangling parameter-dependent effects (trends) and unexplained variability. In addition, we show that this approach is robust to noise in the digital reconstructions of the artifact shapes. Y1 - 2023 U6 - https://doi.org/10.1145/3606698 VL - 16 IS - 4 SP - 1 EP - 26 ER - TY - GEN A1 - Sikorski, Alexander T1 - VoronoiGraph.jl N2 - This Package implements a variation of the Voronoi Graph Traversal algorithm by Polianskii and Pokorny [1]. It constructs a Voronoi Diagram from a set of points by performing a random walk on the graph of the vertices of the diagram. Unlike many other Voronoi implementations this algorithm is not limited to 2 or 3 dimensions and promises good performance even in higher dimensions. Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.6417636 ER - TY - GEN A1 - Tjusila, Gennesaret A1 - Besancon, Mathieu A1 - Turner, Mark A1 - Koch, Thorsten T1 - How Many Clues To Give? A Bilevel Formulation For The Minimum Sudoku Clue Problem N2 - It has been shown that any 9 by 9 Sudoku puzzle must contain at least 17 clues to have a unique solution. This paper investigates the more specific question: given a particular completed Sudoku grid, what is the minimum number of clues in any puzzle whose unique solution is the given grid? We call this problem the Minimum Sudoku Clue Problem (MSCP). We formulate MSCP as a binary bilevel linear program, present a class of globally valid inequalities, and provide a computational study on 50 MSCP instances of 9 by 9 Sudoku grids. Using a general bilevel solver, we solve 95\% of instances to optimality, and show that the solution process benefits from the addition of a moderate amount of inequalities. Finally, we extend the proposed model to other combinatorial problems in which uniqueness of the solution is of interest. T3 - ZIB-Report - 23-15 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-90902 ER - TY - JOUR A1 - Zemann, Berit A1 - Le, Mai-Lee Van A1 - Sherlock, Rob E. A1 - Baum, Daniel A1 - Katija, Kakani A1 - Stach, Thomas T1 - Evolutionary traces of miniaturization in a giant – Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia) JF - Journal of Morphology Y1 - 2023 U6 - https://doi.org/10.1002/jmor.21598 VL - 284 IS - 7 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven T1 - RPExpand (Version 1) T2 - Zenodo Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.7840116 SP - doi: 10.5281/zenodo.7840116 ER - TY - JOUR A1 - Hassan, Irtaza A1 - Donati, Luca A1 - Stensitzki, Till A1 - Keller, Bettina G A1 - Heyne, Karsten A1 - Imhof, Petra T1 - The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations JF - Chemical Physics Letters N2 - We have combined infrared (IR) experiments with molecular dynamics (MD) simulations in solution at finite temperature to analyse the vibrational signature of the small floppy peptide Alanine-Leucine. IR spectra computed from first-principles MD simulations exhibit no distinct differences between conformational clusters of -helix or -sheet-like folds with different orientations of the bulky leucine side chain. All computed spectra show two prominent bands, in good agreement with the experiment, that are assigned to the stretch vibrations of the carbonyl and carboxyl group, respectively. Variations in band widths and exact maxima are likely due to small fluctuations in the backbone torsion angles. Y1 - 2018 U6 - https://doi.org/10.1016/j.cplett.2018.03.026 VL - 698 SP - 227 EP - 233 ER - TY - CHAP A1 - Keller, Bettina G. A1 - Aleksić, Stevan A1 - Donati, Luca T1 - Markov State Models in Drug Design T2 - Biomolecular Simulations in Structure‐Based Drug Discovery N2 - This chapter explains the different ways in which Markov State Models (MSMs) can be helpful in structure-based drug design. MSMs are constructed from the time series of molecular dynamics (MD), which can be generated by classical MD simulations. Several features of the MSMs can be utilized for rational drug design. The discretization of a validated MSM is particularly suited to extract meaningful representatives from the conformational ensemble, because the discretization yields a small number of microstates and mirrors the features of the free energy landscape. Long-lived conformations consist of a set of microstates which show high transition rates within the set and low transition rates to microstates outside of the set. The Bayesian agglomerative clustering engine (BACE) algorithm uses the observed transition counts to extract long-lived conformations from an MSM. By iteratively merging microstates according to the Bayes factor and recalculating the Bayes-factor matrix, the algorithm yields an aggregation of the microstates into long-lived conformations. Y1 - 2018 SN - 1865-0562 U6 - https://doi.org/10.1002/9783527806836.ch4 SP - 67 EP - 86 PB - Wiley-Interscience, Weinheim ER - TY - JOUR A1 - Donati, Luca A1 - Hartmann, Carsten A1 - Keller, Bettina G. T1 - Girsanov reweighting for path ensembles and Markov state models JF - The Journal of Chemical Physics N2 - The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor “on the fly” during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics. Y1 - 2017 U6 - https://doi.org/10.1063/1.4989474 VL - 146 IS - 24 SP - 244112 ER - TY - JOUR A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Girsanov reweighting for metadynamics simulations JF - The Journal of Chemical Physics N2 - Metadynamics is a computational method to explore the phase space of a molecular system. Gaussian functions are added along relevant coordinates on the fly during a molecular-dynamics simulation to force the system to escape from minima in the potential energy function. The dynamics in the resulting trajectory are however unphysical and cannot be used directly to estimate dynamical properties of the system. Girsanov reweighting is a recent method used to construct the Markov State Model (MSM) of a system subjected to an external perturbation. With the combination of these two techniques—metadynamics/Girsanov-reweighting—the unphysical dynamics in a metadynamics simulation can be reweighted to obtain the MSM of the unbiased system. We demonstrate the method on a one-dimensional diffusion process, alanine dipeptide, and the hexapeptide Val-Gly-Val-Ala-Pro-Gly (VGVAPG). The results are in excellent agreement with the MSMs obtained from direct unbiased simulations of these systems. We also apply metadynamics/Girsanov-reweighting to a β-hairpin peptide, whose dynamics is too slow to efficiently explore its phase space by direct simulation Y1 - 2018 U6 - https://doi.org/10.1063/1.5027728 VL - 149 IS - 7 SP - 072335 ER - TY - JOUR A1 - Kieninger, Stefanie A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Dynamical reweighting methods for Markov models JF - Current Opinion in Structural Biology N2 - Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications. Y1 - 2020 U6 - https://doi.org/10.1016/j.sbi.2019.12.018 VL - 61 SP - 124 EP - 131 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus A1 - Keller, Bettina G. T1 - Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux JF - Journal of Physics: Condensed Matter N2 - Molecular dynamics (MD) are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the MD as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker–Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive MD simulations. The square-root approximation of the Fokker–Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used MD simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to $\mathcal{O}\left(1{0}^{6}\right)$ states can be obtained within seconds on a single high-performance compute server if regular grids are used. Y1 - 2021 U6 - https://doi.org/10.1088/1361-648X/abd5f7 VL - 33 IS - 11 SP - 115902 ER - TY - JOUR A1 - Donati, Luca A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Augmented ant colony algorithm for virtual drug discovery JF - Journal of Mathematical Chemistry N2 - Docking is a fundamental problem in computational biology and drug discovery that seeks to predict a ligand’s binding mode and affinity to a target protein. However, the large search space size and the complexity of the underlying physical interactions make docking a challenging task. Here, we review a docking method, based on the ant colony optimization algorithm, that ranks a set of candidate ligands by solving a minimization problem for each ligand individually. In addition, we propose an augmented version that takes into account all energy functions collectively, allowing only one minimization problem to be solved. The results show that our modification outperforms in accuracy and efficiency. Y1 - 2023 U6 - https://doi.org/10.1007/s10910-023-01549-6 VL - 62 SP - 367 EP - 385 ER - TY - JOUR A1 - Plock, Matthias A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Schütte, Christof T1 - Impact Study of Numerical Discretization Accuracy on Parameter Reconstructions and Model Parameter Distributions JF - Metrologia N2 - In optical nano metrology numerical models are used widely for parameter reconstructions. Using the Bayesian target vector optimization method we fit a finite element numerical model to a Grazing Incidence x-ray fluorescence data set in order to obtain the geometrical parameters of a nano structured line grating. Gaussian process, stochastic machine learning surrogate models, were trained during the reconstruction and afterwards sampled with a Markov chain Monte Carlo sampler to determine the distribution of the reconstructed model parameters. The numerical discretization parameters of the used finite element model impact the numerical discretization error of the forward model. We investigated the impact of the polynomial order of the finite element ansatz functions on the reconstructed parameters as well as on the model parameter distributions. We showed that such a convergence study allows to determine numerical parameters which allows for efficient and accurate reconstruction results. Y1 - 2023 U6 - https://doi.org/10.1088/1681-7575/ace4cd VL - 60 SP - 054001 ER - TY - CHAP A1 - Chaukair, Mustafa A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - On the Activation Space of ReLU Equipped Deep Neural Networks T2 - Procedia Computer Science N2 - Modern Deep Neural Networks are getting wider and deeper in their architecture design. However, with an increasing number of parameters the decision mechanisms becomes more opaque. Therefore, there is a need for understanding the structures arising in the hidden layers of deep neural networks. In this work, we present a new mathematical framework for describing the canonical polyhedral decomposition in the input space, and in addition, we introduce the notions of collapsing- and preserving patches, pertinent to understanding the forward map and the activation space they induce. The activation space can be seen as the output of a layer and, in the particular case of ReLU activations, we prove that this output has the structure of a polyhedral complex. Y1 - 2023 U6 - https://doi.org/10.1016/j.procs.2023.08.200 VL - 222 SP - 624 EP - 635 ER - TY - JOUR A1 - Schütte, Christof A1 - Klus, Stefan A1 - Hartmann, Carsten T1 - Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning JF - Acta Numerica N2 - One of the main challenges in molecular dynamics is overcoming the ‘timescale barrier’: in many realistic molecular systems, biologically important rare transitions occur on timescales that are not accessible to direct numerical simulation, even on the largest or specifically dedicated supercomputers. This article discusses how to circumvent the timescale barrier by a collection of transfer operator-based techniques that have emerged from dynamical systems theory, numerical mathematics and machine learning over the last two decades. We will focus on how transfer operators can be used to approximate the dynamical behaviour on long timescales, review the introduction of this approach into molecular dynamics, and outline the respective theory, as well as the algorithmic development, from the early numerics-based methods, via variational reformulations, to modern data-based techniques utilizing and improving concepts from machine learning. Furthermore, its relation to rare event simulation techniques will be explained, revealing a broad equivalence of variational principles for long-time quantities in molecular dynamics. The article will mainly take a mathematical perspective and will leave the application to real-world molecular systems to the more than 1000 research articles already written on this subject. Y1 - 2023 U6 - https://doi.org/10.1017/S0962492923000016 VL - 32 SP - 517 EP - 673 ER - TY - GEN A1 - Pedersen, Jaap A1 - Weinand, Jann Michael A1 - Syranidou, Chloi A1 - Rehfeldt, Daniel T1 - An efficient solver for multi-objective onshore wind farm siting and network integration N2 - Existing planning approaches for onshore wind farm siting and network integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an approach for the multi-objective optimization of turbine locations and their network connection using a Quota Steiner tree problem. Applying a novel transformation on a known directed cut formulation, reduction techniques, and heuristics, we design an exact solver that makes large problem instances solvable and outperforms generic MIP solvers. Although our case studies in selected regions of Germany show large trade-offs between the objective criteria of cost and landscape impact, small burdens on one criterion can significantly improve the other criteria. In addition, we demonstrate that contrary to many approaches for exclusive turbine siting, network integration must be simultaneously optimized in order to avoid excessive costs or landscape impacts in the course of a wind farm project. Our novel problem formulation and the developed solver can assist planners in decision making and help optimize wind farms in large regions in the future. T3 - ZIB-Report - 23-10 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-90590 SN - 1438-0064 ER - TY - JOUR A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - 制約整数計画ソルバ SCIP の並列化 JF - 統計数理 N2 - 制約整数計画(CIP: Constraint Integer Programs)は,制約プログラミング(CP: Constraint Programming),混合整数計画(MIP: Mixed Integer Programming),充足可能性問題(SAT: Satisfability Problem)の研究分野におけるモデリング技術と解法を統合している.その結果,制約整数計画は,広いクラスの最適化問題を扱うことができる.SCIP(Solving Constraint Integer Programs)は,CIP を解くソルバとして実装され,Zuse Institute Berlin(ZIB)の研究者を中心として継続的に拡張が続けられている.本論文では,著者らによって開発された SCIP に対する2 種類の並列化拡張を紹介する.一つは,複数計算ノード間で大規模に並列動作する ParaSCIPである.もう一つは,複数コアと共有メモリを持つ 1 台の計算機上で(スレッド)並列で動作する FiberSCIP である.ParaSCIP は,HLRN II スーパーコンピュータ上で,一つのインスタンスを解くために最大 7,168 コアを利用した動作実績がある.また,統計数理研究所の Fujitsu PRIMERGY RX200S5 上でも,最大 512 コアを利用した動作実績がある.統計数理研究所のFujitsu PRIMERGY RX200S5 上では,これまでに最適解が得られていなかった MIPLIB2010のインスタンスである dg012142 に最適解を与えた. N2 - The paradigm of constraint integer programming (CIP) combines modeling and solving techniques from the fields of constraint programming (CP), mixed-integer programming (MIP) and satisfability problem (SAT). This paradigm allows us to address a wide range of optimization problems. SCIP is an implementation of the idea of CIP and is now being continuously extended by a group of researchers centered at Zuse Institute Berlin (ZIB). This paper introduces two parallel extensions of SCIP. One is ParaSCIP, which is intended to run on a large scale distributed memory computing environment, and the other is FiberSCIP, intended to run on a shared memory computing environment. ParaSCIP has been run successfully on the HLRN II supercomputer utilizing up to 7,168 cores to solve a single difficult MIP. It has also been tested on an ISM supercomputer (Fujitsu PRIMERGY RX200S5 using up to 512 cores). The previously unsolved instance dg012142 from MIPLIB2010 was solved by using the ISM supercomputer. Y1 - 2013 UR - https://www.ism.ac.jp/editsec/toukei/pdf/61-1-047.pdf VL - 61 IS - 1 SP - 47 EP - 78 ER - TY - JOUR A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yasuda, Masaya A1 - Kaji, Shizuo A1 - Yamamura, Keiichiro A1 - Fujisawa, Katsuki T1 - Development and analysis of massive parallelization of a lattice basis reduction algorithm JF - Japan Journal of Industrial and Applied Mathematics N2 - The security of lattice-based cryptography relies on the hardness of solving lattice problems. Lattice basis reduction is a strong tool for solving lattice problems, and the block Korkine–Zolotarev (BKZ) reduction algorithm is the de facto standard in cryptanalysis. We propose a parallel algorithm of BKZ-type reduction based on randomization. Randomized copies of an input lattice basis are independently reduced in parallel, while several basis vectors are shared asynchronously among all processes. There is a trade-off between randomization and information sharing; if a substantial amount of information is shared, all processes might work on the same problem, which diminishes the benefit of parallelization. To monitor the balance between randomness and sharing, we propose a new metric to quantify the variety of lattice bases, and we empirically find an optimal parameter of sharing for high-dimensional lattices. We also demonstrate the effectiveness of our parallel algorithm and metric through experiments from multiple perspectives. Y1 - 2023 U6 - https://doi.org/10.1007/s13160-023-00580-z VL - 40 IS - 1 SP - 13 EP - 56 ER - TY - JOUR A1 - 品野, 勇治 T1 - MIPLIB と Hans Mittelmann’s benchmarks JF - 機関誌「オペレーションズ・リサーチ」 N2 - 混合整数計画法 (Mixed Integer Programming: MIP) は,MIP を解くソフトウェアである MIP ソルバが大規模な現実問題を解けるようになったこともあり,現実問題を解く有用な OR の手法として広く知られるようになった.しかしながら,MIP ソルバの開発に欠かせないベンチマーク・データセットおよび性能測定方法についてはそれほど広く知られているとは言い難い.ベンチマーク・データセットは注意を払って作成しないと,多くのバイアスがかかってしまう.それらのバイアスを可能な限りのぞき,真に有用なベンチマーク・テストの結果を得るためには複数の人数で多大な労力を割く必要がある.本稿では,そのような MIP ソルバ開発の背景として重要な役割を果たしてきた MIPLIB と Hans Mittelmann’s benchmarks について解説する.また,本稿において Hans Mittelmann’s benchmarks は,BENCHMARKS FOR OPTIMIZATION SOFTWAREのページ (http://plato.asu.edu/bench.html) に示されているベンチマークである. Y1 - 2020 UR - https://orsj.org/wp-content/corsj/or65-1/or65_1_49.pdf VL - 65 IS - 1 SP - 49 EP - 56 ER - TY - JOUR A1 - 品野, 勇治 A1 - 藤井, 浩一 T1 - 使ってみよう線形計画ソルバ JF - 機関誌「オペレーションズ・リサーチ」 N2 - 本稿では,線形計画問題を解くソフトウェアである線形計画ソルバの標準的な利用方法と,原稿執筆時点で利用可能なソルバを可能な限り紹介する.筆者らはソルバ開発コミュニティの中で仕事をしているので,この機会に現在のソルバ開発現場の様子も紹介するとともに,各ソルバの特徴として何を紹介するべきかは,できる限り開発者,または,開発者に近い研究者に問い合わせて記述した.本稿は,多くの線形計画ソルバの選択肢がある中で,読者がもつ問題を解くのに最も適当なソルバを選択するための指針を与えることを主たる目的としている. Y1 - 2019 UR - https://orsj.org/wp-content/corsj/or64-4/or64_4_238.pdf VL - 64 IS - 4 SP - 238 EP - 245 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Cover Picture: Resonance Expansion of Quadratic Quantities with Regularized Quasinormal Modes JF - Phys. Status Solidi A Y1 - 2023 U6 - https://doi.org/10.1002/pssa.202370013 VL - 220 SP - 2370013 ER - TY - JOUR A1 - 藤澤, 克樹 A1 - 品野, 勇治 T1 - 最適化と計算の今後 ―大規模問題をどこまで解決できるのか?― JF - 機関誌「オペレーションズ・リサーチ」 N2 - 近年,大規模かつ複雑な最適化問題を高速に解く需要はさまざまな産業界や学術分野において急速に高まりつつある.これからの研究においては最先端理論 (Theory)+超大規模実データ (Practice)+最新計算技術(Computation) の三つを有機的に組み合わせることによって,実用に耐えうる解決策の提示と大規模最適化問題を扱う際の先例となることが求められている.本稿では最適化と計算に関する最新の傾向に触れるとともに,最適化の計算の今後についても考えていきたい. Y1 - 2014 UR - https://orsj.org/wp-content/corsj/or59-1/or59_1_11.pdf VL - 59 IS - 1 SP - 11 EP - 19 ER - TY - JOUR A1 - 品野, 勇治 T1 - 最適化研究における数値実験を中心とした アプリケーション駆動研究サイクル JF - 機関誌「オペレーションズ・リサーチ」 N2 - 最適化研究におけるアプリケーション駆動研究サイクルを紹介する.アプリケーション駆動研究サイクルは,学術機関での研究と企業における研究成果の利用とのつながりを良くする点では優れている.一方で,ソフトウェア開発・維持に多大な労力を要するため,日本の大学や研究機関における実施には困難さが伴う.ZIBにおいてアプリケーション駆動研究サイクルが,比較的うまく機能している背景を説明する.また,日本においてアプリケーション駆動研究サイクルを活性化するための第一歩として,論文投稿時に,論文中の数値実験に利用した全データ提出の義務化を提案したい. Y1 - 2014 UR - https://orsj.org/wp-content/corsj/or59-5/or59_5_247.pdf VL - 59 IS - 5 SP - 247 EP - 253 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(手法の提案) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Proposal of Optimization Method) JF - 第33回エネルギー・資源学会研究発表会講演論文要旨集・講演論文集 N2 - A mixed-integer linear programming (MILP) method utilizing the hierarchical relationship between design and op- eration variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2014 SP - 183 EP - 188 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用階層的関係を考慮した最適化(K-ベスト解の探索) T1 - Optimization ofEnergy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Search for K-Best Solutions) JF - 日本機械学会第11回最適化シンポジウム2014講演論文集 N2 - A mixed-integer linear programming methodutilizing the hierarchical relationship between design and operation variables proposed ot solve the optimal design problem of energy supply systems efficiently is extended ot search K-best solutions: At the upper level, the optimal values ofdesign variables are searched with operation variables relaxed to continuous ones; At the lower level, the values of operation variables are optimized with the values of design variables given tentatively; The obtained solution is used to renew K-best incumbent solutions, and the upper bound for the value of the objective function for K-best solutions is replaced correspondingly. A practical case study is conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2014 SP - 1 EP - 4 ER - TY - JOUR A1 - Taniguchi, Shusuke A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(多目的最適化におけるK-ベスト解の探索) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Search for K-Best Solutions in Multiobjective Optimization) JF - エネルギー・資源学会第31回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed to solve the optimal design problem of energy supply systems efficiently is extended to search K-best solutions in multiobjective optimization: At the upper level, the optimal values of design variables are searched by the branch and bound method with operation variables relaxed to continuous ones; At the lower level, the values of operation variables are optimized independently at the respective periods set for variations in energy demands by the branch and bound method with the values of design variables given tentatively during the search at the upper level. A weighting method is employed for multiobjective optimization, and a weighted sum of the annual total cost and primary energy consumption is adopted as the objective function to be minimized. A practical case study on the optimal design of a cogeneration system is conducted. The validity and effectiveness of the proposed method are clarified, and the trade-off relationship between the annual total cost and primary energy consumption is confirmed. Y1 - 2015 SP - 267 EP - 272 ER - TY - JOUR A1 - Wakayama, Yuki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(時間集約によるモデル縮約とその効果) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation(Model Reduction by Time Aggregation and Its Effect) JF - エネルギー・資源学会第34回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A hierarchical mixed-integer linear programming method to solve optimal design problems of energy supply systems efficiently has been proposed. The original problem is solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of each other at the lower level. In this paper, a method of reducing model by time aggregation is proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. On one hand, the method may decrease the number of design variables and costraints at the upper level, and thus the computation time at the upper level. On the other hand, it may increase the numbers of generated design solution candidates and solved optimal operation problems, and thus the computation time at both the levels. Though a case study on the optimal design of a cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency. Y1 - 2018 SP - 401 EP - 404 ER - TY - JOUR A1 - Wakayama, Yuki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化によるエネルギ ー供給システムの最適設計・運用 (期間のクラスタリングに よるモデル縮約とその効果) T1 - Optimal Design and Operation of Energy Supply Systems by Hierarchical Optimization (Model Reduction by Clustering Periods and Its Effect) JF - 日本機械学会関西支部第93期定時総会講演会講演論文集 N2 - Ahierarchical mixed-integer linear programmingmethod has been proposed to solve optimal design problems of energy supply systems efficiently. In this paper, a method of reducing model by clustering periods is proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Through acase study on the optimaldesign of a cogeneration system, ti is clarified how the model reduction si effective ot enhance the computation efficiency. Y1 - 2018 SP - 259 EP - 260 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 混合整数線形モデルによる エネルギー供給システムのロバスト最適設計 (階層的最適化手法の適用) T1 - Robust Optimal Design of Energy Supply Systems Based on a Mixed-Integer Linear Model (Application of a Hierarchical Optimization Method) JF - エネルギー・資源学会第35回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed- integer linear model for constituent equipment. A robust optimal design problem has been formulated as a three-level min-max- min optimization one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering hierarchical relationships among design variables, uncertain energy demands, and operation variables. However, this method takes a long computation time, and thus it can be applied only to small-scale problems. In this paper, mixed-integer linear programming method in consideration of the hierarchical relationship between design and operation variables is applied to parts of the robust optimal design method which take long computation times to solve problems efficiently. In a case study, this revised method is applied to the robust optimal design of a cogeneration system with a simple configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2019 SP - 163 EP - 168 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの 設計と運用の階層的関係を考慮した最適化 (運用を考慮した期間クラスタリングによるモデル縮約) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Model Reduction by Clustering Periods in Consideration of Operation) JF - エネルギー・資源学会第35回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) methods have been applied widely to such multi-period optimal design problems. A hierarchical MILP method has been proposed to solve the problems very efficiently. In addition, by utilizing features of the hierarchical MILP method, a method of reducing model by clustering periods has also been proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, by utilizing features of the hierarchical MILP method, a method of clustering periods is proposed based on the optimal operational strategies of energy supply systems obtained by solving the relaxed optimal design problem. As a case study, the method is applied to the optimal design of a gas turbine cogeneration system, and it is clarified that the method is effective to enhance the computation efficiency in comparison with a conventional method of clustering periods regularly. Y1 - 2019 SP - 169 EP - 174 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Takeuchi, Kotaro A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (モデル縮約のための期間クラスタリング手法の比較) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Comparison of Time-Period Clustering Methods for Model Reduction) JF - 第38回エネルギー・資源学会研究発表会講演論文集 N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, three clustering methods are applied to time aggregation and compared with one another in terms of the computation efficiency. Especially, the k-medoids method is applied newly in addition to the time-series and operation-based methods applied previously. A case study is conducted on the optimal design of a gas turbine cogeneration system for district energy supply. Through the study, it turns out the k-medoids method is effective to shorten the computation time as compared with the time-series method, although it is necessary to set the number of clusters artifically in both the methods. It also turns out that the operation-based method is more effective than the k-medoids method in terms of the computation efficiency even with the number of clusters set automatically. Y1 - 2019 SP - 109 EP - 114 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化手法の援用による エネルギー供給システムのロバスト最適設計 T1 - Robust Optimal Design of Energy Supply Systems With Aid of a Hierarchical Optimization Method JF - エネルギー・資源学会第36回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed- integer linear model for constituent equipment. A robust optimal design problem has been formulated as a three-level min-max- min optimization one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering hierarchical relationships among design variables, uncertain energy demands, and operation variables. Since this problem must be solved by a special algorithm and is too difficult to solve even using a commercial solver, a hierarchical optimization approach has been applied to solve the problem but its application is limited only to small scale toy problems. In this paper, some strategies are introduced into the hierarchical optimization approach to enhance the computation efficiency for the purpose of applying the approach to large scale practical problems. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system with a complex configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2020 SP - 730 EP - 735 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化手法を用いた エネルギー供給システムのロバスト性評価 T1 - Evaluating Robustness of Energy Supply Systems Using a Hierarchical Optimization Method JF - 日本機械学会関西支部第95期定時総会講演会講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed-integer linear model for constituent equipment. However, this method takes a long computation time, and thus it can be applied only to small-scale problems. In this paper, a hierarchical optimization method is applied to two types of optimization problems for evaluating robustness to solve them efficiently. In a case study, the proposed method is applied to a cogeneration system with a complex configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2020 SP - 1 EP - 4 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの 設計および運用の階層的関係を考慮した最適化 (多目的最適設計へのモデル縮約の適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Application of Model Reduction to Multiobjective Optimal Design) JF - エネルギー・資源学会第36回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) methods have been applied widely to such optimal design problems. A hierarchical MILP method has been proposed to solve the problems very efficiently. In addition, by utilizing features of the hierarchical MILP method, a method of reducing model by clustering periods based on the optimal operational strategies of equipment has been proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, these methods are applied to the multiobjective optimal design of a cogeneration system by considering the annual total cost and primary energy consumption as the objective functions to be minimized. Through a case study, it turns out that the model reduction by the operation-based time-period clustering is effective in terms of the computation efficiency when importance is given to the first objective function, while it is not when importance is given to the second objective function. Y1 - 2020 SP - 724 EP - 729 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化 (k-メドイド法に基づく期間クラスタリングの適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierachical Relationship Between Design and Operation (Application of Time-Period Clustering Based on k-Medoids Method) JF - 日本機械学会関西支部第95期定時総会講演会講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. A hierarchical mixed-integer linear programming method has been proposed to solve such an optimal design problem efficiently. In this paper, a method of reducing model by clustering periods with the k-medoids method is applied to the relaxed optimal design problem at the upper level. Through a case study, it is clarified how the proposed method is effective to enhance the computation efficiency in a large scale optimal design problem. Y1 - 2020 SP - 1 EP - 4 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (蓄エネルギー機器を有するシステムへの適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Application to Systems With Energy Storage Units) JF - 第40回エネルギー・資源学会研究発表会講演論文集 N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies has been extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of re- ducing model is extended by aggregating representative days and sampling times differently in consideration of the characteristics of storage units. A case study is conducted on the optimal design of a gas turbine cogeneration system with a thermal storage unit for district energy supply. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solution as compared with a conventional method. It also turns out that the model reduction with the special time aggregation is effective to shorten the computation time as compared with that without time aggregation in case that the number of candidates for equipment capacities is relatively small. Y1 - 2021 SP - 398 EP - 403 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した設計解の評価) T1 - Derivation and Evaluation of Approximate Optimal Design Solutions of Energy Supply Systems by Time Aggregation (Evaluation of Design Solutions Using Hierarchical Optimization) JF - エネルギー・資源学会第38回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to solve such an optimal design problem with a large number of periods efficiently is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to provide a time aggregation method for deriving aprroximate optimal design solutions and evaluting their values of the objective function. Especially, a method of evaluating design solutions is presented here using both methods of evaluating the robustness under uncertain energy demands and solving optimal design problems by a hierarchical approach. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach. Y1 - 2022 SP - 468 EP - 473 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した近似最適設計) T1 - Derivation and Evaluation of Approximate Optimal Design Solutions of Energy Supply Systems by Time Aggregation (Approximate Optimal Design Using Hierarchical Optimization) JF - 第41回エネルギー・資源学会研究発表会講演論文集 N2 - For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to efficiently solve such an optimal design problem with a large number of periods for variations in energy de- mands is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to propose a time aggregation approach for deriving suitable aprroximate optimal design solutions and evaluting their values of the objective function accurately. This time aggregation approach is realized by combining a robust optimal design method under uncertain energy demands and a hierarchical approach for solving large scale optimal design problems. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective upper and lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach. Y1 - 2022 SP - 144 EP - 148 ER - TY - THES A1 - Grewe, Martin T1 - An Extended 3D Morphable Face Model with Applications in Experimental Psychology N2 - Our faces and facial expressions are an important means of communication and social interaction. One goal of the behavioral sciences is to better understand how the features of the faces that we look at influence our behavior. These include static features like facial proportions or the shape and color of certain parts of a face which primarily constitute facial identity, as well as dynamic movements resulting from the activation of the mimic musculature. Experimental psychology provides an empirical approach to this endeavor. In experiments, participants are typically exposed to images or videos of realistic faces with specifically controlled features. By analysis of the reactions to such stimuli, conclusions can be drawn about the influence of facial features on the participants’ behavior. Psychologists today mostly generate face stimuli with the help of digital tools. Image editing with Photoshop is highly flexible, but also time-consuming and subjective. Using tools like Psychomorph or Fantamorph is easier and more objective, but does not allow specific control over facial features. In contrast, stimulus generation with 3D Morphable Face Models (3DMMs) offers a better balance between objectivity, ease of use, and flexibility. 3DMMs are statistical models which have been determined from 3D scans of real people’s faces and facial expressions. After these training scans have been brought into correspondence, methods like principal component analysis (PCA) can be used to determine the major modes of variation of facial shape and texture in the data. Such modes typically vary the overall facial proportions, expressions, or skin color. They can be individually controlled and flexibly combined to generate new faces and facial expressions. The plausibility of the generated faces can be ensured by having the mode combinations follow the multivariate distribution of the training data. 3DMMs have been mostly used by psychologists for the generation of stimulus images of faces with neutral expression. Static and dynamic stimuli of facial expressions are also of great interest, but generation with 3DMMs is less common. A problem is that the majority of current 3DMMs can only generate facial movements according to the six prototypic expressions of anger, disgust, fear, happiness, sadness, and surprise. More diverse or subtle expressions are often impossible. Among other reasons, this is due to the difficulty in establishing accurate correspondence in the training data. Further, the modes of most 3DMMs were created by means of PCA. These modes often lack interpretability, fail to generate facial details, and rarely provide psychologists a specific control over identity or expression features. Some 3DMMs also generate subtle artifacts that might lead to undesired effects during face perception. They are also less realistic than faces which were designed by artistic experts for recent computer games and animated movies. Last but not least, current 3DMMs have probably not yet been used for interactive experiments in virtual reality (VR) for technical reasons. Although they provide many advantages also beyond the generation of static or dynamic stimuli, the limitations of current 3DMMs have so far prevented a widespread usage in experimental psychology. The goal of this dissertation is to foster the creation and usage of 3DMMs in this context. To this end, we make three major contributions. First, we describe a matching method that establishes correspondence for 3D face scans with a very high accuracy. Unlike the most commonly used methods, it transforms the facial features into a 2D intermediate representation so that they can be aligned to a reference using image registration. We perform experiments with a large database of 3D scans of faces and facial expressions showing that our method outperforms previous approaches. Second, the 3D scans which were previously brought into correspondence are used for the creation of a 3DMM whose resolution is an order of magnitude higher than that of most existing models. We learn a variety of meaningful modes that, e.g., vary features only in specific regions of the face, or that are related to demographic factors such as ethnicity and age. Further, modes of local facial movements are established that can be flexibly combined into a large variety of expressions. We evaluate the quality of the newly created 3DMM in two experiments. Our results show its advantages over previous models, especially the higher degree of realism of dynamic stimuli of facial expressions which were created with our model. Third, we demonstrate that 3DMMs can not only be used for the generation of stimuli. We develop two experimental methods that are readily applicable in experimental psychology. Initially, we create 3D avatar faces with our 3DMM that are readily applicable in VR. They are used in a new open source framework for virtual mirror experiments on self-face perception. A study is conducted which demonstrates the advantages of the framework over previous methods. Furthermore, our 3DMM is used to create a method for improved control of facial asymmetry in existing stimulus photographs. We show that the method accounts for different dimensions of facial asymmetry and is less sensitive than previous approaches to extrinsic factors like the posture of the head. The different methods are evaluated in a study investigating the influence of facial asymmetry on ratings of attractiveness, femininity, and masculinity. The results indicate the benefits and validity of our method. KW - facial modeling KW - 3D morphable face model KW - facial analysis KW - experimental psychology Y1 - 2023 ER - TY - CHAP A1 - Gander, Lia A1 - Krause, Rolf A1 - Weiser, Martin A1 - Costabal, Francisco A1 - Pezzuto, Simone T1 - On the Accuracy of Eikonal Approximations in Cardiac Electrophysiology in the Presence of Fibrosis T2 - Functional Imaging and Modeling of the Heart. FIMH 2023. N2 - Fibrotic tissue is one of the main risk factors for cardiac arrhythmias. It is therefore a key component in computational studies. In this work, we compare the monodomain equation to two eikonal models for cardiac electrophysiology in the presence of fibrosis. We show that discontinuities in the conductivity field, due to the presence of fibrosis, introduce a delay in the activation times. The monodomain equation and eikonal-diffusion model correctly capture these delays, contrarily to the classical eikonal equation. Importantly, a coarse space discretization of the monodomain equation amplifies these delays, even after accounting for numerical error in conduction velocity. The numerical discretization may also introduce artificial conduction blocks and hence increase propagation complexity. Therefore, some care is required when comparing eikonal models to the discretized monodomain equation. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-35302-4_14 VL - 13958 PB - Springer, Cham ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Uram, Samuel A1 - Wolf, Sarah A1 - Conrad, Natasa Djurdjevac A1 - Weiser, Martin T1 - Multilevel Optimization for Policy Design with Agent-Based Epidemic Models JF - Computational Science N2 - Epidemiological models can not only be used to forecast the course of a pandemic like COVID-19, but also to propose and design non-pharmaceutical interventions such as school and work closing. In general, the design of optimal policies leads to nonlinear optimization problems that can be solved by numerical algorithms. Epidemiological models come in different complexities, ranging from systems of simple ordinary differential equations (ODEs) to complex agent-based models (ABMs). The former allow a fast and straightforward optimization, but are limited in accuracy, detail, and parameterization, while the latter can resolve spreading processes in detail, but are extremely expensive to optimize. We consider policy optimization in a prototypical situation modeled as both ODE and ABM, review numerical optimization approaches, and propose a heterogeneous multilevel approach based on combining a fine-resolution ABM and a coarse ODE model. Numerical experiments, in particular with respect to convergence speed, are given for illustrative examples. Y1 - 2024 U6 - https://doi.org/10.1016/j.jocs.2024.102242 VL - 77 SP - 102242 ER - TY - JOUR A1 - Secker, Christopher A1 - Fackeldey, Konstantin A1 - Weber, Marcus A1 - Ray, Sourav A1 - Gorgulla, Christoph A1 - Schütte, Christof T1 - Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists JF - Journal of Cheminformatics N2 - Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the μ-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported β-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale. Y1 - 2023 U6 - https://doi.org/10.1186/s13321-023-00746-4 VL - 15 ER - TY - JOUR A1 - Navayazdani, Esfandiar A1 - Ambellan, Felix A1 - Hanik, Martin A1 - von Tycowicz, Christoph T1 - Sasaki Metric for Spline Models of Manifold-Valued Trajectories JF - Computer Aided Geometric Design N2 - We propose a generic spatiotemporal framework to analyze manifold-valued measurements, which allows for employing an intrinsic and computationally efficient Riemannian hierarchical model. Particularly, utilizing regression, we represent discrete trajectories in a Riemannian manifold by composite Bézier splines, propose a natural metric induced by the Sasaki metric to compare the trajectories, and estimate average trajectories as group-wise trends. We evaluate our framework in comparison to state-of-the-art methods within qualitative and quantitative experiments on hurricane tracks. Notably, our results demonstrate the superiority of spline-based approaches for an intensity classification of the tracks. Y1 - 2023 U6 - https://doi.org/10.1016/j.cagd.2023.102220 VL - 104 SP - 102220 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of en- ergy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been pro- posed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accor- dance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 VL - 181 SP - 782 EP - 792 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Takeuchi, Kotaro A1 - Wakui, Tetsuya T1 - Operation-based time-period clustering for optimal design of energy supply systems by a hierarchical MILP method JF - THE 32ND INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS(ECOS 2019) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, a method of clustering periods has been proposed based on the optimal operational strategies of the systems to avoid a large decrease in the lower bound for the optimal value of the objective function by model reduction. This method has been realized only by solving the relaxed optimal design problem at the upper level in advance. The method can decrease the number of operation variables and constraints at the upper level, and thus can decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the proposed clustering method is effective to enhance the computation efficiency in comparison with the conventional one which clusters periods regularly in time series. Y1 - 2019 SP - 527 EP - 539 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of Design Alternatives for a Gas Turbine Cogeneration Plant Based on Multiobjective K-Best Solutions JF - International Conference on Power Engineering-2019 N2 - To realize the best performance in energy supply, it is an important task to determine types, capacities, and numbers of energy conversion equipment appropriately. It is also necessary to take account of seasonal and hourly variations in energy demands and corresponding operational strategies of equipment. The mixed-integer linear programming (MILP) method has been utilized widely to derive the optimal solution for such a design problem. From the design viewpoint, it is important to generate not only the optimal solution but also suboptimal ones which follow the optimal one without omission, what are called K-best solutions. In this paper, an MILP method utilizing the hierarchical relationship between design and operation variables is applied along with some strategies to efficiently drive K-best solutions of a multiobjective optimal design problem of a gas turbine cogeneration system for district energy supply. The annual total cost and primary energy consumption are adopted as the objective functions to be minimized. A case study is conducted, and K-best solutions with an allowable increase in the value of the combined objective function are derived for each value of the weight for the annual total cost. Through the study, it is clarified how the weight affects the computation time, the number of the K-best solutions, and the design specifications and the values of the objective functions for the K-best solutions. Y1 - 2019 SP - 1112 EP - 1117 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Hiramatsu, Yuto A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model JF - The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified. As a result, it turns out how the values of these performance criteria are close to the optimal ones in relation to the uncertainty in energy demands. This work will be an important step toward developing a multiobjective robust optimal design method. Y1 - 2022 SP - 1937 EP - 1948 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method JF - The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effec- tive to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small. Y1 - 2022 SP - 1891 EP - 1902 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Wakui, Tetsuya T1 - Search for K-best solutions in optimal design of energy supply systems by an extended MILP hierarchical branch and bound method JF - Energy N2 - For the purpose of making a decision in the optimal design of an energy supply system, it is important to investigate not only the optimal solution but also suboptimal ones which follow the optimal one without any omissions, what are called K-best solutions. In this paper, a mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed previ- ously is extended to search the K-best solutions very efficiently. In addition, methods for updating the incumbents are incorporated into the extended method for three options for the criterion set newly in deriving the K-best solutions. This extended method is implemented into open and commercial MILP solvers, and is applied to illustrative and practical case studies, respectively, on the optimal design of cogeneration systems. Through the studies, it turns out that the proposed method is much superior in terms of solution optimality and computation efficiency to a conventional method, and that the computation efficiency to derive one of the K-best solutions by the proposed method increases with the number of K-best solutions. In addition, features of the K-best solutions in the value of objective function are clarified. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2018.02.077 VL - 184 SP - 45 EP - 57 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and Verified Gomory Mixed Integer Cuts in a Rational MIP Framework JF - SIAM Journal on Optimization N2 - This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5% more instances and reduce solving times by 26.8% on the MIPLIB 2017 benchmark test set. Y1 - 2023 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and Verified Gomory Mixed Integer Cuts in a Rational MIP Framework N2 - This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5% more instances and reduce solving times by 26.8% on the MIPLIB 2017 benchmark test set. T3 - ZIB-Report - 23-09 KW - Mixed integer programming, Exact computation, Rational arithmetic, Cutting Planes, Symbolic Computations, Certificate of correctness Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-90159 SN - 1438-0064 ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Effect of inertia force on the interface stability of a tangential-velocity discontinuity in porous media JF - International Journal of Multiphase Flow N2 - The present study investigates the stability of a tangential-velocity discontinuity in porous media during the withdrawing and injecting processes of natural gases from and into an underground gas storage. The focus is placed on analyzing the impact of inertia forces on the interface stability using the Forchheimer equations. Other publications have relied primarily on Darcy's law to describe flow stability in porous media. However, Darcy's law only adequately describes flows in which viscous forces dominate over inertia forces. As the flow rate increases, the significance of inertia forces becomes more pronounced, and Darcy's law becomes insufficient for considering such flows. Our findings indicate that even a slight consideration of the inertia effect leads to permanent destabilization of the discontinuity interface, regardless of the fluid viscosity or the Mach number. In contrast, when the inertia effect is neglected, the interface is stabilized across the entire Mach number range if the fluid viscosity is strong enough. Y1 - 2023 U6 - https://doi.org/10.1016/j.ijmultiphaseflow.2023.104612 VL - 169 ER - TY - JOUR A1 - Tomholt, Lara A1 - Baum, Daniel A1 - Wood, Robert J. A1 - Weaver, James C. T1 - High-throughput segmentation, data visualization, and analysis of sea star skeletal networks JF - Journal of Structural Biology N2 - The remarkably complex skeletal systems of the sea stars (Echinodermata, Asteroidea), consisting of hundreds to thousands of individual elements (ossicles), have intrigued investigators for more than 150 years. While the general features and structural diversity of isolated asteroid ossicles have been well documented in the literature, the task of mapping the spatial organization of these constituent skeletal elements in a whole-animal context represents an incredibly laborious process, and as such, has remained largely unexplored. To address this unmet need, particularly in the context of understanding structure-function relationships in these complex skeletal systems, we present an integrated approach that combines micro-computed tomography, semi-automated ossicle segmentation, data visualization tools, and the production of additively manufactured tangible models to reveal biologically relevant structural data that can be rapidly analyzed in an intuitive manner. In the present study, we demonstrate this high-throughput workflow by segmenting and analyzing entire skeletal systems of the giant knobby star, Pisaster giganteus, at four different stages of growth. The in-depth analysis, presented herein, provides a fundamental understanding of the three-dimensional skeletal architecture of the sea star body wall, the process of skeletal maturation during growth, and the relationship between skeletal organization and morphological characteristics of individual ossicles. The widespread implementation of this approach for investigating other species, subspecies, and growth series has the potential to fundamentally improve our understanding of asteroid skeletal architecture and biodiversity in relation to mobility, feeding habits, and environmental specialization in this fascinating group of echinoderms. Y1 - 2023 U6 - https://doi.org/10.1016/j.jsb.2023.107955 VL - 215 IS - 2 SP - 107955 ER - TY - CHAP A1 - Mukherjee, Deshabrato A1 - Kalas, Benjámin A1 - Burger, Sven A1 - Sáfrán, György A1 - Serényi, Miklós A1 - Fried, Miklós A1 - Petrik, Péter T1 - Nanostructures for in-situ surface-enhanced Kretschmann-Raether ellipsometry T2 - Proc. SPIE Y1 - 2023 U6 - https://doi.org/10.1117/12.2649080 VL - 12428 SP - 124280S ER - TY - THES A1 - Sahu, Manish T1 - Vision-based Context-awareness in Minimally Invasive Surgical Video Streams N2 - Surgical interventions are becoming increasingly complex thanks to modern assistance systems (imaging, robotics, etc.). Minimally invasive surgery in particular places high demands on surgeons due to added surgical complexity and information overload. Therefore, there is a growing need of developing context-aware systems that recognize the current surgical situation in order to derive and present the relevant information to the surgical staff for assistance. Current approaches for deriving contextual cues either utilize specialized hardware that is disruptive to the surgical workflow, or utilize vision-based approaches that require valuable time of surgeons, especially for manual annotations. The main objective of this cumulative dissertation is to improve the existing approaches for three important sub-problems of vision-based context-aware systems, namely surgical phase recognition, surgical instrument recognition and surgical instrument segmentation, while tackling the vision and manual annotation challenges related to these problems. This dissertation demonstrates that vision-based approaches for the three named clinical sub-problems of context-aware systems can be developed in an annotation-scarce setting by employing: domain-specific, deep learning based transfer learning techniques for the surgical instrument and phase recognition tasks; and deep learning based simulation-to-real unsupervised domain adaptation techniques for the surgical instrument segmentation task. The efficacy and real-time performance of the developed approaches have been evaluated on publicly available datasets containing real surgical videos (laparoscopic procedures) that were acquired in an uncontrolled surgical environment. These proposed approaches advance the state-of-the-art for the aforementioned research problems of context-aware systems in the OR and can potentially be utilized for real-time notification of the surgical phase, surgical instrument usage and image-based localization of surgical instruments. Y1 - 2022 ER - TY - THES A1 - Tillmann, Peter T1 - Optimizing bifacial tandem solar cells for realistic operation conditions Y1 - 2023 U6 - https://doi.org/10.17169/refubium-39571 ER - TY - CHAP A1 - Siqueira Rodrigues, Lucas A1 - Nyakatura, John A1 - Zachow, Stefan A1 - Israel, Johann Habakuk T1 - An Immersive Virtual Paleontology Application T2 - 13th International Conference on Human Haptic Sensing and Touch Enabled Computer Applications, EuroHaptics 2022 N2 - Virtual paleontology studies digital fossils through data analysis and visualization systems. The discipline is growing in relevance for the evident advantages of non-destructive imaging techniques over traditional paleontological methods, and it has made significant advancements during the last few decades. However, virtual paleontology still faces a number of technological challenges, amongst which are interaction shortcomings of image segmentation applications. Whereas automated segmentation methods are seldom applicable to fossil datasets, manual exploration of these specimens is extremely time-consuming as it impractically delves into three-dimensional data through two-dimensional visualization and interaction means. This paper presents an application that employs virtual reality and haptics to virtual paleontology in order to evolve its interaction paradigms and address some of its limitations. We provide a brief overview of the challenges faced by virtual paleontology practitioners, a description of our immersive virtual paleontology prototype, and the results of a heuristic evaluation of our design. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-06249-0 SP - 478 EP - 481 ER - TY - JOUR A1 - Ullrich, Julia A1 - Weiser, Martin A1 - Subramaniam, Jayant A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita T1 - The impact of anatomy variation on temperature based time of death estimation JF - International Journal of Legal Medicine N2 - Temperature-based time of death estimation (TTDE) using simulation methods such as the finite element (FE) method promises higher accuracy and broader applicability in nonstandard cooling scenarios than established phenomenological methods. Their accuracy depends crucially on the simulation model to capture the actual situation. The model fidelity in turn hinges on the representation of the corpse’s anatomy in form of computational meshes as well as on the thermodynamic parameters. While inaccuracies in anatomy representation due to coarse mesh resolution are known to have a minor impact on the estimated time of death, the sensitivity with respect to larger differences in the anatomy has so far not been studied. We assess this sensitivity by comparing four independently generated and vastly different anatomical models in terms of the estimated time of death in an identical cooling scenario. In order to isolate the impact of shape variation, the models are scaled to a reference size, and the possible impact of measurement location variation is excluded explicitly, which gives a lower bound on the impact of anatomy on the estimated time of death. Y1 - 2023 U6 - https://doi.org/10.1007/s00414-023-03026-w VL - 137 SP - 1615 EP - 1627 ER - TY - JOUR A1 - Jung, Christian A1 - Nowacka, Anna A1 - Barisin, Tin A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Grzesiak, Szymon A1 - Salamon, Michael A1 - Schladitz, Katja A1 - Redenbach, Claudia A1 - Pahn, Matthias T1 - 3d imaging and analysis of cracks in loaded concrete samples. 12th Conference on Industrial Computed Tomography (iCT) 2023, 27 February - 2 March 2023 in Fürth, Germany JF - e-Journal of Nondestructive Testing N2 - Concrete plays a central role as the standard building material in civil engineering. Experimental characterization of the concrete microstructure and a description of failure mechanisms are important to understand the concrete’s mechanical properties. Computed tomography is a powerful source of information as it yields 3d images of concrete specimens. However, complete visual inspection is often infeasible due to very large image sizes. Hence, automatic methods for crack detection and segmentation are needed. A region-growing algorithm and a 3d U-Net showed promising results in a previous study. Cracks in normal concrete and high-performance concrete that were initiated via tensile tests were investigated. Here, the methods are validated on a more diverse set of concrete types and crack characteristics. Adequate adaptions of the methods are necessary to deal with the complex crack structures. The segmentation results are assessed qualitatively and compared to those of a template matching algorithm which is well-established in industry. Y1 - 2023 U6 - https://doi.org/10.58286/27721 VL - 28 IS - 3 ER - TY - CHAP A1 - Paetsch, Olaf T1 - Possibilities and Limitations of Automatic Feature Extraction shown by the Example of Crack Detection in 3D-CT Images of Concrete Specimen T2 - iCT 2019 N2 - To assess the influence of the alkali-silica reaction (ASR) on pavement concrete 3D-CT imaging has been applied to concrete samples. Prior to imaging these samples have been drilled out of a concrete beam pre-damaged by fatigue loading. The resulting high resolution 3D-CT images consist of several gigabytes of voxels. Current desktop computers can visualize such big datasets without problems but a visual inspection or manual segmentation of features such as cracks by experts can only be carried out on a few slices. A quantitative analysis of cracks requires a segmentation of the whole specimen which could only be done by an automatic feature detection. This arises the question of the reliability of an automatic crack detection algorithm, its certainty and limitations. Does the algorithm find all cracks? Does it find too many cracks? Can parameters of that algorithm, once identified as good, be applied to other samples as well? Can ensemble computing with many crack parameters overcome the difficulties with parameter finding? By means of a crack detection algorithm based on shape recognition (template matching) these questions will be discussed. Since the author has no access to reliable ground truth data of cracks the assessment of the certainty of the automatic crack is restricted to visual inspection by experts. Therefore, an artificial dataset based on a combination of manually segmented cracks processed together with simple image processing algorithms is used to quantify the accuracy of the crack detection algorithm. Part of the evaluation of cracks in concrete samples is the knowledge of the surrounding material. The surrounding material can be used to assess the detected cracks, e.g. micro-cracks within the aggregate-matrix interface may be starting points for cracks on a macro scale. Furthermore, the knowledge of the surrounding material can help to find better parameter sets for the crack detection itself because crack characteristics may vary depending on their surrounding material. Therefore, in addition to a crack detection a complete segmentation of the sample into the components of concrete, such as aggregates, cement matrix and pores is needed. Since such a segmentation task cannot be done manually due to the amount of data, an approach utilizing convolutional neuronal networks stemming from a medical application has been applied. The learning phase requires a ground truth i.e. a segmentation of the components. This has to be created manually in a time-consuming task. However, this segmentation can be used for a quantitative evaluation of the automatic segmentation afterwards. Even though that work has been performed as a short term subtask of a bigger project funded by the German Research Foundation (DFG) this paper discusses problems which may arise in similar projects, too. [1.2MB | id=23664 ] iCT 2019 Session: Short talks Thu 13:50 Auditorium 2019-03 Möglichkeiten und Grenzen automatischer Merkmalserkennung am Beispiel von Risserkennungen in 3D-CT-Aufnahmen von Betonproben O. Paetsch11 Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany Abstract [1MB | id=23104 ] DE DGZfP 2018 Session: Bauwesen 2018-09 Quantitative Rissanalyse im Fahrbahndeckenbeton mit der 3D-Computertomographie D. Meinel125, K. Ehrig128, F. Weise16, O. Paetsch211 1Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany concrete, ROI tomography, in-situ-CT, 3D-CT, Beton, AKR, Feuchtetransport, automatic crack detection Abstract [0.7MB | id=18980 ] DE DGZfP 2015 Session: CT Algorithmen 2016-04 3D Corrosion Detection in Time-dependent CT Images of Concrete O. Paetsch111, D. Baum15, S. Prohaska17, K. Ehrig228, D. Meinel225, G. Ebell24 1Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany CT, multi-angle radiography, defect detection, Feature Extraction, image processing, concrete, corrosion Abstract [0.5MB | id=18043 ] DIR 2015 Session: Quantitative imaging and image processing 2015-08 Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben O. Paetsch111, D. Baum15, G. Ebell24, K. Ehrig228, A. Heyn2, D. Meinel225, S. Prohaska17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Computertomographie [0.4MB | id=17375 ] DE DGZfP 2014 Session: Bauwesen 2015-03 Examination of Damage Processes in Concrete with CT D. Meinel125, K. Ehrig128, V. L’Hostis2, B. Muzeau2, O. Paetsch311 1BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Laboratoire d’Etude du Comportement des Bétons et des Argiles; Commissariat Energie Atomique (CEA)287, Gif-Sur-Yvette, France 3Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany X-ray computed tomography, concrete, corrosion, crack detection, 3D visualization Abstract [4.9MB | id=15692 ] iCT 2014 Session: Non-destructive Testing and 3D Materials Characterisation of... 2014-06 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben O. Paetsch111, D. Baum15, D. Breßler1, K. Ehrig228, D. Meinel225, S. Prohaska1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), statistical analysis, 3D Computed Tomography, visualization, concrete structural damage, automated crack detection [1MB | id=15343 ] DE DGZfP 2013 Session: Computertomographie 2014-03 Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computertomographie O. Paetsch111, K. Ehrig228, D. Meinel225, D. Baum15, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), visualization, crack detection, Visualisierung, computer tomography, template matching, Hessian eigenvalues, ZIBAmira, automated crack detection, percolation [0.9MB | id=14269 ] DE DGZfP 2012 Session: Computertomographie 2013-05 Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography O. Paetsch111, D. Baum15, K. Ehrig228, D. Meinel225, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany computed tomography, template matching, Hessian eigenvalues, crack statistics, visualization, crack surface, ZIBAmira [0.6MB | id=13736 ] iCT 2012 Session: Poster - Analysis and Algorithms 2012-12 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira D. Streicher112, O. Paetsch211, R. Seiler2, S. Prohaska27, M. Krause360 [Profile of Krause] , C. Boller178 1Saarland University74, Saarbrücken, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 3BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany [0.4MB | id=12284 ] DE DGZfP 2011 Session: Bauwesen 2012-05 Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography K. Ehrig128, J. Goebbels153, D. Meinel125, O. Paetsch211, S. Prohaska27, V. Zobel2 1Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany [0.7MB | id=11150 ] DIR 2011 Session: Poster 2011-11 Actual Cooperations 10th International Workshop NDT in Progress 2019 2019 Oct 7-9 11th International Symposium on NDT in Aerospace 2019 2019 Nov 13-15 3rd Singapore International NDT Conference & Exhibition, SINCE 2019 2019 Dec 4-5 10th Conference on Industrial Computed Tomography (iCT) 2020 2020 Feb 4-7 34th European Conference on Acoustic Emission Testing (EWGAE 2020) 2020 Sep 9-11 Contribute Papers and Proceedings to NDT.net Share... Home Exhibition Archive Forum Jobs Members Events Directory NDT A-Z Advertise Privacy Policy Contact About © NDT.net - Where expertise comes together. The Largest Open Access Portal of Nondestructive Testing (NDT)- since 1996 Y1 - 2019 ER - TY - JOUR A1 - Semler, Phillip A1 - Weiser, Martin T1 - Adaptive Gaussian Process Regression for Efficient Building of Surrogate Models in Inverse Problems JF - Inverse Problems N2 - In a task where many similar inverse problems must be solved, evaluating costly simulations is impractical. Therefore, replacing the model y with a surrogate model y(s) that can be evaluated quickly leads to a significant speedup. The approximation quality of the surrogate model depends strongly on the number, position, and accuracy of the sample points. With an additional finite computational budget, this leads to a problem of (computer) experimental design. In contrast to the selection of sample points, the trade-off between accuracy and effort has hardly been studied systematically. We therefore propose an adaptive algorithm to find an optimal design in terms of position and accuracy. Pursuing a sequential design by incrementally appending the computational budget leads to a convex and constrained optimization problem. As a surrogate, we construct a Gaussian process regression model. We measure the global approximation error in terms of its impact on the accuracy of the identified parameter and aim for a uniform absolute tolerance, assuming that y(s) is computed by finite element calculations. A priori error estimates and a coarse estimate of computational effort relate the expected improvement of the surrogate model error to computational effort, resulting in the most efficient combination of sample point and evaluation tolerance. We also allow for improving the accuracy of already existing sample points by continuing previously truncated finite element solution procedures. Y1 - 2023 U6 - https://doi.org/10.1088/1361-6420/ad0028 VL - 39 IS - 12 SP - 125003 ER - TY - CHAP A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Cruz, Alexandros A1 - Wagner, Philipp A1 - Jäger, Klaus A1 - Yoo, Danbi A1 - Lang, Felix A1 - Grischek, Max A1 - Li, Bor A1 - Al-Ashouri, Amran A1 - Köhnen, Eike A1 - Stolterfoht, Martin A1 - Neher, Dieter A1 - Schlatmann, Rutger A1 - Rech, Bernd A1 - Stannowski, Bernd A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Nanooptically Enhanced Perovskite/Silicon Tandem Solar Cells with 29.80% Power Conversion Efficiency T2 - OSA Adv. Photonics Y1 - 2022 U6 - https://doi.org/10.1364/NOMA.2022.JTu4H.2 SP - JTu4H.2 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Newton's Method for Global Free Flight Trajectory Optimization N2 - Globally optimal free flight trajectory optimization can be achieved with a combination of discrete and continuous optimization. A key requirement is that Newton's method for continuous optimization converges in a sufficiently large neighborhood around a minimizer. We show in this paper that, under certain assumptions, this is the case. T3 - ZIB-Report - 23-08 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89876 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Spreckelsen, Klaus A1 - Gotzes, Uwe A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Beimischung von Wasserstoff zum Erdgas: Eine Kapazitätsstudie des deutschen Gasnetzes T1 - Blending hydrogen into natural gas: An assessment of the capacity of the German gas grid JF - gwf Gas + Energie N2 - Die europaische Gasinfrastruktur wird disruptiv in ein zukunftiges dekarbonisiertes Energiesystem verändert; ein Prozess, der angesichts der jüngsten politischen Situation beschleunigt werden muss. Mit einem wachsenden Wasserstoffmarkt wird der pipelinebasierte Transport unter Nutzung der bestehenden Erdgasinfrastruktur wirtschaftlich sinnvoll, trägt zur Erhöhung der öffentlichen Akzeptanz bei und beschleunigt den Umstellungsprozess. In diesem Beitrag wird die maximal technisch machbare Einspeisung von Wasserstoff in das bestehende deutsche Erdgastransportnetz hinsichtlich regulatorischer Grenzwerte der Gasqualität analysiert. Die Analyse erfolgt auf Basis eines transienten Tracking-Modells, das auf dem allgemeinen Pooling-Problem einschließlich Linepack aufbaut. Es zeigt sich, dass das Gasnetz auch bei strengen Grenzwerten gen ̈ugend Kapazität bietet, um für einen großen Teil der bis 2030 geplanten Erzeugungskapazität für grünen Wasserstoff als garantierter Abnehmer zu dienen. N2 - The European gas infrastructure is being disruptively transformed into a future decarbonised energy system; a process that needs to be accelerated given the recent political situation. With a growing hydrogen market, pipeline-based transport using the existing natural gas infrastructure becomes economically viable, helps to increase public acceptance and accelerates the transition process. In this paper, the maximum technically feasible feed-in of hydrogen into the existing German natural gas transport network is analysed with regard to regulatory limits of gas quality. Analysis is based on a transient tracking model that builds on the general pooling problem including linepack. It is shown that even with strict limits, the gas grid offers sufficient capacity to serve as a guaranteed customer for a large part of the green hydrogen generation capacity planned until 2030. Y1 - 2023 PB - Vulkan Verlag ET - 06/2023 ER - TY - GEN A1 - Vohra, Sumit Kumar A1 - Harth, Philipp A1 - Isoe, Yasuko A1 - Bahl, Armin A1 - Fotowat, Haleh A1 - Engert, Florian A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - A Visual Interface for Exploring Hypotheses about Neural Circuits N2 - One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa. T3 - ZIB-Report - 23-07 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89932 SN - 1438-0064 ER - TY - JOUR A1 - Subramaniam, Jayant S. A1 - Hubig, Michael A1 - Muggenthaler, Holger A1 - Schenkl, Sebastian A1 - Ullrich, Julia A1 - Pourtier, Grégroire A1 - Weiser, Martin A1 - Mall, Gita T1 - Sensitivity of temperature-based time since death estimation on measurement location JF - International Journal of Legal Medicine N2 - Rectal temperature measurement (RTM) from crime scenes is an important parameter for temperature-based time of death estimation (TDE). Various influential variables exist in TDE methods like the uncertainty in thermal and environmental parameters. Although RTM depends in particular on the location of measurement position, this relationship has never been investigated separately. The presented study fills this gap using Finite Element (FE) simulations of body cooling. A manually meshed coarse human FE model and an FE geometry model developed from the CT scan of a male corpse are used for TDE sensitivity analysis. The coarse model is considered with and without a support structure of moist soil. As there is no clear definition of ideal rectal temperature measurement location for TDE, possible variations in RTM location (RTML) are considered based on anatomy and forensic practice. The maximum variation of TDE caused by RTML changes is investigated via FE simulation. Moreover, the influence of ambient temperature, of FE model change and of the models positioning on a wet soil underground are also discussed. As a general outcome, we notice that maximum TDE deviations of up to ca. 2-3 h due to RTML deviations have to be expected. The direction of maximum influence of RTML change on TDE generally was on the line caudal to cranial. Y1 - 2023 U6 - https://doi.org/10.1007/s00414-023-03040-y VL - 137 SP - 1815 EP - 1837 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Harth, Philipp A1 - Isoe, Yasuko A1 - Bahl, Armin A1 - Fotowat, Haleh A1 - Engert, Florian A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - A Visual Interface for Exploring Hypotheses about Neural Circuits JF - IEEE Transactions on Visualization and Computer Graphics N2 - One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa. Y1 - 2023 U6 - https://doi.org/10.1109/TVCG.2023.3243668 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - Faster exact solution of sparse MaxCut and QUBO problems JF - Mathematical Programming Computation N2 - The maximum-cut problem is one of the fundamental problems in combinatorial optimization. With the advent of quantum computers, both the maximum-cut and the equivalent quadratic unconstrained binary optimization problem have experienced much interest in recent years. This article aims to advance the state of the art in the exact solution of both problems—by using mathematical programming techniques. The main focus lies on sparse problem instances, although also dense ones can be solved. We enhance several algorithmic components such as reduction techniques and cutting-plane separation algorithms, and combine them in an exact branch-and-cut solver. Furthermore, we provide a parallel implementation. The new solver is shown to significantly outperform existing state-of-the-art software for sparse maximum-cut and quadratic unconstrained binary optimization instances. Furthermore, we improve the best known bounds for several instances from the 7th DIMACS Challenge and the QPLIB, and solve some of them (for the first time) to optimality. Y1 - 2023 U6 - https://doi.org/10.1007/s12532-023-00236-6 VL - 15 SP - 445 EP - 470 ER - TY - JOUR A1 - Boelts, Jan A1 - Harth, Philipp A1 - Gao, Richard A1 - Udvary, Daniel A1 - Yanez, Felipe A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel A1 - Macke, Jakob H T1 - Simulation-based inference for efficient identification of generative models in connectomics JF - bioRxiv N2 - Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neural networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a single rule to fit the empirical data, SBI considers many parametrizations of a wiring rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rules and relies on machine learning methods to estimate a probability distribution (the `posterior distribution over rule parameters conditioned on the data') that characterizes all data-compatible rules. We demonstrate how to apply SBI in connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89890 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Hiramatsu, Yuto A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model JF - Proceedings of the 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified. Y1 - 2022 SP - 1937 EP - 1948 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method JF - PROCEEDINGS OF ECOS 2022 - THE 35 TH INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effective to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small. Y1 - 2022 SP - 1891 EP - 1902 ER - TY - CHAP A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Cutting Plane Selection with Analytic Centers and Multiregression T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research. CPAIOR 2023. N2 - Cutting planes are a crucial component of state-of-the-art mixed-integer programming solvers, with the choice of which subset of cuts to add being vital for solver performance. We propose new distance-based measures to qualify the value of a cut by quantifying the extent to which it separates relevant parts of the relaxed feasible set. For this purpose, we use the analytic centers of the relaxation polytope or of its optimal face, as well as alternative optimal solutions of the linear programming relaxation. We assess the impact of the choice of distance measure on root node performance and throughout the whole branch-and-bound tree, comparing our measures against those prevalent in the literature. Finally, by a multi-output regression, we predict the relative performance of each measure, using static features readily available before the separation process. Our results indicate that analytic center-based methods help to significantly reduce the number of branch-and-bound nodes needed to explore the search space and that our multiregression approach can further improve on any individual method. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-33271-5_4 VL - 13884 SP - 52 EP - 68 PB - Springer ER - TY - JOUR A1 - Helfmann, Luzie A1 - Conrad, Natasa Djurdjevac A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Modelling opinion dynamics under the impact of influencer and media strategies JF - Scientific Reports N2 - Digital communication has made the public discourse considerably more complex, and new actors and strategies have emerged as a result of this seismic shift. Aside from the often-studied interactions among individuals during opinion formation, which have been facilitated on a large scale by social media platforms, the changing role of traditional media and the emerging role of "influencers" are not well understood, and the implications of their engagement strategies arising from the incentive structure of the attention economy even less so. Here we propose a novel opinion dynamics model that accounts for these different roles, namely that media and influencers change their own positions on slower time scales than individuals, while influencers dynamically gain and lose followers. Numerical simulations show the importance of their relative influence in creating qualitatively different opinion formation dynamics: with influencers, fragmented but short-lived clusters emerge, which are then counteracted by more stable media positions. Mean-field approximations by partial differential equations reproduce this dynamic. Based on the mean-field model, we study how strategies of influencers to gain more followers can influence the overall opinion distribution. We show that moving towards extreme positions can be a beneficial strategy for influencers to gain followers. Finally, we demonstrate that optimal control strategies allow other influencers or media to counteract such attempts and prevent further fragmentation of the opinion landscape. Our modelling framework contributes to better understanding the different roles and strategies in the increasingly complex information ecosystem and their impact on public opinion formation. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-46187-9 VL - 13 SP - 19375 ER - TY - GEN A1 - Masing, Berenike A1 - Lindner, Niels A1 - Ebert, Patricia T1 - Forward and Line-Based Cycle Bases for Periodic Timetabling N2 - The optimization of periodic timetables is an indispensable planning task in public transport. Although the periodic event scheduling problem (PESP) provides an elegant mathematical formulation of the periodic timetabling problem that led to many insights for primal heuristics, it is notoriously hard to solve to optimality. One reason is that for the standard mixed-integer linear programming formulations, linear programming relaxations are weak and the integer variables are of pure technical nature and in general do not correlate with the objective value. While the first problem has been addressed by developing several families of cutting planes, we focus on the second aspect. We discuss integral forward cycle bases as a concept to compute improved dual bounds for PESP instances. To this end, we develop the theory of forward cycle bases on general digraphs. Specifically for the application of timetabling, we devise a generic procedure to construct line-based event-activity networks, and give a simple recipe for an integral forward cycle basis on such networks. Finally, we analyze the 16 railway instances of the benchmark library PESPlib, match them to the line-based structure and use forward cycle bases to compute better dual bounds for 14 out of the 16 instances. T3 - ZIB-Report - 23-05 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89731 SN - 1438-0064 ER - TY - GEN A1 - Schiewe, Philine A1 - Goerigk, Marc A1 - Lindner, Niels T1 - Introducing TimPassLib - A library for integrated periodic timetabling and passenger routing N2 - Classic models to derive a timetable for public transport often face a chicken-and-egg situation: A good timetable should offer passengers routes with small travel times, but the route choice of passengers depends on the timetable. While models that fix passenger routes were frequently considered in the literature, integrated models that simultaneously optimize timetables and passenger routes have seen increasing attention lately. This creates a growing need for a set of instances that allows to test and compare new algorithmic developments for the integrated problem. Our paper addresses this requirement by presenting TimPassLib, a new benchmark library of instances for integrated periodic timetabling and passenger routing. T3 - ZIB-Report - 23-06 KW - periodic timetabling KW - optimization in public transport KW - data sets KW - benchmarking Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89741 SN - 1438-0064 ER - TY - JOUR A1 - Melnyk, Kateryna A1 - Weimann, Kuba A1 - Conrad, Tim T1 - Understanding microbiome dynamics via interpretable graph representation learning JF - Scientific Reports N2 - Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of healthy and ill individuals can be complicated due to the large number of complex interactions among microbes. We propose to model these interactions as a time-evolving graph whose nodes are microbes and edges are interactions among them. Motivated by the need to analyse such complex interactions, we develop a method that learns a low-dimensional representation of the time-evolving graph and maintains the dynamics occurring in the high-dimensional space. Through our experiments, we show that we can extract graph features such as clusters of nodes or edges that have the highest impact on the model to learn the low-dimensional representation. This information can be crucial to identify microbes and interactions among them that are strongly correlated with clinical diseases. We conduct our experiments on both synthetic and real-world microbiome datasets. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-29098-7 VL - 13 SP - 2058 ER - TY - GEN A1 - Hosoda, Junko A1 - Maher, Stephen J. A1 - Shinano, Yuji A1 - Villumsen, Jonas Christoffer T1 - A parallel branch-and-bound heuristic for the integrated long-haul and local vehicle routing problem on an adaptive transportation network N2 - Consolidation of commodities and coordination of vehicle routes are fundamental features of supply chain management problems. While locations for consolidation and coordination are typically known a priori, in adaptive transportation networks this is not the case. The identification of such consolidation locations forms part of the decision making process. Supply chain management problems integrating the designation of consolidation locations with the coordination of long haul and local vehicle routing is not only challenging to solve, but also very difficult to formulate mathematically. In this paper, the first mathematical model integrating location clustering with long haul and local vehicle routing is proposed. This mathematical formulation is used to develop algorithms to find high quality solutions. A novel parallel framework is developed that combines exact and heuristic methods to improve the search for high quality solutions and provide valid bounds. The results demonstrate that using exact methods to guide heuristic search is an effective approach to find high quality solutions for difficult supply chain management problems. T3 - ZIB-Report - 23-02 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89700 SN - 1438-0064 ER - TY - CHAP A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Zouhdi, S. ED - Pawlak, D. ED - Kudelski, A. T1 - Contour integral methods for resonance phenomena in nano-optics T2 - The 11th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2021) Y1 - 2021 SN - 2429-1390 SP - 523 ER - TY - CHAP A1 - Movsesyan, Artur A1 - Santiago, Eva Yazmin A1 - Burger, Sven A1 - Correa-Duarte, Miguel A1 - Besteiro, Lucas V. A1 - Wang, Zhiming A1 - Govorov, Alexander O. ED - Zouhdi, S. T1 - The anisotropy of hot carriers’ spatial distribution contrasts the isotropy of photothermal effects in complex and small plasmonic nanocrystals with complex shapes T2 - The 12th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2022) Y1 - 2022 SN - 2429-1390 SP - 285 ER - TY - CHAP A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Zouhdi, S. T1 - Numerical methods for the investigation of resonances in nanophotonics T2 - The 12th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2022) Y1 - 2022 SN - 2429-1390 SP - 247 ER - TY - JOUR A1 - Chen, Ying A1 - Koch, Thorsten A1 - Zakiyeva, Nazgul A1 - Liu, Kailiang A1 - Xu, Zhitong A1 - Chen, Chun-houh A1 - Nakano, Junji A1 - Honda, Keisuke T1 - Article’s scientific prestige: Measuring the impact of individual articles in the web of science JF - Journal of Informetrics N2 - We performed a citation analysis on the Web of Science publications consisting of more than 63 million articles and 1.45 billion citations on 254 subjects from 1981 to 2020. We proposed the Article’s Scientific Prestige (ASP) metric and compared this metric to number of citations (#Cit) and journal grade in measuring the scientific impact of individual articles in the large-scale hierarchical and multi-disciplined citation network. In contrast to #Cit, ASP, that is computed based on the eigenvector centrality, considers both direct and indirect citations, and provides steady-state evaluation cross different disciplines. We found that ASP and #Cit are not aligned for most articles, with a growing mismatch amongst the less cited articles. While both metrics are reliable for evaluating the prestige of articles such as Nobel Prize winning articles, ASP tends to provide more persuasive rankings than #Cit when the articles are not highly cited. The journal grade, that is eventually determined by a few highly cited articles, is unable to properly reflect the scientific impact of individual articles. The number of references and coauthors are less relevant to scientific impact, but subjects do make a difference. Y1 - 2023 U6 - https://doi.org/10.1016/j.joi.2023.101379 VL - 17 IS - 1 SP - 101379 ER - TY - CHAP A1 - Masing, Berenike ED - Trautmann, Norbert ED - Drägi, Mario T1 - Optimal Line Planning in the Parametric City T2 - Operations Research Proceedings 2021. OR 2021. N2 - We formulate the line planning problem in public transport as a mixed integer linear program (MILP), which selects both passenger and vehicle routes, such that travel demands are met with respect to minimized travel times for both operators and users. We apply MILP to the Parametric City, a generic city model developed by Fielbaum et al. [2]. While the infrastructure graph and demand are entirely rotation symmetric, asymmetric optimal line plans can occur. Using group theory, we analyze the properties of symmetric solutions and introduce a symmetry gap to measure their deviation of the optimum. We also develop a 1+1+2√g-approximation algorithm, depending only on the cost related parameter g. Supported by computational experiments, we conclude that in practice symmetric line plans provide good solutions for the line planning problem in the Parametric City. Y1 - 2022 SN - 978-3-031-08623-6 U6 - https://doi.org/10.1007/978-3-031-08623-6_7 SP - 39 EP - 44 PB - Springer, Cham ER - TY - THES A1 - Rabben, Robert Julian T1 - Ein holistischer Ansatz zur Analyse molekularer Konformationen auf der Basis von ISOKANN Y1 - 2022 ER - TY - CHAP A1 - Masing, Berenike A1 - Lindner, Niels A1 - Borndörfer, Ralf ED - Trautmann, Norbert ED - Drägi, Mario T1 - Optimal Line Plans in the Parametric City and the Impact of In-Motion Costs T2 - Operations Research Proceedings 2021 N2 - Line planning in public transport involves determining vehicle routes and assigning frequencies of service such that travel demands are satisfied. We evaluate how line plans, which are optimal with respect to in-motion costs (IMC), the objective function depending purely on arc-lengths for both user and operator costs, performs with respect to the value of resources consumed (VRC). The latter is an elaborate, socio-economic cost function which includes discomfort caused by delay, boarding and alighting times, and transfers. Even though discomfort is a large contributing factor to VRC and is entirely disregarded in IMC,  we observe that the two cost functions are qualitatively comparable. Y1 - 2022 SN - 978-3-031-08623-6 U6 - https://doi.org/10.1007/978-3-031-08623-6_44 SP - 295 EP - 301 PB - Springer, Cham ER - TY - CHAP A1 - Chmiela, Antonia A1 - Gleixner, Ambros A1 - Lichocki, Pawel A1 - Pokutta, Sebastian T1 - Online Learning for Scheduling MIP Heuristics T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research N2 - Mixed Integer Programming (MIP) is NP-hard, and yet modern solvers often solve large real-world problems within minutes. This success can partially be attributed to heuristics. Since their behavior is highly instance-dependent, relying on hard-coded rules derived from empirical testing on a large heterogeneous corpora of benchmark instances might lead to sub-optimal performance. In this work, we propose an online learning approach that adapts the application of heuristics towards the single instance at hand. We replace the commonly used static heuristic handling with an adaptive framework exploiting past observations about the heuristic’s behavior to make future decisions. In particular, we model the problem of controlling Large Neighborhood Search and Diving – two broad and complex classes of heuristics – as a multi-armed bandit problem. Going beyond existing work in the literature, we control two different classes of heuristics simultaneously by a single learning agent. We verify our approach numerically and show consistent node reductions over the MIPLIB 2017 Benchmark set. For harder instances that take at least 1000 seconds to solve, we observe a speedup of 4%. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-33271-5_8 VL - 13884 SP - 114 EP - 123 PB - Springer, Cham ER - TY - CHAP A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - Monoidal strengthening and unique lifting in MIQCPs T2 - Integer Programming and Combinatorial Optimization. IPCO 2023. N2 - Using the recently proposed maximal quadratic-free sets and the well-known monoidal strengthening procedure, we show how to improve inter- section cuts for quadratically-constrained optimization problems by exploiting integrality requirements. We provide an explicit construction that allows an efficient implementation of the strengthened cuts along with computational results showing their improvements over the standard intersection cuts. We also show that, in our setting, there is unique lifting which implies that our strengthening procedure is generating the best possible cut coefficients for the integer variables. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-031-32726-1_7 VL - 13904 SP - 87 EP - 99 ER - TY - JOUR A1 - Ernst, Ariane A1 - Unger, Nathalie A1 - Schütte, Christof A1 - Walter, Alexander A1 - Winkelmann, Stefanie T1 - Rate-limiting recovery processes in neurotransmission under sustained stimulation JF - Mathematical Biosciences N2 - At chemical synapses, an arriving electric signal induces the fusion of vesicles with the presynaptic membrane, thereby releasing neurotransmitters into the synaptic cleft. After a fusion event, both the release site and the vesicle undergo a recovery process before becoming available for reuse again. Of central interest is the question which of the two restoration steps acts as the limiting factor during neurotrans-mission under high-frequency sustained stimulation. In order to investigate this question, we introduce a novel non-linear reaction network which involves explicit recovery steps for both the vesicles and the release sites, and includes the induced time-dependent output current. The associated reaction dynamics are formulated by means of ordinary differential equations (ODEs), as well as via the associated stochastic jump process. While the stochastic jump model describes a single release site, the average over many release sites is close to the ODE solution and shares its periodic structure. The reason for this can be traced back to the insight that recovery dynamics of vesicles and release sites are statistically almost independent. A sensitivity analysis on the recovery rates based on the ODE formulation reveals that neither the vesicle nor the release site recovery step can be identified as the essential rate-limiting step but that the rate- limiting feature changes over the course of stimulation. Under sustained stimulation the dynamics given by the ODEs exhibit transient dynamics leading from an initial depression of the postsynaptic response to an asymptotic periodic orbit, while the individual trajectories of the stochastic jump model lack the oscillatory behavior an asymptotic periodicity of the ODE-solution. Y1 - 2023 U6 - https://doi.org/10.1016/j.mbs.2023.109023 VL - 362 ER - TY - JOUR A1 - Fernandes, Rita A1 - Chaowdhary, Suvrat A1 - Saleh, Noureldin A1 - Mikula, Natalia A1 - Kanevche, Katerina A1 - Berlepsch, Hans A1 - Hosogi, Naoki A1 - Heberle, Joachim A1 - Weber, Marcus A1 - Böttcher, Christoph A1 - Koksch, Beate T1 - Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures JF - Angewandte Chemie N2 - A conjugated Cy5 dye-peptide system reveals the formation of two novel and structurally distinct supramolecular assemblies with photo-physical characteristics of H-type dimers or tetramers, respectively. The molecular ultrastructures are triggered by the complementary interplay of mutual chromophore coupling and pH induced changes in the peptide charge pattern. Y1 - 2022 VL - 61 IS - 48 SP - e202208647 ER - TY - GEN A1 - Prause, Felix A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Tesch, Alexander T1 - Approximating the RSRP with Predictive Maintenance N2 - We study the solution of the rolling stock rotation problem with predictive maintenance (RSRP-PM) by an iterative refinement approach that is based on a state-expanded event-graph. In this graph, the states are parameters of a failure distribution, and paths correspond to vehicle rotations with associated health state approximations. An optimal set of paths including maintenance can be computed by solving an integer linear program. Afterwards, the graph is refined and the procedure repeated. An associated linear program gives rise to a lower bound that can be used to determine the solution quality. Computational results for two instances derived from real world timetables of a German railway company are presented. The results show the effectiveness of the approach and the quality of the solutions. T3 - ZIB-Report - 23-04 KW - Rolling Stock Rotation Planning KW - Predictive Maintenance KW - Integer Linear Programming KW - Heuristic KW - Lower Bound Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89531 SN - 1438-0064 ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Völker, Helena A1 - Gleixner, Ambros T1 - Strengthening SONC Relaxations with Constraints Derived from Variable Bounds N2 - Nonnegativity certificates can be used to obtain tight dual bounds for polynomial optimization problems. Hierarchies of certificate-based relaxations ensure convergence to the global optimum, but higher levels of such hierarchies can become very computationally expensive, and the well-known sums of squares hierarchies scale poorly with the degree of the polynomials. This has motivated research into alternative certificates and approaches to global optimization. We consider sums of nonnegative circuit polynomials (SONC) certificates, which are well-suited for sparse problems since the computational cost depends on the number of terms in the polynomials and does not depend on the degrees of the polynomials. We propose a method that guarantees that given finite variable domains, a SONC relaxation will yield a finite dual bound. This method opens up a new approach to utilizing variable bounds in SONC-based methods, which is particularly crucial for integrating SONC relaxations into branch-and-bound algorithms. We report on computational experiments with incorporating SONC relaxations into the spatial branch-and-bound algorithm of the mixed-integer nonlinear programming framework SCIP. Applying our strengthening method increases the number of instances where the SONC relaxation of the root node yielded a finite dual bound from 9 to 330 out of 349 instances in the test set. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89510 SN - 1438-0064 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Knebel, Sebastian A1 - Shakibaei, Zarin A1 - Pokutta, Sebastian T1 - Low-Rank Tensor Decompositions of Quantum Circuits JF - Journal of Computational Physics N2 - Quantum computing is arguably one of the most revolutionary and disruptive technologies of this century. Due to the ever-increasing number of potential applications as well as the continuing rise in complexity, the development, simulation, optimization, and physical realization of quantum circuits is of utmost importance for designing novel algorithms. We show how matrix product states (MPSs) and matrix product operators (MPOs) can be used to express certain quantum states, quantum gates, and entire quantum circuits as low-rank tensors. This enables the analysis and simulation of complex quantum circuits on classical computers and to gain insight into the underlying structure of the system. We present different examples to demonstrate the advantages of MPO formulations and show that they are more efficient than conventional techniques if the bond dimensions of the wave function representation can be kept small throughout the simulation. Y1 - 2022 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klein, Rupert A1 - Matera, Sebastian A1 - Schmidt, Burkhard T1 - Solving the time-independent Schrödinger equation for chains of coupled excitons and phonons using tensor trains JF - The Journal of Chemical Physics N2 - We demonstrate how to apply the tensor-train format to solve the time-independent Schrödinger equation for quasi-one-dimensional excitonic chain systems with and without periodic boundary conditions. The coupled excitons and phonons are modeled by Fröhlich–Holstein type Hamiltonians with on-site and nearest-neighbor interactions only. We reduce the memory consumption as well as the computational costs significantly by employing efficient decompositions to construct low-rank tensor-train representations, thus mitigating the curse of dimensionality. In order to compute also higher quantum states, we introduce an approach that directly incorporates the Wielandt deflation technique into the alternating linear scheme for the solution of eigenproblems. Besides systems with coupled excitons and phonons, we also investigate uncoupled problems for which (semi-)analytical results exist. There, we find that in the case of homogeneous systems, the tensor-train ranks of state vectors only marginally depend on the chain length, which results in a linear growth of the storage consumption. However, the central processing unit time increases slightly faster with the chain length than the storage consumption because the alternating linear scheme adopted in our work requires more iterations to achieve convergence for longer chains and a given rank. Finally, we demonstrate that the tensor-train approach to the quantum treatment of coupled excitons and phonons makes it possible to directly tackle the phenomenon of mutual self-trapping. We are able to confirm the main results of the Davydov theory, i.e., the dependence of the wave packet width and the corresponding stabilization energy on the exciton–phonon coupling strength, although only for a certain range of that parameter. In future work, our approach will allow calculations also beyond the validity regime of that theory and/or beyond the restrictions of the Fröhlich–Holstein type Hamiltonians. Y1 - 2022 U6 - https://doi.org/10.1063/5.0074948 VL - 156 IS - 2 SP - 024109 ER - TY - JOUR A1 - Nohadani, Omid A1 - Sharma, Kartikey T1 - Optimization under Connected Uncertainty JF - INFORMS Journal on Optimization N2 - Robust optimization methods have shown practical advantages in a wide range of decision-making applications under uncertainty. Recently, their efficacy has been extended to multiperiod settings. Current approaches model uncertainty either independent of the past or in an implicit fashion by budgeting the aggregate uncertainty. In many applications, however, past realizations directly influence future uncertainties. For this class of problems, we develop a modeling framework that explicitly incorporates this dependence via connected uncertainty sets, whose parameters at each period depend on previous uncertainty realizations. To find optimal here-and-now solutions, we reformulate robust and distributionally robust constraints for popular set structures and demonstrate this modeling framework numerically on broadly applicable knapsack and portfolio-optimization problems. Y1 - 2022 U6 - https://doi.org/10.1287/ijoo.2021.0067 VL - 4 IS - 3 SP - 326 EP - 346 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Sharma, Upanshu A1 - Tse, Oliver T1 - Fourier-Cattaneo equation: stochastic origin, variational formulation, and asymptotic limits N2 - We introduce a variational structure for the Fourier-Cattaneo (FC) system which is a second-order hyperbolic system. This variational structure is inspired by the large-deviation rate functional for the Kac process which is closely linked to the FC system. Using this variational formulation we introduce appropriate solution concepts for the FC equation and prove an a priori estimate which connects this variational structure to an appropriate Lyapunov function and Fisher information, the so-called FIR inequality. Finally, we use this formulation and estimate to study the diffusive and hyperbolic limits for the FC system. Y1 - 2022 ER - TY - GEN A1 - Weiser, Martin A1 - Chegini, Fatemeh T1 - Higher-order time integration using spectral deferred correction method (SDC) in a cell by cell discretization of cardiac excitation N2 - This C++ code implements a cell-by-cell model of cardiac excitation using a piecewise-continuous finite element discretization and spectral deferred correction time stepping. The code is based on the Kaskade 7 finite element toolbox and forms a prototype for the µCarp code to be implemented in the Microcard project. Y1 - 2022 U6 - https://doi.org/10.35097/716 ER - TY - JOUR A1 - Ribera Borrell, Enric A1 - Quer, Jannes A1 - Richter, Lorenz A1 - Schütte, Christof T1 - Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics JF - SIAM Journal on Scientific Computing (SISC) N2 - Sampling rare events in metastable dynamical systems is often a computationally expensive task and one needs to resort to enhanced sampling methods such as importance sampling. Since we can formulate the problem of finding optimal importance sampling controls as a stochastic optimization problem, this then brings additional numerical challenges and the convergence of corresponding algorithms might as well suffer from metastabilty. In this article we address this issue by combining systematic control approaches with the heuristic adaptive metadynamics method. Crucially, we approximate the importance sampling control by a neural network, which makes the algorithm in principle feasible for high dimensional applications. We can numerically demonstrate in relevant metastable problems that our algorithm is more effective than previous attempts and that only the combination of the two approaches leads to a satisfying convergence and therefore to an efficient sampling in certain metastable settings. KW - importance sampling KW - stochastic optimal control KW - rare event simulation KW - metastability KW - neural networks KW - metadynamics Y1 - 2023 U6 - https://doi.org/10.1137/22M1503464 VL - 89 IS - 1 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Vigerske, Stefan A1 - Wegscheider, Fabian T1 - Global Optimization of Mixed-Integer Nonlinear Programs with SCIP 8.0 JF - Journal of Global Optimization N2 - For over ten years, the constraint integer programming framework SCIP has been extended by capabilities for the solution of convex and nonconvex mixed-integer nonlinear programs (MINLPs). With the recently published version 8.0, these capabilities have been largely reworked and extended. This paper discusses the motivations for recent changes and provides an overview of features that are particular to MINLP solving in SCIP. Further, difficulties in benchmarking global MINLP solvers are discussed and a comparison with several state-of-the-art global MINLP solvers is provided. Y1 - 2023 U6 - https://doi.org/10.1007/s10898-023-01345-1 ER - TY - GEN ED - Fujisawa, Katsuki ED - Kaji, Shizuo ED - Ishihara, Toru ED - Kondo, Masaaki ED - Shinano, Yuji ED - Tanigawa, Takuji ED - Nakayama, Naoko T1 - データ格付けサービス実現のための数理基盤の構築 Y1 - 2022 UR - https://joint.imi.kyushu-u.ac.jp/wp-content/uploads/2022/12/29d12d46a22d702596713780acde0689-3.pdf SN - 2188-1200 VL - 91 PB - Institute of Mathematics for Industry, Kyushu University CY - Graduate School of Mathematics, Kyushu University Motooka 744, Nishi-ku, Fukuoka, 819-0395, JAPAN ER - TY - GEN ED - Fujisawa, Katsuki ED - Kaji, Shizuo ED - Ishihara, Toru ED - Kondo, Masaaki ED - Shinano, Yuji ED - Tanigawa, Takuji ED - Nakayama, Naoko T1 - Construction of Mathematical Basis for Realizing Data Rating Service Y1 - 2022 UR - https://joint.imi.kyushu-u.ac.jp/wp-content/uploads/2022/12/29d12d46a22d702596713780acde0689-3.pdf SN - 2188-1200 VL - 90 PB - Institute of Mathematics for Industry, Kyushu University CY - Graduate School of Mathematics, Kyushu University Motooka 744, Nishi-ku, Fukuoka, 819-0395, JAPAN ER - TY - JOUR A1 - Ben Soltane, Isam A1 - Colom, Rémi A1 - Stout, Brian A1 - Bonod, Nicolas T1 - Derivation of the Transient and Steady Optical States from the Poles of the S-Matrix JF - Laser Photon. Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202200141 VL - 17 SP - 2200141 ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Vigerske, Stefan A1 - Wegscheider, Fabian T1 - Global Optimization of Mixed-Integer Nonlinear Programs with SCIP 8.0 N2 - For over ten years, the constraint integer programming framework SCIP has been extended by capabilities for the solution of convex and nonconvex mixed-integer nonlinear programs (MINLPs). With the recently published version~8.0, these capabilities have been largely reworked and extended. This paper discusses the motivations for recent changes and provides an overview of features that are particular to MINLP solving in SCIP. Further, difficulties in benchmarking global MINLP solvers are discussed and a comparison with several state-of-the-art global MINLP solvers is provided. T3 - ZIB-Report - 23-01 Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89348 SN - 1438-0064 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Resonance expansion of quadratic quantities with regularized quasinormal modes JF - Phys. Status Solidi A Y1 - 2023 U6 - https://doi.org/10.1002/pssa.202200892 VL - 220 SP - 2200892 ER - TY - JOUR A1 - Wolf, Sarah A1 - Fürst, Steffen A1 - Geiges, Andreas A1 - Laublichler, Manfred A1 - Mielke, Jahel A1 - Steudle, Gesine A1 - Winter, Konstantin A1 - Jaeger, Carlo T1 - The Decision Theatre Triangle for societal challenges – an example case and research needs JF - Journal of Cleaner Production N2 - Tackling societal challenges relating to sustainability requires both an understanding of the underlying complex socio-ecological systems and participation of scientists as well as relevant stakeholders, such as practice experts, decision makers, and citizens. This paper introduces the Decision Theatre Triangle, a method which combines empirical information, mathematical modelling and simulation, and a format for dialogue between scientists and stakeholders. While it builds on previous Decision Theatre work, the new structuring into these three elements emphasizes what is needed for setting up a Decision Theatre for a given challenge. Based on experience with a specific example – sustainable mobility in Germany – it is argued that agent-based models are particularly suitable for Decision Theatres and that the method is useful not only for decision support but also for science communication and co-creation of a deeper knowledge of the system under discussion. As a step towards facilitating a broader use of the Decision Theatre Triangle method, the paper then sketches research needs for each of its three elements, with a focus on mathematical modelling and simulation. Y1 - 2023 U6 - https://doi.org/10.1016/j.jclepro.2023.136299 VL - 394 SP - 136299 ER - TY - THES A1 - Paskin, Martha T1 - Estimating 3D Shape of the Head Skeleton of Basking Sharks Using Annotated Landmarks on a 2D Image N2 - Basking sharks are thought to be one of the most efficient filter-feeding fish in terms of the throughput of water filtered through their gills. Details about the underlying morphology of their branchial region have not been studied due to various challenges in acquiring real-world data. The present thesis aims to facilitate this, by developing a mathematical shape model which constructs the 3D structure of the head skeleton of a basking shark using annotated landmarks on a single 2D image. This is an ill-posed problem as estimating the depth of a 3D object from a single 2D view is, in general, not possible. To reduce this ambiguity, we create a set of pre-defined training shapes in 3D from CT scans of basking sharks. First, the damaged structures of the sharks in the scans are corrected via solving a set of optimization problems, before using them as accurate 3D representations of the object. Then, two approaches are employed for the 2D-to-3D shape fitting problem–an Active Shape Model approach and a Kendall’s Shape Space approach. The former represents a shape as a point on a high-dimensional Euclidean space, whereas the latter represents a shape as an equivalence class of points in this Euclidean space. Kendall’s shape space approach is a novel technique that has not yet been applied in this context, and a comprehensive comparison of the two approaches suggests this approach to be superior for the problem at hand. This can be credited to an improved interpolation of the training shapes. N2 - Riesenhaie zählen zu den effizientesten Filtrierern hinsichtlich des durch die Kiemen gefilterten Wasservolumens. Die Kiemenregion dieser Tiere besitzt eine markante Morphologie, die jedoch bisher nicht umfassend erforscht werden konnte, da es schwierig ist, reale Daten dieser Tiere zu erheben. Die vorliegende Arbeit zielt darauf ab, dies durch die Entwicklung eines mathematischen Formmodels zu ermöglichen, das es erlaubt, die 3D-Struktur des Schädelskeletts anhand von Landmarken, die auf einem 2D-Bild platziert werden, zu rekonstruieren. Die hierzu benötigte Tiefenbestimmung der Landmarken aus einer 2D-Projektion ist ein unterbestimmtes Problem. Wir lösen dies durch die Hinzunahme von Trainingsformen, welche wir aus CT-Scans von Riesenhaien gewinnen. Der Zustand der tomografierten Exemplare erfordert jedoch einen vorhergehenden Korrekturschritt, den wir mit Hilfe eines Optimierungsansatzes lösen, bevor die extrahierten Strukturen als 3D-Trainingsformen dienen können. Um die 3D-Struktur des Schädelskelettes aus 2D-Landmarken zu rekonstruieren, vergleichen wir zwei Ansätze – den sogenannten Active-Shape-Model (ASM)-Ansatz und einen Ansatz basierend auf Kendalls Formenraum. Während eine Form des ASM-Ansatzes durch einen Punkt in einem hochdimensionalen Euklidischen Raum repräsentiert ist, repräsentiert eine Form im Kendall-Formenraum eine Äquivalenzklasse von Punkten des Euklidischen Raumes. Die Anwendung des Kendall-Formenraumes für das beschriebene Problem ist neu und ein umfassender Vergleich der Methoden hat ergeben, dass dieser Ansatz für die spezielle Anwendung zu besseren Ergebnissen führt. Wir führen dies auf die überlegene Interpolation der Trainingsformen in diesem Raum zurück. Y1 - 2022 UR - https://arxiv.org/abs/2207.12687 ER - TY - THES A1 - Hoppmann-Baum, Kai T1 - Mathematical programming for stable control and safe operation of gas transport networks N2 - The fight against climate change makes extreme but inevitable changes in the energy sector necessary. These in turn lead to novel and complex challenges for the transmission system operators (TSOs) of gas transport networks. In this thesis, we consider four different planning problems emerging from real-world operations and present mathematical programming models and solution approaches for all of them. Due to regulatory requirements and side effects of renewable energy production, controlling today's gas networks with their involved topologies is becoming increasingly difficult. Based on the network station modeling concept for approximating the technical capabilities of complex subnetworks, e.g., compressor stations, we introduce a tri-level MIP model to determine important global control decisions. Its goal is to avoid changes in the network elements' settings while deviations from future inflow pressures as well as supplies and demands are minimized. A sequential linear programming inspired post-processing routine is run to derive physically accurate solutions w.r.t. the transient gas flow in pipelines. Computational experiments based on real-world data show that meaningful solutions are quickly and reliably determined. Therefore, the algorithmic approach is used within KOMPASS, a decision support system for the transient network control that we developed together with the Open Grid Europe GmbH (OGE), one of Europe's largest natural gas TSOs. Anticipating future use cases, we adapt the aforementioned algorithmic approach for hydrogen transport. We investigate whether the natural gas infrastructure can be repurposed and how the network control changes when energy-equivalent amounts of hydrogen are transported. Besides proving the need for purpose-built compressors, we observe that, due to the reduced linepack, the network control becomes more dynamic, compression energy increases by 440% on average, and stricter regulatory rules regarding the balancing of supply and demand become necessary. Extreme load flows expose the technical limits of gas networks and are therefore of great importance to the TSOs. In this context, we introduce the Maximum Transportation Problem and the Maximum Potential Transport Moment Problem to determine severe transport scenarios. Both can be modeled as linear bilevel programs where the leader selects supplies and demands, maximizing the follower's transport effort. To solve them, we identify solution-equivalent instances with acyclic networks, provide variable bounds regarding their KKT reformulations, apply the big-M technique, and solve the resulting MIPs. A case study shows that the obtained scenarios exceed the maximum severity values of a provided test set by at least 23%. OGE's transmission system is 11,540km long. Monitoring it is crucial for safe operations. To this end, we discuss the idea of using uncrewed aerial vehicles and introduce the Length-Constrained Cycle Partition Problem to optimize their routing. Its goal is to find a smallest cycle partition satisfying vertex-induced length requirements. Besides a greedy-style heuristic, we propose two MIP models. Combining them with symmetry-breaking constraints as well as valid inequalities and lower bounds from conflict hypergraphs yields a highly performant solution algorithm for this class of problems. Y1 - 2022 UR - https://doi.org/10.14279/depositonce-15837 U6 - https://doi.org/10.14279/depositonce-15837 PB - TU Berlin ER - TY - JOUR A1 - Huynh, Ngoc A1 - Chegini, Fatemeh A1 - Pavarino, Luca A1 - Weiser, Martin A1 - Scacchi, Simone T1 - Convergence analysis of BDDC preconditioners for hybrid DG discretizations of the cardiac cell-by-cell model JF - SIAM Journal on Scientific Computing N2 - A Balancing Domain Decomposition by Constraints (BDDC) preconditioner is constructed and analyzed for the solution of hybrid Discontinuous Galerkin discretizations of reaction-diffusion systems of ordinary and partial differential equations arising in cardiac cell-by-cell models. The latter are different from the classical Bidomain and Monodomain cardiac models based on homogenized descriptions of the cardiac tissue at the macroscopic level, and therefore they allow the representation of individual cardiac cells, cell aggregates, damaged tissues and nonuniform distributions of ion channels on the cell membrane. The resulting discrete cell-by-cell models have discontinuous global solutions across the cell boundaries, hence the proposed BDDC preconditioner is based on appropriate dual and primal spaces with additional constraints which transfer information between cells (subdomains) without influencing the overall discontinuity of the global solution. A scalable convergence rate bound is proved for the resulting BDDC cell-by-cell preconditioned operator, while numerical tests validate this bound and investigate its dependence on the discretization parameters. Y1 - 2023 VL - 45 IS - 6 SP - A2836 EP - A2857 ER - TY - THES A1 - Streubel, Tom T1 - Simulation of Piecewise Smooth Differential Algebraic Equations with Application to Gas Networks Y1 - 2022 UR - https://edoc.hu-berlin.de/handle/18452/25434 U6 - https://doi.org/http://dx.doi.org/10.18452/24688 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles JF - The Journal of Physical Chemistry B N2 - This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the phase flow and of the limit cycle, which controls the dynamics for giant vesicles and dominates the pronouncedly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, which are amenable to analytic treatments that are complemented by numerical solutions, and obtain the period and amplitude of the oscillations as well as the parameter domain, where oscillatory behavior persists. We show that the accuracy of these predictions is highly sensitive to the employed reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The faithful modeling of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpcb.2c09092 VL - 127 IS - 13 SP - 2955 EP - 2967 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Ribera Borrell, Enric A1 - Weber, Marcus T1 - Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN JF - Journal of Mathematical Physics N2 - The dominant eigenfunctions of the Koopman operator characterize the metastabilities and slow-timescale dynamics of stochastic diffusion processes. In the context of molecular dynamics and Markov state modeling, they allow for a description of the location and frequencies of rare transitions, which are hard to obtain by direct simulation alone. In this article, we reformulate the eigenproblem in terms of the ISOKANN framework, an iterative algorithm that learns the eigenfunctions by alternating between short burst simulations and a mixture of machine learning and classical numerics, which naturally leads to a proof of convergence. We furthermore show how the intermediate iterates can be used to reduce the sampling variance by importance sampling and optimal control (enhanced sampling), as well as to select locations for further training (adaptive sampling). We demonstrate the usage of our proposed method in experiments, increasing the approximation accuracy by several orders of magnitude. Y1 - 2024 U6 - https://doi.org/10.1063/5.0140764 VL - 65 SP - 013502 ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Steinke, Thomas A1 - Weiser, Martin T1 - Efficient adaptivity for simulating cardiac electrophysiology with spectral deferred correction methods N2 - The locality of solution features in cardiac electrophysiology simulations calls for adaptive methods. Due to the overhead incurred by established mesh refinement and coarsening, however, such approaches failed in accelerating the computations. Here we investigate a different route to spatial adaptivity that is based on nested subset selection for algebraic degrees of freedom in spectral deferred correction methods. This combination of algebraic adaptivity and iterative solvers for higher order collocation time stepping realizes a multirate integration with minimal overhead. This leads to moderate but significant speedups in both monodomain and cell-by-cell models of cardiac excitation, as demonstrated at four numerical examples. Y1 - 2022 ER - TY - GEN A1 - Ternes, Thomas A1 - Bauer, Karl-Heinz A1 - Brauer, Frank A1 - Drewes, Jürgen A1 - Jewell, Kevin A1 - Joss, Adriano A1 - Oehlmann, Jörg A1 - Radtke, Michael A1 - Schulte-Oehlmann, Ulrike A1 - Schwartz, Thomas A1 - Seel, Peter A1 - Völker, Jeanette A1 - Weber, Lilo A1 - Weber, Marcus T1 - Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen T2 - DWA-Themen N2 - Der DWA-Themenband beschreibt ein Konzept zur weitergehenden Abwasserbehandlung für die Bewertung von Aufbereitungsverfahren, sowohl in einer Pilotphase zur Auswahl von Verfahrensoptionen als auch für die Bewertung großtechnischer Anlagen. Emissionsseitig basiert das Konzept auf bereits regulatorisch definierten Parametern wie anorganischen Stickstoff-Verbindungen oder Phosphat sowie auf neuen noch nicht in der Abwasserverordnung regulierten Parametern. Die immissionsseitige Betrachtung erfolgt auf Basis der rechtlich durch die Europäische Wasserrahmenrichtlinie und andere Anforderungen bindenden Instrumente. Hierfür werden spezifische Vorgehensweisen vorgeschlagen. Anhand zweier ausgewählter Praxisbeispiele wird deutlich, dass es zur Bewertung der Verfahrensoptionen an einem Standort dienlich ist, ausgewählte Reduktionen bzw. Entfernungen von Stoffen, Organismen und Effekten zu bestimmen. Y1 - 2023 VL - T1/2023 PB - DWA ER - TY - CHAP A1 - Rehfeldt, Daniel T1 - Faster Algorithms for Steiner Tree and related Problems: From Theory to Practice T2 - Operations Research Proceedings 2022 Y1 - 2022 ER - TY - JOUR A1 - Rehfeldt, Daniel T1 - Faster Algorithms for Steiner Tree and related Problems: From Theory to Practice JF - OR News: Das Magazin der GOR Y1 - 2022 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Source code and simulation results for computing resonance expansions of quadratic quantities with regularized quasinormal modes T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.7376556 ER - TY - JOUR A1 - Krüger, Tillmann A1 - Leeners, Brigitte A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Engler, Harald A1 - Röblitz, Susanna A1 - Frieling, Helge A1 - Sinke, Christopher A1 - Jahn, Kirsten T1 - The androgen system across the menstrual cycle: Hormonal, (epi-)genetic and psychometric alterations JF - Physiology and Behavior Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.physbeh.2022.114034 ER - TY - JOUR A1 - Fischer-Holzhausen, Sophie A1 - Röblitz, Susanna T1 - Mathematical modelling of follicular growth and ovarian stimulation JF - Current Opinion in Endocrine and Metabolic Research Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.coemr.2022.100385 ER - TY - JOUR A1 - Fischer-Holzhausen, Sophie A1 - Röblitz, Susanna T1 - Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities JF - Journal of Theoretical Biology N2 - We present a modelling and simulation framework for the dynamics of ovarian follicles and key hormones along the hypothalamic-pituitary-gonadal axis throughout consecutive human menstrual cycles. All simulation results (hormone concentrations and ovarian follicle sizes) are in biological units and can easily be compared to clinical data. The model takes into account variability in follicles' response to stimulating hormones, which introduces variability between cycles. The growth of ovarian follicles in waves is an emergent property in our model simulations and further supports the hypothesis that follicular waves are also present in humans. We use Approximate Bayesian Computation and cluster analysis to construct a population of virtual subjects and to study parameter distributions and sensitivities. The model can be used to compare and optimize treatment protocols for ovarian hyperstimulation, thus potentially forming the integral part of a clinical decision support system in reproductive endocrinology. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.jtbi.2022.111150 ER - TY - THES A1 - Chegini, Fatemeh T1 - Multilevel optimization algorithm for Inverse Problem in Electrocardiography N2 - The electric conductivity of cardiac tissue determines excitation propagation and is vital for quantifying ischemia and scar tissue and building personalized models. As scar tissue is generally characterized by different conduction of electrical excitation, we aim to estimate conductivity-related parameters in mathematical excitation models from endocardial mapping data, particularly the anisotropic conductivity tensor in the monodomain equation, which describes the cardiac excitation. Yet, estimating the distributed and anisotropic conductivity tensors reliably and efficiently from endocardial mapping data or electrocardiograms is a challenging inverse problem due to the computational complexity of the monodomain equation; Many expensive high-resolution computations for the monodomain equation on very fine space and time discretizations are involved. Thus, we aim at building an efficient multilevel method for accelerating the estimation procedure combining electrophysiology models of different complex- ity, which uses a computationally cheap eikonal model in addition to the more accurate monodomain model. Distributed parameter estimation, well-known as an ill-posed inverse problem, can be performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface subject to the monodomain model and some regularization, leading to a partial differential equation constrained optimization problem. We formulate this optimization problem, including scar tissue modeling and different regularizations, and design an efficient iterative solver. To this aim, we consider monodomain grid hi- erarchies, monodomain-eikonal model hierarchies, and the combination of both hierarchies in a recursive multilevel trust-region (RMTR) method. On the one hand, both the trust region method’s estimation quality and efficiency, independent of the data, are investigated from several numerical exam- ples. Endocardial mapping data of realistic density appears to be sufficient to provide quantitatively reasonable estimates of the location, size, and shape of scars close to the endocardial surface. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more involved monodomain model for this purpose. Moreover, Eikonal models can accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data. In many situations, eikonal models approximate monodomain models well but are orders of magnitude faster to solve. Thus, eikonal models can utilize them to provide an RMTR acceleration with negligible overhead per iteration, resulting in a practical approach to estimating myocardial scars from endocardial mapping data. In addition, the multilevel solver is faster than a comparable single-level solver. On the other hand, we investigate different optimization approaches based on adjoint gradient computation for computing a maximum posterior estimate: steepest descent, limited memory BFGS, and recursive multilevel trust region methods using mesh hierarchies or heterogeneous model hierarchies. We compare overall performance, asymptotic convergence rate, and pre-asymptotic progress on selected examples in order to assess the benefit of our multifidelity acceleration. Y1 - 2022 ER - TY - CHAP A1 - Fürst, Steffen A1 - Rakow, Christian T1 - Parallelization of large-scale agent-based epidemiological simulations T2 - Proceedings of the 34th European Modeling & Simulation Symposium N2 - Agent-based epidemiological models have been applied widely successfully during the SARS-CoV-2 pandemic and assisted policymakers in assessing the effectiveness of intervention strategies. The computational complexity of agent-based models is still challenging, and therefore it is important to utilize modern multi-core systems as good as possible. In this paper, we are presenting our work on parallelizing the epidemiological simulation model MATSim Episim. Episim combines a large-scale person-centric human mobility model with a mechanistic model of infection and a person-centric disease progression model. In general, the parallelization of agent-based models with an inherent sequential structure — in the case of epidemiological models, the temporal order of the individual movements of the agents — is challenging. Especially when the underlying social network is irregular and dynamic, they require frequent communication between the processing elements. In Episim, however, we were able to take advantage of the fact that people are not contagious on the same day they become infected, and therefore immediate health synchronization is not required. By parallelizing some of the most computationally intensive submodels, we are now able to run MATSim Episim simulations up to eight times faster than the serial version. This makes it feasible to increase the number of agents, e.g. to run simulations for the whole of Germany instead of just Berlin as before. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.46354/i3m.2022.emss.008 ER - TY - CHAP A1 - Brook, Glenn A1 - Fuller, Douglas A1 - Swinburne, John A1 - Christgau, Steffen A1 - Läuter, Matthias A1 - Rodrigues Pelá, Ronaldo A1 - Lewin, Stein A1 - Christian, Tuma A1 - Steinke, Thomas T1 - An Early Scalability Study of Omni-Path Express N2 - This work provides a brief description of Omni-Path Express and the current status of its development, stability, and performance. Basic benchmarks that highlight the gains of OPX over PSM2 are provided, and the results of an initial performance and scalability study of several applications are presented. Y1 - 2022 UR - https://www.ixpug.org/events/isc22-ixpug-workshop U6 - https://doi.org/10.13140/RG.2.2.21353.57442 CY - Hamburg ER - TY - GEN A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Cutting Plane Selection with Analytic Centers and Multiregression N2 - Cutting planes are a crucial component of state-of-the-art mixed-integer programming solvers, with the choice of which subset of cuts to add being vital for solver performance. We propose new distance-based measures to qualify the value of a cut by quantifying the extent to which it separates relevant parts of the relaxed feasible set. For this purpose, we use the analytic centers of the relaxation polytope or of its optimal face, as well as alternative optimal solutions of the linear programming relaxation. We assess the impact of the choice of distance measure on root node performance and throughout the whole branch-and-bound tree, comparing our measures against those prevalent in the literature. Finally, by a multi-output regression, we predict the relative performance of each measure, using static features readily available before the separation process. Our results indicate that analytic center-based methods help to significantly reduce the number of branch-and-bound nodes needed to explore the search space and that our multiregression approach can further improve on any individual method. T3 - ZIB-Report - 22-28 KW - cut selection KW - anlalytic center KW - mixed-integer programming Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89065 SN - 1438-0064 ER - TY - JOUR A1 - Tuncay, Erhun Giray A1 - Erdur, Rıza Cenk A1 - Conrad, Tim T1 - Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics N2 - The aim of Network Alignment in Protein-Protein Interaction Networks is discovering functionally similar regions between compared organisms. One major compromise for solving a network alignment problem is the trade-off among multiple similarity objectives while applying an alignment strategy. An alignment may lose its biological relevance while favoring certain objectives upon others due to the actual relevance of unfavored objectives. One possible solution for solving this issue may be blending the stronger aspects of various alignment strategies until achieving mature solutions. This study proposes a parallel approach called PERSONA that allows aligners to share their partial solutions continuously while they progress. All these aligners pursue their particular heuristics as part of a particle swarm that searches for multi-objective solutions of the same alignment problem in a reactive actor environment. The actors use the stronger portion of a solution as a subgraph that they receive from leading or other actors and send their own stronger subgraphs back upon evaluation of those partial solutions. Moreover, the individual heuristics of each actor takes randomized parameter values at each cycle of parallel execution so that the problem search space can thoroughly be investigated. The results achieved with PERSONA are remarkably optimized and balanced for both topological and node similarity objectives. Y1 - 2023 U6 - https://doi.org/10.1109/TCBB.2022.3231489 VL - 20 IS - 3 SP - 2064 EP - 2077 ER - TY - GEN A1 - Rickert, Lucas A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Burger, Sven A1 - Heindel, Tobias T1 - Data publication for "High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings" T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.7360516 SP - 7360516 ER - TY - JOUR A1 - Rickert, Lucas A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Burger, Sven A1 - Heindel, Tobias T1 - High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings JF - Opt. Express Y1 - 2023 U6 - https://doi.org/10.1364/OE.486060 VL - 31 SP - 14750 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz T1 - Nonasymptotic bounds for suboptimal importance sampling JF - SIAM/ASA Journal on Uncertainty Quantification N2 - Importance sampling is a popular variance reduction method for Monte Carlo estimation, where an evident question is how to design good proposal distributions. While in most cases optimal (zero-variance) estimators are theoretically possible, in practice only suboptimal proposal distributions are available and it can often be observed numerically that those can reduce statistical performance significantly, leading to large relative errors and therefore counteracting the original intention. Previous analysis on importance sampling has often focused on asymptotic arguments that work well in a large deviations regime. In this article, we provide lower and upper bounds on the relative error in a nonasymptotic setting. They depend on the deviation of the actual proposal from optimality, and we thus identify potential robustness issues that importance sampling may have, especially in high dimensions. We particularly focus on path sampling problems for diffusion processes with nonvanishing noise, for which generating good proposals comes with additional technical challenges. We provide numerous numerical examples that support our findings and demonstrate the applicability of the derived bounds. Y1 - 2024 U6 - https://doi.org/10.1137/21M1427760 VL - 12 IS - 2 SP - 309 EP - 346 ER - TY - JOUR A1 - Nüsken, Nikolas A1 - Richter, Lorenz T1 - Interpolating between BSDEs and PINNs: deep learning for elliptic and parabolic boundary value problems JF - Journal of Machine Learning N2 - Solving high-dimensional partial differential equations is a recurrent challenge in economics, science and engineering. In recent years, a great number of computational approaches have been developed, most of them relying on a combination of Monte Carlo sampling and deep learning based approximation. For elliptic and parabolic problems, existing methods can broadly be classified into those resting on reformulations in terms of backward stochastic differential equations (BSDEs) and those aiming to minimize a regression-type L2-error (physics-informed neural networks, PINNs). In this paper, we review the literature and suggest a methodology based on the novel diffusion loss that interpolates between BSDEs and PINNs. Our contribution opens the door towards a unified understanding of numerical approaches for high-dimensional PDEs, as well as for implementations that combine the strengths of BSDEs and PINNs. The diffusion loss furthermore bears close similarities to (least squares) temporal difference objectives found in reinforcement learning. We also discuss eigenvalue problems and perform extensive numerical studies, including calculations of the ground state for nonlinear Schr ¨odinger operators and committor functions relevant in molecular dynamics. Y1 - 2023 U6 - https://doi.org/0.4208/jml.220416 VL - 2 IS - 1 SP - 31 EP - 64 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Pokutta, Sebastian T1 - Accelerated Riemannian Optimization: Handling Constraints with a Prox to Bound Geometric Penalties T2 - Proceedings of Thirty Sixth Conference on Learning Theory N2 - We propose a globally-accelerated, first-order method for the optimization of smooth and (strongly or not) geodesically-convex functions in a wide class of Hadamard manifolds. We achieve the same convergence rates as Nesterov’s accelerated gradient descent, up to a multiplicative geometric penalty and log factors. Crucially, we can enforce our method to stay within a compact set we define. Prior fully accelerated works \emph{resort to assuming} that the iterates of their algorithms stay in some pre-specified compact set, except for two previous methods of limited applicability. For our manifolds, this solves the open question in (Kim and Yang, 2022) about obtaining global general acceleration without iterates assumptively staying in the feasible set.In our solution, we design an accelerated Riemannian inexact proximal point algorithm, which is a result that was unknown even with exact access to the proximal operator, and is of independent interest. For smooth functions, we show we can implement the prox step inexactly with first-order methods in Riemannian balls of certain diameter that is enough for global accelerated optimization. Y1 - 2023 UR - https://proceedings.mlr.press/v195/martinez-rubio23a.html VL - 195 SP - 359 EP - 393 ER - TY - JOUR A1 - Šofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - An Algorithm-independent Measure of Progress for Linear Constraint Propagation JF - Constraints Y1 - 2022 U6 - https://doi.org/10.1007/s10601-022-09338-9 VL - 27 SP - 432 EP - 455 ER - TY - CHAP A1 - Berner, Julius A1 - Richter, Lorenz A1 - Ullrich, Karen T1 - An optimal control perspective on diffusion-based generative modeling T2 - Transactions on Machine Learning Research N2 - We establish a connection between stochastic optimal control and generative models based on stochastic differential equations (SDEs) such as recently developed diffusion probabilistic models. In particular, we derive a Hamilton-Jacobi-Bellman equation that governs the evolution of the log-densities of the underlying SDE marginals. This perspective allows to transfer methods from optimal control theory to generative modeling. First, we show that the evidence lower bound is a direct consequence of the well-known verification theorem from control theory. Further, we develop a novel diffusion-based method for sampling from unnormalized densities -- a problem frequently occurring in statistics and computational sciences. Y1 - 2024 UR - https://openreview.net/forum?id=oYIjw37pTP ER - TY - CHAP A1 - Richter, Lorenz A1 - Berner, Julius T1 - Robust SDE-Based Variational Formulations for Solving Linear PDEs via Deep Learning T2 - Proceedings of the 39th International Conference on Machine Learning, PMLR N2 - The combination of Monte Carlo methods and deep learning has recently led to efficient algorithms for solving partial differential equations (PDEs) in high dimensions. Related learning problems are often stated as variational formulations based on associated stochastic differential equations (SDEs), which allow the minimization of corresponding losses using gradient-based optimization methods. In respective numerical implementations it is therefore crucial to rely on adequate gradient estimators that exhibit low variance in order to reach convergence accurately and swiftly. In this article, we rigorously investigate corresponding numerical aspects that appear in the context of linear Kolmogorov PDEs. In particular, we systematically compare existing deep learning approaches and provide theoretical explanations for their performances. Subsequently, we suggest novel methods that can be shown to be more robust both theoretically and numerically, leading to substantial performance improvements. Y1 - 2022 VL - 162 SP - 18649 EP - 18666 ER - TY - JOUR A1 - Schulze, Kenrick A1 - Peppert, Felix A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Chimeric U-Net–Modifying the standard U-Net towards Explainability JF - bioRxiv Y1 - 2022 U6 - https://doi.org/10.1101/2022.12.01.518699 ER - TY - JOUR A1 - Lang, Annemarie A1 - Vester, Antja A1 - Ferreira-Gomes, M. A1 - Guerra, G.M. A1 - Heinrich, Fredrich R. A1 - Götzke, C.C. A1 - Kurmies, Sebastian A1 - Sunkara, Vikram A1 - Durek, Pawel A1 - Boerckel, Joel D. A1 - Mashreghi, Mir-Farzin T1 - PIPELINE FOR SINGLE CELL SEQUENCING OF HUMAN CHONDROCYTE PELLET CULTURES TO DELINEATE IL-1β MODULATED CHANGES IN CELL HETEROGENEITY JF - Osteoarthritis and Cartilage Y1 - 2022 U6 - https://doi.org/10.1016/j.joca.2022.02.112 VL - 30 IS - Supplement 1 SP - S90 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Lewis, Angus A1 - Nguyen, Giang T. A1 - O'Reilly, Malgorzata M. A1 - Bean, Nigel T1 - A discontinuous Galerkin method for approximating the stationary distribution of stochastic fluid-fluid processes JF - Methodology and Computing in Applied Probability Y1 - 2022 U6 - https://doi.org/10.1007/s11009-022-09945-2 ER - TY - JOUR A1 - Koch, Thorsten A1 - Berthold, Timo A1 - Pedersen, Jaap A1 - Vanaret, Charlie T1 - Progress in mathematical programming solvers from 2001 to 2020 JF - EURO Journal on Computational Optimization N2 - This study investigates the progress made in lp and milp solver performance during the last two decades by comparing the solver software from the beginning of the millennium with the codes available today. On average, we found out that for solving lp/milp, computer hardware got about 20 times faster, and the algorithms improved by a factor of about nine for lp and around 50 for milp, which gives a total speed-up of about 180 and 1,000 times, respectively. However, these numbers have a very high variance and they considerably underestimate the progress made on the algorithmic side: many problem instances can nowadays be solved within seconds, which the old codes are not able to solve within any reasonable time. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejco.2022.100031 VL - 10 SP - 100031 ER - TY - JOUR A1 - Ray, Sourav A1 - Fackeldey, Konstantin A1 - Stein, Christoph A1 - Weber, Marcus T1 - Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane JF - Biophysica N2 - In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the 𝜇-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the 𝜇-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe’s parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane. Y1 - 2023 U6 - https://doi.org/10.3390/biophysica3020017 VL - 3 IS - 2 SP - 263 EP - 275 ER - TY - JOUR A1 - Quer, Jannes A1 - Ribera Borrell, Enric T1 - Connecting Stochastic Optimal Control and Reinforcement Learning JF - Journal of Mathematical Physics N2 - In this paper the connection between stochastic optimal control and reinforcement learning is investigated. Our main motivation is to apply importance sampling to sampling rare events which can be reformulated as an optimal control problem. By using a parameterised approach the optimal control problem becomes a stochastic optimization problem which still raises some open questions regarding how to tackle the scalability to high-dimensional problems and how to deal with the intrinsic metastability of the system. To explore new methods we link the optimal control problem to reinforcement learning since both share the same underlying framework, namely a Markov Decision Process (MDP). For the optimal control problem we show how the MDP can be formulated. In addition we discuss how the stochastic optimal control problem can be interpreted in the framework of reinforcement learning. At the end of the article we present the application of two different reinforcement learning algorithms to the optimal control problem and a comparison of the advantages and disadvantages of the two algorithms. Y1 - 2024 U6 - https://doi.org/10.1063/5.0140665 VL - 65 IS - 8 ER - TY - THES A1 - Rams, Mona Milena T1 - New approaches for unsupervised transcriptomic data analysis based on Dictionary learning Y1 - 2022 ER - TY - THES A1 - Iravani, Sahar T1 - Interpretable Deep Learning Approaches for Biomarker Detection from High-Dimensional Biomedical Data Y1 - 2022 ER - TY - CHAP A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Maristany de las Casas, Pedro T1 - An A* Algorithm for Flight Planning Based on Idealized Vertical Profiles T2 - 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022) N2 - The Flight Planning Problem is to find a minimum fuel trajectory between two airports in a 3D airway network under consideration of the wind. We show that this problem is NP-hard, even in its most basic version. We then present a novel A∗ heuristic, whose potential function is derived from an idealized vertical profile over the remaining flight distance. This potential is, under rather general assumptions, both admissible and consistent and it can be computed efficiently. The method outperforms the state-of-the-art heuristic on real-life instances. Y1 - 2022 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2022.1 VL - 106 SP - 1:1 EP - 1:15 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - A Discrete-Continuous Algorithm for Globally Optimal Free Flight Trajectory Optimization T2 - 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022) N2 - We present an efficient algorithm that finds a globally optimal solution to the 2D Free Flight Trajectory Optimization Problem (aka Zermelo Navigation Problem) up to arbitrary precision in finite time. The algorithm combines a discrete and a continuous optimization phase. In the discrete phase, a set of candidate paths that densely covers the trajectory space is created on a directed auxiliary graph. Then Yen’s algorithm provides a promising set of discrete candidate paths which subsequently undergo a locally convergent refinement stage. Provided that the auxiliary graph is sufficiently dense, the method finds a path that lies within the convex domain around the global minimizer. From this starting point, the second stage will converge rapidly to the optimum. The density of the auxiliary graph depends solely on the wind field, and not on the accuracy of the solution, such that the method inherits the superior asymptotic convergence properties of the optimal control stage. Y1 - 2022 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2022.2 VL - 106 SP - 1 EP - 13 ER - TY - CHAP A1 - Petkovic, Milena A1 - Zakiyeva, Nazgul A1 - Zittel, Janina T1 - Statistical Analysis and Modeling for Detecting Regime Changes in Gas Nomination Time Series T2 - Operations Research Proceedings 2021. OR 2021 N2 - As a result of the legislation for gas markets introduced by the European Union in 2005, separate independent companies have to conduct the transport and trading of natural gas. The current gas market of Germany, which has a market value of more than 54 billion USD, consists of Transmission System Operators (TSO), network users, and traders. Traders can nominate a certain amount of gas anytime and anywhere in the network. Such unrestricted access for the traders, on the other hand, increase the uncertainty in the gas supply management. Some customers’ behaviors may cause abrupt structural changes in gas flow time series. In particular, it is a challenging task for the TSO operators to predict gas nominations 6 to 10 h-ahead. In our study, we aim to investigate the regime changes in time series of nominations to predict the 6 to 10 h-ahead of gas nominations. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-08623-6_29 SP - 188 EP - 193 PB - Springer, Cham ER - TY - CHAP A1 - Zakiyeva, Nazgul A1 - Petkovic, Milena T1 - Modeling and Forecasting Gas Network Flows with Multivariate Time Series and Mathematical Programming Approach T2 - Operations Research Proceedings 2021. OR 2021. N2 - With annual consumption of approx. 95 billion cubic meters and similar amounts of gas just transshipped through Germany to other EU states, Germany’s gas transport system plays a vital role in European energy supply. The complex, more than 40,000 km long high-pressure transmission network is controlled by several transmission system operators (TSOs) whose main task is to provide security of supply in a cost-efficient way. Given the slow speed of gas flows through the gas transmission network pipelines, it has been an essential task for the gas network operators to enhance the forecast tools to build an accurate and effective gas flow prediction model for the whole network. By incorporating the recent progress in mathematical programming and time series modeling, we aim to model natural gas network and predict gas in- and out-flows at multiple supply and demand nodes for different forecasting horizons. Our model is able to describe the dynamics in the network by detecting the key nodes, which may help to build an optimal management strategy for transmission system operators. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-08623-6_31 SP - 200 EP - 205 PB - Springer, Cham ER - TY - CHAP A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis T2 - 2022 IEEE International Conference on Big Data, Posters Y1 - 2022 ER - TY - CHAP A1 - Bader, Jonathan A1 - Witzke, Joel A1 - Becker, Soeren A1 - Lößer, Ansgar A1 - Lehmann, Fabian A1 - Doehler, Leon A1 - Vu, Anh Duc A1 - Kao, Odej T1 - Towards Advanced Monitoring for Scientific Workflows T2 - 2022 IEEE International Conference on Big Data, 11th Workshop on Scalable Cloud Data Management Y1 - 2022 ER - TY - JOUR A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis JF - arXiv Y1 - 2022 U6 - https://doi.org/10.48550/arXiv.2209.05358 SP - 1 EP - 20 ER - TY - GEN A1 - Reidelbach, Marco A1 - Weber, Marcus T1 - MaRDI - The mathematical Research Data Initiative T2 - Aktionstag Forschungsdaten Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.7397588 ER - TY - JOUR A1 - Reidelbach, Marco A1 - Bai, Mei A1 - Zöllner, Martin Sebastian A1 - Schneeberger, Michaela A1 - Kubicek, Katharina A1 - Kirchberg, Henning A1 - Bressler, Christian A1 - Thorwart, Michael A1 - Herrmann, Carmen T1 - Solvent dynamics of aqueous halides before and after photoionization JF - Journal of Physical Chemistry Y1 - 2022 ER - TY - JOUR A1 - Boege, Tobias A1 - Fritze, René A1 - Görgen, Christiane A1 - Hanselmann, Jeroen A1 - Iglezakis, Dorothea A1 - Kastner, Lars A1 - Koprucki, Thomas A1 - Krause, Tabea A1 - Lehrenfeld, Christoph A1 - Polla, Silvia A1 - Reidelbach, Marco A1 - Riedel, Christian A1 - Saak, Jens A1 - Schembera, Björn A1 - Tabelow, Karsten A1 - Weber, Marcus T1 - Research-Data Management Planning in the German Mathematical Community JF - Eur. Math. Soc. Mag. N2 - In this paper we discuss the notion of research data for the field of mathematics and report on the status quo of research-data management and planning. A number of decentralized approaches are presented and compared to needs and challenges faced in three use cases from different mathematical subdisciplines. We highlight the importance of tailoring research-data management plans to mathematicians’ research processes and discuss their usage all along the data life cycle. Y1 - 2023 U6 - https://doi.org/10.4171/mag/152 VL - 130 SP - 40 EP - 47 ER - TY - JOUR A1 - Raharinirina, N. Alexia A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Qualitative Euclidean embedding of Disjoint Sets of Points N2 - We consider two disjoint sets of points with a distance metric, or a proximity function, associated with each set. If each set can be separately embedded into separate Euclidean spaces, then we provide sufficient conditions for the two sets to be jointly embedded in one Euclidean space. In this joint Euclidean embedding, the distances between the points are generated by a specific relation-preserving function. Consequently, the mutual distances between two points of the same set are specific qualitative transformations of their mutual distances in their original space; the pairwise distances between the points of different sets can be constructed from an arbitrary proximity function (might require scaling). Y1 - 2022 UR - https://arxiv.org/abs/2212.00058 ER - TY - GEN A1 - Schütte, Christof A1 - Klus, Stefan A1 - Hartmann, Carsten T1 - Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning N2 - One of the main challenges in molecular dynamics is overcoming the “timescale barrier”, a phrase used to describe that in many realistic molecular systems, biologically important rare transitions occur on timescales that are not accessible to direct numerical simulation, not even on the largest or specifically dedicated supercomputers. This article discusses how to circumvent the timescale barrier by a collection of transfer operator-based techniques that have emerged from dynamical systems theory, numerical mathematics, and machine learning over the last two decades. We will focus on how transfer operators can be used to approximate the dynamical behavior on long timescales, review the introduction of this approach into molecular dynamics, and outline the respective theory as well as the algorithmic development from the early numerics-based methods, via variational reformulations, to modern data-based techniques utilizing and improving concepts from machine learning. Furthermore, its relation to rare event simulation techniques will be explained, revealing a broad equivalence of variational principles for long-time quantities in MD. The article will mainly take a mathematical perspective and will leave the application to real-world molecular systems to the more than 1000 research articles already written on this subject. T3 - ZIB-Report - 22-25 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88637 SN - 1438-0064 ER - TY - GEN A1 - Masing, Berenike A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Periodic Timetabling with Integrated Track Choice for Railway Construction Sites N2 - We propose a mixed-integer linear programming model to generate and optimize periodic timetables with integrated track choice in the context of railway construction sites. When a section of a railway network becomes unavailable, the nearby areas are typically operated close to their capacity limits, and hence carefully modeling headways and allowing flexible routings becomes vital. We therefore discuss first how to integrate headway constraints into the Periodic Event Scheduling Problem (PESP) that do not only prevent overtaking, but also guarantee conflict-free timetables in general and particularly inside stations. Secondly, we introduce a turn-sensitive event-activity network, which is able to integrate routing alternatives for turnarounds at stations, e.g., turning at a platform vs. at a pocket track for metro-like systems. We propose several model formulations to include track choice, and finally evaluate them on six real construction site scenarios on the S-Bahn Berlin network. T3 - ZIB-Report - 22-26 KW - Railway Timetabling KW - Periodic Timetabling KW - Periodic Event Scheduling KW - Train Routing KW - Turnarounds Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88626 SN - 1438-0064 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - The price of symmetric line plans in the Parametric City JF - Transportation Research Part B: Methodological N2 - We consider the line planning problem in public transport in the Parametric City, an idealized model that captures typical scenarios by a (small) number of parameters. The Parametric City is rotation symmetric, but optimal line plans are not always symmetric. This raises the question to quantify the symmetry gap between the best symmetric and the overall best solution. For our analysis, we formulate the line planning problem as a mixed integer linear program, that can be solved in polynomial time if the solutions are forced to be symmetric. We prove that the symmetry gap is small when a specific Parametric City parameter is fixed, and we give an approximation algorithm for line planning in the Parametric City in this case. While the symmetry gap can be arbitrarily large in general, we show that symmetric line plans are a good choice in most practical situations. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88613 VL - 166 SP - 419 EP - 443 ER - TY - JOUR A1 - Raharinirina, N. Alexia A1 - Acevedo-Trejos, Esteban A1 - Merico, Agostino T1 - Modelling the acclimation capacity of coral reefs to a warming ocean JF - PLOS COMPUTATIONAL BIOLOGY N2 - The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming. Y1 - 2022 U6 - https://doi.org/10.1371/journal.pcbi.1010099 ER - TY - THES A1 - Lüdke, David T1 - Neural flow-based deformations for statistical shape modelling N2 - Statistical shape models learn to capture the most characteristic geometric variations of anatomical structures given samples from their population. Accordingly, shape models have become an essential tool for many medical applications and are used in, for example, shape generation, reconstruction, and classification tasks. However, established statistical shape models require precomputed dense correspondence between shapes, often lack robustness, and ignore the global surface topology. This thesis presents a novel neural flow-based shape model that does not require any precomputed correspondence. The proposed model relies on continuous flows of a neural ordinary differential equation to model shapes as deformations of a template. To increase the expressivity of the neural flow and disentangle global, low-frequency deformations from the generation of local, high- frequency details, we propose to apply a hierarchy of flows. We evaluate the performance of our model on two anatomical structures, liver, and distal femur. Our model outperforms state-of-the-art methods in providing an expressive and robust shape prior, as indicated by its generalization ability and specificity. More so, we demonstrate the effectiveness of our shape model on shape reconstruction tasks and find anatomically plausible solutions. Finally, we assess the quality of the emerging shape representation in an unsupervised setting and discriminate healthy from pathological shapes. KW - statistical shape model KW - statistical shape analysis KW - representation learning Y1 - 2022 UR - https://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/searchtype/authorsearch/author/David+L%C3%BCdke/docId/70904/start/0/rows/10 ER - TY - GEN A1 - Berthold, Timo A1 - Mexi, Gioni A1 - Salvagnin, Domenico T1 - Using Multiple Reference Vectors and Objective Scaling in the Feasibility Pump N2 - The Feasibility Pump (FP) is one of the best-known primal heuristics for mixed-integer programming (MIP): more than 15 papers suggested various modifications of all of its steps. So far, no variant considered information across multiple iterations, but all instead maintained the principle to optimize towards a single reference integer point. In this paper, we evaluate the usage of multiple reference vectors in all stages of the FP algorithm. In particular, we use LP-feasible vectors obtained during the main loop to tighten the variable domains before entering the computationally expensive enumeration stage. Moreover, we consider multiple integer reference vectors to explore further optimizing directions and introduce alternative objective scaling terms to balance the contributions of the distance functions and the original MIP objective. Our computational experiments demonstrate that the new method can improve performance on general MIP test sets. In detail, our modifications provide a 29.3% solution quality improvement and 4.0% running time improvement in an embedded setting, needing 16.0% fewer iterations over a large test set of MIP instances. In addition, the method’s success rate increases considerably within the first few iterations. In a standalone setting, we also observe a moderate performance improvement, which makes our version of FP suitable for the two main use-cases of the algorithm. T3 - ZIB-Report - 22-14 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88513 SN - 1438-0064 ER - TY - JOUR A1 - Laguillo-Diego, Alejandra A1 - Kiewisz, Robert A1 - Martí-Gómez, Carlos A1 - Baum, Daniel A1 - Müller-Reichert, Thomas A1 - Vernos, Isabelle T1 - MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles JF - Molecular Biology of the Cell N2 - Faithful chromosome segregation requires the assembly of a bipolar spindle, consisting of two antiparallel microtubule (MT) arrays having most of their minus ends focused at the spindle poles and their plus ends overlapping in the spindle midzone. Spindle assembly, chromosome alignment and segregation require highly dynamic MTs. The plus ends of MTs have been extensively investigated; instead, their minus end structure remains poorly characterized. Here, we used large-scale electron tomography to study the morphology of the MT minus ends in 3D-reconstructed metaphase spindles in HeLa cells. In contrast to the homogeneous open morphology of the MT plus ends at the kinetochores, we found that MT minus ends are heterogeneous showing either open or closed morphologies. Silencing the minus-end specific stabilizer, MCRS1 increased the proportion of open MT minus ends. Altogether, these data suggest a correlation between the morphology and the dynamic state of the MT ends. Taking this heterogeneity of the MT minus end morphologies into account, our work indicates an unsynchronized behavior of MTs at the spindle poles, thus laying the ground for further studies on the complexity of MT dynamics regulation. Y1 - 2022 U6 - https://doi.org/10.1091/mbc.E22-08-0306-T VL - 34 IS - 1 ER - TY - JOUR A1 - Hunkenschröder, Christoph A1 - Pokutta, Sebastian A1 - Weismantel, Robert T1 - Optimizing a low-dimensional convex function over a high-dimensional cub JF - SIAM Journal on Optimization Y1 - 2022 ER - TY - CHAP A1 - MacDonald, Jan A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Interpretable Neural Networks with Frank-Wolfe: Sparse Relevance Maps and Relevance Orderings T2 - Proceedings of the International Conference on Machine Learning Y1 - 2022 ER - TY - CHAP A1 - Tsuji, Kazuma A1 - Tanaka, Ken'ichiro A1 - Pokutta, Sebastian T1 - Pairwise Conditional Gradients without Swap Steps and Sparser Kernel Herding T2 - Proceedings of the International Conference on Machine Learning Y1 - 2022 ER - TY - CHAP A1 - Wäldchen, Stephan A1 - Huber, Felix A1 - Pokutta, Sebastian T1 - Training Characteristic Functions with Reinforcement Learning: XAI-methods Play Connect Four T2 - Proceedings of the International Conference on Machine Learning Y1 - 2022 ER - TY - JOUR A1 - Kossen, Tabea A1 - Hirzel, Manuel A. A1 - Madai, Vince I. A1 - Boenisch, Franziska A1 - Hennemuth, Anja A1 - Hildebrand, Kristian A1 - Pokutta, Sebastian A1 - Sharma, Kartikey A1 - Hilbert, Adam A1 - Sobesky, Jan A1 - Galinovic, Ivana A1 - Khalil, Ahmed A. A1 - Fiebach, Jochen B. A1 - Frey, Dietmar T1 - Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks JF - Frontiers in Artificial Intelligence N2 - Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fréchet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.3389/frai.2022.813842 ER - TY - CHAP A1 - Wirth, Elias A1 - Pokutta, Sebastian T1 - Conditional Gradients for the Approximately Vanishing Ideal T2 - Proceedings of The 25th International Conference on Artificial Intelligence and Statistics N2 - The vanishing ideal of a set of points X is the set of polynomials that evaluate to 0 over all points x in X and admits an efficient representation by a finite set of polynomials called generators. To accommodate the noise in the data set, we introduce the Conditional Gradients Approximately Vanishing Ideal algorithm (CGAVI) for the construction of the set of generators of the approximately vanishing ideal. The constructed set of generators captures polynomial structures in data and gives rise to a feature map that can, for example, be used in combination with a linear classifier for supervised learning. In CGAVI, we construct the set of generators by solving specific instances of (constrained) convex optimization problems with the Pairwise Frank-Wolfe algorithm (PFW). Among other things, the constructed generators inherit the LASSO generalization bound and not only vanish on the training but also on out-sample data. Moreover, CGAVI admits a compact representation of the approximately vanishing ideal by constructing few generators with sparse coefficient vectors. Y1 - 2022 UR - https://proceedings.mlr.press/v151/wirth22a.html VL - 151 SP - 2191 EP - 2209 ER - TY - JOUR A1 - Kamčev, Nina A1 - Spiegel, Christoph T1 - Another note on intervals in the Hales-Jewett theorem JF - Electronic Journal of Combinatorics N2 - The Hales-Jewett Theorem states that any r-colouring of [m]ⁿ contains a monochromatic combinatorial line if n is large enough. Shelah's proof of the theorem implies that for m = 3 there always exists a monochromatic combinatorial line whose set of active coordinates is the union of at most r intervals. For odd r, Conlon and Kamčev constructed r–colourings for which it cannot be fewer than r intervals. However, we show that for even r and large n, any r–colouring of [3]ⁿ contains a monochromatic combinatorial line whose set of active coordinates is the union of at most r−1 intervals. This is optimal and extends a result of Leader and Räty for r=2. Y1 - 2022 U6 - https://doi.org/10.37236/6730 VL - 29 IS - 1 SP - P1.62 ER - TY - CHAP A1 - Parczyk, Olaf A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Szabó, Tibor T1 - Fully Computer-assisted Proofs in Extremal Combinatorics T2 - Proceedings of the AAAI Conference on Artificial Intelligence N2 - We present a fully computer-assisted proof system for solving a particular family of problems in Extremal Combinatorics. Existing techniques using Flag Algebras have proven powerful in the past, but have so far lacked a computational counterpart to derive matching constructive bounds. We demonstrate that common search heuristics are capable of finding constructions far beyond the reach of human intuition. Additionally, the most obvious downside of such heuristics, namely a missing guarantee of global optimality, can often be fully eliminated in this case through lower bounds and stability results coming from the Flag Algebra approach. To illustrate the potential of this approach, we study two related and well-known problems in Extremal Graph Theory that go back to questions of Erdős from the 60s. Most notably, we present the first major improvement in the upper bound of the Ramsey multiplicity of the complete graph on 4 vertices in 25 years, precisely determine the first off-diagonal Ramsey multiplicity number, and settle the minimum number of independent sets of size four in graphs with clique number strictly less than five. Y1 - 2023 U6 - https://doi.org/10.1609/aaai.v37i10.26470 VL - 37 IS - 10 SP - 12482 EP - 12490 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Hoen, Alexander T1 - PaPILO: A Parallel Presolving Library for Integer and Linear Programming with Multiprecision Support JF - INFORMS Journal on Computing N2 - Presolving has become an essential component of modern mixed integer program (MIP) solvers, both in terms of computational performance and numerical robustness. In this paper, we present PaPILO, a new C++ header-only library that provides a large set of presolving routines for MIP and linear programming problems from the literature. The creation of PaPILO was motivated by the current lack of (a) solver-independent implementations that (b) exploit parallel hardware and (c) support multiprecision arithmetic. Traditionally, presolving is designed to be fast. Whenever necessary, its low computational overhead is usually achieved by strict working limits. PaPILO’s parallelization framework aims at reducing the computational overhead also when presolving is executed more aggressively or is applied to large-scale problems. To rule out conflicts between parallel presolve reductions, PaPILO uses a transaction-based design. This helps to avoid both the memory-intensive allocation of multiple copies of the problem and special synchronization between presolvers. Additionally, the use of Intel’s Threading Building Blocks library aids PaPILO in efficiently exploiting recursive parallelism within expensive presolving routines, such as probing, dominated columns, or constraint sparsification. We provide an overview of PaPILO’s capabilities and insights into important design choices. Y1 - 2023 U6 - https://doi.org/10.1287/ijoc.2022.0171 VL - 35 IS - 6 SP - 1329 EP - 1341 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus A1 - Keller, Bettina G. T1 - A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models JF - Journal of Mathematical Physics N2 - Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential U(x) from trajectories that have been generated at a different potential V(x). In this article, we present Girsanov reweighting and Square Root Approximation (SqRA): the first method reweights path probabilities exploiting the Girsanov theorem and can be applied to Markov State Models (MSMs) to reweight transition probabilities; the second method was originally developed to discretize the Fokker-Planck operator into a transition rate matrix, but here we implement it into a reweighting scheme for transition rates. We begin by reviewing the theoretical background of the methods, then present two applications relevant to Molecular Dynamics (MD), highlighting their strengths and weaknesses. Y1 - 2022 U6 - https://doi.org/10.1063/5.0127227 VL - 63 IS - 12 SP - 123306-1 EP - 123306-21 PB - AIP Publishing ER - TY - THES A1 - Ambellan, Felix T1 - Efficient Riemannian Statistical Shape Analysis with Applications in Disease Assessment N2 - In this work, we address the challenge of developing statistical shape models that account for the non-Euclidean nature inherent to (anatomical) shape variation and at the same time offer fast, numerically robust processing and as much invariance as possible regarding translation and rotation, i.e. Euclidean motion. With the aim of doing that we formulate a continuous and physically motivated notion of shape space based on deformation gradients. We follow two different tracks endowing this differential representation with a Riemannian structure to establish a statistical shape model. (1) We derive a model based on differential coordinates as elements in GL(3)+. To this end, we adapt the notion of bi-invariant means employing an affine connection structure on GL(3)+. Furthermore, we perform second-order statistics based on a family of Riemannian metrics providing the most possible invariance, viz. GL(3)+-left-invariance and O(3)-right-invariance. (2) We endow the differential coordinates with a non-Euclidean structure, that stems from a product Lie group of stretches and rotations. This structure admits a bi-invariant metric and thus allows for a consistent analysis via manifold-valued Riemannian statistics. This work further presents a novel shape representation based on discrete fundamental forms that is naturally invariant under Euclidean motion, namely the fundamental coordinates. We endow this representation with a Lie group structure that admits bi-invariant metrics and therefore allows for consistent analysis using manifold-valued statistics based on the Riemannian framework. Furthermore, we derive a simple, efficient, robust, yet accurate (i.e. without resorting to model approximations) solver for the inverse problem that allows for interactive applications. Beyond statistical shape modeling the proposed framework is amenable for surface processing such as quasi-isometric flattening. Additionally, the last part of the thesis aims on shape-based, continuous disease stratification to provide means that objectify disease assessment over the current clinical practice of ordinal grading systems. Therefore, we derive the geodesic B-score, a generalization of the of the Euclidean B-score, in order to assess knee osteoarthritis. In this context we present a Newton-type fixed point iteration for projection onto geodesics in shape space. On the application side, we show that the derived geodesic B-score features, in comparison to its Euclidean counterpart, an improved predictive performance on assessing the risk of total knee replacement surgery. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-refubium-37016-3 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Köppl, Jonas A1 - Djurdjevac, Ana T1 - Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise JF - Entropy N2 - We introduce an agent-based model for co-evolving opinions and social dynamics, under the influence of multiplicative noise. In this model, every agent is characterized by a position in a social space and a continuous opinion state variable. Agents’ movements are governed by the positions and opinions of other agents and similarly, the opinion dynamics are influenced by agents’ spatial proximity and their opinion similarity. Using numerical simulations and formal analyses, we study this feedback loop between opinion dynamics and the mobility of agents in a social space. We investigate the behaviour of this ABM in different regimes and explore the influence of various factors on the appearance of emerging phenomena such as group formation and opinion consensus. We study the empirical distribution, and, in the limit of infinite number of agents, we derive a corresponding reduced model given by a partial differential equation (PDE). Finally, using numerical examples, we show that a resulting PDE model is a good approximation of the original ABM. Y1 - 2022 U6 - https://doi.org/10.3390/e24101352 VL - 24(10) ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Völker, Helena T1 - Strengthening SONC Relaxations with Constraints Derived from Variable Bounds N2 - Certificates of polynomial nonnegativity can be used to obtain tight dual bounds for polynomial optimization problems. We consider Sums of Nonnegative Circuit (SONC) polynomials certificates, which are well suited for sparse problems since the computational cost depends only on the number of terms in the polynomials and does not depend on the degrees of the polynomials. This work is a first step to integrating SONC-based relaxations of polynomial problems into a branch-and-bound algorithm. To this end, the SONC relaxation for constrained optimization problems is extended in order to better utilize variable bounds, since this property is key for the success of a relaxation in the context of branch-and-bound. Computational experiments show that the proposed extension is crucial for making the SONC relaxations applicable to most constrained polynomial optimization problems and for integrating the two approaches. T3 - ZIB-Report - 22-23 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88306 SN - 1438-0064 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus T1 - Assessing transition rates as functions of environmental variables JF - The Journal of Chemical Physics N2 - We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require the sampling of the Grand Canonical Ensemble. For this purpose, we model the molecular system in terms of probable "scenarios", governed by different potential energy functions, which are separately sampled by classical MD simulations. Reweighting the canonical distribution of each scenario according to specific environmental variables, we estimate the grand canonical distribution, then we use the Square Root Approximation (SqRA) method to discretize the Fokker-Planck operator into a rate matrix and the robust Perron Cluster Cluster Analysis (PCCA+) method to coarse-grain the kinetic model. This permits to efficiently estimate the transition rates of conformational states as functions of environmental variables, for example, the local pH at a cell membrane. In this work we formalize the theoretical framework of the procedure and we present a numerical experiment comparing the results with those provided by a constant-pH method based on non-equilibrium Molecular Dynamics Monte Carlo simulations. The method is relevant for the development of new drug design strategies which take into account how the cellular environment influences biochemical processes. Y1 - 2022 U6 - https://doi.org/10.1063/5.0109555 VL - 157 IS - 22 SP - 224103-1 EP - 224103-14 PB - AIP Publishing ER - TY - GEN A1 - Klimpel, Paul ED - Lehnert, Katrin ED - Müller, Anja ED - Rauchut, Franziska ED - Salewski, Laura ED - Urgast, Steff T1 - In Bewegung. Die Rechtsfibel für Digitalisierungsprojekte in Kulturerbe-Einrichtungen N2 - Mitte 2021 bescherte die Urheberrechtsreform neue Chancen für den (offenen) Zugang zum kulturellen Erbe. Die Reform brachte wichtige Veränderungen der rechtlichen Rahmenbedingungen für die Digitalisierung des kulturellen Erbes mit sich. Der Schutz der Gemeinfreiheit für digitale Reproduktionen wurde festgeschrieben, neue Regelungen ermöglichen die Onlinestellung „nicht verfügbarer Werke“ durch öffentliche Einrichtungen des Kulturerbes und erstmals können nun auch in Deutschland erweiterte kollektive Lizenzen umgesetzt werden. Dr. Paul Klimpel (iRights Law) hat die Neuerungen des Urheber*innenrechtsgesetzes (UrhG) in dieser Publikation in den urheberrechtlichen Gesamtkontext eingeordnet. Die Rechtsfibel soll als Orientierungshilfe für die Mitarbeiter*innen in den Kulturinstitutionen dienen. Herausgeber*innen sind das Digitale Deutsche Frauenarchiv (DDF) und das Forschungs- und Kompetenzzentrum Digitalisierung Berlin (digiS). KW - 4062127-3 KW - 4002859-8 KW - 4006439-6 KW - 4040795-0 KW - 4136812-5 KW - 4129060-4 KW - 4233427-5 KW - 4045245-1 KW - 4120677-0 KW - 4011134-9 KW - 4142968-0 KW - 4006568-6 KW - 4045895-7 KW - 4522856-5 KW - 4013134-8 KW - 4067510-5 KW - 4008570-3 KW - 4033560-4 KW - 4123592-7 KW - 4123065-6 KW - 7659230-3 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86485 SN - 978-3-00-074039-8 ET - 1. Auflage ER - TY - CHAP A1 - Klug, Torsten A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Does Laziness Pay Off? - A Lazy-Constraint Approach to Timetabling T2 - 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022) N2 - Timetabling is a classical and complex task for public transport operators as well as for railway undertakings. The general question is: Which vehicle is taking which route through the transportation network in which order? In this paper, we consider the special setting to find optimal timetables for railway systems under a moving block regime. We directly set up on our work of [8 ], i.e., we consider the same model formulation and real-world instances of a moving block headway system. In this paper, we present a repair heuristic and a lazy-constraint approach utilizing the callback features of Gurobi, see [3]. We provide an experimental study of the different algorithmic approaches for a railway network with 100 and up to 300 train requests. The computational results show that the lazy-constraint approach together with the repair heuristic significantly improves our previous approaches. Y1 - 2022 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2022.11 VL - 106 SP - 11:1 EP - 11:8 PB - Schloss Dagstuhl -- Leibniz-Zentrum für Informatik ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Fujisawa, Katsuki A1 - Koch, Thorsten A1 - Nakao, Masahiro A1 - Shinano, Yuji T1 - Computing single-source shortest paths on graphs with over 8 trillion edges N2 - This paper introduces an implementation for solving the single-source shortest path problem on distributed-memory machines. It is tailored to power-law graphs and scales to trillions of edges. The new implementation reached 2nd and 10th place in the latest Graph500 benchmark in June 2022 and handled the largest and second-largest graphs among all participants. T3 - ZIB-Report - 22-22 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88180 SN - 1438-0064 ER - TY - GEN A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles N2 - Our theoretical study concerns an urea-urease-based pH oscillator confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the limit cycle, which controls the dynamics for giant vesicles and dominates the strongly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, amenable to analytic treatments, and show that the accuracy of predictions, including the period of oscillations, is highly sensitive to the choice of the reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The accurate description of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. T3 - ZIB-Report - 22-21 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88179 SN - 1438-0064 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Vertex Covering with Capacitated Trees JF - Networks N2 - The covering of a graph with (possibly disjoint) connected subgraphs is a funda-mental problem in graph theory. In this paper, we study a version to cover a graph’svertices by connected subgraphs subject to lower and upper weight bounds, and pro-pose a column generation approach to dynamically generate feasible and promisingsubgraphs. Our focus is on the solution of the pricing problem which turns out to bea variant of the NP-hard Maximum Weight Connected Subgraph Problem. We com-pare different formulations to handle connectivity, and find that a single-commodityflow formulation performs best. This is notable since the respective literature seemsto have widely dismissed this formulation. We improve it to a new coarse-to-fine flowformulation that is theoretically and computationally superior, especially for largeinstances with many vertices of degree 2 like highway networks, where it provides aspeed-up factor of 5 over the non-flow-based formulations. We also propose a pre-processing method that exploits a median property of weight-constrained subgraphs,a primal heuristic, and a local search heuristic. In an extensive computational studywe evaluate the presented connectivity formulations on different classes of instances,and demonstrate the effectiveness of the proposed enhancements. Their speed-upsessentially multiply to an overall factor of well over 10. Overall, our approach allowsthe reliable solution of instances with several hundreds of vertices in a few min-utes. These findings are further corroborated in a comparison to existing districtingmodels on a set of test instances from the literature Y1 - 2023 U6 - https://doi.org/10.1002/net.22130 VL - 81 IS - 2 SP - 253 EP - 277 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Jayaraj, Abhilash A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches JF - Current Opinion in Chemical Biology N2 - Virtual screening-based approaches to discover initial hit and lead compounds have the potential to reduce both the cost and time of early drug discovery stages, as well as to find inhibitors for even challenging target sites such as protein–protein interfaces. Here in this review, we provide an overview of the progress that has been made in virtual screening methodology and technology on multiple fronts in recent years. The advent of ultra-large virtual screens, in which hundreds of millions to billions of compounds are screened, has proven to be a powerful approach to discover highly potent hit compounds. However, these developments are just the tip of the iceberg, with new technologies and methods emerging to propel the field forward. Examples include novel machine-learning approaches, which can reduce the computational costs of virtual screening dramatically, while progress in quantum-mechanical approaches can increase the accuracy of predictions of various small molecule properties. Y1 - 2022 U6 - https://doi.org/10.1016/j.cbpa.2022.102156 VL - 69 SP - 102156 EP - 102156-12 ER - TY - CHAP A1 - Lindner, Niels A1 - van Lieshout, Rolf T1 - Benders Decomposition for the Periodic Event Scheduling Problem T2 - Operations Research Proceedings 2021 N2 - The Periodic Event Scheduling Problem (PESP) is the central mathematical model behind the optimization of periodic timetables in public transport. We apply Benders decomposition to the incidence-based MIP formulation of PESP. The resulting formulation exhibits particularly nice features: The subproblem is a minimum cost network flow problem, and feasibility cuts are equivalent to the well-known cycle inequalities by Odijk. We integrate the Benders approach into a branch-and-cut framework, and assess the performance of this method on instances derived from the benchmarking library PESPlib. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-08623-6_43 SP - 289 EP - 294 PB - Springer International Publishing CY - Cham ER - TY - GEN ED - D'Emidio, Mattia ED - Lindner, Niels T1 - 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022) N2 - OASIcs, Volume 106, ATMOS 2022, Complete Volume Y1 - 2022 SN - 978-3-95977-259-4 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2022 VL - 106 PB - Schloss Dagstuhl -- Leibniz-Zentrum für Informatik ER - TY - CHAP A1 - Bortoletto, Enrico A1 - Lindner, Niels A1 - Masing, Berenike T1 - Tropical Neighbourhood Search: A New Heuristic for Periodic Timetabling T2 - 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022) N2 - Periodic timetabling is a central aspect of both the long-term organization and the day-to-day operations of a public transportation system. The Periodic Event Scheduling Problem (PESP), the combinatorial optimization problem that forms the mathematical basis of periodic timetabling, is an extremely hard problem, for which optimal solutions are hardly ever found in practice. The most prominent solving strategies today are based on mixed-integer programming, and there is a concurrent PESP solver employing a wide range of heuristics [Borndörfer et al., 2020]. We present tropical neighborhood search (tns), a novel PESP heuristic. The method is based on the relations between periodic timetabling and tropical geometry [Bortoletto et al., 2022]. We implement tns into the concurrent solver, and test it on instances of the benchmarking library PESPlib. The inclusion of tns turns out to be quite beneficial to the solver: tns is able to escape local optima for the modulo network simplex algorithm, and the overall share of improvement coming from tns is substantial compared to the other methods available in the solver. Finally, we provide better primal bounds for five PESPlib instances. Y1 - 2022 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2022.3 VL - 106 SP - 3:1 EP - 3:19 ER - TY - GEN A1 - Fujii, Koichi A1 - Kim, Sunyoung A1 - Kojima, Masakazu A1 - Mittelmann, Hans D. A1 - Shinano, Yuji T1 - The Largest Unsolved QAP Instance Tai256c Can Be Converted into A 256-dimensional Simple BQOP with A Single Cardinality Constraint N2 - Tai256c is the largest unsolved quadratic assignment problem (QAP) instance in QAPLIB; a 1.48% gap remains between the best known feasible objective value and lower bound of the unknown optimal value. This paper shows that the instance can be converted into a 256 dimensional binary quadratic optimization problem (BQOP) with a single cardinality constraint which requires the sum of the binary variables to be 92.The converted BQOP is much simpler than the original QAP tai256c and it also inherits some of the symmetry properties. However, it is still very difficult to solve. We present an efficient branch and bound method for improving the lower bound effectively. A new lower bound with 1.36% gap is also provided. T3 - ZIB-Report - 22-18 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88086 SN - 1438-0064 ER - TY - JOUR A1 - Mohammadzadeh, Saeed A1 - H. Nascimento, Vítor A1 - C. de Lamare, Rodrigo A1 - Hajarolasvadi, Noushin T1 - Robust Beamforming Based on Complex-Valued Convolutional Neural Networks for Sensor Arrays JF - IEEE Signal Processing Letters N2 - Robust adaptive beamforming (RAB) plays a vital role in modern communications by ensuring the reception of high-quality signals. This article proposes a deep learning approach to robust adaptive beamforming. In particular, we propose a novel RAB approach where the sample covariance matrix (SCM) is used as the input of a deep 1D Complex-Valued Convolutional Neural Network (CVCNN). The network employs complex convolutional and pooling layers, as well as a Cartesian Scaled Exponential Linear Unit activation function to directly compute the nearly-optimum weight vector through the training process and without prior knowledge about the direction of arrival of the desired signal. This means that reconstruction of the interference plus noise (IPN) covariance matrix is not required. The trained CVCNN accurately computes the nearly-optimum weight vector for data not used during training. The computed weight vector is employed to estimate the signal-to-interference plus noise ratio. Simulations show that the proposed RAB can provide performance close to that of the optimal beamformer. Y1 - 2022 U6 - https://doi.org/10.1109/LSP.2022.3212637 VL - 29 SP - 2018 EP - 2021 ER - TY - GEN A1 - Petkovic, Milena A1 - Zakiyeva, Nazgul T1 - Mathematical Optimization for Analyzing and Forecasting Nonlinear Network Time Series N2 - This work presents an innovative short to mid-term forecasting model that analyzes nonlinear complex spatial and temporal dynamics in energy networks under demand and supply balance constraints using Network Nonlinear Time Series (TS) and Mathematical Programming (MP) approach. We address three challenges simultaneously, namely, the adjacency matrix is unknown; the total amount in the network has to be balanced; dependence is unnecessarily linear. We use a nonparametric approach to handle the nonlinearity and estimate the adjacency matrix under the sparsity assumption. The estimation is conducted with the Mathematical Optimisation method. We illustrate the accuracy and effectiveness of the model on the example of the natural gas transmission network of one of the largest transmission system operators (TSOs) in Germany, Open Grid Europe. The obtained results show that, especially for shorter forecasting horizons, the proposed method outperforms all considered benchmark models, improving the average nMAPE for 5.1% and average RMSE for 79.6% compared to the second-best model. The model is capable of capturing the nonlinear dependencies in the complex spatial-temporal network dynamics and benefits from both sparsity assumption and the demand and supply balance constraint. T3 - ZIB-Report - 22-19 KW - nonlinear time series KW - mathematical optimization KW - energy networks Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88037 SN - 1438-0064 ER - TY - JOUR A1 - Sechi, Renata A1 - Fackeldey, Konstantin A1 - Chewle, Surahit A1 - Weber, Marcus T1 - SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data JF - Algorithms N2 - This work addresses the problem of determining the number of components from sequential spectroscopic data analyzed by non-negative matrix factorization without separability assumption (SepFree NMF). These data are stored in a matrix M of dimension “measured times” versus “measured wavenumbers” and can be decomposed to obtain the spectral fingerprints of the states and their evolution over time. SepFree NMF assumes a memoryless (Markovian) process to underline the dynamics and decomposes M so that M=WH, with W representing the components’ fingerprints and H their kinetics. However, the rank of this decomposition (i.e., the number of physical states in the process) has to be guessed from pre-existing knowledge on the observed process. We propose a measure for determining the number of components with the computation of the minimal memory effect resulting from the decomposition; by quantifying how much the obtained factorization is deviating from the Markovian property, we are able to score factorizations of a different number of components. In this way, we estimate the number of different entities which contribute to the observed system, and we can extract kinetic information without knowing the characteristic spectra of the single components. This manuscript provides the mathematical background as well as an analysis of computer generated and experimental sequentially measured Raman spectra. Y1 - 2022 U6 - https://doi.org/10.3390/a15090297 VL - 15 IS - 9 SP - 297 ER - TY - CHAP A1 - Parczyk, Olaf A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Szabó, Tibor T1 - New Ramsey Multiplicity Bounds and Search Heuristics T2 - Discrete Mathematics Days N2 - We study two related problems concerning the number of monochromatic cliques in two-colorings of the complete graph that go back to questions of Erdős. Most notably, we improve the 25-year-old upper bounds of Thomason on the Ramsey multiplicity of K4 and K5 and we settle the minimum number of independent sets of size 4 in graphs with clique number at most 4. Motivated by the elusiveness of the symmetric Ramsey multiplicity problem, we also introduce an off-diagonal variant and obtain tight results when counting monochromatic K4 or K5 in only one of the colors and triangles in the other. The extremal constructions for each problem turn out to be blow-ups of a finite graph and were found through search heuristics. They are complemented by lower bounds and stability results established using Flag Algebras, resulting in a fully computer-assisted approach. More broadly, these problems lead us to the study of the region of possible pairs of clique and independent set densities that can be realized as the limit of some sequence of graphs. Y1 - 2022 ER - TY - JOUR A1 - Petkovic, Milena A1 - Zakiyeva, Nazgul T1 - Mathematical Optimization for Analyzing and Forecasting Nonlinear Network Time Series JF - Operations Research Proceedings 2022 N2 - This work presents an innovative short to mid-term forecasting model that analyzes nonlinear complex spatial and temporal dynamics in energy networks under demand and supply balance constraints using Network Nonlinear Time Series (TS) and Mathematical Programming (MP) approach. We address three challenges simultaneously, namely, the adjacency matrix is unknown; the total amount in the network has to be balanced; dependence is unnecessarily linear. We use a nonparametric approach to handle the nonlinearity and estimate the adjacency matrix under the sparsity assumption. The estimation is conducted with the Mathematical Optimisation method. We illustrate the accuracy and effectiveness of the model on the example of the natural gas transmission network of one of the largest transmission system operators (TSOs) in Germany, Open Grid Europe. The obtained results show that, especially for shorter forecasting horizons, proposed method outperforms all considered benchmark models, improving the avarage nMAPE for 5.1% and average RMSE for 79.6% compared to the second-best model. The model is capable to capture the nonlinear dependencies in the complex spatial-temporal network dynamics and benefits from both sparsity assumption and the demand and supply balance constraint. Y1 - 2022 ER - TY - CHAP A1 - Manley, Phillip A1 - Krüger, Jan A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Bodermann, Bernd A1 - Köning, Rainer A1 - Schneider, Philipp-Immanuel T1 - Elementary, my dear Zernike: model order reduction for accelerating optical dimensional microscopy T2 - EPJ Web Conf. Y1 - 2022 U6 - https://doi.org/10.1051/epjconf/202226610010 VL - 266 SP - 10010 ER - TY - CHAP A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Völker, Helena T1 - Strengthening SONC Relaxations with Constraints Derived from Variable Bounds T2 - Proceedings of the Hungarian Global Optimization Workshop HUGO 2022 N2 - Certificates of polynomial nonnegativity can be used to obtain tight dual bounds for polynomial optimization problems. We consider Sums of Nonnegative Circuit (SONC) polynomials certificates, which are well suited for sparse problems since the computational cost depends only on the number of terms in the polynomials and does not depend on the degrees of the polynomials. This work is a first step to integrating SONC-based relaxations of polynomial problems into a branch-and-bound algorithm. To this end, the SONC relaxation for constrained optimization problems is extended in order to better utilize variable bounds, since this property is key for the success of a relaxation in the context of branch-and-bound. Computational experiments show that the proposed extension is crucial for making the SONC relaxations applicable to most constrained polynomial optimization problems and for integrating the two approaches. Y1 - 2022 SP - 41 EP - 44 ER - TY - JOUR A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - Sawfish Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications JF - Adv. Opt. Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202301286 VL - 12 SP - 2301286 ER - TY - CHAP A1 - Krüger, Jan A1 - Manley, Phillip A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Köning, Rainer A1 - Bodermann, Bernd T1 - Untersuchung des Schwingungseinflusses auf gemessene Punktspreizfunktionen in der optischen Mikroskopie T2 - Proc. DGaO Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0287-2022-P005-6 SP - P5 ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Kuen, Lilli A1 - Sekuliĉ, Ivan A1 - Kluge, Julien A1 - Leykauf, Bastian A1 - Krutzik, Markus A1 - Burger, Sven T1 - Boosting quantum optics experiments with Bayesian optimization T2 - Proc. SPIE Y1 - 2022 U6 - https://doi.org/10.1117/12.2632419 VL - 12227 SP - 122270F ER - TY - JOUR A1 - Lücke, Marvin A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Molkethin, Nora A1 - Winkelmann, Stefanie T1 - Large population limits of Markov processes on random networks JF - Stochastic Processes and their Applications N2 - We consider time-continuous Markovian discrete-state dynamics on random networks of interacting agents and study the large population limit. The dynamics are projected onto low-dimensional collective variables given by the shares of each discrete state in the system, or in certain subsystems, and general conditions for the convergence of the collective variable dynamics to a mean-field ordinary differential equation are proved. We discuss the convergence to this mean-field limit for a continuous-time noisy version of the so-called "voter model" on Erdős-Rényi random graphs, on the stochastic block model, as well as on random regular graphs. Moreover, a heterogeneous population of agents is studied. For each of these types of interaction networks, we specify the convergence conditions in dependency on the corresponding model parameters. Y1 - 2023 U6 - https://doi.org/10.1016/j.spa.2023.09.007 VL - 166 ER - TY - CHAP A1 - Mayer, Julius A1 - Baum, Daniel A1 - Ambellan, Felix A1 - von Tycowicz, Christoph T1 - A Soft-Correspondence Approach to Shape-based Disease Grading with Graph Convolutional Networks T2 - Proceedings of Machine Learning Research N2 - Shape analysis provides principled means for understanding anatomical structures from medical images. The underlying notions of shape spaces, however, come with strict assumptions prohibiting the analysis of incomplete and/or topologically varying shapes. This work aims to alleviate these limitations by adapting the concept of soft correspondences. In particular, we present a graph-based learning approach for morphometric classification of disease states that is based on a generalized notion of shape correspondences in terms of functional maps. We demonstrate the performance of the derived classifier on the open-access ADNI database for differentiating normal controls and subjects with Alzheimer’s disease. Notably, our experiment shows that our approach can improve over state-of-the-art from geometric deep learning. Y1 - 2022 VL - 194 SP - 85 EP - 95 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Winkelmann, Stefanie A1 - Klein, Rupert A1 - Höfling, Felix T1 - Chemical diffusion master equation: formulations of reaction-diffusion processes on the molecular level JF - Journal of Mathematical Physics N2 - The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for reaction--diffusion processes. The CDME consists of an infinite ordered family of Fokker--Planck equations, where each level of the ordered family corresponds to a certain number of particles and each particle represents a molecule. The equations at each level describe the spatial diffusion of the corresponding set of particles, and they are coupled to each other via reaction operators --linear operators representing chemical reactions. These operators change the number of particles in the system, and thus transport probability between different levels in the family. In this work, we present three approaches to formulate the CDME and show the relations between them. We further deduce the non-trivial combinatorial factors contained in the reaction operators, and we elucidate the relation to the original formulation of the CDME, which is based on creation and annihilation operators acting on many-particle probability density functions. Finally we discuss applications to multiscale simulations of biochemical systems among other future prospects. Y1 - 2023 U6 - https://doi.org/10.1063/5.0129620 VL - 64 IS - 1 ER - TY - CHAP A1 - Bürger, Johanna A1 - Gundlach, Bastian A1 - Blum, Jürgen A1 - Hayne, Paul A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Lunar regolith properties derived from LRO/Diviner data and thermophysical modelling T2 - Europlanet Science Congress N2 - The Moon as our nearest celestial object is one of the most important bodies for space resource exploration and planetary science. However, knowledge of the physical properties of the lunar regolith is required for the exploitation of lunar resources and for understanding the Moon's geologic history. This knowledge comes mainly from Apollo in-situ experiments and returned samples, but the global distribution of these properties is still poorly understood. Remote sensing measurements offer the opportunity to derive properties of unsampled areas with the help of models. In our study, a microphysical thermal model for the lunar regolith was developed and the simulated surface temperatures were compared with thermal emission measurements from the Diviner radiometer on board the Lunar Reconnaissance Orbiter (LRO) to derive regolith properties. This work expands upon previous investigations of lunar regolith properties using Diviner data, by more directly simulating physical properties such as particle size and porosity. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-92 SP - EPSC2022-92 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - The Rosetta mission to comet 67P/C-G provided a detailed view of the near nucleus environment of an active Jupiter family comet. The continuous monitoring of the gas pressure with the ROSINA experiment at the location of the Rosetta spacecraft in combination with the images of the dust environment acquired by the OSIRIS cameras allows one to test different hypotheses about the origin of the dust and gas emissions. In addition the orbital elements and the rotation axis and spin rate of the nucleus are affected by the gas release. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-281 SP - EPSC2022-281 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Determination of the ice composition near the surface of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - During the apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G) solar irradiation causes varying rates for sublimation of volatile species from the cometary nucleus. Because sublimation processes take place close to the cometary surface, the relative abundance of volatiles in the coma and the ice composition are related to each other. To quantify this relation we assume a model for the expansion of a collisionless gas from the surface into the surrounding space. We use an inverse model approach to relate the in situ measurements of gas densities from the two Rosetta instruments COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) at the positions of the spacecraft to the locations of surface gas emissions during the Rosetta mission 2014-2016. We assume the temporally integrated gas emissions to be representative for the ice composition close to the surface. Our analysis shows characteristic differences in the ice compositions between both hemispheres of 67P/C-G. In particular CO2 ice has a reduced abundance on the northern hemisphere. In contrast to the hemispherical differences, the two lobes do not show significant differences in terms of their ice composition. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-826 SP - EPSC2022-826 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Rooted Maximum Weight Connected Subgraphs with Balancing and Capacity Constraints T2 - Proceedings of the 10th International Network Optimization Conference (INOC), Aachen, Germany, June 7–10, 2022 N2 - Finding connected subgraphs of maximum weight subject to additional constraints on the subgraphs is a common (sub)problem in many applications. In this paper, we study the Maximum Weight Connected Subgraph Problem with a given root node and a lower and upper capacity constraint on the chosen subgraph. In addition, the nodes of the input graph are colored blue and red, and the chosen subgraph is required to be balanced regarding its cumulated blue and red weight. This problem arises as an essential subproblem in district planning applications. We show that the problem is NP-hard and give an integer programming formulation. By exploiting the capacity and balancing condition, we develop a powerful reduction technique that is able to significantly shrink the problem size. In addition, we propose a method to strengthen the LP relaxation of our formulation by identifying conflict pairs, i.e., nodes that cannot be both part of a chosen subgraph. Our computational study confirms the positive impact of the new preprocessing technique and of the proposed conflict cuts. Y1 - 2022 U6 - https://doi.org/10.48786/inoc.2022.12 SP - 63 EP - 68 ER - TY - GEN T1 - Annual Report 2021 T3 - Jahresbericht - 2021 KW - Jahresbericht Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87537 SN - 0934-5892 VL - 2021 ER - TY - GEN A1 - Yueksel-Erguen, Inci A1 - Most, Dieter A1 - Wyrwoll, Lothar A1 - Schmitt, Carlo A1 - Zittel, Janina T1 - Modeling the transition of the multimodal pan-European energy system including an integrated analysis of electricity and gas transport N2 - The European energy system has been through a fundamental transformation since the Paris Agreement to reduce greenhouse gas emissions. The transition involves several energy-generating and consuming sectors emphasizing sector coupling. The increase in the share of renewable energy sources has revealed the need for flexibility in the electri city grid. Thus, holistic planning of pathways towards decarbonized energy systems also involves assessing the gas infrastructure to provide such a flexibility and support for the security of supply. In this paper, we propose a workflow to investigate such optimal energy transition pathways considering sector coupling. This workflow involves an integrated operational analysis of the electricity market, its transmission grid, and the gas grid in high spatio-temporal resolution. In a case study on a pan-European scale between 2020-2050, we show that carbon neutrality can be reached within feasible additional costs and in time. However, the manifestation of the potential pathways strongly depends on political and technological constraints. Sector coupling acts as an enabler of cross-border cooperation to achieve both, decarbonization and security of supply. T3 - ZIB-Report - 22-17 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87774 SN - 1438-0064 ER - TY - CHAP A1 - Euler, Ricardo A1 - Borndörfer, Ralf A1 - Strunk, Timo A1 - Takkula, Tuomo T1 - ULD Build-Up Scheduling with Dynamic Batching in an Air Freight Hub T2 - Operations Research Proceedings 2021 N2 - Air freight is usually shipped in standardized unit load devices (ULDs). The planning process for the consolidation of transit cargo from inbound flights or locally emerging shipments into ULDs for outbound flights is called build-up scheduling. More specifically, outbound ULDs must be assigned a time and a workstation subject to both workstation capacity constraints and the availability of shipments which in turn depends on break-down decisions for incoming ULDs. ULDs scheduled for the same outbound flight should be built up in temporal and spatial proximity. This serves both to minimize overhead in transportation times and to allow workers to move freight between ULDs. We propose to address this requirement by processing ULDs for the same outbound flight in batches. For the above build-up scheduling problem, we introduce a multi-commodity network design model. Outbound flights are modeled as commodities; transit cargo is represented by cargo flow volume and unpack and batch decisions are represented as design variables. The model is solved with a standard MIP solver on a set of benchmark data. For instances with a limited number of resource conflicts, near-optimal solutions are found in under two hours for a whole week of operations. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-08623-6_38 SP - 254 EP - 260 ER - TY - THES A1 - Franz, Henriette T1 - Connected Subgraphs with Budget Constraints: Formulations and Algorithms Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87792 ER - TY - CHAP A1 - Prodanov, Dimiter A1 - Vohra, Sumit Kumar T1 - Active Segmentation: Differential Geometry meets Machine Learning T2 - Proceedings of the 23rd International Conference on Computer Systems and Technologies N2 - Image segmentation is an active area of research for more than 30 years. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. This paper presents a project supported in part by the International Neuroinformatics Coordination Facility through the Google Summer of code. The project resulted in an automated image segmentation and classification platform, called Active Segmentation for ImageJ (AS/IJ). The platform integrates a set of filters computing differential geometrical invariants and combines them with machine learning approaches. Y1 - 2022 U6 - https://doi.org/10.1145/3546118.3546154 SP - 1 EP - 6 ER - TY - JOUR A1 - Becker, Kaitlyn P A1 - Teeple, Clark A1 - Charles, Nicholas A1 - Jung, Yeonsu A1 - Baum, Daniel A1 - Weaver, James C A1 - Mahadevan, L. A1 - Wood, Robert J T1 - Active entanglement enables stochastic, topological grasping JF - PNAS N2 - Grasping, in both biological and engineered mechanisms, can be highly sensitive to the gripper and object morphology, as well as perception and motion planning. Here we circumvent the need for feedback or precise planning by using an array of fluidically-actuated slender hollow elastomeric filaments to actively entangle with objects that vary in geometric and topological complexity. The resulting stochastic interactions enable a unique soft and conformable grasping strategy across a range of target objects that vary in size, weight, and shape. We experimentally evaluate the grasping performance of our strategy, and use a computational framework for the collective mechanics of flexible filaments in contact with complex objects to explain our findings. Overall, our study highlights how active collective entanglement of a filament array via an uncontrolled, spatially distributed scheme provides new options for soft, adaptable grasping. Y1 - 2022 U6 - https://doi.org/10.1073/pnas.2209819119 VL - 119 IS - 42 SP - e2209819119 ER - TY - JOUR A1 - Glatzeder, Korbinian A1 - Komnik, Igor A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Potthast, Wolfgang T1 - Dynamic pressure analysis of novel interpositional knee spacer implants in 3D-printed human knee models JF - Scientific Reports N2 - Alternative treatment methods for knee osteoarthritis (OA) are in demand, to delay the young (< 50 Years) patient’s need for osteotomy or knee replacement. Novel interpositional knee spacers shape based on statistical shape model (SSM) approach and made of polyurethane (PU) were developed to present a minimally invasive method to treat medial OA in the knee. The implant should be supposed to reduce peak strains and pain, restore the stability of the knee, correct the malalignment of a varus knee and improve joint function and gait. Firstly, the spacers were tested in artificial knee models. It is assumed that by application of a spacer, a significant reduction in stress values and a significant increase in the contact area in the medial compartment of the knee will be registered. Biomechanical analysis of the effect of novel interpositional knee spacer implants on pressure distribution in 3D-printed knee model replicas: the primary purpose was the medial joint contact stress-related biomechanics. A secondary purpose was a better understanding of medial/lateral redistribution of joint loading. Six 3D printed knee models were reproduced from cadaveric leg computed tomography. Each of four spacer implants was tested in each knee geometry under realistic arthrokinematic dynamic loading conditions, to examine the pressure distribution in the knee joint. All spacers showed reduced mean stress values by 84–88% and peak stress values by 524–704% in the medial knee joint compartment compared to the non-spacer test condition. The contact area was enlarged by 462–627% as a result of the inserted spacers. Concerning the appreciable contact stress reduction and enlargement of the contact area in the medial knee joint compartment, the premises are in place for testing the implants directly on human knee cadavers to gain further insights into a possible tool for treating medial knee osteoarthritis. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-20463-6 VL - 12 ER - TY - CHAP A1 - Christgau, Steffen A1 - Knaust, Marius A1 - Steinke, Thomas T1 - A First Step towards Support for MPI Partitioned Communication on SYCL-programmed FPGAs T2 - IEEE/ACM International Workshop on Heterogeneous High-performance Reconfigurable Computing, H2RC@SC 2022, Dallas, TX, USA, November 13-18, 2022 N2 - Version 4.0 of the Message Passing Interface standard introduced the concept of Partitioned Communication which adds support for multiple contributions to a communication buffer. Although initially targeted at multithreaded MPI applications, Partitioned Communication currently receives attraction in the context of accelerators, especially GPUs. In this publication it is demonstrated that this communication concept can also be implemented for SYCL-programmed FPGAs. This includes a discussion of the design space and the presentation of a prototypical implementation. Experimental results show that a lightweight implementation on top of an existing MPI library is possible. In addition, the presented approach also reveals issues in both the SYCL and the MPI standard which need to be addresses for improved support of the intended communication style. Y1 - 2022 U6 - https://doi.org/10.1109/H2RC56700.2022.00007 SP - 9 EP - 17 PB - IEEE ER - TY - JOUR A1 - Rej, Sourav A1 - Santiago, Eva Yazmin A1 - Baturina, Olga A1 - Zhang, Yu A1 - Burger, Sven A1 - Kment, Stepan A1 - Govorov, Alexander O. A1 - Naldoni, Alberto T1 - Colloidal Titanium Nitride Nanobars for Broadband Inexpensive Plasmonics and Photochemistry from Visible to Mid-IR Wavelengths JF - Nano Energy Y1 - 2022 U6 - https://doi.org/10.1016/j.nanoen.2022.107989 VL - 104 SP - 107989 ER - TY - JOUR A1 - Ramos Leite, Tiago A1 - Zschiedrich, Lin A1 - Kizilkaya, Orhan A1 - McPeak, Kevin M. T1 - Resonant Plasmonic–Biomolecular Chiral Interactions in the Far-Ultraviolet: Enantiomeric Discrimination of sub-10 nm Amino Acid Films JF - Nano Lett. Y1 - 2022 UR - https://digitalcommons.lsu.edu/chem_engineering_pubs/34/ U6 - https://doi.org/10.1021/acs.nanolett.2c01724 VL - 22 SP - 7343 ER - TY - JOUR A1 - Schmitt, Kira A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Polyp-Cavity Segmentation of Cold-Water Corals guided by Ambient Occlusion and Ambient Curvature JF - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - The segmentation of cavities in three-dimensional images of arbitrary objects is a difficult problem since the cavities are usually connected to the outside of the object without any difference in image intensity. Hence, the information whether a voxel belongs to a cavity or the outside needs to be derived from the ambient space. If a voxel is enclosed by object material, it is very likely that this voxel belongs to a cavity. However, there are dense structures where a voxel might still belong to the outside even though it is surrounded to a large degree by the object. This is, for example, the case for coral colonies. Therefore, additional information needs to be considered to distinguish between those cases. In this paper, we introduce the notion of ambient curvature, present an efficient way to compute it, and use it to segment coral polyp cavities by integrating it into the ambient occlusion framework. Moreover, we combine the ambient curvature with other ambient information in a Gaussian mixture model, trained from a few user scribbles, resulting in a significantly improved cavity segmentation. We showcase the superiority of our approach using four coral colonies of very different morphological types. While in this paper we restrict ourselves to coral data, we believe that the concept of ambient curvature is also useful for other data. Furthermore, our approach is not restricted to curvature but can be easily extended to exploit any properties given on an object's surface, thereby adjusting it to specific applications. Y1 - 2022 U6 - https://doi.org/10.2312/vcbm.20221189 ER - TY - CHAP A1 - Harth, Philipp A1 - Vohra, Sumit A1 - Udvary, Daniel A1 - Oberlaender, Marcel A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - A Stratification Matrix Viewer for Analysis of Neural Network Data T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - The analysis of brain networks is central to neurobiological research. In this context the following tasks often arise: (1) understand the cellular composition of a reconstructed neural tissue volume to determine the nodes of the brain network; (2) quantify connectivity features statistically; and (3) compare these to predictions of mathematical models. We present a framework for interactive, visually supported accomplishment of these tasks. Its central component, the stratification matrix viewer, allows users to visualize the distribution of cellular and/or connectional properties of neurons at different levels of aggregation. We demonstrate its use in four case studies analyzing neural network data from the rat barrel cortex and human temporal cortex. Y1 - 2022 U6 - https://doi.org/10.2312/vcbm.20221194 CY - Vienna, Austria ER - TY - JOUR A1 - Hajarolasvadi, Noushin A1 - Sunkara, Vikram A1 - Khavnekar, Sagar A1 - Beck, Florian A1 - Brandt, Robert A1 - Baum, Daniel T1 - Volumetric macromolecule identification in cryo-electron tomograms using capsule networks JF - BMC Bioinformatics N2 - Background: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macro- molecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. Results: We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an F1−score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the F1-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an F1-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better F1-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the F1-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. Conclusion: Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macro- molecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet. Y1 - 2022 U6 - https://doi.org/10.1186/s12859-022-04901-w VL - 23 IS - 360 ER - TY - CHAP A1 - Dhanakoti, Siva Prasad Chakri A1 - Maddocks, John A1 - Weiser, Martin T1 - Navigation of Concentric Tube Continuum Robots using Optimal Control T2 - Proceedings of the 19th International Conference on Informatics in Control, Automation and Robotics N2 - Recently developed Concentric Tube Continuum Robots (CTCRs) are widely exploited in, for example in minimally invasive surgeries which involve navigating inside narrow body cavities close to sensitive regions. These CTCRs can be controlled by extending and rotating the tubes in order to reach a target point or perform some task. The robot must deviate as little as possible from this narrow space and avoid damaging neighbouring tissue. We consider \emph{open-loop} optimal control of CTCRs parameterized over pseudo-time, primarily aiming at minimizing the robot's working volume during its motion. External loads acting on the system like tip loads or contact with tissues are not considered here. We also discussed the inclusion of tip's orientation in the optimal framework to perform some tasks. We recall a quaternion-based formulation of the robot configuration, discuss discretization, develop optimization objectives addressing different criteria, and investigate their impact on robot path planning for several numerical examples. This optimal framework can be applied to any backbone based continuum robots. Y1 - 2022 U6 - https://doi.org/10.5220/0011271000003271 SP - 146 EP - 154 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian T1 - Large-Scale Performance of the Data-Flow Scheduler (DFS) and FLESnet JF - CBM Progress Report 2021 Y1 - 2022 U6 - https://doi.org/10.15120/GSI-2022-00599 SP - 170 EP - 171 ER - TY - JOUR A1 - Bartels, Tinko A1 - Fisikopoulos, Vissarion A1 - Weiser, Martin T1 - Fast Floating-Point Filters for Robust Predicates JF - BIT Numerical Mathematics N2 - Geometric predicates are at the core of many algorithms, such as the construction of Delaunay triangulations, mesh processing and spatial relation tests. These algorithms have applications in scientific computing, geographic information systems and computer-aided design. With floating-point arithmetic, these geometric predicates can incur round-off errors that may lead to incorrect results and inconsistencies, causing computations to fail. This issue has been addressed using a combination of exact arithmetic for robustness and floating-point filters to mitigate the computational cost of exact computations. The implementation of exact computations and floating-point filters can be a difficult task, and code generation tools have been proposed to address this. We present a new C++ meta-programming framework for the generation of fast, robust predicates for arbitrary geometric predicates based on polynomial expressions. We combine and extend different approaches to filtering, branch reduction, and overflow avoidance that have previously been proposed. We show examples of how this approach produces correct results for data sets that could lead to incorrect predicate results with naive implementations. Our benchmark results demonstrate that our implementation surpasses state-of-the-art implementations. Y1 - 2023 U6 - https://doi.org/10.1007/s10543-023-00975-x VL - 63 ER - TY - JOUR A1 - Beron-Vera, Francisco Javier A1 - Olascoaga, Maria Josefina A1 - Helfmann, Luzie A1 - Miron, Philippe T1 - Sampling-Dependent Transition Paths of Iceland-Scotland Overflow Water JF - Journal of Physical Oceanography N2 - In this note, we apply Transition Path Theory (TPT) from Markov chains to shed light on the problem of Iceland-Scotland Overflow Water (ISOW) equatorward export. A recent analysis of observed trajectories of submerged floats demanded revision of the traditional abyssal circulation theory, which postulates that ISOW should steadily flow along a deep boundary current (DBC) around the subpolar North Atlantic prior to exiting it. The TPT analyses carried out here allow to focus the attention on the portions of flow from the origin of ISOW to the region where ISOW exits the subpolar North Atlantic and suggest that insufficient sampling may be biasing the aforementioned demand. The analyses, appropriately adapted to represent a continuous input of ISOW, are carried out on three time-homogeneous Markov chains modeling the ISOW flow. One is constructed using a high number of simulated trajectories homogeneously covering the flow domain. The other two use much fewer trajectories which heterogeneously cover the domain. The trajectories in the latter two chains are observed trajectories or simulated trajectories subsampled at the observed frequency. While the densely sampled chain supports a well-defined DBC, the more heterogeneously sampled chains do not, irrespective of whether observed or simulated trajectories are used. Studying the sampling sensitivity of the Markov chains, we can give recommendations for enlarging the existing float dataset to improve the significance of conclusions about time-asymptotic aspects of the ISOW circulation. Y1 - 2023 U6 - https://doi.org/10.1175/JPO-D-22-0172.1 VL - 53 IS - 4 SP - 1151 EP - 1160 ER - TY - GEN A1 - Clarner, Jan-Patrick A1 - Tawfik, Christine A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Network-induced Unit Commitment - A model class for investment and production portfolio planning for multi-energy systems N2 - In light of the energy transition production planning of future decarbonized energy systems lead to very large and complex optimization problems. A widely used modeling paradigm for modeling and solving such problems is mathematical programming. While there are various scientific energy system models and modeling tools, most of them do not provide the necessary level of detail or the modeling flexibility to be applicable for industrial usage. Industrial modeling tools, on the other hand, provide a high level of detail and modeling flexibility. However, those models often exhibit a size and complexity that restricts their scope to a time horizon of several months, severely complicating long-term planning. As a remedy, we propose a model class that is detailed enough for real-world usage but still compact enough for long-term planning. The model class is based on a generalized unit commitment problem on a network with investment decisions. The focus lies on the topological dependency of different energy production and transportation units. T3 - ZIB-Report - 22-16 KW - Multi-energy systems KW - Unit commitment KW - Investment planning Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87607 SN - 1438-0064 ER - TY - JOUR A1 - Hosada, Junko A1 - Maher, Stephen A1 - Shinano, Yuji A1 - Villumsen, Jonas Christoffer T1 - Location, transshipment and routing: An adaptive transportation network integrating long-haul and local vehicle routing JF - EURO Journal on Transportation and Logistics Y1 - 2022 U6 - https://doi.org/10.1016/j.ejtl.2022.100091 VL - 11 PB - Elsevier ER - TY - JOUR A1 - Frank, Anna-Simone A1 - Sikorski, Alexander A1 - Röblitz, Susanna T1 - Spectral clustering of Markov chain transition matrices with complex eigenvalues JF - Journal of Computational and Applied Mathematics N2 - The Robust Perron Cluster Analysis (PCCA+) has become a popular spectral clustering algorithm for coarse-graining transition matrices of nearly decomposable Markov chains with transition states. Originally developed for reversible Markov chains, the algorithm only worked for transition matrices with real eigenvalues. In this paper, we therefore extend the theoretical framework of PCCA+ to Markov chains with a complex eigen-decomposition. We show that by replacing a complex conjugate pair of eigenvectors by their real and imaginary components, a real representation of the same subspace is obtained, which is suitable for the cluster analysis. We show that our approach leads to the same results as the generalized PCCA+ (GPCCA), which replaces the complex eigen-decomposition by a conceptually more difficult real Schur decomposition. We apply the method on non-reversible Markov chains, including circular chains, and demonstrate its efficiency compared to GPCCA. The experiments are performed in the Matlab programming language and codes are provided. Y1 - 2024 U6 - https://doi.org/10.1016/j.cam.2024.115791 VL - 444 SP - 115791 ER - TY - GEN A1 - Pedersen, Jaap A1 - Le, Thi Thai A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Optimal discrete pipe sizing for tree-shaped CO2 networks N2 - While energy-intensive industries like the steel industry plan to switch to renewable energy sources, other industries, such as the cement industry, have to rely on carbon capture storage and utilization technologies to reduce the inevitable carbon dioxide (CO2) emissions of their production processes. In this context, we investigate the problem of finding optimal pipeline diameters from a discrete set of diameters for a tree-shaped network transporting captured CO2 from multiple sources to a single sink. The general problem of optimizing arc capacities in potential-based fluid networks is a challenging mixed-integer nonlinear program. Additionally, the behaviour of CO2 is highly sensitive and nonlinear regarding temperature and pressure changes. We propose an iterative algorithm splitting the problem into two parts: a) the pipe-sizing problem under a fixed supply scenario and temperature distribution and b) the thermophysical modelling including mixing effects, the Joule-Thomson effect, and heat exchange with the surrounding environment. We show the effectiveness of our approach by applying our algorithm to a real-world network planning problem for a CO2 network in Western Germany. T3 - ZIB-Report - 22-15 KW - CO2 Transport KW - Network Design KW - Pipeline Sizing Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87574 SN - 1438-0064 ER - TY - GEN A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Source code and simulation data for Computation of eigenfrequency sensitivities using Riesz projections for efficient optimization of nanophotonic resonators T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.6614951 ER - TY - GEN A1 - Plock, Matthias A1 - Andrle, Kas A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Research data and example scripts for the paper "Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction" T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.6359594 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Zumbansen, Maximilian A1 - Weber, Marcus T1 - Parameter estimation on multivalent ITC data sets JF - Scientific Reports N2 - The Wiseman fitting can be used to extract binding parameters from ITC data sets, such as heat of binding, number of binding sites, and the overall dissociation rate. The classical Wiseman fitting assumes a direct binding process and neglects the possibility of intermediate binding steps. In principle, it only provides thermodynamic information and not the kinetics of the process. In this article we show that a concentration dependent dissociation constant could possibly stem from intermediate binding steps. The mathematical form of this dependency can be exploited with the aid of the Robust Perron Cluster Cluster Analysis method. Our proposed extension of the Wiseman fitting rationalizes the concentration dependency, and can probably also be used to determine the kinetic parameters of intermediate binding steps of a multivalent binding process. The novelty of this paper is to assume that the binding rate varies per titration step due to the change of the ligand concentration and to use this information in the Wiseman fitting. We do not claim to produce the most accurate values of the binding parameters, we rather present a novel method of how to approach multivalent bindings from a different angle. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17188-x VL - 12 SP - 13402 ER - TY - CHAP A1 - Rickert, Lucas A1 - Gao, Timm A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Heindel, Tobias T1 - A Plug&Play Telecom-Wavelength Single-Photon Source for Quantum Key Distribution T2 - Quantum 2.0 Y1 - 2022 U6 - https://doi.org/10.1364/QUANTUM.2022.QTu4C.6 SP - QTu4C.6 ER - TY - THES A1 - Helfmann, Luzie T1 - Non-stationary Transition Path Theory with applications to tipping and agent-based models N2 - The interesting dynamical regimes in agent-based models (ABMs) of social dynamics are the transient dynamics leading to metastable or absorbing states, and the transition paths between metastable states possibly caused by external influences. In this thesis, we are particularly interested in the pathways of rare and critical transitions such as the tipping of the public opinion in a population or the forming of social movements. For a detailed quantitative analysis of these transition paths, we consider the agent-based models as Markov chains and employ Transition Path Theory. Since ABMs are usually not considered in stationarity and possibly even forced, we generalize Transition Path Theory to time-dependent dynamics, for example on finite-time intervals or with periodically varying transition probabilities. We also specifically consider the case of dynamics with absorbing states and show how the transitions prior to absorption can be studied. These generalizations can also be useful in other application domains such as for studying tipping in climate models or transitions in molecular models with external stimuli. Another obstacle when analysing the dynamics of agent-based models is the large number of agents resulting in a high-dimensional state space for the model. However, the emergent dynamics of the ABM usually has significantly fewer degrees of freedom and many symmetries enabling a model reduction. On the example of two stationary ABMs we demonstrate how a long model simulation can be employed to find a lower-dimensional parametrization of the state space using a manifold learning algorithm called Diffusion Maps. In the considered models, agents adapt their binary behaviour to the local neighbourhood. When the interaction network consists of several densely connected communities, the dynamics result in a largely coherent behaviour in each community. The low-dimensional structure of the state space is therefore a hypercube. The corners represent metastable states with coherent agent behaviour in each group and the edges correspond to transition paths where agents in a community change their behaviour through a chain reaction. Finally, we can apply Transition Path Theory to the effective dynamics in the reduced space to reveal, for example, the dominant transition paths or the agents that are most indicative of an impending tipping event. Y1 - 2022 UR - https://refubium.fu-berlin.de/handle/fub188/35660 U6 - https://doi.org/http://dx.doi.org/10.17169/refubium-35374 ER - TY - JOUR A1 - Kiewisz, Robert A1 - Fabig, Gunar A1 - Conway, William A1 - Baum, Daniel A1 - Needleman, Daniel A1 - Müller-Reichert, Thomas T1 - Three-dimensional structure of kinetochore-fibers in human mitotic spindles JF - eLife N2 - During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells. Y1 - 2022 U6 - https://doi.org/10.7554/eLife.75459 VL - 11 SP - e75459 ER - TY - JOUR A1 - Caputo, Ariel A1 - Emporio, Marco A1 - Giachetti, Andrea A1 - Cristani, Marco A1 - Borghi, Guido A1 - D'Eusanio, Andrea A1 - Le, Minh-Quan A1 - Nguyen, Hai-Dang A1 - Tran, Minh-Triet A1 - Ambellan, Felix A1 - Hanik, Martin A1 - Navayazdani, Esfandiar A1 - Tycowicz, Christoph von T1 - SHREC 2022 Track on Online Detection of Heterogeneous Gestures JF - Computers and Graphics N2 - This paper presents the outcomes of a contest organized to evaluate methods for the online recognition of heterogeneous gestures from sequences of 3D hand poses. The task is the detection of gestures belonging to a dictionary of 16 classes characterized by different pose and motion features. The dataset features continuous sequences of hand tracking data where the gestures are interleaved with non-significant motions. The data have been captured using the Hololens 2 finger tracking system in a realistic use-case of mixed reality interaction. The evaluation is based not only on the detection performances but also on the latency and the false positives, making it possible to understand the feasibility of practical interaction tools based on the algorithms proposed. The outcomes of the contest's evaluation demonstrate the necessity of further research to reduce recognition errors, while the computational cost of the algorithms proposed is sufficiently low. Y1 - 2022 U6 - https://doi.org/10.1016/j.cag.2022.07.015 VL - 107 SP - 241 EP - 251 ER - TY - JOUR A1 - Berthold, Timo A1 - Mexi, Gioni A1 - Salvagnin, Domenico T1 - Using Multiple Reference Vectors and Objective Scaling in the Feasibility Pump JF - EURO Journal on Computational Optimization N2 - The Feasibility Pump (FP) is one of the best-known primal heuristics for mixed-integer programming (MIP): more than 15 papers suggested various modifications of all of its steps. So far, no variant considered information across multiple iterations, but all instead maintained the principle to optimize towards a single reference integer point. In this paper, we evaluate the usage of multiple reference vectors in all stages of the FP algorithm. In particular, we use LP-feasible vectors obtained during the main loop to tighten the variable domains before entering the computationally expensive enumeration stage. Moreover, we consider multiple integer reference vectors to explore further optimizing directions and introduce alternative objective scaling terms to balance the contributions of the distance functions and the original MIP objective. Our computational experiments demonstrate that the new method can improve performance on general MIP test sets. In detail, our modifications provide a 29.3% solution quality improvement and 4.0% running time improvement in an embedded setting, needing 16.0% fewer iterations over a large test set of MIP instances. In addition, the method’s success rate increases considerably within the first few iterations. In a standalone setting, we also observe a moderate performance improvement, which makes our version of FP suitable for the two main use-cases of the algorithm. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87392 VL - 11 ER - TY - GEN A1 - Bortoletto, Enrico A1 - Lindner, Niels A1 - Masing, Berenike T1 - Tropical Neighbourhood Search: A New Heuristic for Periodic Timetabling N2 - Periodic timetabling is a central aspect of both the long-term organization and the day-to-day operations of a public transportation system. The Periodic Event Scheduling Problem (PESP), the combinatorial optimization problem that forms the mathematical basis of periodic timetabling, is an extremely hard problem, for which optimal solutions are hardly ever found in practice. The most prominent solving strategies today are based on mixed-integer programming, and there is a concurrent PESP solver employing a wide range of heuristics [3]. We present tropical neighborhood search (tns), a novel PESP heuristic. The method is based on the relations between periodic timetabling and tropical geometry [4]. We implement tns into the concurrent solver, and test it on instances of the benchmarking library PESPlib. The inclusion of tns turns out to be quite beneficial to the solver: tns is able to escape local optima for the modulo network simplex algorithm, and the overall share of improvement coming from tns is substantial compared to the other methods available in the solver. Finally, we provide better primal bounds for five PESPlib instances. T3 - ZIB-Report - 22-13 KW - Periodic Timetabling KW - Tropical Geometry KW - Neighbourhood Search KW - Mixed-Integer Programming Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87385 SN - 1438-0064 ER - TY - GEN A1 - Paskin, Martha A1 - Baum, Daniel A1 - Dean, Mason N. A1 - von Tycowicz, Christoph T1 - A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks -- Source Code and Data N2 - Source code and novel dataset of basking shark head skeletons facilitating the reproduction of the results presented in 'A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks' - ECCV 2022. Y1 - 2022 U6 - https://doi.org/10.12752/8730 ER - TY - THES A1 - Niemann, Jan-Hendrik T1 - Learning Reduced Models for Large-Scale Agent-Based Systems N2 - Modeling social systems and studying their dynamical behavior plays an important role in many fields of research. Agent-based modeling provides a high degree of detail into artificial societies by describing the model from the perspective of the agents. The interactions of agents, often characterized by simple rules, lead to complex, time-evolving patterns. Their understanding is of great importance, e.g., for predicting and influencing epidemics. Analysis and simulation, however, often becomes prohibitively time-consuming when the number of agents or the time scale of interest is large. Therefore, this thesis is devoted to learn significantly reduced models of large-scale agent-based systems from simulation data. We show how data-driven methods based on transfer operators can be used to find reduced models represented by ordinary or stochastic differential equations that describe the dynamical behavior of larger groups or entire populations and thus enable the analysis and prediction of agent-based systems. To this end, we first present an extension of EDMD (extended dynamic mode decomposition) called gEDMD to approximate the Koopman generator from data. This method can be used to compute eigenfunctions, eigenvalues, and modes of the generator, as well as for system identification and model reduction of both deterministic and non-deterministic dynamical systems. Secondly, we analyze the long-term behavior of certain agent-based models and their pathwise approximations by stochastic differential equations for large numbers of agents using transfer operators. We show that, under certain conditions, the transfer operator approach connects the pathwise approximations on finite time scales with methods for describing the behavior on possibly exponentially long time scales. As a consequence, we can use the finite-time, pathwise approximations to characterize metastable behavior on long time scales using transfer operators. This can significantly reduce the computational cost. The third part addresses the data-driven model reduction since in many cases no analytical limit models are known or existent. We show how the Koopman operator theory can be used to infer the governing equations of agent-based systems directly from simulation data. Using benchmark problems, we demonstrate that for sufficiently large population sizes the data-driven models agree well with analytical limit equations and, moreover, that the reduced models allow predictions even in cases far from the limit or when no limit equations are known. Lastly, we demonstrate the potential of the presented approach. We present an ansatz for the multi-objective optimization of agent-based systems with the help of data-driven surrogate models based on the Koopman generator. In particular, when limit models are unknown or non-existent, this approach makes multi-objective optimization problems solvable that would otherwise be computationally infeasible due to very expensive objective functions. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-refubium-35530-6 UR - https://refubium.fu-berlin.de/handle/fub188/35530 ER - TY - GEN A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Burger, Sven A1 - Naydenov, Boris T1 - Scripts for quantifying the effect of diamond nano-pillars on the fluorescence of NV centers T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.6558815 ER - TY - JOUR A1 - Lopez-Fraguas, Eduardo A1 - Binkowski, Felix A1 - Burger, Sven A1 - Hagedorn, Sylvia A1 - Garcia-Camara, Braulio A1 - Vergaz, Ricardo A1 - Becker, Christiane A1 - Manley, Phillip T1 - Tripling the light extraction efficiency of a deep ultraviolet LED using a nanostructured p-contact JF - Sci. Rep. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-15499-7 VL - 12 SP - 11480 ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Ehrenfest dynamics implemented in the all-electron package exciting JF - Electron. Struct. N2 - Ehrenfest dynamics combined with real-time time-dependent density functional theory has proven to be a reliable tool to study non-adiabatic molecular dynamics with a reasonable computational cost. Among other possibilities, it allows for assessing in real time electronic excitations generated by ultra-fast laser pulses, as e.g., in pump–probe spectroscopy, and their coupling to the nuclear vibrations even beyond the linear regime. In this work, we present its implementation in the all-electron full-potential package exciting. Three cases are presented as examples: diamond and cubic boron nitride (BN) relaxed after an initial lattice distortion, and cubic BN exposed to a laser pulse. Comparison with the Octopus code exhibits good agreement. Y1 - 2022 U6 - https://doi.org/10.1088/2516-1075/ac7afc VL - 4 SP - 037001 ER - TY - JOUR A1 - Wang, Yujing A1 - Vannucci, Luca A1 - Burger, Sven A1 - Gregersen, Niels T1 - Near-unity efficiency in ridge waveguide-based, on-chip single-photon sources JF - Mater. Quantum Technol. Y1 - 2022 U6 - https://doi.org/10.1088/2633-4356/aca8e8 VL - 2 SP - 045004 ER - TY - JOUR A1 - Obermeier, Patrick E A1 - Heim, Albert A1 - Biere, Barbara A1 - Hage, Elias A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Rath, Barbara A T1 - Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations JF - iScience N2 - To improve the identification and management of viral respiratory infections, we established a clinical and virologic surveillance program for pediatric patients fulfilling pre-defined case criteria of influenza-like illness and viral respiratory infections. The program resulted in a cohort comprising 6,073 patients (56% male, median age 1.6 years, range 0–18.8 years), where every patient was assessed with a validated disease severity score at the point-of-care using the ViVI ScoreApp. We used machine learning and agnostic feature selection to identify characteristic clinical patterns. We tested all patients for human adenoviruses, 571 (9%) were positive. Adenovirus infections were particularly common and mild in children ≥1 month of age but rare and potentially severe in neonates: with lower airway involvement, disseminated disease, and a 50% mortality rate (n = 2/4). In one fatal case, we discovered a novel virus … Y1 - 2022 U6 - https://doi.org/10.1016/j.isci.2022.104276 VL - 25 IS - 5 PB - Cell Press ER - TY - CHAP A1 - Paskin, Martha A1 - Dean, Mason A1 - Baum, Daniel A1 - von Tycowicz, Christoph T1 - A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks T2 - Computer Vision -- ECCV 2022 N2 - 3D shapes provide substantially more information than 2D images. However, the acquisition of 3D shapes is sometimes very difficult or even impossible in comparison with acquiring 2D images, making it necessary to derive the 3D shape from 2D images. Although this is, in general, a mathematically ill-posed problem, it might be solved by constraining the problem formulation using prior information. Here, we present a new approach based on Kendall’s shape space to reconstruct 3D shapes from single monocular 2D images. The work is motivated by an application to study the feeding behavior of the basking shark, an endangered species whose massive size and mobility render 3D shape data nearly impossible to obtain, hampering understanding of their feeding behaviors and ecology. 2D images of these animals in feeding position, however, are readily available. We compare our approach with state-of-the-art shape-based approaches both on human stick models and on shark head skeletons. Using a small set of training shapes, we show that the Kendall shape space approach is substantially more robust than previous methods and always results in plausible shapes. This is essential for the motivating application in which specimens are rare and therefore only few training shapes are available. Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-20086-1_21 SP - 363 EP - 379 PB - Springer Nature Switzerland ER - TY - JOUR A1 - Engel, Maximilian A1 - Olicón-Méndez, Guillermo A1 - Wehlitz, Nathalie A1 - Winkelmann, Stefanie T1 - Synchronization and random attractors in reaction jump processes JF - Journal of Dynamics and Differential Equations N2 - This work explores a synchronization-like phenomenon induced by common noise for continuous-time Markov jump processes given by chemical reaction networks. Based on Gillespie’s stochastic simulation algorithm, a corresponding random dynamical system is formulated in a two-step procedure, at first for the states of the embedded discrete-time Markov chain and then for the augmented Markov chain including random jump times. We uncover a time-shifted synchronization in the sense that—after some initial waiting time—one trajectory exactly replicates another one with a certain time delay. Whether or not such a synchronization behavior occurs depends on the combination of the initial states. We prove this partial time-shifted synchronization for the special setting of a birth-death process by analyzing the corresponding two-point motion of the embedded Markov chain and determine the structure of the associated random attractor. In this context, we also provide general results on existence and form of random attractors for discrete-time, discrete-space random dynamical systems. Y1 - 2024 U6 - https://doi.org/10.1007/s10884-023-10345-4 ER - TY - CHAP A1 - Lüdke, David A1 - Amiranashvili, Tamaz A1 - Ambellan, Felix A1 - Ezhov, Ivan A1 - Menze, Bjoern A1 - Zachow, Stefan T1 - Landmark-free Statistical Shape Modeling via Neural Flow Deformations T2 - Medical Image Computing and Computer Assisted Intervention - MICCAI 2022 N2 - Statistical shape modeling aims at capturing shape variations of an anatomical structure that occur within a given population. Shape models are employed in many tasks, such as shape reconstruction and image segmentation, but also shape generation and classification. Existing shape priors either require dense correspondence between training examples or lack robustness and topological guarantees. We present FlowSSM, a novel shape modeling approach that learns shape variability without requiring dense correspondence between training instances. It relies on a hierarchy of continuous deformation flows, which are parametrized by a neural network. Our model outperforms state-of-the-art methods in providing an expressive and robust shape prior for distal femur and liver. We show that the emerging latent representation is discriminative by separating healthy from pathological shapes. Ultimately, we demonstrate its effectiveness on two shape reconstruction tasks from partial data. Our source code is publicly available (https://github.com/davecasp/flowssm). Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-16434-7_44 VL - 13432 PB - Springer, Cham ER - TY - CHAP A1 - Myers, Adele A1 - Utpala, Saiteja A1 - Talbar, Shubham A1 - Sanborn, Sophia A1 - Shewmake, Christian A1 - Donnat, Claire A1 - Mathe, Johan A1 - Lupo, Umberto A1 - Sonthalia, Rishi A1 - Cui, Xinyue A1 - Szwagier, Tom A1 - Pignet, Arthur A1 - Bergsson, Andri A1 - Hauberg, Søren A1 - Nielsen, Dmitriy A1 - Sommer, Stefan A1 - Klindt, David A1 - Hermansen, Erik A1 - Vaupel, Melvin A1 - Dunn, Benjamin A1 - Xiong, Jeffrey A1 - Aharony, Noga A1 - Pe’er, Itsik A1 - Ambellan, Felix A1 - Hanik, Martin A1 - Navayazdani, Esfandiar A1 - Tycowicz, Christoph von A1 - Miolane, Nina T1 - ICLR 2022 Challenge for Computational Geomerty & Topology: Design and Results T2 - Proceedings of Topology, Algebra, and Geometry in Learning Y1 - 2022 VL - 196 SP - 269 EP - 276 PB - PMLR ER - TY - GEN A1 - Nava-Yazdani, Esfandiar A1 - Hanik, Martin A1 - Ambellan, Felix A1 - von Tycowicz, Christoph T1 - On Gradient Formulas in an Algorithm for the Logarithm of the Sasaki Metric N2 - The Sasaki metric is the canonical metric on the tangent bundle TM of a Riemannian manifold M. It is highly useful for data analysis in TM (e.g., when one is interested in the statistics of a set of geodesics in M). To this end, computing the Riemannian logarithm is often necessary, and an iterative algorithm was proposed by Muralidharan and Fletcher. In this note, we derive approximation formulas of the energy gradients in their algorithm that we use with success. T3 - ZIB-Report - 22-12 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87174 SN - 1438-0064 ER - TY - JOUR A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Karsenti, Asher A1 - Kreinin, Lev A1 - Becker, Christiane T1 - Model-Chain Validation for Estimating the Energy Yield of Bifacial Perovskite/Silicon Tandem Solar Cells JF - Sol. RRL Y1 - 2022 U6 - https://doi.org/10.1002/solr.202200079 VL - 6 SP - 2200079 ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - IOSIG: Declarative I/O-Stream Properties Using Pragmas JF - Datenbank-Spektrum Y1 - 2022 U6 - https://doi.org/10.1007/s13222-022-00419-w VL - 22 IS - 2 SP - 109 EP - 119 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Benner, Peter A1 - Burger, Michael A1 - Göddeke, Dominik A1 - Görgen, Christiane A1 - Himpe, Christian A1 - Heiland, Jan A1 - Koprucki, Thomas A1 - Ohlberger, Mario A1 - Rave, Stephan A1 - Reidelbach, Marco A1 - Saak, Jens A1 - Schöbel, Anita A1 - Tabelow, Karsten A1 - Weber, Marcus T1 - Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative) JF - GAMM Rundbrief Y1 - 2022 IS - 1 SP - 40 EP - 43 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Koopman-based spectral clustering of directed and time-evolving graphs JF - Journal of Nonlinear Science N2 - While spectral clustering algorithms for undirected graphs are well established and have been successfully applied to unsupervised machine learning problems ranging from image segmentation and genome sequencing to signal processing and social network analysis, clustering directed graphs remains notoriously difficult. Two of the main challenges are that the eigenvalues and eigenvectors of graph Laplacians associated with directed graphs are in general complex-valued and that there is no universally accepted definition of clusters in directed graphs. We first exploit relationships between the graph Laplacian and transfer operators and in particular between clusters in undirected graphs and metastable sets in stochastic dynamical systems and then use a generalization of the notion of metastability to derive clustering algorithms for directed and time-evolving graphs. The resulting clusters can be interpreted as coherent sets, which play an important role in the analysis of transport and mixing processes in fluid flows. Y1 - 2022 U6 - https://doi.org/10.1007/s00332-022-09863-0 VL - 33 ER - TY - GEN A1 - Dresen, Christina A1 - Klindt, Marco ED - digiS - Forschungs- und Kompetenzzentrum Digitalisierung Berlin, T1 - Eine kleine Handreichung zur Digitalisierung von Audio- und Videomaterial N2 - Die Handreichung soll Mitarbeiter:innen von kulturellen Einrichtungen bei der Digitalisierung von Audio- und Videomaterial unterstützten. Diese Einführung richtet sich besonders an Personen, die nicht mit dem Thema vertraut sind. Nach einer Einführung in die Geschichte von Ton- und Bildsignalen werden verschiedene Medientypen vorgestellt und der Umgang mit ihnen um eine Digitalisierung zu beginnen. Die Digitalisierung wird im Zusammenhang mit wichtigen Grundbegriffen und Parametern vorgestellt. Abgeschlossen wird die Handreichung durch Hinweise zur Qualitätsprüfung und Archivierung. KW - Digitalisierung KW - Datenkompression KW - Container KW - Codec KW - Tonsignal KW - Bildsignal KW - Bitrate KW - Bildauflösung KW - Bildformat KW - Archiv KW - Langzeitarchivierung KW - Abtastung KW - Restaurierung KW - Archivierung Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86526 ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Viscosity and porosity effects on tangential-discontinuity surface stability in 3D Compressible Media JF - Physics of Fluids N2 - The stability of a flow in porous media relates to the velocity rate of injecting and withdrawing natural gases inside porous storage. We thus aim to analyze the stability of flows in porous media to accelerate the energy transition process. This research examines a flow model of a tangential--velocity discontinuity with porosity and viscosity changes in a three-dimensional (3D) compressible medium because of a co-existence of different gases in a storage. The fluids are assumed to move in a relative motion where the plane y=0 is a tangential-velocity discontinuity surface. We obtain that the critical value of the Mach number to stabilize a tangential discontinuity surface of flows via porous media is smaller than the one of flows in a plane. The critical value of the Mach number M to stabilize a discontinuity surface of the 3D flow is different by a factor |cosθ| compared to the two-dimensional (2D) flow. Here, θ is the angle between velocity and wavenumber vectors. Our results also show that the flow model with viscosity and porosity effects is stable faster than those without these terms. Our analysis is done for both infinite and finite flows. The effect of solid walls along the flow direction could suppress the instability, i.e., the tangential-discontinuity surface is stabilized faster Y1 - 2022 U6 - https://doi.org/10.1063/5.0095970 VL - 34 IS - 7 PB - AIP Publishing ER - TY - GEN A1 - Colom, Remi A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Kivshar, Yuri A1 - Burger, Sven T1 - Source code and simulation results for nanoantennas supporting an enhanced Purcell factor due to interfering resonances T2 - Zenodo Y1 - 2022 U6 - https://doi.org/10.5281/zenodo.6565850 ER - TY - JOUR A1 - Avalos-Ovando, Oscar A1 - Santiago, Eva Yazmin A1 - Movsesyan, Artur A1 - Kong, Xiang-Tian A1 - Yu, Peng A1 - Besteiro, Lucas V. A1 - Khosravi Khorashad, Larousse A1 - Okamoto, Hiromi A1 - Slocik, Joseph M. A1 - Correa-Duarte, Miguel A1 - Comesana-Hermo, Miguel A1 - Liedl, Tim A1 - Markovich, Gil A1 - Burger, Sven A1 - Govorov, Alexander O. T1 - Chiral Bioinspired Plasmonics: A Paradigm Shift for Optical Activity and Photochemistry JF - ACS Photon. Y1 - 2022 U6 - https://doi.org/10.1021/acsphotonics.2c00445 VL - 9 SP - 2219 ER - TY - CHAP A1 - Jäger, Klaus A1 - Sutter, Johannes A1 - Tockhorn, Philipp A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Improving perovskite/silicon tandem solar cells with optical simulations T2 - Proc. SPIE Y1 - 2022 U6 - https://doi.org/10.1117/12.2621255 VL - PC12150 SP - PC1215001 ER - TY - GEN A1 - Berio, Fidji A1 - Bayle, Yann A1 - Agret, Sylvie A1 - Baum, Daniel A1 - Goudemand, Nicolas A1 - Debiais-Thibaud, Mélanie T1 - 3D models related to the publication: Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula T2 - MorphoMuseuM N2 - The present dataset contains the 3D models analyzed in Berio, F., Bayle, Y., Baum, D., Goudemand, N., and Debiais-Thibaud, M. 2022. Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula. It contains the head surfaces of 56 North Atlantic and Mediterranean small-spotted catsharks Scyliorhinus canicula, from which tooth surfaces were further extracted to perform geometric morphometrics and machine learning. Y1 - 2022 U6 - https://doi.org/10.18563/journal.m3.164 ER - TY - JOUR A1 - Berio, Fidji A1 - Bayle, Yann A1 - Baum, Daniel A1 - Goudemand, Nicolas A1 - Debiais-Thibaud, Mélanie T1 - Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula populations JF - PeerJ - Aquatic Biology N2 - Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula exhibits distinct genetic structures, life history traits, and body size differences between populations inhabiting the North Atlantic Ocean and the Mediterranean Sea. In this work, we sample more than 3,000 S. canicula teeth from 56 specimens and provide and use a dataset containing their shape coordinates. We investigate tooth shape and form differences between a Mediterranean and an Atlantic S. canicula population using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils. Y1 - 2022 U6 - https://doi.org/10.7717/peerj.13575 SP - 10:e13575 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Manley, Phillip A1 - Krüger, Jan A1 - Zschiedrich, Lin A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Burger, Sven T1 - Reconstructing phase aberrations for high-precision dimensional microscopy JF - Proc. SPIE Y1 - 2022 U6 - https://doi.org/10.1117/12.2620762 VL - 12137 SP - 121370I ER - TY - GEN A1 - Hennings, Felix A1 - Hoppmann-Baum, Kai A1 - Zittel, Janina T1 - Optimizing transient gas network control for challenging real-world instances using MIP-based heuristics N2 - Optimizing the transient control of gas networks is a highly challenging task. The corresponding model incorporates the combinatorial complexity of determining the settings for the many active elements as well as the non-linear and non-convex nature of the physical and technical principles of gas transport. In this paper, we present the latest improvements of our ongoing work to solve this problem for real-world, large-scale problem instances: By adjusting our mixed-integer non-linear programming model regarding the gas compression capabilities in the network, we reflect the technical limits of the underlying units more accurately while maintaining a similar overall model size. In addition, we introduce a new algorithmic approach that is based on splitting the complexity of the problem by first finding assignments for discrete variables and then determining the continuous variables as locally optimal solution of the corresponding non-linear program. For the first task, we design multiple different heuristics based on concepts for general time-expanded optimization problems that find solutions by solving a sequence of sub-problems defined on reduced time horizons. To demonstrate the competitiveness of our approach, we test our algorithm on particularly challenging historic demand scenarios. The results show that high-quality solutions are obtained reliably within short solving times, making the algorithm well-suited to be applied at the core of time-critical industrial applications. T3 - ZIB-Report - 22-08 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86842 SN - 1438-0064 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Sirbu, Alexei A1 - Stelzer, Nina A1 - de Lanerolle, Primal A1 - Winkelmann, Stefanie A1 - Annibale, Paolo T1 - The Impact of Membrane Protein Diffusion on GPCR Signaling JF - Cells N2 - Spatiotemporal signal shaping in G protein-coupled receptor (GPCR) signaling is now a well-established and accepted notion to explain how signaling specificity can be achieved by a superfamily sharing only a handful of downstream second messengers. Dozens of Gs-coupled GPCR signals ultimately converge on the production of cAMP, a ubiquitous second messenger. This idea is almost always framed in terms of local concentrations, the differences in which are maintained by means of spatial separation. However, given the dynamic nature of the reaction-diffusion processes at hand, the dynamics, in particular the local diffusional properties of the receptors and their cognate G proteins, are also important. By combining some first principle considerations, simulated data, and experimental data of the receptors diffusing on the membranes of living cells, we offer a short perspective on the modulatory role of local membrane diffusion in regulating GPCR-mediated cell signaling. Our analysis points to a diffusion-limited regime where the effective production rate of activated G protein scales linearly with the receptor–G protein complex’s relative diffusion rate and to an interesting role played by the membrane geometry in modulating the efficiency of coupling Y1 - 2022 U6 - https://doi.org/10.3390/cells11101660 VL - 11 IS - 10 SP - 1660 ER - TY - GEN A1 - Fujii, Koichi A1 - Ito, Naoki A1 - Kim, Sunyoung A1 - Kojima, Masakazu A1 - Shinano, Yuji A1 - Toh, Kim-Chuan T1 - 大規模二次割当問題への挑戦 T2 - 統計数理研究所共同研究リポート 453 最適化:モデリングとアルゴリズム33 2022年3月 「大規模二次割当問題への挑戦」 p.84-p.92 N2 - 二次割当問題は線形緩和が弱いことが知られ,強化のため多様な緩和手法が考案されているが,その一つである二重非負値計画緩和( DNN 緩和)及びその解法として近年研究が進んでいるニュートン・ブラケット法を紹介し,それらに基づく分枝限定法の実装及び数値実験結果について報告する. T2 - Solving Large Scale QAPs with DNN-based Branch-and-bound : a progress report T3 - ZIB-Report - 22-11 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86779 SN - 1438-0064 ER - TY - GEN A1 - Kostré, Margarita A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Djurdjevac Conrad, Nataša T1 - Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia N2 - Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process. However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural change in ancient times. T3 - ZIB-Report - 22-10 KW - mesoscale spreading process, network inference, time-evolving network, romanization spreading, scarce data Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86764 SN - 1438-0064 ER - TY - GEN A1 - Bortoletto, Enrico A1 - Lindner, Niels A1 - Masing, Berenike T1 - The tropical and zonotopal geometry of periodic timetables N2 - The Periodic Event Scheduling Problem (PESP) is the standard mathematical tool for optimizing periodic timetabling problems in public transport. A solution to PESP consists of three parts: a periodic timetable, a periodic tension, and integer periodic offset values. While the space of periodic tension has received much attention in the past, we explore geometric properties of the other two components, establishing novel connections between periodic timetabling and discrete geometry. Firstly, we study the space of feasible periodic timetables, and decompose it into polytropes, i.e., polytopes that are convex both classically and in the sense of tropical geometry. We then study this decomposition and use it to outline a new heuristic for PESP, based on the tropical neighbourhood of the polytropes. Secondly, we recognize that the space of fractional cycle offsets is in fact a zonotope. We relate its zonotopal tilings back to the hyperrectangle of fractional periodic tensions and to the tropical neighbourhood of the periodic timetable space. To conclude we also use this new understanding to give tight lower bounds on the minimum width of an integral cycle basis. T3 - ZIB-Report - 22-09 KW - periodic event scheduling KW - tropical geometry KW - zonotopal tilings Y1 - 2022 SN - 1438-0064 ER - TY - JOUR A1 - Eigen, Lennart A1 - Baum, Daniel A1 - Dean, Mason N. A1 - Werner, Daniel A1 - Wölfer, Jan A1 - Nyakatura, John A. T1 - Ontogeny of a tessellated surface: carapace growth of the longhorn cowfish Lactoria cornuta JF - Journal of Anatomy N2 - Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is comprised of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high-throughput fashion, using high-resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g. around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface’s changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box-like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e. where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric and developmental constraints of this species, but also perspectives into natural strategies for constructing mutable tiled architectures. Y1 - 2022 U6 - https://doi.org/10.1111/joa.13692 VL - 241 IS - 3 SP - 565 EP - 580 PB - Wiley ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Modelling the inner coma of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - Based on about 1 million of pressure measurements around comet 67P/Churyumov-Gerasimenko we reconstruct the gas emission across the entire nucleus. Dust particles are seeded in the gas model and the resulting dust distribution follows a daily pattern which agrees with observations if a uniform dust release across the entire sunlit surface is assumed. Y1 - 2018 VL - 12 SP - EPSC2018-115-1 PB - Europlanet Science Congress ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Gas production of comet 67P/Churyumov-Gerasimenko reconstructed from DFMS/COPS data T2 - Europlanet Science Congress N2 - We reconstruct the temporal evolution of surface emissions for the four major gas species H2O, CO2, CO, and O2 emitted during the 2015 apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G). Measurements from the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS) are used to determine the gas sources on the surface with an inverse gas model for the entire coma. For all species, peak production rates and integrated production rates per orbit are evaluated separately for the northern and the southern hemisphere. Complemented with the total mass production, this allows us to estimate the dust-to-gas ratio of the emitted material. Y1 - 2018 VL - 12 SP - EPSC2018-515-1 PB - Europlanet Science Congress ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Matching the activity of comet 67P/Churyumov-Gerasimenko with long-term ground-based astrometry T2 - Europlanet Science Congress N2 - 50 years of astrometric data for comet 67P/C-G (orbital period about 6.45 years) provides a unique opportunity to benchmark non-gravitational acceleration models to the in situ measurements of the volatile release performed from the Rosetta rendezvous mission (2014-2016). Taken together, the Earth-bound and in-situ data yields lower fit errors and serves as a test-case for our ability to deduce thermophysical quantities of cometary nuclei from the Earth-bound observations. Y1 - 2021 U6 - https://doi.org/10.5194/epsc2021-337 VL - 15 SP - EPSC2021-337 PB - Europlanet Science Congress ER - TY - JOUR A1 - Lenz, Ralf A1 - Serrano, Felipe T1 - Tight Convex Relaxations for the Expansion Planning Problem JF - Journal of Optimization Theory and Applications N2 - Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improves the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58%. Y1 - 2022 U6 - https://doi.org/10.1007/s10957-022-02029-8 VL - 194 SP - 325 EP - 352 ER - TY - JOUR A1 - Volkova, Kseniia A1 - Heupel, Julia A1 - Trofimov, Sergei A1 - Betz, Fridtjof A1 - Colom, Rémi A1 - MacQueen, Rowan W. A1 - Akhundzada, Sapida A1 - Reginka, Meike A1 - Ehresmann, Arno A1 - Reithmeier, Johann Peter A1 - Burger, Sven A1 - Popov, Cyril A1 - Naydenov, Boris T1 - Optical and Spin Properties of NV Center Ensembles in Diamond Nano-Pillars JF - Nanomaterials Y1 - 2022 U6 - https://doi.org/10.3390/nano12091516 VL - 12 SP - 1516 ER - TY - JOUR A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Timetable merging for the Periodic Event Scheduling Problem JF - EURO Journal on Transportation and Logistics N2 - We propose a new mixed integer programming based heuristic for computing new benchmark primal solutions for instances of the PESPlib. The PESPlib is a collection of instances for the Periodic Event Scheduling Problem (PESP), comprising periodic timetabling problems inspired by real-world railway timetabling settings, and attracting several international research teams during the last years. We describe two strategies to merge a set of good periodic timetables. These make use of the instance structure and minimum weight cycle bases, finally leading to restricted mixed integer programming formulations with tighter variable bounds. Implementing this timetable merging approach in a concurrent solver, we improve the objective values of the best known solutions for the smallest and largest PESPlib instances by 1.7 and 4.3 percent, respectively. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejtl.2022.100081 VL - 11 SP - 100081 ER - TY - JOUR A1 - Turner, Mark A1 - Koch, Thorsten A1 - Serrano, Felipe A1 - Winkler, Michael T1 - Adaptive Cut Selection in Mixed-Integer Linear Programming JF - Open Journal of Mathematical Optimization N2 - Cutting plane selection is a subroutine used in all modern mixed-integer linear programming solvers with the goal of selecting a subset of generated cuts that induce optimal solver performance. These solvers have millions of parameter combinations, and so are excellent candidates for parameter tuning. Cut selection scoring rules are usually weighted sums of different measurements, where the weights are parameters. We present a parametric family of mixed-integer linear programs together with infinitely many family-wide valid cuts. Some of these cuts can induce integer optimal solutions directly after being applied, while others fail to do so even if an infinite amount are applied. We show for a specific cut selection rule, that any finite grid search of the parameter space will always miss all parameter values, which select integer optimal inducing cuts in an infinite amount of our problems. We propose a variation on the design of existing graph convolutional neural networks, adapting them to learn cut selection rule parameters. We present a reinforcement learning framework for selecting cuts, and train our design using said framework over MIPLIB 2017 and a neural network verification data set. Our framework and design show that adaptive cut selection does substantially improve performance over a diverse set of instances, but that finding a single function describing such a rule is difficult. Code for reproducing all experiments is available at https://github.com/Opt-Mucca/Adaptive-Cutsel-MILP. Y1 - 2023 U6 - https://doi.org/10.5802/ojmo.25 VL - 4 SP - 5 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - The ice composition close to the surface of comet 67P/Churyumov-Gerasimenko JF - ACS Earth and Space Chemistry N2 - The relation between ice composition in the nucleus of comet 67P/Churyumov-Gerasimenko on the one hand and relative abundances of volatiles in the coma on the other hand is important for the interpretation of density measurements in the environment of the cometary nucleus. For the 2015 apparition, in situ measurements from the two ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) sensors COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) determined gas densities at the spacecraft position for the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We derive the spatial distribution of the gas emissions on the complex shape of the nucleus separately for 50 subintervals of the two-year mission time. The most active patches of gas emission are identified on the surface. We retrieve the relation between solar irradiation and observed emissions from these patches. The emission rates are compared to a minimal thermophysical model to infer the surface active fraction of H2O and CO2. We obtain characteristic differences in the ice composition close to the surface between the two hemispheres with a reduced abundance of CO2 ice on the northern hemisphere (locations with positive latitude). We do not see significant differences for the ice composition on the two lobes of 67P/C-G. Y1 - 2022 U6 - https://doi.org/10.1021/acsearthspacechem.1c00378 VL - 6 IS - 5 SP - 1189 EP - 1203 ER - TY - JOUR A1 - Kostré, Margarita A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia JF - Applied Network Science N2 - Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process. However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural change in ancient times. KW - mesoscale spreading process KW - network inference KW - time-evolving network KW - romanization spreading KW - scarce data Y1 - 2022 U6 - https://doi.org/10.1007/s41109-022-00492-w VL - 7 PB - Springer Nature ER - TY - CHAP A1 - Weiser, Martin A1 - Chegini, Fatemeh T1 - Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods T2 - CMBE22 - 7th International Conference on Computational & Mathematical Biomedical Engineering N2 - The highly localized dynamics of cardiac electrophysiology models call for adaptive simulation methods. Unfortunately, the overhead incurred by classical mesh adaptivity turns out to outweigh the performance improvements achieved by reducing the problem size. Here, we explore a different approach to adaptivity based on algebraic degree of freedom subset selection during spectral deferred correction sweeps, which realizes a kind of multirate higher order integration. Numerical experience indicates a significant performance increase compared to uniform simulations. Y1 - 2022 SP - 528 EP - 531 ER - TY - JOUR A1 - Zangerl, Lina Maria A1 - Peters-Kottig, Wolfgang A1 - Oßwald, Achim T1 - Personal Digital Archiving: Eine neue Aufgabe für Öffentliche und Wissenschaftliche Bibliotheken JF - Bibliothek Forschung und Praxis N2 - Die Sicherung und längerfristige Archivierung persönlich relevanter Dokumente und Dateien, in der Fachliteratur als Personal Digital Archiving (PDA) bezeichnet, ist eine für Privatpersonen zunehmend wichtiger werdende Aufgabe. Praktische Anleitungen und weiterführende Hinweise zur Umsetzung dieser Aufgabe gibt die auf unterschiedliche Nutzer:innenperspektiven ausgerichtete Webseite meinDigitalesArchiv.de, die seit 2020 von der nestor-AG PDA bereitgestellt wird. Mit den Informationen dieser Webseite können und sollten Bibliotheken und andere Einrichtungen, die Informationskompetenz vermitteln, Privatpersonen für die Sicherung ihrer persönlichen digitalen Daten sensibilisieren und schulen. Mit der Umsetzung dieser Aufgabe können Öffentliche wie Wissenschaftliche Bibliotheken zur Sicherung auch gesamtgesellschaftlich relevanter Erinnerungsbausteine beitragen. Y1 - 2022 U6 - https://doi.org/10.1515/bfp-2021-0058 VL - 46 IS - 1 SP - 152 EP - 161 ER - TY - JOUR A1 - Lücke, Marvin A1 - Nüske, Feliks T1 - tgEDMD: Approximation of the Kolmogorov Operator in Tensor Train Format JF - Journal of Nonlinear Science N2 - Extracting information about dynamical systems from models learned off simulation data has become an increasingly important research topic in the natural and engineering sciences. Modeling the Koopman operator semigroup has played a central role in this context. As the approximation quality of any such model critically depends on the basis set, recent work has focused on deriving data-efficient representations of the Koopman operator in low-rank tensor formats, enabling the use of powerful model classes while avoiding over-fitting. On the other hand, detailed information about the system at hand can be extracted from models for the infinitesimal generator, also called Kolmogorov backward operator for stochastic differential equations. In this work, we present a data-driven method to efficiently approximate the generator using the tensor train (TT) format. The centerpiece of the method is a TT representation of the tensor of generator evaluations at all data sites. We analyze consistency and complexity of the method, present extensions to practically relevant settings, and demonstrate its applicability to benchmark numerical examples. Y1 - 2022 U6 - https://doi.org/10.1007/s00332-022-09801-0 VL - 32 ER - TY - JOUR A1 - Chen, Ying A1 - Koch, Thorsten A1 - Zakiyeva, Nazgul A1 - Liu, Kailiang A1 - Xu, Zhitong A1 - Chen, Chun-houh A1 - Nakano, Junji A1 - Honda, Keisuke T1 - Article's Scientific Prestige: Measuring the Impact of Individual Articles in the Web of Science N2 - We performed a citation analysis on the Web of Science publications consisting of more than 63 million articles and 1.45 billion citations on 254 subjects from 1981 to 2020. We proposed the Article’s Scientific Prestige (ASP) metric and compared this metric to number of citations (#Cit) and journal grade in measuring the scientific impact of individual articles in the large-scale hierarchical and multi-disciplined citation network. In contrast to #Cit, ASP, that is computed based on the eigenvector centrality, considers both direct and indirect citations, and provides steady-state evaluation cross different disciplines. We found that ASP and #Cit are not aligned for most articles, with a growing mismatch amongst the less cited articles. While both metrics are reliable for evaluating the prestige of articles such as Nobel Prize winning articles, ASP tends to provide more persuasive rankings than #Cit when the articles are not highly cited. The journal grade, that is eventually determined by a few highly cited articles, is unable to properly reflect the scientific impact of individual articles. The number of references and coauthors are less relevant to scientific impact, but subjects do make a difference. T3 - ZIB-Report - 22-07 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86380 VL - 17 IS - 1 SP - 101379 ER - TY - JOUR A1 - Euler, Ricardo A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - Price Optimal Routing in Public Transportation N2 - We consider the price-optimal earliest arrival problem in public transit (POEAP) in which we aim to calculate the Pareto-front of journeys with respect to ticket price and arrival time in a public transportation network. Public transit fare structures are often a combination of various fare strategies such as, e.g., distance-based fares, zone-based fares or flat fares. The rules that determine the actual ticket price are often very complex. Accordingly, fare structures are notoriously difficult to model as it is in general not sufficient to simply assign costs to arcs in a routing graph. Research into POEAP is scarce and usually either relies on heuristics or only considers restrictive fare models that are too limited to cover the full scope of most real-world applications. We therefore introduce conditional fare networks (CFNs), the first framework for representing a large number of real-world fare structures. We show that by relaxing label domination criteria, CFNs can be used as a building block in label-setting multi-objective shortest path algorithms. By the nature of their extensive modeling capabilities, optimizing over CFNs is NP-hard. However, we demonstrate that adapting the multi-criteria RAPTOR (MCRAP) algorithm for CFNs yields an algorithm capable of solving POEAP to optimality in less than 400 ms on average on a real-world data set. By restricting the size of the Pareto-set, running times are further reduced to below 10 ms. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86414 ER - TY - GEN A1 - KOBV (Hrsg.), T1 - KOBV-Sondernewsletter zum 25-jährigen Jubiläum N2 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg wird heute 25 Jahre alt. Seit dem 1. April 1997 entwickelt der KOBV neue Dienstleistungen für Nutzende und Bibliotheken, baut Informationsinfrastrukturen in Berlin und Brandenburg aus, vernetzt Bibliotheken aus der Region und informiert über aktuelle Themen. Im Sondernewsletter geben uns aktuelle und ehemalige KOBV-Mitarbeitende/Mitglieder Antworten auf Fragen zur Entstehung und Weiterentwicklung des Verbundes. Lesen und feiern Sie mit uns zusammen! Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86379 ER - TY - JOUR A1 - Mikula, Natalia A1 - Dörffel, Tom A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - An Interactive Approach for Identifying Structure Definitions JF - Computer Graphics Forum N2 - Our ability to grasp and understand complex phenomena is essentially based on recognizing structures and relating these to each other. For example, any meteorological description of a weather condition and explanation of its evolution recurs to meteorological structures, such as convection and circulation structures, cloud fields and rain fronts. All of these are spatiotemporal structures, defined by time-dependent patterns in the underlying fields. Typically, such a structure is defined by a verbal description that corresponds to the more or less uniform, often somewhat vague mental images of the experts. However, a precise, formal definition of the structures or, more generally, concepts is often desirable, e.g., to enable automated data analysis or the development of phenomenological models. Here, we present a systematic approach and an interactive tool to obtain formal definitions of spatiotemporal structures. The tool enables experts to evaluate and compare different structure definitions on the basis of data sets with time-dependent fields that contain the respective structure. Since structure definitions are typically parameterized, an essential part is to identify parameter ranges that lead to desired structures in all time steps. In addition, it is important to allow a quantitative assessment of the resulting structures simultaneously. We demonstrate the use of the tool by applying it to two meteorological examples: finding structure definitions for vortex cores and center lines of temporarily evolving tropical cyclones. Ideally, structure definitions should be objective and applicable to as many data sets as possible. However, finding such definitions, e.g., for the common atmospheric structures in meteorology, can only be a long-term goal. The proposed procedure, together with the presented tool, is just a first systematic approach aiming at facilitating this long and arduous way. Y1 - 2022 U6 - https://doi.org/10.1111/cgf.14543 VL - 41 IS - 3 SP - 321 EP - 332 ER - TY - JOUR A1 - Schwartz, Stephan T1 - An overview of graph covering and partitioning JF - Discrete Mathematics N2 - While graph covering is a fundamental and well-studied problem, this field lacks a broad and unified literature review. The holistic overview of graph covering given in this article attempts to close this gap. The focus lies on a characterization and classification of the different problems discussed in the literature. In addition, notable results and common approaches are also included. Whenever appropriate, this review extends to the corresponding partitioning problems. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.disc.2022.112884 VL - 345 IS - 8 ER - TY - JOUR A1 - Movsesyan, Artur A1 - Santiago, Eva Yazmin A1 - Burger, Sven A1 - Correa-Duarte, Miguel A1 - Besteiro, Lucas V. A1 - Wang, Zhiming A1 - Govorov, Alexander O. T1 - Plasmonic nanocrystals with complex shapes for photocatalysis and growth: Contrasting anisotropic hot-electron generation with the photothermal effect JF - Adv. Opt. Mater. Y1 - 2022 U6 - https://doi.org/10.1002/adom.202102663 VL - 10 SP - 2102663 ER - TY - JOUR A1 - Udvary, Daniel A1 - Harth, Philipp A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - de Kock, Christiaan P. J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - The Impact of Neuron Morphology on Cortical Network Architecture JF - Cell Reports N2 - The neurons in the cerebral cortex are not randomly interconnected. This specificity in wiring can result from synapse formation mechanisms that connect neurons depending on their electrical activity and genetically defined identity. Here, we report that the morphological properties of the neurons provide an additional prominent source by which wiring specificity emerges in cortical networks. This morphologically determined wiring specificity reflects similarities between the neurons’ axo-dendritic projections patterns, the packing density and cellular diversity of the neuropil. The higher these three factors are the more recurrent is the topology of the network. Conversely, the lower these factors are the more feedforward is the network’s topology. These principles predict the empirically observed occurrences of clusters of synapses, cell type-specific connectivity patterns, and nonrandom network motifs. Thus, we demonstrate that wiring specificity emerges in the cerebral cortex at subcellular, cellular and network scales from the specific morphological properties of its neuronal constituents. Y1 - 2022 U6 - https://doi.org/10.1016/j.celrep.2022.110677 VL - 39 IS - 2 ER - TY - JOUR A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Cruz, Alexandros A1 - Wagner, Philipp A1 - Jäger, Klaus A1 - Yoo, Danbi A1 - Lang, Felix A1 - Grischek, Max A1 - Li, Bor A1 - Li, Jinzhao A1 - Shargaieva, Oleksandra A1 - Unger, Eva A1 - Al-Ashouri, Amran A1 - Köhnen, Eike A1 - Stolterfoth, Martin A1 - Neher, Dieter A1 - Schlatmann, Rutger A1 - Rech, Bernd A1 - Stannowski, Bernd A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Nano-optical designs for high-efficiency monolithic perovskite–silicon tandem solar cells JF - Nat. Nanotechnol. Y1 - 2022 U6 - https://doi.org/10.1038/s41565-022-01228-8 VL - 17 SP - 1214 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Computation of eigenfrequency sensitivities using Riesz projections for efficient optimization of nanophotonic resonators JF - Commun. Phys. Y1 - 2022 U6 - https://doi.org/10.1038/s42005-022-00977-1 VL - 5 SP - 202 ER - TY - JOUR A1 - Müller, Benjamin A1 - Muñoz, Gonzalo A1 - Gasse, Maxime A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Serrano, Felipe T1 - On generalized surrogate duality in mixed-integer nonlinear programming JF - Mathematical Programming N2 - The most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global ϵ-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solvers can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments. Y1 - 2022 U6 - https://doi.org/10.1007/s10107-021-01691-6 VL - 192 IS - 1 SP - 89 EP - 118 ER - TY - CHAP A1 - Knaust, Marius A1 - Seiler, Enrico A1 - Reinert, Knut A1 - Steinke, Thomas T1 - Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA T2 - FPGA '22: Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays N2 - Next-Generation Sequencing technologies generate a vast and exponentially increasing amount of sequence data. The Interleaved Bloom Filter (IBF) is a novel indexing data structure which is state-of-the-art for distributing approximate queries with an in-memory data structure. With it, a main task of sequence analysis pipelines, (approximately) searching large reference data sets for sequencing reads or short sequence patterns like genes, can be significantly accelerated. To meet performance and energy-efficiency requirements, we chose a co-design approach of the IBF data structure on the FPGA platform. Further, our OpenCL-based implementation allows a seamless integration into the widely used SeqAn C++ library for biological sequence analysis. Our algorithmic design and optimization strategy takes advantage of FPGA-specific features like shift register and the parallelization potential of many bitwise operations. We designed a well-chosen schema to partition data across the different memory domains on the FPGA platform using the Shared Virtual Memory concept. We can demonstrate significant improvements in energy efficiency of up to 19x and in performance of up to 5.6x, respectively, compared to a well-tuned, multithreaded CPU reference. Y1 - 2022 U6 - https://doi.org/10.1145/3490422.3502366 SP - 180 EP - 189 ER - TY - CHAP A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Cao, Karl-Kien A1 - Fiand, Fred A1 - Gils, Hans-Christian A1 - Gleixner, Ambros A1 - Khabi, Dmitry A1 - Kempke, Nils A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Wetzel, Manuel T1 - BEAM-ME: Accelerating Linear Energy Systems Models by a Massively Parallel Interior Point Method T2 - NIC Symposium 2020 Y1 - 2020 VL - 50 SP - 345 EP - 352 ER - TY - JOUR A1 - Bonami, Pierre A1 - Gleixner, Ambros A1 - Linderoth, Jeff A1 - Misener, Ruth T1 - Designing and Implementing Algorithms for Mixed-Integer Nonlinear Optimization (Dagstuhl Seminar 18081) JF - Dagstuhl Reports N2 - Mathematical models for optimal decisions often require both nonlinear and discrete components. These mixed-integer nonlinear programs (MINLP) may be used to optimize the energy use of large industrial plants, integrate renewable sources into energy networks, design biological and biomedical systems, and address numerous other applications of societal importance. The first MINLP algorithms and software were designed by application engineers. While these efforts initially proved useful, scientists, engineers, and practitioners have realized that a transformational shift in technology will be required for MINLP to achieve its full potential. MINLP has transitioned to a forefront position in computer science, with researchers actively developing MINLP theory, algorithms, and implementations. Even with their concerted effort, algorithms and available software are often unable to solve practically-sized instances of these important models. Current obstacles include characterizing the computability boundary, effectively exploiting known optimization technologies for specialized classes of MINLP, and effectively using logical formulas holistically throughout algorithms. Y1 - 2018 U6 - https://doi.org/10.4230/DagRep.8.2.64 VL - 8 IS - 2 SP - 64 EP - 87 ER - TY - JOUR A1 - Boltze, Julia A1 - Höllerl, Annika A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Retter, Regina A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Söllner, Konstanze T1 - DeepGreen: Eine Infrastruktur für die Open-Access-Transformation JF - O-Bib. Das Offene Bibliotheksjournal N2 - Mit DeepGreen wurde eine Infrastruktur aufgebaut und etabliert, die Zeitschriftenartikel von wissenschaftlichen Verlagen abholt und berechtigten Bibliotheken zur Veröffentlichung in ihren Repositorien sendet. DeepGreen unterstützt Bibliotheken als Dienstleister für Hochschulen, außeruniversitäre Einrichtungen und die dort tätigen Wissenschaftler*innen, Publikationen auf Open-Access-Repositorien frei zugänglich zu machen und fördert das Zusammenspiel von wissenschaftlichen Einrichtungen und Verlagen. DeepGreen wurde von Januar 2016 bis Juni 2021 von der Deutschen Forschungsgemeinschaft gefördert und wird nun vom Kooperativen Bibliotheksverbund Berlin-Brandenburg, von der Bayerischen Staatsbibliothek und von der Universitätsbibliothek Erlangen-Nürnberg in arbeitsteiliger Eigenleistung für zwei Jahre weiterbetrieben. Der vorliegende Beitrag beleuchtet vielfältige Aspekte bei der Realisierung von DeepGreen und geht auf die Perspektiven dieser zentralen Open-Access-Infrastruktur für deutsche Wissenschaftseinrichtungen ein. Y1 - 2022 U6 - https://doi.org/10.5282/o-bib/5764 VL - 9 IS - 1 ER - TY - JOUR A1 - Ehlers, Sarah A1 - Baum, Daniel A1 - Mühlethaler, Roland A1 - Hoch, Hannelore A1 - Bräunig, Peter T1 - Large abdominal mechanoreceptive sense organs in small plant-dwelling insects JF - Biology Letters N2 - The Hemiptera is the largest non-endopterygote insect order comprising approximately 98,000 recent species. All species of the suborders Cicadomorpha (leafhoppers, spittlebugs, treehoppers and cicadas) and Fulgoromorpha (planthoppers) feed by sucking sap from plant tissues and are thus often vectors for economically important phytopathogens. Except for the cicadas (Cicadomorpha: Cicadoidea: Cicadidae) which produce air-borne sounds, all species of the suborders Cicadomorpha and Fulgoromorpha communicate by vibrational (substrate-borne) signals. While the generation of these signals has been extensively investigated, the mechanisms of perception are poorly understood. This study provides a full description and 3D reconstruction of a large and complex array of six paired chordotonal organs in the first abdominal segments of the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Membracoidea: Cicadellidae). Further we were able to identify homologous organs in the closely related spittlebug Philaenus spumarius (Cicadomorpha: Cercopoidea: Aphrophoridae) and the planthopper Issus coleoptratus (Fulgoromorpha: Fulgoroidea: Issidae). The configuration is congruent with the abdominal chordotonal organs in cicadas, where one of them is an elaborate tympanal organ. This indicates that these organs, together with the tymbal organ constitute a synapomorphy of the Tymbalia (Hemiptera excl. Sternorrhyncha). Our results contribute to the understanding of the evolution from substrate-borne to airborne communication in insects. Y1 - 2022 U6 - https://doi.org/10.1098/rsbl.2022.0078 VL - 18 IS - 4 ER - TY - CHAP A1 - Amiranashvili, Tamaz A1 - Lüdke, David A1 - Li, Hongwei A1 - Menze, Bjoern A1 - Zachow, Stefan T1 - Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions T2 - Medical Imaging with Deep Learning N2 - Reconstructing anatomical shapes from sparse or partial measurements relies on prior knowledge of shape variations that occur within a given population. Such shape priors are learned from example shapes, obtained by segmenting volumetric medical images. For existing models, the resolution of a learned shape prior is limited to the resolution of the training data. However, in clinical practice, volumetric images are often acquired with highly anisotropic voxel sizes, e.g. to reduce image acquisition time in MRI or radiation exposure in CT imaging. The missing shape information between the slices prohibits existing methods to learn a high-resolution shape prior. We introduce a method for high-resolution shape reconstruction from sparse measurements without relying on high-resolution ground truth for training. Our method is based on neural implicit shape representations and learns a continuous shape prior only from highly anisotropic segmentations. Furthermore, it is able to learn from shapes with a varying field of view and can reconstruct from various sparse input configurations. We demonstrate its effectiveness on two anatomical structures: vertebra and femur, and successfully reconstruct high-resolution shapes from sparse segmentations, using as few as three orthogonal slices. Y1 - 2022 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Burdakov, Oleg A1 - Mexi, Gioni A1 - Casselgren, Carl Johan A1 - Koch, Thorsten T1 - Length-Constrained Cycle Partition with an Application to UAV Routing JF - Optimization Methods and Software N2 - This article discusses the Length-Constrained Cycle Partition Problem (LCCP), which constitutes a new generalization of the Travelling Salesperson Problem (TSP). Apart from nonnegative edge weights, the undirected graph in LCCP features a nonnegative critical length parameter for each vertex. A cycle partition, i.e., a vertex-disjoint cycle cover, is a feasible solution for LCCP if the length of each cycle is not greater than the critical length of each vertex contained in it. The goal is to find a feasible partition having a minimum number of cycles. Besides analyzing theoretical properties and developing preprocessing techniques, we propose an elaborate heuristic algorithm that produces solutions of good quality even for large-size instances. Moreover, we present two exact mixed-integer programming formulations (MIPs) for LCCP, which are inspired by well-known modeling approaches for TSP. Further, we introduce the concept of conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a discussion on computational experiments that we conducted using (A)TSPLIB-based problem instances. As a motivating example application, we describe a routing problem where a fleet of uncrewed aerial vehicles (UAVs) must patrol a given set of areas. Y1 - 2022 U6 - https://doi.org/10.1080/10556788.2022.2053972 ER - TY - JOUR A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - Bi-invariant Dissimilarity Measures for Sample Distributions in Lie Groups JF - SIAM Journal on Mathematics of Data Science N2 - Data sets sampled in Lie groups are widespread, and as with multivariate data, it is important for many applications to assess the differences between the sets in terms of their distributions. Indices for this task are usually derived by considering the Lie group as a Riemannian manifold. Then, however, compatibility with the group operation is guaranteed only if a bi-invariant metric exists, which is not the case for most non-compact and non-commutative groups. We show here that if one considers an affine connection structure instead, one obtains bi-invariant generalizations of well-known dissimilarity measures: a Hotelling $T^2$ statistic, Bhattacharyya distance and Hellinger distance. Each of the dissimilarity measures matches its multivariate counterpart for Euclidean data and is translation-invariant, so that biases, e.g., through an arbitrary choice of reference, are avoided. We further derive non-parametric two-sample tests that are bi-invariant and consistent. We demonstrate the potential of these dissimilarity measures by performing group tests on data of knee configurations and epidemiological shape data. Significant differences are revealed in both cases. Y1 - 2022 U6 - https://doi.org/10.1137/21M1410373 VL - 4 IS - 4 SP - 1223 EP - 1249 ER - TY - JOUR A1 - Plock, Matthias A1 - Andrle, Kas A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction JF - Adv. Theory Simul. Y1 - 2022 U6 - https://doi.org/10.1002/adts.202200112 VL - 5 SP - 2200112 ER - TY - JOUR A1 - Dass, Mihir A1 - Kuen, Lilli A1 - Posnjak, Gregor A1 - Burger, Sven A1 - Liedl, Tim T1 - Visible wavelength spectral tuning of absorption and circular dichroism of DNA-assembled Au/Ag core-shell nanorod assemblies JF - Mater. Adv. Y1 - 2022 U6 - https://doi.org/10.1039/D1MA01211H VL - 3 SP - 3438 ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds JF - Journal of Mathematical Imaging and Vision N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends. Y1 - 2022 U6 - https://doi.org/10.1007/s10851-022-01079-x VL - 64 IS - 4 SP - 395 EP - 407 ER - TY - GEN A1 - Hanik, Martin A1 - von Tycowicz, Christoph T1 - Triangle meshes of shadow-recieving surfaces of ancient sundials N2 - This repository contains triangle meshes of the shadow-recieving surfaces of 13 ancient sundials; three of them are from Greece and 10 from Italy. The meshes are in correspondence. Y1 - 2022 U6 - https://doi.org/10.12752/8425 ER - TY - GEN A1 - Turner, Mark A1 - Koch, Thorsten A1 - Serrano, Felipe A1 - Winkler, Michael T1 - Adaptive Cut Selection in Mixed-Integer Linear Programming N2 - Cut selection is a subroutine used in all modern mixed-integer linear programming solvers with the goal of selecting a subset of generated cuts that induce optimal solver performance. These solvers have millions of parameter combinations, and so are excellent candidates for parameter tuning. Cut selection scoring rules are usually weighted sums of different measurements, where the weights are parameters. We present a parametric family of mixed-integer linear programs together with infinitely many family-wide valid cuts. Some of these cuts can induce integer optimal solutions directly after being applied, while others fail to do so even if an infinite amount are applied. We show for a specific cut selection rule, that any finite grid search of the parameter space will always miss all parameter values, which select integer optimal inducing cuts in an infinite amount of our problems. We propose a variation on the design of existing graph convolutional neural networks, adapting them to learn cut selection rule parameters. We present a reinforcement learning framework for selecting cuts, and train our design using said framework over MIPLIB 2017. Our framework and design show that adaptive cut selection does substantially improve performance over a diverse set of instances, but that finding a single function describing such a rule is difficult. Code for reproducing all experiments is available at https://github.com/Opt-Mucca/Adaptive-Cutsel-MILP. T3 - ZIB-Report - 22-04 KW - cut selection KW - mixed-integer linear programming KW - reinforcement learning Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86055 SN - 1438-0064 ER - TY - JOUR A1 - Bremer, Lucas A1 - Jimenez, Carlos A1 - Thiele, Simon A1 - Weber, Ksenia A1 - Huber, Tobias A1 - Rodt, Sven A1 - Herkommer, Alois A1 - Burger, Sven A1 - Höfling, Sven A1 - Giessen, Harald A1 - Reitzenstein, Stephan T1 - Numerical optimization of single-mode fiber- coupled single-photon sources based on semiconductor quantum dots JF - Opt. Express Y1 - 2022 U6 - https://doi.org/10.1364/OE.456777 VL - 30 SP - 15913 ER - TY - JOUR A1 - Lindner, Niels A1 - Reisch, Julian T1 - An analysis of the parameterized complexity of periodic timetabling JF - Journal of Scheduling N2 - Public transportation networks are typically operated with a periodic timetable. The periodic event scheduling problem (PESP) is the standard mathematical modeling tool for periodic timetabling. PESP is a computationally very challenging problem: For example, solving the instances of the benchmarking library PESPlib to optimality seems out of reach. Since PESP can be solved in linear time on trees, and the treewidth is a rather small graph parameter in the networks of the PESPlib, it is a natural question to ask whether there are polynomial-time algorithms for input networks of bounded treewidth, or even better, fixed-parameter tractable algorithms. We show that deciding the feasibility of a PESP instance is NP-hard even when the treewidth is 2, the branchwidth is 2, or the carvingwidth is 3. Analogous results hold for the optimization of reduced PESP instances, where the feasibility problem is trivial. Moreover, we show W[1]-hardness of the general feasibility problem with respect to treewidth, which means that we can most likely only accomplish pseudo-polynomial-time algorithms on input networks with bounded tree- or branchwidth. We present two such algorithms based on dynamic programming. We further analyze the parameterized complexity of PESP with bounded cyclomatic number, diameter, or vertex cover number. For event-activity networks with a special—but standard—structure, we give explicit and sharp bounds on the branchwidth in terms of the maximum degree and the carvingwidth of an underlying line network. Finally, we investigate several parameters on the smallest instance of the benchmarking library PESPlib. Y1 - 2022 U6 - https://doi.org/10.1007/s10951-021-00719-1 VL - 25 SP - 157 EP - 176 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Schütte, Christof A1 - Winkelmann, Stefanie T1 - A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures JF - SIAM Journal on Applied Mathematics N2 - The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit of an infinitely large population, may be described by means of reaction-diffusion partial differential equations. Analyzing and understanding the relation between different mathematical models for reaction-diffusion dynamics is a research topic of steady interest. In this work, we explore a route to the hydrodynamic limit of the RDME which uses gradient structures. Specifically, we elaborate on a method introduced in [J. Maas and A. Mielke, J. Stat. Phys., 181 (2020), pp. 2257–2303] in the context of well-mixed reaction networks by showing that, once it is complemented with an appropriate limit procedure, it can be applied to spatially extended systems with diffusion. Under the assumption of detailed balance, we write down a gradient structure for the RDME and use the method in order to produce a gradient structure for its hydrodynamic limit, namely, for the corresponding RDPDE. Y1 - 2023 U6 - https://doi.org/10.1137/22M1488831 VL - 83 IS - 2 SP - 837 EP - 861 ER - TY - GEN A1 - Dittmann, Antje A1 - Hasler, Tim A1 - Oltmanns, Elias T1 - Archivierungsstrategie für audiovisuelles Material N2 - Im Rahmen ihrer Strategie zur Langzeitarchivierung forscht die Deutsche Kinemathek in einer Kooperation mit dem Zuse-Institut Berlin (ZIB) an der digitalen Langzeitarchivierung von AV-Materialien. Ausgangspunkt des Projektes sind die enormen Dateigrößen und die heterogenen Dateiformate, die einem Werk und einer Fassung zugeordnet werden müssen. Die Verwendung von persistenten Identifikatoren stellt den Lösungsansatz dar. T3 - ZIB-Report - 22-03 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85916 ER - TY - CHAP A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs T2 - Integer Programming and Combinatorial Optimization: 22nd International Conference, IPCO 2021 N2 - The generation of strong linear inequalities for QCQPs has been recently tackled by a number of authors using the intersection cut paradigm - a highly studied tool in integer programming whose flexibility has triggered these renewed efforts in non-linear settings. In this work, we consider intersection cuts using the recently proposed construction of maximal quadratic-free sets. Using these sets, we derive closed-form formulas to compute intersection cuts which allow for quick cut-computations by simply plugging-in parameters associated to an arbitrary quadratic inequality being violated by a vertex of an LP relaxation. Additionally, we implement a cut-strengthening procedure that dates back to Glover and evaluate these techniques with extensive computational experiments. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_10 VL - 22 SP - 134 EP - 147 ER - TY - JOUR A1 - Colom, Remi A1 - Mikheeva, Elena A1 - Achouri, Karim A1 - Zuniga-Perez, Jesus A1 - Bonod, Nicolas A1 - Martin, Olivier J. F. A1 - Burger, Sven A1 - Genevet, Patrice T1 - Crossing of the branch cut: the topological origin of a universal 2π-phase retardation in non-Hermitian metasurfaces JF - Laser Photonics Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202200976 VL - 17 SP - 2200976 ER - TY - THES A1 - Francobaldi, Matteo T1 - Learning to Use Local Cuts N2 - We propose a machine learning approach to address a specific algorithmic question that arises during the solving process of a mixed-integer linear programming problem, namely, whether to use cutting planes only at the root node or also at internal nodes of the branch-and-bound search tree, or equivalently, whether to run a cut-and-branch or rather a branch-and-cut algorithm. Within a supervised regression framework, we develop three machine learning models, Linear Model, Random Forest and Neural Network, for predicting the relative performance between the two methods, local-cut and no-local-cut. Hence, through an extensive computational study conducted with FICO Xpress over a large test bed of problems, we evaluate the produced strategies, and we show that they are able to provide, upon the existing policies, a significant improvement to the performance of the solver. In fact, a variant of the random forest suggested in the present work has already been implemented by the development team of Xpress, and released with version 8.13 of the software. KW - Mathematical Programming KW - Machine Learning KW - Artificial Intelligence Y1 - 2021 ER - TY - JOUR A1 - Dai, Chengxin A1 - Füllgrabe, Anja A1 - Pfeuffer, Julianus A1 - Solovyeva, Elizaveta M. A1 - Deng, Jingwen A1 - Moreno, Pablo A1 - Kamatchinathan, Selvakumar A1 - Kundu, Deepti Jaiswal A1 - George, Nancy A1 - Fexovy, Silvie A1 - Grüning, Björn A1 - Föll, Melanie Christine A1 - Griss, Johannes A1 - Vaudel, Marc A1 - Audain, Enrique A1 - Locard-Paulet, Marie A1 - Turewicz, Michael A1 - Eisenacher, Martin A1 - Uszkoreit, Julian A1 - Van Den Bossche, Tim A1 - Schwämmle, Veit A1 - Webel, Henry A1 - Schulze, Stefan A1 - Bouyssié, David A1 - Jayaram, Savita A1 - Duggineni, Vinay Kumar A1 - Samaras, Patroklos A1 - Wilhelm, Mathias A1 - Choi, Meena A1 - Wang, Mingxun A1 - Kohlbacher, Oliver A1 - Brazma, Alvis A1 - Papatheodorou, Irene A1 - Bandeira, Nuno A1 - Deutsch, Eric W. A1 - Vizcaíno, Juan Antonio A1 - Bai, Mingze A1 - Sachsenberg, Timo A1 - Levitsky, Lev I. A1 - Perez-Riverol, Yasset T1 - A proteomics sample metadata representation for multiomics integration and big data analysis JF - Nature Communications N2 - The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1038/s41467-021-26111-3 VL - 12 IS - 5854 ER - TY - JOUR A1 - Umer, Husen M. A1 - Zhu, Yafeng A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Lehtiö, Janne A1 - Branca, Rui A1 - Perez-Riverol, Yasset T1 - Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides JF - Bioinformatics N2 - We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512). Y1 - 2021 IS - 5 SP - 1470 EP - 1472 PB - Oxford Academic ET - 38 ER - TY - JOUR A1 - Djurdjevac, Ana A1 - Gräser, Carsten A1 - Herbert, Philip J. T1 - Non-stationary incompressible linear fluid equations in a moving domain JF - arXiv N2 - This article considers non-stationary incompressible linear fluid equations in a moving domain. We demonstrate the existence and uniqueness of an appropriate weak formulation of the problem by making use of the theory of time-dependent Bochner spaces. It is not possible to directly apply established evolving Hilbert space theory due to the incompressibility constraint. After we have established the well-posedness, we derive and analyse a time discretisation of the system. Y1 - 2021 ER - TY - JOUR A1 - Alphonse, Amal A1 - Caetano, Diogo A1 - Djurdjevac, Ana A1 - Elliott, Charles M. T1 - Function spaces, time derivatives and compactness for evolving families of Banach spaces with applications to PDEs JF - Journal of Differential Equations N2 - We develop a functional framework suitable for the treatment of partial differential equations and variational problems posed on evolving families of Banach spaces. We propose a definition for the weak time derivative which does not rely on the availability of an inner product or Hilbertian structure and explore conditions under which the spaces of weakly differentiable functions (with values in an evolving Banach space) relate to the classical Sobolev--Bochner spaces. An Aubin--Lions compactness result in this setting is also proved. We then analyse several concrete examples of function spaces over time-evolving spatial domains and hypersurfaces for which we explicitly provide the definition of the time derivative and verify isomorphism properties with the aforementioned Sobolev--Bochner spaces. We conclude with the formulation and proof of well posedness for a class of nonlinear monotone problems on an abstract evolving space (generalising in particular the evolutionary p-Laplace equation on a moving domain or surface) and identify some additional evolutionary problems that can be appropriately formulated with the abstract setting developed in this work. Y1 - 2023 U6 - https://doi.org/10.1016/j.jde.2022.12.032 VL - 353 SP - 268 EP - 338 ER - TY - JOUR A1 - Djurdjevac, Ana T1 - Linear Parabolic Problems in Random Moving Domains N2 - We consider linear parabolic equations on a random non-cylindrical domain. Utilizing the domain mapping method, we write the problem as a partial differential equation with random coefficients on a cylindrical deterministic domain. Exploiting the deterministic results concerning equations on non-cylindrical domains, we state the necessary assumptions about the velocity filed and in addition, about the flow transformation that this field generates. In this paper we consider both cases, the uniformly bounded with respect to the sample and log-normal type transformation. In addition, we give an explicit example of a log-normal type transformation and prove that it does not satisfy the uniformly bounded condition. We define a general framework for considering linear parabolic problems on random non-cylindrical domains. As the first example, we consider the heat equation on a random tube domain and prove its well-posedness. Moreover, as the other example we consider the parabolic Stokes equation which illustrates the case when it is not enough just to study the plain-back transformation of the function, but instead to consider for example the Piola type transformation, in order to keep the divergence free property. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1137/19M1284889 VL - 9 IS - 2 SP - 848 EP - 879 ER - TY - JOUR A1 - Berg, Mascha A1 - Plöntzke, Julia A1 - Siebert, Heike A1 - Röblitz, Susanna T1 - Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations JF - Bulletin of Mathematical Biology N2 - Boolean delay equations (BDEs), with their relatively simple and intuitive mode of modelling, have been used in many research areas including, for example, climate dynamics and earthquake propagation. Their application to biological systems has been scarce and limited to the molecular level. Here, we derive and present two BDE models. One is directly derived from a previously published ordinary differential equation (ODE) model for the bovine estrous cycle, whereas the second model includes a modification of a particular biological mechanism. We not only compare the simulation results from the BDE models with the trajectories of the ODE model, but also validate the BDE models with two additional numerical experiments. One experiment induces a switch in the oscillatory pattern upon changes in the model parameters, and the other simulates the administration of a hormone that is known to shift the estrous cycle in time. The models presented here are the first BDE models for hormonal oscillators, and the first BDE models for drug administration. Even though automatic parameter estimation still remains challenging, our results support the role of BDEs as a framework for the systematic modelling of complex biological oscillators. Y1 - 2021 U6 - https://doi.org/10.1007/s11538-021-00942-z VL - 83 IS - 121 SP - 1 EP - 25 ER - TY - JOUR A1 - Prasad, Anup K. A1 - Tiwari, Chandni A1 - Ray, Sourav A1 - Holden, Stephanie A1 - Armstrong, David A. A1 - Rosengren, K. Johan A1 - Rodger, Alison A1 - Panwar, Ajay S. A1 - Martin, Lisandra L. T1 - Secondary Structure Transitions for a Family of Amyloidogenic, Antimircobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate JF - ChemPlusChem Y1 - 2022 U6 - https://doi.org/10.1002/cplu.202100408 VL - 87 SP - e202100408 ER - TY - THES A1 - Mathew, Maria T1 - Numerical treatment of radiative heat transfer on cooling process N2 - This thesis examines how taking into account surface to surface radiation impacts the cooling process in general. We formulate the non local bound- ary condition after introducing the general setting for the cooling model. In section 3, the mathematical description of the radiative heat transfer is dis- cussed. We cover the implementation of the radiative matrix in section 4, which is followed by a brief explanation of the radiative matrix’s structure and several techniques to dealing with the accompanying challenges. We investigate the importance of radiative heat transport by applying the given approach to a two-dimensional geometry and computing the ensuing cooling curves. We compare the findings of our computation to those ac- quired from experiment conducted and find that they are extremely similar. There is a considerable difference (of about 35%) in the time of cooling of the surface where there is a possibility of influence of radiation from the second surface to that of the surface with no influence at all. Although it is possible to infer that heat convection plays a role in the total result, this has yet to be proved. However, one can clearly see the significance of the surface to surface radiative heat transfer on these parts confirming the research question posed at the begining. The effect of the surface to surface radiative heat transfer has an influence on the resulting cooling time and should be considered in the model. Y1 - 2021 ER - TY - JOUR A1 - Birk, Ralph A1 - Raharinirina, N. Alexia A1 - Fackeldey, Konstantin A1 - Richter, Tonio Sebastian A1 - Weber, Marcus T1 - Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts N2 - In this paper, we explore the relationship patterns between Ancient Egyptian texts of the corpus ``Synodal decrees'', which are originating between 243 and 185 BCE, during the Ptolemaic period. Particularly, we are interested in analyzing the grammatical features of the different texts. Conventional data analysis methods such as correspondence Analysis are very useful to explore the patterns of statistical interdependence between categories of variables. However, it is based on a PCA-like dimension-reduction method and turned out to be unsuitable for our dataset due to the high dimensionality of our data representations. Additionally, the similarity between pairs of texts and pairs of grammatical features is observed through the distance between their representation, but the degree of association between a particular grammatical feature and a text is not. Here, we applied a qualitative Euclidean embedding method that provides a new Euclidean representation of the categories of variables. This new representation of the categories is constructed in such a way that all the patterns of statistical interdependence, similarity, and association, are seen through the Euclidean distance between them. Nevertheless, the PCA-like dimension-reduction method also performed poorly on our new representation. Therefore, we obtained a two-dimensional visualization using non-linear methods such UMAP or t-SNE. Although these dimension-reduction methods reduced the interpretability of interpoint distances, we were still able to identify important similarity patterns between the Synodal text as well as their association patterns with the grammatical features. Y1 - 2021 ER - TY - JOUR A1 - Mokhtari, Zahra A1 - Patterson, Robert I. A. A1 - Höfling, Felix T1 - Spontaneous trail formation in populations of auto-chemotactic walkers JF - New Journal of Physics Y1 - 2022 U6 - https://doi.org/10.1088/1367-2630/ac43ec VL - 24 SP - 013012 ER - TY - JOUR A1 - Gholami, Abbas A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000303 VL - 4 SP - 2000303 ER - TY - JOUR A1 - Klein, Rupert A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Delle Site, Luigi T1 - Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202100071 VL - 4 SP - 2100071 ER - TY - JOUR A1 - Pathania, Yogyata A1 - Chakraborty, Dipanjan A1 - Höfling, Felix T1 - Continuous demixing transition of binary liquids: finite-size scaling from the analysis of sub-systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000235 VL - 4 SP - 2000235 ER - TY - JOUR A1 - Frömberg, Daniela A1 - Höfling, Felix T1 - Generalized master equation for first-passage problems in partitioned spaces JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2021 U6 - https://doi.org/10.1088/1751-8121/abf2ec VL - 54 SP - 215601 ER - TY - JOUR A1 - Hungenberg, Klaus-Dieter A1 - Schwede, Christian A1 - Wulkow, Michael A1 - Wulkow, Niklas T1 - Determination of reactivity ratios for acrylic acid and its dimer from classical parameter estimation and Bayesian approach JF - Canadian Journal of Chemical Engineering N2 - The reactivity ratios of acrylic acid (AA, M1) and its dimer beta-acroyloxypropionic acid (diAA, M2) are determined from cumulative copolymerization data by two different methods: classical parameter estimation (PE) by minimizing the objective function and a Bayesian analysis. Classical PE gives r1 =0.74 and r2 = 1.23 at the minimum of the residual. From the Bayesian analysis, the probability distribution of the parameter sets is obtained, revealing the existence of parameter sets with rather the same probability. The influence of the number of data and the size of the measurement error are discussed. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1002/cjce.24330 SP - 1 EP - 10 ER - TY - JOUR A1 - Driesen, Joshua A1 - El-Khatib, Ziad A1 - Wulkow, Niklas A1 - Joblin, Mitchell A1 - Vasileva, Iskriyana A1 - Glücker, Andreas A1 - Kruspel, Valentin A1 - Vogel, Catherine T1 - Data-Powered Positive Deviance during the SARS-CoV-2 Pandemic—An Ecological Pilot Study of German Districts JF - International Journal of Environmental Research and Public Health N2 - We introduced the mixed-methods Data-Powered Positive Deviance (DPPD) framework as a potential addition to the set of tools used to search for effective response strategies against the SARS-CoV-2 pandemic. For this purpose, we conducted a DPPD study in the context of the early stages of the German SARS-CoV-2 pandemic. We used a framework of scalable quantitative methods to identify positively deviant German districts that is novel in the scientific literature on DPPD, and subsequently employed qualitative methods to identify factors that might have contributed to their comparatively successful reduction of the forward transmission rate. Our qualitative analysis suggests that quick, proactive, decisive, and flexible/pragmatic actions, the willingness to take risks and deviate from standard procedures, good information flows both in terms of data collection and public communication, alongside the utilization of social network effects were deemed highly important by the interviewed districts. Our study design with its small qualitative sample constitutes an exploratory and illustrative effort and hence does not allow for a clear causal link to be established. Thus, the results cannot necessarily be extrapolated to other districts as is. However, the findings indicate areas for further research to assess these strategies’ effectiveness in a broader study setting. We conclude by stressing DPPD’s strengths regarding replicability, scalability, adaptability, as well asits focus on local solutions, which make it a promising framework to be applied in various contexts,e.g., in the context of the Global South. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/ijerph18189765 VL - 18 IS - 9765 SP - 1 EP - 29 ER - TY - JOUR A1 - Stout, Brian A1 - Colom, Remi A1 - Bonod, Nicolas A1 - McPhedran, Ross C T1 - Spectral expansions of open and dispersive optical systems: Gaussian regularization and convergence JF - New J. Phys. Y1 - 2021 U6 - https://doi.org/10.1088/1367-2630/ac10a6 VL - 23 SP - 083004 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Kraus, Luitgard A1 - Sedeno-Noda, Antonio A1 - Borndörfer, Ralf T1 - Targeted multiobjective Dijkstra Algorithm JF - Networks N2 - We introduce the Targeted Multiobjective Dijkstra Algorithm (T-MDA), a label setting algorithm for the One-to-One Multiobjective Shortest Path (MOSP) Problem. It is based on the recently published Multiobjective Dijkstra Algorithm (MDA) and equips it with A*-like techniques. For any explored subpath, a label setting MOSP algorithm decides whether the subpath can be discarded or must be stored as part of the output. A major design choice is how to store subpaths from the moment they are first explored until the mentioned final decision can be made. The T-MDA combines the polynomially bounded size of the priority queue used in the MDA and alazy management of paths that are not in the queue. The running time bounds from the MDA remain valid. In practice, the T-MDA outperforms known algorithms from the literature and the increased memory consumption is negligible. In this paper, we benchmark the T-MDA against an improved version of the state of the art NAMOA∗drOne-to-One MOSP algorithm from the literature on a standard testbed. Y1 - 2023 U6 - https://doi.org/10.1002/net.22174 VL - 82 IS - 3 SP - 277 EP - 298 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - Faster exact solution of sparse MaxCut and QUBO problems T3 - ZIB-Report - 22-02 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85715 SN - 1438-0064 ER - TY - GEN A1 - Charousset-Brignol, Sandrine A1 - van Ackooij, Wim A1 - Oudjane, Nadia A1 - Daniel, Dominique A1 - Noceir, Slimane A1 - Haus, Utz-Uwe A1 - Lazzaro, Alfio A1 - Frangioni, Antonio A1 - Lobato, Rafael A1 - Ghezelsoflu, Ali A1 - Iardella, Niccolò A1 - Galli, Laura A1 - Gorgone, Enrico A1 - dell’Amico, Mauro A1 - Giannelos, Spyros A1 - Moreira, Alex A1 - Strbac, Goran A1 - Borozan, Stefan A1 - Falugi, Paula A1 - Pudjianto, Danny A1 - Wyrwoll, Lothar A1 - Schmitt, Carlo A1 - Franken, Marco A1 - Beulertz, Daniel A1 - Schwaeppe, Henrik A1 - Most, Dieter A1 - Yüksel-Ergün, Inci A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Synergistic approach of multi-energy models for a European optimal energy system management tool T2 - The Project Repository Journal Y1 - 2021 VL - 9 SP - 113 EP - 116 ER - TY - GEN A1 - Most, Dieter A1 - Lothar, Wyrwoll A1 - Schmitt, Carlo A1 - Yüksel-Ergün, Inci T1 - plan4res D2.2 - Case Study 1 Report - Multimodal energy concept for achieving Europe's carbon reduction goals Y1 - 2021 U6 - https://doi.org/10.5281/zenodo.5809338 ER - TY - GEN A1 - Masing, Berenike A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - The Price of Symmetric Line Plans in the Parametric City N2 - We consider the line planning problem in public transport in the Parametric City, an idealized model that captures typical scenarios by a (small) number of parameters. The Parametric City is rotation symmetric, but optimal line plans are not always symmetric. This raises the question to quantify the symmetry gap between the best symmetric and the overall best solution. For our analysis, we formulate the line planning problem as a mixed integer linear program, that can be solved in polynomial time if the solutions are forced to be symmetric. The symmetry gap is provably small when a specific Parametric City parameter is fixed, and we give an approximation algorithm for line planning in the Parametric City in this case. While the symmetry gap can be arbitrarily large in general, we show that symmetric line plans are a good choice in most practical situations. T3 - ZIB-Report - 22-01 KW - line planning KW - mixed integer programming KW - parametric city modeling Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85648 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2020 T3 - Jahresbericht - 2020 KW - Jahresbericht Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85609 SN - 0934-5892 VL - 2020 ER - TY - GEN T1 - Annual Report 2019 T3 - Jahresbericht - 2019 KW - Jahresbericht Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85594 SN - 0934-5892 VL - 2019 ER - TY - GEN T1 - Annual Report 2018 T3 - Jahresbericht - 2018 KW - Jahresbericht Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74971 SN - 0934-5892 VL - 2018 ER - TY - CHAP A1 - Kostre, Margarita A1 - Sunkara, Vikram A1 - Djurdjevac Conrad, Natasa T1 - Inference of historical influence networks T2 - International Conference on Complex Networks & Their Applications Proceedings N2 - We study the romanization process of northern Africa from 50 BC till 300 AD. Our goal is to infer the communication strength between different subregions, based on the evolution of the status of cities. Herefore, we use the general inverse infection model, that infers the weights of a known underlying network, given observations of the spreading on this network. As infection process we choose the SI metapopulation model, where I stands for a city with a Roman status. To solve the minimization problem we use the particle swarm optimization algorithm with a specific choice of parameters. Y1 - 2021 U6 - https://doi.org/10.12752/8558 SP - 110 EP - 113 ET - International Conference on Complex Networks & Their Applications ER - TY - THES A1 - Chemnitz, Robin T1 - Spectral Coarse-Graining of SIS Dynamics on Networks Y1 - 2021 ER - TY - JOUR A1 - Schweigart, Fleur T1 - KARTHAGO, TUNESIEN Datengesteuerte Modellierung des Romanisierungsprozesses in Nordafrika JF - e-Forschungsberichte des Deutschen Archäologischen Instituts. Berlin: Deutsches Archäologisches Institut, Zentrale. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.34780/d469-84h2 VL - Fasc. 1 ER - TY - JOUR A1 - Besançon, Mathieu A1 - Anjos, Miguel F. A1 - Brotcorne, Luce T1 - Complexity of near-optimal robust versions of multilevel optimization problems JF - Optimization Letters N2 - Near-optimality robustness extends multilevel optimization with a limited deviation of a lower level from its optimal solution, anticipated by higher levels. We analyze the complexity of near-optimal robust multilevel problems, where near-optimal robustness is modelled through additional adversarial decision-makers. Near-optimal robust versions of multilevel problems are shown to remain in the same complexity class as the problem without near-optimality robustness under general conditions. Y1 - 2021 U6 - https://doi.org/10.1007/s11590-021-01754-9 VL - 15 IS - 8 SP - 2597 EP - 2610 ER - TY - GEN A1 - Lemke, Mathias A1 - Stein, Lewin A1 - Hölter, Arne A1 - Weinzierl, Stefan T1 - Adjungierten-basierte Synthese und Bestimmung optimaler Treiberfunktionen von Lautsprechern mit komplexer Richtcharakteristik N2 - Die Bestimmung optimaler Treiberfunktionen von Lautsprechern mit frequenzabhängiger Richtcharakteristik ist ein schlecht gestelltes Optimierungsproblem. Zu dessen Lösung haben die Autoren in vorangegangenen Beiträgen eine adjungierten-basierte Methode zur Optimierung von Lautsprecher-Arrays im Zeitbereich vorgestellt [5, 6, 8]. Diese ermöglicht unter anderem die Berücksichtigung von Berandungen und Umgebungseffekten wie Wind, war jedoch bisher auf monopol-artige Quellen beschränkt. Um diese Einschränkung zu beheben, haben die Autoren einen adjungierten-basierten Zeitbereichsansatz mit Finiten-Differenzen (FDTD) zur Synthese komplexer synthetischer Schallquellen durch diskrete, gitter-basierte Monopole vorgestellt [4, 9]. In diesem Beitrag demonstrieren die Autoren die entsprechende Modellierung eines realen Zweiwege-Monitors (A). Zudem wird gezeigt, wie sich die Vielzahl der zur Synthese verwendeten Monopole in eine Lautsprecher-Treiberfunktion überführen lassen (B). Y1 - 2021 SN - 978-3-939296-18-8 U6 - https://doi.org/https://doi.org/10.14279/depositonce-12515 PB - Deutsche Gesellschaft für Akustik e.V. ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeno-Noda, Antonio A1 - Borndörfer, Ralf T1 - An Improved Multiobjective Shortest Path Algorithm JF - Computers & Operations Research N2 - We present a new label-setting algorithm for the Multiobjective Shortest Path (MOSP) problem that computes a minimum complete set of efficient paths for a given instance. The size of the priority queue used in the algorithm is bounded by the number of nodes in the input graph and extracted labels are guaranteed to be efficient. These properties allow us to give a tight output-sensitive running time bound for the new algorithm that can almost be expressed in terms of the running time of Dijkstra’s algorithm for the Shortest Path problem. Hence, we suggest to call the algorithm Multiobjective Dijkstra Algorithm (MDA). The simplified label management in the MDA allows us to parallelize some subroutines. In our computational experiments, we compare the MDA and the classical label-setting MOSP algorithm by Martins, which we improved using new data structures and pruning techniques. On average, the MDA is 2 to 9 times faster on all used graph types. On some instances the speedup reaches an order of magnitude. Y1 - 2021 U6 - https://doi.org/10.1016/j.cor.2021.105424 VL - 135 ER - TY - JOUR A1 - Šofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - Accelerating domain propagation: An efficient GPU-parallel algorithm over sparse matrices JF - Parallel Computing N2 - • Currently, domain propagation in state-of-the-art MIP solvers is single thread only. • The paper presents a novel, efficient GPU algorithm to perform domain propagation. • Challenges are dynamic algorithmic behavior, dependency structures, sparsity patterns. • The algorithm is capable of running entirely on the GPU with no CPU involvement. • We achieve speed-ups of around 10x to 20x, up to 180x on favorably-large instances. Y1 - 2022 U6 - https://doi.org/10.1016/j.parco.2021.102874 VL - 109 SP - 102874 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A computational status update for exact rational mixed integer programming JF - Mathematical Programming N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours. Y1 - 2022 U6 - https://doi.org/10.1007/s10107-021-01749-5 PB - Springer ER - TY - JOUR A1 - Heida, Martin A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension JF - SIAM Journal on Numerical Analysis N2 - We study consistency of cell-centered finite difference methods for elliptic equations with degenerate coefficients in any space dimension $d \geq 2$. This results in order of convergence estimates in the natural weighted energy norm and in the weighted discrete $L^2$-norm on admissible meshes. The cells of meshes under consideration may be very irregular in size. We particularly allow the size of certain cells to remain bounded from below even in the asymptotic limit. For uniform meshes we show that the order of convergence is at least 1 in the energy semi-norm, provided the discrete and continuous solutions exist and the continuous solution has $H^2$ regularity. Y1 - 2022 U6 - https://doi.org/10.20347/WIAS.PREPRINT.2913 ER - TY - GEN A1 - Ambellan, Felix A1 - Hanik, Martin A1 - von Tycowicz, Christoph T1 - Morphomatics: Geometric morphometrics in non-Euclidean shape spaces N2 - Morphomatics is an open-source Python library for (statistical) shape analysis developed within the geometric data analysis and processing research group at Zuse Institute Berlin. It contains prototype implementations of intrinsic manifold-based methods that are highly consistent and avoid the influence of unwanted effects such as bias due to arbitrary choices of coordinates. KW - shape analysis KW - geometric statistics KW - geometric morphometrics Y1 - 2021 U6 - https://doi.org/10.12752/8544 N1 - https://morphomatics.github.io/ ER - TY - GEN A1 - Bertelmann, Roland A1 - Koch, Thorsten A1 - Ceynowa, Klaus A1 - Söllner, Konstanze A1 - Christof, Jürgen A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Putnings, Markus A1 - Pampel, Heinz A1 - Kuberek, Monika A1 - Boltze, Julia A1 - Lohrum, Stefan A1 - Retter, Regina A1 - Höllerl, Annika A1 - Faensen, Katja A1 - Steffen, Ronald A1 - Gross, Matthias A1 - Hoffmann, Cornelia A1 - Haoua, Marsa T1 - DeepGreen: Etablierung und Weiterentwicklung rechtssicherer Workflows zur effizienten Umsetzung von Open-Access-Komponenten in Lizenzvereinbarungen für wissenschaftliche Publikationen – Abschlussbericht N2 - DeepGreen wurde vom 01.08.2018 bis zum 30.06.2021 in einer zweiten Projektphase von der Deutschen Forschungsgemeinschaft (DFG) gefördert. DeepGreen unterstützt Bibliotheken als Dienstleister für Hochschulen, außeruniversitäre Forschungseinrichtungen und die dort tätigen Wissenschaftler:innen dabei, Publikationen auf Open-Access-Repositorien frei zugänglich zu machen und fördert das Zusammenspiel von wissenschaftlichen Einrichtungen und Verlagen. An der zweiten Projektphase waren der Kooperative Bibliotheksverbund Berlin-Brandenburg, die Bayerische Staatsbibliothek, der Bibliotheksverbund Bayern, die Universitätsbibliotheken der Friedrich-Alexander-Universität Erlangen-Nürnberg und der Technischen Universität Berlin und das Helmholtz Open Science Office beteiligt. In dem Projekt wurde erfolgreich eine technische und organisatorische Lösung zur automatisierten Verteilung von Artikeldaten wissenschaftlicher Verlage an institutionelle und fachliche Repositorien entwickelt. In der zweiten Projektphase lag der Fokus auf der Erprobung der Datendrehscheibe in der Praxis und der Ausweitung auf weitere Datenabnehmer und weitere Verlage. Im Anschluss an die DFG-geförderte Projektlaufzeit ist DeepGreen in einen zweijährigen Pilotbetrieb übergegangen. Ziel des Pilotbetriebs ist es, den Übergang in einen bundesweiten Real-Betrieb vorzubereiten. T3 - ZIB-Report - 21-37 KW - Open Access KW - Repositorien KW - DeepGreen Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85420 SN - 1438-0064 ER - TY - CHAP A1 - Rickert, Lucas A1 - Gao, Timm A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Tobias, Heindel T1 - A Quantum Key Distribution Testbed Using Plug&Play Telecom-Wavelength Single-Photons T2 - Quantum Information and Measurement VI Y1 - 2021 U6 - https://doi.org/10.1364/QIM.2021.M2C.1 SP - M2C.1 ER - TY - CHAP A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Nonlinear Hierarchical Model for Longitudinal Data on Manifolds T2 - 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) N2 - Large longitudinal studies provide lots of valuable information, especially in medical applications. A problem which must be taken care of in order to utilize their full potential is that of correlation between intra-subject measurements taken at different times. For data in Euclidean space this can be done with hierarchical models, that is, models that consider intra-subject and between-subject variability in two different stages. Nevertheless, data from medical studies often takes values in nonlinear manifolds. Here, as a first step, geodesic hierarchical models have been developed that generalize the linear ansatz by assuming that time-induced intra-subject variations occur along a generalized straight line in the manifold. However, this is often not the case (e.g., periodic motion or processes with saturation). We propose a hierarchical model for manifold-valued data that extends this to include trends along higher-order curves, namely Bézier splines in the manifold. To this end, we present a principled way of comparing shape trends in terms of a functional-based Riemannian metric. Remarkably, this metric allows efficient, yet simple computations by virtue of a variational time discretization requiring only the solution of regression problems. We validate our model on longitudinal data from the osteoarthritis initiative, including classification of disease progression. Y1 - 2022 U6 - https://doi.org/10.1109/ISBI52829.2022.9761465 SP - 1 EP - 5 ER - TY - CHAP A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yamamura, Keiichiro A1 - Yoshida, Akihiro A1 - Kaji, Shizuo A1 - Yasuda, Masaya A1 - Fujisawa, Katsuki T1 - CMAP-LAP: Configurable Massively Parallel Solver for Lattice Problems T2 - HiPC 2021 proceedings N2 - Lattice problems are a class of optimization problems that are notably hard. There are no classical or quantum algorithms known to solve these problems efficiently. Their hardness has made lattices a major cryptographic primitive for post-quantum cryptography. Several different approaches have been used for lattice problems with different computational profiles; some suffer from super-exponential time, and others require exponential space. This motivated us to develop a novel lattice problem solver, CMAP-LAP, based on the clever coordination of different algorithms that run massively in parallel. With our flexible framework, heterogeneous modules run asynchronously in parallel on a large-scale distributed system while exchanging information, which drastically boosts the overall performance. We also implement full checkpoint-and-restart functionality, which is vital to high-dimensional lattice problems. Through numerical experiments with up to 103,680 cores, we evaluated the performance and stability of our system and demonstrated its high capability for future massive-scale experiments. Y1 - 2021 ER - TY - JOUR A1 - von Lindheim, Johannes A1 - Harikrishnan, Abhishek A1 - Dörffel, Tom A1 - Klein, Rupert A1 - Koltai, Peter A1 - Mikula, Natalia A1 - Müller, Annette A1 - Névir, Peter A1 - Pacey, George A1 - Polzin, Robert A1 - Vercauteren, Nikki T1 - Definition, detection and tracking of persistent structures in atmospheric flows JF - arXiv N2 - Long-lived flow patterns in the atmosphere such as weather fronts, mid-latitude blockings or tropical cyclones often induce extreme weather conditions. As a consequence, their description, detection, and tracking has received increasing attention in recent years. Similar objectives also arise in diverse fields such as turbulence and combustion research, image analysis, and medical diagnostics under the headlines of "feature tracking", "coherent structure detection" or "image registration" - to name just a few. A host of different approaches to addressing the underlying, often very similar, tasks have been developed and successfully used. Here, several typical examples of such approaches are summarized, further developed and applied to meteorological data sets. Common abstract operational steps form the basis for a unifying framework for the specification of "persistent structures" involving the definition of the physical state of a system, the features of interest, and means of measuring their persistence. Y1 - 2021 ER - TY - JOUR A1 - Garcia Santiago, Xavier A1 - Hammerschmidt, Martin A1 - Sachs, Johannes A1 - Burger, Sven A1 - Kwon, Hyunah A1 - Knöller, Marvin A1 - Arens, Tilo A1 - Fischer, Peer A1 - Fernandez-Corbaton, Ivan A1 - Rockstuhl, Carsten T1 - Toward maximally electromagnetically chiral scatterers at optical frequencies JF - ACS Photonics Y1 - 2022 U6 - https://doi.org/10.1021/acsphotonics.1c01887 VL - 9 SP - 1954 ER - TY - GEN A1 - Grewe, C. Martin A1 - Zachow, Stefan T1 - Release of the FexMM for the Open Virtual Mirror Framework N2 - THIS MODEL IS FOR NON-COMMERCIAL RESEARCH PURPOSES. ONLY MEMBERS OF UNIVERSITIES OR NON-COMMERCIAL RESEARCH INSTITUTES ARE ELIGIBLE TO APPLY. 1. Download, fill, and sign the form available from: https://media.githubusercontent.com/media/mgrewe/ovmf/main/data/fexmm_license_agreement.pdf 2. Send the signed form to: fexmm@zib.de NOTE: Use an official email address of your institution for the request. Y1 - 2021 U6 - https://doi.org/10.12752/8532 ER - TY - GEN A1 - Hennings, Felix A1 - Petkovic, Milena A1 - Streubel, Tom T1 - On the Numerical Treatment of Interlaced Target Values - Modeling, Optimization and Simulation of Regulating Valves in Gas Networks N2 - Due to the current and foreseeable shifts in energy production, the trading and transport operations of gas will become more dynamic, volatile, and hence also less predictable. Therefore, computer-aided support in terms of rapid simulation and control optimization will further broaden its importance for gas network dispatching. In this paper, we aim to contribute and openly publish two new mathematical models for regulators, also referred to as control valves, which together with compressors make up the most complex and involved types of active elements in gas network infrastructures. They provide full direct control over gas networks but are in turn controlled via target values, also known as set-point values, themselves. Our models incorporate up to six dynamical target values to define desired transient states for the elements' local vicinity within the network. That is, each pair of every two target values defines a bounding box for the inlet pressure, outlet pressure as well as the passing mass flow of gas. In the proposed models, those target values are prioritized differently and are constantly in competition with each other, which can only be resolved dynamically at run-time of either a simulation or optimization process. Besides careful derivation, we compare simulation and optimization results with predictions of the commercial simulation tool SIMONE. T3 - ZIB-Report - 21-32 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85359 SN - 1438-0064 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Prodanov, Dimiter T1 - The Active Segmentation Platform for Microscopic Image Classification and Segmentation JF - Brain Sciences. 2021 N2 - Image segmentation still represents an active area of research since no universal solution can be identified. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. The article presents an automated image segmentation and classification platform, called Active Segmentation, which is based on ImageJ. The platform integrates expert domain knowledge, providing partial ground truth, with geometrical feature extraction based on multi-scale signal processing combined with machine learning. The approach in image segmentation is exemplified on the ISBI 2012 image segmentation challenge data set. As a second application we demonstrate whole image classification functionality based on the same principles. The approach is exemplified using the HeLa and HEp-2 data sets. Obtained results indicate that feature space enrichment properly balanced with feature selection functionality can achieve performance comparable to deep learning approaches. In summary, differential geometry can substantially improve the outcome of machine learning since it can enrich the underlying feature space with new geometrical invariant objects. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/brainsci11121645 VL - 11 IS - 12 SP - 1645 ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Besançon, Mathieu A1 - Chen, Wei-Kun A1 - Chmiela, Antonia A1 - Donkiewicz, Tim A1 - van Doornmalen, Jasper A1 - Eifler, Leon A1 - Gaul, Oliver A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Graczyk, Christoph A1 - Halbig, Katrin A1 - Hoen, Alexander A1 - Hojny, Christopher A1 - van der Hulst, Rolf A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Matter, Frederic A1 - Mühmer, Erik A1 - Müller, Benjamin A1 - Pfetsch, Marc E. A1 - Rehfeldt, Daniel A1 - Schlein, Steffan A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Sofranac, Boro A1 - Turner, Mark A1 - Vigerske, Stefan A1 - Wegscheider, Fabian A1 - Wellner, Philipp A1 - Weninger, Dieter A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 8.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in SCIP-Jack. T3 - ZIB-Report - 21-41 KW - Constraint integer programming KW - Linear programming KW - Mixed-integer linear programming KW - Mixed-integer nonlinear programming KW - Optimization solver KW - Branch-and-cut KW - Branch-and-price KW - Column generation KW - Parallelization KW - Mixed-integer semidefinite programming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85309 SN - 1438-0064 ER - TY - GEN A1 - Khorsandi, Ramin T1 - Gitram 1.0.0 N2 - Gitram is a software that processes various metadata and data content from GIT and exports them in the format of an XML file. The software is specifically designed for the HPO-navi project. It is also compatible with Opus4 and any other software that can receive data through the sword interface. Gitram process the metadata and the repository content and sends it to Opus4 via the sword interface. The data is taken from a zip file that is stored in the “dataBackup” folder. Users also have an option of saving the data as a document file on Opus. Metadata can also be received from GitLab via a webhook. The entire project is programmed in Python 3.8+ and can be installed on Ubuntu 16 or above. It is open-source and its functionality can be modified to the users needs. Y1 - 2021 U6 - https://doi.org/10.12752/8527 ER - TY - GEN A1 - Shinano, Yuji T1 - UG - Ubiquity Generator Framework v1.0.0beta N2 - UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. v1.0.0: new documentation and cmake, generalization of ug framework, implementation of selfsplitrampup for fiber- and parascip, better memory and time limit handling. KW - parallelization framework KW - branch-and-bound parallelization KW - integer optimization Y1 - 2021 U6 - https://doi.org/10.12752/8521 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Koltai, Péter A1 - Sunkara, Vikram A1 - Schütte, Christof T1 - Data-driven modelling of nonlinear dynamics by barycentric coordinates and memory JF - J. Stat. Phys. N2 - We present a numerical method to model dynamical systems from data. We use the recently introduced method Scalable Probabilistic Approximation (SPA) to project points from a Euclidean space to convex polytopes and represent these projected states of a system in new, lower-dimensional coordinates denoting their position in the polytope. We then introduce a specific nonlinear transformation to construct a model of the dynamics in the polytope and to transform back into the original state space. To overcome the potential loss of information from the projection to a lower-dimensional polytope, we use memory in the sense of the delay-embedding theorem of Takens. By construction, our method produces stable models. We illustrate the capacity of the method to reproduce even chaotic dynamics and attractors with multiple connected components on various examples. Y1 - 2021 ER - TY - GEN A1 - Ribera Borrell, Enric A1 - Quer, Jannes A1 - Richter, Lorenz A1 - Schütte, Christof T1 - Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics N2 - Sampling rare events in metastable dynamical systems is often a computationally expensive task and one needs to resort to enhanced sampling methods such as importance sampling. Since we can formulate the problem of finding optimal importance sampling controls as a stochastic optimization problem, this then brings additional numerical challenges and the convergence of corresponding algorithms might as well suffer from metastabilty. In this article we address this issue by combining systematic control approaches with the heuristic adaptive metadynamics method. Crucially, we approximate the importance sampling control by a neural network, which makes the algorithm in principle feasible for high dimensional applications. We can numerically demonstrate in relevant metastable problems that our algorithm is more effective than previous attempts and that only the combination of the two approaches leads to a satisfying convergence and therefore to an efficient sampling in certain metastable settings. T3 - ZIB-Report - 21-40 KW - importance sampling KW - stochastic optimal control KW - rare event simulation KW - metastability KW - neural networks KW - metadynamics Y1 - 2021 SN - 1438-0064 ER - TY - GEN A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yasuda, Masaya A1 - Kaji, Shizuo A1 - Yamamura, Keiichiro A1 - Fujisawa, Katsuki T1 - Massively parallel sharing lattice basis reduction N2 - For cryptanalysis in lattice-based schemes, the performance evaluation of lattice basis reduction using high-performance computers is becoming increasingly important for the determination of the security level. We propose a distributed and asynchronous parallel reduction algorithm based on randomization and DeepBKZ, which is an improved variant of the block Korkine-Zolotarev (BKZ) reduction algorithm. Randomized copies of a lattice basis are distributed to up to 103,680 cores and independently reduced in parallel, while some basis vectors are shared asynchronously among all processes via MPI. There is a trade-off between randomization and information sharing; if a substantial amount of information is shared, all processes will work on the same problem, thereby diminishing the benefit of parallelization. To monitor this balance between randomness and sharing, we propose a metric to quantify the variety of lattice bases. We empirically find an optimal parameter of sharing for high-dimensional lattices. We demonstrate the efficacy of our proposed parallel algorithm and implementation with respect to both performance and scalability through our experiments. T3 - ZIB-Report - 21-38 KW - Discrete optimization KW - Lattice problem KW - Lattice-based cryptography KW - Shortest vector problem KW - Parallel algorithms KW - Ubiquity Generator Framework Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85209 SN - 1438-0064 N1 - under review ER - TY - THES A1 - Lenz, Ralf T1 - Optimization of Stationary Expansion Planning and Transient Network Control by Mixed-Integer Nonlinear Programming Y1 - 2021 UR - http://dx.doi.org/10.14279/depositonce-12765 U6 - https://doi.org/10.14279/depositonce-12765 ER - TY - GEN A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends. T3 - ZIB-Report - 21-39 KW - Longitudinal KW - Hierarchical Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85187 SN - 1438-0064 N1 - sumbitted to: Journal of Mathematical Imaging and Vision ER - TY - JOUR A1 - Bauer, Wolfgang A1 - Weber, Marcus A1 - Diehl-Wiesenecker, Eva A1 - Galtung, Noa A1 - Prpic, Monika A1 - Somasundaram, Rajan A1 - Tauber, Rudolf A1 - Schwenk, Jochen A1 - Micke, Patrick A1 - Kappert, Kai T1 - Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection JF - Viruses N2 - We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection. We identified distinct plasma proteins linked to the presence and course of COVID-19. These plasma proteomic findings may translate to a protein fingerprint, helping to assist clinical management decisions. Y1 - 2021 U6 - https://doi.org/10.3390/v13122456 VL - 13 IS - 12 SP - 2456 ER - TY - JOUR A1 - Xu, Xiaofei A1 - Chen, Ying A1 - Zhang, Ge A1 - Koch, Thorsten T1 - Modeling functional time series and mixed-type predictors with partially functional autoregressions* JF - Journal of Business and Economic Statistics N2 - In many business and economics studies, researchers have sought to measure the dynamic dependence of curves with high-dimensional mixed-type predictors. We propose a partially functional autoregressive model (pFAR) where the serial dependence of curves is controlled by coefficient operators that are defined on a two-dimensional surface, and the individual and group effects of mixed-type predictors are estimated with a two-layer regularization. We develop an efficient estimation with the proven asymptotic properties of consistency and sparsity. We show how to choose the sieve and tuning parameters in regularization based on a forward-looking criterion. In addition to the asymptotic properties, numerical validation suggests that the dependence structure is accurately detected. The implementation of the pFAR within a real-world analysis of dependence in German daily natural gas flow curves, with seven lagged curves and 85 scalar predictors, produces superior forecast accuracy and an insightful understanding of the dynamics of natural gas supply and demand for the municipal, industry, and border nodes, respectively. Y1 - 2021 U6 - https://doi.org/10.1080/07350015.2021.2011299 SP - 1 EP - 43 ER - TY - THES A1 - Rehfeldt, Daniel T1 - Faster algorithms for Steiner tree and related problems: From theory to practice KW - Steiner tree problem Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85148 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Franz, Henriette A1 - Koch, Thorsten T1 - Optimal Connected Subgraphs: Integer Programming Formulations and Polyhedra JF - Networks Y1 - 2022 U6 - https://doi.org/10.1002/net.22101 VL - 80 IS - 3 SP - 314 EP - 332 PB - Wiley ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Implications, Conflicts, and Reductions for Steiner Trees JF - Mathematical Programming Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01757-5 VL - 197 SP - 903 EP - 966 PB - Springer ER - TY - GEN A1 - Shinano, Yuji T1 - UG - Ubiquity Generator Framework v0.9.1 N2 - UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. For MIP solving, ParaSCIP and FiberSCIP are well debugged and should be stable. For MINLP solving, they are relatively stable, but not as thoroughly debugged. This release version should handle branch-and-cut approaches where subproblems are defined by variable bounds and also by constrains for ug[SCIP,*] ParaSCIP and FiberSCIP). Therefore, problem classes other than MIP or MINLP can be handled, but they have not been tested yet. v0.9.1: Update orbitope cip files. KW - parallelization framework KW - branch-and-bound parallelization KW - integer optimization Y1 - 2020 U6 - https://doi.org/10.12752/8508 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Gorgulla, Christoph A1 - Weber, Marcus T1 - Neue Medikamente dank Supercomputern JF - Spektrum der Wissenschaft N2 - Die aktuelle Pandemie verdeutlicht, wie wichtig es ist, rasch geeignete Arzneimittel zu finden. In Computer­simulationen gelingt das erheblich schneller als im Labor. Gegen das Coronavirus ließen sich auf diese Weise bereits Wirkstoffkandidaten identifizieren. Y1 - 2021 IS - 11 SP - 40 EP - 46 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Liu, Tuo A1 - Hildebrandt, Andrea A1 - Zachow, Stefan T1 - The Open Virtual Mirror Framework for Enfacement Illusions - Enhancing the Sense of Agency With Avatars That Imitate Facial Expressions JF - Behavior Research Methods Y1 - 2022 U6 - https://doi.org/10.3758/s13428-021-01761-9 PB - Springer ER - TY - CHAP A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Schneider, Philipp-Immanuel A1 - Olszewski, Jacek A1 - Poturaj, Krzystof A1 - Wojcik, Grzegorz A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Rodt, Sven A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Stand-alone quantum dot-based single-photon source operating at telecommunication wavelengths T2 - 10th International Conference on Spontaneous Coherence in Excitonic Systems ICSCE10 Y1 - 2020 SP - 39 ER - TY - JOUR A1 - Leser, Ulf A1 - Hilbrich, Marcus A1 - Draxl, Claudia A1 - Eisert, Peter A1 - Grunske, Lars A1 - Hostert, Patrick A1 - Kainmüller, Dagmar A1 - Kao, Odej A1 - Kehr, Birte A1 - Kehrer, Timo A1 - Koch, Christoph A1 - Markl, Volker A1 - Meyerhenke, Henning A1 - Rabl, Tilmann A1 - Reinefeld, Alexander A1 - Reinert, Knut A1 - Ritter, Kerstin A1 - Scheuermann, Björn A1 - Schintke, Florian A1 - Schweikardt, Nicole A1 - Weidlich, Matthias T1 - The Collaborative Research Center FONDA JF - Datenbank-Spektrum Y1 - 2021 U6 - https://doi.org/10.1007/s13222-021-00397-5 VL - 21 IS - 3 SP - 255 EP - 260 ER - TY - JOUR A1 - Colom, Remi A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Kivshar, Yuri A1 - Burger, Sven T1 - Enhanced Purcell factor for nanoantennas supporting interfering resonances JF - Phys. Rev. Research Y1 - 2022 U6 - https://doi.org/10.1103/PhysRevResearch.4.023189 VL - 4 SP - 023189 ER - TY - JOUR A1 - Aigner, Kevin-Martin A1 - Clarner, Jan-Patrick A1 - Liers, Frauke A1 - Martin, Alexander T1 - Robust Approximation of Chance Constrained DC Optimal Power Flow under Decision-Dependent Uncertainty JF - European Journal of Operational Research N2 - We propose a mathematical optimization model and its solution for joint chance constrained DC Optimal Power Flow. In this application, it is particularly important that there is a high probability of transmission limits being satisfied, even in the case of uncertain or fluctuating feed-in from renewable energy sources. In critical network situations where the network risks overload, renewable energy feed-in has to be curtailed by the transmission system operator (TSO). The TSO can reduce the feed-in in discrete steps at each network node. The proposed optimization model minimizes curtailment while ensuring that there is a high probability of transmission limits being maintained. The latter is modeled via (joint) chance constraints that are computationally challenging. Thus, we propose a solution approach based on the robust safe approximation of these constraints. Hereby, probabilistic constraints are replaced by robust constraints with suitably defined uncertainty sets constructed from historical data. The ability to discretely control the power feed-in then leads to a robust optimization problem with decision-dependent uncertainties, i.e. the uncertainty sets depend on decision variables. We propose an equivalent mixed-integer linear reformulation for box uncertainties with the exact linearization of bilinear terms. Finally, we present numerical results for different test cases from the Nesta archive, as well as for a real network. We consider the discrete curtailment of solar feed-in, for which we use real-world weather and network data. The experimental tests demonstrate the effectiveness of this method and run times are very fast. Moreover, on average the calculated robust solutions only lead to a small increase in curtailment, when compared to nominal solutions. Y1 - 2021 ER - TY - JOUR A1 - Zhang, Wei A1 - Li, Tiejun A1 - Schütte, Christof T1 - Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks JF - Journal of Computational Physics N2 - In this paper, we consider the eigenvalue PDE problem of the infinitesimal generators of metastable diffusion processes. We propose a numerical algorithm based on training artificial neural networks for solving the leading eigenvalues and eigenfunctions of such high-dimensional eigenvalue problem. The algorithm is useful in understanding the dynamical behaviors of metastable processes on large timescales. We demonstrate the capability of our algorithm on a high-dimensional model problem, and on the simple molecular system alanine dipeptide. Y1 - 2021 U6 - https://doi.org/10.1016/j.jcp.2022.111377 VL - 465 ER - TY - GEN A1 - Klimpel, Paul ED - Lehnert, Katrin ED - Müller, Anja T1 - Urheberrechtsreform 2021. Neue Chancen für das kulturelle Erbe N2 - Im Juni 2021 fand die jüngste Urheberrechtsreform statt. Sie bietet neue Chancen für das kulturelle Erbe, sei es in den Archiven und Bibliotheken sozialer Bewegungen, kleinen und großen Museen oder staatlichen Archiven und Bibliotheken. Denn die Novelle beinhaltet neue gesetzliche Erlaubnisse, die insbesondere die Online-Stellung von Archivmaterialien (“nicht verfügbare Werke”) und den Schutz der Gemeinfreiheit betreffen. Das vorliegende Bulletin geht komprimiert auf diese Neuerungen ein und erklärt, was sich in Zukunft ändern wird. Darauf aufbauend wird Mitte 2022 eine ausführliche und aktualisierte Publikation zur Rechteklärung erscheinen. Diese Vorveröffentlichung soll erste drängende Fragen klären. Herausgeber:innen sind das Digitale Deutsche Frauenarchiv (DDF) und das Forschungs- und Kompetenzzentrum Digitalisierung Berlin (digiS), die bereits unabhängig voneinander Handreichungen zu rechtlichen Aspekten der Digitalisierung veröffentlichten. KW - 4062127-3 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84315 ET - 1. Auflage ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Garcia-Santiago, Xavier A1 - Wiegand, Benjamin A1 - Anton, Oliver A1 - Krutzik, Markus A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Advances in Bayesian optimization for photonics and quantum atom optics applications T2 - OSA Advanced Photonics Congress Y1 - 2021 U6 - https://doi.org/10.1364/IPRSN.2021.JTh1E.2 SP - JTh1E.2 ER - TY - CHAP A1 - Chmiela, Antonia A1 - Khalil, Elias B. A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Pokutta, Sebastian T1 - Learning to Schedule Heuristics in Branch and Bound T2 - Thirty-fifth Conference on Neural Information Processing Systems, NeurIPS 2021 N2 - Primal heuristics play a crucial role in exact solvers for Mixed Integer Programming (MIP). While solvers are guaranteed to find optimal solutions given sufficient time, real-world applications typically require finding good solutions early on in the search to enable fast decision-making. While much of MIP research focuses on designing effective heuristics, the question of how to manage multiple MIP heuristics in a solver has not received equal attention. Generally, solvers follow hard-coded rules derived from empirical testing on broad sets of instances. Since the performance of heuristics is instance-dependent, using these general rules for a particular problem might not yield the best performance. In this work, we propose the first data-driven framework for scheduling heuristics in an exact MIP solver. By learning from data describing the performance of primal heuristics, we obtain a problem-specific schedule of heuristics that collectively find many solutions at minimal cost. We provide a formal description of the problem and propose an efficient algorithm for computing such a schedule. Compared to the default settings of a state-of-the-art academic MIP solver, we are able to reduce the average primal integral by up to 49% on a class of challenging instances. Y1 - 2021 ER - TY - JOUR A1 - Martens, Kevin A1 - Funck, Timon A1 - Santiago, Eva Y. A1 - Govorov, Alexander O. A1 - Burger, Sven A1 - Liedl, Tim T1 - Onset of Chirality in Plasmonic Meta-Molecules and Dielectric Coupling JF - ACS Nano Y1 - 2022 U6 - https://doi.org/10.1021/acsnano.2c04729 VL - 16 SP - 16143 ER - TY - JOUR A1 - Ahiboz, Doguscan A1 - Andresen, Elina A1 - Manley, Phillip A1 - Resch-Genger, Ute A1 - Würth, Christian A1 - Becker, Christiane T1 - Metasurface-Enhanced Photon Upconversion upon 1550 nm Excitation JF - Adv. Opt. Mater. Y1 - 2021 U6 - https://doi.org/10.1002/adom.202101285 VL - 9 SP - 2101285 ER - TY - GEN A1 - Mokhtari, Zahra A1 - Patterson, Robert I. A. A1 - Höfling, Felix T1 - Spontaneous trail formation in populations of auto-chemotactic walkers N2 - We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive off-lattice computer simulations aiming at the scale of insects, e.g., ants, we identify a number of emerging stationary patterns and obtain qualitatively the non-equilibrium \add{state} diagram of the model, spanned by the strength of the agent--pheromone interaction and the number density of the population. In particular, we demonstrate the spontaneous formation of persistent, macroscopic trails, and highlight some behaviour that is consistent with a dynamic phase transition. This includes a characterisation of the mass of system-spanning trails as a potential order parameter. We also propose a dynamic model for a few macroscopic observables, including the sub-population size of trail-following agents, which captures the early phase of trail formation. T3 - ZIB-Report - 21-36 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84466 SN - 1438-0064 ER - TY - CHAP A1 - Sofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - An Algorithm-Independent Measure of Progress for Linear Constraint Propagation T2 - 27th International Conference on Principles and Practice of Constraint Programming (CP 2021) N2 - Propagation of linear constraints has become a crucial sub-routine in modern Mixed-Integer Programming (MIP) solvers. In practice, iterative algorithms with tolerance-based stopping criteria are used to avoid problems with slow or infinite convergence. However, these heuristic stopping criteria can pose difficulties for fairly comparing the efficiency of different implementations of iterative propagation algorithms in a real-world setting. Most significantly, the presence of unbounded variable domains in the problem formulation makes it difficult to quantify the relative size of reductions performed on them. In this work, we develop a method to measure -- independently of the algorithmic design -- the progress that a given iterative propagation procedure has made at a given point in time during its execution. Our measure makes it possible to study and better compare the behavior of bounds propagation algorithms for linear constraints. We apply the new measure to answer two questions of practical relevance: (i) We investigate to what extent heuristic stopping criteria can lead to premature termination on real-world MIP instances. (ii) We compare a GPU-parallel propagation algorithm against a sequential state-of-the-art implementation and show that the parallel version is even more competitive in a real-world setting than originally reported. Y1 - 2021 U6 - https://doi.org/10.4230/LIPIcs.CP.2021.52 VL - 210 SP - 52:1 EP - 52:17 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - A Safe Computational Framework for Integer Programming applied to Chvátal's Conjecture JF - ACM Transactions on Mathematical Software N2 - We describe a general and safe computational framework that provides integer programming results with the degree of certainty that is required for machine-assisted proofs of mathematical theorems. At its core, the framework relies on a rational branch-and-bound certificate produced by an exact integer programming solver, SCIP, in order to circumvent floating-point roundoff errors present in most state-of-the-art solvers for mixed-integer programs.The resulting certificates are self-contained and checker software exists that can verify their correctness independently of the integer programming solver used to produce the certificate. This acts as a safeguard against programming errors that may be present in complex solver software. The viability of this approach is tested by applying it to finite cases of Chvátal's conjecture, a long-standing open question in extremal combinatorics. We take particular care to verify also the correctness of the input for this specific problem, using the Coq formal proof assistant. As a result we are able to provide a first machine-assisted proof that Chvátal's conjecture holds for all downsets whose union of sets contains seven elements or less. Y1 - 2022 U6 - https://doi.org/10.1145/3485630 VL - 48 IS - 2 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - A Safe Computational Framework for Integer Programming applied to Chvátal's Conjecture N2 - We describe a general and safe computational framework that provides integer programming results with the degree of certainty that is required for machine-assisted proofs of mathematical theorems. At its core, the framework relies on a rational branch-and-bound certificate produced by an exact integer programming solver, SCIP, in order to circumvent floating-point roundoff errors present in most state-of-the-art solvers for mixed-integer programs. The resulting certificates are self-contained and checker software exists that can verify their correctness independently of the integer programming solver used to produce the certificate. This acts as a safeguard against programming errors that may be present in complex solver software. The viability of this approach is tested by applying it to finite cases of Chvátal's conjecture, a long-standing open question in extremal combinatorics. We take particular care to verify also the correctness of the input for this specific problem, using the Coq formal proof assistant. As a result we are able to provide a first machine-assisted proof that Chvátal's conjecture holds for all downsets whose union of sets contains seven elements or less. T3 - ZIB-Report - 21-35 KW - exact rational mixed integer programming KW - extremal combinatorics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84444 SN - 1438-0064 ER - TY - JOUR A1 - Hendel, Gregor A1 - Anderson, Daniel A1 - Le Bodic, Pierre A1 - Pfetsch, Marc T1 - Estimating the Size of Branch-And-Bound Trees JF - INFORMS Journal on Computing N2 - This paper investigates the estimation of the size of Branch-and-Bound (B&B) trees for solving mixed-integer programs. We first prove that the size of the B&B tree cannot be approximated within a factor of~2 for general binary programs, unless P equals NP. Second, we review measures of the progress of the B&B search, such as the gap, and propose a new measure, which we call leaf frequency. We study two simple ways to transform these progress measures into B&B tree size estimates, either as a direct projection, or via double-exponential smoothing, a standard time-series forecasting technique. We then combine different progress measures and their trends into nontrivial estimates using Machine Learning techniques, which yields more precise estimates than any individual measure. The best method we have identified uses all individual measures as features of a random forest model. In a large computational study, we train and validate all methods on the publicly available MIPLIB and Coral general purpose benchmark sets. On average, the best method estimates B&B tree sizes within a factor of 3 on the set of unseen test instances even during the early stage of the search, and improves in accuracy as the search progresses. It also achieves a factor 2 over the entire search on each out of six additional sets of homogeneous instances we have tested. All techniques are available in version 7 of the branch-and-cut framework SCIP. Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2021.1103 ER - TY - GEN A1 - Tack, Alexander A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative (Supplementary Material) T2 - PLOS One N2 - Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies’ shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA A fully automated method is employed to segment six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between healthy and severely arthritic knees yielded BAs of up to 99%, 84% were achieved for diagnosis of early KOA. Substantial agreement with weighted kappa values of 0.73, 0.73, and 0.79 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.60 and 0.75 for prediction of incident KOA and TKR within 5 years, respectively. Quantitative features from automated segmentations yield excellent results for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features as KOA biomarkers should be further evaluated, especially as extensions of CNN-based approaches. To foster such developments we make all segmentations publicly available together with this publication. Y1 - 2021 U6 - https://doi.org/10.12752/8328 N1 - 46,996 automated segmentations for data from the OAI database. VL - 16 IS - 10 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Rooted Maximum Weight Connected Subgraphs with Balancing and Capacity Constraints T3 - ZIB-Report - 21-34 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84427 SN - 1438-0064 ER - TY - GEN A1 - Tack, Alexander A1 - Shestakov, Alexey A1 - Lüdke, David A1 - Zachow, Stefan T1 - A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database N2 - We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences. T3 - ZIB-Report - 21-33 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84415 SN - 1438-0064 ER - TY - JOUR A1 - Tack, Alexander A1 - Shestakov, Alexey A1 - Lüdke, David A1 - Zachow, Stefan T1 - A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database JF - Frontiers in Bioengineering and Biotechnology, section Biomechanics N2 - We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences. Y1 - 2021 U6 - https://doi.org/10.3389/fbioe.2021.747217 SP - 28 EP - 41 ER - TY - JOUR A1 - Mollenhauer, Mattes A1 - Klus, Stefan A1 - Schütte, Christof A1 - Koltai, Péter T1 - Kernel Autocovariance Operators of Stationary Processes: Estimation and Convergence JF - Journal of Machine Learning Research N2 - We consider autocovariance operators of a stationary stochastic process on a Polish space that is embedded into a reproducing kernel Hilbert space. We investigate how empirical estimates of these operators converge along realizations of the process under various conditions. In particular, we examine ergodic and strongly mixing processes and obtain several asymptotic results as well as finite sample error bounds. We provide applications of our theory in terms of consistency results for kernel PCA with dependent data and the conditional mean embedding of transition probabilities. Finally, we use our approach to examine the nonparametric estimation of Markov transition operators and highlight how our theory can give a consistency analysis for a large family of spectral analysis methods including kernel-based dynamic mode decomposition. Y1 - 2022 UR - https://jmlr.org/papers/v23/20-442.html VL - 23 IS - 327 SP - 1 EP - 34 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Mollenhauer, Mattes A1 - Koltai, Péter A1 - Schütte, Christof T1 - Optimal Reaction Coordinates: Variational Characterization and Sparse Computation JF - Multiscale Modelling & Simulation N2 - Reaction coordinates (RCs) are indicators of hidden, low-dimensional mechanisms that govern the long-term behavior of high-dimensional stochastic processes. We present a novel and general variational characterization of optimal RCs and provide conditions for their existence. Optimal RCs are minimizers of a certain loss function, and reduced models based on them guarantee a good approximation of the statistical long-term properties of the original high-dimensional process. We show that for slow-fast systems, metastable systems, and other systems with known good RCs, the novel theory reproduces previous insight. Remarkably, for reversible systems, the numerical effort required to evaluate the loss function scales only with the variability of the underlying, low-dimensional mechanism, and not with that of the full system. The theory provided lays the foundation for an efficient and data-sparse computation of RCs via modern machine learning techniques. Y1 - 2023 U6 - https://doi.org/10.1137/21M1448367 VL - 21 IS - 2 SP - 449 EP - 488 ER - TY - JOUR A1 - Hanik, Martin A1 - Demirtaş, Mehmet Arif A1 - Gharsallaoui, Mohammed Amine A1 - Rekik, Islem T1 - Predicting cognitive scores with graph neural networks through sample selection learning JF - Brain Imaging and Behavior N2 - Analyzing the relation between intelligence and neural activity is of the utmost importance in understanding the working principles of the human brain in health and disease. In existing literature, functional brain connectomes have been used successfully to predict cognitive measures such as intelligence quotient (IQ) scores in both healthy and disordered cohorts using machine learning models. However, existing methods resort to flattening the brain connectome (i.e., graph) through vectorization which overlooks its topological properties. To address this limitation and inspired from the emerging graph neural networks (GNNs), we design a novel regression GNN model (namely RegGNN) for predicting IQ scores from brain connectivity. On top of that, we introduce a novel, fully modular sample selection method to select the best samples to learn from for our target prediction task. However, since such deep learning architectures are computationally expensive to train, we further propose a \emph{learning-based sample selection} method that learns how to choose the training samples with the highest expected predictive power on unseen samples. For this, we capitalize on the fact that connectomes (i.e., their adjacency matrices) lie in the symmetric positive definite (SPD) matrix cone. Our results on full-scale and verbal IQ prediction outperforms comparison methods in autism spectrum disorder cohorts and achieves a competitive performance for neurotypical subjects using 3-fold cross-validation. Furthermore, we show that our sample selection approach generalizes to other learning-based methods, which shows its usefulness beyond our GNN architecture. Y1 - 2022 U6 - https://doi.org/10.1007/s11682-021-00585-7 VL - 16 SP - 1123 EP - 1138 ER - TY - JOUR A1 - Tack, Alexander A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative JF - PLOS One N2 - Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies’ shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA. Six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) are segmented in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between non-arthritic and severely arthritic knees yielded BAs of up to 99%, 84% were achieved for diagnosis of early KOA. Weighted kappa values of 0.73, 0.72, and 0.78 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.61 and 0.76 for prediction of incident KOA and TKR within one year, respectively. Quantitative features from automated segmentations provide novel biomarkers for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features should be further evaluated, especially as extensions of CNN- based approaches. To foster such developments we make all segmentations publicly available together with this publication. Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0258855 VL - 16 IS - 10 ER - TY - CHAP A1 - Ahiboz, Doguscan A1 - Andresen, Elina A1 - Manley, Phillip A1 - Resch Genger, Ute A1 - Würth, Christian A1 - Becker, Christiane T1 - Enhanced Photon Upconversion Using Erbium-Doped Nanoparticles Interacting with Silicon Metasurfaces T2 - IEEE 48th Photovoltaic Specialists Conference (PVSC) Y1 - 2021 U6 - https://doi.org/10.1109/PVSC43889.2021.9518495 SP - 2008 EP - 2010 ER - TY - CHAP A1 - Perevoznik, Dmitrii A1 - Bose, Surajit A1 - Burger, Sven A1 - Demircan, Ayhan A1 - Morgner, Uwe T1 - Photonic components in polymers made by femtosecond pulses T2 - Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC) Y1 - 2021 U6 - https://doi.org/10.1109/CLEO/Europe-EQEC52157.2021.9541906 SP - 1 ER - TY - GEN A1 - Masing, Berenike A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - Optimal Line Plans in the Parametric City and the Impact of In-Motion Costs N2 - Line planning in public transport involves determining vehicle routes and assigning frequencies of service such that travel demands are satisfied. We evaluate how line plans, which are optimal with respect to in-motion costs (IMC), the objective function depending purely on arc-lengths for both user and operator costs, performs with respect to the value of resources consumed (VRC). The latter is an elaborate, socio-economic cost function which includes discomfort caused by delay, boarding and alighting times, and transfers. Even though discomfort is a large contributing factor to VRC and is entirely disregarded in IMC, we observe that the two cost functions are qualitatively comparable. T3 - ZIB-Report - 21-27 KW - line planning KW - public transport KW - mixed-integer prgramming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84195 SN - 1438-0064 ER - TY - JOUR A1 - Roth, Sarah T1 - SAT-Heuristiken für das Periodic Event Scheduling-Problem JF - OR News Y1 - 2021 SN - 1437-2045 IS - 71 ER - TY - JOUR A1 - Beckenbach, Isabel T1 - Von Graphen zu Hypergraphen JF - OR News Y1 - 2020 SN - 1437-2045 IS - 70 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Schmidt genannt Waldschmidt, Daniel T1 - Restricted Adaptivity in Stochastic Scheduling JF - 29th Annual European Symposium on Algorithms (ESA 2021) N2 - We consider the stochastic scheduling problem of minimizing the expected makespan on m parallel identical machines. While the (adaptive) list scheduling policy achieves an approximation ratio of 2, any (non-adaptive) fixed assignment policy has performance guarantee Ω(logm/loglogm). Although the performance of the latter class of policies are worse, there are applications in which non-adaptive policies are desired. In this work, we introduce the two classes of δ-delay and τ-shift policies whose degree of adaptivity can be controlled by a parameter. We present a policy - belonging to both classes - which is an O(loglogm)-approximation for reasonably bounded parameters. In other words, an exponential improvement on the performance of any fixed assignment policy can be achieved when allowing a small degree of adaptivity. Moreover, we provide a matching lower bound for any δ-delay and τ-shift policy when both parameters, respectively, are in the order of the expected makespan of an optimal non-anticipatory policy. Y1 - 2021 U6 - https://doi.org/10.4230/LIPIcs.ESA.2021.79 VL - 204 SP - 79:1 EP - 79:14 ER - TY - JOUR A1 - Sahin, Guvenc A1 - Digehsara, Amin Ahmadi A1 - Borndörfer, Ralf T1 - Efficient Algorithms for the Multi-Period Line Planning Problem in Public Transportation JF - Open Access Series in Informatics (OASIcs), 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021) N2 - In order to plan and schedule a demand-responsive public transportation system, both temporal and spatial changes in demand should be taken into account even at the line planning stage. We study the multi-period line planning problem with integrated decisions regarding dynamic allocation of vehicles among the lines. Given the NP-hard nature of the line planning problem, the multi-period version is clearly difficult to solve for large public transit networks even with advanced solvers. It becomes necessary to develop algorithms that are capable of solving even the very-large instances in reasonable time. For instances which belong to real public transit networks, we present results of a heuristic local branching algorithm and an exact approach based on constraint propagation. Y1 - 2021 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2021.17 VL - 96 SP - 17:1 EP - 17:6 ER - TY - THES A1 - Henning, Erin T1 - Tropical Geometry Approach to Shortest Paths with Parameterized Arc Weights - A Case Study in Public Transportation Networks N2 - In graphical representations of public transportation networks, there is often some degree of uncertainty in the arc values, due to delays or transfer times. This uncertainty can be expressed as a parameterized weight on the transfer arcs. Classical shortest path algorithms often have difficulty handling parameterized arc weights and a tropical geometry approach has been shown as a possible solution. The connection between the classical shortest path problem and tropical geometry is well establish: Tropically multiplying the n × n adjacency matrix of a graph with itself n − 1 times results in the so-called Kleene star, and is a matrix-form solution to the all-pairs shortest path problem. Michael Joswig and Benjamin Schröter showed in their paper The Tropical Geometry of Shortest Paths that the same method can be used to find the solution to the all-pairs shortest path problem even in the case of variable arc weights and they proposed an algorithm to solve the single-target shortest path problem in such a case. The solution takes the form of a polyhedral subdivision of the parameter space. As the number of variable arc weights grows, the time needed to execute an implementation of this algorithm grows exponentially. As the size of a public transportation network grows, the number of variable arc weights grows exponentially as well. However, it has been observed that in public transportation networks, there are usually only a few possible shortest routes. Geometrically, this means that there should be few polyhedra in the polyhedral subdivision. This algorithm is used on an example of a real-world public transportation network and an analysis of the polyhedral subdivision is made. Then a geometrical approach is used to analyze the impact of limiting the number of transfers, and thereby limiting the number of parameterized arcs used, as an estimation of the solution to the all-pairs shortest path problem Y1 - 2020 ER - TY - THES A1 - Bushe, Julian T1 - Rolling Stock Rotation Optimization with Maintenance Paths N2 - Die Planung vom Zugumläufen ist eine der wichtigsten Aufgaben für Eisenbahnun- ternehmen. Dabei spielt auch die Einhaltung von vorgegebenen Wartungsintervallen eine zentrale Rolle für die Sicherheit und Zuverlässigkeit der Schienenfahrzeuge. Wir zeigen, wie man dieses Umlaufplanungsproblem unter Beachtung von Wartungsbe- dingungen mathematisch formuliert, modelliert und löst — sowohl in der Theorie als auch im Anwendungsfall mit Szenarien der DB Fernverkehr AG, einer Konzern- tochter der Deutschen Bahn für den Schienenpersonenfernverkehr. Markus Reuther hat sich in seiner Dissertation [11] mit diesem Problem beschäftigt und es mit Hilfe eines passenden Hypergraphen als gemischt-ganzzahliges Programm modelliert. Neben der Modellierung präsentiert Reuther in seiner Arbeit neuartige algorithmische Ideen, darunter den sogenannten Coarse-to-Fine -Ansatz, bei dem zunächst Teile des Problems auf einer weniger detaillierten ( coarse ) Ebene gelöst werden und diese Lösung dann verwendet wird, um auf effiziente Art und Weise eine Lösung für das ursprüngliche Problem zu finden. Zur Wartungsplanung nutzt Reuther einen Fluss im Hypergraphen, der den Ressourcenverbrauch der Fahrzeuge modelliert. In der linearen Relaxierung des Modells führt dies dazu, dass die Zahl der notwendigen Wartungen systematisch unterschätzt wird. Dadurch bleibt in vielen Fällen eine große Lücke zwischen dem Zielfunktionswert einer optimalen Lösung des ganzzahligen Problems und der untere Schranke, die uns die lineare Relaxierung liefert. Wir nehmen uns in dieser Arbeit dieses Problems an. Wir entwickeln ein auf Pfaden basierendes ganzzahliges Modell für das Umlaufplanungsproblem und zeigen, dass die untere Schranke mindestens so scharf oder schärfer ist als die untere Schranke, die das Modell von Reuther liefert. Um das Modell zu lösen, entwickeln wir einen Algorithmus, der Spaltengenerierung mit dem Coarse-to-Fine-Ansatz von Reuther verbindet. Weiterhin entwickeln wir eine Spaltenauswahlregel zur Beschleunigung des Algorithmus. Das Modell und alle in der Arbeit vorgestellten Algorithmen wur- den im Rahmen der Arbeit implementiert und mit Anwendungsszenarien der DB Fernverkehr AG getestet. Unsere Tests zeigen, dass unser Modell für fast alle Szena- rien deutlich schärfere untere Schranken liefert als das Modell von Reuther. In den getesteten Instanzen konnten wir durch die Verbesserung der unteren Schranke bis zu 99% der Optimalitätslücke schließen. In einem Drittel der Fälle konnten wir durch unseren Ansatz auch für das ganzzahlige Programm verbesserte Zielfunktionswerte erreichen Y1 - 2021 ER - TY - THES A1 - Kraus, Luitgard T1 - A Label Setting Multiobjective Shortest Path FPTAS N2 - Algorithms that solve the shortest path problem can largely be split into the two categories of label setting and label correcting. The Multiobjective Shortest Path (MOSP) problem is a generalization of the classical shortest path problem in terms of the dimension of the cost function. We explore the differences of two similar MOSP label setting algorithms. Furthermore, we present and prove a general method of how to derive Fully Polynomial Time Approximation Schemes (FPTAS) for MOSP label setting algorithms. Finally, we explore two pruning techniques for the one to one variants of exact label setting MOSP algorithms and adapt them to their FPTAS variants. Y1 - 2021 ER - TY - THES A1 - Kühner, Arno T1 - Shortest Paths with Boolean Constraints N2 - For this thesis we study the Constrained Horizontal Flightplanning Problem (CHFPP) for which one has to find the path of minimum cost between airports s and t in a directed graph that respects a set of boolean constraints. To this end we give a survey of three different multilabel algorithms that all use a domination subroutine. We summarize an approach by Knudsen, Chiarandini and Larsen to define this domination and afterwards present our own method which builds on that approach. We suggest different implementation techniques to speed up the computation time, most notably a Reoptimization for an iterative method to solve the problem. Furthermore we implemented the different versions of the algorithm and present statistics on their computation as well as an overview of statistics on the set of real-world constraints that we were given. Finally we present two alternative approaches that tackle the problem, a heuristic with similarities to a Lagrangian relaxation and an approach that makes use of an algorithm which finds the k shortest path of a graph such as the ones of Epstein or Yen. Y1 - 2021 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Höfling, Felix T1 - Stochastic pH oscillations in a model of the urea–urease reaction confined to lipid vesicles JF - J. Phys. Chem. Lett. N2 - The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jpclett.1c03016 VL - 12 SP - 9888 EP - 9893 ER - TY - THES A1 - Rahmati, Niloofar T1 - Resource Constrained APSP-Algorithm with Possible Reloading Stops Y1 - 2021 ER - TY - THES A1 - Lange, Johanna T1 - A Decomposition and Dualization Approach to the Periodic Event Scheduling Problem N2 - Scheduling ist ein wichtiger Forschungsgegenstand im Bereich der diskreten Optimierung. Es geht darum, einen Schedule, d.h. einen Ablaufplan, für gegebene Ereignisse zu finden. Dieser soll optimal hinsichtlich einer Zielfunktion wie zum Beispiel minimaler Dauer oder Kosten sein. Dabei gibt es in der Regel Nebenbedingungen wie Vorrangbeziehungen zwischen den Ereignissen oder zeitliche Einschränkungen, die zu erfüllen sind. Falls die Ereignisse periodisch wiederkehren, spricht man von periodischem Scheduling. Beispiele sind das Erstellen von Zugfahrplänen, die Schaltungvon Ampelsignalen oder die Planung von Produktionsabläufen. Mathematisch können diese Probleme mit dem Periodic Event Scheduling Problem (PESP) modelliert werden, das als gemischt-ganzzahliges Programm formuliert werden kann. In dieser Bachelorarbeit wird ein Ansatz zur Lösung des PESP mittels Zerlegung und Dualisierung entwickelt. In den Kapiteln 2 und 3 werden zunächst die notwendigen graphentheoretischen Grundlagen und das PESP eingeführt. In Kapitel 4 wird das PESP durch Fixierung der ganzzahligen Variablen in lineare Programme zerlegt. Dieses Unterproblem wird dualisiert und wieder in das PESP eingesetzt. Dafür ist eine weitere Nebenbedingung nötig. Im fünften Kapitel behandeln wir die Lösung des teildualisierten PESP. Eine Möglichkeit ist es, sich auf eine Teilmenge der Nebenbedingungen zu beschränken. Eine weitere Möglichkeit ist ein Algorithmus, derähnlich wie BendersZerlegung die Nebenbedingungen dynamisch erzeugt. Dieser Algorithmus wird in Kapitel 6 implementiert und an vier Beispielen getestet. Y1 - 2021 ER - TY - THES A1 - Bortoletto, Enrico T1 - The tropical tiling of periodic timetable space and a dual modulo network simplex algorithm N2 - We propose a tropical interpretation of the solution space of the Periodic Event Scheduling Problem as a collection of polytropes, making use of the characterization of tropical cones as weighted digraph polyhedra. General and geometric properties of the polytropal collection are inspected and understood in connection with the combinatorial properties of the underlying periodic event scheduling instance. Novel algorithmic ideas are presented and tested, making use of the aforementioned theoretical results to solve and optimize the problem. Y1 - 2021 ER - TY - THES A1 - Masing, Berenike T1 - Optimal Line Planning in the Parametric City N2 - One of the fundamental steps in the optimization of public transport is line planning. It involves determining lines and assigning frequencies of service such that costs are minimized while also maximizing passenger comfort and satisfying travel demands. We formulate the problem as a mixed integer linear program that considers all circuit-like lines in a graph and allows free passenger routing. Traveler and operator costs are included in a linear scalarization in the objective. We apply said programming problem to the Parametric City, which is a graph model introduced by Fielbaum, Jara-Díaz and Gschwender that exibly represents different cities. In his dissertation, Fielbaum solved the line planning problem for various parameter choices in the Parametric City. In a first step, we therefore review his results and make comparative computations. Unlike Fielbaum we arrive at the conclusion that the optimal line plan for this model indeed depends on the demand. Consequently, we analyze the line planning problem in-depth: We find equivalent, but easier to compute formulations and provide a lower bound by LP-relaxation, which we show to be equivalent to a multi-commodity flow problem. Further, we examine what impact symmetry has on the solutions. Supported both by computational results as well as by theoretical analysis, we reach the conclusion that symmetric line plans are optimal or near-optimal in the Parametric City. Restricting the model to symmetric line plans allows for a \kappa-factor approximation algorithm for the line planning problem in the Parametric City. Y1 - 2020 ER - TY - JOUR A1 - Schlechte, Thomas A1 - Borndörfer, Ralf A1 - Denißen, Jonas A1 - Heller, Simon A1 - Klug, Torsten A1 - Küpper, Michael A1 - Lindner, Niels A1 - Reuther, Markus A1 - Söhlke, Andreas A1 - Steadman, William T1 - Timetable Optimization for a Moving Block System JF - Journal of Rail Transport Planning & Management N2 - We present an optimization model which is capable of routing and ordering trains on a microscopic level under a moving block regime. Based on a general timetabling definition (GTTP) that allows the plug in of arbitrarily detailed methods to compute running and headway times, we describe a layered graph approach using velocity expansion, and develop a mixed integer linear programming formulation. Finally, we present promising results for a German corridor scenario with mixed traffic, indicating that applying branch-and-cut to our model is able to solve reasonably sized instances with up to hundred trains to optimality. Y1 - 2022 U6 - https://doi.org/10.1016/j.jrtpm.2022.100315 SN - 2210-9706 VL - 22 SP - 100315 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Frömberg, Daniela A1 - Straube, Arthur A1 - Schütte, Christof A1 - Höfling, Felix A1 - Winkelmann, Stefanie T1 - A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations JF - Letters in Mathematical Physics Y1 - 2022 U6 - https://doi.org/10.1007/s11005-022-01539-w VL - 112 IS - 49 ER - TY - JOUR A1 - Lenz, Ralf A1 - Becker, Kai-Helge T1 - Optimization of Capacity Expansion in Potential-driven Networks including Multiple Looping - A comparison of modelling approaches JF - OR Spectrum N2 - In commodity transport networks such as natural gas, hydrogen and water networks, flows arise from nonlinear potential differences between the nodes, which can be represented by so-called "potential-driven" network models. When operators of these networks face increasing demand or the need to handle more diverse transport situations, they regularly seek to expand the capacity of their network by building new pipelines parallel to existing ones ("looping"). The paper introduces a new mixed-integer non-linear programming (MINLP) model and a new non-linear programming (NLP) model and compares these with existing models for the looping problem and related problems in the literature, both theoretically and experimentally. On this basis, we give recommendations about the circumstances under which a certain model should be used. In particular, it turns out that one of our novel models outperforms the existing models. Moreover, the paper is the first to include the practically relevant option that a particular pipeline may be looped several times. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1007/s00291-021-00648-7 VL - 44 SP - 179 EP - 224 ER - TY - CHAP A1 - Lindner, Niels A1 - Maristany de las Casas, Pedro A1 - Schiewe, Philine T1 - Optimal Forks: Preprocessing Single-Source Shortest Path Instances with Interval Data T2 - 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021) N2 - We investigate preprocessing for single-source shortest path queries in digraphs, where arc costs are only known to lie in an interval. More precisely, we want to decide for each arc whether it is part of some shortest path tree for some realization of costs. We show that this problem is solvable in polynomial time by giving a combinatorial algorithm, using optimal structures that we call forks. Our algorithm turns out to be very efficient in practice, and is sometimes even superior in quality to a heuristic developed for the one-to-one shortest path problem in the context of passenger routing in public transport. Y1 - 2021 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2021.7 VL - 96 SP - 7:1 EP - 7:15 ER - TY - CHAP A1 - Lindner, Niels A1 - Liebchen, Christian A1 - Masing, Berenike T1 - Forward Cycle Bases and Periodic Timetabling T2 - 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021) N2 - Periodic timetable optimization problems in public transport can be modeled as mixed-integer linear programs by means of the Periodic Event Scheduling Problem (PESP). In order to keep the branch-and-bound tree small, minimum integral cycle bases have been proven successful. We examine forward cycle bases, where no cycle is allowed to contain a backward arc. After reviewing the theory of these bases, we describe the construction of an integral forward cycle basis on a line-based event-activity network. Adding turnarounds to the instance R1L1 of the benchmark library PESPlib, we computationally evaluate three types of forward cycle bases in the Pareto sense, and come up with significant improvements concerning dual bounds. Y1 - 2021 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2021.2 VL - 96 SP - 2:1 EP - 2:14 ER - TY - CHAP A1 - Carderera, Alejandro A1 - Pokutta, Sebastian A1 - Mathieu, Besançon T1 - Simple steps are all you need: Frank-Wolfe and generalized self-concordant functions T2 - Thirty-fifth Conference on Neural Information Processing Systems, NeurIPS 2021 N2 - Generalized self-concordance is a key property present in the objective function of many important learning problems. We establish the convergence rate of a simple Frank-Wolfe variant that uses the open-loop step size strategy 𝛾𝑡 = 2/(𝑡 + 2), obtaining a O (1/𝑡) convergence rate for this class of functions in terms of primal gap and Frank-Wolfe gap, where 𝑡 is the iteration count. This avoids the use of second-order information or the need to estimate local smoothness parameters of previous work. We also show improved convergence rates for various common cases, e.g., when the feasible region under consideration is uniformly convex or polyhedral. Y1 - 2021 ER - TY - JOUR A1 - Kerdreux, Thomas A1 - d'Aspremont, Alexandre A1 - Pokutta, Sebastian T1 - Local and Global Uniform Convexity Conditions N2 - We review various characterizations of uniform convexity and smoothness on norm balls in finite-dimensional spaces and connect results stemming from the geometry of Banach spaces with scaling inequalities used in analysing the convergence of optimization methods. In particular, we establish local versions of these conditions to provide sharper insights on a recent body of complexity results in learning theory, online learning, or offline optimization, which rely on the strong convexity of the feasible set. While they have a significant impact on complexity, these strong convexity or uniform convexity properties of feasible sets are not exploited as thoroughly as their functional counterparts, and this work is an effort to correct this imbalance. We conclude with some practical examples in optimization and machine learning where leveraging these conditions and localized assumptions lead to new complexity results. Y1 - 2021 ER - TY - JOUR A1 - Bärmann, Andreas A1 - Martin, Alexander A1 - Pokutta, Sebastian A1 - Schneider, Oskar T1 - An Online-Learning Approach to Inverse Optimization Y1 - 2018 ER - TY - CHAP A1 - Carderera, Alejandro A1 - Diakonikolas, Jelena A1 - Lin, Cheuk Yin A1 - Pokutta, Sebastian T1 - Parameter-free Locally Accelerated Conditional Gradients T2 - ICML 2021 N2 - Projection-free conditional gradient (CG) methods are the algorithms of choice for constrained optimization setups in which projections are often computationally prohibitive but linear optimization over the constraint set remains computationally feasible. Unlike in projection-based methods, globally accelerated convergence rates are in general unattainable for CG. However, a very recent work on Locally accelerated CG (LaCG) has demonstrated that local acceleration for CG is possible for many settings of interest. The main downside of LaCG is that it requires knowledge of the smoothness and strong convexity parameters of the objective function. We remove this limitation by introducing a novel, Parameter-Free Locally accelerated CG (PF-LaCG) algorithm, for which we provide rigorous convergence guarantees. Our theoretical results are complemented by numerical experiments, which demonstrate local acceleration and showcase the practical improvements of PF-LaCG over non-accelerated algorithms, both in terms of iteration count and wall-clock time. Y1 - 2021 ER - TY - JOUR A1 - Mathieu, Besançon A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - FrankWolfe.jl: a high-performance and flexible toolbox for Frank-Wolfe algorithms and Conditional Gradients JF - INFORMS Journal on Computing N2 - We present FrankWolfe.jl, an open-source implementation of several popular Frank–Wolfe and conditional gradients variants for first-order constrained optimization. The package is designed with flexibility and high performance in mind, allowing for easy extension and relying on few assumptions regarding the user-provided functions. It supports Julia’s unique multiple dispatch feature, and it interfaces smoothly with generic linear optimization formulations using MathOptInterface.jl. Y1 - 2022 U6 - https://doi.org/10.1287/ijoc.2022.1191 VL - 34 IS - 5 SP - 2383 EP - 2865 ER - TY - JOUR A1 - Bienenstock, Daniel A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - Principled Deep Neural Network Training through Linear Programming N2 - Deep Learning has received significant attention due to its impressive performance in many state-of-the-art learning tasks. Unfortunately, while very powerful, Deep Learning is not well understood theoretically and in particular only recently results for the complexity of training deep neural networks have been obtained. In this work we show that large classes of deep neural networks with various architectures (e.g., DNNs, CNNs, Binary Neural Networks, and ResNets), activation functions (e.g., ReLUs and leaky ReLUs), and loss functions (e.g., Hinge loss, Euclidean loss, etc) can be trained to near optimality with desired target accuracy using linear programming in time that is exponential in the input data and parameter space dimension and polynomial in the size of the data set; improvements of the dependence in the input dimension are known to be unlikely assuming P≠NP, and improving the dependence on the parameter space dimension remains open. In particular, we obtain polynomial time algorithms for training for a given fixed network architecture. Our work applies more broadly to empirical risk minimization problems which allows us to generalize various previous results and obtain new complexity results for previously unstudied architectures in the proper learning setting. Y1 - 2018 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Second-order Conditional Gradient Sliding N2 - Constrained second-order convex optimization algorithms are the method of choice when a high accuracy solution to a problem is needed, due to their local quadratic convergence. These algorithms require the solution of a constrained quadratic subproblem at every iteration. We present the \emph{Second-Order Conditional Gradient Sliding} (SOCGS) algorithm, which uses a projection-free algorithm to solve the constrained quadratic subproblems inexactly. When the feasible region is a polytope the algorithm converges quadratically in primal gap after a finite number of linearly convergent iterations. Once in the quadratic regime the SOCGS algorithm requires O(log(log1/ε)) first-order and Hessian oracle calls and O(log(1/ε)log(log1/ε)) linear minimization oracle calls to achieve an ε-optimal solution. This algorithm is useful when the feasible region can only be accessed efficiently through a linear optimization oracle, and computing first-order information of the function, although possible, is costly. Y1 - 2020 ER - TY - CHAP A1 - Kerdreux, Thomas A1 - d'Aspremont, Alexandre A1 - Pokutta, Sebastian T1 - Projection-Free Optimization on Uniformly Convex Sets T2 - To Appear in Proceedings of AISTATS Y1 - 2020 ER - TY - JOUR A1 - Kerdreux, Thomas A1 - Roux, Christophe A1 - d'Aspremont, Alexandre A1 - Pokutta, Sebastian T1 - Linear Bandits on Uniformly Convex Sets JF - Journal of Machine Learning Research N2 - Linear bandit algorithms yield O~(n√T) pseudo-regret bounds on compact convex action sets K⊂Rn and two types of structural assumptions lead to better pseudo-regret bounds. When K is the simplex or an ℓp ball with p∈]1,2], there exist bandits algorithms with O~(√n√T) pseudo-regret bounds. Here, we derive bandit algorithms for some strongly convex sets beyond ℓp balls that enjoy pseudo-regret bounds of O~(√n√T), which answers an open question from [BCB12, §5.5.]. Interestingly, when the action set is uniformly convex but not necessarily strongly convex, we obtain pseudo-regret bounds with a dimension dependency smaller than O(√n). However, this comes at the expense of asymptotic rates in T varying between O(√T) and O(T). Y1 - 2021 UR - https://www.jmlr.org/papers/v22/21-0277.html VL - 22 IS - 284 SP - 1 EP - 23 ER - TY - JOUR A1 - Roux, Christophe A1 - Pokutta, Sebastian A1 - Wirth, Elias A1 - Kerdreux, Thomas T1 - Efficient Online-Bandit Strategies for Minimax Learning Problems N2 - Several learning problems involve solving min-max problems, e.g., empirical distributional robust learning [Namkoong and Duchi, 2016, Curi et al., 2020] or learning with non-standard aggregated losses [Shalev- Shwartz and Wexler, 2016, Fan et al., 2017]. More specifically, these problems are convex-linear problems where the minimization is carried out over the model parameters w ∈ W and the maximization over the empirical distribution p ∈ K of the training set indexes, where K is the simplex or a subset of it. To design efficient methods, we let an online learning algorithm play against a (combinatorial) bandit algorithm. We argue that the efficiency of such approaches critically depends on the structure of K and propose two properties of K that facilitate designing efficient algorithms. We focus on a specific family of sets Sn,k encompassing various learning applications and provide high-probability convergence guarantees to the minimax values. Y1 - 2021 ER - TY - CHAP A1 - Criado, Francisco A1 - Martínez-Rubio, David A1 - Pokutta, Sebastian T1 - Fast Algorithms for Packing Proportional Fairness and its Dual T2 - Proceedings of the Conference on Neural Information Processing Systems N2 - The proportional fair resource allocation problem is a major problem studied in flow control of networks, operations research, and economic theory, where it has found numerous applications. This problem, defined as the constrained maximization of sum_i log x_i, is known as the packing proportional fairness problem when the feasible set is defined by positive linear constraints and x ∈ R≥0. In this work, we present a distributed accelerated first-order method for this problem which improves upon previous approaches. We also design an algorithm for the optimization of its dual problem. Both algorithms are width-independent. Y1 - 2022 VL - 36 ER - TY - JOUR A1 - Sechi, Renata A1 - Weber, Marcus A1 - Heyne, Karsten T1 - MSM building and projection for the analysis of time-resolved spectra JF - Proceedings in Applied Mathematics and Mechanics N2 - Understanding the kinetics between the components of time-resolved spectra is a crucial step in the study of photo-activatedprocesses. However, modeling the kinetics requires usually some a priori knowledge about the system. In our approach, webuild a Markov State Model (MSM) from the spectral data, and obtain a Koopman transition matrix K(t). With genPCCA,an invariant subspace projection, we project the process into its metastable components. The result of the application of gen-PCCA is a transition matrix Kc(t), from which we can read the transition probability between the metastable components of the reaction. We discuss the application of this analysis method to the transient absorption spectrum of brominated Al-corrole Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?https://onlinelibrary.wiley.com/doi/10.1002/pamm.202100102 IS - 21 SP - e202100102 ER - TY - THES A1 - Moldenhauer, Marian T1 - Adaptive Algorithms in Optimization under PDE Constraints N2 - In this thesis, adaptive algorithms in optimization under PDE constraints have been inves- tigated. In its application, the aim of optimization is to increase the longevity of implants, namely the hip joint implant, and in doing so to minimize stress shielding and simultaneously minimize the influence of locally high stresses, that, above a threshold value, are malign to the bone structure. Under the constraint of the equilibrium of forces, describing an elastodynamic setup, coupled with a contact inequality condition, a computationally expensive problem formulation is given. The first step to make the solution of the given problem possible and efficient was to change over to the spatial equilibrium equation, thus rendering an elastostatic setup. Subsequently the intrinsically dynamic motions – trajectories in the load domain – were converted to the static setup. Thus, the trajectories are marginalized to the load domain and characterized with probability distributions. Therefore the solving of the PDE constraint, the contact problem, is simplified. Yet in the whole optimization process, the solving of the PDE, the spatial equilibrium equation together with the contact condition has the most expensive contribution still and hence needed further reduction. This was achieved by application of Kriging interpolation to the load responses of the integrated distribution of stress difference and the maximum stresses. The interpolation of the two response surfaces only needs comparatively few PDE solves to set up the models. Moreover, the Kriging models can be adaptively extended by sequentially adding sample-response pairs. For this the Kriging inherent variance is used to estimate ideal new sample locations with maximum variance values. In doing so, the overall interpolation variance and therefore the interpolation error is reduced. For the integration of the integrated stress differences and penalty values on the relative high dimensional load domain Monte Carlo integration was implemented, averting the curse of dimension. Here, the motion’s probability distribution combined with patient specific data of motion frequencies is taken advantage of, making obsolete the use of the otherwise necessary importance sampling. Throughout the optimization, the FE-discretization error and the subsequently attached errors entering the solution process via PDE discretization and approximative solving of the PDE, Kriging interpolation and Monte Carlo integration need to decrease. While the FE-discretization error and the solution of the elastostatic contact problem were assumed precise enough, numerics showed, that the interpolation and integration errors can be controlled by adaptive refinement of the respective methods. For this purpose comparable error quantities for the particular algorithms were introduced and effectively put to use. For the implant position’s optimization, the derivative of the objective function was derived using the implicit function theorem. As the FE-discretization changes with implant position modifications big enough, a special line search had to be used to deal with the discontinuities in the objective function. The interplay and performance of the subalgorithms was demonstrated numerically on a reduced 2D setup of a hip joint with and without the implant. Consequently the load domain and the control variable were also limited to the 2D case. Y1 - 2021 ER - TY - JOUR A1 - Berthold, Timo A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - MILP. Try. Repeat. JF - Proceedings of the 13th International Conference on the Practice and Theory of Automated Timetabling - PATAT 2021 Y1 - 2021 VL - 2 ER - TY - THES A1 - Shestakov, Alexey T1 - A Deep Learning Method for Automated Detection of Meniscal Tears in Meniscal Sub-Regions in 3D MRI Data N2 - This work presents a fully automated pipeline, centered around a deep neural network, as well as a method to train that network in an efficient manner, that enables accurate detection of lesions in meniscal anatomical subregions. The network architecture is based on a transformer encoder/decoder. It is trained on DESS and tuned on IW TSE 3D MRI scans sourced from the Osteoarthritis Initiative. Furthermore, it is trained in a multilabel, and multitask fashion, using an auxiliary detection head. The former enables implicit localisation of meniscal defects, that to the best of my knowledge, has not yet been reported elsewhere. The latter enables efficient learning on the entire 3D MRI volume. Thus, the proposed method does not require any expert knowledge at inference. Aggregated inference results from two datasets resulted in an overall AUCROC result of 0.90, 0.91 and 0.93 for meniscal lesion detection anywhere in the knee, in medial and in lateral menisci respectively. These results compare very well to the related work, even though only a fraction of the data has been utilized. Clinical applicability and benefit is yet to be determined. KW - Machine Learning KW - Computational Diagnosis KW - Knee Osteoarthritis Y1 - 2021 ER - TY - THES A1 - Krause, Jan T1 - Investigation of Options to Handle 3D MRI Data via Convolutional Neural Networks Application in Knee Osteoarthritits Classification KW - Machine Learning KW - Computational Diagnosis KW - Knee Osteoarthritis Y1 - 2021 ER - TY - THES A1 - Mexi, Gioni T1 - New Ideas for the Feasibility Pump: Using Multiple Reference Vectors Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83724 ER - TY - JOUR A1 - Doerffel, Tom A1 - Papke, Ariane A1 - Klein, Rupert A1 - Ernst, Natalia A1 - Smolarkiewicz, Piotr K. T1 - Dynamics of tilted atmospheric vortices under asymmetric diabatic heating JF - Theoretical and Computational Fluid Dynamics N2 - Päschke et al. (J Fluid Mech, 2012) studied the nonlinear dynamics of strongly tilted vortices subject to asymmetric diabatic heating by asymptotic methods. They found, inter alia, that an azimuthal Fourier mode 1 heating pattern can intensify or attenuate such a vortex depending on the relative orientation of the tilt and the heating asymmetries. The theory originally addressed the gradient wind regime which, asymptotically speaking, corresponds to vortex Rossby numbers of order unity in the limit. Formally, this restricts the applicability of the theory to rather weak vortices. It is shown below that said theory is, in contrast, uniformly valid for vanishing Coriolis parameter and thus applicable to vortices up to low hurricane strengths. An extended discussion of the asymptotics as regards their physical interpretation and their implications for the overall vortex dynamics is also provided in this context. The paper’s second contribution is a series of three-dimensional numerical simulations examining the effect of different orientations of dipolar diabatic heating on idealized tropical cyclones. Comparisons with numerical solutions of the asymptotic equations yield evidence that supports the original theoretical predictions of Päschke et al. In addition, the influence of asymmetric diabatic heating on the time evolution of the vortex centerline is further analyzed, and a steering mechanism that depends on the orientation of the heating dipole is revealed. Finally, the steering mechanism is traced back to the correlation of dipolar perturbations of potential temperature, induced by the vortex tilt, and vertical velocity, for which diabatic heating not necessarily needs to be responsible, but which may have other origins. Y1 - 2021 U6 - https://doi.org/10.1007/s00162-021-00591-x VL - 35 IS - 6 SP - 831 EP - 873 ER - TY - THES A1 - Punjabi, Dev T1 - Orientation-invariant Dense Correspondence using Graph Convolutional Neural Networks Y1 - 2021 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Kamada, Hiroki A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - A hierarchical optimization approach to robust design of energy supply systems based on a mixed-integer linear model JF - Energy N2 - In designing energy supply systems, designers should heighten the robustness in performance criteria against the uncertainty in energy demands. In this paper, a robust optimal design method using a hierarchical mixed-integer linear programming (MILP) method is proposed to maximize the robustness of energy supply systems under uncertain energy demands based on a mixed-integer linear model. A robust optimal design problem is formulated as a three-level min-max-min MILP one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering relationships among integer design variables, uncertain energy demands, and integer and continuous operation variables. This problem is solved by evaluating upper and lower bounds for the minimum of the maximum regret of the performance criterion repeatedly outside, and evaluating lower and upper bounds for the maximum regret repeatedly inside. Different types of optimization problems are solved by applying a hierarchical MILP method developed for ordinary optimal design problems without and with its modifications. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system. Through the study, its validity and effectiveness are ascertained, and some features of the obtained robust designs are clarified. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2021.120343 VL - 229 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Takeuchi, Kotaro A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Effect of model reduction by time aggregation in multiobjective optimal design of energy supply systems by a hierarchical MILP method JF - Energy N2 - The mixed-integer linear programming (MILP) method has been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, a method of reducing model by time aggregation has been proposed to search design candidates accurately and efficiently at the upper level. In this paper, the hierarchical MILP method and model reduction by time aggregation are applied to the multiobjective optimal design. The methods of clustering periods by the order of time series, by the k-medoids method, and based on an operational strategy are applied for the model reduction. As a case study, the multiobjective optimal design of a gas turbine cogeneration system is investigated by adopting the annual total cost and primary energy consumption as the objective functions, and the clustering methods are compared with one another in terms of the computation efficiency. It turns out that the model reduction by any clustering method is effective to enhance the computation efficiency when importance is given to minimizing the first objective function, but that the model reduction only by the k-medoids method is effective very limitedly when importance is given to minimizing the second objective function. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2021.120505 VL - 228 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Saitenmacher, René A1 - Walther, Tom T1 - Improved models for operation modes of complex compressor stations JF - Mathematical Methods of Operations Research N2 - We study combinatorial structures in large-scale mixed-integer (nonlinear) programming problems arising in gas network optimization. We propose a preprocessing strategy exploiting the observation that a large part of the combinatorial complexity arises in certain subnetworks. Our approach analyzes these subnetworks and the combinatorial structure of the flows within these subnetworks in order to provide alternative models with a stronger combinatorial structure that can be exploited by off-the-shelve solvers. In particular, we consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. We propose a refined model that allows to precompute tighter bounds for each operation mode and a number of model variants based on the refined model exploiting these tighter bounds. We provide a procedure to obtain the refined model from the input data for the original model. This procedure is based on a nontrivial reduction of the graph representing the gas flow through the compressor station in an operation mode. We evaluate our model variants on reference benchmark data, showing that they reduce the average running time between 10% for easy instances and 46% for hard instances. Moreover, for three of four considered networks, the average number of search tree nodes is at least halved, showing the effectivity of our model variants to guide the solver’s search. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s00186-021-00745-x VL - 94 SP - 171 EP - 195 ER - TY - CHAP A1 - Pedersen, Jaap A1 - Hoppmann-Baum, Kai A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Blending hydrogen into natural gas: An assessment of the capacity of the German gas grid T2 - Operations Research Proceedings 2021 N2 - In the transition towards a pure hydrogen infrastructure, repurposing the existing natural gas infrastructure is considered. In this study, the maximal technically feasible injection of hydrogen into the existing German natural gas transmission network is analysed with respect to regulatory limits regarding the gas quality. We propose a transient tracking model based on the general pooling problem including linepack. The analysis is conducted using real-world hourly gas flow data on a network of about 10,000 km length. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1007/978-3-031-08623-6_28 SP - 182 EP - 187 ER - TY - JOUR A1 - Petkovic, Milena A1 - Chen, Ying A1 - Gamrath, Inken A1 - Gotzes, Uwe A1 - Hadjidimitrou, Natalia Selini A1 - Zittel, Janina A1 - Xu, Xiaofei A1 - Koch, Thorsten T1 - A hybrid approach for high precision prediction of gas flows JF - Energy Systems N2 - About 23% of the German energy demand is supplied by natural gas. Additionally, for about the same amount Germany serves as a transit country. Thereby, the German network represents a central hub in the European natural gas transport network. The transport infrastructure is operated by transmissions system operators (TSOs). The number one priority of the TSOs is to ensure the security of supply. However, the TSOs have only very limited knowledge about the intentions and planned actions of the shippers (traders). Open Grid Europe (OGE), one of Germany’s largest TSO, operates a high-pressure transport network of about 12,000 km length. With the introduction of peak-load gas power stations, it is of great importance to predict in- and out-flow of the network to ensure the necessary flexibility and security of supply for the German Energy Transition (“Energiewende”). In this paper, we introduce a novel hybrid forecast method applied to gas flows at the boundary nodes of a transport network. This method employs an optimized feature selection and minimization. We use a combination of a FAR, LSTM and mathematical programming to achieve robust high-quality forecasts on real-world data for different types of network nodes. Y1 - 2022 U6 - https://doi.org/10.1007/s12667-021-00466-4 VL - 13 SP - 383 EP - 408 ER - TY - JOUR A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide T1 - Effect of depth discontinuity on interfacial stability of tangential-velocity discontinuity in shallow-water flow JF - Physics Letters A N2 - It is well known as the Kelvin-Helmholtz instability (KHI) that an interface of tangential velocity discontinuity is necessarily unstable, regardless of the velocity difference's strength. However, the KHI is suppressed for shallow water flows if the Froude number, defined by the ratio of the velocity difference to the gravity wave's speed, is sufficiently large. In this investigation, we examine the effect of the depth difference of two fluid layers on the KHI. The depth difference enhances instability. Given the Froude number in the instability range, the growth rate sensitively depends on the depth ratio and increases monotonically with the depth ratio difference from unity. The critical value of the Froude number for stabilization varies with the depth ratio and attains the minimum value √8 for equal depth. This behavior is verified by asymptotic analysis. Y1 - 2022 U6 - https://doi.org/10.1016/j.physleta.2022.128073 VL - 436 SP - 128073 PB - ELSEVIER ER - TY - GEN A1 - Petkovic, Milena A1 - Zakiyeva, Nazgul A1 - Zittel, Janina T1 - Statistical analysis and modeling for detecting regime changes in gas nomination time series N2 - As a result of the legislation for gas markets introduced by the European Union in 2005, separate independent companies have to conduct the transport and trading of natural gas. The current gas market of Germany, which has a market value of more than 54 billion USD, consists of Transmission System Operators (TSO), network users, and traders. Traders can nominate a certain amount of gas anytime and anywhere in the network. Such unrestricted access for the traders, on the other hand, increase the uncertainty in the gas supply management. Some customers’ behaviors may cause abrupt structural changes in gas flow time series. In particular, it is a challenging task for the TSO operators to predict gas nominations 6 to 10 hours ahead. In our study, we aim to investigate the regime changes in the time series of nominations to predict the 6 to 10 hours ahead of gas nominations. T3 - ZIB-Report - 21-22 KW - Time series Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82988 SN - 1438-0064 ER - TY - GEN A1 - Zakiyeva, Nazgul A1 - Petkovic, Milena T1 - Modeling and forecasting gas network flows with multivariate time series and mathematical programming approach N2 - With annual consumption of approx. 95 billion cubic me-ters and similar amounts of gas just transshipped through Germany toother EU states, Germany’s gas transport system plays a vital role inEuropean energy supply. The complex, more than 40,000 km long high-pressure transmission network is controlled by several transmission sys-tem operators (TSOs) whose main task is to provide security of supplyin a cost-efficient way. Given the slow speed of gas flows through the gastransmission network pipelines, it has been an essential task for the gasnetwork operators to enhance the forecast tools to build an accurate andeffective gas flow prediction model for the whole network. By incorpo-rating the recent progress in mathematical programming and time seriesmodeling, we aim to model natural gas network and predict gas in- andout-flows at multiple supply and demand nodes for different forecastinghorizons. Our model is able to describe the dynamics in the network bydetecting the key nodes, which may help to build an optimal manage-ment strategy for transmission system operators. T3 - ZIB-Report - 21-23 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82966 SN - 1438-0064 ER - TY - JOUR A1 - Petkovic, Milena A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Deep learning for spatio-temporal supply anddemand forecasting in natural gas transmission networks JF - Energy Science and Engineering N2 - Germany is the largest market for natural gas in the European Union, with an annual consumption of approx. 95 billion cubic meters. Germany's high-pressure gas pipeline network is roughly 40,000 km long, which enables highly fluctuating quantities of gas to be transported safely over long distances. Considering that similar amounts of gas are also transshipped through Germany to other EU states, it is clear that Germany's gas transport system is essential to the European energy supply. Since the average velocity of gas in a pipeline is only 25km/h, an adequate high-precision, high-frequency forecasting of supply and demand is crucial for efficient control and operation of such a transmission network. We propose a deep learning model based on spatio-temporal convolutional neural networks (DLST) to tackle the problem of gas flow forecasting in a complex high-pressure transmission network. Experiments show that our model effectively captures comprehensive spatio-temporal correlations through modeling gas networks and consistently outperforms state-of-the-art benchmarks on real-world data sets by at least 21%. The results demonstrate that the proposed model can deal with complex nonlinear gas network flow forecasting with high accuracy and effectiveness. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1002/ese3.932 ER - TY - JOUR A1 - Moewis, Philippe A1 - Kaiser, René A1 - Trepczynski, Adam A1 - von Tycowicz, Christoph A1 - Krahl, Leonie A1 - Ilg, Ansgar A1 - Holz, Johannes A1 - Duda, Georg T1 - Patient specific resurfacing implant knee surgery in subjects with early osteoarthritis results in medial pivot and lateral femoral rollback during flexion: A retrospective pilot study JF - Knee Surgery, Sports Traumatology, Arthroscopy N2 - Purpose. Metallic resurfacing implants have been developed for the treatment of early, focal, small, condylar and trochlear osteoarthritis (OA) lesions. They represent an option for patients who are either too young to fulfill the criteria for total knee arthroplasty (TKA) or too old for biological treatment. Although relevant clinical evidence has been collected for different resurfacing types, the in vivo post-operative knee kinematics remains unknown. The present study aims to measure and analyse the knee joint kinematics in subjects with patient-specific Episealer implants Methods. Retrospective study design. Fluoroscopic analyses during high flexion activities (unloaded flexion-extension and loaded lunge) were conducted at >12 months post-surgery in ten Episealer knees. The post-operative knee joint kinematics was compared to equally assessed kinematic from ten healthy knees, twenty G-Curve TKA knees and 10 J-Curve knees. Pre- and postoperative clinical data of the Episealer knees were collected using a visual analog scale (VAS), the EQ 5d Health Questionnaire and the Knee Injury and Osteoarthritis Outcome Score (KOOS). Results. During unloaded flexion-extension and loaded lunge, the medial condyle in the Episealer knees remained relative stationary, indicating a medial pivot, while the lateral condyle translated consistently towards posterior. Similarly, reduced movement of the medial condyle and posterior translation of the lateral condyle was also observed in the healthy knees, although to a lesser extent. In contrast, the kinematics of both TKA cohorts during unloaded flexion-extension showed a tendency towards anterior displacement in the medial compartment, which led to significant differences in comparison with the Episealer knees. In the lateral compartment, a certain degree of femoral rollback was noted in the G-Curve TKA cohort. Improved scores were observed in the Episealer subjects between the preoperative and 1-year postoperative follow-up. Conclusion. At 12 months postsurgery, a physiological-like knee kinematics was observed in the group of patient-specific reconstructed chondral/osteochondral lesions by means of a resurfacing Episealer implant strategy. Considering that these patients are physically active and do not fulfill the criteria for TKA, the group is hard to be compared to TKA patients which usually are less active and more challenging. Nevertheless, the comparison to either healthy knee kinematics as well as to TKA reconstructed knees with different implant designs showed a more physiological-like kinematics in the resurfacing implants that seems more appropriate for such a patient group. Despite positive results, careful clinical follow-up of treated patients is recommended for the long-term OA progression. Further investigations need to be encouraged not only in larger patient groups but also in a prospective manner to assess the pre- to postoperative kinematic changes. Y1 - 2021 U6 - https://doi.org/10.1007/s00167-021-06749-8 ER - TY - CHAP A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Katz, Eugene A1 - Becker, Christiane T1 - Relaxed current-matching constraints by bifacial operation and luminescent coupling in perovskite/silicon tandem solar cells T2 - 2021 IEEE 48th Photovoltaic Specialists Conference (PVSC) Y1 - 2021 U6 - https://doi.org/10.1109/PVSC43889.2021.9518891 SP - 1086 ER - TY - GEN A1 - Euler, Ricardo A1 - Borndörfer, Ralf A1 - Strunk, Timo A1 - Takkula, Tuomo T1 - ULD Build-Up Scheduling with Dynamic Batching in an Air Freight Hub N2 - Air freight is usually shipped in standardized unit load devices (ULDs). The planning process for the consolidation of transit cargo from inbound flights or locally emerging shipments into ULDs for outbound flights is called build-up scheduling. More specifically, outbound ULDs must be assigned a time and a workstation subject to both workstation capacity constraints and the availability of shipments which in turn depends on break-down decisions for incoming ULDs. ULDs scheduled for the same outbound flight should be built up in temporal and spatial proximity. This serves both to minimize overhead in transportation times and to allow workers to move freight between ULDs. We propose to address this requirement by processing ULDs for the same outbound flight in batches. For the above build-up scheduling problem, we introduce a multi-commodity network design model. Outbound flights are modeled as commodities; transit cargo is represented by cargo flow volume and unpack and batch decisions are represented as design variables. The model is solved with standard MIP solvers on a set of benchmark data. For instances with a limited number of resource conflicts, near-optimal solutions are found in under two hours for a whole week of operations. T3 - ZIB-Report - 21-31 KW - Logistics KW - Airline Applications Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83482 SN - 1438-0064 ER - TY - GEN A1 - Niemann, Jan-Hendrik A1 - Schütte, Christof A1 - Klus, Stefan T1 - Simulation data: Data-driven model reduction of agent-based systems using the Koopman generator T2 - PLOS ONE Y1 - 2021 U6 - https://doi.org/http://doi.org/10.5281/zenodo.4522119 N1 - This repository contains the simulation data for the article "Data-driven model reduction of agent-based systems using the Koopman generator" by Jan-Hendrik Niemann, Stefan Klus and Christof Schütte. The archive complete_voter_model.zip contains the simulation results for the extended voter model on a complete graph for the parameters given in the corresponding txt-files to learn a reduced SDE model. The files are of the form [types, time steps, samples, training points].The archive dependency.zip contains additional simulation results of the form [types, time steps, samples, training points] to learn a reduced SDE model. The parameters used are given in the corresponding txt-files.The archive random_voter_model.zip contains the simulation results to learn a reduced SDE model for the given adjacency matrix within the archive. The file aggregate_state is of the form [training points, types, time steps, samples]. The file full_state is of the form [training points, agents, time steps, samples].The archive predator_prey_model.zip contains the simulation results to learn a reduced SDE model and calculation of the mean value of the agent-based model. The data is of the form [types, time steps, samples, training points] and [samples, time steps, types].The archive two_clustered_voter_model.zip contains the simulation results for the extended voter model on a graph with two clusters for the given adjacency matrices to learn a reduced SDE model. The file aggregate_state is of the form [training points, types, time steps, samples]. The file full_state is of the form [training points, agents, time steps, samples]. VL - 16 IS - 5 ER - TY - JOUR A1 - Oehme, Stephan A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Bartek, Benjamin A1 - Lippert, Annika A1 - von Tycowicz, Christoph A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Jung, Tobias T1 - PCL insufficient patients with increased translational and rotational passive knee joint laxity have no increased range of anterior–posterior and rotational tibiofemoral motion during level walking JF - Scientific Reports Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17328-3 VL - 12 IS - 1 SP - 1 EP - 11 ER - TY - JOUR A1 - Tierno, Pietro A1 - Johansen, Tom H. A1 - Straube, Arthur T1 - Thermally active nanoparticle clusters enslaved by engineered domain wall traps JF - Nature Commun. N2 - The stable assembly of fluctuating nanoparticle clusters on a surface represents a technological challenge of widespread interest for both fundamental and applied research. Here we demonstrate a technique to stably confine in two dimensions clusters of interacting nanoparticles via size-tunable, virtual magnetic traps. We use cylindrical Bloch walls arranged to form a triangular lattice of ferromagnetic domains within an epitaxially grown ferrite garnet film. At each domain, the magnetic stray field generates an effective harmonic potential with a field tunable stifness. The experiments are combined with theory to show that the magnetic confinement is effectively harmonic and pairwise interactions are of dipolar nature, leading to central, strictly repulsive forces. For clusters of magnetic nanoparticles, the stationary collective states arise from the competition between repulsion, confinement and the tendency to fill the central potential well. Using a numerical simulation model as a quantitative map between the experiment and theory we explore the field-induced crystallization process for larger clusters and unveil the existence of three different dynamical regimes. The present method provides a model platform for investigations of the collective phenomena emerging when strongly confined nanoparticle clusters are forced to move in an idealized, harmonic-like potential. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-25931-7 VL - 12 SP - 5813 ER - TY - GEN A1 - Hosoda, Junko A1 - Maher, Stephen J. A1 - Shinano, Yuji A1 - Villumsen, Jonas Christoffer T1 - Location, transshipment and routing: An adaptive transportation network integrating long-haul and local vehicle routing N2 - The routing of commodities is a tactical problem in supply chain management that aims to synchronise transportation services connecting a network of warehouses and consolidation locations. This paper considers the routing of commodities in a transportation network that is flexible in response to demand through changes to regional warehouse clustering and the designation of consolidation locations. Traditionally, warehouse clustering and consolidation locations are determined as part of strategic planning that is performed months to years in advance of operations---limiting the flexibility in transportation networks to respond to changes in demand. A mathematical programming-based algorithmic framework is proposed to integrate the strategic decisions of location planning with tactical decisions of vehicle routing and synchronisation. A multi-armed bandit problem is developed to explore warehouse clustering decisions and exploit those that lead to small transportation costs. An extensive computational study will show that the proposed algorithmic framework effectively integrates strategic and tactical planning decisions to reduce the overall transportation costs. T3 - ZIB-Report - 21-12 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83438 ER - TY - JOUR A1 - Ayanbayev, Birzhan A1 - Klebanov, Ilja A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Γ-convergence of Onsager–Machlup functionals: II. Infinite product measures on Banach spaces JF - Inverse Problems Y1 - 2022 U6 - https://doi.org/10.1088/1361-6420/ac3f82 VL - 38 IS - 2 ER - TY - JOUR A1 - Ayanbayev, Birzhan A1 - Klebanov, Ilja A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Γ-convergence of Onsager–Machlup functionals: I. With applications to maximum a posteriori estimation in Bayesian inverse problems JF - Inverse Problems Y1 - 2022 U6 - https://doi.org/10.1088/1361-6420/ac3f81 VL - 38 IS - 2 ER - TY - JOUR A1 - Sekuboyina, Anjany A1 - Husseini, Malek E. A1 - Bayat, Amirhossein A1 - Löffler, Maximilian A1 - Liebl, Hans A1 - Li, Hongwei A1 - Tetteh, Giles A1 - Kukačka, Jan A1 - Payer, Christian A1 - Štern, Darko A1 - Urschler, Martin A1 - Chen, Maodong A1 - Cheng, Dalong A1 - Lessmann, Nikolas A1 - Hu, Yujin A1 - Wang, Tianfu A1 - Yang, Dong A1 - Xu, Daguang A1 - Ambellan, Felix A1 - Amiranashvili, Tamaz A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Lehnert, Sebastian A1 - Lirio, Marilia A1 - de Olaguer, Nicolás Pérez A1 - Ramm, Heiko A1 - Sahu, Manish A1 - Tack, Alexander A1 - Zachow, Stefan A1 - Jiang, Tao A1 - Ma, Xinjun A1 - Angerman, Christoph A1 - Wang, Xin A1 - Brown, Kevin A1 - Kirszenberg, Alexandre A1 - Puybareau, Élodie A1 - Chen, Di A1 - Bai, Yiwei A1 - Rapazzo, Brandon H. A1 - Yeah, Timyoas A1 - Zhang, Amber A1 - Xu, Shangliang A1 - Hou, Feng A1 - He, Zhiqiang A1 - Zeng, Chan A1 - Xiangshang, Zheng A1 - Liming, Xu A1 - Netherton, Tucker J. A1 - Mumme, Raymond P. A1 - Court, Laurence E. A1 - Huang, Zixun A1 - He, Chenhang A1 - Wang, Li-Wen A1 - Ling, Sai Ho A1 - Huynh, Lê Duy A1 - Boutry, Nicolas A1 - Jakubicek, Roman A1 - Chmelik, Jiri A1 - Mulay, Supriti A1 - Sivaprakasam, Mohanasankar A1 - Paetzold, Johannes C. A1 - Shit, Suprosanna A1 - Ezhov, Ivan A1 - Wiestler, Benedikt A1 - Glocker, Ben A1 - Valentinitsch, Alexander A1 - Rempfler, Markus A1 - Menze, Björn H. A1 - Kirschke, Jan S. T1 - VerSe: A Vertebrae labelling and segmentation benchmark for multi-detector CT images JF - Medical Image Analysis N2 - Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://github.com/anjany/verse. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102166 VL - 73 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, F.J. A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, J. A1 - Weiser, Martin A1 - Wende, Florian T1 - The HighPerMeshes Framework for Numerical Algorithms on Unstructured Grids JF - Concurrency and Computation: Practice and Experience N2 - Solving PDEs on unstructured grids is a cornerstone of engineering and scientific computing. Heterogeneous parallel platforms, including CPUs, GPUs, and FPGAs, enable energy-efficient and computationally demanding simulations. In this article, we introduce the HPM C++-embedded DSL that bridges the abstraction gap between the mathematical formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different programming models on the other hand. Thus, the HPM DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HPM DSL, and demonstrate its usage with three examples. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters, is presented. A code generator and a matching back end allow the acceleration of HPM code with GPUs. Finally, the achievable performance and scalability are demonstrated for different example problems. Y1 - 2022 U6 - https://doi.org/10.1002/cpe.6616 VL - 34 IS - 14 ER - TY - GEN A1 - Lindner, Niels A1 - van Lieshout, Rolf T1 - Benders Decomposition for the Periodic Event Scheduling Problem N2 - The Periodic Event Scheduling Problem (PESP) is the central mathematical model behind the optimization of periodic timetables in public transport. We apply Benders decomposition to the incidence-based MIP formulation of PESP. The resulting formulation exhibits particularly nice features: The subproblem is a minimum cost network flow problem, and feasibility cuts are equivalent to the well-known cycle inequalities by Odijk. We integrate the Benders approach into a branch-and-cut framework, and assess the performance of this method on instances derived from the benchmarking library PESPlib. T3 - ZIB-Report - 21-29 KW - Periodic Timetabling KW - Periodic Event Scheduling Problem KW - Benders Decomposition KW - Mixed-Integer Programming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83338 SN - 1438-0064 ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Kopanicakova, Alena A1 - Weiser, Martin A1 - Krause, Rolf T1 - Quantitative Analysis of Nonlinear MultifidelityOptimization for Inverse Electrophysiology T2 - Domain Decomposition Methods in Science and Engineering XXVI N2 - The electric conductivity of cardiac tissue determines excitation propagation and is important for quantifying ischemia and scar tissue and for building personalized models. Estimating conductivity distributions from endocardial mapping data is a challenging inverse problem due to the computational complexity of the monodomain equation, which describes the cardiac excitation. For computing a maximum posterior estimate, we investigate different optimization approaches based on adjoint gradient computation: steepest descent, limited memory BFGS, and recursive multilevel trust region methods, which are using mesh hierarchies or heterogeneous model hierarchies. We compare overall performance, asymptotic convergence rate, and pre-asymptotic progress on selected examples in order to assess the benefit of our multifidelity acceleration. Y1 - 2022 SP - 65 EP - 76 PB - Springer ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Error Bounds for Discrete-Continuous Free Flight Trajectory Optimization JF - Journal of Optimization Theory and Applications N2 - Flight planning, the computation of optimal routes in view of flight time and fuel consumption under given weather conditions, is traditionally done by finding globally shortest paths in a predefined airway network. Free flight trajectories, not restricted to a network, have the potential to reduce the costs significantly, and can be computed using locally convergent continuous optimal control methods. Hybrid methods that start with a discrete global search and refine with a fast continuous local optimization combine the best properties of both approaches, but rely on a good switchover, which requires error estimates for discrete paths relative to continuous trajectories. Based on vertex density and local complete connectivity, we derive localized and a priori bounds for the flight time of discrete paths relative to the optimal continuous trajectory, and illustrate their properties on a set of benchmark problems. It turns out that localization improves the error bound by four orders of magnitude, but still leaves ample opportunities for tighter bounds using a posteriori error estimators. Y1 - 2023 U6 - https://doi.org/10.1007/s10957-023-02264-7 VL - 198 SP - 830 EP - 856 ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Gwalt, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Siewert, Frank A1 - Soltwisch, Victor T1 - Shape- and Element-Sensitive Reconstruction of Periodic Nanostructures with Grazing Incidence X-ray Fluorescence Analysis and Machine Learning JF - Nanomaterials Y1 - 2021 U6 - https://doi.org/10.3390/nano11071647 VL - 11 SP - 1647 ER - TY - GEN A1 - Ehlers, Sarah A1 - Wessel, Andreas A1 - Baum, Daniel T1 - Segmentation of abdominal chordotonal organs based on semithin serial sections in the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Cicadellidae) N2 - For mating, leafhoppers (Cicadellidae) use substrate-borne vibrational signals to communicate. We provide the first complete description of the abdominal chordotonal organs that enable the perception of these signals. This supplementary data provides the aligned stack of 450 semithin serial sections of the first and second abdominal segment of an adult male Rhododendron leafhopper (Graphocephala fennahi). Further, this supplementary data comprises the segmentation files of five chordotonal organs, the exoskeleton, the segmental nerves and the spiracles of the first and the second abdominal segment. Due to time limitations, the structures of only one half of the body were segmented. The specimen was caught by hand net in September 2018 in Berlin-Tiergarten, Germany. Samples were embedded in Araldite® 502 resin and cut transversally in 1 μm thick sections using a Leica ultramicrotome and a DIATOME Histo Jumbo 6.0 mm diamond knife. Sections were placed on microscopic slides and stained with methylene blue/azur II. The images were taken by means of a 3DHISTECH PANNORAMIC SCAN II slide scanner in the Institute of Pathology Charité in Berlin-Mitte, Germany. Images with a voxel size of 0.273809 μm x 0.273809 μm x 1 μm where obtained. The images were converted from MRXS-files to TIFF-files with the 3DHistech software Slide Converter 2.3. Using Photoshop, the images were cropped to the same canvas size and artefacts were removed. All further steps, such as alignment and segmentation, were done with the software Amira. In order to facilitate the further processing of the dataset, the voxels where resampled to a size of 0.547619 μm x 0.547619 μm x 1 μm. Y1 - 2021 U6 - https://doi.org/10.12752/8326 N1 - Supplementary data to reproduce and understand the description of the morphology of the abdominal chordotonal organs in Graphocephala fennahi. ER - TY - JOUR A1 - Nitzke, Isabel A1 - Fackeldey, Konstantin A1 - Vrabec, Jadran T1 - Long range corrections for inhomogeneous fluids containing a droplet or a bubble JF - Molecular Simulation N2 - Long range corrections for molecular simulations of inhomogeneous fluids with a spherical interface are presented. Correction terms for potential energy, force and virial are derived for the monatomic Lennard–Jones fluid. The method is generalised to the Mie potential and arbitrary molecular structures, employing a numerically efficient centre of mass cut-off scheme. The results are validated by a series of droplet simulations for one-centre and two-centre Lennard–Jones fluids with different cut-off radii rc. Systems with rc=8σ provide a check of self-consistence. Further, a system containing a bubble is investigated for the one-centre Lennard–Jones fluid. The equilibrium properties are almost completely independent on the cut-off radius. In comparison with vapour–liquid equilibrium data for systems without a curved interface, all properties show the expected behaviour. Simulation data are used to approximate the surface tension, which is in good agreement with the findings for planar interfaces, thus verifying the present corrections. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1080/08927022.2021.1954639 SP - 1 EP - 14 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Casel, Katrin A1 - Issac, Davis A1 - Niklanovits, Aikaterini A1 - Schwartz, Stephan A1 - Zeif, Ziena T1 - Connected k-partition of k-connected graphs and c-claw-free graphs T2 - Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, APPROX/RANDOM 2021 N2 - A connected partition is a partition of the vertices of a graph into sets that induce connected subgraphs. Such partitions naturally occur in many application areas such as road networks, and image processing. In these settings, it is often desirable to partition into a fixed number of parts of roughly of the same size or weight. The resulting computational problem is called Balanced Connected Partition (BCP). The two classical objectives for BCP are to maximize the weight of the smallest, or minimize the weight of the largest component. We study BCP on c-claw-free graphs, the class of graphs that do not have K_{1,c} as an induced subgraph, and present efficient (c −1)-approximation algorithms for both objectives. In particular, for 3-claw-free graphs, also simply known as claw-free graphs, we obtain a 2-approximation. Due to the claw-freeness of line graphs, this also implies a 2-approximation for the edge-partition version of BCP in general graphs. A harder connected partition problem arises from demanding a connected partition into k parts that have (possibly) heterogeneous target weights w_1, ..., w_k. In the 1970s Győri and Lovász showed that if G is k-connected and the target weights sum to the total size of G, such a partition exists. However, to this day no polynomial algorithm to compute such partitions exists for k > 4. Towards finding such a partition T_1, ..., T_k in k-connected graphs for general k, we show how to efficiently compute connected partitions that at least approximately meet the target weights, subject to the mild assumption that each w_i is greater than the weight of the heaviest vertex. In particular, we give a 3-approximation for both the lower and the upper bounded version i.e. we guarantee that each T_i has weight at least w_i/3 or that each T_i has weight most 3w_i, respectively. Also, we present a both-side bounded version that produces a connected partition where each T_i has size at least w_i/3 and at most max({r, 3})w_i, where r ≥1 is the ratio between the largest and smallest value in w_1, ..., w_k. In particular for the balanced version, i.e. w_1 = w_2 = ... = w_k, this gives a partition with 1/3 w_i ≤ w(T_i) ≤ 3w_i. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0030-drops-147200 VL - 207 SP - 27:1 EP - 27:14 PB - Schloss Dagstuhl - Leibniz-Zentrum für Informatik ER - TY - JOUR A1 - Raharinirina, Alexia N. A1 - Peppert, Felix A1 - von Kleist, Max A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments JF - Patterns N2 - Single-cell RNA sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealized due to technical and computational challenges. In this work we focus on the latter, which is under-represented in the literature. We took a systemic approach by subdividing the GRN inference into three fundamental components: data pre-processing, feature extraction, and inference. We observed that the regulatory signature is captured in the statistical moments of scRNA-seq data and requires computationally intensive minimization solvers to extract it. Furthermore, current data pre-processing might not conserve these statistical moments. Although our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking—finding computationally feasible multi-dimensional statistics of data—is imperative for designing GRN inference methods. Y1 - 2021 U6 - https://doi.org/10.1016/j.patter.2021.100332 VL - 2 IS - 9 ER - TY - GEN A1 - Masing, Berenike T1 - Optimal Line Planning in the Parametric City N2 - We formulate the line planning problem in public transport as a mixed integer linear program (MILP), which selects both passenger and vehicle routes, such that travel demands are met with respect to minimized travel times for both operators and users. We apply MILP to the Parametric City, a generic city model developed by Fielbaum et al. While the infrastructure graph and demand are entirely rotation symmetric, asymmetric optimal line plans can occur. Using group theory, we analyze the properties of symmetric solutions and introduce a symmetry gap to measure their deviation of the optimum. We also develop a 1+(1+\sqrt{2})/g-approximation algorithm, depending only on the cost related parameter g. Supported by computational experiments, we conclude that in practice symmetric line plans provide good solutions for the line planning problem in the Parametric City. T3 - ZIB-Report - 21-26 KW - line planning KW - city modelling KW - symmetry KW - mixed integer programming KW - approximation algorithm Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83238 SN - 1438-0064 ER - TY - CHAP A1 - Perevoznik, Dmitrii A1 - Bose, Surajit A1 - Burger, Sven A1 - Demircan, Ayhan A1 - Morgner, Uwe T1 - Writing Photonic Components in Polymers Using Femtosecond Pulses T2 - Conference on Lasers and Electro-Optics (CLEO) Y1 - 2021 U6 - https://doi.org/10.1364/CLEO_AT.2021.ATh4P.4 SP - ATh4P.4 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Finding Minimum Balanced Separators - an Exact Approach T2 - Operations Research Proceedings 2021 N2 - Balanced separators are node sets that split the graph into size bounded components. They find applications in different theoretical and practical problems. In this paper we discuss how to find a minimum set of balanced separators in node weighted graphs. Our contribution is a new and exact algorithm that solves Minimum Balanced Separators by a sequence of Hitting Set problems. The only other exact method appears to be a mixed-integer program (MIP) for the edge weighted case. We adapt this model to node weighted graphs and compare it to our approach on a set of instances, resembling transit networks. It shows that our algorithm is far superior on almost all test instances. T3 - ZIB-Report - 21-25 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83138 SN - 1438-0064 SP - 154 EP - 159 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 24 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple_PriPro, CaDiCaL_PriPro and CaDiCaL_PriPro_no_bin T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 N1 - CaDiCaL_PriPro won the Special Innovation Price at the SAT Competition 2021 SP - 25 ER - TY - CHAP A1 - Schnauber, Peter A1 - Schall, Johannes A1 - Bounouar, Samir A1 - Srinivasan, Kartik A1 - Davanco, Marcelo A1 - Song, Jin-Dong A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Deterministically fabricated quantum dot – waveguide systems for on-chip quantum optics T2 - Proc. SPIE Y1 - 2021 U6 - https://doi.org/10.1117/12.2596042 VL - 11806 SP - 118060G ER - TY - JOUR A1 - Wang, Junyang A1 - Cockayne, Jon A1 - Chkrebtii, Oksana A1 - Sullivan, T. J. A1 - Oates, Chris T1 - Bayesian numerical methods for nonlinear partial differential equations JF - Statistics and Computing Y1 - 2021 U6 - https://doi.org/10.1007/s11222-021-10030-w VL - 31 IS - 5 ER - TY - JOUR A1 - Negrin-Montecelo, Yoel A1 - Movsesyan, Artur A1 - Gao, Jie A1 - Burger, Sven A1 - Wang, Zhiming A1 - Nlate, Sylvain A1 - Pouget, Emilie A1 - Oda, Reiko A1 - Comesana-Hermo, Miguel A1 - Govorov, Alexander O. A1 - Correa-Duarte, Miguel T1 - Chiral Generation of Hot Carriers for Polarization-Sensitive Plasmonic Photocatalysis with Hybrid Nanostructures JF - J. Am. Chem. Soc. Y1 - 2022 U6 - https://doi.org/10.1021/jacs.1c10526 VL - 144 SP - 1663 ER - TY - CHAP A1 - Schwarz, R. A1 - Lacalandra, F. A1 - Schewe, L. A1 - Bettinelli, A. A1 - Vigo, D. A1 - Bischi, A. A1 - Parriani, T. A1 - Martelli, E. A1 - Vuik, K. A1 - Lenz, R. A1 - Madsen, H. A1 - Blanco, I. A1 - Guericke, D. A1 - Yüksel-Ergün, I. A1 - Zittel, J. T1 - Network and Storage T2 - Mathematical Optimization for Efficient and Robust Energy Networks N2 - Natural gas is considered by many to be the most important energy source for the future. The objectives of energy commodities strategic problems can be mainly related to natural gas and deal with the definition of the “optimal” gas pipelines design which includes a number of related sub problems such as: Gas stations (compression) location and Gas storage locations, as well as compression station design and optimal operation. Y1 - 2020 SN - 978-3-030-57442-0 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-57442-0_6 VL - 4 PB - Springer ER - TY - CHAP A1 - Diekerhof, M. A1 - Monti, A. A1 - Lebedeva, E. A1 - Tkaczyk, A. H. A1 - Yüksel-Ergün, I. A1 - Zittel, J. A1 - Escudero, L. F. A1 - Soroudi, A. A1 - Helmberg, C. A1 - Kanovíc, Ž. A1 - Petkovic, M. A1 - Lacalandra, F. A1 - Frangioni, A. A1 - Lee, J. A1 - De Filippo, A. A1 - Lombardi, M. A1 - Milano, M. A1 - Ezran, P. A1 - Haddad, Y. T1 - Production and Demand Management T2 - Mathematical Optimization for Efficient and Robust Energy Networks N2 - Demand Side Management (DSM) is usually considered as a process of energy consumption shifting from peak hours to off-peak times. DSM does not always reduce total energy consumption, but it helps to meet energy demand and supply. For example, it balances variable generation from renewables (such as solar and wind) when energy demand differs from renewable generation. Y1 - 2020 SN - 978-3-030-57442-0 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-57442-0_1 VL - 4 PB - Springer ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven T1 - RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2021 U6 - https://doi.org/10.1016/j.softx.2021.100763 VL - 15 SP - 100763 ER - TY - JOUR A1 - Hennings, Felix T1 - Large-scale empirical study on the momentum equation's inertia term JF - Journal of Natural Gas Science and Engineering N2 - A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation, which is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems. Y1 - 2021 U6 - https://doi.org/10.1016/j.jngse.2021.104153 VL - 95 PB - Elsevier ER - TY - JOUR A1 - Wu, Tong A1 - Arrivault, Denis A1 - Duruflé, Marc A1 - Gras, Alexandre A1 - Binkowski, Felix A1 - Burger, Sven A1 - Yan, Wei A1 - Lalanne, Philippe T1 - Efficient hybrid method for the modal analysis of optical microcavities and nanoresonators JF - J. Opt. Soc. Am. A Y1 - 2021 U6 - https://doi.org/10.1364/JOSAA.428224 VL - 38 SP - 1224 ER - TY - JOUR A1 - Picht, Thomas A1 - Le Calve, Maxime A1 - Tomasello, Rosario A1 - Fekonja, Lucius A1 - Gholami, Mohammad Fardin A1 - Bruhn, Matthias A1 - Zwick, Carola A1 - Rabe, Jürgen P. A1 - Müller-Birn, Claudia A1 - Vajkoczy, Peter A1 - Sauer, Igor M. A1 - Zachow, Stefan A1 - Nyakatura, John A. A1 - Ribault, Patricia A1 - Pulvermüller, Friedemann T1 - A note on neurosurgical resection and why we need to rethink cutting JF - Neurosurgery Y1 - 2021 U6 - https://doi.org/10.1093/neuros/nyab326 VL - 89 IS - 5 SP - 289 EP - 291 ER - TY - GEN A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven T1 - RPExpand: Software for Riesz projection expansion of resonance phenomena [Source Code] Y1 - 2021 U6 - https://doi.org/10.24433/CO.2372084.v1 ER - TY - JOUR A1 - Sipiran, Ivan A1 - Lazo, Patrick A1 - Lopez, Cristian A1 - Bagewadi, Nihar A1 - Bustos, Benjamin A1 - Dao, Hieu A1 - Gangisetty, Shankar A1 - Hanik, Martin A1 - Ho-Thi, Ngoc-Phuong A1 - Holenderski, Mike A1 - Jarnikov, Dmitri A1 - Labrada, Arniel A1 - Lengauer, Stefan A1 - Licandro, Roxane A1 - Nguyen, Dinh-Huan A1 - Nguyen-Ho, Thang-Long A1 - Pérez Rey, Luis A. A1 - Pham, Bang-Dang A1 - Pham, Minh-Khoi A1 - Preiner, Reinhold A1 - Schreck, Tobias A1 - Trinh, Quoc-Huy A1 - Tonnaer, Loek A1 - von Tycowicz, Christoph A1 - Vu-Le, The-Anh T1 - SHREC 2021: Retrieval of Cultural Heritage Objects JF - Computers and Graphics N2 - This paper presents the methods and results of the SHREC’21 contest on a dataset of cultural heritage (CH) objects. We present a dataset of 938 scanned models that have varied geometry and artistic styles. For the competition, we propose two challenges: the retrieval-by-shape challenge and the retrieval-by-culture challenge. The former aims at evaluating the ability of retrieval methods to discriminate cultural heritage objects by overall shape. The latter focuses on assessing the effectiveness of retrieving objects from the same culture. Both challenges constitute a suitable scenario to evaluate modern shape retrieval methods in a CH domain. Ten groups participated in the contest: thirty runs were submitted for the retrieval-by-shape task, and twenty-six runs were submitted for the retrieval-by-culture challenge. The results show a predominance of learning methods on image-based multi-view representations to characterize 3D objects. Nevertheless, the problem presented in our challenges is far from being solved. We also identify the potential paths for further improvements and give insights into the future directions of research. Y1 - 2021 U6 - https://doi.org/10.1016/j.cag.2021.07.010 VL - 100 SP - 1 EP - 20 ER - TY - GEN A1 - Pedersen, Jaap A1 - Hoppmann-Baum, Kai A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Blending hydrogen into natural gas: An assessment of the capacity of the German gas grid; Technical Report N2 - In the transition towards a pure hydrogen infrastructure, utilizing the existing natural gas infrastructure is a necessity. In this study, the maximal technically feasible injection of hydrogen into the existing German natural gas transmission network is analysed with respect to regulatory limits regarding the gas quality. We propose a transient tracking model based on the general pooling problem including linepack. The analysis is conducted using real-world hourly gas flow data on a network of about 10,000 km length. T3 - ZIB-Report - 21-21 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82838 SN - 1438-0064 ER - TY - THES A1 - Pakhomov, Anton T1 - Efficient modeling and optimization of surface second-harmonic generation from nanophotonic components Y1 - 2021 U6 - https://doi.org/10.22032/dbt.49369 ER - TY - THES A1 - Tiwari, Sofi T1 - Facial Landmark Detection on 3D Surface Scans using Geometric Deep Learning N2 - Facial landmark detection on 3D scans is an active area of research. Most of the recent work focus on using statistical techniques and Deep Learning architectures to make the task of landmark detection an automated one. Recently, there has been an increasing interest in the field of Geometric Deep Learning that learns features directly from 3D data and offers a promising approach to improve the task of facial landmark detection. In this thesis, we investigate three different ways to improve an existing Geometric Deep Learning method for landmark detection on non-aligned face meshes. Our method offers promising results on meshes that are rotated up to 90° and outperforms the inter-rater variability obtained from the ground truth. KW - anthropometry Y1 - 2021 ER - TY - GEN A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yamamura, Keiichiro A1 - Yoshida, Akihiro A1 - Kaji, Shizuo A1 - Yasuda, Masaya A1 - Fujisawa, Katsuki T1 - CMAP-LAP: Configurable Massively Parallel Solver for Lattice Problems N2 - Lattice problems are a class of optimization problems that are notably hard. There are no classical or quantum algorithms known to solve these problems efficiently. Their hardness has made lattices a major cryptographic primitive for post-quantum cryptography. Several different approaches have been used for lattice problems with different computational profiles; some suffer from super-exponential time, and others require exponential space. This motivated us to develop a novel lattice problem solver, CMAP-LAP, based on the clever coordination of different algorithms that run massively in parallel. With our flexible framework, heterogeneous modules run asynchronously in parallel on a large-scale distributed system while exchanging information, which drastically boosts the overall performance. We also implement full checkpoint-and-restart functionality, which is vital to high-dimensional lattice problems. Through numerical experiments with up to 103,680 cores, we evaluated the performance and stability of our system and demonstrated its high capability for future massive-scale experiments. T3 - ZIB-Report - 21-16 KW - Discrete optimization KW - Lattice problem KW - Lattice-based cryptography KW - Shortest vector problem KW - Parallel algorithms KW - Ubiquity Generator Framework Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82802 SN - 1438-0064 N1 - Revised version is accepted to HiPC 2021 ER - TY - GEN A1 - Ray, Sourav A1 - Thies, Arne A1 - Sunkara, Vikram A1 - Wulkow, Hanna A1 - Celik, Özgür A1 - Yergöz, Fatih A1 - Schütte, Christof A1 - Stein, Christoph A1 - Weber, Marcus A1 - Winkelmann, Stefanie T1 - Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design N2 - Initiated by mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands in normal versus diseased (inflamed) environments, we previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. Uniquely, this design recognised that GPCRs function differently under pathological versus healthy conditions. We now present a novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels associated with parameters of inflamed tissue (pH, radicals). By means of molecular dynamics simulations, we also assessed qualitative changes of the reaction rates due to additional disulfide bridges inside the GPCR binding pocket and used these rates for stochastic simulations of the corresponding reaction jump process. The modelling results were validated with in vitro experiments measuring calcium currents and G-protein activation. We found markedly reduced G-protein dissociation and calcium channel inhibition induced by NFEPP at normal pH, and enhanced constitutive G-protein activation but lower probability of ligand binding with increasing radical concentrations. These results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account. T3 - ZIB-Report - 21-19 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82797 SN - 1438-0064 ER - TY - GEN A1 - Koch, Thorsten A1 - Berthold, Timo A1 - Pedersen, Jaap A1 - Vanaret, Charlie T1 - Progress in Mathematical Programming Solvers from 2001 to 2020 N2 - This study investigates the progress made in LP and MILP solver performance during the last two decades by comparing the solver software from the beginning of the millennium with the codes available today. On average, we found out that for solving LP/MILP, computer hardware got about 20 times faster, and the algorithms improved by a factor of about nine for LP and around 50 for MILP, which gives a total speed-up of about 180 and 1,000 times, respectively. However, these numbers have a very high variance and they considerably underestimate the progress made on the algorithmic side: many problem instances can nowadays be solved within seconds, which the old codes are not able to solve within any reasonable time. T3 - ZIB-Report - 21-20 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82779 SN - 1438-0064 ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian A1 - Masing, Berenike T1 - Forward Cycle Bases and Periodic Timetabling N2 - Periodic timetable optimization problems in public transport can be modeled as mixed-integer linear programs by means of the Periodic Event Scheduling Problem (PESP). In order to keep the branch-and-bound tree small, minimum integral cycle bases have been proven successful. We examine forward cycle bases, where no cycle is allowed to contain a backward arc. After reviewing the theory of these bases, we describe the construction of an integral forward cycle basis on a line-based event-activity network. Adding turnarounds to the instance \texttt{R1L1} of the benchmark library PESPlib, we computationally evaluate three types of forward cycle bases in the Pareto sense, and come up with significant improvements concerning dual bounds. T3 - ZIB-Report - 21-18 KW - Periodic Timetabling KW - Cycle Bases KW - Mixed Integer Programming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82756 SN - 1438-0064 ER - TY - JOUR A1 - Thies, Arne A1 - Sunkara, Vikram A1 - Ray, Sourav A1 - Wulkow, Hanna A1 - Celik, M. Özgür A1 - Yergöz, Fatih A1 - Schütte, Christof A1 - Stein, Christoph A1 - Weber, Marcus A1 - Winkelmann, Stefanie T1 - Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design JF - Scientific Reports N2 - We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. The design process of NFEPP was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present an additional and novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels and their dependence on parameters of inflamed and healthy tissue (pH, radicals). The model is validated against in vitro experimental data for the ligands NFEPP and fentanyl at different pH values and radical concentrations. We observe markedly reduced binding affinity and calcium channel inhibition for NFEPP at normal pH compared to lower pH, in contrast to the effect of fentanyl. For increasing radical concentrations, we find enhanced constitutive G-protein activation but reduced ligand binding affinity. Assessing the different effects, the results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-27699-w VL - 13 IS - 607 ER - TY - JOUR A1 - Ernst, Ariane A1 - Schütte, Christof A1 - Sigrist, Stephan A1 - Winkelmann, Stefanie T1 - Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics JF - Mathematical Biosciences N2 - Neurotransmission at chemical synapses relies on the calcium-induced fusion of synaptic vesicles with the presynaptic membrane. The distance to the calcium channels determines the release probability and thereby the postsynaptic signal. Suitable models of the process need to capture both the mean and the variance observed in electrophysiological measurements of the postsynaptic current. In this work, we propose a method to directly compute the exact first- and second-order moments for signals generated by a linear reaction network under convolution with an impulse response function, rendering computationally expensive numerical simulations of the underlying stochastic counting process obsolete. We show that the autocorrelation of the process is central for the calculation of the filtered signal’s second-order moments, and derive a system of PDEs for the cross-correlation functions (including the autocorrelations) of linear reaction networks with time-dependent rates. Finally, we employ our method to efficiently compare different spatial coarse graining approaches for a specific model of synaptic vesicle fusion. Beyond the application to neurotransmission processes, the developed theory can be applied to any linear reaction system that produces a filtered stochastic signal. Y1 - 2022 U6 - https://doi.org/10.1016/j.mbs.2021.108760 VL - 343 ER - TY - GEN A1 - Lindner, Niels A1 - Maristany de las Casas, Pedro A1 - Schiewe, Philine T1 - Optimal Forks: Preprocessing Single-Source Shortest Path Instances with Interval Data N2 - We investigate preprocessing for single-source shortest path queries in digraphs, where arc costs are only known to lie in an interval. More precisely, we want to decide for each arc whether it is part of some shortest path tree for some realization of costs. We show that this problem is solvable in polynomial time by giving a combinatorial algorithm, using optimal structures that we call forks. Our algorithm turns out to be very efficient in practice, and is sometimes even superior in quality to a heuristic developed for the one-to-one shortest path problem in the context of passenger routing in public transport. T3 - ZIB-Report - 21-17 KW - Preprocessing Shortest Path Problems KW - Interval Data KW - Graph Algorithms Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82716 SN - 1438-0064 ER - TY - GEN A1 - Ernst, Ariane A1 - Schütte, Christof A1 - Sigrist, Stephan A1 - Winkelmann, Stefanie T1 - Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics N2 - Neurotransmission at chemical synapses relies on the calcium-induced fusion of synaptic vesicles with the presynaptic membrane. The distance to the calcium channels determines the release probability and thereby the postsynaptic signal. Suitable models of the process need to capture both the mean and the variance observed in electrophysiological measurements of the postsynaptic current. In this work, we propose a method to directly compute the exact first- and second-order moments for signals generated by a linear reaction network under convolution with an impulse response function, rendering computationally expensive numerical simulations of the underlying stochastic counting process obsolete. We show that the autocorrelation of the process is central for the calculation of the filtered signal’s second-order moments, and derive a system of PDEs for the cross-correlation functions (including the autocorrelations) of linear reaction networks with time-dependent rates. Finally, we employ our method to efficiently compare different spatial coarse graining approaches for a specific model of synaptic vesicle fusion. Beyond the application to neurotransmission processes, the developed theory can be applied to any linear reaction system that produces a filtered stochastic signal. T3 - ZIB-Report - 21-15 KW - linear reaction networks KW - cross-correlation KW - neurotransmission Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82674 SN - 1438-0064 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Schuster, Ingmar T1 - Markov Chain Importance Sampling - a highly efficient estimator for MCMC JF - Journal of Computational and Graphical Statistics N2 - Markov chain (MC) algorithms are ubiquitous in machine learning and statistics and many other disciplines. Typically, these algorithms can be formulated as acceptance rejection methods. In this work we present a novel estimator applicable to these methods, dubbed Markov chain importance sampling (MCIS), which efficiently makes use of rejected proposals. For the unadjusted Langevin algorithm, it provides a novel way of correcting the discretization error. Our estimator satisfies a central limit theorem and improves on error per CPU cycle, often to a large extent. As a by-product it enables estimating the normalizing constant, an important quantity in Bayesian machine learning and statistics. Y1 - 2020 U6 - https://doi.org/10.1080/10618600.2020.1826953 ER - TY - JOUR A1 - Lantzsch, Ina A1 - Yu, Che-Hang A1 - Chen, Yu-Zen A1 - Zimyanin, Vitaly A1 - Yazdkhasti, Hossein A1 - Lindow, Norbert A1 - Szentgyoergyi, Erik A1 - Pani, Ariel M A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Fürthauer, Sebastian A1 - Redemann, Stefanie T1 - Microtubule reorganization during female meiosis in C. elegans JF - eLife N2 - Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic \textit{Caenorhabditis elegans} spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin. Y1 - 2021 U6 - https://doi.org/10.7554/eLife.58903 VL - 10 SP - e58903 ER - TY - GEN A1 - Rusch, Beate A1 - Peters-Kottig, Wolfgang A1 - Boltze, Julia A1 - Brandtner, Andreas A1 - Degkwitz, Andreas A1 - Kirsch, Simona A1 - Koch, Thorsten A1 - Lohrum, Stefan A1 - Müller, Anja A1 - Mutter, Moritz A1 - Seeliger, Frank A1 - Stanek, Ursula T1 - KOBV Jahresbericht 2019-2020 N2 - Der aktuelle KOBV-Jahresbericht informiert darüber, was in den Mitgliedsbibliotheken und Partnerprojekten in den letzten beiden Jahren passiert ist und was sich in der Verbundzentrale und in der Bibliothekslandschaft ändert. Die Ausgabe 2019/2020 enthält den Schwerpunktteil »Digitalisierung« mit verschiedenen Perspektiven auf die digitale Arbeitswelt. T3 - KOBV-Jahresbericht - 2019-2020 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82474 SN - 1438-0064 CY - Berlin ER - TY - JOUR A1 - Plock, Matthias A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Recent advances in Bayesian optimization with applications to parameter reconstruction in optical nano-metrology JF - Proc. SPIE Y1 - 2021 U6 - https://doi.org/10.1117/12.2592266 VL - 11783 SP - 117830J ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Vertex Covering with Capacitated Trees N2 - The covering of a graph with (possibly disjoint) connected subgraphs is a fundamental problem in graph theory. In this paper, we study a version to cover a graph's vertices by connected subgraphs subject to lower and upper weight bounds, and propose a column generation approach to dynamically generate feasible and promising subgraphs. Our focus is on the solution of the pricing problem which turns out to be a variant of the NP-hard Maximum Weight Connected Subgraph Problem. We compare different formulations to handle connectivity, and find that a single-commodity flow formulation performs best. This is notable since the respective literature seems to have dismissed this formulation. We improve it to a new coarse-to-fine flow formulation that is theoretically and computationally superior, especially for large instances with many vertices of degree 2 like highway networks, where it provides a speed-up factor of 10 over the non-flow-based formulations. We also propose a preprocessing method that exploits a median property of weight constrained subgraphs, a primal heuristic, and a local search heuristic. In an extensive computational study we evaluate the presented connectivity formulations on different classes of instances, and demonstrate the effectiveness of the proposed enhancements. Their speed-ups essentially multiply to an overall factor of 20. Overall, our approach allows the reliabe solution of instances with several hundreds of nodes in a few minutes. These findings are further corroborated in a comparison to existing districting models on a set of test instances from the literature. T3 - ZIB-Report - 21-14 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82616 SN - 1438-0064 ER - TY - GEN A1 - Jäger, Klaus A1 - Sutter, Johannes A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Becker, Christiane T1 - Optical simulations of nanotextured perovskite/silicon tandem solar cell T2 - HZB Data Service Y1 - 2021 U6 - https://doi.org/10.5442/ND000005 ER - TY - GEN A1 - Raharinirina, N. Alexia A1 - Weber, Marcus A1 - Birk, Ralph A1 - Fackeldey, Konstantin A1 - Klasse, Sarah M. A1 - Richter, Tonio Sebastian T1 - Different Tools and Results for Correspondence Analysis N2 - This is a list of codes generated from ancient egyptian texts. The codes are used for a correspondence analysis (CA). Codes and CA software are available from the linked webpage. Y1 - 2021 U6 - https://doi.org/10.12752/8257 N1 - A detailed description of the software can be found in the code repository at https://github.com/AlexiaNomena/Correspondence_Analysis_User_Friendly (repository version of CA software might include updates). ER - TY - JOUR A1 - Torun, Cem Güney A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Munns, Joseph H.D. A1 - Schröder, Tim T1 - Optimized diamond inverted nanocones for enhanced color center to fiber coupling JF - Appl. Phys. Lett. Y1 - 2021 U6 - https://doi.org/10.1063/5.0050338 VL - 118 SP - 234002 ER - TY - JOUR A1 - Alzaatreh, Ayman A1 - Aljarrah, Mohammad A1 - Almagambetova, Ayanna A1 - Zakiyeva, Nazgul T1 - On the Regression Model for Generalized Normal Distributions JF - Entropy N2 - The traditional linear regression model that assumes normal residuals is applied extensively in engineering and science. However, the normality assumption of the model residuals is often ineffective. This drawback can be overcome by using a generalized normal regression model that assumes a non-normal response. In this paper, we propose regression models based on generalizations of the normal distribution. The proposed regression models can be used effectively in modeling data with a highly skewed response. Furthermore, we study in some details the structural properties of the proposed generalizations of the normal distribution. The maximum likelihood method is used for estimating the parameters of the proposed method. The performance of the maximum likelihood estimators in estimating the distributional parameters is assessed through a small simulation study. Applications to two real datasets are given to illustrate the flexibility and the usefulness of the proposed distributions and their regression models. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/e23020173 VL - 23 IS - 2 SP - 173 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Denißen, Jonas A1 - Heller, Simon A1 - Klug, Torsten A1 - Küpper, Michael A1 - Lindner, Niels A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Söhlke, Andreas A1 - Steadman, William T1 - Microscopic Timetable Optimization for a Moving Block System N2 - We present an optimization model which is capable of routing and ordering trains on a microscopic level under a moving block regime. Based on a general timetabling definition (GTTP) that allows the plug in of arbitrarily detailed methods to compute running and headway times, we describe a layered graph approach using velocity expansion, and develop a mixed integer linear programming formulation. Finally, we present promising results for a German corridor scenario with mixed traffic, indicating that applying branch-and-cut to our model is able to solve reasonably sized instances with up to hundred trains to optimality. T3 - ZIB-Report - 21-13 KW - Moving Block KW - Railway Track Allocation KW - Railway Timetabling KW - Train Routing Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82547 SN - 1438-0064 ER - TY - CHAP A1 - Baumann, Tobias A1 - Noack, Matthias A1 - Steinke, Thomas T1 - Performance Evaluation and Improvements of the PoCL Open-Source OpenCL Implementation on Intel CPUs T2 - IWOCL'21: International Workshop on OpenCL N2 - The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs – which run 92 % of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy. Y1 - 2021 U6 - https://doi.org/10.1145/3456669.3456698 ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Interface stability of compressible fluids in porous media JF - Physics of Fluids N2 - The stability of flows in porous media plays a vital role in transiting energy supply from natural gas to hydrogen, especially for estimating the usability of existing underground gas storage infrastructures. Thus, this research aims to analyze the interface stability of the tangential-velocity discontinuity between two compressible gases by using Darcy's model to include the porosity effect. The results shown in this research will be a basis for considering whether underground gas storages in porous material can be used to store hydrogen. We show the relation between the Mach number M, the viscosity \mu, and the porosity \epsilon on the stability of the interface. This interface stability affects gases' withdrawal and injection processes, thus will help us to determine the velocity which with gas can be extracted and injected into the storage effectively. By imposing solid walls along the flow direction, the critical values of these parameters regarding the stability of the interface are smaller than when considering no walls. The consideration of bounded flows approaches the problem more realistically. In particular, this analysis plays a vital role when considering two-dimensional gas flows in storages and pipes. Y1 - 2021 U6 - https://doi.org/10.1063/5.0059336 VL - 33 IS - 8 SP - 084102 PB - AIP Publishing ER - TY - JOUR A1 - Tillmann, Peter A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Höhn, Oliver A1 - Becker, Christiane A1 - Jäger, Klaus T1 - Optimizing metal grating back reflectors for III-V-on-silicon multijunction solar cells JF - Opt. Express Y1 - 2021 U6 - https://doi.org/10.1364/OE.426761 VL - 29 SP - 22517 ER - TY - CHAP A1 - Clausecker, Robert A1 - Schintke, Florian T1 - A Measure of Quality for IDA* Heuristics T2 - Proceedings of the Fourteenth International Symposium on Combinatorial Search (SoCS 2021) Y1 - 2021 N1 - Best SoCS21 paper award SP - 55 EP - 63 ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - Journal of Microscopy N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists. Y1 - 2021 U6 - https://doi.org/10.1111/jmi.13039 VL - 284 IS - 1 SP - 25 EP - 44 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Çınaroğlu, Süleyman A1 - Fischer, Patrick D. A1 - Fackeldey, Konstantin A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization JF - Special Issue Artificial Intelligence & Deep Learning Approaches for Structural Bioinformatics N2 - The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/ijms22115807 VL - 22 IS - 11 SP - 5807 ER - TY - JOUR A1 - Toulkeridou, Evropi A1 - Gutierrez, Carlos Enrique A1 - Baum, Daniel A1 - Doya, Kenji A1 - Economo, Evan P. T1 - Automated segmentation of insect anatomy from micro-CT images using deep learning JF - bioRxiv Y1 - 2021 U6 - https://doi.org/10.1101/2021.05.29.446283 ER - TY - JOUR A1 - Hoppmann-Baum, Kai T1 - On the Complexity of Computing Maximum and Minimum Min‐Cost‐Flows JF - Networks N2 - Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time. Y1 - 2021 U6 - https://doi.org/10.1002/net.22060 ER - TY - JOUR A1 - Gao, Timm A1 - Rickert, Lucas A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Heindel, Tobias T1 - A quantum key distribution testbed using a plug&play telecom-wavelength single-photon source JF - Appl. Phys. Rev. Y1 - 2022 U6 - https://doi.org/10.1063/5.0070966 VL - 9 SP - 011412 ER - TY - CHAP A1 - Gamrath, Gerwin A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - An LP-based heuristic for Inspector Scheduling T2 - Proceedings of the 13th International Conference on the Practice and Theory of Automated Timetabling - PATAT 2021: Volume I N2 - We present a heuristic based on linear programming (LP) for the integrated tour and crew roster planning of toll enforcement inspectors. Their task is to enforce the proper paying of a distance-based toll on German motorways. This leads to an integrated tour planning and duty rostering problem; it is called Toll Enforcement Problem (TEP). We tackle the TEP by a standard multi-commodity flow model with some extensions in order to incorporate the control tours. The heuristic consists of two variants. The first, called Price & Branch, is a column generation approach to solve the model’s LP relaxation by pricing tour and roster arc variables. Then, we compute an integer feasible solution by restricting to all variables that were priced. The second is a coarse-to-fine approach. Its basic idea is projecting variables to an aggregated variable space, which is much smaller. The aim is to spend as much algorithmic effort in this coarse model as possible. For both heuristic procedures we will show that feasible solutions of high quality can be computed even for large scale industrial instances. Y1 - 2021 UR - https://patatconference.org/patat2020/proceedings/ VL - 1 SP - 77 EP - 86 ER - TY - GEN A1 - Pflüger, Mika A1 - Kline, R Joseph A1 - Fernández Herrero, Analía A1 - Hammerschmidt, Martin A1 - Soltwisch, Victor A1 - Krumrey, Michael T1 - Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering [Source Code] Y1 - 2020 U6 - https://doi.org/10.24433/CO.0953516.v2 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian T1 - Load balancing mechanism for FLESnet JF - CBM Progress Report 2020 Y1 - 2021 U6 - https://doi.org/10.15120/GSI-2021-00421 SP - 156 EP - 157 ER - TY - THES A1 - Badel, Raphael T1 - Registration-based Tracking of Regions Defined by Level Sets of Time-dependent Scalar Fields N2 - This thesis is concerned with the wide field of feature tracking in time-dependent data. Many solutions already exist for the tracking of various features in scalar fields that are given as discrete time steps. In the field of meteorology, recently published precipitation data of the COSMO-REA2 reanalysis system gave rise to the analysis of precipitation at a convective scale for which a tracking of precipitation cells over time is desired. A previous study indicated that a tracking based on the widely used overlap criterion does not perform well for the reanalysis data. Based on a novel set of requirements, a new approach to the tracking of regions in time-dependent scalar fields is developed in the course of this thesis and applied in a prototypical study to example datasets of the COSMO-REA2 system. Despite the concrete motivation of using the developed method for subsequent studies of precipitation, the tracking approach is designed to be applicable for arbitrary scalar quantities that can conceptually be given on uniform grids of arbitrary dimensions. Based on a detailed description of the utilized methods, this thesis presents a novel tracking solution whose correspondence identification is based on image registration of successive time steps in combination with a hierarchical watershed segmentation by means of which features are extracted. The proposed implementation allows for an efficient generation of tracking results under the premise that the registration-based correspondence information has been precomputed. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82264 ER - TY - JOUR A1 - Li, Jianning A1 - Pimentel, Pedro A1 - Szengel, Angelika A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Estacio, Laura A1 - Doenitz, Christian A1 - Ramm, Heiko A1 - Shi, Haochen A1 - Chen, Xiaojun A1 - Matzkin, Franco A1 - Newcombe, Virginia A1 - Ferrante, Enzo A1 - Jin, Yuan A1 - Ellis, David G. A1 - Aizenberg, Michele R. A1 - Kodym, Oldrich A1 - Spanel, Michal A1 - Herout, Adam A1 - Mainprize, James G. A1 - Fishman, Zachary A1 - Hardisty, Michael R. A1 - Bayat, Amirhossein A1 - Shit, Suprosanna A1 - Wang, Bomin A1 - Liu, Zhi A1 - Eder, Matthias A1 - Pepe, Antonio A1 - Gsaxner, Christina A1 - Alves, Victor A1 - Zefferer, Ulrike A1 - von Campe, Cord A1 - Pistracher, Karin A1 - Schäfer, Ute A1 - Schmalstieg, Dieter A1 - Menze, Bjoern H. A1 - Glocker, Ben A1 - Egger, Jan T1 - AutoImplant 2020 - First MICCAI Challenge on Automatic Cranial Implant Design JF - IEEE Transactions on Medical Imaging N2 - The aim of this paper is to provide a comprehensive overview of the MICCAI 2020 AutoImplant Challenge. The approaches and publications submitted and accepted within the challenge will be summarized and reported, highlighting common algorithmic trends and algorithmic diversity. Furthermore, the evaluation results will be presented, compared and discussed in regard to the challenge aim: seeking for low cost, fast and fully automated solutions for cranial implant design. Based on feedback from collaborating neurosurgeons, this paper concludes by stating open issues and post-challenge requirements for intra-operative use. Y1 - 2021 U6 - https://doi.org/10.1109/TMI.2021.3077047 SN - 0278-0062 VL - 40 IS - 9 SP - 2329 EP - 2342 ER - TY - GEN A1 - Schmitt, Carlo A1 - Wyrwoll, Lothar A1 - Moser, Albert A1 - Yueksel-Erguen, Inci T1 - Integration of Flexible Distributed Energy Resource Models into a Market Coupling-based Lagrangian Relaxation of the pan-European Electricity Market N2 - This report presents a method to integrate highly flexible technology models for distributed energy resources such as electric vehicles, power-to-heat systems, or home battery systems into a Lagrangian relaxation of the pan-European day-ahead electricity market (EULR). These flexible technology models are highly sensitive to the changes of Lagrangian multipliers within the iterative Lagrangian relaxation process, leading to volatile behavior. Furthermore, they show a high concurrency in their market behavior due to their technical homogeneity. Therefore, the method proposed in this report is an extension of the existing EULR modeling approach to improve the model's convergence. The methodological extension comprises a convex combination of iteration solutions for the Lagrangian relaxation subproblems similar to Dantzig-Wolfe decomposition. An exemplary case study shows the effectiveness of this extended approach. T3 - ZIB-Report - 21-11 KW - Electricity Market Simulation KW - Lagrangian Relaxation KW - Distributed Energy Resources Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82238 SN - 1438-0064 ER - TY - JOUR A1 - Boeth, Heide A1 - Biesen, Robert A1 - Hollnagel, Jeremias A1 - Herrmann, Sandra A1 - Ehrig, Rainald A1 - Pelli, Lorenzo A1 - Taylor, William R. A1 - Duda, Georg A1 - Buttgereit, Frank T1 - Quantification of morning stiffness to assess disease activity and treatment effects in rheumatoid arthritis JF - Rheumatology N2 - Objectives The clinical parameter “morning stiffness” is widely used to assess the status of rheumatoid arthritis (RA), but its accurate quantitative assessment in a clinical setting has not yet been successful. This lack of individual quantification limits both personalized medication and efficacy evaluation in the treatment of RA. Methods We have developed a novel technology to assess passive resistance of the metacarpophalangeal (MCP) III joint (stiffness) and its Passive Range of Motion (PRoM). Within this pilot study, nineteen female postmenopausal RA patients and nine healthy controls were examined in the evening as well as in the morning of the following day. To verify the specificity of the biomechanical quantification, eleven patients with RA were assessed both prior to and ∼3 h after glucocorticoid therapy. Results While the healthy controls showed only minor changes between afternoon and morning, in RA patients mean±SD PRoM decreased significantly by 18 ± 22% and stiffness increased significantly by 20 ± 18% in the morning compared with the previous afternoon. We found a significant positive correlation between RA activity and biomechanical measures. Glucocorticoids significantly increased mean PRoM by 16 ± 11% and reduced mean stiffness by 23 ± 22%. Conclusion This technology allowed mechanical stiffness to be quantified in MCP joints, and has demonstrated high sensitivity in respect to disease status as well as medication effect in RA patients. Such non-invasive, low risk, and rapid assessment of biomechanical joint stiffness opens a novel avenue for judging therapy efficacy in patients with RA, and potentially also in other non-RA inflammatory joint diseases. Y1 - 2021 U6 - https://doi.org/10.1093/rheumatology/keab323 VL - 60 IS - 11 SP - 5282 EP - 5291 ER - TY - JOUR A1 - Peppert, Felix A1 - von Kleist, Max A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks JF - IEEE Transactions on Neural Networks and Learning Systems N2 - Deep convolutional neural networks (DCNNs) are routinely used for image segmentation of biomedical data sets to obtain quantitative measurements of cellular structures like tissues. These cellular structures often contain gaps in their boundaries, leading to poor segmentation performance when using DCNNs like the U-Net. The gaps can usually be corrected by post-hoc computer vision (CV) steps, which are specific to the data set and require a disproportionate amount of work. As DCNNs are Universal Function Approximators, it is conceivable that the corrections should be obsolete by selecting the appropriate architecture for the DCNN. In this article, we present a novel theoretical framework for the gap-filling problem in DCNNs that allows the selection of architecture to circumvent the CV steps. Combining information-theoretic measures of the data set with a fundamental property of DCNNs, the size of their receptive field, allows us to formulate statements about the solvability of the gap-filling problem independent of the specifics of model training. In particular, we obtain mathematical proof showing that the maximum proficiency of filling a gap by a DCNN is achieved if its receptive field is larger than the gap length. We then demonstrate the consequence of this result using numerical experiments on a synthetic and real data set and compare the gap-filling ability of the ubiquitous U-Net architecture with variable depths. Our code is available at https://github.com/ai-biology/dcnn-gap-filling. Y1 - 2022 U6 - https://doi.org/10.1109/TNNLS.2021.3072746 VL - 33 IS - 11 SP - 6194 EP - 6205 ER - TY - JOUR A1 - Jin, Liangbing A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide T1 - Frictional effect on stability of discontinuity interface in tangential velocity of a shallow-water flow JF - Physics Letters A N2 - We examine a frictional effect on the linear stability of an interface of discontinuity in tangential velocity. The fluid is moving with uniform velocity U in a region but is at rest in the other, and the bottom surface is assumed to exert drag force, quadratic in velocity, on the thin fluid layer. In the absence of the drag, the instability of the Kelvin-Helmholtz type is suppressed for U>√8 c, with c being the propagating speed of the gravity wave. We find by asymptotic analyses for both small and large values of the drag strength that the drag, regardless of its strength, makes the flow unstable for the whole range of the Froude number U/c. Y1 - 2019 U6 - https://doi.org/10.1016/j.physleta.2019.125839 VL - 383 IS - 26 SP - 125839 ER - TY - JOUR A1 - Le, Thi Thai T1 - Kelvin-Helmholtz instability in a shallow-water flow with a finite width JF - Journal of Mathematical Physics N2 - We examine an effect of side walls on the linear stability of an interface of tangential-velocity discontinuity in shallow-water flow. The flow is pure horizontal in the plane xy, and the fluid is bounded in a finite width 2d in the y− direction. In region 0 < y < d, the fluid is moving with uniform velocity U but is at rest for −d < y < 0. Without side walls, the flow is unstable for a velocity difference U<√8c U < √8 c, with c being the velocity of gravity waves. In this work, we show that if the velocity difference U is smaller than 2c, the interface is always destabilized, also known as the flow is unstable. The unstable region of an infinite width model is shrunken by the effects of side walls in the case of narrow width, while there is no range for the Froude number for stabilization in the case of large width. These results play an important role in predicting the wave propagations and have a wide application in the fields of industry. As a result of the interaction of waves and the mean flow boundary, the flow is unstable, which is caused by a decrease in the kinetic energy of disturbance. Y1 - 2019 U6 - https://doi.org/10.1063/1.5126321 VL - 60 IS - 1 SP - 123101 PB - AIP Publishing ER - TY - JOUR A1 - Dellnitz, Michael A1 - Hüllermeier, Eyke A1 - Lücke, Marvin A1 - Ober-Blöbaum, Sina A1 - Offen, Christian A1 - Peitz, Sebastian A1 - Pfannschmidt, Karlson T1 - Efficient Time-Stepping for Numerical Integration Using Reinforcement Learning JF - SIAM Journal on Scientific Computing Y1 - 2023 U6 - https://doi.org/10.1137/21M1412682 VL - 45 IS - 2 SP - A579 EP - A595 ER - TY - JOUR A1 - Lücke, Marvin A1 - Lu, Jingyi A1 - Quevedo, Daniel E. T1 - Coding for secrecy in remote state estimation with an adversary JF - IEEE Transactions on Automatic Control N2 - We study the problem of remote state estimation in the presence of an eavesdropper. A sensor transmits state information over a packet-dropping link to a legitimate user. This information is randomly overheard by an eavesdropper. To reduce information leakage to the eavesdropper, previous studies have shown that by encoding the estimate with the acknowledgments (Acks), perfect secrecy can be achieved. However, this strategy greatly relies on the accuracy of the Acks and may easily fail if the Acks are compromised by cyberattacks. In this article, we tackle this issue by proposing to switch between sending an encoded state and sending the plain state to stay resilient against fake Acks. Specifically, we assume the Acks to be randomly attacked and derive recursive expressions for the minimum-mean-squared error estimates and error covariance matrices at the legitimate user and at the eavesdropper. Based upon this, we propose a transmission policy that depends on the probability of synchronization. We formulate a partially observable Markov decision process to model the evolution of the synchronization status and derive associated optimal transmission policies. Numerical examples are provided to verify the theoretical results. Y1 - 2022 U6 - https://doi.org/10.1109/TAC.2022.3169839 VL - 67 IS - 9 SP - 4955 EP - 4962 ER - TY - JOUR A1 - Liang, YongTian A1 - Piao, Chengji A1 - Beuschel, Christine B. A1 - Toppe, David A1 - Kollipara, Laxmikanth A1 - Bogdanow, Boris A1 - Maglione, Marta A1 - Lützkendorf, Janine A1 - See, Jason Chun Kit A1 - Huang, Sheng A1 - Conrad, Tim A1 - Kintscher, Ulrich A1 - Madeo, Frank A1 - Liu, Fan A1 - Sickmann, Albert A1 - Sigrist, Stephan J. T1 - eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction JF - Cell Reports Y1 - 2021 U6 - https://doi.org/10.1016/j.celrep.2021.108941 VL - 35 IS - 2 ER - TY - GEN A1 - Lenz, Ralf T1 - Pipe Merging for Transient Gas Network Problems N2 - In practice, transient gas transport problems frequently have to be solved for large-scale gas networks. Gas network optimization problems typically belong to the class of Mixed-Integer Nonlinear Programming Problems (MINLP). However current state-of-the-art MINLP solvers are not yet mature enough to solve large-scale real-world instances. Therefore, an established approach in practice is to solve the problems with respect to a coarser representation of the network and thereby reducing the size of the underlying model. Two well-known aggregation methods that effectively reduce the network size are parallel and serial pipe merges. However, these methods have only been studied in stationary gas transport problems so far. This paper closes this gap and presents parallel and serial pipe merging methods in the context of transient gas transport. To this end, we introduce the concept of equivalent and heuristic subnetwork replacements. For the heuristic methods, we conduct a huge empirical evaluation based on real-world data taken from one of the largest gas networks in Europe. It turns out that both, parallel and serial pipe merging can be considered as appropriate aggregation methods for real-world transient gas flow problems. T3 - ZIB-Report - 21-10 KW - Pipe merging KW - Network aggregation KW - Gas network optimization KW - Transient gas flow transport KW - Nonlinear Programming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82116 SN - 1438-0064 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Moschner, Johann A1 - Koksch, Beate A1 - Netz, Roland A1 - Schütte, Christof T1 - Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis JF - The European Physical Journal B Y1 - 2021 U6 - https://doi.org/10.1140/epjb/s10051-021-00200-0 VL - 94 ER - TY - JOUR A1 - Cryille W., Combettes A1 - Spiegel, Christoph A1 - Pokutta, Sebastian T1 - Projection-Free Adaptive Gradients for Large-Scale Optimization N2 - The complexity in large-scale optimization can lie in both handling the objective function and handling the constraint set. In this respect, stochastic Frank-Wolfe algorithms occupy a unique position as they alleviate both computational burdens, by querying only approximate first-order information from the objective and by maintaining feasibility of the iterates without using projections. In this paper, we improve the quality of their first-order information by blending in adaptive gradients. We derive convergence rates and demonstrate the computational advantage of our method over the state-of-the-art stochastic Frank-Wolfe algorithms on both convex and nonconvex objectives. The experiments further show that our method can improve the performance of adaptive gradient algorithms for constrained optimization. Y1 - 2020 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Deep Neural Network Training with Frank-Wolfe N2 - This paper studies the empirical efficacy and benefits of using projection-free first-order methods in the form of Conditional Gradients, a.k.a. Frank-Wolfe methods, for training Neural Networks with constrained parameters. We draw comparisons both to current state-of-the-art stochastic Gradient Descent methods as well as across different variants of stochastic Conditional Gradients. In particular, we show the general feasibility of training Neural Networks whose parameters are constrained by a convex feasible region using Frank-Wolfe algorithms and compare different stochastic variants. We then show that, by choosing an appropriate region, one can achieve performance exceeding that of unconstrained stochastic Gradient Descent and matching state-of-the-art results relying on L2-regularization. Lastly, we also demonstrate that, besides impacting performance, the particular choice of constraints can have a drastic impact on the learned representations. Y1 - 2020 ER - TY - JOUR A1 - Baum, Daniel A1 - Herter, Felix A1 - Larsen, John Møller A1 - Lichtenberger, Achim A1 - Raja, Rubina T1 - Revisiting the Jerash Silver Scroll: a new visual data analysis approach JF - Digital Applications in Archaeology and Cultural Heritage N2 - This article revisits a complexly folded silver scroll excavated in Jerash, Jordan in 2014 that was digitally examined in 2015. In this article we apply, examine and discuss a new virtual unfolding technique that results in a clearer image of the scroll’s 17 lines of writing. We also compare it to the earlier unfolding and discuss progress in general analytical tools. We publish the original and the new images as well as the unfolded volume data open access in order to make these available to researchers interested in optimising unfolding processes of various complexly folded materials. Y1 - 2021 U6 - https://doi.org/10.1016/j.daach.2021.e00186 VL - 21 SP - e00186 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Borndörfer, Ralf A1 - Kraus, Luitgard A1 - Sedeño-Noda, Antonio T1 - An FPTAS for Dynamic Multiobjective Shortest Path Problems JF - Algorithms N2 - The Dynamic Multiobjective Shortest Path problem features multidimensional costs that can depend on several variables and not only on time; this setting is motivated by flight planning applications and the routing of electric vehicles. We give an exact algorithm for the FIFO case and derive from it an FPTAS for both, the static Multiobjective Shortest Path (MOSP) problems and, under mild assumptions, for the dynamic problem variant. The resulting FPTAS is computationally efficient and beats the known complexity bounds of other FPTAS for MOSP problems. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/a14020043 VL - 14 IS - 2 SP - 1 EP - 22 ER - TY - JOUR A1 - Liu, Yongtao A1 - Zhou, Zhiguang A1 - Wang, Fan A1 - Kewes, Günter A1 - Wen, Shihui A1 - Burger, Sven A1 - Wakiani, Majid Ebrahimi A1 - Xi, Peng A1 - Yang, Jiong A1 - Yang, Xusan A1 - Benson, Oliver A1 - Jin, Dayong T1 - Axial localization and tracking of self-interference nanoparticles by lateral point spread functions JF - Nat. Commun. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-22283-0 VL - 12 SP - 2019 ER - TY - JOUR A1 - Herter, Felix A1 - Hege, Hans-Christian A1 - Hadwiger, Markus A1 - Lepper, Verena A1 - Baum, Daniel T1 - Thin-Volume Visualization on Curved Domains JF - Computer Graphics Forum N2 - Thin, curved structures occur in many volumetric datasets. Their analysis using classical volume rendering is difficult because parts of such structures can bend away or hide behind occluding elements. This problem cannot be fully compensated by effective navigation alone, because structure-adapted navigation in the volume is cumbersome and only parts of the structure are visible in each view. We solve this problem by rendering a spatially transformed view into the volume so that an unobscured visualization of the entire curved structure is obtained. As a result, simple and intuitive navigation becomes possible. The domain of the spatial transform is defined by a triangle mesh that is topologically equivalent to an open disc and that approximates the structure of interest. The rendering is based on ray-casting in which the rays traverse the original curved sub-volume. In order to carve out volumes of varying thickness, the lengths of the rays as well as the position of the mesh vertices can be easily modified in a view-controlled manner by interactive painting. We describe a prototypical implementation and demonstrate the interactive visual inspection of complex structures from digital humanities, biology, medicine, and materials science. Displaying the structure as a whole enables simple inspection of interesting substructures in their original spatial context. Overall, we show that transformed views utilizing ray-casting-based volume rendering supported by guiding surface meshes and supplemented by local, interactive modifications of ray lengths and vertex positions, represent a simple but versatile approach to effectively visualize thin, curved structures in volumetric data. Y1 - 2021 U6 - https://doi.org/10.1111/cgf.14296 VL - 40 IS - 3 SP - 147 EP - 157 PB - Wiley-Blackwell Publishing Ltd. CY - United Kingdom ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - Osteoarthritis and Cartilage Y1 - 2021 U6 - https://doi.org/10.1016/j.joca.2021.03.007 VL - 29 IS - 6 SP - 905 EP - 914 ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. T3 - ZIB-Report - 21-09 KW - Statistical shape analysis KW - Osteoarthritis KW - Geometric statistics KW - Riemannian manifolds Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81930 SN - 1438-0064 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Hobbie, Hannes A1 - Schönheit, David A1 - Koch, Thorsten A1 - Möst, Dominik A1 - Gleixner, Ambros T1 - A massively parallel interior-point solver for LPs with generalized arrowhead structure, and applications to energy system models JF - European Journal of Operational Research N2 - Linear energy system models are a crucial component of energy system design and operations, as well as energy policy consulting. If detailed enough, such models lead to large-scale linear programs, which can be intractable even for the best state-of-the-art solvers. This article introduces an interior-point solver that exploits common structures of energy system models to efficiently run in parallel on distributed-memory systems. The solver is designed for linear programs with doubly-bordered block-diagonal constraint matrix and makes use of a Schur complement based decomposition. In order to handle the large number of linking constraints and variables commonly observed in energy system models, a distributed Schur complement preconditioner is used. In addition, the solver features a number of more generic techniques such as parallel matrix scaling and structure-preserving presolving. The implementation is based on the solver PIPS-IPM. We evaluate the computational performance on energy system models with up to four billion nonzero entries in the constraint matrix—and up to one billion columns and one billion rows. This article mainly concentrates on the energy system model ELMOD, which is a linear optimization model representing the European electricity markets by the use of a nodal pricing market-clearing. It has been widely applied in the literature on energy system analyses in recent years. However, it will be demonstrated that the new solver is also applicable to other energy system models. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejor.2021.06.063 VL - 296 IS - 1 SP - 60 EP - 71 ER - TY - CHAP A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Implications, conflicts, and reductions for Steiner trees T2 - Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021 Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_33 SP - 473 EP - 487 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - On the exact solution of prize-collecting Steiner tree problems JF - INFORMS Journal on Computing Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2021.1087 ER - TY - GEN A1 - Hennings, Felix T1 - Large-scale empirical study on the momentum equation's inertia term N2 - A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation since it is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems. T3 - ZIB-Report - 21-08 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81881 SN - 1438-0064 ER - TY - JOUR A1 - Jäger, Klaus A1 - Sutter, Johannes A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Becker, Christiane T1 - Prospects of light management in perovskite/silicon tandem solar cells JF - Nanophotonics Y1 - 2021 U6 - https://doi.org/10.1515/nanoph-2020-0674 VL - 10 SP - 1991 ER - TY - JOUR A1 - Gelss, Patrick A1 - Klus, Stefan A1 - Schuster, Ingmar A1 - Schütte, Christof T1 - Feature space approximation for kernel-based supervised learning JF - Knowledge-Based Sytems Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.knosys.2021.106935 VL - 221 PB - Elsevier ER - TY - JOUR A1 - del Razo, Mauricio J. A1 - Dibak, Manuel A1 - Schütte, Christof A1 - Noé, Frank T1 - Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics JF - The Journal of Chemical Physics Y1 - 2021 U6 - https://doi.org/10.1063/5.0060314 VL - 155 IS - 12 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Telgmann, Regina A1 - Hungenberg, Klaus-Dieter A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Deterministic and Stochastic Parameter Estimation for Polymer Reaction Kinetics I: Theory and Simple Examples JF - Macromolecular Theory and Simulations N2 - Two different approaches to parameter estimation (PE) in the context of polymerization are introduced, refined, combined, and applied. The first is classical PE where one is interested in finding parameters which minimize the distance between the output of a chemical model and experimental data. The second is Bayesian PE allowing for quantifying parameter uncertainty caused by experimental measurement error and model imperfection. Based on detailed descriptions of motivation, theoretical background, and methodological aspects for both approaches, their relation are outlined. The main aim of this article is to show how the two approaches complement each other and can be used together to generate strong information gain regarding the model and its parameters. Both approaches and their interplay in application to polymerization reaction systems are illustrated. This is the first part in a two-article series on parameter estimation for polymer reaction kinetics with a focus on theory and methodology while in the second part a more complex example will be considered. Y1 - 2021 U6 - https://doi.org/10.1002/mats.202100017 VL - 30 ER - TY - JOUR A1 - Binkowski, Felix A1 - Wu, Tong A1 - Lalanne, Philippe A1 - Burger, Sven A1 - Govorov, Alexander O. T1 - Hot Electron Generation through Near-Field Excitation of Plasmonic Nanoresonators JF - ACS Photonics Y1 - 2021 U6 - https://doi.org/10.1021/acsphotonics.1c00231 VL - 8 SP - 1243 ER - TY - GEN A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Vigerske, Stefan T1 - A Computational Study of Perspective Cuts N2 - The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to nonconvex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time. T3 - ZIB-Report - 21-07 KW - perspective cuts, mixed-integer nonlinear programming, nonconvex optimization, computational study Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81821 SN - 1438-0064 ER - TY - JOUR A1 - Tawfik, Christine A1 - Gendron, Bernard A1 - Limbourg, Sabine T1 - An iterative two-stage heuristic algorithm for a bilevel service network design and pricing model JF - European Journal of Operational Research N2 - Building upon earlier research, we revisit a bilevel formulation of service design and pricing for freight networks, with the aim of investigating its algorithmic aspects. The model adds substantial computational challenges to the existing literature, as it deals with general integer network design variables. An iterative heuristic algorithm is introduced, based on the concepts of inverse optimization and neighbourhood search. The procedure alternates between two versions of restricted formulations of the model while inducing promising changes into the service assignments. The approach has proven a high performance for all of the considered real-world instances. Its efficiency rests on its ability to deliver results within a close proximity to those obtained by the exact solver in terms of quality, yet within a significantly smaller amount of time, and to land feasible solutions for the large-sized instances that could not be previously solved. In line with the sustainable transport goals, a deeper observation of the transport management side highlights the strategy of the algorithm favouring freight consolidation and achieving high load factors. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.ejor.2021.07.052 PB - Elsevier CY - European Journal of Operational Research ER - TY - THES A1 - Dill, Sabrina T1 - Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection N2 - In this thesis we investigate the task of automatically detecting phases in surgical workflow in endoscopic video data. For this, we employ deep learning approaches that solely rely on frame-wise visual information, instead of using additional signals or handcrafted features. While previous work has mainly focused on tool presence and temporal information for this task, we reason that additional global information about the context of a frame might benefit the phase detection task. We propose novel deep learning architectures: a convolutional neural network (CNN) based model for the tool detection task only, called Clf-Net, as well as a model which performs joint (context) feature learning and tool classification to incorporate information about the context, which we name Context-Clf-Net. For the phase detection task lower-dimensional feature vectors are extracted, which are used as input to recurrent neural networks in order to enforce temporal constraints. We compare the performance of an online model, which only considers previous frames up to the current time step, to that of an offline model that has access to past and future information. Experimental results indicate that the tool detection task benefits strongly from the introduction of context information, as we outperform both Clf-Net results and stateof-the-art methods. Regarding the phase detection task our results do not surpass state-of-the-art methods. Furthermore, no improvement of using features learned by the Context-Clf-Net is observed in the phase detection task for both online and offline versions Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81745 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres JF - Nondestructive Testing and Evaluation N2 - We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres. Y1 - 2020 U6 - https://doi.org/10.1080/10589759.2020.1774583 VL - 35 IS - 3 SP - 328 EP - 341 ER - TY - JOUR A1 - Pakhomov, Anton V. A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Modeling of surface-induced second-harmonic generation from multilayer structures by the transfer matrix method JF - Opt. Express Y1 - 2021 U6 - https://doi.org/10.1364/OE.417066 VL - 29 SP - 9098 ER - TY - THES A1 - Pedersen, Jaap T1 - Multiperiod Optimal Power Flow Problem In Distribution System Planning N2 - Growing demand, distributed generation, such as renewable energy sources (RES), and the increasing role of storage systems to mitigate the volatility of RES on a medium voltage level, push existing distribution grids to their limits. Therefore, necessary network expansion needs to be evaluated to guarantee a safe and reliable electricity supply in the future taking these challenges into account. This problem is formulated as an optimal power flow (OPF) problem which combines network expansion, volatile generation and storage systems, minimizing network expansion and generation costs. As storage systems introduce a temporal coupling into the system, a multiperiod OPF problem is needed and analysed in this thesis. To reduce complexity, the network expansion problem is represented in a continuous nonlinear programming formulation by using fundamental properties of electrical engeneering. This formulation is validated succesfully against a common mixed integer programming approach on a 30 and 57 bus network with respect to solution and computing time. As the OPF problem is, in general, a nonconvex, nonlinear problem and, thus, hard to solve, convex relaxations of the power flow equations have gained increasing interest. Sufficient conditions are represented which guarantee exactness of a second-order cone (SOC) relaxation of an operational OPF in radial networks. In this thesis, these conditions are enhanced for the network expansion planning problem. Additionally, nonconvexities introduced by the choice of network expansion variables are relaxed by using McCormick envelopes. These relaxations are then applied on the multiperiod OPF and compared to the original problem on a 30 and a 57 bus network. In particular, the computational time is decreased by an order up to 10^2 by the SOC relaxation while it provides either an exact solution or a sufficient lower bound on the original problem. Finally, a sensitivity study is performed on weights of network expansion costs showing strong dependency of both the solution of performed expansion and solution time on the chosen weights. KW - multiperiod optimal power flow, distribution network planning, battery storage Y1 - 2020 ER - TY - JOUR A1 - Le, Thi Thai T1 - Effect of water depth on Kelvin - Helmholtz instability in a shallow-water flow JF - Journal of Mathematical Physics N2 - It is well known that the interface between two regions of an incompressible ideal fluid flow moving in a relative motion is necessarily destabilized, regardless of the velocity difference's strength. This phenomenon is the so-called Kelvin-Helmholtz instability (KHI). However, a large number of works demonstrated a surprising result that the instability is suppressed for shallow water flows; the interface is stabilized if the Froude number, defined by the velocity difference's ratio to the gravity wave's speed, is sufficiently large. In a limited way, these authors have been used the shallow-water equations without the higher-order effect of the dispersive terms. Thus, this investigation aims to examine these higher-order dispersive effects to analyze the interface stability problem of tangential-velocity discontinuity in shallow-water flows. In particular, we use the Green-Naghdi equations to introduce the dispersive terms related to the depth and the depth-averaged horizontal velocities of the fluid. We show that the interface stability depends on the Froude number (i.e., the velocity difference's strength) and the water depth. A critical value of the Froude number to stabilize the interface is smaller than the case of no dispersive terms, and the flow in a deeper region is more stable than in a shallower one. We also consider the distribution of kinetic and potential energy to clarify a feature characteristic of a large class of instabilities in shallow water flow. The instability of flows is caused by the decrease in the kinetic energy during the perturbation of waves. This phenomenon is known as negative energy modes and plays a vital role in applying the model to industrial equipment. A conclusion is that the equipartition of energies occurs if and only if the velocity difference is zero and the water depth is shallow enough to ignore the dispersive terms. Y1 - 2021 U6 - https://doi.org/10.1063/1.5145060 VL - 62 IS - 10 PB - AIP Publishing ER - TY - JOUR A1 - Anderson, Lovis A1 - Turner, Mark A1 - Koch, Thorsten T1 - Generative deep learning for decision making in gas networks JF - Mathematical Methods of Operations Research N2 - A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5%. Y1 - 2022 U6 - https://doi.org/10.1007/s00186-022-00777-x VL - 95 SP - 503 EP - 532 PB - Springer Nature ER - TY - JOUR A1 - Manley, Phillip A1 - Segantini, Michele A1 - Ahiboz, Doguscan A1 - Hammerschmidt, Martin A1 - Arnaoutakis, Georgios A1 - MacQueen, Rowan W. A1 - Burger, Sven A1 - Becker, Christiane T1 - Double-layer metasurface for enhanced photon up-conversion JF - APL Photon. Y1 - 2021 U6 - https://doi.org/10.1063/5.0040839 VL - 6 SP - 036103 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Kurths, Jürgen A1 - Schütte, Christof T1 - Statistical analysis of tipping pathways in agent-based models JF - Eur. Phys. J. Spec. Top. N2 - Agent-based models are a natural choice for modeling complex social systems. In such models simple stochastic interaction rules for a large population of individuals on the microscopic scale can lead to emergent dynamics on the macroscopic scale, for instance a sudden shift of majority opinion or behavior. Here we are introducing a methodology for studying noise-induced tipping between relevant subsets of the agent state space representing characteristic configurations. Due to a large number of interacting individuals, agent-based models are high-dimensional, though usually a lower-dimensional structure of the emerging collective behaviour exists. We therefore apply Diffusion Maps, a non-linear dimension reduction technique, to reveal the intrinsic low-dimensional structure. We characterize the tipping behaviour by means of Transition Path Theory, which helps gaining a statistical understanding of the tipping paths such as their distribution, flux and rate. By systematically studying two agent-based models that exhibit a multitude of tipping pathways and cascading effects, we illustrate the practicability of our approach. Y1 - 2021 U6 - https://doi.org/10.1140/epjs/s11734-021-00191-0 VL - 230 SP - 3249 EP - 3271 ER - TY - CHAP A1 - Pedersen, Jaap A1 - Schachler, Birgit A1 - Heider, Anya A1 - Pleßmann, Guido T1 - Distribution System Planning with Battery Storage using Multiperiod Optimal Power Flow T2 - 14th International Renewable Energy Storage Conference 2020 (IRES 2020) N2 - The ongoing energy transition introduces new challenges for distribution networks and brings about the need to expand existing power grid capacities. In order to contain network expansion and with it economic costs, utilization of various flexibility options to reduce expansion needs is discussed. This paper proposes a multiperiod optimal power flow (MPOPF) approach with a new continuous network expansion formulation to optimize the deployment of flexibility options under the objective of minimizing network expansion costs. In a comparison of the newly proposed continuous network expansion formulation with an existing mixed integer formulation and a continuous interpretation of the latter the here proposed formulation is shown to be useful in order to obtain a solvable problem and contain computational efforts. The presented MPOPF including the flexibility options storage units and curtailment is then assessed on synthetic medium voltage grids and applied to evaluate the benefit of a combined vs. a stepwise optimization of these flexibility options. It is demonstrated that using a local solver the proposed approach is applicable and yields a solution in reasonable time. Furthermore, it is shown that the combined optimization generally leads to a more efficient utilization of the considered flexibility options and therefore lower grid expansion costs than the stepwise consideration. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.2991/ahe.k.210202.007 VL - 6 SP - 41 EP - 48 ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Gwalt, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Siewert, Frank A1 - Soltwisch, Victor T1 - GIXRF and machine learning as metrological tools for shape and element sensitive reconstructions of periodic nanostructures JF - Proc. SPIE Y1 - 2021 U6 - https://doi.org/10.1117/12.2586082 VL - 11611 SP - 116110R ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Timetable Merging for the Periodic Event Scheduling Problem N2 - We propose a new mixed integer programming based heuristic for computing new benchmark primal solutions for instances of the PESPlib. The PESPlib is a collection of instances for the Periodic Event Scheduling Problem (PESP), comprising periodic timetabling problems inspired by real-world railway timetabling settings, and attracting several international research teams during the last years. We describe two strategies to merge a set of good periodic timetables. These make use of the instance structure and minimum weight cycle bases, finally leading to restricted mixed integer programming formulations with tighter variable bounds. Implementing this timetable merging approach in a concurrent solver, we improve the objective values of the best known solutions for the smallest and largest PESPlib instances by 1.7 and 4.3 percent, respectively. T3 - ZIB-Report - 21-06 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Railway Timetabling KW - PESPlib KW - Benchmark Solutions KW - Mixed Integer Programming Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81587 SN - 1438-0064 ER - TY - JOUR A1 - Hembus, Jessica A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Bader, Rainer T1 - Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants JF - Applied Sciences N2 - Currently, new materials for knee implants need to be extensively and expensive tested in a knee wear simulator in a realized design. However, using a rolling-sliding test bench, these materials can be examined under the same test conditions but with simplified geometries. In the present study, the test bench was optimized, and forces were adapted to the physiological contact pressure in the knee joint using the available geometric parameters. Various polymers made of polyethylene and polyurethane articulating against test wheels made of cobalt-chromium and aluminum titanate were tested in the test bench using adapted forces based on ISO 14243-1. Polyurethane materials showed distinctly higher wear rates than polyethylene materials and showed inadequate wear resistance for use as knee implant material. Thus, the rolling-sliding test bench is an adaptable test setup for evaluating newly developed bearing materials for knee implants. It combines the advantages of screening and simulator tests and allows testing of various bearing materials under physiological load and tribological conditions of the human knee joint. The wear behavior of different material compositions and the influence of surface geometry and quality can be initially investigated without the need to produce complex implant prototypes of total knee endoprosthesis or interpositional spacers. Y1 - 2021 U6 - https://doi.org/10.3390/app11041886 VL - 11 IS - 4 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Zonker, Johannes A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading JF - Mathematical Biosciences N2 - Agent based models (ABMs) are a useful tool for modeling spatio-temporal population dynamics, where many details can be included in the model description. Their computational cost though is very high and for stochastic ABMs a lot of individual simulations are required to sample quantities of interest. Especially, large numbers of agents render the sampling infeasible. Model reduction to a metapopulation model leads to a significant gain in computational efficiency, while preserving important dynamical properties. Based on a precise mathematical description of spatio-temporal ABMs, we present two different metapopulation approaches (stochastic and piecewise deterministic) and discuss the approximation steps between the different models within this framework. Especially, we show how the stochastic metapopulation model results from a Galerkin projection of the underlying ABM onto a finite-dimensional ansatz space. Finally, we utilize our modeling framework to provide a conceptual model for the spreading of COVID-19 that can be scaled to real-world scenarios. Y1 - 2021 U6 - https://doi.org/10.1016/j.mbs.2021.108619 VL - 336 PB - Elsevier ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis T2 - Proc. Information Processing in Medical Imaging (IPMI) N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-78191-0_14 SP - 177 EP - 188 ER - TY - JOUR A1 - Gemander, Patrick A1 - Chen, Wei-Kun A1 - Weninger, Dieter A1 - Gottwald, Leona A1 - Gleixner, Ambros T1 - Two-row and two-column mixed-integer presolve using hashing-based pairing methods JF - EURO Journal on Computational Optimization N2 - In state-of-the-art mixed-integer programming solvers, a large array of reduction techniques are applied to simplify the problem and strengthen the model formulation before starting the actual branch-and-cut phase. Despite their mathematical simplicity, these methods can have significant impact on the solvability of a given problem. However, a crucial property for employing presolve techniques successfully is their speed. Hence, most methods inspect constraints or variables individually in order to guarantee linear complexity. In this paper, we present new hashing-based pairing mechanisms that help to overcome known performance limitations of more powerful presolve techniques that consider pairs of rows or columns. Additionally, we develop an enhancement to one of these presolve techniques by exploiting the presence of set-packing structures on binary variables in order to strengthen the resulting reductions without increasing runtime. We analyze the impact of these methods on the MIPLIB 2017 benchmark set based on an implementation in the MIP solver SCIP. Y1 - 2020 U6 - https://doi.org/10.1007/s13675-020-00129-6 VL - 8 IS - 3-4 SP - 205 EP - 240 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Zittel, Janina A1 - Gotzes, Uwe A1 - Spreckelsen, Eva-Maria A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - An Optimization Approach for the Transient Control of Hydrogen Transport Networks JF - Mathematical Methods of Operations Research Y1 - 2021 IS - Special Issue on Energy Networks ER - TY - JOUR A1 - Zakiyeva, Nazgul A1 - Xu, X. T1 - Nonlinear network autoregressive model with application to natural gas network forecasting JF - Mathematics Japonica T3 - ZIB-Report - 21-24 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81025 ER - TY - GEN A1 - Bertelmann, Roland A1 - Boltze, Julia A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Faensen, Katja A1 - Groß, Matthias A1 - Hoffmann, Cornelia A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Retter, Regina A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Söllner, Konstanze A1 - Steffen, Ronald A1 - Wannick, Eike T1 - DeepGreen: Open-Access-Transformation in der Informationsinfrastruktur – Anforderungen und Empfehlungen, Version 1.0 N2 - DeepGreen ist ein Service, der es teilnehmenden institutionellen Open-Access-Repositorien,Open-Access-Fachrepositorien und Forschungsinformationssystemen erleichtert, für sie relevante Verlagspublikationen in zyklischer Abfolge mithilfe von Schnittstellen Open Access zur Verfügung zu stellen. Die entsprechende Bandbreite an Relationen zwischen den Akteuren, diverse lizenzrechtliche Rahmenbedingungen sowie technische Anforderungen gestalten das Thema komplex. Ziel dieser Handreichung ist es, neben all diesen Themen, die begleitend beleuchtet werden, im Besonderen Empfehlungen für die reibungslose Nutzung der Datenübertragung zu liefern. Außerdem werden mithilfe einer vorangestellten Workflow- Evaluierung Unterschiede und Besonderheiten in den Arbeitsschritten bei institutionellen Open-Access-Repositorien und Open-Access-Fachrepositorien aufgezeigt und ebenfalls mit Empfehlungen angereichert. T3 - ZIB-Report - 21-03 KW - Open Access KW - Zweitveröffentlichung KW - Bibliotheken KW - Verlage Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81503 SN - 1438-0064 ER - TY - CHAP A1 - Thostrup, Lasse A1 - Skrzypczak, Jan A1 - Jasny, Matthias A1 - Ziegler, Tobias A1 - Binnig, Carsten T1 - DFI: The Data Flow Interface for High-Speed Networks T2 - SIGMOD '21: International Conference on Management of Data Y1 - 2021 U6 - https://doi.org/10.1145/3448016.3452816 SP - 1825 EP - 1837 PB - ACM ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian T1 - Combining XOR and Partner Checkpointing for Resilient Multilevel Checkpoint/Restart T2 - 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) Y1 - 2021 U6 - https://doi.org/10.1109/IPDPS49936.2021.00036 SP - 277 EP - 288 ER - TY - GEN A1 - Lenz, Ralf A1 - Serrano, Felipe T1 - Tight Convex Relaxations for the Expansion Planning Problem N2 - Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improve the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58%. T3 - ZIB-Report - 21-05 KW - Convex envelopes KW - Mixed-Integer Nonlinear Programming KW - Expansion planning of energy networks Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81459 SN - 1438-0064 ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Instability of a tangential discontinuity surface in a three-dimensional compressible medium JF - Physics of Fluids N2 - Compressible flows appear in many natural and technological processes, for instance, the flow of natural gases in a pipe system. Thus, a detailed study of the stability of tangential velocity discontinuity in compressible media is relevant and necessary. The first early investigation in two-dimensional (2D) media was given more than 70 years ago. In this article, we continue investigating the stability in three-dimensional (3D) media. The idealized statement of this problem in an infinite spatial space was studied by Syrovatskii in 1954. However, the omission of the absolute sign of cos θ with θ being the angle between vectors of velocity and wave number in a certain inequality produced the inaccurate conclusion that the flow is always unstable for entire values of the Mach number M. First, we revisit this case to arrive at the correct conclusion, namely that the discontinuity surface is stabilized for a large Mach number with a given value of the angle θ. Next, we introduce a real finite spatial system such that it is bounded by solid walls along the flow direction. We show that the discontinuity surface is stable if and only if the dispersion relation equation has only real roots, with a large value of the Mach number; otherwise, the surface is always unstable. In particular, we show that a smaller critical value of the Mach number is required to make the flow in a narrow channel stable. Y1 - 2021 U6 - https://doi.org/10.1063/5.0033753 VL - 33 IS - 1 SP - 016106 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Pokutta, Sebastian A1 - Schütte, Christof A1 - Weiser, Martin T1 - CINDy: Conditional gradient-based Identification of Non-linear Dynamics – Noise-robust recovery JF - Journal of Computational and Applied Mathematics N2 - Governing equations are essential to the study of nonlinear dynamics, often enabling the prediction of previously unseen behaviors as well as the inclusion into control strategies. The discovery of governing equations from data thus has the potential to transform data-rich fields where well-established dynamical models remain unknown. This work contributes to the recent trend in data-driven sparse identification of nonlinear dynamics of finding the best sparse fit to observational data in a large library of potential nonlinear models. We propose an efficient first-order Conditional Gradient algorithm for solving the underlying optimization problem. In comparison to the most prominent alternative algorithms, the new algorithm shows significantly improved performance on several essential issues like sparsity-induction, structure-preservation, noise robustness, and sample efficiency. We demonstrate these advantages on several dynamics from the field of synchronization, particle dynamics, and enzyme chemistry. Y1 - 2021 ER - TY - JOUR A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Theory and simulation of open systems out of equilibrium JF - The Journal of Chemical Physics N2 - We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations. Y1 - 2020 U6 - https://doi.org/10.1063/5.0014065 VL - 153 SP - 101102 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Finite-size corrections for the static structure factor of a liquid slab with open boundaries JF - The Journal of Chemical Physics N2 - The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures. Y1 - 2020 U6 - https://doi.org/10.1063/5.0017923 VL - 153 SP - 054119 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Kurchan, Jorge A1 - Liu, Andrea J. T1 - Fluctuation distributions of energy minima in complex landscapes JF - Physical Review Research N2 - We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin-glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and nontrivial finite-size scaling. Based on this, we propose a picture of gradient-descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for nonconvex complex landscapes, rationalizing the commonality that we find across models. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevResearch.3.013061 VL - 3 IS - 1 SP - 013061 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - A Discrete-Continuous Algorithm for Free Flight Planning N2 - We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach. T3 - ZIB-Report - 20-33 KW - shortest path KW - flight planning KW - free flight KW - discrete-continuous algorithm KW - optimal control KW - discrete optimization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81343 SN - 1438-0064 ER - TY - GEN A1 - Fujii, Koichi A1 - Ito, Naoki A1 - Kim, Sunyoung A1 - Kojima, Masakazu A1 - Shinano, Yuji A1 - Toh, Kim-Chuan T1 - Solving Challenging Large Scale QAPs N2 - We report our progress on the project for solving larger scale quadratic assignment problems (QAPs). Our main approach to solve large scale NP-hard combinatorial optimization problems such as QAPs is a parallel branch-and-bound method efficiently implemented on a powerful computer system using the Ubiquity Generator(UG) framework that can utilize more than 100,000 cores. Lower bounding procedures incorporated in the branch-and-bound method play a crucial role in solving the problems. For a strong lower bounding procedure, we employ the Lagrangian doubly nonnegative (DNN) relaxation and the Newton-bracketing method developed by the authors’ group. In this report, we describe some basic tools used in the project including the lower bounding procedure and branching rules, and present some preliminary numerical results. Our next target problem is QAPs with dimension at least 50, as we have succeeded to solve tai30a and sko42 from QAPLIB for the first time. T3 - ZIB-Report - 21-02 KW - QAP KW - Parallel Branch-and-Bound Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81303 SN - 1438-0064 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A Computational Status Update for Exact Rational Mixed Integer Programming N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 6.6x over the original framework and 2.8 times as many instances solved within a time limit of two hours. T3 - ZIB-Report - 21-04 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81298 SN - 1438-0064 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A Computational Status Update for Exact Rational Mixed Integer Programming JF - Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021 N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 6.6x over the original framework and 2.8 times as many instances solved within a time limit of two hours. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_12 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose Segmentation of surgical instruments in endoscopic video streams is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods We introduce a teacher–student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the challenges in simulation-to-real unsupervised domain adaptation for endoscopic image segmentation. Results Empirical results on three datasets highlight the effectiveness of the proposed framework over current approaches for the endoscopic instrument segmentation task. Additionally, we provide analysis of major factors affecting the performance on all datasets to highlight the strengths and failure modes of our approach. Conclusions We show that our proposed approach can successfully exploit the unlabeled real endoscopic video frames and improve generalization performance over pure simulation-based training and the previous state-of-the-art. This takes us one step closer to effective segmentation of surgical instrument in the annotation scarce setting. Y1 - 2021 U6 - https://doi.org/10.1007/s11548-021-02383-4 N1 - Honorary Mention: Machine Learning for Computer-Assisted Intervention (CAI) Award @IPCAI2021 N1 - Honorary Mention: Audience Award for Best Innovation @IPCAI2021 VL - 16 SP - 849 EP - 859 PB - Springer Nature ER - TY - GEN A1 - Borndörfer, Ralf A1 - Tesch, Alexander A1 - Sagnol, Guillaume T1 - Algorithmen unterstützen OP-Planung T2 - Management & Krankenhaus N2 - Mathematische Algorithmen können durch Vorhersage von Unsicherheiten optimierte OP-Pläne berechnen, sodass mehrere Zielkriterien wie Überstunden, Wartezeit und Ausfälle im OP minimiert werden. Y1 - 2019 IS - 12 SP - 20 PB - Wiley ER - TY - JOUR A1 - Pronzato, Luc A1 - Sagnol, Guillaume T1 - Removing inessential points in c- and A-optimal design JF - Journal of Statistical Planning and Inference N2 - A design point is inessential when it does not contribute to an optimal design, and can therefore be safely discarded from the design space. We derive three inequalities for the detection of such inessential points in c-optimal design: the first two are direct consequences of the equivalence theorem for c-optimality; the third one is derived from a second-order cone programming formulation of c-optimal design. Elimination rules for A-optimal design are obtained as a byproduct. When implemented within an optimization algorithm, each inequality gives a screening test that may provide a substantial acceleration by reducing the size of the problem online. Several examples are presented with a multiplicative algorithm to illustrate the effectiveness of the approach. Y1 - 2021 UR - https://hal.archives-ouvertes.fr/hal-02868664 U6 - https://doi.org/10.1016/j.jspi.2020.11.011 VL - 213 SP - 233 EP - 252 ER - TY - JOUR A1 - Duarte, Belmiro A1 - Sagnol, Guillaume T1 - Approximate and exact optimal designs for 2^k factorial experiments for generalized linear models via second order cone programming JF - Statistical Papers N2 - Model-based optimal designs of experiments (M-bODE) for nonlinear models are typically hard to compute. The literature on the computation of M-bODE for nonlinear models when the covariates are categorical variables, i.e. factorial experiments, is scarce. We propose second order cone programming (SOCP) and Mixed Integer Second Order Programming (MISOCP) formulations to find, respectively, approximate and exact A- and D-optimal designs for 2𝑘 factorial experiments for Generalized Linear Models (GLMs). First, locally optimal (approximate and exact) designs for GLMs are addressed using the formulation of Sagnol (J Stat Plan Inference 141(5):1684–1708, 2011). Next, we consider the scenario where the parameters are uncertain, and new formulations are proposed to find Bayesian optimal designs using the A- and log det D-optimality criteria. A quasi Monte-Carlo sampling procedure based on the Hammersley sequence is used for computing the expectation in the parametric region of interest. We demonstrate the application of the algorithm with the logistic, probit and complementary log–log models and consider full and fractional factorial designs. Y1 - 2020 U6 - https://doi.org/10.1007/s00362-018-01075-7 VL - 61 SP - 2737 EP - 2767 ER - TY - GEN A1 - Petkovic, Milena A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Deep learning for spatio-temporal supply and demand forecasting in natural gas transmission networks N2 - Germany is the largest market for natural gas in the European Union, with an annual consumption of approx. 95 billion cubic meters. Germany's high-pressure gas pipeline network is roughly 40,000 km long, which enables highly fluctuating quantities of gas to be transported safely over long distances. Considering that similar amounts of gas are also transshipped through Germany to other EU states, it is clear that Germany's gas transport system is essential to the European energy supply. Since the average velocity of gas in a pipeline is only 25km/h, an adequate high-precision, high-frequency forecasting of supply and demand is crucial for efficient control and operation of such a transmission network. We propose a deep learning model based on spatio-temporal convolutional neural networks (DLST) to tackle the problem of gas flow forecasting in a complex high-pressure transmission network. Experiments show that our model effectively captures comprehensive spatio-temporal correlations through modeling gas networks and consistently outperforms state-of-the-art benchmarks on real-world data sets by at least 21$\%$. The results demonstrate that the proposed model can deal with complex nonlinear gas network flow forecasting with high accuracy and effectiveness. T3 - ZIB-Report - 21-01 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81221 SN - 1438-0064 ER - TY - CHAP A1 - Estacio, Laura A1 - Ehlke, Moritz A1 - Tack, Alexander A1 - Castro-Gutierrez, Eveling A1 - Lamecker, Hans A1 - Mora, Rensso A1 - Zachow, Stefan T1 - Unsupervised Detection of Disturbances in 2D Radiographs T2 - 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) N2 - We present a method based on a generative model for detection of disturbances such as prosthesis, screws, zippers, and metals in 2D radiographs. The generative model is trained in an unsupervised fashion using clinical radiographs as well as simulated data, none of which contain disturbances. Our approach employs a latent space consistency loss which has the benefit of identifying similarities, and is enforced to reconstruct X-rays without disturbances. In order to detect images with disturbances, an anomaly score is computed also employing the Frechet distance between the input X-ray and the reconstructed one using our generative model. Validation was performed using clinical pelvis radiographs. We achieved an AUC of 0.77 and 0.83 with clinical and synthetic data, respectively. The results demonstrated a good accuracy of our method for detecting outliers as well as the advantage of utilizing synthetic data. Y1 - 2021 U6 - https://doi.org/10.1109/ISBI48211.2021.9434091 SP - 367 EP - 370 ER - TY - GEN A1 - Anderson, Lovis A1 - Turner, Mark A1 - Koch, Thorsten T1 - Generative deep learning for decision making in gas networks N2 - A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5%. T3 - ZIB-Report - 20-38 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81103 SN - 1438-0064 ER - TY - JOUR A1 - Schneck, Jakob A1 - Weiser, Martin A1 - Wende, Florian T1 - Impact of mixed precision and storage layout on additive Schwarz smoothers JF - Numerical Linear Algebra with Applications N2 - The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth-bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage. Y1 - 2021 U6 - https://doi.org/10.1002/nla.2366 VL - 28 IS - 4 ER - TY - JOUR A1 - Scott, Philip A1 - Santiago, Xavier Garcia A1 - Beutel, Dominik A1 - Rockstuhl, Carsten A1 - Wegener, Martin A1 - Fernandez-Corbaton, Ivan T1 - On enhanced sensing of chiral molecules in optical cavities JF - Appl. Phys. Rev. Y1 - 2020 U6 - https://doi.org/10.1063/5.0025006 VL - 7 SP - 041413 ER - TY - JOUR A1 - Streubel, Tom A1 - Tischendorf, Caren A1 - Griewank, Andreas T1 - Piecewise Polynomial Taylor Expansions - The Generalization of Faà di Bruno's Formula JF - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 N2 - We present an extension of Taylor's Theorem for the piecewise polynomial expansion of non-smooth evaluation procedures involving absolute value operations. Evaluation procedures are computer programs of mathematical functions in closed form expression and allow a different treatment of smooth operations or calls to the absolute value function. The well known classical Theorem of Taylor defines polynomial approximations of sufficiently smooth functions and is widely used for the derivation and analysis of numerical integrators for systems of ordinary differential- or differential-algebraic equations, for the construction of solvers for continuous non-linear optimization of finite dimensional objective functions and for root solving of non-linear systems of equations. The long term goal is the stabilization and acceleration of already known methods and the derivation of new methods by incorporating piecewise polynomial Taylor expansions. The herein provided proof of the higher order approximation quality of the new generalized expansions is constructive and allows efficiently designed algorithms for the execution and computation of the piecewise polynomial expansions. As a demonstration towards the ultimate goal we will derive a prototype of a {\$}{\$}k{\$}{\$}k-step method on the basis of polynomial interpolation and the proposed generalized expansions. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-55240-4_3 IS - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 SP - 63 EP - 82 PB - Springer International Publishing ER - TY - GEN A1 - Becker, Christiane A1 - Jäger, Klaus A1 - Burger, Sven T1 - Nanophotonics for Solar Energy T2 - Sol. Energy Mater. Sol. Cells Y1 - 2021 U6 - https://doi.org/10.1016/j.solmat.2020.110916 VL - 221 SP - 110916 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Klus, Stefan A1 - Schütte, Christof T1 - Data-driven model reduction of agent-based systems using the Koopman generator JF - PLOS ONE N2 - The dynamical behavior of social systems can be described by agent-based models. Although single agents follow easily explainable rules, complex time-evolving patterns emerge due to their interaction. The simulation and analysis of such agent-based models, however, is often prohibitively time-consuming if the number of agents is large. In this paper, we show how Koopman operator theory can be used to derive reduced models of agent-based systems using only simulation or real-world data. Our goal is to learn coarse-grained models and to represent the reduced dynamics by ordinary or stochastic differential equations. The new variables are, for instance, aggregated state variables of the agent-based model, modeling the collective behavior of larger groups or the entire population. Using benchmark problems with known coarse-grained models, we demonstrate that the obtained reduced systems are in good agreement with the analytical results, provided that the numbers of agents is sufficiently large. Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0250970 VL - 16 IS - 5 ER - TY - JOUR A1 - Chewle, Surahit A1 - Emmerling, Franziska A1 - Weber, Marcus T1 - Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study JF - Crystals N2 - The choice of solvents influences crystalline solid formed during the crystallization of active pharmaceutical ingredients (API). The underlying effects are not always well understood because of the complexity of the systems. Theoretical models are often insufficient to describe this phenomenon. In this study, the crystallization behavior of the model drug paracetamol in different solvents was studied based on experimental and molecular dynamics data. The crystallization process was followed in situ using time-resolved Raman spectroscopy. Molecular dynamics with simulated annealing algorithm was used for an atomistic understanding of the underlying processes. The experimental and theoretical data indicate that paracetamol molecules adopt a particular geometry in a given solvent predefining the crystallization of certain polymorphs. Y1 - 2020 U6 - https://doi.org/10.3390/cryst10121107 VL - 10 IS - 12 SP - 1107 ER - TY - JOUR A1 - Gotzes, Uwe A1 - Hoppmann-Baum, Kai T1 - Bounding the final rank during a round robin tournament with integer programming JF - Operational Research N2 - This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s12351-020-00546-w VL - 1866-1505 ER - TY - GEN A1 - Prause, Felix A1 - Hoppmann-Baum, Kai A1 - Defourny, Boris A1 - Koch, Thorsten T1 - The Maximum Diversity Assortment Selection Problem N2 - In this paper, we introduce the Maximum Diversity Assortment Selection Problem (MADASS), which is a generalization of the 2-dimensional Cutting Stock Problem (2CSP). Given a set of rectangles and a rectangular container, the goal of 2CSP is to determine a subset of rectangles that can be placed in the container without overlapping, i.e., a feasible assortment, such that a maximum area is covered. In MADASS, we need to determine a set of feasible assortments, each of them covering a certain minimum threshold of the container, such that the diversity among them is maximized. Thereby, diversity is defined as minimum or average normalized Hamming-Distance of all assortment pairs. The MADASS Problem was used in the 11th AIMMS-MOPTA Competition in 2019. The methods we describe in this article and the computational results won the contest. In the following, we give a definition of the problem, introduce a mathematical model and solution approaches, determine upper bounds on the diversity, and conclude with computational experiments conducted on test instances derived from the 2CSP literature. T3 - ZIB-Report - 20-34 KW - Combinatorial Optimization KW - Mixed Integer Programming KW - 2-dim Cutting Stock Problem KW - Maximum Diversity Problem Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81039 SN - 1438-0064 ER - TY - JOUR A1 - Wulkow, Hanna A1 - Conrad, Tim A1 - Djurdjevac Conrad, Natasa A1 - Müller, Sebastian A. A1 - Nagel, Kai A1 - Schütte, Christof T1 - Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts JF - PLOS One Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0249676 VL - 16 IS - 4 PB - Public Library of Science ER - TY - THES A1 - Ehlke, Moritz T1 - 3D Reconstruction of Anatomical Structures from 2D X-ray Images Y1 - 2020 UR - https://depositonce.tu-berlin.de/handle/11303/12753 U6 - https://doi.org/https://doi.org/10.14279/depositonce-11553 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - A Discrete-Continuous Algorithm for Free Flight Planning JF - Algorithms N2 - We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach. KW - shortest path KW - flight planning KW - free flight KW - discrete-continuous algorithm KW - optimal control KW - discrete optimization Y1 - 2020 U6 - https://doi.org/10.3390/a14010004 SN - 1438-0064 VL - 14 IS - 1 SP - 4 PB - MDPI ER - TY - JOUR A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms JF - Medical Image Analysis N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. Additionally, as planar configurations form a submanifold in shape space, our representation allows for effective estimation of quasi-isometric surfaces flattenings. We evaluate the performance of our model w.r.t. shape-based classification of hippocampus and femur malformations due to Alzheimer's disease and osteoarthritis, respectively. In particular, we achieve state-of-the-art accuracies outperforming the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102178 VL - 73 ER - TY - JOUR A1 - Schienle, Adam A1 - Maristany de las Casas, Pedro A1 - Blanco, Marco T1 - A Priori Search Space Pruning in the Flight Planning Problem N2 - We study the Flight Planning Problem for a single aircraft, where we look for a minimum cost path in the airway network, a directed graph. Arc evaluation, such as weather computation, is computationally expensive due to non-linear functions, but required for exactness. We propose several pruning methods to thin out the search space for Dijkstra's algorithm before the query commences. We do so by using innate problem characteristics such as an aircraft's tank capacity, lower and upper bounds on the total costs, and in particular, we present a method to reduce the search space even in the presence of regional crossing costs. We test all pruning methods on real-world instances, and show that incorporating crossing costs into the pruning process can reduce the number of nodes by 90\% in our setting. T3 - ZIB-Report - 20-32 Y1 - 2019 U6 - https://doi.org/https://doi.org/10.4230/OASIcs.ATMOS.2019.8 SN - 1438-0064 ER - TY - GEN A1 - Maristany de las Casas, Pedro A1 - Borndörfer, Ralf A1 - Kraus, Luitgard A1 - Sedeño-Noda, Antonio T1 - An FPTAS for Dynamic Multiobjective Shortest Path Problems N2 - We propose in this paper the Dynamic Multiobjective Shortest Problem. It features multidimensional states that can depend on several variables and not only on time; this setting is motivated by flight planning and electric vehicle routing applications. We give an exact algorithm for the FIFO case and derive from it an FPTAS, which is computationally efficient. It also features the best known complexity in the static case. T3 - ZIB-Report - 20-31 KW - Multiobjective Shortest Paths KW - Time Dependent Shortest Paths KW - Multiobjective Approximation Algorithms KW - Flight Planning Problem Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80954 ER - TY - JOUR A1 - Sekuboyina, Anjany A1 - Bayat, Amirhossein A1 - Husseini, Malek E. A1 - Löffler, Maximilian A1 - Li, Hongwei A1 - Tetteh, Giles A1 - Kukačka, Jan A1 - Payer, Christian A1 - Štern, Darko A1 - Urschler, Martin A1 - Chen, Maodong A1 - Cheng, Dalong A1 - Lessmann, Nikolas A1 - Hu, Yujin A1 - Wang, Tianfu A1 - Yang, Dong A1 - Xu, Daguang A1 - Ambellan, Felix A1 - Amiranashvili, Tamaz A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Lehnert, Sebastian A1 - Lirio, Marilia A1 - de Olaguer, Nicolás Pérez A1 - Ramm, Heiko A1 - Sahu, Manish A1 - Tack, Alexander A1 - Zachow, Stefan A1 - Jiang, Tao A1 - Ma, Xinjun A1 - Angerman, Christoph A1 - Wang, Xin A1 - Wei, Qingyue A1 - Brown, Kevin A1 - Wolf, Matthias A1 - Kirszenberg, Alexandre A1 - Puybareau, Élodie A1 - Valentinitsch, Alexander A1 - Rempfler, Markus A1 - Menze, Björn H. A1 - Kirschke, Jan S. T1 - VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images JF - arXiv Y1 - 2020 ER - TY - JOUR A1 - Tack, Alexander A1 - Preim, Bernhard A1 - Zachow, Stefan T1 - Fully automated Assessment of Knee Alignment from Full-Leg X-Rays employing a "YOLOv4 And Resnet Landmark regression Algorithm" (YARLA): Data from the Osteoarthritis Initiative JF - Computer Methods and Programs in Biomedicine N2 - We present a method for the quantification of knee alignment from full-leg X-Rays. A state-of-the-art object detector, YOLOv4, was trained to locate regions of interests (ROIs) in full-leg X-Ray images for the hip joint, the knee, and the ankle. Residual neural networks (ResNets) were trained to regress landmark coordinates for each ROI.Based on the detected landmarks the knee alignment, i.e., the hip-knee-ankle (HKA) angle, was computed. The accuracy of landmark detection was evaluated by a comparison to manually placed landmarks for 360 legs in 180 X-Rays. The accuracy of HKA angle computations was assessed on the basis of 2,943 X-Rays. Results of YARLA were compared to the results of two independent image reading studies(Cooke; Duryea) both publicly accessible via the Osteoarthritis Initiative. The agreement was evaluated using Spearman's Rho, and weighted kappa as well as regarding the correspondence of the class assignment (varus/neutral/valgus). The average difference between YARLA and manually placed landmarks was less than 2.0+- 1.5 mm for all structures (hip, knee, ankle). The average mismatch between HKA angle determinations of Cooke and Duryea was 0.09 +- 0.63°; YARLA resulted in a mismatch of 0.10 +- 0.74° compared to Cooke and of 0.18 +- 0.64° compared to Duryea. Cooke and Duryea agreed almost perfectly with respect to a weighted kappa value of 0.86, and showed an excellent reliability as measured by a Spearman's Rho value of 0.99. Similar values were achieved by YARLA, i.e., a weighted kappa value of0.83 and 0.87 and a Spearman's Rho value of 0.98 and 0.99 to Cooke and Duryea,respectively. Cooke and Duryea agreed in 92% of all class assignments and YARLA did so in 90% against Cooke and 92% against Duryea. In conclusion, YARLA achieved results comparable to those of human experts and thus provides a basis for an automated assessment of knee alignment in full-leg X-Rays. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.cmpb.2021.106080 VL - 205 IS - 106080 ER - TY - JOUR A1 - Udvary, Daniel A1 - Harth, Philipp A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - de Kock, Christiaan P. J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - A Theory for the Emergence of Neocortical Network Architecture JF - BioRxiv Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1101/2020.11.13.381087 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Liu, Tuo A1 - Kahl, Christoph A1 - Andrea, Hildebrandt A1 - Zachow, Stefan T1 - Statistical Learning of Facial Expressions Improves Realism of Animated Avatar Faces JF - Frontiers in Virtual Reality Y1 - 2021 U6 - https://doi.org/10.3389/frvir.2021.619811 VL - 2 SP - 1 EP - 13 PB - Frontiers ER - TY - JOUR A1 - Lindner, Niels T1 - Hypersurfaces with defect JF - Journal of Algebra N2 - A projective hypersurface X⊆P^n has defect if h^i(X) ≠ h^i(P^n) for some i∈{n,…,2n−2} in a suitable cohomology theory. This occurs for example when X⊆P^4 is not Q-factorial. We show that hypersurfaces with defect tend to be very singular: In characteristic 0, we present a lower bound on the Tjurina number, where X is allowed to have arbitrary isolated singularities. For X with mild singularities, we prove a similar result in positive characteristic. As an application, we obtain an estimate on the asymptotic density of hypersurfaces without defect over a finite field. Y1 - 2020 U6 - https://doi.org/10.1016/j.jalgebra.2020.02.022 VL - 555 SP - 1 EP - 35 ER - TY - CHAP A1 - Löbel, Fabian A1 - Lindner, Niels A1 - Borndörfer, Ralf ED - Neufeld, Janis S. ED - Buscher, Udo ED - Lasch, Rainer ED - Möst, Dominik ED - Schönberger, Jörn T1 - The Restricted Modulo Network Simplex Method for Integrated Periodic Timetabling and Passenger Routing T2 - Operations Research Proceedings 2019 N2 - The Periodic Event Scheduling Problem is a well-studied NP-hard problem with applications in public transportation to find good periodic timetables. Among the most powerful heuristics to solve the periodic timetabling problem is the modulo network simplex method. In this paper, we consider the more difficult version with integrated passenger routing and propose a refined integrated variant to solve this problem on real-world-based instances. Y1 - 2020 SN - 978-3-030-48438-5 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-48439-2_92 SP - 757 EP - 763 PB - Springer International Publishing CY - Cham ER - TY - CHAP A1 - Lindner, Niels A1 - Liebchen, Christian ED - Huisman, Dennis ED - Zaroliagis, Christos D. T1 - Determining all integer vertices of the PESP polytope by flipping arcs T2 - 20th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2020) N2 - We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. We finally present better dual bounds for the smallest and largest instance of the benchmarking library PESPlib. Y1 - 2020 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2020.5 VL - 85 SP - 5:1 EP - 5:18 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - THES A1 - Santiago, Xavier Garcia T1 - Numerical methods for shape optimization of photonic nanostructures Y1 - 2021 U6 - https://doi.org/10.5445/IR/1000131006 ER - TY - JOUR A1 - Mielke, Alexander A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence JF - Continuum Mechanics and Thermodynamics N2 - This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories. Y1 - 2021 U6 - https://doi.org/10.1007/s00161-020-00932-x VL - 33 SP - 611 EP - 637 PB - Springer ER - TY - JOUR A1 - Schiela, Anton A1 - Stöcklein, Matthias A1 - Weiser, Martin T1 - A primal dual projection algorithm for efficient constraint preconditioning JF - SIAM Journal on Scientific Computing N2 - We consider a linear iterative solver for large scale linearly constrained quadratic minimization problems that arise, for example, in optimization with PDEs. By a primal-dual projection (PDP) iteration, which can be interpreted and analysed as a gradient method on a quotient space, the given problem can be solved by computing sulutions for a sequence of constrained surrogate problems, projections onto the feasible subspaces, and Lagrange multiplier updates. As a major application we consider a class of optimization problems with PDEs, where PDP can be applied together with a projected cg method using a block triangular constraint preconditioner. Numerical experiments show reliable and competitive performance for an optimal control problem in elasticity. Y1 - 2021 U6 - https://doi.org/10.1137/20M1380739 VL - 43 IS - 6 SP - A4095 EP - A4120 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Euler, Ricardo A1 - Karbstein, Marika T1 - Ein Graphen-basiertes Modell zur Beschreibung von Preissystemen im öffentlichen Nahverkehr JF - HEUREKA 21 N2 - In dieser Arbeit wird ein graphenbasiertes Modell zur Einbindung von Preissystemen des öffentlichen Nahverkehrs in Routing-Algorithmen vorgestellt. Jeder Knoten des Graphen repräsentiert einen abstrakten Preiszustand einer Route und ist an einen tatsächlichen Preis gekoppelt. Damit sind sehr einfache und konzise Beschreibungen von Tarifstrukturen möglich, diesich algorithmisch behandeln lassen. Durch das zeitgleiche Tracken eines Pfades im Routinggraphen im Ticketgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Dies ermöglicht die Berechnung von preisoptimalen Routen. An den Tarifsystemen der Verkehrsverbünde MDV (Mitteldeutscher Verkehrsverbund) und VBB (Verkehrsverbund Berlin-Brandenburg) wird die Konstruktion des Modells detailliert erläutert. Y1 - 2021 UR - https://verlag.fgsv-datenbanken.de/tagungsbaende?kat=HEUREKA&subkat=FGSV+002%2F127+%282021%29&fanr=&va=&titel=&text=&autor=&tagungsband=1256&_titel=Ein+Graphen-basiertes+Modell+zur+Beschreibung+von+Preissystemen+im+%C3%B6ffentlichen+Nahverkehr VL - 002/127 SP - 1 EP - 15 PB - FGSV CY - Stuttgart ER - TY - JOUR A1 - Koch, Thorsten A1 - Schmidt, Martin A1 - Hiller, Benjamin A1 - Pfetsch, Marc A1 - Geißler, Björn A1 - Henrion, René A1 - Joormann, Imke A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Schewe, Lars A1 - Schultz, Rüdiger T1 - Capacity Evaluation for Large-Scale Gas Networks JF - German Success Stories in Industrial Mathematics Y1 - 2020 SN - 978-3-030-81454-0 U6 - https://doi.org/10.1007/978-3-030-81455-7 VL - 35 SP - 23 EP - 28 ER - TY - CHAP A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - An exact high performance solver for Steiner tree problems in graphs and related problems T2 - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 Y1 - 2020 PB - Springer ER - TY - JOUR A1 - Koch, Thorsten A1 - Chen, Ying A1 - Lim, Kian Guan A1 - Xu, Xiaofei A1 - Zakiyeva, Nazgul T1 - A review study of functional autoregressive models with application to energy forecasting JF - WIREs Computational Statistics Y1 - 2020 U6 - https://doi.org/10.1002/wics.1525 N1 - https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=7693&context=lkcsb_research ER - TY - JOUR A1 - Chen, Ying A1 - Zakiyeva, Nazgul A1 - Zhu, Bangzhu A1 - Koch, Thorsten T1 - Modeling and Forecasting the Dynamics of the Natural Gas Transmission Network in Germany with the Demand and Supply Balance Constraint JF - Applied Energy Y1 - 2020 U6 - https://doi.org/10.1016/j.apenergy.2020.115597 N1 - https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3646636 IS - 278 ER - TY - CHAP A1 - Pfetsch, Marc A1 - Pokutta, Sebastian T1 - IPBoost – Non-Convex Boosting via Integer Programming T2 - Proceedings of ICML Y1 - 2020 N1 - URL of the Code: https://www2.mathematik.tu-darmstadt.de/~pfetsch/ipboost.html N1 - URL of the Slides: https://app.box.com/s/8dpvmls88suouy11bkpwufhu7iiz6dxl N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/02/13/ipboost-abstract.html ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness T2 - Proceedings of ICML Y1 - 2020 N1 - URL of the Poster: https://app.box.com/s/24vbh1s2vib11upqyepzen3lzdl13skr N1 - URL of the Slides: https://app.box.com/s/fmjxhfdpiqubm28upf563ohy8t8fgl3a N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/06/03/unreasonable-abstract.html N1 - https://www.youtube.com/watch?v=VB1e0HrDmVo ER - TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Locally Accelerated Conditional Gradients T2 - Proceedings of AISTATS Y1 - 2020 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: http://proceedings.mlr.press/v108/diakonikolas20a/diakonikolas20a.pdf N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html N1 - https://slideslive.com/38930107/locally-accelerated-conditional-gradients?ref=account-folder-52123-folders ER - TY - JOUR A1 - Faenza, Yuri A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - New Limits of Treewidth-based tractability in Optimization JF - Mathematical Programming Y1 - 2020 U6 - https://doi.org/10.1007/s10107-020-01563-5 N1 - URL of the PDF: http://link.springer.com/article/10.1007/s10107-020-01563-5 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2018/09/22/treewidth-abstract.html VL - 191 SP - 559 EP - 594 ER - TY - JOUR A1 - Anari, N. A1 - Haghtalab, N. A1 - Naor, S. A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Structured Robust Submodular Maximization: Offline and Online Algorithms JF - INFORMS Journal on Computing Y1 - 2020 ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Boosting Frank-Wolfe by Chasing Gradients T2 - Proceedings of ICML Y1 - 2020 N1 - Additional Note: github code: https://github.com/cyrillewcombettes/boostfw N1 - URL of the Code: https://colab.research.google.com/drive/1TSOVjDFF1X2ADBo_adHLsUVrblSutRKw N1 - URL of the Slides: https://app.box.com/s/wwj247r5d456q0778p9b9y1jm6txuifb N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/03/16/boostFW.html N1 - https://www.youtube.com/watch?v=BfyV0C5FRbE ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2019.04.066 VL - 181 SP - 782 EP - 792 ER - TY - CHAP A1 - Shinano, Yuji A1 - Tateiwa, N. A1 - Nakamura, S. A1 - Yoshida, A. A1 - Yasuda, M. A1 - Kaji, S. A1 - Fujisawa, K. T1 - Massive Parallelization for Finding Shortest Lattice Vectors Based on Ubiquity Generator Framework T2 - 2020 SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (SC) N2 - Lattice-based cryptography has received attention as a next-generation encryption technique, because it is believed to be secure against attacks by classical and quantum computers. Its essential security depends on the hardness of solving the shortest vector problem (SVP). In the cryptography, to determine security levels, it is becoming significantly more important to estimate the hardness of the SVP by high-performance computing. In this study, we develop the world’s first distributed and asynchronous parallel SVP solver, the MAssively Parallel solver for SVP (MAP-SVP). It can parallelize algorithms for solving the SVP by applying the Ubiquity Generator framework, which is a generic framework for branch-and-bound algorithms. The MAP-SVP is suitable for massive-scale parallelization, owing to its small memory footprint, low communication overhead, and rapid checkpoint and restart mechanisms. We demonstrate its performance and scalability of the MAP-SVP by using up to 100,032 cores to solve instances of the Darmstadt SVP Challenge. Y1 - 2020 U6 - https://doi.org/10.1109/SC41405.2020.00064 SP - 834 EP - 848 ER - TY - CHAP A1 - Mortagy, Hassan A1 - Gupta, Swati A1 - Pokutta, Sebastian T1 - Walking in the Shadow: A New Perspective on Descent Directions for Constrained Minimization T2 - Proceedings of NeurIPS Y1 - 2020 N1 - URL of the Code: https://github.com/pokutta/Walking-in-the-Shadow N1 - URL of the Poster: https://app.box.com/s/y266djezdjdidsswaopvdcnsnkp8774i N1 - URL of the Slides: https://app.box.com/s/wjhpe4nh8kv5pw6vl5jbp902v3mksivs ER - TY - CHAP A1 - Sofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - Accelerating Domain Propagation: an Efficient GPU-Parallel Algorithm over Sparse Matrices T2 - 2020 IEEE/ACM 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3) N2 - Fast domain propagation of linear constraints has become a crucial component of today's best algorithms and solvers for mixed integer programming and pseudo-boolean optimization to achieve peak solving performance. Irregularities in the form of dynamic algorithmic behaviour, dependency structures, and sparsity patterns in the input data make efficient implementations of domain propagation on GPUs and, more generally, on parallel architectures challenging. This is one of the main reasons why domain propagation in state-of-the-art solvers is single thread only. In this paper, we present a new algorithm for domain propagation which (a) avoids these problems and allows for an efficient implementation on GPUs, and is (b) capable of running propagation rounds entirely on the GPU, without any need for synchronization or communication with the CPU. We present extensive computational results which demonstrate the effectiveness of our approach and show that ample speedups are possible on practically relevant problems: on state-of-the-art GPUs, our geometric mean speed-up for reasonably-large instances is around 10x to 20x and can be as high as 195x on favorably-large instances. Y1 - 2020 U6 - https://doi.org/10.1109/IA351965.2020.00007 N1 - URL of the Slides: https://app.box.com/s/qy0pjmhtbm7shk2ypxjxlh2sj4nudvyu N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/09/20/gpu-prob.html SP - 1 EP - 11 ER - TY - JOUR A1 - Devriendt, Jo A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search JF - Constraints N2 - Conflict-driven pseudo-Boolean solvers optimize 0-1 integer linear programs by extending the conflict-driven clause learning (CDCL) paradigm from SAT solving. Though pseudo-Boolean solvers have the potential to be exponentially more efficient than CDCL solvers in theory, in practice they can sometimes get hopelessly stuck even when the linear programming (LP) relaxation is infeasible over the reals. Inspired by mixed integer programming (MIP), we address this problem by interleaving incremental LP solving with cut generation within the conflict-driven pseudo-Boolean search. This hybrid approach, which for the first time combines MIP techniques with full-blown conflict analysis operating directly on linear inequalities using the cutting planes method, significantly improves performance on a wide range of benchmarks, approaching a "best-of-both-worlds" scenario between SAT-style conflict-driven search and MIP-style branch-and-cut. Y1 - 2021 U6 - https://doi.org/10.1007/s10601-020-09318-x VL - 26 SP - 26 EP - 55 ER - TY - CHAP A1 - Pokutta, Sebastian T1 - Restarting Algorithms: Sometimes there is Free Lunch T2 - Proceedings of CPAIOR Y1 - 2020 N1 - URL of the Slides: https://app.box.com/s/8ps8bhjv2phhy182xn55iurk9t3o1xc3 N1 - https://www.youtube.com/watch?v=v3Xzoda2_gQ ER - TY - JOUR A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Salvagnin, Domenico T1 - An exploratory computational analysis of dual degeneracy in mixed-integer programming JF - EURO Journal on Computational Optimization N2 - Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable–constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates. Y1 - 2020 U6 - https://doi.org/10.1007/s13675-020-00130-z IS - 8 SP - 241 EP - 246 ER - TY - JOUR A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict Analysis for MINLP JF - INFORMS Journal on Computing N2 - The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality. Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2020.1050 VL - 33 IS - 2 SP - 421 EP - 435 ER - TY - JOUR A1 - Lang, Annemarie A1 - Helfmeier, Sarah A1 - Stefanowski, Jonathan A1 - Kuppe, Aditi A1 - Sunkara, Vikram A1 - Pfeiffenberger, Moritz A1 - Wolter, Angelique A1 - Damerau, Alexandra A1 - Hemmati-Sadeghi, Shabnam A1 - Ringe, Jochen A1 - Haag, Rainer A1 - Hauser, Anja E. A1 - Löhning, Max A1 - Perka, Carsten A1 - Duda, Georg A1 - Hoff, Paula A1 - Schmidt-Bleek, Katharina A1 - Gaber, Timo A1 - Buttgereit, Frank T1 - HIF-stabilization prevents delayed fracture healing JF - bioarxiv Y1 - 2020 U6 - https://doi.org/10.1101/2020.07.02.182832 ER - TY - JOUR A1 - Csizmadia, Zsolt A1 - Berthold, Timo T1 - The confined primal integral: a measure to benchmark heuristic MINLP solvers against global MINLP solvers JF - Mathematical Programming N2 - It is a challenging task to fairly compare local solvers and heuristics against each other and against global solvers. How does one weigh a faster termination time against a better quality of the found solution? In this paper, we introduce the confined primal integral, a new performance measure that rewards a balance of speed and solution quality. It emphasizes the early part of the solution process by using an exponential decay. Thereby, it avoids that the order of solvers can be inverted by choosing an arbitrarily large time limit. We provide a closed analytic formula to compute the confined primal integral a posteriori and an incremental update formula to compute it during the run of an algorithm. For the latter, we show that we can drop one of the main assumptions of the primal integral, namely the knowledge of a fixed reference solution to compare against. Furthermore, we prove that the confined primal integral is a transitive measure when comparing local solves with different final solution values. Finally, we present a computational experiment where we compare a local MINLP solver that uses certain classes of cutting planes against a solver that does not. Both versions show very different tendencies w.r.t. average running time and solution quality, and we use the confined primal integral to argue which of the two is the preferred setting. Y1 - 2020 U6 - https://doi.org/10.1007/s10107-020-01547-5 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - bioarxiv (Accepted in Osteoarthr. Cartil.) Y1 - 2020 U6 - https://doi.org/10.1101/2020.06.13.148056 ER - TY - JOUR A1 - Laydon, Daniel J. A1 - Sunkara, Vikram A1 - Boelen, Lies A1 - Bangham, Charles R. M. A1 - Asquith, Becca T1 - The relative contributions of infectious and mitotic spread to HTLV-1 persistence JF - PLOS Computational Biology Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007470 ER - TY - GEN A1 - Hoppmann-Baum, Kai A1 - Mexi, Gioni A1 - Burdakov, Oleg A1 - Casselgren, Carl Johan A1 - Koch, Thorsten T1 - Length-Constrained Cycle Partition with an Application to UAV Routing N2 - In this article, we discuss the Length-Constrained Cycle Partition Problem (LCCP). Besides edge weights, the undirected graph in LCCP features an individual critical weight value for each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is a feasible solution if the length of each cycle is not greater than the critical weight of each of the vertices in the cycle. The goal is to find a feasible partition with the minimum number of cycles. In this article, we discuss theoretical properties, preprocessing techniques, and two mixed-integer programming models (MIP) for LCCP both inspired by formulations for the closely related Travelling Salesperson Problem (TSP). Further, we introduce conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a report on computational experiments conducted on (A)TSPLIB-based instances. As an example, we use a routing problem in which a fleet of uncrewed aerial vehicles (UAVs) patrols a set of areas. T3 - ZIB-Report - 20-30 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80489 SN - 1438-0064 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Takeuchi, Kotaro A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Effect of Model Reduction by Time Aggregation in Multiobjective Optimal Design of Energy Supply Systems by a Hierarchical MILP Method T2 - Conference N2 - The mixed-integer linear programming (MILP) method has been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems effi- ciently. As one of the strategies to enhance the computation efficiency furthermore, a method of reducing model by time aggregation has been proposed to search design candidates accurately and efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method and model reduction by time aggregation are applied to the multiobjective optimal design. In applying the model reduc- tion, the methods of clustering periods by the order of time series, based on an operational strategy, and by the k-medoids method are applied. As a case study, the multiobjective optimal design of a gas turbine cogeneration system with a practical configuration is investigated by adopting the annual total cost and pri- mary energy consumption as the objective functions to be minimized simultaneously, and the clustering methods are compared with one another in terms of the computation efficiency. It turns out that the model reduction by any clustering method is effective to enhance the computation efficiency when importance is given to minimizing the first objective function. It also turns out that the model reduction only by the k- medoids method is effective very limitedly when importance is given to minimizing the second objective function. Y1 - 2020 SP - 627 EP - 639 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Kamada, Hiroki A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - A Hierarchical Optimization Approach to Robust Design of Energy Supply Systems Based on a Mixed-Integer Linear Model T2 - Conference N2 - In designing energy supply systems, designers should heighten the robustness in performance criteria against the uncertainty in energy demands. In this paper, a robust optimal design method using a hierarchi- cal mixed-integer linear programming (MILP) method is proposed to maximize the robustness of energy sup- ply systems under uncertain energy demands based on a mixed-integer linear model. A robust optimal design problem is formulated as a three-level min-max-min MILP one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret cri- terion, and considering relationships among integer design variables, uncertain energy demands, and inte- ger and continuous operation variables. This problem is solved by evaluating upper and lower bounds for the minimum of the maximum regret of the performance criterion repeatedly outside, and evaluating lower and upper bounds for the maximum regret repeatedly inside. Since these different types of optimization problems are difficult to solve even using commercial MILP solvers, they are solved by applying a hierarchi- cal MILP method developed for ordinary optimal design problems with its modifications. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system. Through the study, its validity and effectiveness are ascertained, and some features of the obtained robust designs are clarified. Y1 - 2020 SP - 601 EP - 613 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Eßer, Thomas A1 - Frankenberger, Patrick A1 - Huck, Andreas A1 - Jobmann, Christoph A1 - Krostitz, Boris A1 - Kuchenbecker, Karsten A1 - Moorhagen, Kai A1 - Nagl, Philipp A1 - Peterson, Michael A1 - Reuther, Markus A1 - Schang, Thilo A1 - Schoch, Michael A1 - Schülldorf, Hanno A1 - Schütz, Peter A1 - Therolf, Tobias A1 - Waas, Kerstin A1 - Weider, Steffen T1 - Deutsche Bahn Schedules Train Rotations Using Hypergraph Optimization JF - Informs Journal on Applied Analytics N2 - Deutsche Bahn (DB) operates a large fleet of rolling stock (locomotives, wagons, and train sets) that must be combined into trains to perform rolling stock rotations. This train composition is a special characteristic of railway operations that distinguishes rolling stock rotation planning from the vehicle scheduling problems prevalent in other industries. DB models train compositions using hyperarcs. The resulting hypergraph models are ad-dressed using a novel coarse-to-fine method that implements a hierarchical column genera-tion over three levels of detail. This algorithm is the mathematical core of DB’s fleet em-ployment optimization (FEO) system for rolling stock rotation planning. FEO’s impact within DB’s planning departments has been revolutionary. DB has used it to support the company’s procurements of its newest high-speed passenger train fleet and its intermodal cargo locomotive fleet for cross-border operations. FEO is the key to successful tendering in regional transport and to construction site management in daily operations. DB’s plan-ning departments appreciate FEO’s high-quality results, ability to reoptimize (quickly), and ease of use. Both employees and customers benefit from the increased regularity of operations. DB attributes annual savings of 74 million euro, an annual reduction of 34,000 tons of CO2 emissions, and the elimination of 600 coupling operations in cross-border operations to the implementation of FEO. Y1 - 2021 U6 - https://doi.org/10.1287/inte.2020.1069 VL - 51 IS - 1 SP - 42 EP - 62 ER - TY - JOUR A1 - Sahin, Guvenc A1 - Ahmadi, Amin A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Multi-period line planning with resource transfers JF - Transportation Research Part C: Emerging Technologies N2 - Urban transportation systems are subject to a high level of variation and fluctuation in demand over the day. When this variation and fluctuation are observed in both time and space, it is crucial to develop line plans that are responsive to demand. A multi-period line planning approach that considers a changing demand during the planning horizon is proposed. If such systems are also subject to limitations of resources, a dynamic transfer of resources from one line to another throughout the planning horizon should also be considered. A mathematical modelling framework is developed to solve the line planning problem with a cost-oriented approach considering transfer of resources during a finite length planning horizon of multiple periods. We use real-life public transportation network data for our computational results. We analyze whether or not multi-period solutions outperform single period solutions in terms of feasibility and relevant costs. The importance of demand variation on multi-period solutions is investigated. We evaluate the impact of resource transfer constraints on the effectiveness of solutions. We also study the effect of period lengths along with the problem parameters that are significant for and sensitive to the optimality of solutions. Y1 - 2020 U6 - https://doi.org/10.1016/j.trc.2020.102726 VL - 119 SP - 102726 ER - TY - JOUR A1 - Iravani, Sahar A1 - Conrad, Tim T1 - An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics N2 - Analyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Additionally, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Based on the trained neural networks, we show how biomarkers can be identified using layer-wise relevance propagation. This enables detecting discriminating regions of the data and the design of more robust networks. One of the main advantages over other established methods is that no explicit preprocessing step is needed in our DLearnMS framework. Our evaluation shows that DLearnMS outperforms conventional LC-MS biomarker detection approaches in identifying fewer false positive peaks while maintaining a comparable amount of true positives peaks. Y1 - 2023 U6 - https://doi.org/10.1109/tcbb.2022.3141656 VL - 20 IS - 1 SP - 151 EP - 161 ER - TY - JOUR A1 - Rams, Mona A1 - Conrad, Tim T1 - Dictionary learning allows model-free pseudotime estimation of transcriptomics data JF - BMC Genomics Y1 - 2022 U6 - https://doi.org/10.1186/s12864-021-08276-9 VL - 23 PB - BioMed Central ER - TY - JOUR A1 - Weimann, K. A1 - Conrad, Tim T1 - Transfer Learning for ECG Classification JF - Scientific Reports N2 - Remote monitoring devices, which can be worn or implanted, have enabled a more effective healthcare for patients with periodic heart arrhythmia due to their ability to constantly monitor heart activity. However, these devices record considerable amounts of electrocardiogram (ECG) data that needs to be interpreted by physicians. Therefore, there is a growing need to develop reliable methods for automatic ECG interpretation to assist the physicians. Here, we use deep convolutional neural networks (CNN) to classify raw ECG recordings. However, training CNNs for ECG classification often requires a large number of annotated samples, which are expensive to acquire. In this work, we tackle this problem by using transfer learning. First, we pretrain CNNs on the largest public data set of continuous raw ECG signals. Next, we finetune the networks on a small data set for classification of Atrial Fibrillation, which is the most common heart arrhythmia. We show that pretraining improves the performance of CNNs on the target task by up to 6.57%, effectively reducing the number of annotations required to achieve the same performance as CNNs that are not pretrained. We investigate both supervised as well as unsupervised pretraining approaches, which we believe will increase in relevance, since they do not rely on the expensive ECG annotations. The code is available on GitHub at https://github.com/kweimann/ecg-transfer-learning. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-84374-8 VL - 11 ER - TY - JOUR A1 - Le Duc, Huy A1 - Conrad, Tim T1 - A light-weight and highly flexible software system for analyzing large bio-medical datasets JF - Future Generation Computer Systems Y1 - 2020 ER - TY - JOUR A1 - Juds, Carmen A1 - Schmidt, Johannes A1 - Weller, Michael A1 - Lange, Thorid A1 - Conrad, Tim A1 - Boerner, Hans T1 - Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces JF - Journal of the American Chemical Society N2 - Phage display biopanning with Illumina next-generation sequencing (NGS) is applied to reveal insights into peptide-based adhesion domains for polypropylene (PP). One biopanning round followed by NGS selects robust PP-binding peptides that are not evident by Sanger sequencing. NGS provides a significant statistical base that enables motif analysis, statistics on positional residue depletion/enrichment, and data analysis to suppress false-positive sequences from amplification bias. The selected sequences are employed as water-based primers for PP?metal adhesion to condition PP surfaces and increase adhesive strength by 100\% relative to nonprimed PP. Y1 - 2020 U6 - https://doi.org/10.1021/jacs.0c03482 VL - 142 IS - 24 SP - 10624 EP - 10628 ER - TY - JOUR A1 - Cvetkovic, Nada A1 - Conrad, Tim A1 - Lie, Han Cheng T1 - A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes JF - Multiscale Modeling & Simulation Y1 - 2021 U6 - https://doi.org/10.1137/20M1329354 VL - 19 IS - 1 SP - 242 EP - 266 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Melnyk, Kateryna A1 - Montavon, Grègoire A1 - Klus, Stefan A1 - Conrad, Tim T1 - Graph Kernel Koopman Embedding for Human Microbiome Analysis JF - Applied Network Science N2 - More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to directly analyze human microbiome and its influence on the health status. Microbial communities are monitored over long periods of time and the associations between their members are explored. These relationships can be described by a time-evolving graph. In order to understand responses of the microbial community members to a distinct range of perturbations such as antibiotics exposure or diseases and general dynamical properties, the time-evolving graph of the human microbial communities has to be analyzed. This becomes especially challenging due to dozens of complex interactions among microbes and metastable dynamics. The key to solving this problem is the representation of the time-evolving graphs as fixed-length feature vectors preserving the original dynamics. We propose a method for learning the embedding of the time-evolving graph that is based on the spectral analysis of transfer operators and graph kernels. We demonstrate that our method can capture temporary changes in the time-evolving graph on both synthetic data and real-world data. Our experiments demonstrate the efficacy of the method. Furthermore, we show that our method can be applied to human microbiome data to study dynamic processes. Y1 - 2020 U6 - https://doi.org/10.1007/s41109-020-00339-2 VL - 5 IS - 96 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Katz, Eugene A. A1 - Becker, Christiane T1 - Perovskite/silicon tandem solar cells: Effect of luminescent coupling and bifaciality JF - Sol. RRL Y1 - 2021 U6 - https://doi.org/10.1002/solr.202000628 VL - 5 SP - 2000628 ER - TY - CHAP A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Katz, Eugene A. A1 - Becker, Christiane T1 - Simulating bifacial perovskite/silicon tandem solar cells in large PV fields T2 - OSA Advanced Photonics Congress Y1 - 2020 U6 - https://doi.org/10.1364/PVLED.2020.PvTh1G.3 SP - PvTh1G.3 ER - TY - JOUR A1 - Chegini, Fatemeh A1 - Kopanicakova, Alena A1 - Krause, Rolf A1 - Weiser, Martin T1 - Efficient Identification of Scars using Heterogeneous Model Hierarchies JF - EP Europace N2 - Aims. Detection and quantification of myocardial scars are helpful both for diagnosis of heart diseases and for building personalized simulation models. Scar tissue is generally charac­terized by a different conduction of electrical excitation. We aim at estimating conductivity-related parameters from endocardial mapping data, in particular the conductivity tensor. Solving this inverse problem requires computationally expensive monodomain simulations on fine discretizations. Therefore, we aim at accelerating the estimation using a multilevel method combining electrophysiology models of different complexity, namely the mono­domain and the eikonal model. Methods. Distributed parameter estimation is performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface, subject to the mono­domain model and regularization, leading to a constrained optimization problem. We formulate this optimization problem, including the modeling of scar tissue and different regularizations, and design an efficient iterative solver. We consider monodomain grid hierarchies and monodomain-eikonal model hierarchies in a recursive multilevel trust-region method. Results. From several numerical examples, both the efficiency of the method and the estimation quality, depending on the data, are investigated. The multilevel solver is significantly faster than a comparable single level solver. Endocardial mapping data of realistic density appears to be just sufficient to provide quantitatively reasonable estimates of location, size, and shape of scars close to the endocardial surface. Conclusion. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more accurate but more expensive monodomain model for this purpose. Still, eikonal models can be utilized to accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data. Y1 - 2021 U6 - https://doi.org/10.1093/europace/euaa402 VL - 23 SP - i113 EP - i122 ER - TY - JOUR A1 - Stein, Lewin A1 - Straube, Florian A1 - Weinzierl, Stefan A1 - Lemke, Mathias T1 - Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach JF - Acoustical Society of America N2 - An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774–1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1121/10.0002425 VL - 148 IS - 5 SP - 3075 EP - 3085 PB - The Journal of the Acoustical Society of America ER - TY - CHAP A1 - Lemke, Mathias A1 - Stein, Lewin T1 - Adjoint-Based Identification of Sound Sources for Sound Reinforcement and Source Localization T2 - Notes on Numerical Fluid Mechanics and Multidisciplinary Design N2 - The identification of sound sources is a common problem in acoustics. Different parameters are sought, among these are signal and position of the sources. We present an adjoint-based approach for sound source identification, which employs computational aeroacoustic techniques. Two different applications are presented as a proof-of-concept: optimization of a sound reinforcement setup and the localization of (moving) sound sources. Y1 - 2020 SN - 978-3-030-52429-6 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-52429-6_17 VL - 145 SP - 263 EP - 278 PB - Springer, Cham ER - TY - GEN A1 - Lemke, Mathias A1 - Stein, Lewin A1 - Hölter, Arne A1 - Straube, Florian A1 - Weinzierl, Stefan ED - Peissig, Jürgen T1 - Synthese komplexer Richtcharakteristiken für eine Schallfeldoptimierung im Zeitbereich N2 - Die Bestimmung optimaler Treiberfunktionen von Lautsprechern in beliebiger Anordnung ist ein schlecht gestelltes Optimierungsproblem, da die Anzahl der Quellen immer erheblich kleiner als die Anzahl der Empfänger ist. Typischerweise werden frequenz-basierte Löser eingesetzt. In einem vorangegangenen Beitrag haben die Autoren einen Adjungierten-basierten Ansatz vorgestellt, um optimale Treiberfunktionen im Zeitbereich zu bestimmen. Die Methode erlaubt es, inhomogene Windprofile und Temperaturschichtungen einzubeziehen, die typischerweise bei auf der Wellengleichung beruhenden Lösungen nicht berücksichtigt werden. Daru ̈ber hinaus können komplexe Geometrien und Randbedingungen berücksichtigt werden. Bisher war diese Methode auf Monopolquellen beschränkt. Hier stellen die Autoren eine Erweiterung des Ansatzes in Bezug auf eine Adjungierten-basierte Monopolsynthese vor, die es ermöglicht, auch Quellen mit komplexen Richtcharakteristiken zu betrachten. Das Verfahren wird für typische Quellsignale und ein repräsentatives Lautsprechermodell mit komplexer Richtcharakteristik validiert. Y1 - 2020 SN - 978-3939296171 U6 - https://doi.org/https://doi.org/10.14279/depositonce-9997 PB - Deutsche Gesellschaft für Akustik e.V. ER - TY - JOUR A1 - Montefusco, Alberto A1 - Peletier, Mark A. A1 - Öttinger, Hans Christian T1 - A Framework of Nonequilibrium Statistical Mechanics. II. Coarse-Graining JF - Journal of Non-Equilibrium Thermodynamics N2 - For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green–Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green–Kubo-like scheme. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0069 VL - 46 IS - 1 SP - 15 EP - 33 PB - De Gruyter ER - TY - JOUR A1 - Öttinger, Hans Christian A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations JF - Journal of Non-Equilibrium Thermodynamics N2 - Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green–Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0068 VL - 46 IS - 1 SP - 1 EP - 13 PB - De Gruyter ER - TY - THES A1 - Eshtewy, Neveen Ali Salem T1 - Mathematical Modeling of Metabolic-Genetic Networks Y1 - 2020 ER - TY - THES A1 - Venkatareddy, Narendra Lagumaddepalli T1 - Revealing secrets of mussel-glue mimetic peptides - From advanced NMR to computational process modelling Y1 - 2020 ER - TY - JOUR A1 - Sechi, Renata A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Estimation of the Koopman Generator by Newton's Extrapolation JF - Multiscale Modeling and Simulation N2 - This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods. Y1 - 2020 U6 - https://doi.org/10.1137/20M1333006 VL - 19 IS - 2 SP - 758 EP - 774 PB - SIAM ER - TY - JOUR A1 - Sikorski, Alexander A1 - Weber, Marcus A1 - Schütte, Christof T1 - The Augmented Jump Chain JF - Advanced Theory and Simulations N2 - Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated. Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000274 VL - 4 IS - 4 PB - Wiley-VCH ER - TY - BOOK A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Numerische Mathematik 3. Adaptive Lösung partieller Differentialgleichungen Y1 - 2020 SN - 978-3-11-069168-9 U6 - https://doi.org/10.1515/9783110689655 PB - de Gruyter ET - 2 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Sperber, Wolfram A1 - Chrapary, Hagen T1 - swMATH: A Publication-based Approach to Mathematical Software JF - SIAM Newsletter N2 - The growing importance of mathematical software in everyday life—in applications such as internet communication, traffic, and artificial intelligence—necessitates advances in software documentation services to raise awareness of existing packages and their usage. Such information helps potential software developers and users make informed choices about packages that could advance their work in modeling, simulation, and analysis. At the same time, software presents novel challenges to information services that require the development of new methods and means of processing. swMATH provides users with an overview of a broad range of mathematical software and extends documentation services for publications related to such software. It acts as a counterpart to the established abstracting and reviewing services for mathematical publications and has nearly 30,000 entries, making it one of the most comprehensive documentation services in mathematics. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80099 VL - Volume 53 IS - Number 06 | July/August 2020 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Lenz, Ralf A1 - Gotzes, Uwe A1 - Heinecke, Nina A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - Optimal Operation of Transient Gas Transport Networks JF - Optimization and Engineering N2 - In this paper, we describe an algorithmic framework for the optimal operation of transient gas transport networks consisting of a hierarchical MILP formulation together with a sequential linear programming inspired post-processing routine. Its implementation is part of the KOMPASS decision support system, which is currently used in an industrial setting. Real-world gas transport networks are controlled by operating complex pipeline intersection areas, which comprise multiple compressor units, regulators, and valves. In the following, we introduce the concept of network stations to model them. Thereby, we represent the technical capabilities of a station by hand-tailored artificial arcs and add them to network. Furthermore, we choose from a predefined set of flow directions for each network station and time step, which determines where the gas enters and leaves the station. Additionally, we have to select a supported simple state, which consists of two subsets of artificial arcs: Arcs that must and arcs that cannot be used. The goal is to determine a stable control of the network satisfying all supplies and demands. The pipeline intersections, that are represented by the network stations, were initially built centuries ago. Subsequently, due to updates, changes, and extensions, they evolved into highly complex and involved topologies. To extract their basic properties and to model them using computer-readable and optimizable descriptions took several years of effort. To support the dispatchers in controlling the network, we need to compute a continuously updated list of recommended measures. Our motivation for the model presented here is to make fast decisions on important transient global control parameters, i.e., how to route the flow and where to compress the gas. Detailed continuous and discrete technical control measures realizing them, which take all hardware details into account, are determined in a subsequent step. In this paper, we present computational results from the KOMPASS project using detailed real-world data. Y1 - 2020 U6 - https://doi.org/10.1007/s11081-020-09584-x VL - 22 SP - 735 EP - 781 ER - TY - JOUR A1 - Prause, Felix A1 - Hoppmann-Baum, Kai A1 - Defourny, Boris A1 - Koch, Thorsten T1 - The maximum diversity assortment selection problem JF - Mathematical Methods of Operations Research N2 - In this article, we introduce the Maximum Diversity Assortment Selection Problem (MDASP), which is a generalization of the two-dimensional Knapsack Problem (2D-KP). Given a set of rectangles and a rectangular container, the goal of 2D-KP is to determine a subset of rectangles that can be placed in the container without overlapping, i.e., a feasible assortment, such that a maximum area is covered. MDASP is to determine a set of feasible assortments, each of them covering a certain minimum threshold of the container, such that the diversity among them is maximized. Thereby, diversity is defined as the minimum or average normalized Hamming distance of all assortment pairs. MDASP was the topic of the 11th AIMMS-MOPTA Competition in 2019. The methods described in this article and the resulting computational results won the contest. In the following, we give a definition of the problem, introduce a mathematical model and solution approaches, determine upper bounds on the diversity, and conclude with computational experiments conducted on test instances derived from the 2D-KP literature. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s00186-021-00740-2 VL - 93 SP - 521 EP - 554 PB - Mathematical Methods of Operations Research ER - TY - CHAP A1 - Hoppmann-Baum, Kai A1 - Mexi, Gioni A1 - Burdakov, Oleg A1 - Casselgren, Carl Johan A1 - Koch, Thorsten ED - Hebrard, Emmanuel ED - Musliu, Nysret T1 - Minimum Cycle Partition with Length Requirements T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research N2 - In this article we introduce a Minimum Cycle Partition Problem with Length Requirements (CPLR). This generalization of the Travelling Salesman Problem (TSP) originates from routing Unmanned Aerial Vehicles (UAVs). Apart from nonnegative edge weights, CPLR has an individual critical weight value associated with each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is regarded as a feasible solution if the length of each cycle, which is the sum of the weights of its edges, is not greater than the critical weight of each of its vertices. The goal is to find a feasible partition, which minimizes the number of cycles. In this article, a heuristic algorithm is presented together with a Mixed Integer Programming (MIP) formulation of CPLR. We furthermore introduce a conflict graph, whose cliques yield valid constraints for the MIP model. Finally, we report on computational experiments conducted on TSPLIB-based test instances. Y1 - 2020 SN - 978-3-030-58941-7 U6 - https://doi.org/10.1007/978-3-030-58942-4_18 VL - 12296 SP - 273 EP - 282 PB - Springer International Publishing CY - Cham ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Implications, conflicts, and reductions for Steiner trees T3 - ZIB-Report - 20-28 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80039 SN - 1438-0064 ER - TY - GEN A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs N2 - The generation of strong linear inequalities for QCQPs has been recently tackled by a number of authors using the intersection cut paradigm - a highly studied tool in integer programming whose flexibility has triggered these renewed efforts in non-linear settings. In this work, we consider intersection cuts using the recently proposed construction of maximal quadratic-free sets. Using these sets, we derive closed-form formulas to compute intersection cuts which allow for quick cut-computations by simply plugging-in parameters associated to an arbitrary quadratic inequality being violated by a vertex of an LP relaxation. Additionally, we implement a cut-strengthening procedure that dates back to Glover and evaluate these techniques with extensive computational experiments. KW - Intersection cuts KW - QCQPs KW - Quadratic-free sets Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79994 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Fackeldey, Konstantin A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method JF - Supercomputing Frontiers and Innovations N2 - Structure-based virtual screening approaches have the ability to dramatically reduce the time and costs associated to the discovery of new drug candidates. Studies have shown that the true hit rate of virtual screenings improves with the scale of the screened ligand libraries. Therefore, we have recently developed an open source drug discovery platform (VirtualFlow), which is able to routinely carry out ultra-large virtual screenings. One of the primary challenges of molecular docking is the circumstance when the protein is highly dynamic or when the structure of the protein cannot be captured by a static pose. To accommodate protein dynamics, we report the extension of VirtualFlow to allow the docking of ligands using a grey wolf optimization algorithm using the docking program GWOVina, which substantially improves the quality and efficiency of flexible receptor docking compared to AutoDock Vina. We demonstrate the linear scaling behavior of VirtualFlow utilizing GWOVina up to 128 000 CPUs. The newly supported docking method will be valuable for drug discovery projects in which protein dynamics and flexibility play a significant role. Y1 - 2020 U6 - https://doi.org/10.14529/jsfi200301 VL - 7 IS - 3 SP - 4 EP - 12 ER - TY - JOUR A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - On the abs-polynomial expansion of piecewise smooth functions JF - Optimization Methods and Software N2 - Tom Streubel has observed that for functions in abs-normal form, generalized Taylor expansions of arbitrary order $\bar d-1$ can be generated by algorithmic piecewise differentiation. Abs-normal form means that the real or vector valued function is defined by an evaluation procedure that involves the absolute value function $|...|$ apart from arithmetic operations and $\bar d$ times continuously differentiable univariate intrinsic functions. The additive terms in Streubel's expansion are abs-polynomial, i.e. involve neither divisions nor intrinsics. When and where no absolute values occur, Moore's recurrences can be used to propagate univariate Taylor polynomials through the evaluation procedure with a computational effort of $\mathcal O({\bar d}^2)$, provided all univariate intrinsics are defined as solutions of linear ODEs. This regularity assumption holds for all standard intrinsics, but for irregular elementaries one has to resort to Faa di Bruno's formula, which has exponential complexity in $\bar d$. As already conjectured we show that the Moore recurrences can be adapted for regular intrinsics to the abs-normal case. Finally, we observe that where the intrinsics are real analytic the expansions can be extended to infinite series that converge absolutely on spherical domains. Y1 - 2020 U6 - https://doi.org/10.1080/10556788.2020.1817448 PB - Taylor & Francis ER - TY - JOUR A1 - Martens, Kevin A1 - Binkowski, Felix A1 - Nguyen, Linh A1 - Hu, Li A1 - Govorov, Alexander O. A1 - Burger, Sven A1 - Liedl, Tim T1 - Long- and Short-Ranged Chiral Interactions in DNA Assembled Plasmonic Chains JF - Nat. Commun. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-22289-8 VL - 12 SP - 2025 ER - TY - GEN A1 - Musiał, Anna A1 - Żołnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wojcik, Grzegorz A1 - Mergo, Paweł A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Lauritsen, Kristian A1 - Bülter, Andreas A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Rodt, Sven A1 - Urbanczyk, Wacław A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Front Cover: Plug&Play Fiber‐Coupled 73 kHz Single‐Photon Source Operating in the Telecom O‐Band (Adv. Quantum Technol. 6/2020) T2 - Adv. Quantum Technol. Y1 - 2020 U6 - https://doi.org/10.1002/qute.202070061 VL - 3 SP - 2070061 ER - TY - JOUR A1 - Sharma, Upanshu A1 - Zhang, Wei T1 - Non-reversible sampling schemes on submanifolds JF - SIAM Journal on Numerical Analysis N2 - Calculating averages with respect to probability measures on submanifolds is often necessary in various application areas such as molecular dynamics, computational statistical mechanics and Bayesian statistics. In recent years, various numerical schemes have been proposed in the literature to study this problem based on appropriate reversible constrained stochastic dynamics. In this paper we present and analyse a non-reversible generalisation of the projection-based scheme developed by one of the authors [ESAIM: M2AN, 54 (2020), pp. 391-430]. This scheme consists of two steps - starting from a state on the submanifold, we first update the state using a non-reversible stochastic differential equation which takes the state away from the submanifold, and in the second step we project the state back onto the manifold using the long-time limit of a ordinary differential equation. We prove the consistency of this numerical scheme and provide quantitative error estimates for estimators based on finite-time running averages. Furthermore, we present theoretical analysis which shows that this scheme outperforms its reversible counterpart in terms of asymptotic variance. We demonstrate our findings on an illustrative test example. Y1 - 2020 U6 - https://doi.org/10.1137/20M1378752 VL - 59 IS - 6 SP - 2989 EP - 3031 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian T1 - Towards Log-Less, Fine-Granular State Machine Replication JF - Datenbank Spektrum Y1 - 2020 U6 - https://doi.org/10.1007/s13222-020-00358-4 VL - 20 IS - 3 SP - 231 EP - 241 ER - TY - GEN A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Zittel, Janina A1 - Gotzes, Uwe A1 - Spreckelsen, Eva-Maria A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - From Natural Gas towards Hydrogen - A Feasibility Study on Current Transport Network Infrastructure and its Technical Control N2 - This study examines the usability of a real-world, large-scale natural gas transport infrastructure for hydrogen transport. We investigate whether a converted network can transport the amounts of hydrogen necessary to satisfy current energy demands. After introducing an optimization model for the robust transient control of hydrogen networks, we conduct computational experiments based on real-world demand scenarios. Using a representative network, we demonstrate that replacing each turbo compressor unit by four parallel hydrogen compressors, each of them comprising multiple serial compression stages, and imposing stricter rules regarding the balancing of in- and outflow suffices to realize transport in a majority of scenarios. However, due to the reduced linepack there is an increased need for technical and non-technical measures leading to a more dynamic network control. Furthermore, the amount of energy needed for compression increases by 364% on average. T3 - ZIB-Report - 20-27 KW - Hydrogen Transport KW - Hydrogen Infrastructure KW - Network Flows KW - Mixed Integer Programming KW - Energiewende Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79901 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Herter, Felix A1 - Lepper, Verena T1 - Jerash Silver Scroll: Virtually Unfolded Volume T2 - figshare N2 - A new virtual unfolding technique was applied to a silver scroll excavated in Jerash, Jordan, in 2014. As result of the unfolding, 17 lines of writing are clearly visible in the unfolded volumetric data that is published here. Y1 - 2020 U6 - https://doi.org/10.6084/m9.figshare.12145236 ER - TY - THES A1 - Löbel, Fabian T1 - Implementing the Network Simplex for Hypergraphs N2 - The well-known network simplex algorithm is a powerful tool to solve flow problems on graphs. Based on a recent dissertation by Isabel Beckenbach, we develop the necessary theory to extend the network simplex to capacitated flow problems on hypergraphs and implement this new variant. We then attempt to solve instances arising from real-life vehicle rotation planning problems. Y1 - 2020 ER - TY - THES A1 - Löbel, Fabian T1 - Solving Integrated Timetabling and Passenger Routing Problems Using the Modulo Network Simplex Algorithm N2 - Common models and solving approaches for the problem of periodic timetabling, that is, determining periodic arrival and departure times of a given public transportation network’s lines so that the total weighted travel time of all passengers is minimized, fail to take passenger behavior into account. Current research is attempting to resolve this issue and first results show a positive impact on solution quality. This thesis aims to give a brief overview of literature on the topic of timetabling and to then state a heuristic approach to Integrated Timetabling by blending passenger behavior into the Modulo Network Simplex algorithm, which is part of the research carried out by the author’s study group at the Zuse Institut Berlin in the framework of MATHEON’s research project MI-3 supported by the Einstein Foundation Berlin. Y1 - 2017 ER - TY - JOUR A1 - Soares, Ana Prates A1 - Baum, Daniel A1 - Hesse, Bernhard A1 - Kupsch, Andreas A1 - Müller, Bernd A1 - Zaslansky, Paul T1 - Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming JF - Dental Materials Y1 - 2020 U6 - https://doi.org/10.1016/j.dental.2020.10.018 VL - 37 IS - 2 SP - 201 EP - 211 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Oster, Mathias A1 - Sallandt, Leon A1 - Schneider, Reinhold T1 - Approximative Policy Iteration for Exit Time Feedback Control Problems driven by Stochastic Differential Equations using Tensor Train format JF - SIAM Journal on Multiscale Modeling and Simulation N2 - We consider a stochastic optimal exit time feedback control problem. The Bellman equation is solved approximatively via the Policy Iteration algorithm on a polynomial ansatz space by a sequence of linear equations. As high degree multi-polynomials are needed, the corresponding equations suffer from the curse of dimensionality even in moderate dimensions. We employ tensor-train methods to account for this problem. The approximation process within the Policy Iteration is done via a Least-Squares ansatz and the integration is done via Monte-Carlo methods. Numerical evidences are given for the (multi dimensional) double well potential and a three-hole potential. Y1 - 2022 U6 - https://doi.org/10.1137/20M1372500 VL - 20 IS - 1 SP - 379 EP - 403 ER - TY - JOUR A1 - Pimentel, Pedro A1 - Szengel, Angelika A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Estacio, Laura A1 - Doenitz, Christian A1 - Ramm, Heiko ED - Li, Jianning ED - Egger, Jan T1 - Automated Virtual Reconstruction of Large Skull Defects using Statistical Shape Models and Generative Adversarial Networks BT - First Challenge, AutoImplant 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings JF - Towards the Automatization of Cranial Implant Design in Cranioplasty N2 - We present an automated method for extrapolating missing regions in label data of the skull in an anatomically plausible manner. The ultimate goal is to design patient-speci� c cranial implants for correcting large, arbitrarily shaped defects of the skull that can, for example, result from trauma of the head. Our approach utilizes a 3D statistical shape model (SSM) of the skull and a 2D generative adversarial network (GAN) that is trained in an unsupervised fashion from samples of healthy patients alone. By � tting the SSM to given input labels containing the skull defect, a First approximation of the healthy state of the patient is obtained. The GAN is then applied to further correct and smooth the output of the SSM in an anatomically plausible manner. Finally, the defect region is extracted using morphological operations and subtraction between the extrapolated healthy state of the patient and the defective input labels. The method is trained and evaluated based on data from the MICCAI 2020 AutoImplant challenge. It produces state-of-the art results on regularly shaped cut-outs that were present in the training and testing data of the challenge. Furthermore, due to unsupervised nature of the approach, the method generalizes well to previously unseen defects of varying shapes that were only present in the hidden test dataset. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-64327-0_3 N1 - Best Paper Award VL - 12439 SP - 16 EP - 27 PB - Springer International Publishing ET - 1 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Non-gravitational force model vs observation: the trajectory and rotation-axis of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - The determination of non-gravitational forces based on precise astrometry is one of the main tools to establish the cometary character of interstellar and solar-system objects. The Rosetta mission to comet 67P/C-G provided the unique opportunity to benchmark Earth-bound estimates of non-gravitational forces with in-situ data. We determine the accuracy of the standard Marsden and Sekanina parametrization of non-gravitational forces with respect to the observed dynamics. Additionally we analyse the rotation-axis changes (orientation and period) of 67P/C-G. This comparison provides a reference case for future cometary missions and sublimation models for non-gravitational forces. Y1 - 2020 U6 - https://doi.org/10.5194/epsc2020-403 VL - 14 SP - EPSC2020-403 PB - Europlanet Science Congress ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Gas production for 14 species on comet 67P/Churyumov-Gerasimenko from 2014-2016 T2 - Europlanet Science Congress N2 - During a two year period between 2014 and 2016 the coma of comet 67P/Churyumov-Gerasimenko (67P/C-G) has been probed by the Rosetta spacecraft. Density data for 14 gas species was recorded with the COmet Pressure Sensor (COPS) and the Double Focusing Mass Spectrometer (DFMS) being two sensors of the ROSINA instrument. The combination with an inverse gas model yields emission rates on each of 3996 surface elements of a surface shape for the cometary nucleus. The temporal evolution of gas production, of relative abundances, and peak productions weeks after perihelion are investigated. Solar irradiation and gas production are in a complex relation revealing features differing for gas species, for mission time, and for the hemispheres of the comet. This characterization of gas composition allows one to correlate 67P/C-G to other solar and interstellar comets, their formation conditions and nucleus properties, see [Bodewits D., et al., 2020 Nature Astronomy]. Y1 - 2020 U6 - https://doi.org/10.5194/epsc2020-319 VL - 14 SP - EPSC2020-319 PB - Europlanet Science Congress ER - TY - CHAP A1 - Christgau, Steffen A1 - Steinke, Thomas T1 - Leveraging a Heterogeneous Memory System for a Legacy Fortran Code: The Interplay of Storage Class Memory, DRAM and OS T2 - 2020 IEEE/ACM Workshop on Memory Centric High Performance Computing (MCHPC) N2 - Large capacity Storage Class Memory (SCM) opens new possibilities for workloads requiring a large memory footprint. We examine optimization strategies for a legacy Fortran application on systems with an heterogeneous memory configuration comprising SCM and DRAM. We present a performance study for the multigrid solver component of the large-eddy simulation framework PALM for different memory configurations with large capacity SCM. An important optimization approach is the explicit assignment of storage locations depending on the data access characteristic to take advantage of the heterogeneous memory configuration. We are able to demonstrate that an explicit control over memory locations provides better performance compared to transparent hardware settings. As on aforementioned systems the page management by the OS appears as critical performance factor, we study the impact of different huge page settings. Y1 - 2020 SN - 978-0-7381-1067-7 U6 - https://doi.org/10.1109/MCHPC51950.2020.00008 SP - 17 EP - 24 PB - IEEE ER - TY - JOUR A1 - Fischer, Sophie A1 - Ehrig, Rainald A1 - Schäfer, Stefan A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Egli, Marcel A1 - Ille, Fabian A1 - Krüger, Tillmann H. C. A1 - Leeners, Brigitte A1 - Röblitz, Susanna T1 - Mathematical Modelling and Simulation Provides Evidence for New Strategies of Ovarian Stimulation JF - Frontiers in Endocrinology N2 - New approaches to ovarian stimulation protocols, such as luteal start, random start or double stimulation, allow for flexibility in ovarian stimulation at different phases of the menstrual cycle which is especially useful when time for assisted reproductive technology is limited, e.g. for emergency fertility preservation in cancer patients. It has been proposed that the success of these methods is based on the continuous growth of multiple cohorts ("waves") of follicles throughout the menstrual cycle which leads to the availability of ovarian follicles for ovarian controlled stimulation at several time points. Though several preliminary studies have been published, their scientific evidence has not been considered as being strong enough to integrate these results into routine clinical practice. This work aims at adding further scientific evidence about the efficiency of variable-start protocols and underpinning the theory of follicular waves by using mathematical modelling and numerical simulations. For this purpose, we have modified and coupled two previously published models, one describing the time course of hormones and one describing competitive follicular growth in a normal menstrual cycle. The coupled model is used to test stimulation protocols in silico. Simulation results show the occurrence of follicles in a wave-like manner during a normal menstrual cycle and qualitatively predict the outcome of ovarian stimulation initiated at different time points of the menstrual cycle. Y1 - 2021 U6 - https://doi.org/10.3389/fendo.2021.613048 VL - 12 ER - TY - GEN A1 - Yueksel-Erguen, Inci A1 - Zittel, Janina A1 - Wang, Ying A1 - Hennings, Felix A1 - Koch, Thorsten T1 - Lessons learned from gas network data preprocessing N2 - The German high-pressure natural gas transport network consists of thousands of interconnected elements spread over more than 120,000 km of pipelines built during the last 100 years. During the last decade, we have spent many person-years to extract consistent data out of the available sources, both public and private. Based on two case studies, we present some of the challenges we encountered. Preparing consistent, high-quality data is surprisingly hard, and the effort necessary can hardly be overestimated. Thus, it is particularly important to decide which strategy regarding data curation to adopt. Which precision of the data is necessary? When is it more efficient to work with data that is just sufficiently correct on average? In the case studies we describe our experiences and the strategies we adopted to deal with the obstacles and to minimize future effort. Finally, we would like to emphasize that well-compiled data sets, publicly available for research purposes, provide the grounds for building innovative algorithmic solutions to the challenges of the future. T3 - ZIB-Report - 20-13 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78262 SN - 1438-0064 ER - TY - GEN A1 - Maristany de las Casas, Pedro A1 - Sedeno-Noda, Antonio A1 - Borndörfer, Ralf T1 - An Improved Multiobjective Shortest Path Algorithm N2 - We present a new label-setting algorithm for the Multiobjective Shortest Path (MOSP) problem that computes the minimal complete set of efficient paths for a given instance. The size of the priority queue used in the algorithm is bounded by the number of nodes in the input graph and extracted labels are guaranteed to be efficient. These properties allow us to give a tight output-sensitive running time bound for the new algorithm that can almost be expressed in terms of the running time of Dijkstra's algorithm for the Shortest Path problem. Hence, we suggest to call the algorithm \emph{Multiobjective Dijkstra Algorithm} (MDA). The simplified label management in the MDA allows us to parallelize some subroutines. In our computational experiments, we compare the MDA and the classical label-setting MOSP algorithm by Martins', which we improved using new data structures and pruning techniques. On average, the MDA is $\times2$ to $\times9$ times faster on all used graph types. On some instances the speedup reaches an order of magnitude. T3 - ZIB-Report - 20-26 KW - Multiobjective Shortest Path Problem KW - Output-Sensitive Multiobjective Combinatorial Problems KW - Network Optimization Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79712 SN - 1438-0064 ER - TY - JOUR A1 - Miron, Philippe A1 - Beron-Vera, Francisco A1 - Helfmann, Luzie A1 - Koltai, Péter T1 - Transition paths of marine debris and the stability of the garbage patches JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - We used transition path theory (TPT) to infer "reactive" pathways of floating marine debris trajectories. The TPT analysis was applied on a pollution-aware time-homogeneous Markov chain model constructed from trajectories produced by satellite-tracked undrogued buoys from the NOAA Global Drifter Program. The latter involved coping with the openness of the system in physical space, which further required an adaptation of the standard TPT setting. Directly connecting pollution sources along coastlines with garbage patches of varied strengths, the unveiled reactive pollution routes represent alternative targets for ocean cleanup efforts. Among our specific findings we highlight: constraining a highly probable pollution source for the Great Pacific Garbage Patch; characterizing the weakness of the Indian Ocean gyre as a trap for plastic waste; and unveiling a tendency of the subtropical gyres to export garbage toward the coastlines rather than to other gyres in the event of anomalously intense winds. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1063/5.0030535 VL - 31 IS - 3 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sprungk, Björn A1 - Sullivan, T. J. T1 - The linear conditional expectation in Hilbert space JF - Bernoulli Y1 - 2021 U6 - https://doi.org/10.3150/20-BEJ1308 VL - 27 IS - 4 SP - 2299 EP - 2299 ER - TY - GEN A1 - Sunkara, Vikram A1 - Raharinirina, N. Alexia A1 - Peppert, Felix A1 - von Kleist, Max A1 - Schütte, Christof T1 - Inferring Gene Regulatory Networks from Single Cell RNA-seq Temporal Snapshot Data Requires Higher Order Moments N2 - Due to the increase in accessibility and robustness of sequencing technology, single cell RNA-seq (scRNA-seq) data has become abundant. The technology has made significant contributions to discovering novel phenotypes and heterogeneities of cells. Recently, there has been a push for using single-- or multiple scRNA-seq snapshots to infer the underlying gene regulatory networks (GRNs) steering the cells' biological functions. To date, this aspiration remains unrealised. In this paper, we took a bottom-up approach and curated a stochastic two gene interaction model capturing the dynamics of a complete system of genes, mRNAs, and proteins. In the model, the regulation was placed upstream from the mRNA on the gene level. We then inferred the underlying regulatory interactions from only the observation of the mRNA population through~time. We could detect signatures of the regulation by combining information of the mean, covariance, and the skewness of the mRNA counts through time. We also saw that reordering the observations using pseudo-time did not conserve the covariance and skewness of the true time course. The underlying GRN could be captured consistently when we fitted the moments up to degree three; however, this required a computationally expensive non-linear least squares minimisation solver. There are still major numerical challenges to overcome for inference of GRNs from scRNA-seq data. These challenges entail finding informative summary statistics of the data which capture the critical regulatory information. Furthermore, the statistics have to evolve linearly or piece-wise linearly through time to achieve computational feasibility and scalability. T3 - ZIB-Report - 20-25 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79664 SN - 1438-0064 ER - TY - JOUR A1 - Weber, Marcus A1 - Weitere Autoren, ED - Reichardt, Christine T1 - DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten JF - Beuth Verlag N2 - Dieses Dokument legt Parameter und Formate für die Übertragung sprachbasierter Daten zwischen verschiedenen KI-Ökosystemen fest. Y1 - 2020 ER - TY - JOUR A1 - Rabben, Robert Julian A1 - Ray, Sourav A1 - Weber, Marcus T1 - ISOKANN: Invariant subspaces of Koopman operators learned by a neural network JF - The Journal of Chemical Physics N2 - The problem of determining the rate of rare events in dynamical systems is quite well-known but still difficult to solve. Recent attempts to overcome this problem exploit the fact that dynamic systems can be represented by a linear operator, such as the Koopman operator. Mathematically, the rare event problem comes down to the difficulty in finding invariant subspaces of these Koopman operators K. In this article, we describe a method to learn basis functions of invariant subspaces using an artificial neural Network. Y1 - 2020 U6 - https://doi.org/10.1063/5.0015132 VL - 153 IS - 11 SP - 114109 ER - TY - JOUR A1 - Villatoro, José A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Weber, Marcus A1 - Löhmannsröben, Hans-Gerd T1 - Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities JF - Analytical and Bioanalytical Chemistry N2 - A new ion mobility (IM) spectrometer, enabling mobility measurements in the pressure range between 5 and 500 mbar and in the reduced field strength range E/N of 5–90 Td, was developed and characterized. Reduced mobility (K0) values were studied under low E/N (constant value) as well as high E/N (deviation from low field K0) for a series of molecular ions in nitrogen. Infrared matrix-assisted laser desorption ionization (IR-MALDI) was used in two configurations: a source working at atmospheric pressure (AP) and, for the first time, an IR-MALDI source working with a liquid (aqueous) matrix at sub-ambient/reduced pressure (RP). The influence of RP on IR-MALDI was examined and new insights into the dispersion process were gained. This enabled the optimization of the IM spectrometer for best analytical performance. While ion desolvation is less efficient at RP, the transport of ions is more efficient, leading to intensity enhancement and an increased number of oligomer ions. When deciding between AP and RP IR-MALDI, a trade-off between intensity and resolving power has to be considered. Here, the low field mobility of peptide ions was first measured and compared with reference values from ESI-IM spectrometry (at AP) as well as collision cross sections obtained from molecular dynamics simulations. The second application was the determination of the reduced mobility of various substituted ammonium ions as a function of E/N in nitrogen. The mobility is constant up to a threshold at high E/N. Beyond this threshold, mobility increases were observed. This behavior can be explained by the loss of hydrated water molecules. Y1 - 2020 U6 - https://doi.org/10.1007/s00216-020-02735-0 VL - 412 SP - 5247 EP - 5260 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Sirbu, Alexei A1 - Stelzer, Nina A1 - Lohse, Martin J. A1 - Schütte, Christof A1 - Annibale, Paolo T1 - Quantitative spectroscopy of single molecule interaction times JF - Optic Letters N2 - Single molecule fluorescence tracking provides information at nanometer-scale and millisecond-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can be characterized well, the quantitative insight is more limited when interactions between two indistinguishable molecules occur. We address this aspect by developing a theoretical foundation for a spectroscopy of interaction times, i.e., the inference of interaction from imaging data. A non-trivial crossover between a power law to an exponential behavior of the distribution of the interaction times is highlighted, together with the dependence of the exponential term upon the microscopic reaction affinity. Our approach is validated with simulated and experimental datasets. Y1 - 2021 U6 - https://doi.org/10.1364/OL.413030 VL - 46 IS - 7 SP - 1538 EP - 1541 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Rockstuhl, Carsten A1 - Decker, Manuel T1 - Modeling Optical Materials at the Single Scatterer Level: The Transition from Homogeneous to Heterogeneous Materials JF - Adv. Theory Simul. Y1 - 2020 U6 - https://doi.org/10.1002/adts.202000192 VL - 3 SP - 2000192 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Schneider, Philipp-Immanuel T1 - Bayesian optimization with improved scalability and derivative information for efficient design of nanophotonic structures JF - J. Light. Technol. Y1 - 2021 U6 - https://doi.org/10.1109/JLT.2020.3023450 VL - 39 SP - 167 ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - bioRxiv N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. Y1 - 2020 U6 - https://doi.org/10.1101/2020.05.28.120899 ER - TY - THES A1 - Betz, Fridtjof T1 - Investigation and application of contour integral methods for resonance expansion in nanophotonics Y1 - 2020 ER - TY - CHAP A1 - Hartung, Marc A1 - Kaiser, Benjamin T1 - Crafted Benchmarks with Artificial Community Structure and Known Complexity T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 89 EP - 90 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Hartung, Marc T1 - PauSat T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 34 EP - 35 ER - TY - CHAP A1 - Hartung, Marc T1 - CTSat: C++ Template Abstractions for Dynamic Interchangeable SAT Solver Features T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 32 EP - 33 ER - TY - GEN A1 - Schwartz, Stephan T1 - An Overview of Graph Covering and Partitioning N2 - While graph covering is a fundamental and well-studied problem, this field lacks a broad and unified literature review. The holistic overview of graph covering given in this article attempts to close this gap. The focus lies on a characterization and classification of the different problems discussed in the literature. In addition, notable results and common approaches are also included. Whenever appropriate, our review extends to the corresponding partioning problems. T3 - ZIB-Report - 20-24 KW - Graph Covering KW - Graph Partitioning Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79431 SN - 1438-0064 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - The gas production of 14 species from comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data from 2014-2016 JF - Monthly Notices of the Royal Astronomical Society N2 - The coma of comet 67P/Churyumov-Gerasimenko has been probed by the Rosetta spacecraft and shows a variety of different molecules. The ROSINA COmet Pressure Sensor and the Double Focusing Mass Spectrometer provide in-situ densities for many volatile compounds including the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We fit the observed densities during the entire comet mission between August 2014 and September 2016 to an inverse coma model. We retrieve surface emissions on a cometary shape with 3996 triangular elements for 50 separated time intervals. For each gas we derive systematic error bounds and report the temporal evolution of the production, peak production, and the time-integrated total production. We discuss the production for the two lobes of the nucleus and for the northern and southern hemispheres. Moreover we provide a comparison of the gas production with the seasonal illumination. Y1 - 2020 U6 - https://doi.org/10.1093/mnras/staa2643 VL - 498 IS - 3 SP - 3995 EP - 4004 PB - Monthly Notices of the Royal Astronomical Society ER - TY - JOUR A1 - Ramin, Elham A1 - Bestuzheva, Ksenia A1 - Gargalo, Carina A1 - Ramin, Danial A1 - Schneider, Carina A1 - Ramin, Pedram A1 - Flores-Alsina, Xavier A1 - Andersen, Maj M. A1 - Gernaey, Krist V. T1 - Incremental design of water symbiosis networks with prior knowledge: The case of an industrial park in Kenya JF - Science of the Total Environment N2 - Industrial parks have a high potential for recycling and reusing resources such as water across companies by creating symbiosis networks. In this study, we introduce a mathematical optimization framework for the design of water network integration in industrial parks formulated as a large-scale standard mixed-integer non-linear programming (MINLP) problem. The novelty of our approach relies on i) developing a multi-level incremental optimization framework for water network synthesis, ii) including prior knowledge of demand growth and projected water scarcity to evaluate the significance of water-saving solutions, iii) incorporating a comprehensive formulation of water network synthesis problem including multiple pollutants and different treatment units and iv) performing a multi-objective optimization of the network including freshwater savings and relative cost of the network. The significance of the proposed optimization framework is illustrated by applying it to an existing industrial park in a water-scarce region in Kenya. Firstly, we illustrated the benefits of including prior knowledge to prevent an over-design of the network at the early stages. In the case study, we achieved a more flexible and expandable water network with 36% lower unit cost at the early stage and 15% lower unit cost at later stages for the overall maximum freshwater savings of 25%. Secondly, multi-objective analysis suggests an optimum freshwater savings of 14% to reduce the unit cost of network by half. Moreover, the significance of symbiosis networks is highlighted by showing that intra-company connections can only achieve a maximum freshwater savings of 17% with significantly higher unit cost (+45%). Finally, we showed that the values of symbiosis connectivity index in the Pareto front correspond to higher freshwater savings, indicating the significant role of the symbiosis network in the industrial park under study. This is the first study, where all the above elements have been taken into account simultaneously for the design of a water reuse network. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.scitotenv.2020.141706 VL - 751 ER - TY - JOUR A1 - Ray, Sourav A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Weber, Marcus T1 - How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs JF - Molecular Simulation N2 - Molecular simulations of ligand–receptor interactions are a computational challenge, especially when their association- (‘on’-rate) and dissociation- (‘off’-rate) mechanisms are working on vastly differing timescales. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenyl propionamide (NFEPP) in a μ-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab. Y1 - 2020 U6 - https://doi.org/10.1080/08927022.2020.1839660 VL - 46 IS - 18 SP - 1443 EP - 1452 PB - Taylor and Francis ER - TY - GEN A1 - Klimpel, Paul T1 - Kulturelles Erbe digital – eine kleine Rechtsfibel N2 - Kunst- und Kulturinstitutionen beschäftigen sich zunehmend mit der Digitalisierung ihrer Sammlungen, auch und gerade im Angesicht der Pandemie 2020. Dabei spielen nicht nur technische und organisatorische Fragen eine Rolle, vor allem rechtliche Aspekte führen oft zu Unsicherheit bei der digitalen Zugänglichmachung der Daten. Um diesen Unsicherheiten kompakt zu begegnen, gibt digiS die "Rechtsfibel" in Zusammenarbeit mit iRights und Paul Klimpel als Autor heraus. Darin werden unter anderem konkrete Fragen des Urheberrechts zu verschiedenen Objektgattungen, Lizenzfragen, Persönlichkeitsrecht und Datenschutz, die Online-Präsentation von Digitalisaten und zur Archivierung behandelt. Die Handreichung soll Mitarbeiter*innen in Kultur(-erbe)einrichtungen ermutigen, sich mit den rechtlichen Fragen bei der Digitalisierung auseinanderzusetzen, indem sie die vielen Facetten dieses Bereichs verständlich darstellt. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78644 SN - 9783752987645 ER - TY - CHAP A1 - Colom, Rémi A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Quasi-normal mode expansion as a tool for the design of nanophotonic devices T2 - EPJ Web Conf. Y1 - 2020 U6 - https://doi.org/10.1051/epjconf/202023805008 VL - 238 SP - 05008 ER - TY - CHAP A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Rémi A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Modal expansion of optical far-field quantities using quasinormal modes T2 - EPJ Web Conf. Y1 - 2020 U6 - https://doi.org/10.1051/epjconf/202023805007 VL - 238 SP - 05007 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, Franz-Josef A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, Jürgen A1 - Weiser, Martin A1 - Wende, Florian T1 - HighPerMeshes - A Domain-Specific Language for Numerical Algorithms on Unstructured Grids JF - Euro-Par 2020: Parallel Processing Workshops. N2 - Solving partial differential equations on unstructured grids is a cornerstone of engineering and scientific computing. Nowadays, heterogeneous parallel platforms with CPUs, GPUs, and FPGAs enable energy-efficient and computationally demanding simulations. We developed the HighPerMeshes C++-embedded Domain-Specific Language (DSL) for bridging the abstraction gap between the mathematical and algorithmic formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different parallel programming and runtime models on the other hand. Thus, the HighPerMeshes DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HighPer-Meshes DSL, and demonstrate its usage with three examples, a Poisson and monodomain problem, respectively, solved by the continuous finite element method, and the discontinuous Galerkin method for Maxwell’s equation. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters is presented. Finally, the achievable performance and scalability are demonstrated for a typical example problem on a multi-core CPU cluster. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-71593-9_15 SP - 185 EP - 196 PB - Springer ER - TY - THES A1 - Schotte, Merlind T1 - Finite-Elemente-Techniken zur mechanischen Stabilitätsanalyse der Hyomandibula von Rochen N2 - Haie und Rochen sind die einzigen Wirbeltiere, die sich durch ein Knorpelskelett auszeichnen, das mit winzigen mineralisierten Elementen bedeckt ist, die sogenannten Tesserae. Obwohl dieser mineralisierte Knorpel seit hunderten von Millionen Jahren ein charakteristisches Merkmal dieser Tiere ist, ist der funktionelle Vorteil dieses Gewebestruktur bisher unklar geblieben. In dieser Masterarbeit wird diese Struktur mithilfe der Finite-Elemente-Methode(FEM) untersucht, wobei biologische Informationen zu den Muskeln und der geometrischen Gegebenheiten aus einem hochaufgelösten, kontrastgefärbten μCT-Scan einer Stechrochenhyomandibula verwendet werden. Für die Analyse werden Computer-Aided-Design(CAD)-Modelle und FE-Modelle konstruiert sowie vorhandene Methoden erweitert, um bei den Berechnungen die Charakteristika des biologischen Objektes bestmöglich zu berücksichtigen. Die Modelle bauen auf einer Segmentierung der Hyomandibula auf, wobei die mehreren tausend Tesserae in diesem Datensatz bereits voneinander isoliert sind. Für die Modellierung der Hyomandibula wird als erstes ein CAD-Modell konstruiert. Bei dieser Konstruktion wird eine Tesserae-Mittelfläche erstellt und im Anschluss nach innen und außen verschoben. Der nächste Schritt basiert auf dem Einbau von Zwischenwänden, die die Tesserae voneinander separieren. Auf Grundlage dieses Modells wird ein Tetraedergitter generiert, das die Basis für den zweiten Teil dieser Arbeit darstellt - die Berechnungen mit der FEM. Die wesentliche Aufgabe des zweiten Teils beinhaltet die Konstruktion eines FE-Modells, das in die lineare FEM einzuordnen ist. In dieses fließen die Randbedingungen und die Materialeigenschaften des Skelettelements ein. Mithilfe der FEM lassen sich die durch Krafteinwirkung auftretenden Verschiebungen und Spannungen der Hyomandibula ermitteln. Die Ergebnisse geben Rückschlüsse über das Verhalten des Materials, die Besonderheiten der Geometrie und damit über die Stabilität des Objektes. Der dritte Teil der Abschlussarbeit beschäftigt sich mit zusätzlichen Anpassungen und Änderungen der Modelle (CAD-Modell und FE-Modell), um diese Resultate mit dem Modell zu vergleichen, das der Biologie am nächsten kommt. Diese Anpassungen beinhalten das Variieren der Dicke der mineralisierten Schicht, die Konstellation des Materials und den Abstand zwischen den Tesserae. Die Ergebnisse zeigen, dass sowohl die Tesserae-Struktur als auch die zwischen den Tesserae liegenden Kollagenfasern vermutlich keinen Einfluss auf die Mechanik und dementsprechend die Stabilität haben. Jedoch lassen die unterschiedlichen Resultate im Fall verschieden gewählter Tesserae-Dicken annehmen, dass diese sehr wohl einen Einfluss besitzen. N2 - Sharks and rays are the only vertebrates characterized by a peculiar cartilage skeleton covered with minute mineralized tiles called tesserae. Although this tessellated cartilage has been a defining feature of this lineage for hundreds of millions of years, the functional advantage of this tissue design has remained obscure. In this Master’s thesis, the finite element method (FEM) is used to investigate the role of tiling in the skeleton, using biological information on the muscles and shape from a high-resolution, contrast-stained μCT-scan of a stingray hyomandibula. For this purpose, computer aided design (CAD) models and FE models are constructed and existing methods will be extended to take the best possible account of the characteristics of the biological object. The analysis builds from a segmentation of the hyomandibula, with the dataset’s several thousand tesserae pre-isolated from one another. For the modeling of the hyomandibula a CAD model is constructed. In this construction, a medial surface is created using the tesserae which is subsequently moved to the inside and outside. The next step is to integrate partition walls separating the tesserae elements. Based on this model, a tetrahedral grid is then generated, which is the content of the second part of this thesis, the calculation with the FEM. A finite element model is constructed including boundary conditions and material properties of the skeletal element to compute the results using the linear FEM theory. The FEM is used to determine the displacements and stresses resulting from biological forces acting on the hyomandibula. The results allow conclusions of the material behavior, geometric characteristics (tesselation) and therefore the object stability. Important contributions of this thesis are additional adjustments and changes to the models (CAD model and FE model) to make it more appropriate to study the biological data at hand. The tesserae thickness, the length of the collagenious fibres and the constellation of the material are the parameters, which are changed. In contrast to the tesserae thicknesses, the results suggest that both the arrangement of the tesserae and its interposed collagen fibers have no substantial influence on the mechanics. Y1 - 2018 ER - TY - JOUR A1 - Würth, Christian A1 - Manley, Phillip A1 - Voigt, Robert A1 - Ahiboz, Doguscan A1 - Becker, Christiane A1 - Resch-Genger, Ute T1 - Metasurface enhanced sensitized photon upconversion: towards highly efficient low power upconversion applications and nano-scale E-field sensors JF - Nano Lett. Y1 - 2020 U6 - https://doi.org/10.1021/acs.nanolett.0c02548 VL - 20 SP - 6682 ER - TY - JOUR A1 - Bonnet, Luc A1 - Akian, Jean-Luc A1 - Savin, Éric A1 - Sullivan, T. J. T1 - Adaptive reconstruction of imperfectly-observed monotone functions, with applications to uncertainty quantification JF - Algorithms N2 - Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design. Y1 - 2020 U6 - https://doi.org/10.3390/a13080196 VL - 13 IS - 8 SP - 196 ER - TY - THES A1 - Spenger, Jonas T1 - Using Blockchain for Tamper-Proof Broadcast Protocols N2 - We present the tamper-resistant broadcast abstraction of the Bitcoin blockchain, and show how it can be used to implement tamper-resistant replicated state machines. The tamper-resistant broadcast abstraction provides functionality to: broadcast, deliver, and verify messages. The tamper-resistant property ensures: 1) the probabilistic protection against byzantine behaviour, and 2) the probabilistic verifiability that no tampering has occurred. In this work, we study various tamper-resistant broadcast protocols for: different environmental models (public/permissioned, bounded/unbounded, byzantine fault tolerant (BFT)/non-BFT, native/non-native); as well as different properties, such as ordering guarantees (FIFO-order, causal-order, total-order), and delivery guarantees (validity, agreement, uniform). This way, we can match the protocol to the required environment model and consistency model of the replicated state machine. We implemented the tamper-resistant broadcast abstraction as a proof of concept. The results show that the implemented tamper-resistant broadcast protocols can compete on throughput and latency with other state-of-the-art broadcast technologies. Use cases, such as a tamper-resistant file system, supply chain tracking, and a timestamp server highlight the expressiveness of the abstraction. In conclusion, the tamper-resistant broadcast protocols provide a powerful interface, with clear semantics and tunable settings, enabling the design of tamper-resistant applications. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79165 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Das, Krishna M. Padmanabha A1 - Leigh, Kendra E A1 - Cespugli, Marco A1 - Fischer, Patrick D. A1 - Wang, Zi-Fu A1 - Tesseyre, Guilhem A1 - Pandita, Shreya A1 - Shnapir, Alex A1 - Calderaio, Anthony A1 - Hutcheson, Colin A1 - Gechev, Minko A1 - Rose, Alexander A1 - Lewis, Noam A1 - Yaffe, Erez A1 - Luxenburg, Roni A1 - Herce, Henry D. A1 - Durmaz, Vedat A1 - Halazonetis, Thanos D. A1 - Fackeldey, Konstantin A1 - Patten, Justin J. A1 - Chuprina, Alexander A1 - Dziuba, Igor A1 - Plekhova, Alla A1 - Moroz, Yurii A1 - Radchenko, Dmytro A1 - Tarkhanova, Olga A1 - Yavnyuk, Irina A1 - Gruber, Christian C. A1 - Yust, Ryan A1 - Payne, Dave A1 - Näär, Anders M. A1 - Namchuk, Mark N. A1 - Davey, Robert A. A1 - Wagner, Gerhard A1 - Kinney, Jamie A1 - Arthanari, Haribabu T1 - A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening JF - iScience N2 - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development. Y1 - 2021 U6 - https://doi.org/10.26434/chemrxiv.12682316 VL - 24 IS - 2 SP - 102021 PB - CellPress ER - TY - CHAP A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - Bi-invariant Two-Sample Tests in Lie Groups for Shape Analysis T2 - Shape in Medical Imaging N2 - We propose generalizations of the T²-statistics of Hotelling and the Bhattacharayya distance for data taking values in Lie groups. A key feature of the derived measures is that they are compatible with the group structure even for manifolds that do not admit any bi-invariant metric. This property, e.g., assures analysis that does not depend on the reference shape, thus, preventing bias due to arbitrary choices thereof. Furthermore, the generalizations agree with the common definitions for the special case of flat vector spaces guaranteeing consistency. Employing a permutation test setup, we further obtain nonparametric, two-sample testing procedures that themselves are bi-invariant and consistent. We validate our method in group tests revealing significant differences in hippocampal shape between individuals with mild cognitive impairment and normal controls. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-61056-2_4 SP - 44 EP - 54 PB - Springer International Publishing CY - Cham ER - TY - JOUR A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Colom, Rémi A1 - Kegelmann, Lukas A1 - Al-Ashouri, Amran A1 - Roß, Marcel A1 - Jäger, Klaus A1 - Unold, Thomas A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Improved Quantum Efficiency by Advanced Light Management in Nanotextured Solution-Processed Perovskite Solar Cells JF - ACS Photonics Y1 - 2020 U6 - https://doi.org/10.1021/acsphotonics.0c00935 VL - 7 SP - 2589 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Franz, Henriette A1 - Koch, Thorsten T1 - Optimal Connected Subgraphs: Formulations and Algorithms T3 - ZIB-Report - 20-23 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79094 SN - 1438-0064 ER - TY - BOOK A1 - Hadjidimitriou, Natalia Selini A1 - Frangioni, Antonio A1 - Lodi, Andrea A1 - Koch, Thorsten ED - Hadjidimitriou, Natalia Selini ED - Frangioni, Antonio ED - Lodi, Andrea ED - Koch, Thorsten T1 - Mathematical Optimization for Efficient and Robust Energy Networks Y1 - 2020 SN - 978-3-030-57441-3 U6 - https://doi.org/10.1007/978-3-030-57442-0 VL - 4 PB - Springer ER - TY - GEN A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Analyzing laparoscopic cholecystectomy with deep learning: automatic detection of surgical tools and phases T2 - 28th International Congress of the European Association for Endoscopic Surgery (EAES) N2 - Motivation: The ever-rising volume of patients, high maintenance cost of operating rooms and time consuming analysis of surgical skills are fundamental problems that hamper the practical training of the next generation of surgeons. The hospitals prefer to keep the surgeons busy in real operations over training young surgeons for obvious economic reasons. One fundamental need in surgical training is the reduction of the time needed by the senior surgeon to review the endoscopic procedures performed by the young surgeon while minimizing the subjective bias in evaluation. The unprecedented performance of deep learning ushers the new age of data-driven automatic analysis of surgical skills. Method: Deep learning is capable of efficiently analyzing thousands of hours of laparoscopic video footage to provide an objective assessment of surgical skills. However, the traditional end-to-end setting of deep learning (video in, skill assessment out) is not explainable. Our strategy is to utilize the surgical process modeling framework to divide the surgical process into understandable components. This provides the opportunity to employ deep learning for superior yet automatic detection and evaluation of several aspects of laparoscopic cholecystectomy such as surgical tool and phase detection. We employ ZIBNet for the detection of surgical tool presence. ZIBNet employs pre-processing based on tool usage imbalance, a transfer learned 50-layer residual network (ResNet-50) and temporal smoothing. To encode the temporal evolution of tool usage (over the entire video sequence) that relates to the surgical phases, Long Short Term Memory (LSTM) units are employed with long-term dependency. Dataset: We used CHOLEC 80 dataset that consists of 80 videos of laparoscopic cholecystectomy performed by 13 surgeons, divided equally for training and testing. In these videos, up to three different tools (among 7 types of tools) can be present in a frame. Results: The mean average precision of the detection of all tools is 93.5 ranging between 86.8 and 99.3, a significant improvement (p <0.01) over the previous state-of-the-art. We observed that less frequent tools like Scissors, Irrigator, Specimen Bag etc. are more related to phase transitions. The overall precision (recall) of the detection of all surgical phases is 79.6 (81.3). Conclusion: While this is not the end goal for surgical skill analysis, the development of such a technological platform is essential toward a data-driven objective understanding of surgical skills. In future, we plan to investigate surgeon-in-the-loop analysis and feedback for surgical skill analysis. Y1 - 2020 UR - https://academy.eaes.eu/eaes/2020/28th/298882/manish.sahu.analyzing.laparoscopic.cholecystectomy.with.deep.learning.html?f=listing%3D0%2Abrowseby%3D8%2Asortby%3D2 ER - TY - JOUR A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Surgical phase recognition by learning phase transitions JF - Current Directions in Biomedical Engineering (CDBME) N2 - Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/cdbme-2020-0037 N1 - Nomination for the Best-Paper Award VL - 6 IS - 1 SP - 20200037 PB - De Gruyter ER - TY - CHAP A1 - Sahu, Manish A1 - Strömsdörfer, Ronja A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III N2 - Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-59716-0_75 VL - 12263 PB - Springer Nature ER - TY - JOUR A1 - Röhl, Susanne A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the minimal rebinding effect for non-reversible processes JF - Multiscale Modeling and Simulation N2 - The aim of this paper is to investigate the rebinding effect, a phenomenon describing a "short-time memory" which can occur when projecting a Markov process onto a smaller state space. For guaranteeing a correct mapping by the Markov State Model, we assume a fuzzy clustering in terms of membership functions, assigning degrees of membership to each state. The macro states are represented by the membership functions and may be overlapping. The magnitude of this overlap is a measure for the strength of the rebinding effect, caused by the projection and stabilizing the system. A minimal bound for the rebinding effect included in a given system is computed as the solution of an optimization problem. Based on membership functions chosen as a linear combination of Schur vectors, this generalized approach includes reversible as well as non-reversible processes. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1137/20M1334966 VL - 19 IS - 1 SP - 460 EP - 477 ER - TY - JOUR A1 - Siefke, Thomas A1 - Hurtado, Carol A1 - Dickmann, Johannes A1 - Dickmann, Walter A1 - Käseberg, Tim A1 - Meyer, Jan A1 - Burger, Sven A1 - Zeitner, Uwe A1 - Bodermann, Bernd A1 - Kroker, Stefanie T1 - Quasi-bound states in the continuum for deep subwavelength structural information retrieval for DUV nano-optical polarizers JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.396044 VL - 28 SP - 23122 ER - TY - GEN A1 - Berthold, Timo A1 - Witzig, Jakob T1 - Conflict Analysis for MINLP N2 - The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality. T3 - ZIB-Report - 20-20 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78964 SN - 1438-0064 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Skrzypczak, Jan T1 - Transactions on Red-black and AVL trees in NVRAM JF - arXiv Y1 - 2020 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Röhm, Jonas A1 - Niknejad, Amir A1 - Chewle, Surahit A1 - Weber, Marcus T1 - Analyzing Raman Spectral Data without Separabiliy Assumption JF - Journal of Mathematical Chemistry N2 - Raman spectroscopy is a well established tool for the analysis of vibration spectra, which then allow for the determination of individual substances in a chemical sample, or for their phase transitions. In the Time-Resolved-Raman-Sprectroscopy the vibration spectra of a chemical sample are recorded sequentially over a time interval, such that conclusions for intermediate products (transients) can be drawn within a chemical process. The observed data-matrix M from a Raman spectroscopy can be regarded as a matrix product of two unknown matrices W and H, where the first is representing the contribution of the spectra and the latter represents the chemical spectra. One approach for obtaining W and H is the non-negative matrix factorization. We propose a novel approach, which does not need the commonly used separability assumption. The performance of this approach is shown on a real world chemical example. Y1 - 2021 U6 - https://doi.org/10.1007/s10910-020-01201-7 VL - 3 IS - 59 SP - 575 EP - 596 PB - Springer ER - TY - JOUR A1 - Straube, Arthur A1 - Kowalik, Bartosz G. A1 - Netz, Roland R. A1 - Höfling, Felix T1 - Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures JF - Commun. Phys. N2 - Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with theory, we show that friction in liquids emerges abruptly at a characteristic frequency, beyond which viscous liquids appear as non-dissipative, elastic solids. Concomitantly, the molecules experience Brownian forces that display persistent correlations. A critical test of the generalised Stokes–Einstein relation, mapping the friction of single molecules to the visco-elastic response of the macroscopic sample, disproves the relation for Newtonian fluids, but substantiates it exemplarily for water and a moderately supercooled liquid. The employed approach is suitable to yield insights into vitrification mechanisms and the intriguing mechanical properties of soft materials. Y1 - 2020 U6 - https://doi.org/10.1038/s42005-020-0389-0 VL - 3 SP - 126 PB - Nature ER - TY - JOUR A1 - Anzt, H. A1 - Bach, F. A1 - Druskat, S. A1 - Löffler, F. A1 - Loewe, A. A1 - Renard, B. Y. A1 - Seemann, G. A1 - Struck, A. A1 - Achhammer, E. A1 - Appell, F. A1 - Bader, M. A1 - Brusch, L. A1 - Busse, C. A1 - Chourdakis, G. A1 - Dabrowski, P. W. A1 - Ebert, P. A1 - Flemisch, B. A1 - Friedl, S. A1 - Fritzsch, B. A1 - Funk, M. D. A1 - Gast, V. A1 - Goth, F. A1 - Grad, J.-N. A1 - Hermann, Sibylle A1 - Hohmann, F. A1 - Janosch, S. A1 - Kutra, D. A1 - Linxweiler, J. A1 - Muth, T. A1 - Peters-Kottig, Wolfgang A1 - Rack, F. A1 - Raters, F. H. C. A1 - Rave, S. A1 - Reina, G. A1 - Reißig, M. A1 - Ropinski, T. A1 - Schaarschmidt, J. A1 - Seibold, H. A1 - Thiele, J. P. A1 - Uekermann, B. A1 - Unger, S. A1 - Weeber, R. T1 - An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations] JF - F1000Research N2 - Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. KW - Sustainable Software Development KW - Research Software Y1 - 2020 U6 - https://doi.org/10.12688/f1000research.23224.1 IS - 9:295 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Koltai, Péter A1 - Schütte, Christof T1 - Memory-Based Reduced Modelling and Data-Based Estimation of Opinion Spreading JF - Journal of Nonlinear Science N2 - We investigate opinion dynamics based on an agent-based model and are interested in predicting the evolution of the percentages of the entire agent population that share an opinion. Since these opinion percentages can be seen as an aggregated observation of the full system state, the individual opinions of each agent, we view this in the framework of the Mori–Zwanzig projection formalism. More specifically, we show how to estimate a nonlinear autoregressive model (NAR) with memory from data given by a time series of opinion percentages, and discuss its prediction capacities for various specific topologies of the agent interaction network. We demonstrate that the inclusion of memory terms significantly improves the prediction quality on examples with different network topologies. Y1 - 2021 U6 - https://doi.org/10.1007/s00332-020-09673-2 VL - 31 ER - TY - GEN A1 - Oltmanns, Elias A1 - Hasler, Tim T1 - Outline of an archiving strategy for digital audiovisual material N2 - This is the documentation on current results of a research project jointly conducted by Stiftung Deutsche Kinemathek (SDK) and Zuse Institute Berlin (ZIB). In this project, we are working on a practical yet sustainable archiving solution for audiovisual material. In the course of the project two major obstacles were identified: 1) Metadata is collected according to standards established in the community but lacking a prescribed serialisation format. 2) Storage size of audiovisual material and time scales of production processes make it often impractical to defer submission for archival storage until all components have arrived and can be processed in one go. T3 - ZIB-Report - 20-22 KW - long term preservation, digital audiovisual material, METS, EBUCore, PID, handle Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78840 SN - 1438-0064 ER - TY - JOUR A1 - Alves, Sónia A1 - Ehrig, Rainald A1 - Raffalt, Peter C. A1 - Bender, Alwina A1 - Duda, Georg A1 - Agres, Alison N. T1 - Quantifying Asymmetry in Gait: A Weighted Universal Symmetry Index to Evaluate 3D Ground Reaction Forces JF - Frontiers in Bioengineering and Biotechnology N2 - Though gait asymmetry is used as a metric of functional recovery in clinical rehabilitation, there is no consensus on an ideal method for its evaluation. Various methods have been proposed but are limited in scope, as they can often use only positive signals or discrete values extracted from time-scale data as input. By defining five symmetry axioms, a framework for benchmarking existing methods was established and a new method was described here for the first time: the weighted universal symmetry index (wUSI), which overcomes limitations of other methods. Both existing methods and the wUSI were mathematically compared to each other and in respect to their ability to fulfill the proposed symmetry axioms. Eligible methods that fulfilled these axioms were then applied using both discrete and continuous approaches to ground reaction force (GRF) data collected from healthy gait, both with and without artificially induced asymmetry using a single instrumented elbow crutch. The wUSI with a continuous approach was the only symmetry method capable of determining GRF asymmetries in different walking conditions in all three planes of motion. When used with a continuous approach, the wUSI method was able to detect asymmetries while avoiding artificial inflation, a common problem reported in other methods. In conclusion, the wUSI is proposed as a universal method to quantify three-dimensional GRF asymmetries, which may also be expanded to other biomechanical signals. Y1 - 2020 ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Determining all integer vertices of the PESP polytope by flipping arcs N2 - We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. These produce better dual bounds for the smallest and largest instance of the benchmarking library PESPlib. T3 - ZIB-Report - 20-19 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Mixed Integer Programming Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78793 SN - 1438-0064 ER - TY - JOUR A1 - Zhang, Wei T1 - Some new results on relative entropy production, time reversal, and optimal control of time-inhomogeneous diffusion processes JF - Journal of Mathematical Physics N2 - This paper studies time-inhomogeneous nonequilibrium diffusion processes, including both Brownian dynamics and Langevin dynamics. We derive upper bounds of the relative entropy production of the time-inhomogeneous process with respect to the transient invariant probability measures. We also study the time reversal of the reverse process in Crooks' fluctuation theorem. We show that the time reversal of the reverse process coincides with the optimally controlled forward process that leads to zero variance importance sampling estimator based on Jarzynski's equality. Y1 - 2021 U6 - https://doi.org/10.1063/5.0038740 VL - 62 IS - 4 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Handling Compute-Node Failures in FLESnet JF - CBM Progress Report 2019 Y1 - 2020 SN - 978-3-9815227-8-5 U6 - https://doi.org/10.15120/GSI-2020-00904 SP - 167 EP - 168 ER - TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - Macroscale mesenchymal condensation to study cytokine-driven cellular and matrix-related changes during cartilage degradation JF - Biofabrication N2 - Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics. Y1 - 2020 U6 - https://doi.org/10.1088/1758-5090/aba08f VL - 12 IS - 4 ER - TY - CHAP A1 - Bärring, Olof A1 - Lopez, Maite Barroso A1 - Cancio, German A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - et al., T1 - Towards automation of computing fabrics using tools from the fabric management workpackage of the EU DataGrid project T2 - Computing in High Energy and Nuclear Physics (CHEP03) Y1 - 2003 SP - 1 EP - 8 ER - TY - GEN A1 - Bittracher, Andreas A1 - Schütte, Christof T1 - A probabilistic algorithm for aggregating vastly undersampled large Markov chains N2 - Model reduction of large Markov chains is an essential step in a wide array of techniques for understanding complex systems and for efficiently learning structures from high-dimensional data. We present a novel aggregation algorithm for compressing such chains that exploits a specific low-rank structure in the transition matrix which, e.g., is present in metastable systems, among others. It enables the recovery of the aggregates from a vastly undersampled transition matrix which in practical applications may gain a speedup of several orders of mag- nitude over methods that require the full transition matrix. Moreover, we show that the new technique is robust under perturbation of the transition matrix. The practical applicability of the new method is demonstrated by identifying a reduced model for the large-scale traffic flow patterns from real-world taxi trip data. T3 - ZIB-Report - 20-21 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78688 UR - https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/7587 SN - 1438-0064 ER - TY - JOUR A1 - Pakhomov, Anton A1 - Löchner, Franz A1 - Zschiedrich, Lin A1 - Saravi, Sina A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Far-field polarization signatures of surface optical nonlinearity in noncentrosymmetric semiconductors JF - Sci. Rep. Y1 - 2020 U6 - https://doi.org/10.1038/s41598-020-67186-0 VL - 10 SP - 10545 ER - TY - CHAP A1 - Iamnitchi, Adriana A1 - Trunfio, Paolo A1 - Ledlie, Jonathan A1 - Schintke, Florian T1 - Peer-to-Peer Computing T2 - Euro-Par 2010 - Parallel Processing Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15277-1_42 VL - 6271 SP - 444 EP - 445 ER - TY - CHAP A1 - Miller, Barton P. A1 - Labarta, Jesús A1 - Schintke, Florian A1 - Simon, Jens T1 - Performance Evaluation, Analysis and Optimization T2 - Euro-Par 2002 Parallel Processing Y1 - 2002 U6 - https://doi.org/10.1007/3-540-45706-2_15 VL - 2400 SP - 131 EP - 131 ER - TY - CHAP A1 - Allen, Gabrielle A1 - Dramlitsch, Thomas A1 - Goodale, Tom A1 - Lanfermann, Gerd A1 - Radke, Thomas A1 - Seidel, Edward A1 - Kielmann, Thilo A1 - Verstoep, Kees A1 - Balaton, Zoltán A1 - Kacsuk, Péter A1 - Szalai, Ferenc A1 - Gehring, Jörn A1 - Keller, Axel A1 - Streit, Achim A1 - Matyska, Ludek A1 - Ruda, Miroslav A1 - Krenek, Ales A1 - Knipp, Harald A1 - Merzky, André A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Ludwiczak, Bogdan A1 - Nabrzyski, Jarek A1 - Pukacki, Juliusz A1 - Kersken, Hans-Peter A1 - Aloisio, Giovanni A1 - Cafaro, Massimo A1 - Ziegler, Wolfgang A1 - Russell, Michael T1 - Early experiences with the EGrid testbed T2 - Proceedings First IEEE/ACM International Symposium on Cluster Computing and the Grid Y1 - 2001 U6 - https://doi.org/10.1109/CCGRID.2001.923185 SP - 130 EP - 137 ER - TY - THES A1 - Kruber, Nico T1 - Approximate Distributed Set Reconciliation with Defined Accuracy Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:11-110-18452/22105-6 UR - https://doi.org/10.18452/21294 ER - TY - JOUR A1 - Kostre, Margarita A1 - Schütte, Christof A1 - Noé, Frank A1 - del Razo Sarmina, Mauricio T1 - Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs JF - Multiscale Modeling & Simulation N2 - Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications. Y1 - 2021 U6 - https://doi.org/10.1137/20M1352739 VL - 19 IS - 4 SP - 1659 EP - 1683 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Weiss, Selina A1 - Grewe, Carl Martin A1 - Olderbak, Sally A1 - Goecke, Benjamin A1 - Kaltwasser, Laura A1 - Hildebrandt, Andrea T1 - Symmetric or not? A holistic approach to the measurement of fluctuating asymmetry from facial photographs JF - Personality and Individual Differences Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1016/j.paid.2020.110137 VL - 166 SP - 1 EP - 12 ER - TY - JOUR A1 - Scholtz, Gerhard A1 - Knötel, David A1 - Baum, Daniel T1 - D’Arcy W. Thompson’s Cartesian transformations: a critical evaluation JF - Zoomorphology N2 - The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00494-1 VL - 139 SP - 293 EP - 308 ER - TY - JOUR A1 - Weiss, Selina A1 - Grewe, Carl Martin A1 - Olderbak, Sally A1 - Goecke, Benjamin A1 - Kaltwasser, Laura A1 - Hildebrandt, Andrea T1 - Symmetric or not? A holistic approach to the measurement of fluctuating asymmetry from facial photographs JF - PsyArXiv Y1 - 2020 U6 - https://doi.org/10.31234/osf.io/s534t N1 - preprint of https://doi.org/10.1016/j.paid.2020.110137 ER - TY - JOUR A1 - Shi, Liping A1 - Evlyukhin, Andrey B. A1 - Reinhardt, Carsten A1 - Babushkin, Ihar A1 - Zenin, Vladimir A. A1 - Burger, Sven A1 - Malureanu, Radu A1 - Chichkov, Boris N. A1 - Morgner, Uwe A1 - Kovacev, Milutin T1 - Progressive Self-Boosting Anapole-Enhanced Deep-Ultraviolet Third Harmonic During Few-Cycle Laser Radiation JF - ACS Photonics Y1 - 2020 U6 - https://doi.org/10.1021/acsphotonics.0c00753 VL - 7 SP - 1655 ER - TY - CHAP A1 - Christgau, Steffen A1 - Steinke, Thomas T1 - Porting a Legacy CUDA Stencil Code to oneAPI T2 - 2020 IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2020, New Orleans, LA, USA, May 18-22, 2020 N2 - Recently, Intel released the oneAPI programming environment. With Data Parallel C++ (DPC++), oneAPI enables codes to target multiple hardware architectures like multi-core CPUs, GPUs, and even FPGAs or other hardware using a single source. For legacy codes that were written for Nvidia GPUs, a compatibility tool is provided which facilitates the transition to the SYCL-based DPC++ programming language. This paper presents early experiences when using both the compatibility tool and oneAPI as well the employed extension to the SYCL programming standard for the tsunami simulation code easyWave. A performance study compares the original code running on Xeon processors using OpenMP as well as CUDA with the performance of the DPC++ counter part on multicore CPUs as well as integrated GPUs. Y1 - 2020 SN - 978-1-7281-7445-7 U6 - https://doi.org/10.1109/IPDPSW50202.2020.00070 SP - 359 EP - 367 PB - IEEE CY - New Orleans ER - TY - GEN A1 - Clausecker, Robert T1 - The Quality of Heuristic Functions for IDA* N2 - The aim of this thesis is to deepen our understand of how IDA* heuristics influence the number of nodes expanded during search. To this end, we develop Korf's formula for the number of expanded nodes into a heuristic quality η which expresses the quality of a heuristic function as a constant factor on the number of expanded nodes, independent of a particular problem instance. We proceed to show how to compute η for some common kinds of heuristics and how to estimate η by means of a random sample for arbitrary heuristics. Using the value of η for some concrete examples, we then inspect for which parts of the search space the values of h(v) are particularly critical to the performance of the heuristic, allowing us to build better heuristics for future problems. This report originally appeared as a master thesis at Humboldt University of Berlin. T3 - ZIB-Report - 20-17 KW - IDA* heuristic search sampling random walks Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78489 SN - 1438-0064 ER - TY - GEN A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - On the abs-polynomial expansion of piecewise smooth functions N2 - Tom Streubel has observed that for functions in abs-normal form, generalized Taylor expansions of arbitrary order $\bar d-1$ can be generated by algorithmic piecewise differentiation. Abs-normal form means that the real or vector valued function is defined by an evaluation procedure that involves the absolute value function $|...|$ apart from arithmetic operations and $\bar d$ times continuously differentiable univariate intrinsic functions. The additive terms in Streubel's expansion are abs-polynomial, i.e. involve neither divisions nor intrinsics. When and where no absolute values occur, Moore's recurrences can be used to propagate univariate Taylor polynomials through the evaluation procedure with a computational effort of $\mathcal O({\bar d}^2)$, provided all univariate intrinsics are defined as solutions of linear ODEs. This regularity assumption holds for all standard intrinsics, but for irregular elementaries one has to resort to Faa di Bruno's formula, which has exponential complexity in $\bar d$. As already conjectured we show that the Moore recurrences can be adapted for regular intrinsics to the abs-normal case. Finally, we observe that where the intrinsics are real analytic the expansions can be extended to infinite series that converge absolutely on spherical domains. T3 - ZIB-Report - 20-14 KW - Nonsmooth Taylor polynomial/series KW - forward mode propagation KW - abs-normal form KW - abs-linear form KW - absolute convergence KW - Moore recurrences KW - quadratic complexity Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78448 SN - 1438-0064 ER - TY - GEN A1 - Ray, Sourav A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Weber, Marcus T1 - How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs N2 - Molecular simulations of ligand-receptor interactions are a computational challenge, especially when their association- (``on''-rate) and dissociation- (``off''-rate) mechanisms are working on vastly differing timescales. In addition, the timescale of the simulations themselves is, in practice, orders of magnitudes smaller than that of the mechanisms; which further adds to the complexity of observing these mechanisms, and of drawing meaningful and significant biological insights from the simulation. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)- N-phenyl propionamide (NFEPP) in a $\mu$-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab, who investigated the influence of pH on the inhibitory constant of fentanyl and NFEPP (Spahn et al. 2017). MD simulations are far more accessible and cost-effective than in vitro and in vivo studies. Especially in the context of the current opioid crisis, MD simulations can aid in unravelling molecular functionality and assist in clinical decision-making; the approaches presented in this paper are a pertinent step forward in this direction. T3 - ZIB-Report - 20-18 KW - Opioid, Ligand-Receptor Interaction, Binding Kinetics, Molecular Dynamics, Metadynamics, SQRA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78437 SN - 1438-0064 ER - TY - JOUR A1 - Serrano, Felipe A1 - Schwarz, Robert A1 - Gleixner, Ambros T1 - On the relation between the extended supporting hyperplane algorithm and Kelley’s cutting plane algorithm JF - Journal of Global Optimization N2 - Recently, Kronqvist et al. (J Global Optim 64(2):249–272, 2016) rediscovered the supporting hyperplane algorithm of Veinott (Oper Res 15(1):147–152, 1967) and demonstrated its computational benefits for solving convex mixed integer nonlinear programs. In this paper we derive the algorithm from a geometric point of view. This enables us to show that the supporting hyperplane algorithm is equivalent to Kelley’s cutting plane algorithm (J Soc Ind Appl Math 8(4):703–712, 1960) applied to a particular reformulation of the problem. As a result, we extend the applicability of the supporting hyperplane algorithm to convex problems represented by a class of general, not necessarily convex nor differentiable, functions. Y1 - 2020 U6 - https://doi.org/10.1007/s10898-020-00906-y VL - 78 SP - 161 EP - 179 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael T1 - Solving Previously Unsolved MIP Instances with ParaSCIP on Supercomputers by using up to 80,000 Cores N2 - Mixed-integer programming (MIP) problem is arguably among the hardest classes of optimization problems. This paper describes how we solved 21 previously unsolved MIP instances from the MIPLIB benchmark sets. To achieve these results we used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper, we describe the basic parallelization mechanism of ParaSCIP, improvements of the dynamic load balancing and novel techniques to exploit the power of parallelization for MIP solving. We give a detailed overview of computing times and statistics for solving open MIPLIB instances. T3 - ZIB-Report - 20-16 KW - Mixed Integer Programming, Parallel processing, Node merging, Racing, ParaSCIP, Ubiquity Generator Framework, MIPLIB Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78393 SN - 1438-0064 ER - TY - JOUR A1 - Mrowiński, Paweł A1 - Schnauber, Peter A1 - Kaganskiy, Arsenty A1 - Schall, Johannes A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Directional single-photon emission from deterministic quantum dot waveguide structures JF - Phys. Status Solidi RRL Y1 - 2020 U6 - https://doi.org/10.1002/pssr.202000115 VL - 14 SP - 2000115 ER - TY - CHAP A1 - Schintke, Florian A1 - Simon, Jens A1 - Reinefeld, Alexander T1 - A Cache Simulator for Shared Memory Systems T2 - Computational Science - ICCS 2001 Y1 - 2001 U6 - https://doi.org/10.1007/3-540-45718-6_62 VL - 2074 SP - 569 EP - 578 ER - TY - CHAP A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - Hennemuth, Anja A1 - von Tycowicz, Christoph T1 - Nonlinear Regression on Manifolds for Shape Analysis using Intrinsic Bézier Splines T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) N2 - Intrinsic and parametric regression models are of high interest for the statistical analysis of manifold-valued data such as images and shapes. The standard linear ansatz has been generalized to geodesic regression on manifolds making it possible to analyze dependencies of random variables that spread along generalized straight lines. Nevertheless, in some scenarios, the evolution of the data cannot be modeled adequately by a geodesic. We present a framework for nonlinear regression on manifolds by considering Riemannian splines, whose segments are Bézier curves, as trajectories. Unlike variational formulations that require time-discretization, we take a constructive approach that provides efficient and exact evaluation by virtue of the generalized de Casteljau algorithm. We validate our method in experiments on the reconstruction of periodic motion of the mitral valve as well as the analysis of femoral shape changes during the course of osteoarthritis, endorsing Bézier spline regression as an effective and flexible tool for manifold-valued regression. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-59719-1_60 SP - 617 EP - 626 PB - Springer International Publishing CY - Cham ER - TY - GEN A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. T3 - ZIB-Report - 20-12 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78237 SN - 1438-0064 ER - TY - JOUR A1 - Hoang, Margaux A1 - Garnier, Philippe A1 - Lasue, Jeremie A1 - Rème, Henri A1 - Capria, Maria Teresa A1 - Altwegg, Kathrin A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin T1 - Investigating the Rosetta/RTOF observations of comet 67P/Churyumov-Gerasimenko using a comet nucleus model: Influence of dust mantle and trapped CO JF - Astronomy & Astrophysics N2 - Context. Cometary outgassing is induced by the sublimation of ices and the ejection of dust originating from the nucleus. Therefore measuring the composition and dynamics of the cometary gas provides information concerning the interior composition of the body. Nevertheless, the bulk composition differs from the coma composition, and numerical models are required to simulate the main physical processes induced by the illumination of the icy body. Aims. The objectives of this study are to bring new constraints on the interior composition of the nucleus of comet 67P/Churyumov-Gerasimenko (hereafter 67P) by comparing the results of a thermophysical model applied to the nucleus of 67P and the coma measurements made by the Reflectron-type Time-Of-Flight (RTOF) mass spectrometer. This last is one of the three instruments of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA), used during the Rosetta mission. Methods. Using a thermophysical model of the comet nucleus, we studied the evolution of the stratigraphy (position of the sublimation and crystallisation fronts), the temperature of the surface and subsurface, and the dynamics and spatial distribution of the volatiles (H2O, CO2 and CO). We compared them with the in situ measurements from ROSINA/RTOF and an inverse coma model. Results. We observed the evolution of the surface and near surface temperature, and the deepening of sublimation fronts. The thickness of the dust layer covering the surface strongly influences the H2O outgassing but not the more volatiles species. The CO outgassing is highly sensitive to the initial CO/H2O ratio, as well as to the presence of trapped CO in the amorphous ice. Conclusions. The study of the influence of the initial parameters on the computed volatile fluxes and the comparison with ROSINA/RTOF measurements provide a range of values for an initial dust mantle thickness and a range of values for the volatile ratio. These imply the presence of trapped CO. Nevertheless, further studies are required to reproduce the strong change of behaviour observed in RTOF measurements between September 2014 and February 2015. Y1 - 2020 U6 - https://doi.org/10.1051/0004-6361/201936655 VL - 638 SP - A106 ER - TY - JOUR A1 - Willsch, Maraike A1 - Friedrich, Frank A1 - Baum, Daniel A1 - Jurisch, Ivo A1 - Ohl, Michael T1 - A comparative description of the mesosomal musculature in Sphecidae and Ampulicidae (Hymenoptera, Apoidea) using 3D techniques JF - Deutsche Entomologische Zeitschrift N2 - Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper. Y1 - 2020 U6 - https://doi.org/10.3897/dez.67.49493 VL - 67 IS - 1 SP - 51 EP - 67 ER - TY - GEN A1 - Lindner, Niels A1 - Reisch, Julian T1 - Parameterized Complexity of Periodic Timetabling N2 - Public transportation networks are typically operated with a periodic timetable. The Periodic Event Scheduling Problem (PESP) is the standard mathematical modelling tool for periodic timetabling. Since PESP can be solved in linear time on trees, it is a natural question to ask whether there are polynomial-time algorithms for input networks of bounded treewidth. We show that deciding the feasibility of a PESP instance is NP-hard even when the treewidth is 2, the branchwidth is 2, or the carvingwidth is 3. Analogous results hold for the optimization of reduced PESP instances, where the feasibility problem is trivial. To complete the picture, we present two pseudo-polynomial-time dynamic programming algorithms solving PESP on input networks with bounded tree- or branchwidth. We further analyze the parameterized complexity of PESP with bounded cyclomatic number, diameter, or vertex cover number. For event-activity networks with a special -- but standard -- structure, we give explicit and sharp bounds on the branchwidth in terms of the maximum degree and the carvingwidth of an underlying line network. Finally, we investigate several parameters on the smallest instance of the benchmarking library PESPlib. T3 - ZIB-Report - 20-15 KW - Parameterized complexity KW - Periodic timetabling KW - Treewidth KW - Branchwidth KW - Carvingwidth KW - Periodic Event Scheduling Problem Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78314 SN - 1438-0064 ER - TY - JOUR A1 - Farchmin, Nando A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Wurm, Matthias A1 - Bodermann, Bernd A1 - Bär, Markus A1 - Heidenreich, Sebastian T1 - Efficient Bayesian inversion for shape reconstruction of lithography masks JF - J. Micro/Nanolith. MEMS MOEMS Y1 - 2020 U6 - https://doi.org/10.1117/1.JMM.19.2.024001 VL - 19 SP - 024001 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Flat optics in high numerical aperture broadband imaging systems JF - J. Opt. Y1 - 2020 U6 - https://doi.org/10.1088/2040-8986/ab8ea2 VL - 22 SP - 065607 ER - TY - JOUR A1 - Feis, Joshua A1 - Beutel, Dominik A1 - Köpfler, Julian A1 - Santiago, Xavier Garcia A1 - Rockstuhl, Carsten A1 - Wegener, Martin A1 - Fernandez-Corbaton, Ivan T1 - Helicity-Preserving Optical Cavity Modes for Enhanced Sensing of Chiral Molecules JF - Phys. Rev. Lett. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.033201 VL - 124 SP - 033201 ER - TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - GEN A1 - Ege, Yannic A1 - Foth, Christian A1 - Baum, Daniel A1 - Wirkner, Christian S. A1 - Richter, Stefan T1 - Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability N2 - An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time. T3 - ZIB-Report - 20-09 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77744 SN - 1438-0064 ER - TY - BOOK A1 - Reuter, Bernhard T1 - Generalisierte Markov-Modellierung N2 - Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zustände ermöglichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der für das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschränkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzuklären. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu führt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1–40)-Peptids durch und modelliert diese. Y1 - 2020 SN - 978-3-658-29711-4 U6 - https://doi.org/10.1007/978-3-658-29712-1 PB - Springer Spektrum, Wiesbaden ER - TY - JOUR A1 - Colom, Rémi A1 - Stout, Brian A1 - Bonod, Nicolas T1 - Modal Expansion of the Impulse Response Function for Predicting the Time Dynamics of Open Optical Cavities JF - arXiv Y1 - 2020 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - On the exact solution of prize-collecting Steiner tree problems T3 - ZIB-Report - 20-11 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78174 SN - 1438-0064 ER - TY - JOUR A1 - Lelievre, Tony A1 - Stoltz, Gabriel A1 - Zhang, Wei T1 - Multiple projection MCMC algorithms on submanifolds JF - IMA Journal of Numerical Analysis N2 - We propose new Markov Chain Monte Carlo algorithms to sample probability distributions on submanifolds, which generalize previous methods by allowing the use of set-valued maps in the proposal step of the MCMC algorithms. The motivation for this generalization is that the numerical solvers used to project proposed moves to the submanifold of interest may find several solutions. We show that the new algorithms indeed sample the target probability measure correctly, thanks to some carefully enforced reversibility property. We demonstrate the interest of the new MCMC algorithms on illustrative numerical examples. Y1 - 2022 U6 - https://doi.org/10.1093/imanum/drac006 ER - TY - GEN A1 - Hendel, Gregor A1 - Anderson, Daniel A1 - Le Bodic, Pierre A1 - Pfetsch, Marc T1 - Estimating the Size of Branch-And-Bound Trees N2 - This paper investigates the estimation of the size of Branch-and-Bound (B&B) trees for solving mixed-integer programs. We first prove that the size of the B&B tree cannot be approximated within a factor of~2 for general binary programs, unless P equals NP. Second, we review measures of the progress of the B&B search, such as the gap, and propose a new measure, which we call leaf frequency. We study two simple ways to transform these progress measures into B&B tree size estimates, either as a direct projection, or via double-exponential smoothing, a standard time-series forecasting technique. We then combine different progress measures and their trends into nontrivial estimates using Machine Learning techniques, which yields more precise estimates than any individual measure. The best method we have identified uses all individual measures as features of a random forest model. In a large computational study, we train and validate all methods on the publicly available MIPLIB and Coral general purpose benchmark sets. On average, the best method estimates B&B tree sizes within a factor of 3 on the set of unseen test instances even during the early stage of the search, and improves in accuracy as the search progresses. It also achieves a factor 2 over the entire search on each out of six additional sets of homogeneous instances we have tested. All techniques are available in version 7 of the branch-and-cut framework SCIP. T3 - ZIB-Report - 20-02 KW - mixed integer programming KW - machine learning KW - branch and bound KW - forecasting Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78144 SN - 1438-0064 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - RMWPaxos: Fault-Tolerant In-Place Consensus Sequences JF - IEEE Transactions on Parallel and Distributed Systems Y1 - 2020 U6 - https://doi.org/10.1109/TPDS.2020.2981891 SN - 1045-9219 VL - 31 IS - 10 SP - 2392 EP - 2405 ER - TY - GEN A1 - Gamrath, Gerald A1 - Anderson, Daniel A1 - Bestuzheva, Ksenia A1 - Chen, Wei-Kun A1 - Eifler, Leon A1 - Gasse, Maxime A1 - Gemander, Patrick A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Halbig, Katrin A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Le Bodic, Pierre A1 - Maher, Stephen J. A1 - Matter, Frederic A1 - Miltenberger, Matthias A1 - Mühmer, Erik A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Tawfik, Christine A1 - Vigerske, Stefan A1 - Wegscheider, Fabian A1 - Weninger, Dieter A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 7.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming frame- work SCIP. This paper discusses enhancements and extensions contained in version 7.0 of the SCIP Optimization Suite. The new version features the parallel presolving library PaPILO as a new addition to the suite. PaPILO 1.0 simplifies mixed-integer linear op- timization problems and can be used stand-alone or integrated into SCIP via a presolver plugin. SCIP 7.0 provides additional support for decomposition algorithms. Besides im- provements in the Benders’ decomposition solver of SCIP, user-defined decomposition structures can be read, which are used by the automated Benders’ decomposition solver and two primal heuristics. Additionally, SCIP 7.0 comes with a tree size estimation that is used to predict the completion of the overall solving process and potentially trigger restarts. Moreover, substantial performance improvements of the MIP core were achieved by new developments in presolving, primal heuristics, branching rules, conflict analysis, and symmetry handling. Last, not least, the report presents updates to other components and extensions of the SCIP Optimization Suite, in particular, the LP solver SoPlex and the mixed-integer semidefinite programming solver SCIP-SDP. T3 - ZIB-Report - 20-10 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78023 SN - 1438-0064 ER - TY - JOUR A1 - Musiał, Anna A1 - Żołnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wojcik, Grzegorz A1 - Mergo, Paweł A1 - Kamil, Dybka A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Lauritsen, Kristian A1 - Bülter, Andreas A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Rodt, Sven A1 - Urbanczyk, Wacław A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Plug&play fibre-coupled 73 kHz single-photon source operating in the telecom O-band JF - Adv. Quantum Technol. Y1 - 2020 U6 - https://doi.org/10.1002/qute.202000018 VL - 3 SP - 2000018 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Rémi A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Quasinormal mode expansion of optical far-field quantities JF - Phys. Rev. B Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevB.102.035432 VL - 102 SP - 035432 ER - TY - GEN A1 - Most, Dieter A1 - Giannelos, Spyros A1 - Yueksel-Erguen, Inci A1 - Beulertz, Daniel A1 - Haus, Utz-Uwe A1 - Charousset-Brignol, Sandrine A1 - Frangioni, Antonio T1 - A Novel Modular Optimization Framework for Modelling Investment and Operation of Energy Systems at European Level N2 - Project plan4res (www.plan4res.eu) involves the development of a modular framework for the modeling and analysis of energy system strategies at the European level. It will include models describing the investment and operation decisions for a wide variety of technologies related to electricity and non-electricity energy sectors across generation, consumption, transmission and distribution. The modularity of the framework allows for detailed modelling of major areas of energy systems that can help stakeholders from different backgrounds to focus on specific topics related to the energy landscape in Europe and to receive relevant outputs and insights tailored to their needs. The current paper presents a qualitative description of key concepts and methods of the novel modular optimization framework and provides insights into the corresponding energy landscape. T3 - ZIB-Report - 20-08 KW - energy systems analysis and optimization KW - simulation and planning under uncertainty KW - renewables integration KW - sector coupling KW - climate change impact Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78079 SN - 1438-0064 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Boeszoermnyi, Andras A1 - Wang, Zi-Fu A1 - Fischer, Patrick D. A1 - Coote, Paul A1 - Das, Krishna M. Padmanabha A1 - Malets, Yehor S. A1 - Radchenko, Dmytro S. A1 - Moroz, Yurii A1 - Scott, David A. A1 - Fackeldey, Konstantin A1 - Hoffmann, Moritz A1 - Iavniuk, Iryna A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - An open-source drug discovery platform enables ultra-large virtual screens JF - Nature N2 - On average, an approved drug today costs $2-3 billion and takes over ten years to develop1. In part, this is due to expensive and time-consuming wet-lab experiments, poor initial hit compounds, and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening (SBVS) has the potential to mitigate these problems. With SBVS, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large compound databases exist, the ability to carry out large-scale SBVSs on computer clusters in an accessible, efficient, and flexible manner has remained elusive. Here we designed VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large ligand libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we have prepared the largest and freely available ready-to-dock ligand library available, with over 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened over 1 billion compounds and discovered a small molecule inhibitor (iKeap1) that engages KEAP1 with nanomolar affinity (Kd = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. We also identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify binders with high affinity for target proteins. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1038/s41586-020-2117-z VL - 580 SP - 663 EP - 668 PB - Springer Nature ER - TY - JOUR A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Kniasew, Dimitri A1 - Schlögel, Dominik A1 - Martin, Alexander A1 - Weninger, Dieter T1 - Tackling Industrial-Scale Supply Chain Problems by Mixed-Integer Programming JF - Journal of Computational Mathematics N2 - The modeling flexibility and the optimality guarantees provided by mixed-integer programming greatly aid the design of robust and future-proof decision support systems. The complexity of industrial-scale supply chain optimization, however, often poses limits to the application of general mixed-integer programming solvers. In this paper we describe algorithmic innovations that help to ensure that MIP solver performance matches the complexity of the large supply chain problems and tight time limits encountered in practice. Our computational evaluation is based on a diverse set, modeling real-world scenarios supplied by our industry partner SAP. Y1 - 2019 U6 - https://doi.org/10.4208/jcm.1905-m2019-0055 VL - 37 SP - 866 EP - 888 ER - TY - JOUR A1 - Witzig, Jakob A1 - Gleixner, Ambros T1 - Conflict-Driven Heuristics for Mixed Integer Programming JF - INFORMS Journal on Computing N2 - Two essential ingredients of modern mixed-integer programming (MIP) solvers are diving heuristics that simulate a partial depth-first search in a branch-and-bound search tree and conflict analysis of infeasible subproblems to learn valid constraints. So far, these techniques have mostly been studied independently: primal heuristics under the aspect of finding high-quality feasible solutions early during the solving process and conflict analysis for fathoming nodes of the search tree and improving the dual bound. Here, we combine both concepts in two different ways. First, we develop a diving heuristic that targets the generation of valid conflict constraints from the Farkas dual. We show that in the primal this is equivalent to the optimistic strategy of diving towards the best bound with respect to the objective function. Secondly, we use information derived from conflict analysis to enhance the search of a diving heuristic akin to classical coefficient diving. The computational performance of both methods is evaluated using an implementation in the source-open MIP solver SCIP. Experiments are carried out on publicly available test sets including Miplib 2010 and Cor@l. Y1 - 2020 U6 - https://doi.org/10.1287/ijoc.2020.0973 VL - 33 IS - 2 SP - 706 EP - 720 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Hendel, Gregor A1 - Gamrath, Gerald A1 - Achterberg, Tobias A1 - Bastubbe, Michael A1 - Berthold, Timo A1 - Christophel, Philipp M. A1 - Jarck, Kati A1 - Koch, Thorsten A1 - Linderoth, Jeff A1 - Lübbecke, Marco A1 - Mittelmann, Hans A1 - Ozyurt, Derya A1 - Ralphs, Ted A1 - Salvagnin, Domenico A1 - Shinano, Yuji T1 - MIPLIB 2017: Data-Driven Compilation of the 6th Mixed-Integer Programming Library JF - Mathematical Programming Computation N2 - We report on the selection process leading to the sixth version of the Mixed Integer Programming Library. Selected from an initial pool of over 5,000 instances, the new MIPLIB 2017 collection consists of 1,065 instances. A subset of 240 instances was specially selected for benchmarking solver performance. For the first time, the compilation of these sets was done using a data-driven selection process supported by the solution of a sequence of mixed integer optimization problems, which encoded requirements on diversity and balancedness with respect to instance features and performance data. Y1 - 2021 U6 - https://doi.org/10.1007/s12532-020-00194-3 VL - 13 IS - 3 SP - 443 EP - 490 ER - TY - GEN A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. T3 - ZIB-Report - 20-04 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77087 SN - 1438-0064 ER - TY - CHAP A1 - Rodt, Sven A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Heindel, Tobias A1 - Bounouar, Samir A1 - Kantner, Markus A1 - Koprucki, Thomas A1 - Bandelow, Uwe A1 - Burger, Sven A1 - Reitzenstein, Stephan ED - Kneissl, Michael ED - Knorr, Andreas ED - Reitzenstein, Stephan ED - Hoffmann, Axel T1 - Deterministic Quantum Devices for Optical Quantum Communication T2 - Semiconductor Nanophotonics Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-35656-9_8 VL - 194 SP - 285 EP - 359 PB - Springer CY - Cham ER - TY - JOUR A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Lindow, Norbert A1 - Powers, James A. A1 - Cota, Vanessa A1 - Quintanilla, Luis J. A1 - Brugués, Jan A1 - Prohaska, Steffen A1 - Chu, Diana S. A1 - Müller-Reichert, Thomas T1 - Sperm-specific meiotic chromosome segregation in C. elegans JF - eLife Y1 - 2020 U6 - https://doi.org/10.7554/eLife.50988 VL - 9 SP - e50988 ER - TY - GEN A1 - Mollenhauer, Mattes A1 - Schuster, Ingmar A1 - Klus, Stefan A1 - Schütte, Christof ED - Junge, Oliver ED - Schütze, O. ED - Froyland, Gary ED - Ober-Blobaum, S. ED - Padberg-Gehle, K. T1 - Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces T2 - Advances om Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on his 60th birthday Y1 - 2020 SN - 978-3-030-51264-4 U6 - https://doi.org/10.1007/978-3-030-51264-4_5 VL - 304 SP - 109 EP - 131 PB - Springer International ER - TY - GEN A1 - Bittracher, Andreas A1 - Schütte, Christof ED - Junge, Oliver ED - Schütze, O. ED - Froyland, Gary ED - Ober-Blobaum, S. ED - Padberg-Gehle, E. T1 - A weak characterization of slow variables in stochastic dynamical systems T2 - Advances in Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on the occasion of his 60th birthday Y1 - 2020 SN - 978-3-030-51264-4 U6 - https://doi.org/10.1007/978-3-030-51264-4_6 VL - 304 SP - 132 EP - 150 PB - Springer International ER - TY - THES A1 - Wulkow, Hanna T1 - Regularization of Elliptic Partial Differential Equations using Neural Networks N2 - This thesis presents a method for interpolating data using a neural network. The data is sparse and perturbed and is used as training data for a small neural network. For severely perturbed data, the network does not manage to find a smooth interpolation. But as the data resembles the solution to the one-dimensional and time-independent heat equation, the weak form of this PDE and subsequently its functional can be written down. If the functional is minimized, a solution to the weak form of the heat equation is found. The functional is now added to the traditional loss function of a neural network, the mean squared error between the network prediction and the given data, in order to smooth out fluctuations and interpolate between distanced grid points. This way, the network minimizes both the mean squared error and the functional, resulting in a smoother curve that can be used to predict u(x) for any grid point x. KW - elliptic partial differential equations KW - neural networks Y1 - 2020 ER - TY - THES A1 - Semler, Phillip T1 - Mixed finite elements in cloth simulation N2 - This master thesis investigates the use and behaviour of a mixed finite element formulation for the simulation of garments. The garment is modelled as an isotropic shell and is related to its mid-surface by energetic degeneration. Based on this, an energy functional is constructed, which contains the deformation and the mid-surface vector as degree of freedom. It is then shown why this problem does not correspond to a saddle point problem, but to a non-convex energy minimization. The implementation of the energy minimization takes place with the ZIB-internal FE framework Kaskade7.4, whereby a geometric linear and different geometric non-linear problems are examined, whereby for a selected, non-linear example a comparison is made with an existing implementation on basis of Morley elements. The further evaluations include the analysis of the quantitative and qualitative results, the used solution method, the behaviour of the system energy as well as the used CPU time. KW - cloth simulation KW - shell elements KW - mixed finite elements Y1 - 2020 ER - TY - JOUR A1 - Temp, Julia A1 - Labuz, Dominika A1 - Negrete, Roger A1 - Sunkara, Vikram A1 - Machelska, Halina T1 - Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis JF - Osteoarthritis and Cartilage Y1 - 2019 U6 - https://doi.org/10.1016/j.joca.2019.11.003 ER - TY - JOUR A1 - Sunkara, Vikram T1 - On the Properties of the Reaction Counts Chemical Master Equation JF - Entropy N2 - The reaction counts chemical master equation (CME) is a high-dimensional variant of the classical population counts CME. In the reaction counts CME setting, we count the reactions which have fired over time rather than monitoring the population state over time. Since a reaction either fires or not, the reaction counts CME transitions are only forward stepping. Typically there are more reactions in a system than species, this results in the reaction counts CME being higher in dimension, but simpler in dynamics. In this work, we revisit the reaction counts CME framework and its key theoretical results. Then we will extend the theory by exploiting the reactions counts’ forward stepping feature, by decomposing the state space into independent continuous-time Markov chains (CTMC). We extend the reaction counts CME theory to derive analytical forms and estimates for the CTMC decomposition of the CME. This new theory gives new insights into solving hitting times-, rare events-, and a priori domain construction problems. Y1 - 2019 U6 - https://doi.org/10.3390/e21060607 VL - 21 IS - 6 SP - 607 ER - TY - JOUR A1 - Haase, Tobias A1 - Sunkara, Vikram A1 - Kohl, Benjamin A1 - Meier, Carola A1 - Bußmann, Patricia A1 - Becker, Jessica A1 - Jagielski, Michal A1 - von Kleist, Max A1 - Ertel, Wolfgang T1 - Discerning the spatio-temporal disease patterns of surgically induced OA mouse models JF - PLOS One N2 - Osteoarthritis (OA) is the most common cause of disability in ageing societies, with no effective therapies available to date. Two preclinical models are widely used to validate novel OA interventions (MCL-MM and DMM). Our aim is to discern disease dynamics in these models to provide a clear timeline in which various pathological changes occur. OA was surgically induced in mice by destabilisation of the medial meniscus. Analysis of OA progression revealed that the intensity and duration of chondrocyte loss and cartilage lesion formation were significantly different in MCL-MM vs DMM. Firstly, apoptosis was seen prior to week two and was narrowly restricted to the weight bearing area. Four weeks post injury the magnitude of apoptosis led to a 40–60% reduction of chondrocytes in the non-calcified zone. Secondly, the progression of cell loss preceded the structural changes of the cartilage spatio-temporally. Lastly, while proteoglycan loss was similar in both models, collagen type II degradation only occurred more prominently in MCL-MM. Dynamics of chondrocyte loss and lesion formation in preclinical models has important implications for validating new therapeutic strategies. Our work could be helpful in assessing the feasibility and expected response of the DMM- and the MCL-MM models to chondrocyte mediated therapies. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0213734 VL - 14 IS - 4 PB - PLOS One ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Burger, Sven ED - Kaltenbacher, Manfred T1 - Spectral resonance expansion by Riesz projections T2 - 14 th International Conference on Mathematical and Numerical Aspects of Wave Propagation Book of Abstracts Y1 - 2019 U6 - https://doi.org/10.34726/waves2019 SP - 234 ER - TY - THES A1 - Baumann, Felix T1 - Impact of Contact Surfaces on the Death Estimation N2 - The determination of time of death is one of the central tasks in forensic medicine. A standard method of time of death estimation elies on matching temperature measurements of the corpse with a post-mortem cooling model. In addition to widely used empirical post-mortem models, modelling based on a precise mathematical simulation of the cooling process have been gaining popularity. The simulation based cooling models and the resulting time of death estimates dependon a large variety of parameters. These include hermal properties for different body tissue types, environmental conditions such as temperature and air flow, and the presence of clothing and coverings. In this thesis we focus on a specific arameter - the contact between corpse and underground - and investigate its influence on the time of death estimation. Resulting we aim to answer the question whether it is necessary to consider contact mechanics in the underlying mathematical cooling model. KW - time of death estimation KW - contact mechanics KW - heat equation KW - inverse problems Y1 - 2020 ER - TY - CHAP A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven ED - Novotny, Lukas ED - Quidant, Romain T1 - Numerical Investigation of Integrated Single-Photon Emitters in Low-Index-Contrast Waveguides T2 - Nanophotonics: Foundations & Applications, CSF Conference Book of Abstracts Y1 - 2019 SP - B11 ER - TY - JOUR A1 - Klus, Stefan A1 - Husic, Brooke E. A1 - Mollenhauer, Mattes A1 - Noe, Frank T1 - Kernel methods for detecting coherent structures in dynamical data JF - Chaos: An Interdisciplinary Journal of Nonlinear Science Y1 - 2019 U6 - https://doi.org/10.1063/1.5100267 VL - 29 IS - 12 ER - TY - JOUR A1 - Ege, Yannic A1 - Foth, Christian A1 - Baum, Daniel A1 - Wirkner, Christian S. A1 - Richter, Stefan T1 - Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability JF - Zoomorphology N2 - An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00488-z VL - 139 SP - 421 EP - 432 ER - TY - THES A1 - Kostré, Margarita T1 - Hybrid Models and Simulations of Reaction-Diffusion Processes N2 - In this thesis,we are interested in multiscale models for particle-based reaction diffusion (PBRD) simulations,where we focus on coupling particle-based simulations to macroscopic chemical reservoirs. These reservoirs are given by a mean concentration of chemical species that can vary in time and space. We model these reservoirs as reaction-diffusion partial differential equations (PDEs). The goal of this work is to achieve a mathematically consistent coupling between the PBRD simulations and the reaction-diffusion PDEs. Y1 - 2019 ER - TY - GEN A1 - Becker, Kai-Helge A1 - Hiller, Benjamin T1 - Efficient Enumeration of Acyclic Graph Orientations with Sources or Sinks Revisited N2 - In a recent paper, Conte et al. [CGMR2017] presented an algorithm for enumerating all acyclic orientations of a graph G=(V,E) with a single source (and related orientations) with delay O(|V||E|). In this paper we revisit the problem by going back to an early paper by de Fraysseix et al. [FMR1995], who proposed an algorithm for enumerating all bipolar orientations of a graph based on a recursion formula. We first formalize de Fraysseix et al.'s algorithm for bipolar orientations and determine that its delay is also O(|V||E|). We then apply their recursion formula to the case of Conte et al.'s enumeration problem and show that this yields a more efficient enumeration algorithm with delay O(\sqrt(|V|)|E|). Finally, a way to further streamline the algorithm that leads to a particularly simple implementation is suggested. T3 - ZIB-Report - 20-05 KW - acyclic orientations KW - enumeration algorithm KW - multiple sources and sinks KW - bipolar orientations Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77684 SN - 1438-0064 ER - TY - CHAP A1 - Krause, Rolf A1 - Weiser, Martin T1 - Multilevel augmented Lagrangian solvers for overconstrained contact formulations T2 - ESAIM: ProcS N2 - Multigrid methods for two-body contact problems are mostly based on special mortar discretizations, nonlinear Gauss-Seidel solvers, and solution-adapted coarse grid spaces. Their high computational efficiency comes at the cost of a complex implementation and a nonsymmetric master-slave discretization of the nonpenetration condition. Here we investigate an alternative symmetric and overconstrained segment-to-segment contact formulation that allows for a simple implementation based on standard multigrid and a symmetric treatment of contact boundaries, but leads to nonunique multipliers. For the solution of the arising quadratic programs, we propose augmented Lagrangian multigrid with overlapping block Gauss-Seidel smoothers. Approximation and convergence properties are studied numerically at standard test problems. Y1 - 2021 U6 - https://doi.org/10.1051/proc/202171175 VL - 71 SP - 175 EP - 184 ER - TY - CHAP A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven ED - Reitzenstein, Stephan ED - Heindel, Tobias T1 - Numerical Studies of Integrated Single-Photon Emitters in Low-Index-Contrast Waveguides T2 - 7th International Workshop on Engineering of Quantum Emitter Properties (EQEP) Y1 - 2019 SP - 49 ER - TY - THES A1 - Basaleh, Rascha T1 - Prediction and Analysis of Drugs Inducing Liver Injury (DILI) using ProTox-II Computational-Tool Y1 - 2019 ER - TY - CHAP A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Höhne, Theresa A1 - Zschiedrich, Lin ED - Reitzenstein, Stephan ED - Heindel, Tobias T1 - Numerical methods for simulation and optimization of the extraction efficiency from quantum-dot based single-photon emitters T2 - 7th International Workshop on Engineering of Quantum Emitter Properties (EQEP) Y1 - 2019 SP - 20 ER - TY - THES A1 - Boz, Seyma T1 - Classification of the toxicity profile of the withdrawn drugs using computational prediction platform ProTox-II Y1 - 2019 ER - TY - THES A1 - Wachsmann, Ole T1 - Computational Models for the prediction of drug-induced Nephrotoxicity Y1 - 2019 ER - TY - THES A1 - Rabben, Robert Julian T1 - Bestimmung invarianter Unterräume des Koopman-Operators einer Overdamped Langevin-Dynamik mithilfe eines Muli-Layer Neural Networks Y1 - 2019 ER - TY - THES A1 - Hoffmann, Lara T1 - Automating PCCA+ applied to Eye-Tracking Data Y1 - 2019 ER - TY - CHAP A1 - Binkowski, Felix A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Matijević, Milica ED - Krstić, Marko ED - Beličev, Petra T1 - Numerical optimization of resonant nanophotonic devices T2 - The Seventh International School and Conference on Photonics (PHOTONICA Belgrade) Y1 - 2019 SN - 978-86-7306-153-5 SP - 10 ER - TY - THES A1 - Zumbansen, Max T1 - Parameter estimation of multivalent processes on ITC datasets Y1 - 2019 ER - TY - THES A1 - Donati, Luca T1 - Reweighting methods for Molecular Dynamics N2 - The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems. An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations. In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed. The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation. We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-refubium-24541-6 PB - Freie Universität Berlin ER - TY - THES A1 - Reidelbach, Marco T1 - Optimal Network Generation for the Simulation of Proton Transfer Processes Y1 - 2019 ER - TY - CHAP A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Santiago, Xavier Garcia A1 - Betz, Fridtjof A1 - Burger, Sven ED - Saastamoinen, Kimmo T1 - Spectral Expansion of the Scattering Response of Resonant Nanostructures T2 - EOS Topical Meeting on Diffractive Optics Y1 - 2019 SN - 978-952-68553-8-7 SP - 1 ER - TY - THES A1 - Omari, Mohamed T1 - A Mathematical Model of Bovine Metabolism and Reproduction: Application to Feeding Strategies, Drug Administration and Experimental Design Y1 - 2019 ER - TY - JOUR A1 - Brüning, Jan A1 - Hildebrandt, Thomas A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Lamecker, Hans A1 - Szengel, Angelika A1 - Amiridze, Natalja A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity JF - Scientific Reports N2 - This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations. Integral measures of the nasal resistance, wall shear stresses (WSS) and velocities were calculated as well as cross-sectional areas (CSA). Furthermore, individual WSS and static pressure distributions were mapped onto the average geometry. The average geometry featured an overall more regular shape that resulted in less resistance, reduced wall shear stresses and velocities compared to the median of the 25 geometries. Spatial distributions of WSS and pressure of average geometry agreed well compared to the average distributions of all individual geometries. The minimal CSA of the average geometry was larger than the median of all individual geometries (83.4 vs. 74.7 mm²). The airflow observed within the average geometry of the healthy nasal cavity did not equal the average airflow of the individual geometries. While differences observed for integral measures were notable, the calculated values for the average geometry lay within the distributions of the individual parameters. Spatially resolved parameters differed less prominently. Y1 - 2020 UR - https://rdcu.be/b2irD U6 - https://doi.org/10.1038/s41598-020-60755-3 VL - 3755 IS - 10 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Burger, Sven ED - Asquini, Rita T1 - Light-matter Interaction in Optical Resonators: Spectral Expansion by Riesz Projection T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 1067 ER - TY - CHAP A1 - Kewes, Günter A1 - Binkowski, Felix A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Stete, Felix A1 - Koopman, Wouter A1 - Bargheer, Matias A1 - Benson, Oliver ED - Asquini, Rita T1 - Line Broadening Mechanisms in Hybrid Plasmonic Systems for Strong Coupling T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 704 ER - TY - CHAP A1 - Burger, Sven A1 - Binkowski, Felix A1 - Zschiedrich, Lin ED - Asquini, Rita T1 - Finite Element Simulations of Optical Resonances in Dispersive Nanoresonators T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 699 ER - TY - CHAP A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Asquini, Rita T1 - Computing Optical Resonances in Plasmonic Systems Using a Contour Integral Method T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 1068 ER - TY - THES A1 - Amiridze, Natalja T1 - Morphological indicators for limitations in nasal breathing T1 - Morphologische Indikatoren für Einschränkungen der Nasenatmung N2 - In order to better understand the relationship between shape of the nasal cavity and to find objective classification for breathing obstruction, a population of 25 cases of healthy nasal cavity and 27 cases with diagnosed nasal airway obstruction (NAO) was examined for correlations between morphological, clinical and CFD parameters. For this purpose a workflow was implemented in Tcl to perform automatic measurements of morphological parameters of nasal cavity surfaces in Amira, which has as output a table with all estimated values. Furthermore, the statistical analysis was designed using Python to find the most probable subset of parameters that are predictors of nasal cavity pathology and consisted of correlation analysis, the selection of the best possible subset of parameters that could be used as predictors of clinically stated pathology of the nasal cavity by a logistic regression classifier. As a result, 10 most promising parameters were identified: mean distance between the two isthmuses, left isthmus contour, area ratio between the two isthmuses, left isthmus height, height ratio between the two isthmuses, left isthmus width, right isthmus width, right isthmus hydraulic diameter, mean distance of septal curvature between the septum enclosing walls of the nasal cavity, velocities volume average by expiration. As it turns out, most parameters refer to the isthmus region. This was to be expected since this region plays an important role in the airflow system of the nasal cavity. Y1 - 2020 ER - TY - CHAP A1 - Becker, Christiane A1 - Manley, Phillip A1 - Jäger, Klaus A1 - Eisenhauer, David A1 - Sutter, Johannes A1 - Albrecht, Steve A1 - Zheng, Kaibo A1 - Pullerits, Tonu A1 - Burger, Sven ED - Zhoudi, Said ED - Topa, Antonio T1 - Nanophotonic enhanced perovskite-silicon solar cell devices T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 858 ER - TY - CHAP A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane ED - Zhoudi, Said ED - Topa, Antonio T1 - Nanophotonic Enhancement of Light Out-Coupling for Deep-UV LEDs T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 745 ER - TY - CHAP A1 - Burger, Sven A1 - Binkowski, Felix A1 - Zschiedrich, Lin ED - Zhoudi, Said ED - Topa, Antonio T1 - Computing resonances in nano-photonic devices using Riesz-projection-based methods T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 92 ER - TY - GEN ED - Ernst, Oliver ED - Nobile, Fabio ED - Schillings, Claudia ED - Sullivan, T. J. T1 - Uncertainty Quantification, 11-15 March 2019 T2 - Oberwolfach Reports Y1 - 2019 U6 - https://doi.org/10.4171/OWR/2019/12 VL - 16 IS - 1 SP - 695 EP - 772 ER - TY - THES A1 - Wohlfeil, Benjamin T1 - Integrated fiber grating couplers in silicon photonics Y1 - 2015 U6 - https://doi.org/10.14279/depositonce-4521 ER - TY - GEN A1 - Klimpel, Paul T1 - Kleine Handreichung zum Umgang mit historischen Fotos bei Online-Projekten N2 - Historische Fotos online zu stellen, ist rechtlich betrachtet in vielfacher Hinsicht problematisch. Zum einen ist dies nur zulässig, wenn hierfür entsprechende urheberrechtliche Nutzungsrechte vorliegen oder die Fotos inzwischen gemeinfrei sind. Allerdings unterscheidet das Recht zwischen Fotos als Werken und bloßen „Knipsbildern“, was sich vor allem darauf auswirkt, wie lange Fotos urheberrechtlich geschützt sind. Auf die urheberrechtlichen Fragen bei der Online-Veröffentlichung von Fotos wird im ersten Teil eingegangen. Sind auf Fotos Personen erkennbar, so sind auch die Persönlichkeitsrechte der Abgebildeten zu beachten. In der Regel ist die Online-Veröffentlichung nur mit Zustimmung der Abgebildeten zulässig. Nur in bestimmten Ausnahmefällen dürfen solche Fotos auch ohne ausdrückliche Zustimmung genutzt werden. Hiermit beschäftigt sich der zweite Teil dieser kleinen Handreichung Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77215 ER - TY - JOUR A1 - Rams, Mona A1 - Conrad, Tim T1 - Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting JF - it - Information Technology Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/itit-2019-0048 SN - 2196-7032 VL - 62 IS - 3-4 PB - De Gruyter CY - Oldenbourg ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara A1 - Hoppe, Christian T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care JF - Clinical Microbiology and Infection Y1 - 2019 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 SN - 1469-0691 VL - 25 IS - 3 SP - 380.e9 EP - 380.e16 ER - TY - CHAP A1 - Iravani, Sahar A1 - Conrad, Tim ED - Holzinger, A. ED - Kieseberg, P. ED - Tjoa, A. ED - Weippl, E. T1 - Deep Learning for Proteomics Data for Feature Selection and Classification T2 - Machine Learning and Knowledge Extraction. CD-MAKE 2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-29726-8_19 VL - 11713 PB - Springer, Cham ER - TY - JOUR A1 - Koltai, Péter A1 - Lie, Han Cheng A1 - Plonka, Martin T1 - Fréchet differentiable drift dependence of Perron–Frobenius and Koopman operators for non-deterministic dynamics JF - Nonlinearity N2 - We prove the Fréchet differentiability with respect to the drift of Perron–Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron–Frobenius and Koopman operators. Y1 - 2019 U6 - https://doi.org/10.1088/1361-6544/ab1f2a VL - 32 IS - 11 SP - 4232 EP - 4257 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Winkelmann, Stefanie A1 - Wolf, Sarah A1 - Schütte, Christof T1 - Agent-based modeling: Population limits and large timescales JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - Modeling, simulation and analysis of interacting agent systems is a broad field of research, with existing approaches reaching from informal descriptions of interaction dynamics to more formal, mathematical models. In this paper, we study agent-based models (ABMs) given as continuous-time stochastic processes and their pathwise approximation by ordinary and stochastic differential equations (ODEs and SDEs, respectively) for medium to large populations. By means of an appropriately adapted transfer operator approach we study the behavior of the ABM process on long time scales. We show that, under certain conditions, the transfer operator approach allows to bridge the gap between the pathwise results for large populations on finite timescales, i.e., the SDE limit model, and approaches built to study dynamical behavior on long time scales like large deviation theory. The latter provides a rigorous analysis of rare events including the associated asymptotic rates on timescales that scale exponentially with the population size. We demonstrate that it is possible to reveal metastable structures and timescales of rare events of the ABM process by finite-length trajectories of the SDE process for large enough populations. This approach has the potential to drastically reduce computational effort for the analysis of ABMs. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77309 SN - 1438-0064 VL - 31 IS - 3 ER - TY - JOUR A1 - Sun, Yahui A1 - Rehfeldt, Daniel A1 - Brazil, Marcus A1 - Thomas, Doreen A1 - Halgamuge, Saman T1 - A Physarum-Inspired Algorithm for Minimum-Cost Relay Node Placement in Wireless Sensor Networks JF - IEEE/ACM Transactions on Networking Y1 - 2020 U6 - https://doi.org/10.1109/TNET.2020.2971770 ER - TY - THES A1 - Meitzner, Felix T1 - Influence of Ordinary Differential Equations on Neural Networks N2 - In this thesis, I want to analyze how neural networks trained to resemble a given function based on particular values react to additional knowledge about the function in terms of a differential equation that the function satisfies. In the first chapter, I will recall the definition of initial value problems and discuss the existence and uniqueness of their solutions, as well as touch on a method to numerically approximate them. Furthermore, I will give a mathematical introduction to neural networks. Then, I will consider a system of two first-order differential equations and test how their solution will be approximated by a neural net. In the next step, I want to see how added noise to the training data and the influence of the differential equation on the loss functional of the neural net will affect the error of the predicted solution against the exact data. Furthermore, I will test if this influence can help reduce the amount of necessary data points in order to reach similar degrees of accuracy. Y1 - 2019 ER - TY - THES A1 - Ribera Borrell, Enric T1 - From ergodic infinite-time to finite-time transition path theory Y1 - 2019 ER - TY - THES A1 - Gaedke-Merzhäuser, Lisa T1 - Adaptive Multigrid Solvers for Space-Time Discretisations Y1 - 2019 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Ribera Borrell, Enric A1 - Schütte, Christof A1 - Koltai, Peter T1 - Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics JF - Journal of Nonlinear Science Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s00332-020-09652-7 VL - 30 SP - 3321 EP - 3366 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Becker, Christiane T1 - Detailed illumination model for bifacial solar cells JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.383570 VL - 28 SP - 4751 ER - TY - THES A1 - Weltsch, André T1 - Fast Approximation of Equations of transient Gasflow Y1 - 2018 ER - TY - THES A1 - Mexi, Gioni T1 - Node Partitioning and Subtours Creation Problem (NPSC) Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77094 ER - TY - THES A1 - Bender, Wilhelm T1 - On a Novel Approach for Global Optimization of Non-Convex Problems N2 - In this work new approaches for global optimization are developed. We move from theoretical connections in complexity theory to very practical results in protein-ligand docking. In regard to the efficiency of the suggested optimizer, continuity methods are motivated, that yield an improved optimization method. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77074 ER - TY - JOUR A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage JF - Bone N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. Y1 - 2020 U6 - https://doi.org/10.1016/j.bone.2020.115264 VL - 134 SP - 115264 ER - TY - CHAP A1 - Serrano, Felipe A1 - Muñoz, Gonzalo T1 - Maximal Quadratic-Free Sets T2 - Integer Programming and Combinatorial Optimization: 21th International Conference, IPCO 2020 N2 - The intersection cut paradigm is a powerful framework that facilitates the generation of valid linear inequalities, or cutting planes, for a potentially complex set S. The key ingredients in this construction are a simplicial conic relaxation of S and an S-free set: a convex zone whose interior does not intersect S. Ideally, such S-free set would be maximal inclusion-wise, as it would generate a deeper cutting plane. However, maximality can be a challenging goal in general. In this work, we show how to construct maximal S-free sets when S is defined as a general quadratic inequality. Our maximal S-free sets are such that efficient separation of a vertex in LP-based approaches to quadratically constrained problems is guaranteed. To the best of our knowledge, this work is the first to provide maximal quadratic-free sets. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-45771-6_24 SP - 307 EP - 321 ER - TY - THES A1 - Wegscheider, Fabian T1 - Exploiting Symmetry in Mixed-Integer Nonlinear Programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77055 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Schiela, Anton A1 - Weiser, Martin T1 - Kaskade 7 - a Flexible Finite Element Toolbox JF - Computers and Mathematics with Applications N2 - Kaskade 7 is a finite element toolbox for the solution of stationary or transient systems of partial differential equations, aimed at supporting application-oriented research in numerical analysis and scientific computing. The library is written in C++ and is based on the \textsc{Dune} interface. The code is independent of spatial dimension and works with different grid managers. An important feature is the mix-and-match approach to discretizing systems of PDEs with different ansatz and test spaces for all variables. We describe the mathematical concepts behind the library as well as its structure, illustrating its use at several examples on the way. Y1 - 2021 U6 - https://doi.org/10.1016/j.camwa.2020.02.011 VL - 81 SP - 444 EP - 458 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Olthoff, Mats T1 - A Solution Approach to the Vehicle Routing Problem with Perishable Goods N2 - This paper focuses on a special case of vehicle routing problem where perishable goods are considered. Deliveries have to be performed until a due date date, which may vary for different products. Storing products is prohibited. Since late deliveries have a direct impact on the revenues for these products, a precise demand prediction is important. In our practical case the product demands and vehicle driving times for the product delivery are dependent on weather conditions, i.e., temperatures, wind, and precipitation. In this paper the definition and a solution approach to the Vehicle Routing Problem with Perishable Goods is presented. The approach includes a procedure how historical weather data is used to predict demands and driving times. Its run time and solution quality is evaluated on different data sets given by the MOPTA Competition 2018. T3 - ZIB-Report - 20-03 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77020 SN - 1438-0064 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Olthoff, Mats T1 - A Solution Approach to the Vehicle Routing Problem with Perishable Goods T2 - Operations Research 2019 Proceedings N2 - This paper focuses on a special case of vehicle routing problem where perishable goods are considered. Deliveries have to be performed until a due date date, which may vary for different products. Storing products is prohibited. Since late deliveries have a direct impact on the revenues for these products, a precise demand prediction is important. In our practical case the product demands and vehicle driving times for the product delivery are dependent on weather conditions, i.e., temperatures, wind, and precipitation. In this paper the definition and a solution approach to the Vehicle Routing Problem with Perishable Goods is presented. The approach includes a procedure how historical weather data is used to predict demands and driving times. Its run time and solution quality is evaluated on different data sets given by the MOPTA Competition 2018. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77020 ER - TY - CHAP A1 - Weinhold, Carsten A1 - Lackorzynski, Adam A1 - Bierbaum, Jan A1 - Küttler, Martin A1 - Planeta, Maksym A1 - Weisbach, Hannes A1 - Hille, Matthias A1 - Härtig, Hermann A1 - Margolin, Alexander A1 - Sharf, Dror A1 - Levy, Ely A1 - Gak, Pavel A1 - Barak, Amnon A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Lieber, Matthias A1 - Nagel, Wolfgang T1 - FFMK: A Fast and Fault-Tolerant Microkernel-Based System for Exascale Computing T2 - Software for Exascale Computing - SPPEXA 2016-2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-47956-5_16 SP - 483 EP - 516 PB - Springer ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - General design formalism for highly efficient flat optics for broadband applications JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.386573 VL - 28 SP - 6452 ER - TY - JOUR A1 - Tesch, Alexander T1 - A Polyhedral Study of Event-Based Models for the Resource-Constrained Project Scheduling Problem JF - Journal of Scheduling N2 - We consider event-based Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP) that represent an alternative to the common time-indexed model (DDT) of Pritsker et al. (1969) for the case where the underlying time horizon is large or job processing times are subject to huge variations. In contrast to the time-indexed model, the size of event-based models does not depend on the time horizon. For two event-based formulations OOE and SEE of Koné et al. (2011) we present new valid inequalities that dominate the original formulation. Additionally, we introduce a new event-based model: the Interval Event-Based Model (IEE). We deduce linear transformations between all three models that yield the strict domination order IEE > SEE > OOE for their linear programming (LP) relaxations, meaning that IEE has the strongest linear relaxation among the event-based models. We further show that the popular DDT formulation can be retrieved from IEE by certain polyhedral operations, thus giving a unifying view on a complete branch of MIP formulations for the RCPSP. In addition, we analyze the computational performance of all presented models on test instances of the PSPLIB (Kolisch and Sprecher 1997). Y1 - 2020 ER - TY - JOUR A1 - Chen, Ying A1 - Xu, Xiuqin A1 - Koch, Thorsten T1 - Day-ahead high-resolution forecasting of natural gas demand and supply in Germany with a hybrid model JF - Applied Energy N2 - As the natural gas market is moving towards short-term planning, accurate and robust short-term forecasts of the demand and supply of natural gas is of fundamental importance for a stable energy supply, a natural gas control schedule, and transport operation on a daily basis. We propose a hybrid forecast model, Functional AutoRegressive and Convolutional Neural Network model, based on state-of-the-art statistical modeling and artificial neural networks. We conduct short-term forecasting of the hourly natural gas flows of 92 distribution nodes in the German high-pressure gas pipeline network, showing that the proposed model provides nice and stable accuracy for different types of nodes. It outperforms all the alternative models, with an improved relative accuracy up to twofold for plant nodes and up to fourfold for municipal nodes. For the border nodes with rather flat gas flows, it has an accuracy that is comparable to the best performing alternative model. KW - Natural gas flow forecasting KW - Neural network KW - Hybrid model KW - Functional autoregressive Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1016/j.apenergy.2019.114486 VL - 262 IS - 114486 ER - TY - JOUR A1 - Khorashad, Larousse Khosravi A1 - Besteiro, Lucas V. A1 - Correa-Duarte, Miguel A1 - Burger, Sven A1 - Wang, Zhiming M. A1 - Govorov, Alexander O. T1 - Hot electrons generated in chiral plasmonic nanocrystals as a mechanism for surface photochemistry and chiral growth JF - J. Am. Chem. Soc. Y1 - 2020 U6 - https://doi.org/10.1021/jacs.9b11124 VL - 142 SP - 4193 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Teckentrup, Aretha T1 - Error bounds for some approximate posterior measures in Bayesian inference JF - Numerical Mathematics and Advanced Applications ENUMATH 2019 Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-55874-1_26 SP - 275 EP - 283 PB - Springer ER - TY - BOOK A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Stochastic Dynamics in Computational Biology T3 - Frontiers in Applied Dynamical Systems: Reviews and Tutorials Y1 - 2020 SN - 978-3-030-62386-9 U6 - https://doi.org/10.1007/978-3-030-62387-6 VL - 8 PB - Springer International Publishing ER - TY - JOUR A1 - Stoop, Ralph L. A1 - Straube, Arthur A1 - Johansen, Tom H. A1 - Tierno, Pietro T1 - Collective directional locking of colloidal monolayers on a periodic substrate JF - Phys. Rev. Lett. N2 - We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.058002 VL - 124 SP - 058002 ER - TY - GEN A1 - Serrano, Felipe A1 - Muñoz, Gonzalo T1 - Maximal Quadratic-Free Sets N2 - The intersection cut paradigm is a powerful framework that facilitates the generation of valid linear inequalities, or cutting planes, for a potentially complex set S. The key ingredients in this construction are a simplicial conic relaxation of S and an S-free set: a convex zone whose interior does not intersect S. Ideally, such S-free set would be maximal inclusion-wise, as it would generate a deeper cutting plane. However, maximality can be a challenging goal in general. In this work, we show how to construct maximal S-free sets when S is defined as a general quadratic inequality. Our maximal S-free sets are such that efficient separation of a vertex in LP-based approaches to quadratically constrained problems is guaranteed. To the best of our knowledge, this work is the first to provide maximal quadratic-free sets. T3 - ZIB-Report - 19-56 KW - MINLP KW - Quadratic Optimization KW - Cutting planes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-76922 SN - 1438-0064 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Compression Challenges in Large Scale Partial Differential Equation Solvers JF - Algorithms N2 - Solvers for partial differential equations (PDEs) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that need to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to the relatively small arithmetic intensity, and increasingly due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers over the recent decades. This paper surveys data compression challenges and discusses examples of corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to the main memory. We illustrate concepts for particular methods, with examples, and give references to alternatives. Y1 - 2019 U6 - https://doi.org/10.3390/a12090197 VL - 12 IS - 9 SP - 197 ER - TY - JOUR A1 - Straube, Arthur A1 - Pagès, Josep M. A1 - Tierno, Pietro A1 - Ignés-Mullol, Jordi A1 - Sagués, Francesc T1 - Collective dynamics and conformal ordering in electrophoretically driven nematic colloids JF - Phys. Rev. Research N2 - We present a theoretical framework to understand the collective dynamics of an ensemble of electrophoretically driven colloidal particles that are forced to assemble around a single topological defect in a nematic liquid crystal by an alternating current electric field. Our generic model combines phoretic propulsion with electrostatic interactions and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while nematic elasticity plays a subdominant role. Simulations based on this model fully capture the collective organization process observed in the experiments and other striking effects as the emergence of conformal ordering and a nearly frequency-independent repulsive interaction above 10Hz. Our results demonstrate the importance of hydrodynamic interactions on the assembly of driven microscale matter in anisotropic media. Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevResearch.1.022008 VL - 1 SP - 022008 ER - TY - JOUR A1 - Abbott, Joshua L. A1 - Straube, Arthur A1 - Aarts, Dirk G. A. L. A1 - Dullens, Roel P. A. T1 - Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape JF - New J. Phys. N2 - A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking. Y1 - 2019 U6 - https://doi.org/10.1088/1367-2630/ab3765 VL - 21 SP - 083027 ER - TY - CHAP A1 - Mayer, Florian A1 - Knaust, Marius A1 - Philippsen, Michael T1 - OpenMP on FPGAs—A Survey T2 - OpenMP: Conquering the Full Hardware Spectrum N2 - Due to the ubiquity of OpenMP and the rise of FPGA-based accelerators in the HPC world, several research groups have attempted to bring the two together by building OpenMP-to-FPGA compilers. This paper is a survey of the current state of the art (with a focus on the OpenMP target pragma). It first introduces and explains a design space for the compilers. Design space dimensions include how FPGA infrastructure is generated, how work is distributed, and where/how target outlining is done. A table concisely condenses the available information on the surveyed projects which are also summarized and compared. The paper concludes with possible future research directions. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-28596-8_7 SP - 94 EP - 108 ER - TY - CHAP A1 - Knaust, Marius A1 - Mayer, Florian A1 - Steinke, Thomas T1 - OpenMP to FPGA Offloading Prototype Using OpenCL SDK T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) N2 - Field-programmable gate arrays (FPGAs) are of great interest for future high-performance computing and data analytics systems, since they are capable of efficient, highly-parallel data processing. Even though high-level synthesis became more popular in the last years, the effort of porting existing scientific software onto FPGAs is still considerable. We propose to use OpenMP target offloading as a solution, which we implement in a first prototype, making use of the preexisting OpenCL SDK of the FPGA vendor. Early results demonstrate the feasibility of this approach and also reveal that further optimizations will be necessary such that code can be written in an FPGA-agnostic way. Y1 - 2019 U6 - https://doi.org/10.1109/IPDPSW.2019.00072 SP - 387 EP - 390 ER - TY - JOUR A1 - Pflüger, Mika A1 - Kline, R. Joseph A1 - Fernández Herrero, Analia A1 - Hammerschmidt, Martin A1 - Soltwisch, Victor A1 - Krumrey, Michael T1 - Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering JF - J. Micro Nanolithogr. MEMS MOEMS Y1 - 2020 U6 - https://doi.org/10.1117/1.JMM.19.1.014001 VL - 19 SP - 014001 ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Optimal degree of centralization of liquidity management T2 - Proceedings of 22nd Australasian Finance and Banking Conference Y1 - 2009 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1458963 ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Rank of random half-integral polytopes T2 - Electronic Notes in Discrete Mathematics Y1 - 2010 UR - http://www.box.net/shared/0zx04174bg N1 - Additional Note: doi:10.1016/j.endm.2010.05.053 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.endm.2010.05.053 VL - 36 SP - 415 EP - 422 ER - TY - CHAP A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Cutting-planes for weakly-coupled 0/1 second order cone programs T2 - Electronic Notes in Discrete Mathematics Y1 - 2010 UR - http://www.box.net/shared/4k2qtsl65k N1 - Additional Note: doi:10.1016/j.endm.2010.05.093 N1 - URL of the PDF: http://dx.doi.org/j.endm.2010.05.093 VL - 36 SP - 735 EP - 742 ER - TY - CHAP A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Geometric mean maximization in the presence of discrete decisions T2 - Proceedings of 23rd Australasian Finance and Banking Conference Y1 - 2010 ER - TY - CHAP A1 - Martin, Alexander A1 - Müller, J. A1 - Pokutta, Sebastian T1 - On clearing coupled day-ahead electricity markets T2 - Proceedings of 23rd Australasian Finance and Banking Conference Y1 - 2010 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1660528 N1 - Additional Note: doi:10.1080/10556788.2013.823544 ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Schulz, A.S. T1 - On the rank of generic cutting-plane proof systems T2 - Proceedings of IPCO, Lecture Notes in Computer Science Y1 - 2010 UR - http://www.optimization-online.org/DB_HTML/2013/02/3782.html N1 - Additional Note: doi:10.1007/978-3-642-13036-6_34 N1 - URL of the PDF: http://dx.doi.org/10.1007/978-3-642-13036-6_34 VL - 6080 SP - 450 EP - 463 ER - TY - CHAP A1 - Dey, Santanu Sabush A1 - Pokutta, Sebastian T1 - Design and verify: a new scheme for generating cutting-planes T2 - Proceedings of IPCO, Lecture Notes in Computer Science Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2011/04/3002.html N1 - Additional Note: DOI: 10.1007/978-3-642-20807-2_12 VL - 6655 SP - 143 EP - 155 ER - TY - CHAP A1 - Helmke, H. A1 - Gluchshenko, O. A1 - Martin, Alexander A1 - Peter, A. A1 - Pokutta, Sebastian A1 - Siebert, U. T1 - Optimal Mixed-Mode Runway Scheduling T2 - Proceedings of DACS Y1 - 2011 UR - http://www.box.net/shared/34p1ea2of7exdgq7tlty ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - A network model for bank lending capacity T2 - Proceedings of Systemic Risk, Basel III, Financial Stability and Regulation Y1 - 2011 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1773964 ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Optimal Planning under Basel III Regulations T2 - Proceedings of 24th Australasian Finance and Banking Conference Y1 - 2011 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1914800 ER - TY - CHAP A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Steurer, D. T1 - Approximation Limits of Linear Programs (Beyond Hierarchies) T2 - Proceedings of FOCS Y1 - 2012 ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - An algebraic view on symmetric extended formulations T2 - Proceedings of ISCO, Lecture Notes in Computer Science Y1 - 2012 VL - 7422 IS - 141--152 ER - TY - CHAP A1 - Fiorini, Samuel A1 - Massar, S. A1 - Pokutta, Sebastian A1 - Tiwary, H.R. A1 - de Wolf, R. T1 - Linear vs. Semidefinite Extended Formulations: Exponential Separation and Strong Lower Bounds T2 - Proceedings of STOC Y1 - 2012 ER - TY - CHAP A1 - Schmaltz, Christian A1 - Pokutta, Sebastian A1 - Heidorn, Thomas A1 - Andrae, Silvio T1 - How to make regulators and shareholders happy under Basel III T2 - Proceedings of the 26th Australasian Finance and Banking Conference Y1 - 2013 UR - http://ssrn.com/abstract=2179490 N1 - Additional Note: 10.1016/j.jbankfin.2014.05.031 ER - TY - CHAP A1 - Briët, Jop A1 - Dadush, Daniel A1 - Pokutta, Sebastian T1 - On the existence of 0/1 polytopes with high semidefinite extension complexity T2 - Proceedings of ESA Y1 - 2013 ER - TY - CHAP A1 - Braun, Gabor A1 - Pokutta, Sebastian T1 - Foundations of Computer Science (FOCS), 2013 IEEE 54th Annual Symposium T2 - Foundations of Computer Science (FOCS), 2013 IEEE 54th Annual Symposium Y1 - 2013 UR - http://eccc.hpi-web.de/report/2013/056 SP - 688 EP - 697 ER - TY - CHAP A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian T1 - Average case polyhedral complexity of the maximum stable set problem T2 - Proceedings of RANDOM Y1 - 2014 N1 - Additional Note: http://www.dagstuhl.de/dagpub/978-3-939897-74-3 N1 - URL of the PDF: http://www.dagstuhl.de/dagpub/978-3-939897-74-3 ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Xie, Y. T1 - Info-Greedy Sequential Adaptive Compressed Sensing T2 - Proceedings of 52nd Annual Allerton Conference on Communication, Control, and Computing Y1 - 2014 ER - TY - CHAP A1 - Bazzi, Abbas A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Svensson, Ola T1 - Small linear programs cannot approximate Vertex Cover within a factor of 2 - epsilon T2 - Proceedings of FOCS Y1 - 2015 N1 - URL of the Slides: https://app.box.com/s/00aqupo722bbpmdcyzwt8xmfqzyu14iy ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - The matching polytope does not admit fully-polynomial size relaxation schemes T2 - Proceeedings of SODA Y1 - 2015 ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Inapproximability of combinatorial problems via small LPs and SDPs T2 - Proceeedings of STOC Y1 - 2015 ER - TY - CHAP A1 - Pokutta, Sebastian T1 - Information Theory and Polyhedral Combinatorics T2 - Proceedings of 53rd Annual Allerton Conference on Communication, Control, and Computing Y1 - 2015 N1 - Additional Note: http://ieeexplore.ieee.org/abstract/document/7447134/ N1 - URL of the PDF: http://ieeexplore.ieee.org/abstract/document/7447134/ ER - TY - CHAP A1 - Song, R. A1 - Xie, Y. A1 - Pokutta, Sebastian T1 - Sequential Sensing with Model Mismatch T2 - Proceedings of ISIT Y1 - 2015 ER - TY - CHAP A1 - Xie, Y. A1 - Li, Q. A1 - Pokutta, Sebastian T1 - Supervised Online Subspace Tracking T2 - Proceedings of Asilomar Conference on Signals, Systems, and Computers Y1 - 2015 ER - TY - CHAP A1 - Roy, Aurko A1 - Pokutta, Sebastian T1 - Hierarchical Clustering via Spreading Metrics T2 - Proceedings of NIPS Y1 - 2016 N1 - Additional Note: http://https://papers.nips.cc/paper/by-source-2016-1199 https://arxiv.org/abs/1610.09269 N1 - URL of the PDF: https://papers.nips.cc/paper/by-source-2016-1199 ER - TY - CHAP A1 - Braun, Gábor A1 - Roy, Aurko A1 - Pokutta, Sebastian T1 - Stronger Reductions for Extended Formulations T2 - Proceedings of IPCO Y1 - 2016 ER - TY - CHAP A1 - Braun, Gábor A1 - Brown-Cohen, Jonah A1 - Huq, Arefin A1 - Pokutta, Sebastian A1 - Raghavendra, Prasad A1 - Weitz, Benjamin A1 - Zink, Daniel T1 - The matching problem has no small symmetric SDP T2 - Proceddings of SODA 2016 Y1 - 2016 N1 - URL of the PDF: http://ieeexplore.ieee.org/abstract/document/7447134/ ER - TY - CHAP A1 - Roy, Aurko A1 - Xu, Huan A1 - Pokutta, Sebastian T1 - Reinforcement Learning under Model Mismatch T2 - Proceedings of NIPS Y1 - 2017 N1 - Additional Note: http://https://papers.nips.cc/paper/by-source-2016-1199 https://arxiv.org/abs/1610.09269 ER - TY - CHAP A1 - Bärmann, Andreas A1 - Pokutta, Sebastian A1 - Schneider, Oskar T1 - Emulating the Expert: Inverse Optimization through Online Learning T2 - Proceedings of the International Conference on Machine Learning (ICML) Y1 - 2017 N1 - URL of the PDF: http://proceedings.mlr.press/v70/barmann17a.html N1 - URL of the Poster: https://app.box.com/s/h3ychkv99il7oyzw7sym8la5lhit3elg N1 - URL of the Slides: https://app.box.com/s/7ti8sz8mf5s2znn1qo32in4jxy5gjnn1 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2018/11/25/expertLearning-abstract.html ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Lazifying Conditional Gradient Algorithms T2 - Proceedings of the International Conference on Machine Learning (ICML) Y1 - 2017 N1 - URL of the PDF: http://proceedings.mlr.press/v70/braun17a N1 - URL of the Poster: https://app.box.com/s/lysscdg17ytpz7mqr0tu2djffyqvkl6a N1 - URL of the Slides: https://app.box.com/s/zsp0hixjz2ha23u1vuyosijjkjdh8kj7 ER - TY - CHAP A1 - Arumugam, Keerthi Suria Kumar A1 - Kadampot, Ishaque Ashar A1 - Tahmasbi, Mehrdad A1 - Shah, Shaswat A1 - Bloch, Matthieu A1 - Pokutta, Sebastian T1 - Modulation Recognition Using Side Information and Hybrid Learning T2 - Proceedings of IEEE DySPAN Y1 - 2017 ER - TY - CHAP A1 - Lan, G. A1 - Pokutta, Sebastian A1 - Zhou, Y. A1 - Zink, Daniel T1 - Conditional Accelerated Lazy Stochastic Gradient Descent T2 - Proceedings of the International Conference on Machine Learning (ICML) Y1 - 2017 N1 - URL of the PDF: http://proceedings.mlr.press/v70/lan17a.html N1 - URL of the Poster: https://app.box.com/s/wnwym0p3eby54abb5bidnz7gznlkentq ER - TY - CHAP A1 - Inanlouganji, A. A1 - Pedrielli, G. A1 - Fainekos, G. A1 - Pokutta, Sebastian T1 - Continuous Simulation Optimization with Model Mismatch Using Gaussian Process Regression T2 - Proceedings of the 2018 Winter Simulation Conference Y1 - 2018 ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Efficient algorithms for robust submodular maximization under matroid constraints T2 - ICML Workshop Paper Y1 - 2018 N1 - Additional Note: https://arxiv.org/abs/1807.09405 N1 - URL of the PDF: https://sites.google.com/view/icml2018nonconvex/papers ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Tu, Dan A1 - Wright, Stephen T1 - Blended Conditional Gradients: the unconditioning of conditional gradients T2 - Proceedings of ICML Y1 - 2019 N1 - Additional Note: https://arxiv.org/abs/1805.07311 N1 - URL of the Code: https://github.com/pokutta/bcg N1 - URL of the PDF: http://proceedings.mlr.press/v97/braun19a/braun19a.pdf N1 - URL of the Poster: https://app.box.com/s/nmmm671jd72i397nysa8emfnzh1hn6hf N1 - URL of the Slides: https://app.box.com/s/xbx3z7ws6dxvl3rzgj4jp6forigycooe N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/02/18/bcg-abstract.html ER - TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Breaking the Curse of Dimensionality (Locally) to Accelerate Conditional Gradients T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_26.pdf N1 - URL of the Poster: https://app.box.com/s/d7p038u7df422q4jsccbmj15mngqv2ws N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Blended Matching Pursuit T2 - Proceedings of NeurIPS Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/17XYIxnCcJjKswba9mAaXFWnNGVZdsaXQ N1 - URL of the PDF: https://papers.nips.cc/paper/8478-blended-matching-pursuit N1 - URL of the Poster: https://app.box.com/s/j6lbh49udjd45krhxcypufxwdofw6br8 N1 - URL of the Slides: https://app.box.com/s/8lfktq6h3dqp9t2gqydu2tp8h2uxgz7m N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/27/bmp-abstract.html ER - TY - CHAP A1 - Kerdreux, T. A1 - d’Aspremont, A. A1 - Pokutta, Sebastian T1 - Restarting Frank-Wolfe T2 - Proceedings of AISTATS Y1 - 2019 N1 - URL of the PDF: http://proceedings.mlr.press/v89/kerdreux19a/kerdreux19a.pdf N1 - URL of the Slides: https://app.box.com/s/prd32r6xmuef2k4gah23rd0egllz9rv5 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/02/restartfw-abstract.html ER - TY - CHAP A1 - Anari, N. A1 - Haghtalab, N. A1 - Naor, S. A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Structured Robust Submodular Maximization: Offline and Online Algorithms T2 - Proceedings of AISTATS Y1 - 2019 N1 - URL of the PDF: http://proceedings.mlr.press/v89/anari19a/anari19a.pdf ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_16.pdf N1 - URL of the Poster: https://app.box.com/s/24vbh1s2vib11upqyepzen3lzdl13skr ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Strüngmann, L. T1 - The Chase radical and reduced products JF - Journal of Pure and Applied Algebra Y1 - 2007 N1 - Additional Note: doi:10.1016/j.jpaa.2007.02.007 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jpaa.2007.02.007 VL - 211 SP - 532 EP - 540 ER - TY - JOUR A1 - Droste, M. A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Absolute graphs with prescribed endomorphism monoid JF - Semigroup Forum Y1 - 2008 N1 - URL of the PDF: http://dx.doi.org/doi:10.1007/s00233-007-9029-1 VL - 76 SP - 256 EP - 267 ER - TY - JOUR A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Construction of dual modules using Martin’s axiom JF - Journal of Algebra Y1 - 2008 N1 - Additional Note: doi:10.1016/j.jalgebra.2008.06.017 N1 - URL of the PDF: https://www.sciencedirect.com/science/article/pii/S0021869308003153 VL - 320 SP - 2388 EP - 2404 ER - TY - JOUR A1 - Heldt, D. A1 - Kreuzer, M. A1 - Pokutta, Sebastian A1 - Poulisse, H. T1 - Approximate Computation of zero-dimensional polynomial ideals JF - Journal of Symbolic Computation Y1 - 2009 N1 - Additional Note: doi:10.1016/j.jsc.2008.11.010 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jsc.2008.11.010 VL - 44 SP - 1566 EP - 1591 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Stauffer, G. T1 - France Telecom Workforce Scheduling Problem: a challenge JF - RAIRO-Operations Research Y1 - 2009 N1 - Additional Note: DOI: 10.1051/ro/2009025 N1 - URL of the PDF: http://dx.doi.org/10.1051/ro/2009025 IS - 43 SP - 375 EP - 386 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Random half-integral polytopes JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/11/2813.html N1 - Additional Note: doi:10.1016/j.orl.2011.03.003 VL - 39 IS - 3 SP - 204 EP - 207 ER - TY - JOUR A1 - Haus, Utz-Uwe A1 - Hemmecke, R. A1 - Pokutta, Sebastian T1 - Reconstructing biochemical cluster networks JF - Journal of Mathematical Chemistry Y1 - 2011 N1 - URL of the PDF: http://dx.doi.org/10.1007/s10910-011-9892-6 VL - 49 IS - 10 SP - 2441 EP - 2456 ER - TY - JOUR A1 - Letchford, A.N. A1 - Pokutta, Sebastian A1 - Schulz, A.S. T1 - On the membership problem for the 0,1/2-closure JF - Operations Research Letters Y1 - 2011 UR - http://www.box.net/shared/zxx88q38l3 N1 - Additional Note: doi:10.1016/j.orl.2011.07.003 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.07.003 VL - 39 IS - 5 SP - 301 EP - 304 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schulz, A.S. T1 - Integer-empty polytopes in the 0/1-cube with maximal Gomory-Chvátal rank JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/12/2850.html N1 - Additional Note: doi:10.1016/j.orl.2011.09.004 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.09.004 VL - 39 IS - 6 SP - 457 EP - 460 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Managing liquidity: Optimal degree of centralization JF - Journal of Banking and Finance KW - Real options Y1 - 2011 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1458963 U6 - https://doi.org/DOI: 10.1016/j.jbankfin.2010.07.001 SN - 0378-4266 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jbankfin.2010.07.001 VL - 35 SP - 627 EP - 638 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Stauffer, G. T1 - Lower bounds for the Chvátal-Gomory rank in the 0/1 cube JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/09/2748.html N1 - Additional Note: doi:10.1016/j.orl.2011.03.001 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.03.001 VL - 39 IS - 3 SP - 200-203 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Rigid abelian groups and the probabilistic method JF - Contemporary Mathematics Y1 - 2012 N1 - Additional Note: doi:/10.1090/conm/576 N1 - URL of the PDF: http://dx.doi.org/10.1090/conm/576 VL - 576 SP - 17 EP - 30 ER - TY - JOUR A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Absolutely rigid fields and Shelah’s absolutely rigid trees JF - Contemporary Mathematics Y1 - 2012 UR - http://www.box.net/shared/numjyo0qxmpsz9dposyt N1 - Additional Note: doi:/10.1090/conm/576 N1 - URL of the PDF: http://dx.doi.org/10.1090/conm/576 VL - 576 SP - 105 EP - 128 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Optimal Planning under Basel III Regulations JF - Cass-Capco Institute Paper Series on Risk Y1 - 2012 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1914800 N1 - Additional Note: http://www.capco.com/capco-institute/capco-journal/journal-34-cass-capco-institute-paper-series-on-risk N1 - URL of the PDF: http://www.capco.com/capco-institute/capco-journal/journal-34-cass-capco-institute-paper-series-on-risk VL - 34 ER - TY - JOUR A1 - Kroll, C. A1 - Pokutta, Sebastian T1 - Just a perfect day: developing a happiness optimised day schedule JF - Journal of Economic Psychology Y1 - 2013 N1 - Additional Note: doi:/10.1016/j.joep.2012.09.015 N1 - URL of the PDF: http://www.sciencedirect.com/science/article/pii/S0167487012001158 VL - 34 SP - 210 EP - 217 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - VanVyve, M. T1 - A note on the extension complexity of the knapsack polytope JF - Operations Research Letters Y1 - 2013 UR - http://www.optimization-online.org/DB_HTML/2013/02/3787.html N1 - Additional Note: DOI information: 10.1016/j.orl.2013.03.010 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2013.03.010 VL - 41 SP - 347 EP - 350 ER - TY - JOUR A1 - Schmaltz, Christian A1 - Pokutta, Sebastian A1 - Heidorn, Thomas A1 - Andrae, Silvio T1 - How to make regulators and shareholders happy under Basel III JF - Journal of Banking and Finance Y1 - 2014 UR - http://ssrn.com/abstract=2179490 N1 - Additional Note: 10.1016/j.jbankfin.2014.05.031 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jbankfin.2014.05.031 SP - 311 EP - 325 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - A short proof for the polyhedrality of the Chvátal-Gomory closure of a compact convex set JF - Operations Research Letters Y1 - 2014 N1 - Additional Note: 10.1016/j.orl.2014.05.004 VL - 42 SP - 307 EP - 310 ER - TY - JOUR A1 - Dey, Santanu Sabush A1 - Pokutta, Sebastian T1 - Design and verify: a new scheme for generating cutting-planes JF - Mathematical Programming A Y1 - 2014 UR - http://www.optimization-online.org/DB_HTML/2011/04/3002.html N1 - Additional Note: DOI: 10.1007/978-3-642-20807-2_12 VL - 145 SP - 199 EP - 222 ER - TY - JOUR A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Computing discrete expected utility maximizing portfolios JF - Journal of Investing Y1 - 2014 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1662729 VL - 23 IS - 4 SP - 121 EP - 132 ER - TY - JOUR A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Symmetry-exploiting cuts for a class of mixed-0/1 second order cone programs JF - Discrete Optimization Y1 - 2014 UR - http://www.optimization-online.org/DB_HTML/2010/06/2652.html N1 - Additional Note: doi:10.1016/j.disopt.2014.04.002 VL - 13 SP - 23 EP - 35 ER - TY - JOUR A1 - Martin, Alexander A1 - Müller, J. A1 - Pokutta, Sebastian T1 - Strict linear prices in non-convex European day-ahead electricity markets JF - Optimization Methods and Software Y1 - 2014 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1660528 N1 - Additional Note: 10.1080/10556788.2013.823544 N1 - URL of the PDF: http://dx.doi.org/10.1080/10556788.2013.823544 VL - 29 IS - 1 SP - 189 EP - 221 ER - TY - JOUR A1 - Briët, Jop A1 - Dadush, Daniel A1 - Pokutta, Sebastian T1 - On the existence of 0/1 polytopes with high semidefinite extension complexity JF - Mathematical Programming B Y1 - 2015 VL - 153 IS - 1 SP - 179 EP - 199 ER - TY - JOUR A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Steurer, D. T1 - Approximation Limits of Linear Programs (Beyond Hierarchies) JF - Mathematics of Operations Research Y1 - 2015 VL - 40 IS - 3 SP - 179 EP - 199 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - The matching polytope does not admit fully-polynomial size relaxation schemes JF - IEEE Transactions on Information Theory Y1 - 2015 N1 - Additional Note: doi:10.1109/TIT.2015.2465864 N1 - URL of the PDF: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7182355 VL - 61 IS - 10 SP - 1 EP - 11 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Xie, Y. T1 - Info-Greedy Sequential Adaptive Compressed Sensing JF - IEEE Journal of Selected Topics in Signal Processing Y1 - 2015 VL - 9 IS - 4 SP - 601 EP - 611 ER - TY - JOUR A1 - Fiorini, Samuel A1 - Massar, S. A1 - Pokutta, Sebastian A1 - Tiwary, H.R. A1 - de Wolf, R. T1 - Exponential Lower Bounds for Polytopes in Combinatorial Optimization JF - Journal of the ACM Y1 - 2015 N1 - URL of the PDF: https://doi.org/10.1145/2716307 VL - 62 IS - 2 SP - 1 EP - 17 ER - TY - JOUR A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian T1 - Average case polyhedral complexity of the maximum stable set problem JF - Mathematical Programming A Y1 - 2016 N1 - Additional Note: http://www.dagstuhl.de/dagpub/978-3-939897-74-3 N1 - URL of the PDF: https://rdcu.be/7uOy VL - 160 IS - 1 SP - 407 EP - 431 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - A polyhedral characterization of Border Bases JF - SIAM Journal on Discrete Mathematics Y1 - 2016 VL - 30 IS - 1 SP - 239 EP - 265 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Common information and unique disjointness JF - Algorithmica Y1 - 2016 UR - http://eccc.hpi-web.de/report/2013/056 N1 - URL of the PDF: https://rdcu.be/6b9u VL - 76 IS - 3 SP - 597 EP - 629 ER - TY - JOUR A1 - Gatzert, Nadine A1 - Pokutta, Sebastian A1 - Vogl, Nikolai T1 - Convergence of Capital and Insurance Markets: Pricing Aspects of Index-Linked Catastrophic Loss Instruments JF - to appear in Journal of Risk and Insurance Y1 - 2016 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2320370 ER - TY - JOUR A1 - Bärmann, Andreas A1 - Heidt, Andreas A1 - Martin, Alex A1 - er, A1 - Pokutta, Sebastian A1 - Thurner, Christoph T1 - Polyhedral Approximation of Ellipsoidal Uncertainty Sets via Extended Formulations - a computational case study JF - Computational Management Science Y1 - 2016 UR - http://www.optimization-online.org/DB_HTML/2014/02/4245.html N1 - Additional Note: http://link.springer.com/article/10.1007/s10287-015-0243-0 DOI:10.1007/s10287-015-0243-0 N1 - URL of the PDF: http://link.springer.com/article/10.1007/s10287-015-0243-0 VL - 13 IS - 2 SP - 151 EP - 193 ER - TY - JOUR A1 - Roy, Aurko A1 - Pokutta, Sebastian T1 - Hierarchical Clustering via Spreading Metrics JF - Journal of Machine Learning Research (JMLR) Y1 - 2017 N1 - Additional Note: http://https://papers.nips.cc/paper/by-source-2016-1199 N1 - URL of the PDF: http://jmlr.org/papers/v18/17-081.html VL - 18 SP - 1 EP - 35 ER - TY - JOUR A1 - Bodur, Merve A1 - Del Pia, Alberto A1 - Dey, Santanu Sabush A1 - Molinaro, Marco A1 - Pokutta, Sebastian T1 - Aggregation-based cutting-planes for packing and covering Integer Programs JF - to appear in Mathematical Programming A Y1 - 2017 N1 - Additional Note: doi:10.1007/s10107-017-1192-x N1 - URL of the PDF: http://dx.doi.org/10.1007/s10107-017-1192-x ER - TY - JOUR A1 - Bazzi, Abbas A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Svensson, Ola T1 - Small linear programs cannot approximate Vertex Cover within a factor of 2 - epsilon JF - to appear in Mathematics of Operations Research Y1 - 2017 N1 - URL of the Slides: https://app.box.com/s/00aqupo722bbpmdcyzwt8xmfqzyu14iy ER - TY - JOUR A1 - Braun, Gábor A1 - Guzmán, C. A1 - Pokutta, Sebastian T1 - Unifying Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization JF - IEEE Transactions of Information Theory Y1 - 2017 N1 - Additional Note: doi:10.1109/TIT.2017.2701343 http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7919238 N1 - URL of the PDF: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7919238 VL - 63 IS - 7 SP - 4709 EP - 4724 ER - TY - JOUR A1 - Braun, Gábor A1 - Jain, R. A1 - Lee, T. A1 - Pokutta, Sebastian T1 - Information-theoretic approximations of the nonnegative rank JF - Computational Complexity Y1 - 2017 UR - http://eccc.hpi-web.de/report/2013/158 VL - 26 IS - 1 SP - 147 EP - 197 ER - TY - JOUR A1 - Christensen, H. A1 - Khan, A. A1 - Pokutta, Sebastian A1 - Tetali, P. T1 - Multidimensional Bin Packing and Other Related Problems: A survey JF - to appear in Computer Science Review Y1 - 2017 N1 - Additional Note: http://www.sciencedirect.com/science/article/pii/S1574013716301356 http://www.sciencedirect.com/science/article/pii/S1574013716301356 N1 - URL of the PDF: http://www.sciencedirect.com/science/article/pii/S1574013716301356 ER - TY - JOUR A1 - Martin, Alex A1 - Müller, J. A1 - Pape, S. A1 - Peter, A. A1 - Pokutta, Sebastian A1 - Winter, T. T1 - Pricing and clearing combinatorial markets with singleton and swap orders JF - Mathematical Methods of Operations Research Y1 - 2017 VL - 85 IS - 2 SP - 155 EP - 177 ER - TY - JOUR A1 - Knueven, B. A1 - Ostrowski, J. A1 - Pokutta, Sebastian T1 - Detecting Almost Symmetries in Graphs JF - to appear in Mathematical Programming C Y1 - 2017 UR - http://www.optimization-online.org/DB_HTML/2015/09/5117.html N1 - URL of the PDF: http://link.springer.com/article/10.1007/s12532-017-0124-3 ER - TY - JOUR A1 - Braun, Gábor A1 - Brown-Cohen, Jonah A1 - Huq, Arefin A1 - Pokutta, Sebastian A1 - Raghavendra, Prasad A1 - Weitz, Benjamin A1 - Zink, Daniel T1 - The matching problem has no small symmetric SDP JF - Mathematical Programming A Y1 - 2017 N1 - Additional Note: DOI 10.1007/s10107-016-1098-z N1 - URL of the PDF: http://dx.doi.org/10.1007/s10107-016-1098-z VL - 165 IS - 2 SP - 643 EP - 662 ER - TY - JOUR A1 - Le Bodic, P. A1 - Pfetsch, Marc A1 - Pavelka, J. A1 - Pokutta, Sebastian T1 - Solving MIPs via Scaling-based Augmentation JF - Discrete Optimization Y1 - 2018 N1 - Additional Note: doi: 10.1016/j.disopt.2017.08.004 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.disopt.2017.08.004 VL - 27 SP - 1 EP - 25 ER - TY - JOUR A1 - Braun, Gábor A1 - Roy, Aurko A1 - Pokutta, Sebastian T1 - Stronger Reductions for Extended Formulations JF - to appear in Mathematical Programming B Y1 - 2018 N1 - Additional Note: available at \url{http://arxiv.org/abs/1512.04932} ER - TY - JOUR A1 - Song, R. A1 - Xie, Y. A1 - Pokutta, Sebastian T1 - On the effect of model mismatch for sequential Info-Greedy Sensing JF - EURASIP Journal on Advances in Signal Processing Y1 - 2018 N1 - URL of the PDF: https://asp-eurasipjournals.springeropen.com/articles/10.1186/s13634-018-0551-y ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Affine Reductions for LPs and SDPs JF - Mathematical Programming A Y1 - 2019 N1 - URL of the PDF: http://rdcu.be/EPf9 VL - 173 IS - 1 SP - 281 EP - 312 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Lazifying Conditional Gradient Algorithms JF - Journal of Machine Learning Research (JMLR) Y1 - 2019 N1 - URL of the PDF: http://jmlr.org/papers/v20/18-114.html N1 - URL of the Slides: https://app.box.com/s/zsp0hixjz2ha23u1vuyosijjkjdh8kj7 VL - 20 IS - 71 SP - 1 EP - 42 ER - TY - JOUR A1 - Becker, Fabian A1 - Djurdjevac Conrad, Natasa A1 - Eser, Raphael A. A1 - Helfmann, Luzie A1 - Schütt, Brigitta A1 - Schütte, Christof A1 - Zonker, Johannes T1 - The Furnace and the Goat—A spatio-temporal model of the fuelwood requirement for iron metallurgy on Elba Island, 4th century BCE to 2nd century CE JF - PLOS ONE Y1 - 2020 UR - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241133 U6 - https://doi.org/10.1371/journal.pone.0241133 VL - 15 SP - 1 EP - 37 PB - Public Library of Science ER - TY - CHAP A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Geodesic Mixed Effects Model in Kendall's Shape Space T2 - Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA) N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and apply the approach for the estimation of group trends and statistical testing of 3D shapes derived from an open access longitudinal imaging study on osteoarthritis. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-33226-6_22 VL - 11846 SP - 209 EP - 218 ER - TY - CHAP A1 - Müller, Benjamin A1 - Muñoz, Gonzalo A1 - Gasse, Maxime A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Serrano, Felipe T1 - On Generalized Surrogate Duality in Mixed-Integer Nonlinear Programming T2 - Integer Programming and Combinatorial Optimization: 21th International Conference, IPCO 2020 N2 - The most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global epsilon-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solver can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-45771-6_25 SP - 322 EP - 337 ER - TY - CHAP A1 - Devriendt, Jo A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search T2 - Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2020 N2 - Conflict-driven Pseudo-Boolean (PB) solvers optimize 0-1 integer linear programs by extending the conflict-driven clause learning (CDCL) paradigm from SAT solving. Though PB solvers have the potential to be exponentially more efficient than CDCL solvers in theory, in practice they can sometimes get hopelessly stuck even when the linear program (LP) relaxation is infeasible over the reals. Inspired by mixed integer programming (MIP), we address this problem by interleaving incremental LP solving with cut generation within the conflict-driven PB search. This hybrid approach, which for the first time combines MIP techniques with full-blown conflict analysis over linear inequalities using the cutting planes method, significantly improves performance on a wide range of benchmarks, approaching a "best of two worlds" scenario between SAT-style conflict-driven search and MIP-style branch-and-cut. Y1 - 2020 VL - 12296 SP - xxiv EP - xxvi PB - Springer ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - Sullivan, T. J. A1 - von Tycowicz, Christoph T1 - Geodesic Analysis in Kendall's Shape Space with Epidemiological Applications JF - Journal of Mathematical Imaging and Vision N2 - We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall’s shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone. Y1 - 2020 U6 - https://doi.org/10.1007/s10851-020-00945-w VL - 62 IS - 4 SP - 549 EP - 559 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Peitz, Sebastian A1 - Niemann, Jan-Hendrik A1 - Clementi, Cecilia A1 - Schütte, Christof T1 - Data-driven approximation of the Koopman generator: Model reduction, system identification, and control JF - Physica D: Nonlinear Phenomena Y1 - 2020 U6 - https://doi.org/10.1016/j.physd.2020.132416 VL - 406 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Klus, Stefan A1 - Hamzi, Boumediene A1 - Schütte, Christof T1 - Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds JF - Journal of Nonlinear Science N2 - We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework for the computation of optimal reaction coordinates of such systems that is based on learning a parameterization of a low-dimensional transition manifold in a certain function space. In this article, we enhance this approach by embedding and learning this transition manifold in a reproducing kernel Hilbert space, exploiting the favorable properties of kernel embeddings. Under mild assumptions on the kernel, the manifold structure is shown to be preserved under the embedding, and distortion bounds can be derived. This leads to a more robust and more efficient algorithm compared to the previous parameterization approaches. Y1 - 2021 U6 - https://doi.org/10.1007/s00332-020-09668-z VL - 31 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Schütte, Christof T1 - A probabilistic algorithm for aggregating vastly undersampled large Markov chains JF - Physica D: Nonlinear Phenomena Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75874 VL - 416 ER - TY - JOUR A1 - Möller, Jan A1 - Isbilir, Ali A1 - Sungkaworn, Titiwat A1 - Osberg, Brenda A1 - Karathanasis, Christos A1 - Sunkara, Vikram A1 - Grushevsky, Eugene O A1 - Bock, Andreas A1 - Annibale, Paolo A1 - Heilemann, Mike A1 - Schütte, Christof A1 - Lohse, Martin J. T1 - Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision JF - Nature Chemical Biology Y1 - 2020 U6 - https://doi.org/10.1038/s41589-020-0566-1 VL - 16 SP - 946 EP - 954 ER - TY - CHAP A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict-Free Learning for Mixed Integer Programming T2 - Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2020 N2 - Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-58942-4_34 IS - 12296 SP - 521 EP - 530 PB - Springer, Cham. ER - TY - JOUR A1 - Rössig, Ansgar A1 - Petkovic, Milena T1 - Advances in Verification of ReLU Neural Networks JF - Journal of Global Optimization N2 - We consider the problem of verifying linear properties of neural networks. Despite their success in many classification and prediction tasks, neural networks may return unexpected results for certain inputs. This is highly problematic with respect to the application of neural networks for safety-critical tasks, e.g. in autonomous driving. We provide an overview of algorithmic approaches that aim to provide formal guarantees on the behavior of neural networks. Moreover, we present new theoretical results with respect to the approximation of ReLU neural networks. On the other hand, we implement a solver for verification of ReLU neural networks which combines mixed integer programming (MIP) with specialized branching and approximation techniques. To evaluate its performance, we conduct an extensive computational study. For that we use test instances based on the ACAS Xu System and the MNIST handwritten digit data set. Our solver is publicly available and able to solve the verification problem for instances which do not have independent bounds for each input neuron. Y1 - 2020 U6 - https://doi.org/10.1007/s10898-020-00949-1 PB - Springer ER - TY - THES A1 - Rössig, Ansgar T1 - Verification of Neural Networks KW - Neural Network Verification Y1 - 2019 ER - TY - JOUR A1 - Schulz, Robert A1 - Yamamoto, Kenji A1 - Klossek, André A1 - Rancan, Fiorenza A1 - Vogt, Annika A1 - Schütte, Christof A1 - Rühl, Eckart A1 - Netz, Roland R. T1 - Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin JF - Biophysical Journal N2 - Based on experimental drug concentration profiles in healthy as well as tape-stripped ex vivo human skin, we model the penetration of the antiinflammatory drug dexamethasone into the skin layers by the one-dimensional generalized diffusion equation. We estimate the position-dependent free-energy and diffusivity profiles by solving the conjugated minimization problem, in which the only inputs are concentration profiles of dexamethasone in skin at three consecutive penetration times. The resulting free-energy profiles for damaged and healthy skin show only minor differences. In contrast, the drug diffusivity in the first 10 μm of the upper skin layer of damaged skin is 200-fold increased compared to healthy skin, which reflects the corrupted barrier function of tape-stripped skin. For the case of healthy skin, we examine the robustness of our method by analyzing the behavior of the extracted skin parameters when the number of input and output parameters are reduced. We also discuss techniques for the regularization of our parameter extraction method. Y1 - 2019 U6 - https://doi.org/10.1016/j.bpj.2019.07.027 VL - 117 IS - 5 SP - 998 EP - 1008 ER - TY - CHAP A1 - Benner, Peter A1 - Grundel, Sara A1 - Himpe, Christian A1 - Huck, Christoph A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - Gas Network Benchmark Models T2 - Applications of Differential-Algebraic Equations: Examples and Benchmarks N2 - The simulation of gas transportation networks becomes increasingly more important as its use-cases broaden to more complex applications. Classically, the purpose of the gas network was the transportation of predominantly natural gas from a supplier to the consumer for long-term scheduled volumes. With the rise of renewable energy sources, gas-fired power plants are often chosen to compensate for the fluctuating nature of the renewables, due to their on-demand power generation capability. Such an only short-term plannable supply and demand setting requires sophisticated simulations of the gas network prior to the dispatch to ensure the supply of all customers for a range of possible scenarios and to prevent damages to the gas network. In this work we describe the modeling of gas networks and present benchmark systems to test implementations and compare new or extended models. Y1 - 2019 SN - 978-3-030-03718-5 U6 - https://doi.org/10.1007/11221_2018_5 SP - 171 EP - 197 PB - Springer International Publishing ER - TY - GEN ED - Dalitz, Wolfgang T1 - alsoMATH - A Database for Mathematical Algorithms and Software N2 - Mathematical publications are an important resource for the devel- opment of machine-based methods for mathematical knowledge man- agement. This article describes the publication-based approach to improve the information and the access to two important classes of mathematical research, mathematical software and mathematical algo- rithms. The publication-based approach is based on analyzing links and the structure of mathematical publications. It has been used to build the swMATH service which provides comprehensive information about mathematical software and algorithms. Y1 - 2019 U6 - https://doi.org/http://cl-informatik.uibk.ac.at/cek/cicm-wip-tentative/ VL - 2019 PB - Cezary Kaliszyk ER - TY - JOUR A1 - Omari, Mohamed A1 - Lange, Alexander A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows JF - Biology Direct Y1 - 2019 U6 - https://doi.org/10.1186/s13062-019-0256-7 VL - 15 ER - TY - JOUR A1 - Manley, Phillip A1 - Walde, Sebastian A1 - Hagedorn, Sylvia A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Nanopatterned Sapphire Substrates in Deep-UV LEDs: Is there an Optical Benefit? JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.379438 VL - 28 SP - 3619 ER - TY - JOUR A1 - Banyassady, Bahareh A1 - Barba, Luis A1 - Mulzer, Wolfgang T1 - Time-Space Trade-Offs for Computing Euclidean Minimum Spanning Trees JF - Journal of Computational Geometry (JoCG) N2 - We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set S of n point-sites in the plane. More precisely, we assume that S resides in a random-access memory that can only be read. The edges of the Euclidean minimum spanning tree EMST(S) have to be reported sequentially, and they cannot be accessed or modified afterwards. There is a parameter s in {1, ..., n} so that the algorithm may use O(s) cells of read-write memory (called the workspace) for its computations. Our goal is to find an algorithm that has the best possible running time for any given s between 1 and n. We show how to compute EMST(S) in O(((n^3)/(s^2)) log s) time with O(s) cells of workspace, giving a smooth trade-off between the two best-known bounds O(n^3) for s = 1 and O(n log n) for s = n. For this, we run Kruskal's algorithm on the "relative neighborhood graph" (RNG) of S. It is a classic fact that the minimum spanning tree of RNG(S) is exactly EMST(S). To implement Kruskal's algorithm with O(s) cells of workspace, we define s-nets, a compact representation of planar graphs. This allows us to efficiently maintain and update the components of the current minimum spanning forest as the edges are being inserted. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?https://jocg.org/index.php/jocg/article/view/473 VL - 11(1) SP - 525 EP - 547 ER - TY - JOUR A1 - Banyassady, Bahareh A1 - Chiu, Man-Kwun A1 - Korman, Matias A1 - Mulzer, Wolfgang A1 - van Renssen, André A1 - Roeloffzen, Marcel A1 - Seiferth, Paul A1 - Stein, Yannik A1 - Vogtenhuber, Birgit A1 - Willert, Max T1 - Routing in polygonal domains JF - Computational Geometry, Theory and Applications N2 - We consider the problem of routing a data packet through the visibility graph of a polygonal domain P with n vertices and h holes. We may preprocess P to obtain a "label" and a "routing table" for each vertex of P. Then, we must be able to route a data packet between any two vertices p and q of P, where each step must use only the label of the target node q and the routing table of the current node. For any fixed epsilon > 0, we present a routing scheme that always achieves a routing path whose length exceeds the shortest path by a factor of at most 1 + epsilon. The labels have O(log n) bits, and the routing tables are of size O(((epsilon^-1)+h)log n). The preprocessing time is O((n^2)log n). It can be improved to O(n^2) for simple polygons. Y1 - 2019 U6 - https://doi.org/10.1016/j.comgeo.2019.101593 VL - 87 PB - Elsevier ER - TY - JOUR A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Temp, Julia A1 - Seitz, Viola A1 - Kloner, Michael A1 - Negrete, Roger A1 - Rodriguez-Gaztelumendi, Antonio A1 - Weber, Marcus A1 - Machelska, Halina A1 - Stein, Christoph T1 - pKa of opioid ligands as a discriminating factor for side effects JF - Scientific Reports N2 - The non-selective activation of central and peripheral opioid receptors is a major shortcoming of currently available opioids. Targeting peripheral opioid receptors is a promising strategy to preclude side effects. Recently, we showed that fentanyl-derived μ-opioid receptor (MOR) agonists with reduced acid dissociation constants (pKa) due to introducing single fluorine atoms produced injury-restricted antinociception in rat models of inflammatory, postoperative and neuropathic pain. Here, we report that a new double-fluorinated compound (FF6) and fentanyl show similar pKa, MOR affinity and [35S]-GTPγS binding at low and physiological pH values. In vivo, FF6 produced antinociception in injured and non-injured tissue, and induced sedation and constipation. The comparison of several fentanyl derivatives revealed a correlation between pKa values and pH-dependent MOR activation, antinociception and side effects. An opioid ligand's pKa value may be used as discriminating factor to design safer analgesics. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-55886-1 VL - 9 SP - 19344 ER - TY - JOUR A1 - Christgau, Steffen A1 - Schnor, Bettina T1 - Comparing MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor JF - Mitteilungen - Gesellschaft für Informatik e. V., Parallel-Algorithmen und Rechnerstrukturen, ISSN 0177-0454, 28. PARS-Workshop Y1 - 2020 IS - 35 SP - 121 EP - 132 ER - TY - JOUR A1 - Dibak, Manuel A1 - Fröhner, Christoph A1 - Noé, Frank A1 - Höfling, Felix T1 - Diffusion-influenced reaction rates in the presence of pair interactions JF - The Journal of Chemical Physics N2 - The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi’s volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction–diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction–diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions. Y1 - 2019 U6 - https://doi.org/10.1063/1.5124728 VL - 151 SP - 164105 ER - TY - JOUR A1 - Venkatareddy, Narendra Lagumaddepalli A1 - Wilke, Patrick A1 - Ernst, Natalia A1 - Horch, Justus A1 - Weber, Marcus A1 - Dallmann, Andre A1 - Börner, Hans G. T1 - Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces JF - Advanced Materials Interfaces N2 - Mussel glue‐proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel‐glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l‐Dopa)) that was previously selected by phage‐display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full‐length adhesion domain at Al2O3 surfaces are provided by a divergent‐convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full‐length peptide. The peptide is divided into two submotifs, each containing one Dopa “anchor” (Motif‐1 and 2). The analysis proves Motif‐1 to constitute a dynamic Al2O3 binder and adopting an “M”‐structure with multiple surface contacts. Motif‐2 binds stronger by two surface contacts, forming a compact “C”‐structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full‐length peptide adhering to Al2O3. Y1 - 2019 U6 - https://doi.org/10.1002/admi.201900501 VL - 6 IS - 13 SP - 1900501 ER - TY - JOUR A1 - Weber, Marcus T1 - Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung JF - KA Korrespondenz Abwasser, Abfall Y1 - 2019 VL - 7 SP - 551 EP - 557 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Hartmann, Laura A1 - Weber, Marcus T1 - Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC JF - Computation N2 - In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies. Y1 - 2019 U6 - https://doi.org/10.3390/computation7030046 VL - 7 IS - 3 SP - 46 ER - TY - JOUR A1 - Ziesche, Ralf F. A1 - Arlt, Tobias A1 - Finegan, Donal P. A1 - Heenan, Thomas M.M. A1 - Tengattini, Alessandro A1 - Baum, Daniel A1 - Kardjilov, Nikolay A1 - Markötter, Henning A1 - Manke, Ingo A1 - Kockelmann, Winfried A1 - Brett, Dan J.L. A1 - Shearing, Paul R. T1 - 4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique JF - Nature Communications N2 - The temporally and spatially resolved tracking of lithium intercalation and electrode degradation processes are crucial for detecting and understanding performance losses during the operation of lithium-batteries. Here, high-throughput X-ray computed tomography has enabled the identification of mechanical degradation processes in a commercial Li/MnO2 primary battery and the indirect tracking of lithium diffusion; furthermore, complementary neutron computed tomography has identified the direct lithium diffusion process and the electrode wetting by the electrolyte. Virtual electrode unrolling techniques provide a deeper view inside the electrode layers and are used to detect minor fluctuations which are difficult to observe using conventional three dimensional rendering tools. Moreover, the ‘unrolling’ provides a platform for correlating multi-modal image data which is expected to find wider application in battery science and engineering to study diverse effects e.g. electrode degradation or lithium diffusion blocking during battery cycling. Y1 - 2020 U6 - https://doi.org/10.1038/s41467-019-13943-3 VL - 11 SP - 777 ER - TY - CHAP A1 - Wende, Florian T1 - C++ Data Layout Abstractions through Proxy Types T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 14th International Workshop on Automatic Performance Tunings (iWAPT) N2 - Programs that process linearly indexed fields with structured element types in a data-parallel way usually suffer from the fact that compilers fail to generate efficient code if the selected data layout appears inappropriate for the chosen target architecture. If their internal heuristics cannot proof a performance gain from a data-parallel execution, compilers may fall back to scalar code generation. Data access through proxy types together with a customized container is one means to assist the compiler in generating efficient machine code in these cases without changing the user code. We present an automated proxy-type generator (using Clang’s LibTooling) and a configurable C++ container that supports different data layouts in a transparent way. Y1 - 2019 U6 - https://doi.org/10.1109/IPDPSW.2019.00126 SP - 758 EP - 767 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Döpking, Sandra A1 - Burger, Sven A1 - Matera, Sebastian T1 - Field Heterogeneities and Their Impact on Photocatalysis: Combining Optical and Kinetic Monte Carlo Simulations on the Nanoscale JF - J. Phys. Chem. C Y1 - 2020 U6 - https://doi.org/10.1021/acs.jpcc.9b11469 VL - 124 SP - 3177 ER - TY - CHAP A1 - Kantner, Markus A1 - Höhne, Theresa A1 - Koprucki, Thomas A1 - Burger, Sven A1 - Wünsche, Hans-Jürgen A1 - Schmidt, Frank A1 - Mielke, Alexander A1 - Bandelow, Uwe ED - Kneissl, Michael ED - Knorr, Andreas ED - Reitzenstein, Stephan ED - Hoffmann, Axel T1 - Multi-dimensional modeling and simulation of semiconductor nanophotonic devices T2 - Semiconductor Nanophotonics Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-35656-9_7 VL - 194 SP - 241 EP - 283 PB - Springer CY - Cham ER - TY - CHAP A1 - von Tycowicz, Christoph T1 - Towards Shape-based Knee Osteoarthritis Classification using Graph Convolutional Networks T2 - 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI 2020) N2 - We present a transductive learning approach for morphometric osteophyte grading based on geometric deep learning. We formulate the grading task as semi-supervised node classification problem on a graph embedded in shape space. To account for the high-dimensionality and non-Euclidean structure of shape space we employ a combination of an intrinsic dimension reduction together with a graph convolutional neural network. We demonstrate the performance of our derived classifier in comparisons to an alternative extrinsic approach. Y1 - 2020 U6 - https://doi.org/10.1109/ISBI45749.2020.9098687 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - A Cut Separation Approach for the Rolling Stock Rotation Problem with Vehicle Maintenance T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - For providing railway services the company’s railway rolling stock is one if not the most important ingredient. It decides about the number of passenger or cargo trips the company can offer, about the quality a passenger experiences the train ride and it is often related to the image of the company itself. Thus, it is highly desired to have the available rolling stock in the best shape possible. Moreover, in many countries, as Germany where our industrial partner DB Fernverkehr AG (DBF) is located, laws enforce regular vehicle inspections to ensure the safety of the passengers. This leads to rolling stock optimization problems with complex rules for vehicle maintenance. This problem is well studied in the literature for example see Maroti and Kroon 2005, or Cordeau et. al. 2001 for applications including vehicle maintenance. The contribution of this paper is a new algorithmic approach to solve the Rolling Stock Rotation Problem for the ICE high speed train fleet of DBF with included vehicle maintenance. It is based on a relaxation of a mixed integer linear programming model with an iterative cut generation to enforce the feasibility of a solution of the relaxation in the solution space of the original problem. The resulting mixed integer linear programming model is based on a hypergraph approach presented in Borndörfer et. al. 2015. The new approach is tested on real world instances modeling different scenarios for the ICE high speed train network in Germany and compared to the approaches of Reuther 2017 that are in operation at DB Fernverkehr AG. The approach shows a significant reduction of the run time to produce solutions with comparable or even better objective function values. T3 - ZIB-Report - 19-61 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75501 SN - 1438-0064 ER - TY - JOUR A1 - Mohr, Gunther A1 - Altenburg, Simon J. A1 - Ulbricht, Alexander A1 - Heinrich, Philipp A1 - Baum, Daniel A1 - Maierhofer, Christiane A1 - Hilgenberg, Kai T1 - In-situ defect detection in laser powder bed fusion by using thermography and optical tomography – comparison to computed tomography JF - Metals Y1 - 2020 U6 - https://doi.org/10.3390/met10010103 VL - 10 IS - 1 SP - 103 ER - TY - CHAP A1 - Kramer, Tobias T1 - Transient capture of electrons in magnetic fields, or: comets in the restricted three-body problem T2 - Journal of Physics: Conference Series N2 - The motion of celestial bodies in astronomy is closely related to the orbits of electrons encircling an atomic nucleus. Bohr and Sommerfeld presented a quantization scheme of the classical orbits to analyze the eigenstates of the hydrogen atom. Here we discuss another close connection of classical trajectories and quantum mechanical states: the transient dynamics of objects around a nucleus. In this setup a comet (or an electron) is trapped for a while in the vicinity of parent object (Jupiter or an atomic nucleus), but eventually escapes after many revolutions around the center of attraction. Y1 - 2020 U6 - https://doi.org/10.1088/1742-6596/1612/1/012019 VL - 1612 SP - 012019 ET - Symmetries in Science XVIII ER - TY - JOUR A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs JF - SIAM J. Sci. Comput. N2 - To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE-constrained optimization. In order to develop an efficient fully time-parallel algorithm, we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and the adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a nonlinear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches. Y1 - 2019 U6 - https://doi.org/10.1137/19M1239313 VL - 41 IS - 6 SP - C603 EP - C626 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodríguez, Mirta T1 - Effect of disorder and polarization sequences on two-dimensional spectra of light harvesting complexes JF - Photosynthesis Research N2 - Two-dimensional electronic spectra (2DES) provide unique ways to track the energy transfer dynamics in light-harvesting complexes. The interpretation of the peaks and structures found in experimentally recorded 2DES is often not straightforward, since several processes are imaged simultaneously. The choice of specific pulse polarization sequences helps to disentangle the sometimes convoluted spectra, but brings along other disturbances. We show by detailed theoretical calculations how 2DES of the Fenna-Matthews-Olson complex are affected by rotational and conformational disorder of the chromophores. Y1 - 2020 U6 - https://doi.org/10.1007/s11120-019-00699-6 VL - 144 SP - 147 EP - 154 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas ED - Cacchiani, Valentina ED - Marchetti-Spaccamela, Alberto T1 - A Cut Separation Approach for the Rolling Stock Rotation Problem with Vehicle Maintenance T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - For providing railway services the company's railway rolling stock is one if not the most important ingredient. It decides about the number of passenger or cargo trips the company can offer, about the quality a passenger experiences the train ride and it is often related to the image of the company itself. Thus, it is highly desired to have the available rolling stock in the best shape possible. Moreover, in many countries, as Germany where our industrial partner DB Fernverkehr AG (DBF) is located, laws enforce regular vehicle inspections to ensure the safety of the passengers. This leads to rolling stock optimization problems with complex rules for vehicle maintenance. This problem is well studied in the literature for example see [Maróti and Kroon, 2005; Gábor Maróti and Leo G. Kroon, 2007], or [Cordeau et al., 2001] for applications including vehicle maintenance. The contribution of this paper is a new algorithmic approach to solve the Rolling Stock Rotation Problem for the ICE high speed train fleet of DBF with included vehicle maintenance. It is based on a relaxation of a mixed integer linear programming model with an iterative cut generation to enforce the feasibility of a solution of the relaxation in the solution space of the original problem. The resulting mixed integer linear programming model is based on a hypergraph approach presented in [Ralf Borndörfer et al., 2015]. The new approach is tested on real world instances modeling different scenarios for the ICE high speed train network in Germany and compared to the approaches of [Reuther, 2017] that are in operation at DB Fernverkehr AG. The approach shows a significant reduction of the run time to produce solutions with comparable or even better objective function values. Y1 - 2019 UR - https://drops.dagstuhl.de/opus/volltexte/2019/11413/ U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.1 VL - 75 SP - 1:1 EP - 1:12 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms JF - Photoacoustics N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. Y1 - 2020 U6 - https://doi.org/10.1016/j.pacs.2019.100157 VL - 17 SP - 100157 ER - TY - GEN A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. T3 - ZIB-Report - 19-60 KW - quantitative photoacoustic imaging KW - blood oxygen saturation KW - inverse problem KW - model-based inversion KW - Monte Carlo KW - spectral unmixing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75416 SN - 1438-0064 ER - TY - GEN A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures N2 - In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor. The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection. Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures. T3 - ZIB-Report - 19-30 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73739 SN - 1438-0064 ER - TY - CHAP A1 - Hartung, Marc A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Pinpoint Data Races via Testing and Classification T2 - 2019 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW); 3rd International Workshop on Software Faults (IWSF 2019) Y1 - 2019 U6 - https://doi.org/10.1109/ISSREW.2019.00100 SP - 386 EP - 393 ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian T1 - Multilevel Checkpoint/Restart for Large Computational Jobs on Distributed Computing Resources T2 - 2019 IEEE 38th Symposium on Reliable Distributed Systems (SRDS) Y1 - 2019 U6 - https://doi.org/10.1109/SRDS47363.2019.00025 SP - 143 EP - 152 ER - TY - GEN A1 - Becker, Kai-Helge A1 - Hiller, Benjamin T1 - Improved optimization models for potential-driven network flow problems via ASTS orientations N2 - The class of potential-driven network flow problems provides important models for a range of infrastructure networks that lead to hard-to-solve MINLPs in real-world applications. On large-scale meshed networks the relaxations usually employed are rather weak due to cycles in the network. To address this situation, we introduce the concept of ASTS orientations, a generalization of bipolar orientations, as a combinatorial relaxation of feasible solutions of potential-driven flow problems, study their structure, and show how they can be used to strengthen existing relaxations and thus provide improved optimization models. Our computational results indicate that ASTS orientations can be used to derive much stronger bounds on the flow variables than existing bound tightening methods and to yield significant performance improvements for an existing state-of-the-art MILP model for large-scale gas networks. T3 - ZIB-Report - 19-58 KW - potential-driven network flows KW - mixed-integer nonlinear programming KW - ASTS orientations KW - bipolar orientations Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75347 SN - 1438-0064 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Schuster, Ingmar A1 - Sullivan, T. J. T1 - A rigorous theory of conditional mean embeddings JF - SIAM Journal on Mathematics of Data Science Y1 - 2020 U6 - https://doi.org/10.1137/19M1305069 VL - 2 IS - 3 SP - 583 EP - 606 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict-Free Learning for Mixed Integer Programming N2 - Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set. T3 - ZIB-Report - 19-59 KW - mixed integer programming KW - conflict analysis KW - dual proof analysis KW - no-good learning KW - solution learning Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75338 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Linear Programming using Limited-Precision Oracles N2 - Since the elimination algorithm of Fourier and Motzkin, many different methods have been developed for solving linear programs. When analyzing the time complexity of LP algorithms, it is typically either assumed that calculations are performed exactly and bounds are derived on the number of elementary arithmetic operations necessary, or the cost of all arithmetic operations is considered through a bit-complexity analysis. Yet in practice, implementations typically use limited-precision arithmetic. In this paper we introduce the idea of a limited-precision LP oracle and study how such an oracle could be used within a larger framework to compute exact precision solutions to LPs. Under mild assumptions, it is shown that a polynomial number of calls to such an oracle and a polynomial number of bit operations, is sufficient to compute an exact solution to an LP. This work provides a foundation for understanding and analyzing the behavior of the methods that are currently most effective in practice for solving LPs exactly. T3 - ZIB-Report - 19-57 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75316 SN - 1438-0064 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Linear Programming using Limited-Precision Oracles JF - Mathematical Programming N2 - Since the elimination algorithm of Fourier and Motzkin, many different methods have been developed for solving linear programs. When analyzing the time complexity of LP algorithms, it is typically either assumed that calculations are performed exactly and bounds are derived on the number of elementary arithmetic operations necessary, or the cost of all arithmetic operations is considered through a bit-complexity analysis. Yet in practice, implementations typically use limited-precision arithmetic. In this paper we introduce the idea of a limited-precision LP oracle and study how such an oracle could be used within a larger framework to compute exact precision solutions to LPs. Under mild assumptions, it is shown that a polynomial number of calls to such an oracle and a polynomial number of bit operations, is sufficient to compute an exact solution to an LP. This work provides a foundation for understanding and analyzing the behavior of the methods that are currently most effective in practice for solving LPs exactly. Y1 - 2020 U6 - https://doi.org/10.1007/s10107-019-01444-6 VL - 183 IS - 1-2 SP - 525 EP - 554 ER - TY - GEN A1 - Müller, Benjamin A1 - Muñoz, Gonzalo A1 - Gasse, Maxime A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Serrano, Felipe T1 - On Generalized Surrogate Duality in Mixed-Integer Nonlinear Programming N2 - The most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global epsilon-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solver can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments. T3 - ZIB-Report - 19-55 KW - surrogate relaxation KW - MINLP KW - nonconvex optimization Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75179 SN - 1438-0064 ER - TY - CHAP A1 - Hartung, Marc T1 - ZIB_Glucose: Luby Blocked Restarts and Dynamic Vivification T2 - Proceedings of SAT Race 2019 : Solver and Benchmark Descriptions Y1 - 2019 SP - 43 EP - 44 ER - TY - CHAP A1 - Clausecker, Robert A1 - Reinefeld, Alexander T1 - Zero-Aware Pattern Databases with 1-Bit Compression for Sliding Tile Puzzles T2 - Proceedings of the Twelfth International Symposium on Combinatorial Search (SoCS 2019) Y1 - 2019 UR - https://aaai.org/ocs/index.php/SOCS/SOCS19/paper/view/18326 SP - 35 EP - 43 ER - TY - CHAP A1 - Beulertz, Daniel A1 - Charousset-Brignol, Sandrine A1 - Most, Dieter A1 - Giannelos, Spyros A1 - Yueksel-Erguen, Inci T1 - Development of a Modular Framework for Future Energy System Analysis T2 - 54th International Universities Power Engineering Conference (UPEC) N2 - This paper gives an overview of the modeling framework that is being developed within the Horizon2020 project plan4res. In the context of energy transition, integration of high shares of renewable energies will play a vital role for achieving the proposed climate targets. This brings new challenges to modeling tools, including data construction, implementation and solution techniques. In order to address these challenges, plan4res aims to create a well-structured and highly modular framework that will provide insights into the needs of future energy systems. An overview of the central modeling aspects is given in this paper. Finally, three case studies are presented that show the adequacy and relevance of the proposed optimization framework. Y1 - 2019 U6 - https://doi.org/10.1109/UPEC.2019.8893472 ER - TY - CHAP A1 - Lindner, Niels A1 - Liebchen, Christian ED - Cacchiani, Valentina ED - Marchetti-Spaccamela, Alberto T1 - New Perspectives on PESP: T-Partitions and Separators T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - In the planning process of public transportation companies, designing the timetable is among the core planning steps. In particular in the case of periodic (or cyclic) services, the Periodic Event Scheduling Problem (PESP) is well-established to compute high-quality periodic timetables. We are considering algorithms for computing good solutions for the very basic PESP with no additional extra features as add-ons. The first of these algorithms generalizes several primal heuristics that had been proposed in the past, such as single-node cuts and the modulo network simplex algorithm. We consider partitions of the graph, and identify so-called delay cuts as a structure that allows to generalize several previous heuristics. In particular, when no more improving delay cut can be found, we already know that the other heuristics could not improve either. The second of these algorithms turns a strategy, that had been discussed in the past, upside-down: Instead of gluing together the network line-by-line in a bottom-up way, we develop a divide-and-conquer-like top-down approach to separate the initial problem into two easier subproblems such that the information loss along their cutset edges is as small as possible. We are aware that there may be PESP instances that do not fit well the separator setting. Yet, on the RxLy-instances of PESPlib in our experimental computations, we come up with good primal solutions and dual bounds. In particular, on the largest instance (R4L4), this new separator approach, which applies a state-of-the-art solver as subroutine, is able to come up with better dual bounds than purely applying this state-of-the-art solver in the very same time. Y1 - 2019 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.2 VL - 75 SP - 2:1 EP - 2:18 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - CHAP A1 - Euler, Ricardo A1 - Borndörfer, Ralf T1 - A Graph- and Monoid-based Framework for Price-Sensitive Routing in Local Public Transportation Networks T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - We present a novel framework to mathematically describe the fare systems of local public transit companies. The model allows the computation of a provably cheapest itinerary even if prices depend on a number of parameters and non-linear conditions. Our approach is based on a ticket graph model to represent tickets and their relation to each other. Transitions between tickets are modeled via transition functions over partially ordered monoids and a set of symbols representing special properties of fares (e.g. surcharges). Shortest path algorithms rely on the subpath optimality property. This property is usually lost when dealing with complicated fare systems. We restore it by relaxing domination rules for tickets depending on the structure of the ticket graph. An exemplary model for the fare system of Mitteldeutsche Verkehrsbetriebe (MDV) is provided. By integrating our framework in the multi-criteria RAPTOR algorithm we provide a price-sensitive algorithm for the earliest arrival problem and assess its performance on data obtained from MDV. We discuss three preprocessing techniques that improve run times enough to make the algorithm applicable for real-time queries. Y1 - 2019 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.12 VL - 75 SP - 12:1 EP - 12:15 ER - TY - JOUR A1 - Oltmanns, Elias A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang A1 - Kuper, Heinz-Günter T1 - Different Preservation Levels: The Case of Scholarly Digital Editions JF - Data Science Journal N2 - Ensuring the long-term availability of research data forms an integral part of data management services. Where OAIS compliant digital preservation has been established in recent years, in almost all cases the services aim at the preservation of file-based objects. In the Digital Humanities, research data is often represented in highly structured aggregations, such as Scholarly Digital Editions. Naturally, scholars would like their editions to remain functionally complete as long as possible. Besides standard components like webservers, the presentation typically relies on project specific code interacting with client software like webbrowsers. Especially the latter being subject to rapid change over time invariably makes such environments awkward to maintain once funding has ended. Pragmatic approaches have to be found in order to balance the curation effort and the maintainability of access to research data over time. A sketch of four potential service levels aiming at the long-term availability of research data in the humanities is outlined: (1) Continuous Maintenance, (2) Application Conservation, (3) Application Data Preservation, and (4) Bitstream Preservation. The first being too costly and the last hardly satisfactory in general, we suggest that the implementation of services by an infrastructure provider should concentrate on service levels 2 and 3. We explain their strengths and limitations considering the example of two Scholarly Digital Editions. KW - Digital Preservation Y1 - 2019 U6 - https://doi.org/10.5334/dsj-2019-051 VL - 18 IS - 1(51) ER - TY - GEN A1 - Omari, Mohamed A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - A pharmacokinetic-pharmacodynamic model for single dose administration of Dexamethasone in dairy cows N2 - We present a mechanistic pharmacokinetic-pharmacodynamic model to simulate the effect of dexamethasone on the glucose metabolism in dairy cows. The coupling of the pharmacokinetic model to the pharmacodynamic model is based on mechanisms underlying homeostasis regulation by dexamethasone. In particular, the coupling takes into account the predominant role of dexamethasone in stimulating glucagon secretion, glycogenolysis and lipolysis and in impairing the sensitivity of cells to insulin. Simulating the effect of a single dose of dexamethasone on the physiological behaviour of the system shows that the adopted mechanisms are able to induce a temporary hyperglycemia and hyperinsulinemia, which captures the observed data in non-lactating cows. In lactating cows, the model simulations show that a single dose of dexamethasone reduces the lipolytic effect, owing to the reduction of glucose uptake by the mammary gland. T3 - ZIB-Report - 19-53 KW - systems biology; modelling; differential equations; metabolism; nutrition; bovine; fertility; reproduction; hormones; follicles; Dexamethasone; PK-PD Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75043 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Giliard, Nicole A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Leitlinien zum Umgang mit Forschungsdaten am Zuse-Institut Berlin N2 - Die nachhaltige Sicherung und Bereitstellung von Forschungsdaten dienen nicht nur der Reproduzierbarkeit früherer Ergebnisse, sondern in hohem Maße auch der Erzielung künftiger Ergebnisse mit dem Ziel, die Qualität, Produktivität und Wettbewerbsfähigkeit der Wissenschaft zu fördern. Die folgenden Grundsätze gelten als Leitlinien zur Handhabung von Forschungsdaten im ZIB. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73781 CY - Berlin ER - TY - JOUR A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Becker, Christiane T1 - Minimising levelised cost of electricity of bifacial solar panel arrays using Bayesian optimisation JF - Sustain. Energy Fuels Y1 - 2020 U6 - https://doi.org/10.1039/C9SE00750D VL - 4 SP - 254 ER - TY - THES A1 - Mattes, Dirk T1 - Ein System zur deterministischen Wiedergabe von verteilten Algorithmen auf Anwendungsebene Y1 - 2019 ER - TY - JOUR A1 - Girolami, Mark A. A1 - Ipsen, Ilse C. F. A1 - Oates, Chris A1 - Owen, Art B. A1 - Sullivan, T. J. T1 - Editorial: Special edition on probabilistic numerics JF - Statistics and Computing Y1 - 2019 U6 - https://doi.org/doi:10.1007/s11222-019-09892-y VL - 29 IS - 6 SP - 1181 EP - 1183 ER - TY - JOUR A1 - Hennings, Felix A1 - Anderson, Lovis A1 - Hoppmann-Baum, Kai A1 - Turner, Mark A1 - Koch, Thorsten T1 - Controlling transient gas flow in real-world pipeline intersection areas JF - Optimization and Engineering N2 - Compressor stations are the heart of every high-pressure gas transport network. Located at intersection areas of the network they are contained in huge complex plants, where they are in combination with valves and regulators responsible for routing and pushing the gas through the network. Due to their complexity and lack of data compressor stations are usually dealt with in the scientific literature in a highly simplified and idealized manner. As part of an ongoing project with one of Germany's largest Transmission System Operators to develop a decision support system for their dispatching center, we investigated how to automatize control of compressor stations. Each station has to be in a particular configuration, leading in combination with the other nearby elements to a discrete set of up to 2000 possible feasible operation modes in the intersection area. Since the desired performance of the station changes over time, the configuration of the station has to adapt. Our goal is to minimize the necessary changes in the overall operation modes and related elements over time, while fulfilling a preset performance envelope or demand scenario. This article describes the chosen model and the implemented mixed integer programming based algorithms to tackle this challenge. By presenting extensive computational results on real world data we demonstrate the performance of our approach. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s11081-020-09559-y VL - 22 SP - 687 EP - 734 PB - Springer Nature ET - 2 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Scheduling data streams for low latency and high throughput on a Cray XC40 using Libfabric JF - Concurrency and Computation Practice and Experience Y1 - 2020 U6 - https://doi.org/10.1002/cpe.5563 VL - 32 IS - 20 SP - 1 EP - 14 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo A1 - Heinz, Stefan T1 - Computational Aspects of Infeasibility Analysis in Mixed Integer Programming N2 - The analysis of infeasible subproblems plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications, obtained by domain propagation, that led to infeasibility. The result of this analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept is called conflict graph analysis and has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. Every ray of the dual LP provides a set of multipliers that can be used to generate a single new globally valid linear constraint. This method is called dual proof analysis. The main contribution of this paper is twofold. Firstly, we present three enhancements of dual proof analysis: presolving via variable cancellation, strengthening by applying mixed integer rounding functions, and a filtering mechanism. Further, we provide an intense computational study evaluating the impact of every presented component regarding dual proof analysis. Secondly, this paper presents the first integrated approach to use both conflict graph and dual proof analysis simultaneously within a single MIP solution process. All experiments are carried out on general MIP instances from the standard public test set MIPLIB 2017; the presented algorithms have been implemented within the non-commercial MIP solver SCIP and the commercial MIP solver FICO Xpress. T3 - ZIB-Report - 19-54 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74962 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2017 T3 - Jahresbericht - 2017 KW - Jahresbericht Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74948 SN - 0934-5892 VL - 2017 ER - TY - JOUR A1 - Rusch, Beate A1 - Boltze, Julia A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Staub, Hedda T1 - DeepGreen - DeepGold: Open-Access-Transformation - Entwicklung und Perspektiven JF - GMS Medizin - Bibliothek - Information N2 - Das deutsche Projekt DeepGreen (https://deepgreen.kobv.de/de/deepgreen/) arbeitet an einer automatisierten Lösung, um Artikeldaten (Volltexte und Metadaten) von wissenschaftlichen Verlagen abzuholen und an Repositorien zu liefern, die diese Artikel wiederum Open Access veröffentlichen können. Ausgangspunkt für das Projekt sind die überregional geförderten deutschen Allianz-Lizenzen. Diese enthalten eine Open-Access-Komponente, die es Autor*innen oder deren Institution erlaubt, ihre Artikel nach einer verkürzten Embargofrist in einem Repositorium ihrer Wahl Open Access zugänglich zu machen. DeepGreen wird seit 2016 von der Deutschen Forschungsgemeinschaft gefördert (1. Förderphase: 01.2016–12.2017; 2. Förderphase: 08.2018–07.2020) und besteht aus einem Konsortium aus 6 Institutionen: Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV), Bayerische Staatsbibliothek (BSB), Bibliotheksverbund Bayern (BVB), Universitätsbibliothek der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum Potsdam (GFZ), Universitätsbibliothek der Technischen Universität Berlin (TUBB). Y1 - 2019 U6 - https://doi.org/10.3205/mbi000432 VL - 19 IS - 1-2 ER - TY - JOUR A1 - Nyakatura, John A1 - Baumgarten, Roxane A1 - Baum, Daniel A1 - Stark, Heiko A1 - Youlatos, Dionisios T1 - Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel JF - Mammalian Biology N2 - In individuals of similar body mass representing closely related species with different lifestyles, muscle architectural properties can be assumed to reflect adaptation to differing, lifestyle-related functional demands. We here employ a fiber recognition algorithm on contrast-enhanced micro-computed tomography (μCT) scans of one specimen each of an arboreal (Sciurus vulgaris) and a fossorial (Spermophilus citellus) sciuromorph rodent. The automated approach accounts for potential heterogeneity of architectural properties within a muscle by analyzing all fascicles that compose a muscle. Muscle architectural properties (volume, fascicle length, and orientation, and force-generating capacity) were quantified in 14 hindlimb (hip, knee, and ankle) extensor muscles and compared between specimens. We expected the arboreal squirrel to exhibit greater force-generating capacity and a greater capacity for length change allowing more powerful hindlimb extension. Generally and mostly matching our expectations, the S. vulgaris specimen had absolutely and relatively larger extensor muscles than the S. citellus specimen which were thus metabolically more expensive and demonstrate the relatively larger investment into powerful hindlimb extension necessary in the arboreal context. We conclude that detailed quantitative data on hindlimb muscle internal structure as was gathered here for a very limited sample further lends support to the notion that muscle architecture reflects adaptation to differential functional demands in closely related species with different locomotor behaviors and lifestyles. Y1 - 2019 U6 - https://doi.org/10.1016/j.mambio.2019.10.007 VL - 99 SP - 71 EP - 80 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Improving the throughput of a scalable FLESnet using the Data-Flow Scheduler JF - CBM Progress Report 2018 Y1 - 2019 SN - 978-3-9815227-6-1 U6 - https://doi.org/10.15120/GSI-2019-01018 SP - 149 EP - 150 ER - TY - GEN A1 - Chen, Ying A1 - Koch, Thorsten A1 - Xu, Xiaofei T1 - Regularized partially functional autoregressive model with application to high-resolution natural gas forecasting in Germany N2 - We propose a partially functional autoregressive model with exogenous variables (pFAR) to describe the dynamic evolution of the serially correlated functional data. It provides a unit� ed framework to model both the temporal dependence on multiple lagged functional covariates and the causal relation with ultrahigh-dimensional exogenous scalar covariates. Estimation is conducted under a two-layer sparsity assumption, where only a few groups and elements are supposed to be active, yet without knowing their number and location in advance. We establish asymptotic properties of the estimator and investigate its unite sample performance along with simulation studies. We demonstrate the application of pFAR with the high-resolution natural gas flows in Germany, where the pFAR model provides insightful interpretation as well as good out-of-sample forecast accuracy. T3 - ZIB-Report - 19-34 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74880 SN - 1438-0064 ER - TY - GEN A1 - Christof, Jürgen A1 - Conrad-Rempel, Steffi A1 - Degkwitz, Andreas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Happel, Hans-Gerd A1 - Hasler, Tim A1 - Heiss, Alexandra A1 - Kaminsky, Uta A1 - Kant, Oliver A1 - Kende, Jiří A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Müller, Anja A1 - Mutter, Moritz A1 - Peters-Kottig, Wolfgang A1 - Quitzsch, Nicole A1 - Rusch, Beate A1 - Schwidder, Jens A1 - Stanek, Ursula A1 - Weihe, Signe A1 - Zeyns, Andrea T1 - KOBV Jahresbericht 2015-2016 N2 - Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV). T3 - KOBV-Jahresbericht - 2015-2016 KW - KOBV KW - Jahresbericht Y1 - 2017 SN - 0934-5892 VL - 2015-2016 IS - 2015-2016 SP - 1 EP - 64 ER - TY - GEN A1 - Aust, Sonja A1 - Conrad-Rempel, Steffi A1 - Degkwitz, Andreas A1 - Golz, Bettina A1 - Hasler, Tim A1 - Heiss, Alexandra A1 - Keidel, Petra A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Lill, Monika A1 - Lohrum, Stefan A1 - Müller, Anja A1 - Peters-Kottig, Wolfgang A1 - Quitzsch, Nicole A1 - Rusch, Beate A1 - Schwidder, Jens A1 - Sischke, Gabriele A1 - Stanek, Ursula A1 - Taylor, Viola A1 - Weihe, Signe A1 - Wyrwol, Christiane A1 - Happel, Hans-Gerd T1 - KOBV Jahresbericht 2013-2014 N2 - Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV). T3 - KOBV-Jahresbericht - 2013-2014 KW - KOBV KW - Jahresbericht Y1 - 2015 SN - 0934-5892 VL - 2013-2014 IS - 2013-2014 SP - 1 EP - 56 ER - TY - GEN T1 - KOBV Jahresbericht 2011-2012 N2 - Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV). T3 - KOBV-Jahresbericht - 2011-2012 KW - KOBV KW - Jahresbericht Y1 - 2013 SN - 0934-5892 VL - 2011-2012 SP - 1 EP - 46 ER - TY - GEN T1 - KOBV Jahresbericht 2010 N2 - Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV). T3 - KOBV-Jahresbericht - 2010 KW - KOBV KW - Jahresbericht Y1 - 2019 SN - 0934-5892 VL - 2010 SP - 1 EP - 36 ER - TY - GEN A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Rusch, Beate A1 - Biernacka, Katarzyna A1 - Brandtner, Andreas A1 - Christof, Jürgen A1 - Czechowska, Dr. Ilona A1 - Degkwitz, Andreas A1 - Euler, Prof. Dr. Ellen A1 - Freyberg, Linda A1 - Geukes, Dr. Albert A1 - Happel, Hans-Gerd A1 - Helbig, Kerstin A1 - Hübner, Andreas A1 - Mohnke, Janett A1 - Mutter, Moritz A1 - Seeliger, Frank A1 - Stanek, Ursula A1 - Voigt, Michaela A1 - Winterhalter, Dr. Christian A1 - Zeyns, Andrea A1 - Kaminsky, Uta A1 - Boltze, Julia A1 - Conrad-Rempel, Steffi A1 - Gerlach, Viktoria A1 - Heidingsfelder, Nicole A1 - Kant, Oliver A1 - Lohrum, Stefan A1 - Müller, Anja A1 - Peters-Kottig, Wolfgang A1 - Schwidder, Jens A1 - Weihe, Signe A1 - Bauknecht, Anne-Beatrix A1 - Krauß, Frieder T1 - KOBV Jahresbericht 2017-2018 N2 - Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV). T3 - KOBV-Jahresbericht - 2017-2018 KW - KOBV KW - Jahresbericht Y1 - 2019 SN - 1438-0064 IS - 2017-2018 SP - 1 EP - 63 ER - TY - GEN A1 - Christgau, Steffen A1 - Schnor, Bettina T1 - MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor N2 - MPI passive target synchronization offers exclusive and shared locks. These are the building blocks for the implementation of applications with Readers & Writers semantic, like for example distributed hash tables. This paper discusses the implementation of MPI passive target synchronization on a non-cache-coherent multicore, the Intel Single-Chip Cloud Computer. The considered algorithms differ in their communication style (message based versus shared memory), their data structures (centralized versus distributed) and their semantics (with/without Writer preference). It is shown that shared memory approaches scale very well and deliver good performance, even in absence of cache coherence. T3 - ZIB-Report - 19-52 KW - process synchronization KW - programming models and systems for manycores KW - MPI Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74774 SN - 1438-0064 ER - TY - JOUR A1 - Heller, Eric J. A1 - Fleischmann, Ragnar A1 - Kramer, Tobias T1 - Branched Flow N2 - In many physical situations involving diverse length scales, waves or rays representing them travel through media characterized by spatially smooth, random, modest refractive index variations. "Primary" diffraction (by individual sub-wavelength features) is absent. Eventually the weak refraction leads to imperfect focal "cusps". Much later, a statistical regime characterized by momentum diffusion is manifested. An important intermediate regime is often overlooked, one that is diffusive only in an ensemble sense. Each realization of the ensemble possesses dramatic ray limit structure that guides the waves (in the same sense that ray optics is used to design lens systems). This structure is a universal phenomenon called branched flow. Many important phenomena develop in this intermediate regime. Here we give examples and some of the physics of this emerging field. Y1 - 2019 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Lindner, Niels A1 - Roth, Sarah T1 - A Concurrent Approach to the Periodic Event Scheduling Problem JF - Journal of Rail Transport Planning & Management N2 - We introduce a concurrent solver for the periodic event scheduling problem (PESP). It combines mixed integer programming techniques, the modulo network simplex method, satisfiability approaches, and a new heuristic based on maximum cuts. Running these components in parallel speeds up the overall solution process. This enables us to significantly improve the current upper and lower bounds for all benchmark instances of the library PESPlib. Y1 - 2020 U6 - https://doi.org/10.1016/j.jrtpm.2019.100175 SN - 2210-9706 IS - 15 SP - 100175 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika A1 - Lindner, Niels T1 - Separation of cycle inequalities in periodic timetabling JF - Discrete Optimization N2 - Cycle inequalities play an important role in the polyhedral study of the periodic timetabling problem in public transport. We give the first pseudo-polynomial time separation algorithm for cycle inequalities, and we contribute a rigorous proof for the pseudo-polynomial time separability of the change-cycle inequalities. Moreover, we provide several NP-completeness results, indicating that pseudo-polynomial time is best possible. The efficiency of these cutting planes is demonstrated on real-world instances of the periodic timetabling problem. Y1 - 2020 U6 - https://doi.org/10.1016/j.disopt.2019.100552 IS - 35 SP - 100552 ER - TY - GEN A1 - Maher, Stephen J. A1 - Ralphs, Ted A1 - Shinano, Yuji T1 - Assessing the Effectiveness of (Parallel) Branch-and-bound Algorithms N2 - Empirical studies are fundamental in assessing the effectiveness of implementations of branch-and-bound algorithms. The complexity of such implementations makes empirical study difficult for a wide variety of reasons. Various attempts have been made to develop and codify a set of standard techniques for the assessment of optimization algorithms and their software implementations; however, most previous work has been focused on classical sequential algorithms. Since parallel computation has become increasingly mainstream, it is necessary to re-examine and modernize these practices. In this paper, we propose a framework for assessment based on the notion that resource consumption is at the heart of what we generally refer to as the “effectiveness” of an implementation. The proposed framework carefully distinguishes between an implementation’s baseline efficiency, the efficacy with which it utilizes a fixed allocation of resources, and its scalability, a measure of how the efficiency changes as resources (typically additional computing cores) are added or removed. Efficiency is typically applied to sequential implementations, whereas scalability is applied to parallel implementations. Efficiency and scalability are both important contributors in determining the overall effectiveness of a given parallel implementation, but the goal of improved efficiency is often at odds with the goal of improved scalability. Within the proposed framework, we review the challenges to effective evaluation and discuss the strengths and weaknesses of existing methods of assessment. T3 - ZIB-Report - 19-03 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74702 ER - TY - CHAP A1 - Schnauber, Peter A1 - Schall, Johannes A1 - Bounouar, Samir A1 - Höhne, Theresa A1 - Park, Suk-In A1 - Ryu, Geun-Hwan A1 - Heindel, Tobias A1 - Burger, Sven A1 - Song, Jin-Dong A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Deterministic integration of quantum dots into on-chip multi-mode interference couplers via in-situ electron beam lithography T2 - Conference on Lasers and Electro-Optics Europe and European Quantum Electronics Conference (CLEO/EQEC) Y1 - 2019 U6 - https://doi.org/10.1109/CLEOE-EQEC.2019.8872583 SP - EB2.2 ER - TY - JOUR A1 - Pulaj, Jonad T1 - Cutting planes for families implying Frankl's conjecture JF - Mathematics of Computation N2 - We find previously unknown families of sets which ensure Frankl's conjecture holds for all families that contain them using an algorithmic framework. The conjecture states that for any nonempty finite union-closed (UC) family there exists an element of the ground set in at least half the sets of the considered UC family. Poonen's Theorem characterizes the existence of weights which determine whether a given UC family implies the conjecture for all UC families which contain it. We design a cutting-plane method that computes the explicit weights which satisfy the existence conditions of Poonen's Theorem. This method enables us to answer several open questions regarding structural properties of UC families, including the construction of a counterexample to a conjecture of Morris from 2006. Y1 - 2019 U6 - https://doi.org/10.1090/mcom/3461 ER - TY - GEN A1 - Sahin, Guvenc A1 - Ahmadi, Amin A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Multi-Period Line Planning with Resource Transfers N2 - Urban transportation systems are subject to a high level of variation and fluctuation in demand over the day. When this variation and fluctuation are observed in both time and space, it is crucial to develop line plans that are responsive to demand. A multi-period line planning approach that considers a changing demand during the planning horizon is proposed. If such systems are also subject to limitations of resources, a dynamic transfer of resources from one line to another throughout the planning horizon should also be considered. A mathematical modelling framework is developed to solve the line planning problem with transfer of resources during a finite length planning horizon of multiple periods. We analyze whether or not multi-period solutions outperform single period solutions in terms of feasibility and relevant costs. The importance of demand variation on multi-period solutions is investigated. We evaluate the impact of resource transfer constraints on the effectiveness of solutions. We also study the effect of line type designs and question the choice of period lengths along with the problem parameters that are significant for and sensitive to the optimality of solutions. T3 - ZIB-Report - 19-51 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74662 SN - 1438-0064 ER - TY - JOUR A1 - Gotzes, Uwe T1 - Ein neuer Ansatz zur Optimierung des Bilanzausgleichs in einem Gasmarktgebiet JF - Zeitschrift für Energiewirtschaft N2 - Im BDEW/VKU/GEODE-Leitfaden Krisenvorsorge Gas ist zu lesen, dass als oberster Grundsatz zur Vermeidung von Versorgungsengpässen in Gasversorgungssystemen gilt, möglichst laufend einen Bilanzausgleich in allen Teilen des Netzes zu erreichen. Wir entwickeln Modelle zur Optimierung des laufenden Bilanzausgleichs. Als Gasversorgungssystem betrachten wir modellhaft die Fernleitungsnetze eines Marktgebiets. Als Teile des Gasversorgungssystems fassen wir vereinfachend die jeweiligen Netze der Fernleitungsnetzbetreiber auf. Die Optimierung erfolgt in zwei Schritten. Im ersten Schritt wird der optimale Einsatz netzbezogener Maßnahmen ermittelt. Beispiele für netzbezogene Maßnahmen sind die Nutzung von Netzpuffer und Mengenverlagerungen mit anderen Infrastrukturbetreibern. Falls sich die Bilanzen durch netzbezogene Maßnahmen nicht vollständig ausgleichen lassen, werden Fehlmengen angesetzt, die so gleichmäßig wie möglich auf die Teile des Netzes verteilt werden. Im zweiten Schritt werden die verbliebenen Fehlmengen, welche in der Regel durch marktbezogene Maßnahmen bereinigt werden, regulierungskonform auf möglichst große Teile des Gasversorgungssystems verteilt. Im Ergebnis erhalten wir ein transparentes, gerechtes, flexibel parametrier- und erweiterbares Verfahren, welches zyklisch im Dispatchingprozess eingesetzt werden kann, um die Integrität der Netze zu unterstützen. Dies wird an Beispielen verdeutlicht. Y1 - 2019 U6 - https://doi.org/10.1007/s12398-019-00257-6 ER - TY - JOUR A1 - Żołnacz, Kinga A1 - Musiał, Anna A1 - Srocka, Nicole A1 - Große, Jan A1 - Schlösinger, Maximilian A1 - Schneider, Philipp-Immanuel A1 - Kravets, Oleh A1 - Mikulicz, Monika A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wójcik, Grzegorz A1 - Mergo, Paweł A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dłubek, Michał A1 - Rodt, Sven A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Sęk, Grzegorz A1 - Reitzenstein, Stephan A1 - Urbańczyk, Wacław T1 - Method for direct coupling of a semiconductor quantum dot to an optical fiber for single-photon source applications JF - Opt. Express Y1 - 2019 U6 - https://doi.org/10.1364/OE.27.026772 VL - 27 SP - 26772 ER - TY - GEN A1 - Gotzes, Uwe A1 - Hoppmann, Kai T1 - Bounds for the final ranks during a round robin tournament T2 - Operational Research - An International Journal (ORIJ) N2 - This article answers two kinds of questions regarding the Bundesliga which is Germany's primary football (soccer) competition having the highest average stadium attendance worldwide. First "At any point of the season, what final rank will a certain team definitely reach?" and second "At any point of the season, what final rank can a certain team at most reach?". Although we focus especially on the Bundesliga, the models that we use to answer the two questions can easily be adopted to league systems that are similar to that of the Bundesliga. T3 - ZIB-Report - 19-50 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74638 ER - TY - GEN A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Geodesic Mixed Effects Model in Kendall's Shape Space T2 - Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA) N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and apply the approach for the estimation of group trends and statistical testing of 3D shapes derived from an open access longitudinal imaging study on osteoarthritis. T3 - ZIB-Report - 19-49 KW - Shape Space KW - Kendall Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74621 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Schiela, Anton A1 - Weiser, Martin T1 - Kaskade 7 -- a Flexible Finite Element Toolbox N2 - Kaskade 7 is a finite element toolbox for the solution of stationary or transient systems of partial differential equations, aimed at supporting application-oriented research in numerical analysis and scientific computing. The library is written in C++ and is based on the Dune interface. The code is independent of spatial dimension and works with different grid managers. An important feature is the mix-and-match approach to discretizing systems of PDEs with different ansatz and test spaces for all variables. We describe the mathematical concepts behind the library as well as its structure, illustrating its use at several examples on the way. T3 - ZIB-Report - 19-48 KW - finite elements KW - generic programming KW - partial differential equations Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74616 SN - 1438-0064 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weissenböck, Johannes A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science JF - Computer Graphics Forum N2 - We present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list‐based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber‐reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well‐considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis‐)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13688 VL - 38 IS - 3 SP - 273 EP - 283 ER - TY - JOUR A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Fiand, Frederik A1 - Cao, Karl-Kiên A1 - Gils, Hans Christian A1 - Wetzel, Manuel A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Khabi, Dmitry T1 - BEAM-ME: Ein interdisziplinärer Beitrag zur Erreichung der Klimaziele JF - OR-News : das Magazin der GOR Y1 - 2019 IS - 66 SP - 6 EP - 8 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Hellmeier, Florian A1 - Bruening, Jan Joris A1 - Spuler, Andreas A1 - Hege, Hans-Christian A1 - Voss, Samuel A1 - Janiga, Gábor A1 - Saalfeld, Sylvia A1 - Beuing, Oliver A1 - Berg, Philipp T1 - Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters JF - BioMedical Engineering OnLine N2 - Background Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures. Materials 26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values. Results A large variability of relative uncertainties in the range between 3.9 and 179.8% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80% were found for some curvature parameters. Conclusions Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models. Y1 - 2019 U6 - https://doi.org/10.1186/s12938-019-0657-y VL - 18 IS - 35 ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - An as-invariant-as-possible GL+(3)-based Statistical Shape Model N2 - We describe a novel nonlinear statistical shape model basedon differential coordinates viewed as elements of GL+(3). We adopt an as-invariant-as possible framework comprising a bi-invariant Lie group mean and a tangent principal component analysis based on a unique GL+(3)-left-invariant, O(3)-right-invariant metric. Contrary to earlier work that equips the coordinates with a specifically constructed group structure, our method employs the inherent geometric structure of the group-valued data and therefore features an improved statistical power in identifying shape differences. We demonstrate this in experiments on two anatomical datasets including comparison to the standard Euclidean as well as recent state-of-the-art nonlinear approaches to statistical shape modeling. T3 - ZIB-Report - 19-46 KW - Statistical shape analysis KW - Tangent principal component analysis KW - Lie groups KW - Classification KW - Manifold valued statistics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74566 SN - 1438-0064 ER - TY - JOUR A1 - Lang, Annemarie A1 - Fischer, Lisa A1 - Weber, Marie-Christin A1 - Gaber, Timo A1 - Ehrig, Rainald A1 - Röblitz, Susanna A1 - Buttgereit, Frank T1 - Combining in vitro simulation and in silico modelling towards a sophisticated human osteoarthritis model JF - Osteoarthritis and Cartilage N2 - Our project aimed at building an in silico model based on our recently developed in vitro osteoarthritis (OA) model seeking for refinement of the model to enhance validity and translatability towards the more sophisticated simulation of OA. In detail, the previously 3D in vitro model is based on 3D chondrogenic constructs generated solely from human bone marrow derived mesenchymal stromal cells (hMSCs). Besides studying the normal state of the model over 3 weeks, the in vitro model was treated with interleukin-1β (IL-1β) and tumor necrosis factor alpha (TNFα) to mimic an OA-like environment. Y1 - 2019 U6 - https://doi.org/10.1016/j.joca.2019.02.277 VL - 27 SP - S183 ER - TY - CHAP A1 - Baum, Daniel ED - Bock von Wülfingen, Bettina T1 - An Evaluation of Color Maps for Visual Data Exploration T2 - Science in Color: Visualizing Achromatic Knowledge Y1 - 2019 SP - 147 EP - 161 PB - De Gruyter CY - Berlin ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - A Surface-Theoretic Approach for Statistical Shape Modeling N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. We evaluate the performance of our model w.r.t. shape-based classification of pathological malformations of the human knee and show that it outperforms the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing natural biological shape variability, we carry out an analysis of specificity and generalization ability. T3 - ZIB-Report - 19-20 KW - Statistical shape analysis KW - Principal geodesic analysis KW - Lie groups KW - Classification KW - Manifold valued statistics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74497 SN - 1438-0064 ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - An as-invariant-as-possible GL+(3)-based Statistical Shape Model T2 - Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA) N2 - We describe a novel nonlinear statistical shape model basedon differential coordinates viewed as elements of GL+(3). We adopt an as-invariant-as possible framework comprising a bi-invariant Lie group mean and a tangent principal component analysis based on a unique GL+(3)-left-invariant, O(3)-right-invariant metric. Contrary to earlier work that equips the coordinates with a specifically constructed group structure, our method employs the inherent geometric structure of the group-valued data and therefore features an improved statistical power in identifying shape differences. We demonstrate this in experiments on two anatomical datasets including comparison to the standard Euclidean as well as recent state-of-the-art nonlinear approaches to statistical shape modeling. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-33226-6_23 VL - 11846 SP - 219 EP - 228 PB - Springer ER - TY - THES A1 - Mangalgiri, Gauri T1 - Development of Titanium Dioxide Metasurfaces and Nanosoupbowls for Optically Enhancing Silicon Photocathodes Y1 - 2019 U6 - https://doi.org/10.18452/20160 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Schneider, Philipp-Immanuel A1 - Binkowski, Felix A1 - Burger, Sven T1 - Numerical optimization of resonant photonic devices T2 - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2534348 VL - 11057 SP - 1105702 ER - TY - GEN A1 - Özel, M. Neset A1 - Kulkarni, Abhishek A1 - Hasan, Amr A1 - Brummer, Josephine A1 - Moldenhauer, Marian A1 - Daumann, Ilsa-Maria A1 - Wolfenberg, Heike A1 - Dercksen, Vincent J. A1 - Kiral, F. Ridvan A1 - Weiser, Martin A1 - Prohaska, Steffen A1 - von Kleist, Max A1 - Hiesinger, Peter Robin T1 - Serial synapse formation through filopodial competition for synaptic seeding factors N2 - Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses. T3 - ZIB-Report - 19-45 KW - filopodia KW - growth cone dynamics KW - brain wiring KW - 2-photon microscopy KW - model Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74397 SN - 1438-0064 ER - TY - GEN A1 - Behrens, Kathrin A1 - Bertelmann, Roland A1 - Boltze, Julia A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Hammerl, Michaela A1 - Haoua, Marsa A1 - Heermann, Petra A1 - Hoffmann, Cornelia A1 - Höhnow, Tobias A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Staub, Hedda A1 - Wannick, Eike T1 - DeepGreen - Open Access Transformation: Eine Handreichung für institutionelle Repositorien BT - Version 1.0 N2 - Mit dem DFG-geförderten Projekt DeepGreen soll eine automatisierte, rechtssichere Lösung entwickelt werden, um Artikeldaten von wissenschaftlichen Verlagen abzuholen und anschließend, nach Ablauf etwaiger lizenzrechtlicher Embargofristen, an berechtigte Repositorien zu verteilen und somit in den Open Access zu überführen. Dabei liegt der Fokus auf den DFG-geförderten und überregional verhandelten Allianz-Lizenzen, mit spezieller Open-Access-Komponente. Die vorliegende Handreichung richtet sich speziell an die Betreiber institutioneller Repositorien und stellt Empfehlungen und einen Workflow bereit, um eine erfolgreiche Veröffentlichung, der durch die DeepGreen-Datendrehscheibe zugeordneten Artikel, zu ermöglichen. Die Handreichung basiert auf den bisherigen Erfahrungen der DeepGreen-Projektbeteiligten. T3 - ZIB-Report - 19-31 KW - Open Access KW - Open-Access-Transformation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74438 SN - 1438-0064 ER - TY - CHAP A1 - Jäger, Klaus A1 - Jošt, Marko A1 - Sutter, Johannes A1 - Tockhorn, Philipp A1 - Köhnen, Eike A1 - Eisenhauer, David A1 - Manley, Phillip A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Improving Monolithic Perovskite/Silicon Tandem Solar Cells From an Optical Viewpoint T2 - OSA Advanced Photonics Congress Y1 - 2019 U6 - https://doi.org/10.1364/PVLED.2019.PM4C.2 SP - PM4C.2 ER - TY - THES A1 - Beckenbach, Isabel T1 - Matchings and Flows in Hypergraphs N2 - In this dissertation, we study matchings and flows in hypergraphs using combinatorial methods. These two problems are among the best studied in the field of combinatorial optimization. As hypergraphs are a very general concept, not many results on graphs can be generalized to arbitrary hypergraphs. Therefore, we consider special classes of hypergraphs, which admit more structure, to transfer results from graph theory to hypergraph theory. In Chapter 2, we investigate the perfect matching problem on different classes of hypergraphs generalizing bipartite graphs. First, we give a polynomial time approximation algorithm for the maximum weight matching problem on so-called partitioned hypergraphs, whose approximation factor is best possible up to a constant. Afterwards, we look at the theorems of König and Hall and their relation. Our main result is a condition for the existence of perfect matchings in normal hypergraphs that generalizes Hall’s condition for bipartite graphs. In Chapter 3, we consider perfect f-matchings, f-factors, and (g,f)-matchings. We prove conditions for the existence of (g,f)-matchings in unimodular hypergraphs, perfect f-matchings in uniform Mengerian hypergraphs, and f-factors in uniform balanced hypergraphs. In addition, we give an overview about the complexity of the (g,f)-matching problem on different classes of hypergraphs generalizing bipartite graphs. In Chapter 4, we study the structure of hypergraphs that admit a perfect matching. We show that these hypergraphs can be decomposed along special cuts. For graphs it is known that the resulting decomposition is unique, which does not hold for hypergraphs in general. However, we prove the uniqueness of this decomposition (up to parallel hyperedges) for uniform hypergraphs. In Chapter 5, we investigate flows on directed hypergraphs, where we focus on graph-based directed hypergraphs, which means that every hyperarc is the union of a set of pairwise disjoint ordinary arcs. We define a residual network, which can be used to decide whether a given flow is optimal or not. Our main result in this chapter is an algorithm that computes a minimum cost flow on a graph-based directed hypergraph. This algorithm is a generalization of the network simplex algorithm. N2 - Diese Arbeit untersucht Matchings und Flüsse in Hypergraphen mit Hilfe kombinatorischer Methoden. In Graphen gehören diese Probleme zu den grundlegendsten der kombinatorischen Optimierung. Viele Resultate lassen sich nicht von Graphen auf Hypergraphen verallgemeinern, da Hypergraphen ein sehr abstraktes Konzept bilden. Daher schauen wir uns bestimmte Klassen von Hypergraphen an, die mehr Struktur besitzen, und nutzen diese aus um Resultate aus der Graphentheorie zu übertragen. In Kapitel 2 betrachten wir das perfekte Matchingproblem auf Klassen von „bipartiten“ Hypergraphen, wobei es verschiedene Möglichkeiten gibt den Begriff „bipartit“ auf Hypergraphen zu definieren. Für sogenannte partitionierte Hypergraphen geben wir einen polynomiellen Approximationsalgorithmus an, dessen Gütegarantie bis auf eine Konstante bestmöglich ist. Danach betrachten wir die Sätze von Konig und Hall und untersuchen deren Zusammenhang. Unser Hauptresultat ist eine Bedingung für die Existenz von perfekten Matchings auf normalen Hypergraphen, die Halls Bedingung für bipartite Graphen verallgemeinert. Als Verallgemeinerung von perfekten Matchings betrachten wir in Kapitel 3 perfekte f-Matchings, f-Faktoren und (g, f)-Matchings. Wir beweisen Bedingungen für die Existenz von (g, f)-Matchings auf unimodularen Hypergraphen, perfekten f-Matchings auf uniformen Mengerschen Hypergraphen und f-Faktoren auf uniformen balancierten Hypergraphen. Außerdem geben wir eine Übersicht über die Komplexität des (g, f)-Matchingproblems auf verschiedenen Klassen von Hypergraphen an, die bipartite Graphen verallgemeinern. In Kapitel 4 untersuchen wir die Struktur von Hypergraphen, die ein perfektes Matching besitzen. Wir zeigen, dass diese Hypergraphen entlang spezieller Schnitte zerlegt werden können. Für Graphen weiß man, dass die so erhaltene Zerlegung eindeutig ist, was im Allgemeinen für Hypergraphen nicht zutrifft. Wenn man jedoch uniforme Hypergraphen betrachtet, dann liefert jede Zerlegung die gleichen unzerlegbaren Hypergraphen bis auf parallele Hyperkanten. Kapitel 5 beschäftigt sich mit Flüssen in gerichteten Hypergraphen, wobei wir Hypergraphen betrachten, die auf gerichteten Graphen basieren. Das bedeutet, dass eine Hyperkante die Vereinigung einer Menge von disjunkten Kanten ist. Wir definieren ein Residualnetzwerk, mit dessen Hilfe man entscheiden kann, ob ein gegebener Fluss optimal ist. Unser Hauptresultat in diesem Kapitel ist ein Algorithmus, um einen Fluss minimaler Kosten zu finden, der den Netzwerksimplex verallgemeinert. KW - Matchings KW - Balanced Hypergraphs KW - Normal Hypergraphs KW - Mengerian Hypergraphs KW - Factors KW - Tight Cuts KW - Network Flows Y1 - 2019 UR - http://nbn-resolving.de/urn:nbn:de:kobv:188-refubium-24385-6 ER - TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - In vitro and in silico modeling of cellular and matrix-related changes during the early phase of osteoarthritis JF - BioRxiv N2 - Understanding the pathophysiological processes of osteoarthritis (OA) require adequate model systems. Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific parts of the disease. This study aimed to combine in vitro and in silico modeling to describe cellular and matrix-related changes during the early phase of OA. We developed an in vitro OA model based on scaffold-free cartilage-like constructs (SFCCs), which was mathematically modeled using a partial differential equation (PDE) system to resemble the processes during the onset of OA. SFCCs were produced from mesenchymal stromal cells and analyzed weekly by histology and qPCR to characterize the cellular and matrix-related composition. To simulate the early phase of OA, SFCCs were treated with interleukin-1β (IL-1β), tumor necrosis factor α (TNFα) and examined after 3 weeks or cultivated another 3 weeks without inflammatory cytokines to validate the regeneration potential. Mathematical modeling was performed in parallel to the in vitro experiments. SFCCs expressed cartilage-specific markers, and after stimulation an increased expression of inflammatory markers, matrix degrading enzymes, a loss of collagen II (Col-2) and a reduced cell density was observed which could be partially reversed by retraction of stimulation. Based on the PDEs, the distribution processes within the SFCCs, including those of IL-1β, Col-2 degradation and cell number reduction was simulated. By combining in vitro and in silico methods, we aimed to develop a valid, efficient alternative approach to examine and predict disease progression and new therapeutic strategies. Y1 - 2019 U6 - https://doi.org/10.1101/725317 ER - TY - JOUR A1 - Krämer, Martin A1 - Maggioni, Marta A1 - Brisson, Nicholas A1 - Zachow, Stefan A1 - Teichgräber, Ulf A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - T1 and T2* mapping of the human quadriceps and patellar tendons using ultra-short echo-time (UTE) imaging and bivariate relaxation parameter-based volumetric visualization JF - Magnetic Resonance Imaging N2 - Quantification of magnetic resonance (MR)-based relaxation parameters of tendons and ligaments is challenging due to their very short transverse relaxation times, requiring application of ultra-short echo-time (UTE) imaging sequences. We quantify both T1 and T2⁎ in the quadriceps and patellar tendons of healthy volunteers at a field strength of 3 T and visualize the results based on 3D segmentation by using bivariate histogram analysis. We applied a 3D ultra-short echo-time imaging sequence with either variable repetition times (VTR) or variable flip angles (VFA) for T1 quantification in combination with multi-echo acquisition for extracting T2⁎. The values of both relaxation parameters were subsequently binned for bivariate histogram analysis and corresponding cluster identification, which were subsequently visualized. Based on manually-drawn regions of interest in the tendons on the relaxation parameter maps, T1 and T2⁎ boundaries were selected in the bivariate histogram to segment the quadriceps and patellar tendons and visualize the relaxation times by 3D volumetric rendering. Segmentation of bone marrow, fat, muscle and tendons was successfully performed based on the bivariate histogram analysis. Based on the segmentation results mean T2⁎ relaxation times, over the entire tendon volumes averaged over all subjects, were 1.8 ms ± 0.1 ms and 1.4 ms ± 0.2 ms for the patellar and quadriceps tendons, respectively. The mean T1 value of the patellar tendon, averaged over all subjects, was 527 ms ± 42 ms and 476 ms ± 40 ms for the VFA and VTR acquisitions, respectively. The quadriceps tendon had higher mean T1 values of 662 ms ± 97 ms (VFA method) and 637 ms ± 40 ms (VTR method) compared to the patellar tendon. 3D volumetric visualization of the relaxation times revealed that T1 values are not constant over the volume of both tendons, but vary locally. This work provided additional data to build upon the scarce literature available on relaxation times in the quadriceps and patellar tendons. We were able to segment both tendons and to visualize the relaxation parameter distributions over the entire tendon volumes. Y1 - 2019 U6 - https://doi.org/10.1016/j.mri.2019.07.015 VL - 63 IS - 11 SP - 29 EP - 36 ER - TY - CHAP A1 - Neumann, Mario A1 - Hellwich, Olaf A1 - Zachow, Stefan T1 - Localization and Classification of Teeth in Cone Beam CT using Convolutional Neural Networks T2 - Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC) N2 - In dentistry, software-based medical image analysis and visualization provide efficient and accurate diagnostic and therapy planning capabilities. We present an approach for the automatic recognition of tooth types and positions in digital volume tomography (DVT). By using deep learning techniques in combination with dimensionality reduction through non-planar reformatting of the jaw anatomy, DVT data can be efficiently processed and teeth reliably recognized and classified, even in the presence of imaging artefacts, missing or dislocated teeth. We evaluated our approach, which is based on 2D Convolutional Neural Networks (CNNs), on 118 manually annotated cases of clinical DVT datasets. Our proposed method correctly classifies teeth with an accuracy of 94% within a limit of 2mm distance to ground truth labels. Y1 - 2019 SN - 978-3-00-063717-9 SP - 182 EP - 188 ER - TY - CHAP A1 - Joachimsky, Robert A1 - Ma, Lihong A1 - Icking, Christian A1 - Zachow, Stefan T1 - A Collision-Aware Articulated Statistical Shape Model of the Human Spine T2 - Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC) N2 - Statistical Shape Models (SSMs) are a proven means for model-based 3D anatomy reconstruction from medical image data. In orthopaedics and biomechanics, SSMs are increasingly employed to individualize measurement data or to create individualized anatomical models to which implants can be adapted to or functional tests can be performed on. For modeling and analysis of articulated structures, so called articulated SSMs (aSSMs) have been developed. However, a missing feature of aSSMs is the consideration of collisions in the course of individual fitting and articulation. The aim of our work was to develop aSSMs that handle collisions between components correctly. That way it becomes possible to adjust shape and articulation in view of a physically and geometrically plausible individualization. To be able to apply collision-aware aSSMs in simulation and optimisation, our approach is based on an e� cient collision detection method employing Graphics Processing Units (GPUs). Y1 - 2019 SP - 58 EP - 64 ER - TY - THES A1 - Joachimsky, Robert T1 - Approaching Spinal Kinematics using a Collision-Aware Articulated Deformable Model N2 - Statistical Shape Models (SSMs) allow for a compact representation of shape and shape variation and they are a proven means for model-based 3D anatomy reconstruction from medical image data. In orthopaedics and biomechanics, SSMs are increasingly employed to individualize measurement data or to create individualized anatomical models. The human spine is a versatile and complex articulated structure and thus is an interesting candidate to be modeled using an advanced type of SSMs. For modeling and analysis of articulated structures, so called articulated SSMs (aSSMs) have been developed. However, a missing feature of aSSMs is the consideration of collisions in the course of individual fitting and articulation. The aim of this thesis is to develop an aSSM of two adjacent vertebrae that handles collisions between components correctly. The model will incorporate the two major aspects of variability: Shape of a single vertebra and the relative positioning of neighboring vertebrae. That way it becomes possible to adjust shape and articulation in view of a physically and geometrically plausible individualization. To be able to apply collision-aware aSSMs in simulation and optimisation in future work, the approach is based on a parallelized collision detection method employing Graphics Processing Units (GPUs). KW - Spine Modeling KW - Spinal Kinematics KW - GPU-Accelerated Collision Detection KW - Spherical Shell Y1 - 2019 ER - TY - GEN A1 - Breugem, Thomas A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Schulz, Christof T1 - A Three-Phase Heuristic for Cyclic Crew Rostering with Fairness Requirements N2 - In this paper, we consider the Cyclic Crew Rostering Problem with Fairness Requirements (CCRP-FR). In this problem, attractive cyclic rosters have to be constructed for groups of employees, considering multiple, a priori determined, fairness levels. The attractiveness follows from the structure of the rosters (e.g., sufficient rest times and variation in work), whereas fairness is based on the work allocation among the different roster groups. We propose a three-phase heuristic for the CCRP-FR, which combines the strength of column generation techniques with a large-scale neighborhood search algorithm. The design of the heuristic assures that good solutions for all fairness levels are obtained quickly, and can still be further improved if additional running time is available. We evaluate the performance of the algorithm using real-world data from Netherlands Railways, and show that the heuristic finds close to optimal solutions for many of the considered instances. In particular, we show that the heuristic is able to quickly find major improvements upon the current sequential practice: For most instances, the heuristic is able to increase the attractiveness by at least 20% in just a few minutes. T3 - ZIB-Report - 19-43 KW - Crew Planning KW - Column Generation KW - Variable-Depth Neighborhood Search Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74297 SN - 1438-0064 ER - TY - GEN A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri N2 - The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”. T3 - ZIB-Report - 19-44 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74338 SN - 1438-0064 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Hobbie, Hannes A1 - Schönheit, David A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Möst, Dominik T1 - A massively parallel interior-point solver for linear energy system models with block structure N2 - Linear energy system models are often a crucial component of system design and operations, as well as energy policy consulting. Such models can lead to large-scale linear programs, which can be intractable even for state-of-the-art commercial solvers|already the available memory on a desktop machine might not be sufficient. Against this backdrop, this article introduces an interior-point solver that exploits common structures of linear energy system models to efficiently run in parallel on distributed memory systems. The solver is designed for linear programs with doubly bordered block-diagonal constraint matrix and makes use of a Schur complement based decomposition. Special effort has been put into handling large numbers of linking constraints and variables as commonly observed in energy system models. In order to handle this strong linkage, a distributed preconditioning of the Schur complement is used. In addition, the solver features a number of more generic techniques such as parallel matrix scaling and structure-preserving presolving. The implementation is based on the existing parallel interior-point solver PIPS-IPM. We evaluate the computational performance on energy system models with up to 700 million non-zero entries in the constraint matrix, and with more than 200 million columns and 250 million rows. This article mainly concentrates on the energy system model ELMOD, which is a linear optimization model representing the European electricity markets by the use of a nodal pricing market clearing. It has been widely applied in the literature on energy system analyses during the recent years. However, it will be demonstrated that the new solver is also applicable to other energy system models. T3 - ZIB-Report - 19-41 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74321 SN - 1438-0064 N1 - In the meantime, this report got published as a journal article: https://opus4.kobv.de/opus4-zib/frontdoor/index/index/searchtype/authorsearch/author/Hannes+Hobbie/docId/8191/start/1/rows/10 Please use this journal reference when citing this work. ER - TY - JOUR A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri JF - Journal of Cultural Heritage N2 - The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”. Y1 - 2020 U6 - https://doi.org/10.1016/j.culher.2019.07.007 VL - 41 SP - 264 EP - 269 PB - Elsevier ER - TY - GEN A1 - Baum, Daniel T1 - An Evaluation of Color Maps for Visual Data Exploration T3 - ZIB-Report - 19-42 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74259 SN - 1438-0064 ER - TY - JOUR A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms JF - Integrative And Comparative Biology N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. Y1 - 2019 U6 - https://doi.org/10.1093/icb/icz117 ER - TY - CHAP A1 - Paetsch, Olaf T1 - Possibilities and Limitations of Automatic Feature Extraction shown by the Example of Crack Detection in 3D-CT Images of Concrete Specimen T2 - iCT 2019 N2 - To assess the influence of the alkali-silica reaction (ASR) on pavement concrete 3D-CT imaging has been applied to concrete samples. Prior to imaging these samples have been drilled out of a concrete beam pre-damaged by fatigue loading. The resulting high resolution 3D-CT images consist of several gigabytes of voxels. Current desktop computers can visualize such big datasets without problems but a visual inspection or manual segmentation of features such as cracks by experts can only be carried out on a few slices. A quantitative analysis of cracks requires a segmentation of the whole specimen which could only be done by an automatic feature detection. This arises the question of the reliability of an automatic crack detection algorithm, its certainty and limitations. Does the algorithm find all cracks? Does it find too many cracks? Can parameters of that algorithm, once identified as good, be applied to other samples as well? Can ensemble computing with many crack parameters overcome the difficulties with parameter finding? By means of a crack detection algorithm based on shape recognition (template matching) these questions will be discussed. Since the author has no access to reliable ground truth data of cracks the assessment of the certainty of the automatic crack is restricted to visual inspection by experts. Therefore, an artificial dataset based on a combination of manually segmented cracks processed together with simple image processing algorithms is used to quantify the accuracy of the crack detection algorithm. Part of the evaluation of cracks in concrete samples is the knowledge of the surrounding material. The surrounding material can be used to assess the detected cracks, e.g. micro-cracks within the aggregate-matrix interface may be starting points for cracks on a macro scale. Furthermore, the knowledge of the surrounding material can help to find better parameter sets for the crack detection itself because crack characteristics may vary depending on their surrounding material. Therefore, in addition to a crack detection a complete segmentation of the sample into the components of concrete, such as aggregates, cement matrix and pores is needed. Since such a segmentation task cannot be done manually due to the amount of data, an approach utilizing convolutional neuronal networks stemming from a medical application has been applied. The learning phase requires a ground truth i.e. a segmentation of the components. This has to be created manually in a time-consuming task. However, this segmentation can be used for a quantitative evaluation of the automatic segmentation afterwards. Even though that work has been performed as a short term subtask of a bigger project funded by the German Research Foundation (DFG) this paper discusses problems which may arise in similar projects, too. Y1 - 2019 ER - TY - CHAP A1 - Paetsch, Olaf T1 - Möglichkeiten und Grenzen automatischer Merkmalserkennung am Beispiel von Risserkennungen in 3D-CT-Aufnahmen von Betonproben N2 - Die Auswertungen der großen Datenmengen moderner bildgebender Verfahren der ZfP können manuell kaum noch bewältigt werden. Hochauflösende 3D-CT-Aufnahmen bestehen oft aus über 1000 Schichtbildern mit einer Datenmenge von mehreren Gigabytes. Aktuelle Computer können diese zwar problemlos visualisieren und erlauben somit eine visuelle Inspektion, aber die möglichst vollständige Erkennung bestimmter Merkmale in den Daten und deren qualitative wie quantitative Auswertung ist durch Experten manuell nicht mehr zu bewältigen. Das gilt insbesondere im Kontext der Schadensaufklärung für die quantitative Analyse verschiedenartig induzierter Risse in Betonen (z.B. durch mechanische Belastungen sowie Frost, Sulfat und Alkali-Kieselsäure-Reaktion). Eine dazu notwendige Segmentierung und Merkmalserkennung kann nur automatisch durchgeführt werden. Dabei ergibt sich (auch fast automatisch) die Frage nach der Verlässlichkeit der verwendeten Algorithmen. Inwieweit kann man davon ausgehen, dass alle gesuchten Merkmale auch tatsächlich gefunden worden sind? Sind die gefundenen Merkmale quantitativ auswertbar und wie wirken sich Parameteränderungen auf die Ergebnisse aus? Sollten immer dieselben, einmal mit gutem Ergebnis angewandten, Parameter auch bei anderen Proben zur besseren Vergleichbarkeit genutzt werden? Anhand eines Risserkennungsalgorithmus basierend auf Formerkennung und Bildverarbeitung wird die Problematik diskutiert. Als Grundlage zur Bewertung des Ansatzes dienen 3D-CT-Aufnahmen von geschädigten Betonprobekörpern und Datensätze, in denen sich aufgrund ihres homogenen Aufbaus mit einfachen Mitteln Risse sicher und eindeutig erkennen lassen. Zur Auswertung der erkannten Risse gehört auch deren Einbettung in das umliegende Material. Das erfordert neben einer automatischen Risserkennung auch eine Segmentierung des gesamten Probekörpers in Zementsteinmatrix, Gesteinskörnung und Porenraum. Da eine solche Segmentierung aufgrund der Datenmenge nur schwer manuell erfolgen kann, werden erste Ergebnisse aus einer Segmentierung mit Hilfe selbstlernender Convolutional Neural Networks gezeigt. Y1 - 2018 PB - iCT 2019 CY - https://www.ndt.net/article/ctc2019/papers/iCT2019_Full_paper_29.pdf ER - TY - CHAP A1 - Hartung, Marc A1 - Schintke, Florian T1 - Learned Clause Minimization in Parallel SAT Solvers T2 - Pragmatics of SAT 2019 N2 - Learned clauses minimization (LCM) let to performance improvements of modern SAT solvers especially in solving hard SAT instances. Despite the success of LCM approaches in sequential solvers, they are not widely incorporated in parallel SAT solvers. In this paper we explore the potential of LCM for parallel SAT solvers by defining multiple LCM approaches based on clause vivification, comparing their runtime in different SAT solvers and discussing reasons for performance gains and losses. Results show that LCM only boosts performance of parallel SAT solvers on a fraction of SAT instances. More commonly applying LCM decreases performance. Only certain LCM approaches are able to improve the overall performance of parallel SAT solvers. Y1 - 2019 UR - http://www.pragmaticsofsat.org/2019/ SP - 1 EP - 11 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Dispersion-engineered nanocomposites enable achromatic diffractive optical elements JF - Optica Y1 - 2019 U6 - https://doi.org/10.1364/OPTICA.6.001031 VL - 6 SP - 1031 ER - TY - CHAP A1 - Skrzypczak, Jan A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Linearizable State Machine Replication of State-Based CRDTs without Logs T2 - Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, PODC 2019 N2 - General solutions of state machine replication have to ensure that all replicas apply the same commands in the same order, even in the presence of failures. Such strict ordering incurs high synchronization costs due to the use of distributed consensus or a leader. This paper presents a protocol for linearizable state machine replication of conflict-free replicated data types (CRDTs) that neither requires consensus nor a leader. By leveraging the properties of state-based CRDTs—in particular the monotonic growth of a join semilattice—synchronization overhead is greatly reduced. In addition, updates just need a single round trip and modify the state ‘in-place’ without the need for a log. Furthermore, the message size overhead for coordination consists of a single counter per message. While reads in the presence of concurrent updates are not wait-free without a coordinator, we show that more than 97 % of reads can be handled in one or two round trips under highly concurrent accesses. Our protocol achieves high throughput without auxiliary processes such as command log management or leader election. It is well suited for all practical scenarios that need linearizable access on CRDT data on a fine-granular scale. Y1 - 2019 U6 - https://doi.org/10.1145/3293611.3331568 SP - 455 EP - 457 ER - TY - JOUR A1 - Mrowinski, Paweł A1 - Schnauber, Peter A1 - Gutsche, Philipp A1 - Kaganskiy, Arsenty A1 - Schall, Johannes A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Directional emission of a deterministically fabricated quantum dot – Bragg reflection multi-mode waveguide system JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.9b00369 VL - 6 SP - 2231 ER - TY - CHAP A1 - Gleixner, Ambros A1 - Kempke, Nils-Christian A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Uslu, Svenja T1 - First Experiments with Structure-Aware Presolving for a Parallel Interior-Point Method T2 - Operations Research Proceedings 2019 N2 - In linear optimization, matrix structure can often be exploited algorithmically. However, beneficial presolving reductions sometimes destroy the special structure of a given problem. In this article, we discuss structure-aware implementations of presolving as part of a parallel interior-point method to solve linear programs with block-diagonal structure, including both linking variables and linking constraints. While presolving reductions are often mathematically simple, their implementation in a high-performance computing environment is a complex endeavor. We report results on impact, performance, and scalability of the resulting presolving routines on real-world energy system models with up to 700 million nonzero entries in the constraint matrix. KW - block structure KW - energy system models KW - interior-point method KW - high performance computing KW - linear programming KW - parallelization KW - presolving KW - preprocessing Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-48439-2_13 SP - 105 EP - 111 PB - Springer International Publishing ET - 1 ER - TY - GEN A1 - Rössig, Ansgar T1 - Verification of Neural Networks T3 - ZIB-Report - 19-40 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74174 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Kempke, Nils-Christian A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Uslu, Svenja T1 - First Experiments with Structure-Aware Presolving for a Parallel Interior-Point Method N2 - In linear optimization, matrix structure can often be exploited algorithmically. However, beneficial presolving reductions sometimes destroy the special structure of a given problem. In this article, we discuss structure-aware implementations of presolving as part of a parallel interior-point method to solve linear programs with block-diagonal structure, including both linking variables and linking constraints. While presolving reductions are often mathematically simple, their implementation in a high-performance computing environment is a complex endeavor. We report results on impact, performance, and scalability of the resulting presolving routines on real-world energy system models with up to 700 million nonzero entries in the constraint matrix. T3 - ZIB-Report - 19-39 KW - block structure KW - energy system models KW - interior-point method KW - high performance computing KW - linear programming KW - parallelization KW - presolving KW - preprocessing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74084 SN - 1438-0064 ER - TY - THES A1 - Neumann, Mario T1 - Localization and Classification of Teeth in Cone Beam Computed Tomography using 2D CNNs N2 - In dentistry, software-based medical image analysis and visualization provide effcient and accurate diagnostic and therapy planning capabilities. We present an approach for the automatic recognition of tooth types and positions in digital volume tomography (DVT). By using deep learning techniques in combination with dimension reduction through non-planar reformatting of the jaw anatomy, DVT data can be effciently processed and teeth reliably recognized and classified, even in the presence of imaging artefacts, missing or dislocated teeth. We evaluated our approach, which is based on 2D Convolutional Neural Networks (CNNs), on 118 manually annotated cases of clinical DVT datasets. Our proposed method correctly classifies teeth with an accuracy of 94% within a limit of 2mm distancr to ground truth landmarks. KW - Dental Imaging KW - Tooth Classification KW - Dimension Reduction KW - Image Reformatting Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74045 ER - TY - GEN A1 - Serrano, Felipe T1 - Visible points, the separation problem, and applications to MINLP N2 - In this paper we introduce a technique to produce tighter cutting planes for mixed-integer non-linear programs. Usually, a cutting plane is generated to cut off a specific infeasible point. The underlying idea is to use the infeasible point to restrict the feasible region in order to obtain a tighter domain. To ensure validity, we require that every valid cut separating the infeasible point from the restricted feasible region is still valid for the original feasible region. We translate this requirement in terms of the separation problem and the reverse polar. In particular, if the reverse polar of the restricted feasible region is the same as the reverse polar of the feasible region, then any cut valid for the restricted feasible region that \emph{separates} the infeasible point, is valid for the feasible region. We show that the reverse polar of the \emph{visible points} of the feasible region from the infeasible point coincides with the reverse polar of the feasible region. In the special where the feasible region is described by a single non-convex constraint intersected with a convex set we provide a characterization of the visible points. Furthermore, when the non-convex constraint is quadratic the characterization is particularly simple. We also provide an extended formulation for a relaxation of the visible points when the non-convex constraint is a general polynomial. Finally, we give some conditions under which for a given set there is an inclusion-wise smallest set, in some predefined family of sets, whose reverse polars coincide. T3 - ZIB-Report - 19-38 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74016 SN - 1438-0064 ER - TY - CHAP A1 - Hiremath, Kirankumar A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Finite elements based numerical solution of nonlocal hydrodynamic Drude model of nano-plasmonic scatterers T2 - 12th International Conference on Fiber Optics and Photonics Y1 - 2014 U6 - https://doi.org/10.1364/PHOTONICS.2014.M3D.4 SP - M3D.4 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Optimization of handouts for rolling stock rotations JF - Journal of Rail Transport Planning & Management N2 - A railway operator creates (rolling stock) rotations in order to have a precise master plan for the operation of a timetable by railway vehicles. A rotation is considered as a cycle that multiply traverses a set of operational days while covering trips of the timetable. As it is well known, the proper creation of rolling stock rotations by, e.g., optimization algorithms is challenging and still a topical research subject. Nevertheless, we study a completely different but strongly related question in this paper, i.e.: How to visualize a rotation? For this purpose, we introduce a basic handout concept, which directly leads to the visualization, i.e., handout of a rotation. In our industrial application at DB Fernverkehr AG, the handout is exactly as important as the rotation itself. Moreover, it turns out that also other European railway operators use exactly the same methodology (but not terminology). Since a rotation can have many handouts of different quality, we show how to compute optimal ones through an integer program (IP) by standard software. In addition, a construction as well as an improvement heuristic are presented. Our computational results show that the heuristics are a very reliable standalone approach to quickly find near-optimal and even optimal handouts. The efficiency of the heuristics is shown via a computational comparison to the IP approach. Y1 - 2019 U6 - https://doi.org/10.1016/j.jrtpm.2019.02.001 IS - 10 SP - 1 EP - 8 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Schlechte, Thomas T1 - Re-optimizing ICE Rotations after a Tunnel Breakdown near Rastatt T2 - Proceedings of the 8th International Conference on Railway Operations Modelling and Analysis - RailNorrköping 2019 N2 - Planning rolling stock movements in industrial passenger railway applications isa long-term process based on timetables which are also often valid for long periods of time. For these timetables and rotation plans, i.e., plans of railway vehicle movements are constructed as templates for these periods. During operation the rotation plans are affected by all kinds of unplanned events. An unusal example for that is the collapse of a tunnel ceiling near Rastatt in southern Germany due to construction works related to the renewal of the central station in Stuttgart. As a result the main railway connection between Stuttgart and Frankfurt am Main, located on top of the tunnel, had to be closed from August 12th to October 2nd 2017. This had a major impact on the railway network in southern Germany. Hence, all rotation plans and train schedules for both passenger and cargo traffic had to be revised. In this paper we focus on a case study for this situation and compute new rotation plans via mixed integer programming for the ICE high speed fleet of DB Fernverkehr AG one of the largest passenger railway companies in Europe. In our approach we take care of some side constraints to ensure a smooth continuation of the rotation plans after the disruption has ended. Y1 - 2019 UR - http://www.ep.liu.se/ecp/article.asp?issue=069&article=011&volume= SN - 978-91-7929-992-7 SN - 1650-3686 VL - Linköping Electronic Conference Proceedings IS - 069 SP - 160 EP - 168 PB - Linköping University Electronic Press, Linköpings universitet CY - Linköping, Sweden ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Re-optimizing ICE Rotations after a Tunnel Breakdown near Rastatt N2 - Planning rolling stock movements in industrial passenger railway applications isa long-term process based on timetables which are also often valid for long periods of time. For these timetables and rotation plans, i.e., plans of railway vehicle movements are constructed as templates for these periods. During operation the rotation plans are affected by all kinds of unplanned events. An unusal example for that is the collapse of a tunnel ceiling near Rastatt in southern Germany due to construction works related to the renewal of the central station in Stuttgart. As a result the main railway connection between Stuttgart and Frankfurt am Main, located on top of the tunnel, had to be closed from August 12th to October 2nd 2017. This had a major impact on the railway network in southern Germany. Hence, all rotation plans and train schedules for both passenger and cargo traffic had to be revised. In this paper we focus on a case study for this situation and compute new rotation plans via mixed integer programming for the ICE high speed fleet of DB Fernverkehr AG one of the largest passenger railway companies in Europe. In our approach we take care of some side constraints to ensure a smooth continuation of the rotation plans after the disruption has ended. T3 - ZIB-Report - 19-02 KW - case study KW - re-optimization KW - railway rolling stock optimization KW - mixed integer programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73976 SN - 1438-0064 ER - TY - CHAP A1 - Berthold, Timo A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schade, Stanley A1 - Schlechte, Thomas T1 - Strategic Planning of Rolling Stock Rotations for Public Tenders T2 - Proceedings of the 8th International Conference on Railway Operations Modelling and Analysis - RailNorrköping 2019 N2 - Since railway companies have to apply for long-term public contracts to operate railway lines in public tenders, the question how they can estimate the operating cost for long-term periods adequately arises naturally. We consider a rolling stock rotation problem for a time period of ten years, which is based on a real world instance provided by an industry partner. We use a two stage approach for the cost estimation of the required rolling stock. In the first stage, we determine a weekly rotation plan. In the second stage, we roll out this weekly rotation plan for a longer time period and incorporate scheduled maintenance treatments. We present a heuristic approach and a mixed integer programming model to implement the process of the second stage. Finally, we discuss computational results for a real world tendering scenario. Y1 - 2019 UR - http://www.ep.liu.se/ecp/article.asp?issue=069&article=009&volume= SN - 978-91-7929-992-7 SN - 1650-3686 VL - Linköping Electronic Conference Proceedings IS - 069 SP - 148 EP - 159 PB - Linköping University Electronic Press, Linköpings universitet ER - TY - CHAP A1 - Fröhler, Bernhard A1 - da Cunha Melo, Lucas A1 - Weissenböck, Johannes A1 - Kastner, Johann A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Gröller, Eduard M. A1 - Sanctorum, Jonathan A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Heinzl, Christoph T1 - Tools for the analysis of datasets from X-ray computed tomography based on Talbot-Lau grating interferometry T2 - Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy – iCT 2019, February 13-15, 2019) N2 - This work introduces methods for analyzing the three imaging modalities delivered by Talbot-Lau grating interferometry X-ray computed tomography (TLGI-XCT). The first problem we address is providing a quick way to show a fusion of all three modal- ities. For this purpose the tri-modal transfer function widget is introduced. The widget controls a mixing function that uses the output of the transfer functions of all three modalities, allowing the user to create one customized fused image. A second problem prevalent in processing TLGI-XCT data is a lack of tools for analyzing the segmentation process of such multimodal data. We address this by providing methods for computing three types of uncertainty: From probabilistic segmentation algorithms, from the voxel neighborhoods as well as from a collection of results. We furthermore introduce a linked views interface to explore this data. The techniques are evaluated on a TLGI-XCT scan of a carbon-fiber reinforced dataset with impact damage. We show that the transfer function widget accelerates and facilitates the exploration of this dataset, while the uncertainty analysis methods give insights into how to tweak and improve segmentation algorithms for more suitable results. Y1 - 2019 N1 - PDF | open access: https://www.ndt.net/article/ctc2019/papers/iCT2019_Full_paper_52.pdf IS - paper 52 ER - TY - JOUR A1 - Farchmin, Nando A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Wurm, Matthias A1 - Bär, Markus A1 - Heidenreich, Sebastian T1 - Efficient global sensitivity analysis for silicon line gratings using polynomial chaos JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2525978 VL - 11057 SP - 110570J ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Scholze, Frank A1 - Beckhoff, Burkhard A1 - Soltwisch, Victor T1 - Grazing incidence x-ray fluorescence based characterization of nanostructures for element sensitive profile reconstruction JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2526082 VL - 11057 SP - 110570M ER - TY - GEN A1 - Löbel, Fabian A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - The Restricted Modulo Network Simplex Method for Integrated Periodic Timetabling and Passenger Routing N2 - The Periodic Event Scheduling Problem is a well-studied NP-hard problem with applications in public transportation to find good periodic timetables. Among the most powerful heuristics to solve the periodic timetabling problem is the modulo network simplex method. In this paper, we consider the more difficult version with integrated passenger routing and propose a refined integrated variant to solve this problem on real-world-based instances. T3 - ZIB-Report - 19-36 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Integrated Passenger Routing KW - Shortest Routes in Public Transport Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73868 SN - 1438-0064 ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian T1 - New Perspectives on PESP: T-Partitions and Separators N2 - In the planning process of public transportation companies, designing the timetable is among the core planning steps. In particular in the case of periodic (or cyclic) services, the Periodic Event Scheduling Problem (PESP) is well-established to compute high-quality periodic timetables. We are considering algorithms for computing good solutions for the very basic PESP with no additional extra features as add-ons. The first of these algorithms generalizes several primal heuristics that had been proposed in the past, such as single-node cuts and the modulo network simplex algorithm. We consider partitions of the graph, and identify so-called delay cuts as a structure that allows to generalize several previous heuristics. In particular, when no more improving delay cut can be found, we already know that the other heuristics could not improve either. The second of these algorithms turns a strategy, that had been discussed in the past, upside-down: Instead of gluing together the network line-by-line in a bottom-up way, we develop a divide-and-conquer-like top-down approach to separate the initial problem into two easier subproblems such that the information loss along their cutset edges is as small as possible. We are aware that there may be PESP instances that do not fit well the separator setting. Yet, on the RxLy-instances of PESPlib in our experimental computations, we come up with good primal solutions and dual bounds. In particular, on the largest instance (R4L4), this new separator approach, which applies a state-of-the-art solver as subroutine, is able to come up with better dual bounds than purely applying this state-of-the-art solver in the very same time. T3 - ZIB-Report - 19-35 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Graph Partitioning KW - Graph Separators KW - Balanced Cuts Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73853 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. T3 - ZIB-Report - 19-33 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73841 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy Compression for Large Scale PDE Problems N2 - Solvers for partial differential equations (PDE) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that needs to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to relatively small arithmetic intensity, and increasingly so due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers during the last decades. This paper surveys data compression challenges and corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to main memory. Exemplarily, we illustrate concepts at particular methods, and give references to alternatives. T3 - ZIB-Report - 19-32 KW - partial differential equation KW - data compression KW - floating point compression KW - lossy compression Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73817 SN - 1438-0064 ER - TY - JOUR A1 - Sullivan, T. J. T1 - Contributed discussion on the article "A Bayesian conjugate gradient method" JF - Bayesian Analysis N2 - The recent article "A Bayesian conjugate gradient method" by Cockayne, Oates, Ipsen, and Girolami proposes an approximately Bayesian iterative procedure for the solution of a system of linear equations, based on the conjugate gradient method, that gives a sequence of Gaussian/normal estimates for the exact solution. The purpose of the probabilistic enrichment is that the covariance structure is intended to provide a posterior measure of uncertainty or confidence in the solution mean. This note gives some comments on the article, poses some questions, and suggests directions for further research. Y1 - 2019 U6 - https://doi.org/10.1214/19-BA1145 VL - 14 IS - 3 SP - 985 EP - 989 ER - TY - JOUR A1 - Chen, Ying A1 - Chua, Wee Song A1 - Koch, Thorsten T1 - Forecasting day-ahead high-resolution natural-gas demand and supply in Germany JF - Applied Energy N2 - Forecasting natural gas demand and supply is essential for an efficient operation of the German gas distribution system and a basis for the operational decisions of the transmission system operators. The German gas market is moving towards more short-term planning, in particular, day-ahead contracts. This increases the difficulty that the operators in the dispatching centre are facing, as well as the necessity of accurate forecasts. This paper presents a novel predictive model that provides day-ahead forecasts of the high resolution gas flow by developing a Functional AutoRegressive model with eXogenous variables (FARX). The predictive model allows the dynamic patterns of hourly gas flows to be described in a wide range of historical profiles, while also taking the relevant determinants data into account. By taking into account a richer set of information, FARX provides stronger performance in real data analysis, with both accuracy and high computational efficiency. Compared to several alternative models in out-of-sample forecasts, the proposed model can improve forecast accuracy by at least 12% and up to 5-fold for one node, 3% to 2-fold and 2-fold to 4-fold for the other two nodes. The results show that lagged 1-day gas flow and nominations are important predictors, and with their presence in the forecast model, temperature becomes insignificant for short-term predictions. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1016/j.apenergy.2018.06.137 IS - Volume 228 SP - 1091 EP - 1110 ER - TY - GEN A1 - Gamrath, Inken A1 - Petkovic, Milena T1 - Prediction of Intermitted Flows in Large Gas Networks T3 - ZIB-Report - 19-29 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73717 SN - 1438-0064 ER - TY - THES A1 - Scheizel, Jenia T1 - A fast Flow based Heuristic for MIP modelled SCM Problems Y1 - 2018 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Elijazyfer, Ziena A1 - Schwartz, Stephan T1 - Approximating Balanced Graph Partitions N2 - We consider the problem of partitioning a weighted graph into k connected components of similar weight. In particular, we consider the two classical objectives to maximize the lightest part or to minimize the heaviest part. For a partitioning of the vertex set and for both objectives, we give the first known approximation results on general graphs. Specifically, we give a $\Delta$-approximation where $\Delta$ is the maximum degree of an arbitrary spanning tree of the given graph. Concerning the edge partition case, we even obtain a 2-approximation for the min-max and the max-min problem, by using the claw-freeness of line graphs. T3 - ZIB-Report - 19-25 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73675 SN - 1438-0064 ER - TY - GEN A1 - Hennings, Felix A1 - Anderson, Lovis A1 - Hoppmann, Kai A1 - Turner, Mark A1 - Koch, Thorsten T1 - Controlling transient gas flow in real-world pipeline intersection areas N2 - Compressor stations are the heart of every high-pressure gas transport network. Located at intersection areas of the network they are contained in huge complex plants, where they are in combination with valves and regulators responsible for routing and pushing the gas through the network. Due to their complexity and lack of data compressor stations are usually dealt with in the scientific literature in a highly simplified and idealized manner. As part of an ongoing project with one of Germany's largest Transmission System Operators to develop a decision support system for their dispatching center, we investigated how to automatize control of compressor stations. Each station has to be in a particular configuration, leading in combination with the other nearby elements to a discrete set of up to 2000 possible feasible operation modes in the intersection area. Since the desired performance of the station changes over time, the configuration of the station has to adapt. Our goal is to minimize the necessary changes in the overall operation modes and related elements over time, while fulfilling a preset performance envelope or demand scenario. This article describes the chosen model and the implemented mixed integer programming based algorithms to tackle this challenge. By presenting extensive computational results on real world data we demonstrate the performance of our approach. T3 - ZIB-Report - 19-24 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73645 SN - 1438-0064 ER - TY - GEN A1 - Hoppmann, Kai A1 - Hennings, Felix A1 - Lenz, Ralf A1 - Gotzes, Uwe A1 - Heinecke, Nina A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - Optimal Operation of Transient Gas Transport Networks T3 - ZIB-Report - 19-23 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73639 SN - 1438-0064 ER - TY - GEN A1 - Petkovic, Milena A1 - Chen, Ying A1 - Gamrath, Inken A1 - Gotzes, Uwe A1 - Hadjidimitriou, Natalia Selini A1 - Zittel, Janina A1 - Xu, Xiaofei A1 - Koch, Thorsten T1 - A Hybrid Approach for High Precision Prediction of Gas Flows N2 - About 20% of the German energy demand is supplied by natural gas. Ad- ditionally, for about twice the amount Germany serves as a transit country. Thereby, the German network represents a central hub in the European natural gas transport network. The transport infrastructure is operated by so-called transmissions system operators or TSOs. The number one priority of the TSOs is to ensure security of supply. However, the TSOs have no knowledge of the intentions and planned actions of the shippers (traders). Open Grid Europe (OGE), one of Germany’s largest TSO, operates a high- pressure transport network of about 12.000 km length. Since flexibility and security of supply is of utmost importance to the German Energy Transition (“Energiewende”) especially with the introduction of peak-load gas power stations, being able to predict in- and out-flow of the network is of great importance. In this paper we introduce a new hybrid forecast method applied to gas flows at the boundary nodes of a transport network. The new method employs optimized feature minimization and selection. We use a combination of an FAR, LSTM DNN and mathematical programming to achieve robust high quality forecasts on real world data for different types of network nodes. Keywords: Gas Forecast, Time series, Hybrid Method, FAR, LSTM, Mathematical Optimisation T3 - ZIB-Report - 19-26 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73525 SN - 1438-0064 ER - TY - CHAP A1 - Rehfeldt, Daniel A1 - Shinano, Yuji A1 - Koch, Thorsten T1 - SCIP-Jack: An exact high performance solver for Steiner tree problems in graphs and related problems BT - Proceedings of the 7th International Conference on High Performance Scientific Computing T2 - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 N2 - The Steiner tree problem in graphs is one of the classic combinatorial optimization problems. Furthermore, many related problems, such as the rectilinear Steiner tree problem or the maximum-weight connected subgraph problem, have been described in the literature—with a wide range of practical applications. To embrace this wealth of problem classes, the solver SCIP-JACK has been developed as an exact framework for classic Steiner tree and 11 related problems. Moreover, the solver comes with both shared- and distributed memory extensions by means of the UG framework. Besides its versatility, SCIP-JACK is highly competitive for most of the 12 problem classes it can solve, as for instance demonstrated by its top ranking in the recent PACE 2018 Challenge. This article describes the current state of SCIP-JACK and provides up-to-date computational results, including several instances that can now be solved for the first time to optimality. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-55240-4_10 PB - Springer ER - TY - CHAP A1 - Shinano, Yuji A1 - Rehfeldt, Daniel A1 - Gally, Tristan T1 - An Easy Way to Build Parallel State-of-the-art Combinatorial Optimization Problem Solvers: A Computational Study on Solving Steiner Tree Problems and Mixed Integer Semidefinite Programs by using ug[SCIP-*,*]-libraries T2 - Proceedings of the 9th IEEE Workshop Parallel / Distributed Combinatorics and Optimization N2 - Branch-and-bound (B&B) is an algorithmic framework for solving NP-hard combinatorial optimization problems. Although several well-designed software frameworks for parallel B&B have been developed over the last two decades, there is very few literature about successfully solving previously intractable combinatorial optimization problem instances to optimality by using such frameworks.The main reason for this limited impact of parallel solvers is that the algorithmic improvements for specific problem types are significantly greater than performance gains obtained by parallelization in general. Therefore, in order to solve hard problem instances for the first time, one needs to accelerate state-of-the-art algorithm implementations. In this paper, we present a computational study for solving Steiner tree problems and mixed integer semidefinite programs in parallel. These state-of-the-art algorithm implementations are based on SCIP and were parallelized via the ug[SCIP-*,*]-libraries---by adding less than 200 lines of glue code. Despite the ease of their parallelization, these solvers have the potential to solve previously intractable instances. In this paper, we demonstrate the convenience of such a parallelization and present results for previously unsolvable instances from the well-known PUC benchmark set, widely regarded as the most difficult Steiner tree test set in the literature. Y1 - 2019 U6 - https://doi.org/10.1109/IPDPSW.2019.00095 SP - 530 EP - 541 PB - IEEE ER - TY - CHAP A1 - Noack, Matthias A1 - Focht, Erich A1 - Steinke, Thomas T1 - Heterogeneous Active Messages for Offloading on the NEC SX-Aurora TSUBASA T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Heterogeneity in Computing Workshop (HCW 2019) N2 - The NEC SX-Aurora TSUBASA is a new generation of vector processing architectures that combines a standard Intel Xeon host with the newly developed NEC Vector Engine co-processor cards. One way to use these co-processors is offloading suitable parts of the program from the host to the Vector Engines. Currently, the only vendor-provided offloading solutions are the low-level Vector Engine Offloading (VEO) library, and a builtin reverse-offloading mechanism named VHcall. In this work, we extend the portable Heterogeneous Active Messages (HAM) based HAM-Offload framework with support for the NEC SX-Aurora TSUBASA. Therefore, we design, implement, and evaluate two messaging protocols aimed at minimising offloading cost. This sheds some light on how to achieve fast communication between host CPU and the Vector Engines of the NEC SX-Aurora TSUBASA. Compared with VEO, the DMA-based protocol reduces offloading overhead by a factor of 13×. The resulting framework enables users to write portable offload applications with low overhead, that do neither require a language extension like OpenMP, nor a special language like OpenCL. Existing HAM-Offload applications are now ready to run on the NEC SX-Aurora TSUBASA. Y1 - 2019 ER - TY - CHAP A1 - Noack, Matthias T1 - Heterogeneous Active Messages (HAM) — Implementing Lightweight Remote Procedure Calls in C++ T2 - Proceedings of the 5th International Workshop on OpenCL, The Distributed & Heterogeneous Programming in C/C++ (DHPCC++ 2019) Conference N2 - We present HAM (Heterogeneous Active Messages), a C++-only active messaging solution for heterogeneous distributed systems.Combined with a communication protocol, HAM can be used as a generic Remote Procedure Call (RPC) mechanism. It has been used in HAM-Offload to implement a low-overhead offloading framework for inter- and intra-node offloading between different architectures including accelerators like the Intel Xeon Phi x100 series and the NEC SX-Aurora TSUBASA Vector Engine. HAM uses template meta-programming to implicitly generate active message types and their corresponding handler functions. Heterogeneity is enabled by providing an efficient address translation mechanism between the individual handler code addresses of processes running different binaries on different architectures, as well a hooks to inject serialisation and deserialisation code on a per-type basis. Implementing such a solution in modern C++ sheds some light on the shortcomings and grey areas of the C++ standard when it comes to distributed and heterogeneous environments. Y1 - 2019 U6 - https://doi.org/10.1145/3318170.3318195 ER - TY - CHAP A1 - Shinano, Yuji A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Building Optimal Steiner Trees on Supercomputers by Using up to 43,000 Cores T2 - Integration of Constraint Programming, Artificial Intelligence, and Operations Research. CPAIOR 2019 N2 - SCIP-JACK is a customized, branch-and-cut based solver for Steiner tree and related problems. ug [SCIP-JACK, MPI] extends SCIP-JACK to a massively parallel solver by using the Ubiquity Generator (UG) framework. ug [SCIP-JACK, MPI] was the only solver that could run on a distributed environment at the (latest) 11th DIMACS Challenge in 2014. Furthermore, it could solve three well-known open instances and updated 14 best-known solutions to instances from the benchmark libary STEINLIB. After the DIMACS Challenge, SCIP-JACK has been considerably improved. However, the improvements were not reflected on ug [SCIP- JACK, MPI]. This paper describes an updated version of ug [SCIP-JACK, MPI], especially branching on constrains and a customized racing ramp-up. Furthermore, the different stages of the solution process on a supercomputer are described in detail. We also show the latest results on open instances from the STEINLIB. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-19212-9_35 VL - 11494 SP - 529 EP - 539 PB - Springer ER - TY - GEN A1 - Omari, Mohamed A1 - Lange, Alexander A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - A Mathematical Model for the Influence of Glucose-Insulin Dynamics on the Estrous Cycle in Dairy Cows N2 - Nutrition plays a crucial role in regulating reproductive hormones and follicular development in cattle. This is visible particularly during the time of negative energy balance at the onset of milk production after calving. Here, elongated periods of anovulation have been observed, resulting from alterations in luteiniz- ing hormone concentrations, likely caused by lower glucose and insulin concen- trations in the blood. The mechanisms that result in a reduced fertility are not completely understood, although a close relationship to the glucose-insulin metabolism is widely supported. Following this idea, a mathematical model of the hormonal network combining reproductive hormones and hormones that are coupled to the glucose compartments within the body of the cow was developed. The model is built on ordinary differential equations and relies on previously introduced models on the bovine estrous cycle and the glucose-insulin dynam- ics. Necessary modifications and coupling mechanisms are thoroughly discussed. Depending on the composition and the amount of food, in particular the glu- cose content in the dry matter, the model quantifies reproductive hormones and follicular development over time. Simulation results for different nutritional regimes in lactating and non-lactating dairy cows are examined and compared with experimental studies. Regarding its applicability, this work is an early attempt towards developing in silico feeding strategies and may eventually help refining and reducing animal experiments. T3 - ZIB-Report - 19-22 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73475 SN - 1438-0064 ER - TY - GEN A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - From interacting agents to density-based modeling with stochastic PDEs N2 - Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models. T3 - ZIB-Report - 19-21 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73456 SN - 1438-0064 ER - TY - CHAP A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Nanocomposites – A Route to better and smaller optical Elements? T2 - Optical Design and Fabrication 2019 Y1 - 2019 U6 - https://doi.org/10.1364/OFT.2019.OT2A.2 SP - OT2A.2 ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - Modal analysis for nanoplasmonics with nonlocal material properties JF - Phys. Rev. B Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevB.100.155406 VL - 100 SP - 155406 ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - A Surface-Theoretic Approach for Statistical Shape Modeling T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part IV N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. We evaluate the performance of our model w.r.t. shape-based classification of pathological malformations of the human knee and show that it outperforms the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model’s ability of capturing natural biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-32251-9_3 VL - 11767 SP - 21 EP - 29 PB - Springer ER - TY - JOUR A1 - Zhang, Wei A1 - Klus, Stefan A1 - Conrad, Tim A1 - Schütte, Christof T1 - Learning chemical reaction networks from trajectory data JF - SIAM Journal on Applied Dynamical Systems (SIADS) N2 - We develop a data-driven method to learn chemical reaction networks from trajectory data. Modeling the reaction system as a continuous-time Markov chain and assuming the system is fully observed,our method learns the propensity functions of the system with predetermined basis functions by maximizing the likelihood function of the trajectory data under l^1 sparse regularization. We demonstrate our method with numerical examples using synthetic data and carry out an asymptotic analysis of the proposed learning procedure in the infinite-data limit. Y1 - 2019 U6 - https://doi.org/10.1137/19M1265880 VL - 18 IS - 4 SP - 2000 EP - 2046 ER - TY - JOUR A1 - Thiel, Denise A1 - Djurdjevac Conrad, Natasa A1 - Ntini, Evgenia A1 - Peschutter, Ria A1 - Siebert, Heike A1 - Marsico, Annalisa T1 - Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis JF - BMC Bioinformatics N2 - Background: Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of ’guilt-by-association’, no strategy exists so far which identifies mRNA-lncRNA functional modules based on the 3D chromatin interaction graph. Results: To better understand the function of chromatin interactions in the context of lncRNA-mediated gene regulation, we have developed a multi-step graph analysis approach to examine the RNA polymerase II ChIA-PET chromatin interaction network in the K562 human cell line. We have annotated the network with gene and lncRNA coordinates, and chromatin states from the ENCODE project. We used centrality measures, as well as an adaptation of our previously developed Markov State Models (MSM) clustering method, to gain a better understanding of lncRNAs in transcriptional regulation. The novelty of our approach resides in the detection of fuzzy regulatory modules based on network properties and their optimization based on co-expression analysis between genes and gene-lncRNA pairs. This results in our method returning more bona fide regulatory modules than other state-of-the art approaches for clustering on graphs. Conclusions: Interestingly, we find that lncRNA network hubs tend to be significantly enriched in evolutionary conserved lncRNAs and enhancer-like functions. We validated regulatory functions for well known lncRNAs, such as MALAT1 and the enhancer-like lncRNA FALEC. In addition, by investigating the modular structure of bigger components we mine putative regulatory functions for uncharacterized lncRNAs. Y1 - 2019 U6 - https://doi.org/10.1186/s12859-019-2900-8 VL - 20 IS - 1471-2105 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - From interacting agents to density-based modeling with stochastic PDEs JF - Communications in Applied Mathematics and Computational Science N2 - Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models. Y1 - 2021 U6 - https://doi.org/10.2140/camcos.2021.16.1 VL - 16 IS - 1 SP - 1 EP - 32 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Linearizable State Machine Replication of State-Based CRDTs without Logs JF - arXiv N2 - General solutions of state machine replication have to ensure that all replicas apply the same commands in the same order, even in the presence of failures. Such strict ordering incurs high synchronization costs caused by distributed consensus or by the use of a leader. This paper presents a protocol for linearizable state machine replication of conflict-free replicated data types (CRDTs) that neither requires consensus nor a leader. By leveraging the properties of state-based CRDTs - in particular the monotonic growth of a join semilattice - synchronization overhead is greatly reduced. In addition, updates just need a single round trip and modify the state `in-place' without the need for a log. Furthermore, the message size overhead for coordination consists of a single counter per message. While reads in the presence of concurrent updates are not wait-free without a coordinator, we show that more than 97% of reads can be handled in one or two round trips under highly concurrent accesses. Our protocol achieves high throughput without auxiliary processes like command log management or leader election. It is well suited for all practical scenarios that need linearizable access on CRDT data on a fine-granular scale. Y1 - 2019 ER - TY - CHAP A1 - Alonso, Gustavo A1 - Binnig, Carsten A1 - Pandis, Ippokratis A1 - Salem, Kenneth A1 - Skrzypczak, Jan A1 - Stutsman, Ryan A1 - Thostrup, Lasse A1 - Wang, Tianzheng A1 - Wang, Zeke A1 - Ziegler, Tobias T1 - DPI: The Data Processing Interface for Modern Networks T2 - 9th Biennial Conference on Innovative Data Systems Research N2 - As data processing evolves towards large scale, distributed platforms, the network will necessarily play a substantial role in achieving efficiency and performance. Increasingly, switches, network cards, and protocols are becoming more flexible while programmability at all levels (aka, software defined networks) opens up many possibilities to tailor the network to data processing applications and to push processing down to the network elements. In this paper, we propose DPI, an interface providing a set of simple yet powerful abstractions flexible enough to exploit features of modern networks (e.g., RDMA or in-network processing) suitable for data processing. Mirroring the concept behind the Message Passing Interface (MPI) used extensively in high-performance computing, DPI is an interface definition rather than an implementation so as to be able to bridge different networking technologies and to evolve with them. In the paper we motivate and discuss key primitives of the interface and present a number of use cases that show the potential of DPI for data-intensive applications, such as analytic engines and distributed database systems. Y1 - 2019 ER - TY - GEN A1 - Hoppmann, Kai T1 - On the Complexity of the Maximum Minimum Cost Flow Problem N2 - Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity and an associated length, together with nonempty supply-intervals for the sources and nonempty demand-intervals for the sinks. The goal of the Maximum Minimum Cost Flow Problem (MMCF) is to find fixed supply and demand values within these intervals, such that the optimal objective value of the induced Minimum Cost Flow Problem (MCF) is maximized. In this paper, we show that MMCF is APX-hard and remains NP-hard in the uncapacitated case. T3 - ZIB-Report - 19-19 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73359 SN - 1438-0064 ER - TY - CHAP A1 - Salem, Farouk A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Scheduling Data Streams for Low Latency and High Throughput on a Cray XC40 Using Libfabric T2 - CUG Conference Proceedings N2 - Achieving efficient many-to-many communication on a given network topology is a challenging task when many data streams from different sources have to be scattered concurrently to many destinations with low variance in arrival times. In such scenarios, it is critical to saturate but not to congest the bisectional bandwidth of the network topology in order to achieve a good aggregate throughput. When there are many concurrent point-to-point connections, the communication pattern needs to be dynamically scheduled in a fine-grained manner to avoid network congestion (links, switches), overload in the node’s incoming links, and receive buffer overflow. Motivated by the use case of the Compressed Baryonic Matter experiment (CBM), we study the performance and variance of such communication patterns on a Cray XC40 with different routing schemes and scheduling approaches. We present a distributed Data Flow Scheduler (DFS) that reduces the variance of arrival times from all sources at least 30 times and increases the achieved aggregate bandwidth by up to 50%. Y1 - 2019 ER - TY - GEN A1 - Serrano, Felipe A1 - Schwarz, Robert A1 - Gleixner, Ambros T1 - On the Relation between the Extended Supporting Hyperplane Algorithm and Kelley’s Cutting Plane Algorithm N2 - Recently, Kronqvist et al. (2016) rediscovered the supporting hyperplane algorithm of Veinott (1967) and demonstrated its computational benefits for solving convex mixed-integer nonlinear programs. In this paper we derive the algorithm from a geometric point of view. This enables us to show that the supporting hyperplane algorithm is equivalent to Kelley's cutting plane algorithm applied to a particular reformulation of the problem. As a result, we extend the applicability of the supporting hyperplane algorithm to convex problems represented by general, not necessarily convex, differentiable functions that satisfy a mild condition. T3 - ZIB-Report - 19-18 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73253 SN - 1438-0064 ER - TY - CHAP A1 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan ED - Rea, Paul M. T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy T2 - Biomedical Visualisation N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. Y1 - 2019 SN - 978-3-030-19384-3 SN - 978-3-030-19385-0 U6 - https://doi.org/10.1007/978-3-030-19385-0_5 VL - 3 IS - 1156 SP - 67 EP - 84 PB - Springer Nature Switzerland AG ET - 1 ER - TY - JOUR A1 - Becker, Christiane A1 - Burger, Sven A1 - Jäger, Klaus T1 - Nanooptische Simulationen für optoelektronische Anwendungen JF - Photonik: Fachzeitschrift für die optischen Technologien Y1 - 2019 SN - 1432-9778 VL - 2019 IS - 2 SP - 42 EP - 45 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Eisert, Jens A1 - Schütte, Christof T1 - Multidimensional Approximation of Nonlinear Dynamical Systems JF - Journal of Computational and Nonlinear Dynamics N2 - A key task in the field of modeling and analyzing nonlinear dynamical systems is the recovery of unknown governing equations from measurement data only. There is a wide range of application areas for this important instance of system identification, ranging from industrial engineering and acoustic signal processing to stock market models. In order to find appropriate representations of underlying dynamical systems, various data-driven methods have been proposed by different communities. However, if the given data sets are high-dimensional, then these methods typically suffer from the curse of dimensionality. To significantly reduce the computational costs and storage consumption, we propose the method multidimensional approximation of nonlinear dynamical systems (MANDy) which combines data-driven methods with tensor network decompositions. The efficiency of the introduced approach will be illustrated with the aid of several high-dimensional nonlinear dynamical systems. Y1 - 2019 U6 - https://doi.org/10.1115/1.4043148 VL - 14 IS - 6 ER - TY - JOUR A1 - Reuter, Bernhard A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Generalized Markov modeling of nonreversible molecular kinetics JF - The Journal of Chemical Physics N2 - Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems. Y1 - 2019 U6 - https://doi.org/10.1063/1.5064530 VL - 17 IS - 150 SP - 174103 ER - TY - JOUR A1 - Ernst, Natalia A1 - Fackeldey, Konstantin A1 - Volkamer, Andrea A1 - Opatz, Oliver A1 - Weber, Marcus T1 - Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes JF - Molecular Simulation N2 - Molecular simulations are often used to analyse the stability of protein–ligand complexes. The stability can be characterised by exit rates or using the exit time approach, i.e. by computing the expected holding time of the complex before its dissociation. However determining exit rates by straightforward molecular dynamics methods can be challenging for stochastic processes in which the exit event occurs very rarely. Finding a low variance procedure for collecting rare event statistics is still an open problem. In this work we discuss a novel method for computing exit rates which uses results of Robust Perron Cluster Analysis (PCCA+). This clustering method gives the possibility to define a fuzzy set by a membership function, which provides additional information of the kind ‘the process is being about to leave the set’. Thus, the derived approach is not based on the exit event occurrence and, therefore, is also applicable in case of rare events. The novel method can be used to analyse the temperature effect of protein–ligand systems through the differences in exit rates, and, thus, open up new drug design strategies and therapeutic applications. Y1 - 2019 U6 - https://doi.org/10.1080/08927022.2019.1610949 VL - 45 IS - 11 SP - 904 EP - 911 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Pauwels, Edouard T1 - An unexpected connection between Bayes A-optimal designs and the group lasso JF - Statistical Papers N2 - We show that the A-optimal design optimization problem over m design points in R^n is equivalent to minimizing a quadratic function plus a group lasso sparsity inducing term over n x m real matrices. This observation allows to describe several new algorithms for A-optimal design based on splitting and block coordinate decomposition. These techniques are well known and proved powerful to treat large scale problems in machine learning and signal processing communities. The proposed algorithms come with rigorous convergence guarantees and convergence rate estimate stemming from the optimization literature. Performances are illustrated on synthetic benchmarks and compared to existing methods for solving the optimal design problem. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73059 VL - 60 IS - 2 SP - 215 EP - 234 ER - TY - JOUR A1 - Delle Site, Luigi A1 - Krekeler, Christian A1 - Whittaker, John A1 - Agarwal, Animesh A1 - Klein, Rupert A1 - Höfling, Felix T1 - Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir JF - Advanced Theory and Simulations N2 - The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed. Y1 - 2019 U6 - https://doi.org/10.1002/adts.201900014 VL - 2 SP - 1900014 ER - TY - GEN A1 - Berthold, Timo A1 - Gamrath, Gerald A1 - Salvagnin, Domenico T1 - Exploiting Dual Degeneracy in Branching N2 - Branch-and-bound methods for mixed-integer programming (MIP) are traditionally based on solving a linear programming (LP) relaxation and branching on a variable which takes a fractional value in the (single) computed relaxation optimum. In this paper, we study branching strategies for mixed-integer programs that exploit the knowledge of multiple alternative optimal solutions (a cloud ) of the current LP relaxation. These strategies naturally extend common methods like most infeasible branching, strong branching, pseudocost branching, and their hybrids, but we also propose a novel branching rule called cloud diameter branching. We show that dual degeneracy, a requirement for alternative LP optima, is present for many instances from common MIP test sets. Computational experiments show significant improvements in the quality of branching decisions as well as reduced branching effort when using our modifications of existing branching rules. We discuss different ways to generate a cloud of solutions and present extensive computational results showing that through a careful implementation, cloud modifications can speed up full strong branching by more than 10 % on standard test sets. Additionally, by exploiting degeneracy, we are also able to improve the state-of-the-art hybrid branching rule and reduce the solving time on affected instances by almost 20 % on average. T3 - ZIB-Report - 19-17 KW - mixed integer programming KW - branching rule KW - search strategy KW - dual degeneracy Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73028 SN - 1438-0064 ER - TY - GEN A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - 3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent N2 - Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori. T3 - ZIB-Report - 19-16 KW - quantitative photoacoustic imaging KW - blood oxygen saturation KW - inverse problem KW - model-based inversion KW - Monte Carlo KW - spectral unmixing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72995 SN - 1438-0064 ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - 3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent JF - Journal of Biomedical Optics N2 - Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori. Y1 - 2019 U6 - https://doi.org/10.1117/1.JBO.24.6.066001 VL - 24 IS - 6 SP - 066001 ER - TY - JOUR A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Ehrig, Rainald A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - Model Based Exploration of Hypokalemia in Dairy Cows JF - Scientific Reports N2 - Hypokalemia, characterized by too low serum potassium levels, is a severe mineral disorder which can be life threatening. It is increasingly diagnosed in veterinarian healthcare and a topic of ongoing research. In this paper, we explore the different originating conditions of hypokalemia: reduced potassium intake, increased excretion, acid-base disturbances, or increased insulin, by using a dynamic mathematical model for potassium balance in non-lactating and lactating cows. Simulations are compared with literature. The results give insights into the network dynamics and point to scenarios on which experimental effort should be focused. Application of mathematical models can assist in experimental planning as well as the reduction, refinement and replacement of animal experiments. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-22596-0 VL - 12, 19781 ER - TY - JOUR A1 - Graf, Florian A1 - Feis, Joshua A1 - Santiago, Xavier Garcia A1 - Wegener, Martin A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan T1 - Achiral, Helicity Preserving, and Resonant Structures for Enhanced Sensing of Chiral Molecules JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.8b01454 VL - 6 SP - 482 ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - An auxiliary field approach for computing optical resonances in dispersive media JF - J. Eur. Opt. Soc.-Rapid Y1 - 2019 U6 - https://doi.org/10.1186/s41476-019-0098-z VL - 15 SP - 3 ER - TY - THES A1 - Niemann, Jan-Hendrik T1 - A Dynamic Memory Approach for Consensus Problems with Packet Loss Y1 - 2019 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Using Gaussian process regression for efficient parameter reconstruction JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2513268 VL - 10959 SP - 1095911 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Determining 2D photonic crystal geometries from reflectance spectra with a reduced basis method T2 - Proc. Europ. Opt. Soc. Ann. Meet. 2016 (EOSAM) Y1 - 2016 SN - 978-1-5108-4796-5 SP - 281 ER - TY - CHAP A1 - Barth, Carlo A1 - Roder, Sebastian A1 - Brodoceanu, Daniel A1 - Kraus, Tobias A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Increased fluorescence of PbS quantum dots on photonic crystal slab structures T2 - Proc. Europ. Opt. Soc. Ann. Meet. 2016 (EOSAM) Y1 - 2016 SN - 978-1-5108-4796-5 SP - 181 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Pomplun, Jan A1 - Burger, Sven T1 - Finite elements for nano-optics applications T2 - Proc. Europ. Opt. Soc. Ann. Meet. 2016 (EOSAM) Y1 - 2016 SN - 978-1-5108-4796-5 SP - 178 ER - TY - CHAP A1 - Lassila, Antti A1 - Shpak, Maksim A1 - Vaigu, A. A1 - Smid, M. A1 - Velasco, A. A1 - Pokatilov, A. A1 - Fatadin, I. A1 - Ferguson, R. A1 - Robinson, D. A1 - Walbaum, T. A1 - Burger, Sven A1 - Haapalainen, Mertsi A1 - Vahimaa, P. A1 - Lukner, H. A1 - Pernice, W. A1 - Pitwon, R. A1 - Deninger, A. A1 - Morel, Jacques A1 - Castagna, Natascia A1 - Peters, O. A1 - Husu, H. T1 - Joint research for photonics fibres, waveguides and interconnects T2 - Proc. Europ. Opt. Soc. Ann. Meet. 2016 (EOSAM) Y1 - 2016 SN - 978-1-5108-4796-5 SP - 25 ER - TY - GEN A1 - Shinano, Yuji A1 - Rehfeldt, Daniel A1 - Galley, Tristan T1 - An Easy Way to Build Parallel State-of-the-art Combinatorial Optimization Problem Solvers: A Computational Study on Solving Steiner Tree Problems and Mixed Integer Semidefinite Programs by using ug[SCIP-*,*]-libraries N2 - Branch-and-bound (B&B) is an algorithmic framework for solving NP-hard combinatorial optimization problems. Although several well-designed software frameworks for parallel B&B have been developed over the last two decades, there is very few literature about successfully solving previously intractable combinatorial optimization problem instances to optimality by using such frameworks.The main reason for this limited impact of parallel solvers is that the algorithmic improvements for specific problem types are significantly greater than performance gains obtained by parallelization in general. Therefore, in order to solve hard problem instances for the first time, one needs to accelerate state-of-the-art algorithm implementations. In this paper, we present a computational study for solving Steiner tree problems and mixed integer semidefinite programs in parallel. These state-of-the-art algorithm implementations are based on SCIP and were parallelized via the ug[SCIP-*,*]-libraries---by adding less than 200 lines of glue code. Despite the ease of their parallelization, these solvers have the potential to solve previously intractable instances. In this paper, we demonstrate the convenience of such a parallelization and present results for previously unsolvable instances from the well-known PUC benchmark set, widely regarded as the most difficult Steiner tree test set in the literature. T3 - ZIB-Report - 19-14 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72804 SN - 1438-0064 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Outgassing induced acceleration of comet 67P/Churyumov-Gerasimenko JF - Astronomy & Astrophysics N2 - Cometary activity affects the orbital motion and rotation state due to sublimation induced forces. The availability of precise rotation-axis orientation and position data from the Rosetta mission allows one to accurately determine the outgassing of comet Churyumov-Gerasimenko/67P (67P). We derive the observed non-gravitational acceleration of 67P directly from the Rosetta spacecraft trajectory. From the non-gravitational acceleration we recover the diurnal outgassing variations and study a possible delay of the sublimation response with respect to the peak solar illumination. This allows us to compare the non-gravitational acceleration of 67P with expectations based on empirical models and common assumptions about the sublimation process. We use an iterative orbit refinement and Fourier decomposition of the diurnal activity to derive the outgassing induced non-gravitational acceleration. The uncertainties of the data reduction are established by a sensitivity analysis of an ensemble of best-fit orbits for comet 67P. We find that the Marsden non-gravitational acceleration parameters reproduce part of the non-gravitational acceleration but need to be augmented by an analysis of the nucleus geometry and surface illumination to draw conclusions about the sublimation process on the surface. The non-gravitational acceleration follows closely the subsolar latitude (seasonal illumination), with a small lag angle with respect to local noon around perihelion. The observed minor changes of the rotation axis do not favor forced precession models for the non-gravitational acceleration. In contrast to the sublimation induced torques, the non-gravitational acceleration does not put strong constraints on localized active areas on the nucleus. We find a close agreement of the orbit deduced non-gravitational acceleration and the water production independently derived from Rosetta in-situ measurement. Y1 - 2019 U6 - https://doi.org/10.1051/0004-6361/201935229 VL - 630 SP - A4 ER - TY - JOUR A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Gleixner, Ambros T1 - Using two-dimensional Projections for Stronger Separation and Propagation of Bilinear Terms JF - SIAM Journal on Optimization N2 - One of the most fundamental ingredients in mixed-integer nonlinear programming solvers is the well- known McCormick relaxation for a product of two variables x and y over a box-constrained domain. The starting point of this paper is the fact that the convex hull of the graph of xy can be much tighter when computed over a strict, non-rectangular subset of the box. In order to exploit this in practice, we propose to compute valid linear inequalities for the projection of the feasible region onto the x-y-space by solving a sequence of linear programs akin to optimization-based bound tightening. These valid inequalities allow us to employ results from the literature to strengthen the classical McCormick relaxation. As a consequence, we obtain a stronger convexification procedure that exploits problem structure and can benefit from supplementary information obtained during the branch-and bound algorithm such as an objective cutoff. We complement this by a new bound tightening procedure that efficiently computes the best possible bounds for x, y, and xy over the available projections. Our computational evaluation using the academic solver SCIP exhibit that the proposed methods are applicable to a large portion of the public test library MINLPLib and help to improve performance significantly. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72767 VL - 30 IS - 2 SP - 1339 EP - 1365 ER - TY - GEN A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Gleixner, Ambros T1 - Using two-dimensional Projections for Stronger Separation and Propagation of Bilinear Terms N2 - One of the most fundamental ingredients in mixed-integer nonlinear programming solvers is the well- known McCormick relaxation for a product of two variables x and y over a box-constrained domain. The starting point of this paper is the fact that the convex hull of the graph of xy can be much tighter when computed over a strict, non-rectangular subset of the box. In order to exploit this in practice, we propose to compute valid linear inequalities for the projection of the feasible region onto the x-y-space by solving a sequence of linear programs akin to optimization-based bound tightening. These valid inequalities allow us to employ results from the literature to strengthen the classical McCormick relaxation. As a consequence, we obtain a stronger convexification procedure that exploits problem structure and can benefit from supplementary information obtained during the branch-and bound algorithm such as an objective cutoff. We complement this by a new bound tightening procedure that efficiently computes the best possible bounds for x, y, and xy over the available projections. Our computational evaluation using the academic solver SCIP exhibit that the proposed methods are applicable to a large portion of the public test library MINLPLib and help to improve performance significantly. T3 - ZIB-Report - 19-15 KW - mixed-integer quadratically constrained programs KW - nonconvex KW - global optimization KW - separation KW - propagation KW - projection KW - bilinear terms Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72759 SN - 1438-0064 ER - TY - JOUR A1 - Bernal, David E. A1 - Vigerske, Stefan A1 - Trespalacios, Francisco A1 - Grossmann, Ignacio E. T1 - Improving the performance of DICOPT in convex MINLP problems using a feasibility pump JF - Optimization Methods and Software N2 - The solver DICOPT is based on an outer-approximation algorithm used for solving mixed- integer nonlinear programming (MINLP) problems. This algorithm is very effective for solving some types of convex MINLPs. However, there are certain problems that are diffcult to solve with this algorithm. One of these problems is when the nonlinear constraints are so restrictive that the nonlinear subproblems produced by the algorithm are infeasible. This problem is addressed in this paper with a feasibility pump algorithm, which modifies the objective function in order to efficiently find feasible solutions. It has been implemented as a preprocessing algorithm for DICOPT. Computational comparisons with previous versions of DICOPT and other MINLP solvers on a set of convex MINLPs demonstrate the effectiveness of the proposed algorithm in terms of solution quality and solving time. Y1 - 2017 ER - TY - JOUR A1 - Tawfik, Christine A1 - Limbourg, Sabine T1 - A Bilevel Model for Network Design and Pricing Based on a Level-of-Service Assessment JF - Transportation Science N2 - Within a wide view to stimulate intermodal transport, this paper is devoted to the examination of the intrinsically related problems of designing freight carrying services and determining their associated prices as observed by the shipper firms. A path-based multicommodity formulation is developed for a medium-term planning horizon, from the perspective of an intermodal operator. In the quest of incorporating nonprice attributes, two approaches are proposed to depict a realistic assessment of the service quality. First, frequency delay constraints are added to the upper level problem. Second, based on a random utility model, behavioural concepts are integrated in the expression of the lower level as a logistics costs minimization problem. Exact tests are invoked on real-world instances, demonstrating the capability of the presented approaches of reaching reasonable results within acceptable computation times and optimality gaps. The broader level-of-service perspective imposes additional costs on the service providers, although to a lesser extent on long-distance freight corridors, as indicated by the computed market share and net profit. Further experiments are conducted to test the impact of certain transport management instruments (e.g. subsidies and service capacities) on the modal split, as well as to assess the intermodality’s future based on a scenario analysis methodology. Y1 - 2019 U6 - https://doi.org/10.1287/trsc.2019.0906 VL - 53 IS - 6 SP - 1609 EP - 1626 PB - Informs CY - Transportation Science ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging (MRI) that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs).The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures.The shape models and neural networks employed are trained using data from the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets from the SKI10 challenge.For the first time, an accuracy equivalent to the inter-observer variability of human readers is achieved in this challenge.Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We make the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation.In conclusion, combining localized classification via CNNs with statistical anatomical knowledge via SSMs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. T3 - ZIB-Report - 19-06 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72704 SN - 1438-0064 N1 - Innovation Excellence Award 2020 ER - TY - GEN A1 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. T3 - ZIB-Report - 19-13 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72699 SN - 1438-0064 ER - TY - JOUR A1 - Berthold, Timo A1 - Farmer, James A1 - Heinz, Stefan A1 - Perregaard, Michael T1 - Parallelization of the FICO Xpress Optimizer JF - Optimization Methods and Software N2 - Computing hardware has mostly thrashed out the physical limits for speeding up individual computing cores. Consequently, the main line of progress for new hardware is growing the number of computing cores within a single CPU. This makes the study of efficient parallelization schemes for computation-intensive algorithms more and more important. A natural precondition to achieving reasonable speedups from parallelization is maintaining a high workload of the available computational resources. At the same time, reproducibility and reliability are key requirements for software that is used in industrial applications. In this paper, we present the new parallelization concept for the state-of-the-art MIP solver FICO Xpress-Optimizer. MIP solvers like Xpress are expected to be deterministic. This inevitably results in synchronization latencies which render the goal of a satisfying workload a challenge in itself. We address this challenge by following a partial information approach and separating the concepts of simultaneous tasks and independent threads from each other. Our computational results indicate that this leads to a much higher CPU workload and thereby to an improved, almost linear, scaling on modern high-performance CPUs. As an added value, the solution path that Xpress takes is not only deterministic in a fixed environment, but also, to a certain extent, thread-independent. This paper is an extended version of Berthold et al. [Parallelization of the FICO Xpress-Optimizer, in Mathematical Software – ICMS 2016: 5th International Conference, G.-M. Greuel, T. Koch, P. Paule, and A. Sommere, eds., Springer International Publishing, Berlin, 2016, pp. 251–258] containing more detailed technical descriptions, illustrative examples and updated computational results. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1333612 VL - 33 IS - 3 SP - 518 EP - 529 ER - TY - GEN A1 - Anderson, Daniel A1 - Hendel, Gregor A1 - Le Bodic, Pierre A1 - Viernickel, Jan Merlin T1 - Clairvoyant Restarts in Branch-and-Bound Search Using Online Tree-Size Estimation N2 - We propose a simple and general online method to measure the search progress within the Branch-and-Bound algorithm, from which we estimate the size of the remaining search tree. We then show how this information can help solvers algorithmically at runtime by designing a restart strategy for Mixed-Integer Programming (MIP) solvers that decides whether to restart the search based on the current estimate of the number of remaining nodes in the tree. We refer to this type of algorithm as clairvoyant. Our clairvoyant restart strategy outperforms a state-of-the-art solver on a large set of publicly available MIP benchmark instances. It is implemented in the MIP solver SCIP and will be available in future releases. T3 - ZIB-Report - 19-11 KW - Mixed-Integer Programming solvers KW - Restart KW - Progress measures KW - tree-size estimates Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72653 SN - 1438-0064 ER - TY - JOUR A1 - Rettig, Anika A1 - Haase, Tobias A1 - Pletnyov, Alexandr A1 - Kohl, Benjamin A1 - Ertel, Wolfgang A1 - von Kleist, Max A1 - Sunkara, Vikram T1 - SLCV – A Supervised Learning - Computer Vision combined strategy for automated muscle fibre detection in cross sectional images JF - PeerJ N2 - Muscle fibre cross sectional area (CSA) is an important biomedical measure used to determine the structural composition of skeletal muscle, and it is relevant for tackling research questions in many different fields of research. To date, time consuming and tedious manual delineation of muscle fibres is often used to determine the CSA. Few methods are able to automatically detect muscle fibres in muscle fibre cross sections to quantify CSA due to challenges posed by variation of bright- ness and noise in the staining images. In this paper, we introduce SLCV, a robust semi-automatic pipeline for muscle fibre detection, which combines supervised learning (SL) with computer vision (CV). SLCV is adaptable to different staining methods and is quickly and intuitively tunable by the user. We are the first to perform an error analysis with respect to cell count and area, based on which we compare SLCV to the best purely CV-based pipeline in order to identify the contribution of SL and CV steps to muscle fibre detection. Our results obtained on 27 fluorescence-stained cross sectional images of varying staining quality suggest that combining SL and CV performs signifi- cantly better than both SL based and CV based methods with regards to both the cell separation- and the area reconstruction error. Furthermore, applying SLCV to our test set images yielded fibre detection results of very high quality, with average sensitivity values of 0.93 or higher on different cluster sizes and an average Dice Similarity Coefficient (DSC) of 0.9778. T3 - ZIB-Report - 19-10 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72639 PB - PeerJ CY - PeerJ ER - TY - JOUR A1 - Achterberg, Tobias A1 - Bixby, Robert E. A1 - Gu, Zonghao A1 - Rothberg, Edward A1 - Weninger, Dieter T1 - Presolve Reductions in Mixed Integer Programming JF - INFORMS Journal on Computing N2 - Mixed integer programming has become a very powerful tool for modeling and solving real-world planning and scheduling problems, with the breadth of applications appearing to be almost unlimited. A critical component in the solution of these mixed-integer programs is a set of routines commonly referred to as presolve. Presolve can be viewed as a collection of preprocessing techniques that reduce the size of and, more importantly, improve the ``strength'' of the given model formulation, that is, the degree to which the constraints of the formulation accurately describe the underlying polyhedron of integer-feasible solutions. As our computational results will show, presolve is a key factor in the speed with which we can solve mixed-integer programs, and is often the difference between a model being intractable and solvable, in some cases easily solvable. In this paper we describe the presolve functionality in the Gurobi commercial mixed-integer programming code. This includes an overview, or taxonomy of the different methods that are employed, as well as more-detailed descriptions of several of the techniques, with some of them appearing, to our knowledge, for the first time in the literature. Y1 - 2019 ER - TY - GEN A1 - Sakurai, Daisuke A1 - Hege, Hans-Christian A1 - Kuhn, Alexander A1 - Rust, Henning A1 - Kern, Bastian A1 - Breitkopf, Tom-Lukas T1 - An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences N2 - In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features – which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data. T3 - ZIB-Report - 17-50 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72617 SN - 1438-0064 ER - TY - GEN A1 - Sakurai, Daisuke A1 - Ono, Kenji A1 - Carr, Hamish A1 - Nonaka, Jorji A1 - Kawanabe, Tomohiro ED - Carr, Hamish ED - Fujishiro, Issei ED - Sadlo, Filip ED - Takahashi, Shigeo T1 - Flexible Fiber Surfaces: A Reeb-Free Approach T2 - Topological Methods in Data Analysis and Visualization V N2 - The fiber surface generalizes the popular isosurface to multi-fields, so that pre-images can be visualized as surfaces. As with the isosurface, however, the fiber surface suffers from visual occlusion. We propose to avoid such occlusion by restricting the components to only the relevant ones with a new component-wise flexing algorithm. The approach, flexible fiber surface, generalizes the manipulation idea found in the flexible isosurface for the fiber surface. The flexible isosurface in the original form, however, relies on the contour tree. For the fiber surface, this corresponds to the Reeb space, which is challenging for both the computation and user interaction. We thus take a Reeb-free approach, in which one does not compute the Reeb space. Under this constraint, we generalize a few selected interactions in the flexible isosurface and discuss the implication of the restriction. Y1 - 2019 PB - Springer ER - TY - GEN A1 - Sakurai, Daisuke A1 - Ono, Kenji A1 - Carr, Hamish A1 - Nonaka, Jorji A1 - Kawanabe, Tomohiro T1 - Flexible Fiber Surfaces: A Reeb-Free Approach N2 - The fiber surface generalizes the popular isosurface to multi-fields, so that pre-images can be visualized as surfaces. As with the isosurface, however, the fiber surface suffers from visual occlusion. We propose to avoid such occlusion by restricting the components to only the relevant ones with a new component-wise flexing algorithm. The approach, flexible fiber surface, generalizes the manipulation idea found in the flexible isosurface for the fiber surface. The flexible isosurface in the original form, however, relies on the contour tree. For the fiber surface, this corresponds to the Reeb space, which is challenging for both the computation and user interaction. We thus take a Reeb-free approach, in which one does not compute the Reeb space. Under this constraint, we generalize a few selected interactions in the flexible isosurface and discuss the implication of the restriction. T3 - ZIB-Report - 19-09 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72599 SN - 1438-0064 ER - TY - JOUR A1 - Chrapary, Hagen A1 - Dalitz, Wolfgang A1 - Neun, Winfried A1 - Sperber, Wolfram T1 - Design, Concepts, and State of the Art of the swMATH Service JF - Mathematics in Computer Science N2 - In this paper, the concepts and design for an efficient information service for mathematical software and further mathematical research data are presented. The publication-based approach and the web-based approach are the main building blocks of the service and will be discussed. Heuristic methods are used for identification, extraction, and ranking of information about software and other mathematical research data. The methods provide not only information about the research data but also link software and mathematical research data to the scientific context. Y1 - 2017 U6 - https://doi.org/10.1007/s11786-017-0305-5 VL - 11 IS - 3-4 SP - 469 EP - 481 ER - TY - JOUR A1 - Munguia, Lluis-Miquel A1 - Oxberry, Geoffrey A1 - Rajan, Deepak A1 - Shinano, Yuji T1 - Parallel PIPS-SBB: Multi-Level Parallelism For Stochastic Mixed-Integer Programs JF - Computational Optimization and Applications N2 - PIPS-SBB is a distributed-memory parallel solver with a scalable data distribution paradigm. It is designed to solve MIPs with a dual-block angular structure, which is characteristic of deterministic-equivalent Stochastic Mixed-Integer Programs (SMIPs). In this paper, we present two different parallelizations of Branch & Bound (B&B), implementing both as extensions of PIPS-SBB, thus adding an additional layer of parallelism. In the first of the proposed frameworks, PIPS-PSBB, the coordination and load-balancing of the different optimization workers is done in a decentralized fashion. This new framework is designed to ensure all available cores are processing the most promising parts of the B&B tree. The second, ug[PIPS-SBB,MPI], is a parallel implementation using the Ubiquity Generator (UG), a universal framework for parallelizing B&B tree search that has been successfully applied to other MIP solvers. We show the effects of leveraging multiple levels of parallelism in potentially improving scaling performance beyond thousands of cores. Y1 - 2019 U6 - https://doi.org/10.1007/s10589-019-00074-0 ER - TY - CHAP A1 - Péron, Martin A1 - Bartlett, Peter L. A1 - Becker, Kai-Helge A1 - Helmstedt, Kate A1 - Chadès, Iadine T1 - Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks T2 - COMPASS '18 Proceedings of the 1st ACM SIGCAS Conference on Computing and Sustainable Societies N2 - Inspired by the problem of best managing the invasive mosquito Aedes albopictus across the 17 Torres Straits islands of Australia, we aim at solving a Markov decision process on large Susceptible-Infected-Susceptible (SIS) networks that are highly connected. While dynamic programming approaches can solve sequential decision-making problems on sparsely connected networks, these approaches are intractable for highly connected networks. Inspired by our case study, we focus on problems where the probability of nodes changing state is low and propose two approximate dynamic programming approaches. The first approach is a modified version of value iteration where only those future states that are similar to the current state are accounted for. The second approach models the state space as continuous instead of binary, with an on-line algorithm that takes advantage of Bellman's adapted equation. We evaluate the resulting policies through simulations and provide a priority order to manage the 17 infested Torres Strait islands. Both algorithms show promise, with the continuous state approach being able to scale up to high dimensionality (50 nodes). This work provides a successful example of how AI algorithms can be designed to tackle challenging computational sustainability problems. Y1 - 2018 U6 - https://doi.org/10.1145/3209811.3209814 PB - ACM ER - TY - BOOK A1 - Abbink, Erwin A1 - Bärmann, Andreas A1 - Bešinovic, Nikola A1 - Bohlin, Markus A1 - Cacchiani, Valentina A1 - Caimi, Gabrio A1 - de Fabris, Stefano A1 - Dollevoet, Twan A1 - Fischer, Frank A1 - Fügenschuh, Armin A1 - Galli, Laura A1 - Goverde, Rob M.P. A1 - Hansmann, Ronny A1 - Homfeld, Henning A1 - Huisman, Dennis A1 - Johann, Marc A1 - Klug, Torsten A1 - Törnquist Krasemann, Johanna A1 - Kroon, Leo A1 - Lamorgese, Leonardo A1 - Liers, Frauke A1 - Mannino, Carlo A1 - Medeossi, Giorgio A1 - Pacciarelli, Dario A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Schmidt, Marie A1 - Schöbel, Anita A1 - Schülldorf, Hanno A1 - Stieber, Anke A1 - Stiller, Sebastian A1 - Toth, Paolo A1 - Zimmermann, Uwe ED - Borndörfer, Ralf ED - Klug, Torsten ED - Lamorgese, Leonardo ED - Mannino, Carlo ED - Reuther, Markus ED - Schlechte, Thomas T1 - Handbook of Optimization in the Railway Industry N2 - This book promotes the use of mathematical optimization and operations research methods in rail transportation. The editors assembled thirteen contributions from leading scholars to present a unified voice, standardize terminology, and assess the state-of-the-art. There are three main clusters of articles, corresponding to the classical stages of the planning process: strategic, tactical, and operational. These three clusters are further subdivided into five parts which correspond to the main phases of the railway network planning process: network assessment, capacity planning, timetabling, resource planning, and operational planning. Individual chapters cover: Simulation Capacity Assessment Network Design Train Routing Robust Timetabling Event Scheduling Track Allocation Blocking Shunting Rolling Stock Crew Scheduling Dispatching Delay Propagation Y1 - 2018 SN - 978-3-319-72152-1 U6 - https://doi.org/10.1007/978-3-319-72153-8 VL - 268 PB - Springer Verlag ER - TY - CHAP A1 - Berthold, Timo A1 - Perregaard, Michael A1 - Mészáros, Csaba T1 - Four Good Reasons to Use an Interior Point Solver Within a MIP Solver T2 - Kliewer N., Ehmke J., Borndörfer R. (eds) Operations Research Proceedings 2017 N2 - “Interior point algorithms are a good choice for solving pure LPs or QPs, but when you solve MIPs, all you need is a dual simplex” This is the common conception which disregards that an interior point solution provides some unique structural insight into the problem at hand. In this paper, we will discuss some of the benefits that an interior point solver brings to the solution of difficult MIPs within FICO Xpress. This includes many different components of the MIP solver such as branching variable selection, primal heuristics, preprocessing, and of course the solution of the LP relaxation. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_22 SP - 159 EP - 164 ER - TY - CHAP A1 - Serrano, Felipe T1 - Intersection cuts for factorable MINLP T2 - A. Lodi, V. Nagarajan (eds), Integer Programming and Combinatorial Optimization: 20th International Conference, IPCO 2019 N2 - Given a factorable function f, we propose a procedure that constructs a concave underestimor of f that is tight at a given point. These underestimators can be used to generate intersection cuts. A peculiarity of these underestimators is that they do not rely on a bounded domain. We propose a strengthening procedure for the intersection cuts that exploits the bounds of the domain. Finally, we propose an extension of monoidal strengthening to take advantage of the integrality of the non-basic variables. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-17953-3_29 VL - 11480 SP - 385 EP - 398 ER - TY - THES A1 - Prendke, Mona T1 - Comparison of 2D and 3D CNNs for Classification of Knee MRI Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72439 ER - TY - THES A1 - Dill, Sabrina Patricia T1 - Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection Y1 - 2018 ER - TY - JOUR A1 - Hettich, G. A1 - Schierjott, R. A. A1 - Schilling, C. A1 - Maas, A. A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Lamecker, Hans A1 - Grupp, T. M. T1 - Validation of a Statistical Shape Model for Acetabular Bone Defect Analysis JF - ISTA 2018 London Abstract Book N2 - Acetabular bone defects are still challenging to quantify. Numerous classification schemes have been proposed to categorize the diverse kinds of defects. However, these classification schemes are mainly descriptive and hence it remains difficult to apply them in pre-clinical testing, implant development and pre-operative planning. By reconstructing the native situation of a defect pelvis using a Statistical Shape Model (SSM), a more quantitative analysis of the bone defects could be performed. The aim of this study is to develop such a SSM and to validate its accuracy using relevant clinical scenarios and parameters. Y1 - 2018 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Schmidt, Nora Laura A1 - Lamecker, Hans A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - The Healthy Nasal Cavity - Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon’s Perspective JF - Facial Plastic Surgery N2 - Functional surgery on the nasal framework requires referential criteria to objectively assess nasal breathing for indication and follow-up. Thismotivated us to generate amean geometry of the nasal cavity based on a statistical shape model. In this study, the authors could demonstrate that the introduced nasal cavity’s mean geometry features characteristics of the inner shape and airflow, which are commonly observed in symptom-free subjects. Therefore, the mean geometry might serve as a reference-like model when one considers qualitative aspects. However, to facilitate quantitative considerations and statistical inference, further research is necessary. Additionally, the authorswere able to obtain details about the importance of the isthmus nasi and the inferior turbinate for the intranasal airstream. KW - statistical shape model KW - nasal cavity KW - nasal breathing KW - nasal airflow KW - isthmus nasi KW - inferior turbinate Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677721 VL - 35 IS - 1 SP - 9 EP - 13 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Goubergrits, Leonid T1 - Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery JF - Facial Plastic Surgery N2 - Successful functional surgery on the nasal framework requires reliable and comprehensive diagnosis. In this regard, the authors introduce a new methodology: Digital Analysis of Nasal Airflow (diANA). It is based on computational fluid dynamics, a statistical shape model of the healthy nasal cavity and rhinologic expertise. diANA necessitates an anonymized tomographic dataset of the paranasal sinuses including the complete nasal cavity and, when available, clinical information. The principle of diANA is to compare the morphology and the respective airflow of an individual nose with those of a reference. This enablesmorphometric aberrations and consecutive flow field anomalies to localize and quantify within a patient’s nasal cavity. Finally, an elaborated expert opinion with instructive visualizations is provided. Using diANA might support surgeons in decision-making, avoiding unnecessary surgery, gaining more precision, and target-orientation for indicated operations. KW - nasal airflow simulation KW - nasal breathing KW - statistical shape model KW - diANA KW - nasal obstruction KW - rhinorespiratory homeostasis Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677720 VL - 35 IS - 1 SP - 1 EP - 8 ER - TY - GEN A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Röblitz, Susanna T1 - A mathematical modelling approach to the insight of dynamic networks: Potassium homeostasis and glucose-insulin in dairy cows T2 - ADSA 2018 Annual Meeting N2 - Lactating dairy cows require a particular composition of nutritional ingredients depending on their production status. The optimal supply of energy and minerals in diet, one of them potassium, is indispensable for the prevention of disbalances like hypokalemia or hypoglycaemia. Potassium balance in cows is the result of potassium intake, distribution in the organism, and excretion, and closely interacts with glucose and electrolyte metabolism, in which postpartum veterinary treatments frequently intervene. We present a mechanistic, dynamic model for potassium balance together with a glucose insulin model in non-lactating and lactating dairy cows based on ordinary differential equations. Parameter values were obtained from data of a clinical trial as well as from literature. To verify the mechanistic functioning of the model, we validate the model by comparing simulation outcomes with clinical study findings. Furthermore we perform numerical experiments and compare them with expected behaviour according to mechanistic knowledge. The results give insight into the dynamic behaviour of the network and open the way for further open questions and hypothesis to be tested. Y1 - 2018 UR - https://www.adsa.org/Portals/0/SiteContent/Docs/Meetings/PastMeetings/Annual/2018/223.pdf VL - 101 Suppl. 2 SP - 226 EP - 227 PB - American Dairy Science Association ET - Journal of Dairy Science ER - TY - JOUR A1 - Hendel, Gregor T1 - Adaptive Large Neighborhood Search for Mixed Integer Programming JF - Mathematical Programming Computation N2 - Large Neighborhood Search (LNS) heuristics are among the most powerful but also most expensive heuristics for mixed integer programs (MIP). Ideally, a solver learns adaptively which LNS heuristics work best for the MIP problem at hand in order to concentrate its limited computational budget. To this end, this work introduces Adaptive Large Neighborhood Search (ALNS) for MIP, a primal heuristic that acts a framework for eight popular LNS heuristics such as Local Branching and Relaxation Induced Neighborhood Search (RINS). We distinguish the available LNS heuristics by their individual search domains, which we call neighborhoods. The decision which neighborhood should be executed is guided by selection strategies for the multi armed bandit problem, a related optimization problem during which suitable actions have to be chosen to maximize a reward function. In this paper, we propose an LNS-specific reward function to learn to distinguish between the available neighborhoods based on successful calls and failures. A second, algorithmic enhancement is a generic variable fixing priorization, which ALNS employs to adjust the subproblem complexity as needed. This is particularly useful for some neighborhoods which do not fix variables by themselves. The proposed primal heuristic has been implemented within the MIP solver SCIP. An extensive computational study is conducted to compare different LNS strategies within our ALNS framework on a large set of publicly available MIP instances from the MIPLIB and Coral benchmark sets. The results of this simulation are used to calibrate the parameters of the bandit selection strategies. A second computational experiment shows the computational benefits of the proposed ALNS framework within the MIP solver SCIP. Y1 - 2018 ER - TY - JOUR A1 - Wende, Florian A1 - Marsman, Martijn A1 - Kim, Jeongnim A1 - Vasilev, Fedor A1 - Zhao, Zhengji A1 - Steinke, Thomas T1 - OpenMP in VASP: Threading and SIMD JF - International Journal of Quantum Chemistry N2 - The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version, as well as a 2x increased performance of collective operations using the multiple-endpoint MPI feature. The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9x performance gain on AVX512 platforms with the Intel compiler. Y1 - 2018 U6 - https://doi.org/10.1002/qua.25851 IS - Emerging Architectures in Computational Chemistry SP - e25851 PB - Wiley Online Library ER - TY - CHAP A1 - Dalitz, Wolfgang A1 - Chrapary, Hagen T1 - Software Products, Software Versions, Archiving of Software, and swMATH T2 - Mathematical Software – ICMS 2018 N2 - Management of software information is difficult for various reasons. First, software typically cannot be reduced to a single object: information about software is an aggregate of software code, APIs, documentation, installations guides, tutorials, user interfaces, test data, dependencies on hardware and other software, etc. Moreover, secondary information about software, especially use cases and experience with employing the software, is important to communicate. Second, typically named software, which we term here a `software product', is taken to stand for all versions of the software which can have different features and properties and may produced different results from the same input data. Software production is a dynamic process and software development is, increasingly, widely distributed. Therefore GitHub, GitLab, Bitbucket and other platforms for sharing are used. Information about software is alos provided in different locations, on websites, repositories, portals, etc. Each resource provides information about software from a particular point of view, but the information is often not linked together. Therefore swMATH has developed a conception which covers portals and a search engines for mathematical software, persistent and citable landing pages for specific software, and a method for software archiving. Based on the publication-based approach, swMATH collects and analyses semi-automatically the existing information about mathematical software found on the Web and makes it available in a user-oriented way. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-96418-8_15 SP - 123 EP - 127 ER - TY - CHAP A1 - Dalitz, Wolfgang A1 - Chrapary, Hagen A1 - Sperber, Wolfram T1 - Software Knowledge Management and swMATH T2 - Fachgruppe Didaktik der Mathematik der Universität Paderborn N2 - Mathematische Software ist heute ein weitverbreitetes Werkzeug in der Forschung, aber auch in der mathematischen Bildung. Die Anzahl mathematischer Softwareprodukte wächst, nicht zuletzt durch die Anforderungen der Anwender, stark. Anders als für mathematische Publikationen sind für das Management mathematischer Software viele Fragen offen und werden noch diskutiert, etwa die Standardisierung von Software Zitationen. Der Aufbau einer effizienten Infrastruktur für Software ist eine notwendige Voraussetzung für die Überprüfung von Forschungsergebnissen, die mittels Software erzielt worden sind und wichtig für die Entscheidung, ob eine bestimmte Software zur Lösung eines Problems verwendet werden soll. Das swMATH [1] Portal gibt einen weitgehend vollständigen Überblick über die existierende mathematische Software. Es ist ein Dienst entstanden, der automatisiert die im Web vorhandenen Informationen zu einer Software identifiziert, auswertet und verfügbar macht. Der Dienst soll insbesondere durch die Verknüpfung mit anderen Quellen, etwa dem Internet Archive, persistente Informationen über ein Software Produkt und dessen Versionen liefern. Y1 - 2018 U6 - https://doi.org/10.17877/DE290R-19281 SP - 401 EP - 404 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model Reduction by Time Aggregation for Optimal Design of Energy Supply Systems by an MILP Hierarchical Branch and Bound Method T2 - Proceedings of the 31st International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2018) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems effi- ciently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solu- tion. The method can decrease the number of design variables and constraints at the upper level, and thus may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2018 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayamaa, Yuji A1 - Wakui, Tetsuya T1 - Optimal Design of a Gas Turbine Cogeneration Plant by a Hierarchical Optimization Method With Parallel Computing T2 - ASME Turbo Expo 2018: Turbomachinery Technical Conference and Exposition N2 - To attain the highest performance of energy supply systems, it is necessary to rationally determine types, capacities, and numbers of equipment in consideration of their operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) approaches have been applied widely to such optimal design problems. The authors have proposed a MILP method utilizing the hierarchical relationship between design and operation variables to solve the optimal design problems of energy supply systems efficiently. In addition, some strategies to enhance the computation efficiency have been adopted: bounding procedures at both the levels and ordering of the optimal operation problems at the lower level. In this paper, as an additional strategy to enhance the computation efficiency, parallel computing is adopted to solve multiple optimal operation problems in parallel at the lower level. In addition, the effectiveness of each and combinations of the strategies adopted previously and newly is investigated. This hierarchical optimization method is applied to an optimal design of a gas turbine cogeneration plant, and its validity and effectiveness are clarified through some case studies. Y1 - 2018 UR - http://proceedings.asmedigitalcollection.asme.org/proceeding.aspx?articleid=2700845 VL - 3 ER - TY - CHAP A1 - Anderson, Daniel A1 - Hendel, Gregor A1 - Le Bodic, Pierre A1 - Viernickel, Jan Merlin T1 - Clairvoyant Restarts in Branch-and-Bound Search Using Online Tree-Size Estimation T2 - AAAI-19: Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence N2 - We propose a simple and general online method to measure the search progress within the branch-and-bound algorithm, from which we estimate the size of the remaining search tree. We then show how this information can help solvers algorithmically at runtime by designing a restart strategy for Mixed-Integer Programming (MIP) solvers that decides whether to restart the search based on the current estimate of the number of remaining nodes in the tree. We refer to this type of algorithm as clairvoyant. Our clairvoyant restart strategy outperforms a state-of-the-art solver on a large set of publicly available MIP benchmark instances. It is implemented in the MIP solver SCIP and will be available in future releases. Y1 - 2018 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Hijazi, Hassan A1 - Coffrin, Carleton T1 - Convex Relaxations for Quadratic On/Off Constraints and Applications to Optimal Transmission Switching JF - INFORMS Journal on Computing N2 - This paper studies mixed-integer nonlinear programs featuring disjunctive constraints and trigonometric functions and presents a strengthened version of the Convex Quadratic relaxation of the Optimal Transmission Switching problem. We first characterize the convex hull of univariate quadratic on/off constraints in the space of original variables using perspective functions. We then introduce new tight quadratic relaxations for trigonometric functions featuring variables with asymmetrical bounds. These results are used to further tighten recent convex relaxations introduced for the Optimal Transmission Switching problem in Power Systems. Using the proposed improvements, along with bound propagation, on 23 medium-size test cases in the PGLib benchmark library with a relaxation gap of more than 1%, we reduce the gap to less than 1% on 5 instances. The tightened model has promising computational results when compared to state-of-the-art formulations. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1287/ijoc.2019.0900 VL - 32 IS - 3 SP - 682 EP - 696 PB - INFORMS Institute for Operations Research and the Management Sciences CY - 5521 Research Park Drive, Suite 200, Catonsville, MD 21228 USA ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Koltai, Peter A1 - Nevir, Peter A1 - Rust, Henning A1 - Schild, Axel A1 - Weber, Marcus T1 - From metastable to coherent sets - Time-discretization schemes JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - In this article, we show that these well-established spectral algorithms (like PCCA+, Perron Cluster Cluster Analysis) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-time-discretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application. Y1 - 2019 U6 - https://doi.org/10.1063/1.5058128 VL - 29 SP - 012101 EP - 012101 ER - TY - GEN A1 - Witzig, Jakob A1 - Gleixner, Ambros T1 - Conflict-Driven Heuristics for Mixed Integer Programming N2 - Two essential ingredients of modern mixed-integer programming (MIP) solvers are diving heuristics that simulate a partial depth-first search in a branch-and-bound search tree and conflict analysis of infeasible subproblems to learn valid constraints. So far, these techniques have mostly been studied independently: primal heuristics under the aspect of finding high-quality feasible solutions early during the solving process and conflict analysis for fathoming nodes of the search tree and improving the dual bound. Here, we combine both concepts in two different ways. First, we develop a diving heuristic that targets the generation of valid conflict constraints from the Farkas dual. We show that in the primal this is equivalent to the optimistic strategy of diving towards the best bound with respect to the objective function. Secondly, we use information derived from conflict analysis to enhance the search of a diving heuristic akin to classical coefficient diving. The computational performance of both methods is evaluated using an implementation in the source-open MIP solver SCIP. Experiments are carried out on publicly available test sets including Miplib 2010 and Cor@l. T3 - ZIB-Report - 19-08 KW - mixed integer programming; primal heuristics; conflict analysis; branch-and-bound Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72204 SN - 1438-0064 ER - TY - JOUR A1 - Seeber, L. A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Obermeier, Patrick A1 - Chen, X. A1 - Karsch, K. A1 - Muehlhans, S. A1 - Tief, Franziska A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Educating parents about the vaccination status of their children: A user-centered mobile application JF - Preventive Medicine Reports N2 - Parents are often uncertain about the vaccination status of their children. In times of vaccine hesitancy, vaccination programs could benefit from active patient participation. The Vaccination App (VAccApp) was developed by the Vienna Vaccine Safety Initiative, enabling parents to learn about the vaccination status of their children, including 25 different routine, special indication and travel vaccines listed in the WHO Immunization Certificate of Vaccination (WHO-ICV). Between 2012 and 2014, the VAccApp was validated in a hospital-based quality management program in Berlin, Germany, in collaboration with the Robert Koch Institute. Parents of 178 children were asked to transfer the immunization data of their children from the WHO-ICV into the VAccApp. The respective WHO-ICV was photocopied for independent, professional data entry (gold standard). Demonstrating the status quo in vaccine information reporting, a Recall Group of 278 parents underwent structured interviews for verbal immunization histories, without the respective WHO-ICV. Only 9% of the Recall Group were able to provide a complete vaccination status; on average 39% of the questions were answered correctly. Using the WHO-ICV with the help of the VAccApp resulted in 62% of parents providing a complete vaccination status; on average 95% of the questions were answered correctly. After using the VAccApp, parents were more likely to remember key aspects of the vaccination history. User-friendly mobile applications empower parents to take a closer look at the vaccination record, thereby taking an active role in providing accurate vaccination histories. Parents may become motivated to ask informed questions and to keep vaccinations up-to-date. Y1 - 2017 U6 - https://doi.org/10.1016/j.pmedr.2017.01.002 VL - 5 SP - 241 EP - 250 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Vybiral, Jan A1 - Kutyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinformatics N2 - Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 SP - 1 EP - 20 ER - TY - JOUR A1 - Borong, Shao A1 - Cannistraci, Carlo A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data JF - Genomics and Computational Biology N2 - Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type. Y1 - 2017 U6 - https://doi.org/http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e57 VL - 3 IS - 3 SP - 1 EP - 13 ER - TY - CHAP A1 - Jayrannejad, Fahrnaz A1 - Conrad, Tim T1 - Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining T2 - Springer Lecture Notes in Artificial Intelligence N2 - Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set. Y1 - 2017 SP - studi ER - TY - CHAP A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Linear Programming using Limited-Precision Oracles T2 - A. Lodi, V. Nagarajan (eds), Integer Programming and Combinatorial Optimization: 20th International Conference, IPCO 2019 N2 - Linear programming is a foundational tool for many aspects of integer and combinatorial optimization. This work studies the complexity of solving linear programs exactly over the rational numbers through use of an oracle capable of returning limited-precision LP solutions. It is shown that a polynomial number of calls to such an oracle and a polynomial number of bit operations, is sufficient to compute an exact solution to an LP. Previous work has often considered oracles that provide solutions of an arbitrary specified precision. While this leads to polynomial-time algorithms, the level of precision required is often unrealistic for practical computation. In contrast, our work provides a foundation for understanding and analyzing the behavior of the methods that are currently most effective in practice for solving LPs exactly. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-17953-3_30 SP - 399 EP - 412 ER - TY - JOUR A1 - Lelièvre, Tony A1 - Zhang, Wei T1 - Pathwise estimates for effective dynamics: the case of nonlinear vectorial reaction coordinates JF - Multiscale Modeling and Simulation N2 - Effective dynamics using conditional expectation was proposed in [F. Legoll and T. Lelièvre, Nonlinearity, 2010] to approximate the essential dynamics of high-dimensional diffusion processes along a given reaction coordinate. The approximation error of the effective dynamics when it is used to approximate the behavior of the original dynamics has been considered in recent years. As a continuation of the previous work [F. Legoll, T. Lelièvre, and S. Olla, Stoch. Process. Appl, 2017], in this paper we obtain pathwise estimates for effective dynamics when the reaction coordinate function is either nonlinear or vector-valued. Y1 - 2018 U6 - https://doi.org/10.1137/18M1186034 IS - 17 SP - 1019 EP - 1051 ER - TY - JOUR A1 - Zhang, Wei T1 - Ergodic SDEs on submanifolds and related numerical sampling schemes JF - ESAIM: Mathematical Modelling and Numerical Analysis N2 - In many applications, it is often necessary to sample the mean value of certain quantity with respect to a probability measure $\mu$ on the level set of a smooth function ξ:R^d→R^k, 1≤k300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. Y1 - 2018 U6 - https://doi.org/10.1016/j.ultramic.2018.08.015 VL - 195 SP - 157 EP - 170 ER - TY - THES A1 - Helfmann, Luzie T1 - Stochastic Modeling of Interacting Agent Systems Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71887 ER - TY - JOUR A1 - Kork, F. A1 - Spies, Claudia A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 ER - TY - JOUR A1 - Obermeier, Patrick A1 - Heim, A. A1 - Biere, Barbara A1 - Hage, E. A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Clinical characteristics and disease severity associated with adenovirus infections in infants and children - discovery of a novel adenovirus, HAdV-D80 JF - Clinical Infectious Diseases Y1 - 2018 ER - TY - THES A1 - Anderson, Lovis T1 - The Computation of the Volume of the Union of Polytopes via a Sweep-Plane Algorithm N2 - Das Thema dieser Arbeit ist ein Volumen-Algorithmus für die Vereinigung von Polytopen. Der Algorithmus basiert auf der Arbeit von Bieri und Nef. Er berechnet das Volumen der Vereinigung von Polytopen mit einem Sweep-Verfahren. Dabei wird eine Hyperebene im Raum verschoben und das Volumen auf der einen Seite der Hyperebene berechnet. Umso weiter die Hyperebene verschobe wird, desto größer ist auch der Halbraum. Unser Algorithmus berechnet das Volumen einer Vereinigung von Polytopen geschnitten mit dem Halbraum der Sweep-Ebene als eine Funktion abhängig von der Veschiebung. Ab einem gewissen Punkt liegt der Körper dabei komplett im Halbraum der Sweep-Ebene und das Volumen bleibt konstant. Unser Algorithmus unterscheidet sich in zwei Punkten von dem Algorithmus von Bieri und Nef. Erstens funktioniert er nur auf der Vereinigung von Polytopen, wohingegen der Algorithmus von Bieri und Nef für Nef-Polyeder funktioniert. Diese sind eine Verallgemeinerung von Polyedern, die auch die Klasse der Vereinigung von Polytopen umfasst. Für uns ist das allerdings kein Nachteil, da unsere Datensätze zu Vereinigungen von Polytopen führen. Zweitens ist unser Algorithmus in zwei Teile aufgeteilt. Im ersten Teil wird eine Datenstruktur entwickelt, aus der im zweiten Teil zusammen mit einer Richtung die Sweep-Ebenen-Volumenfunktion berechnet wird. Der Großteil der Komplexität liegt im ersten Teil des Algorithmus. Das hat den Vorteil, dass wir die Volumenfunktionen für viele verschiedene Richtungen berechnen können. So können Einblicke in die Struktur des Körpers gewonnen werden. Der Algorithmus beruht auf zwei verschiedenen Zerlegungsansätzen. Zuerst können wir mit Hilfe von Anordnungen von Hyperebenen eine Vereinigung von Polytopen in ihre Zellen zerlegen. Dabei berufen wir uns auf die Arbeit von Gerstner und Holtz, in der das Konzept der Positionsvektoren eingeführt wird. Diese nutzen wir um die Ecken und ihre benachbarten Zellen zu bestimmen. So erhalten wir eine Zerlegung unserer Vereinigung in Zellen, deren paarweise Schnitte kein Volumen haben. Das zweite Zerlegungskonzept ist die konische Zerlegung, wie sie von Lawrence eingeführt wurde. Mit Hilfe dieser können wir die Indikatorfunktion eines Polytops als die Summe der Indikatorfunktionen seiner Vorwärtskegel schreiben. Die Sweep-Ebenen Volumenfunktionen können dann leicht mit Hilfe einer altbekannten Formel für das Volumen von Simplices berechnet werden. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71829 ER - TY - JOUR A1 - Dartsch, Maria A1 - Dulski, Sebastian A1 - Engels, Frauke A1 - Gran, Meike A1 - Kende, Jiri A1 - Lohrum, Stefan A1 - Porth, Robert A1 - Ristau, Ute A1 - Rüter, Christian A1 - Sabisch, Andreas A1 - Stumm, Birgit A1 - Taylor, Viola A1 - Voß, Michael T1 - Einführung des cloudbasierten Bibliothekssystems Alma in Berlin – ein Erfahrungsbericht JF - ABI Technik - Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen N2 - Die enge Zusammenarbeit der vier Berliner Universitätsbibliotheken1 reicht weit zurück. Bereits vor der Jahrtausendwende haben die Berliner Universitätsbibliotheken (UBs) gemeinsam das Bibliothekssystem Aleph 500 ausgewählt und implementiert, danach folgten weitere Systeme – das Linking System SFX, die Digitale Bibliothek MetaLib und das Bibliotheksportal Primo. Es war daher folgerichtig und selbstverständlich, dass auch die Auswahl und Implementierung eines neuen Bibliothekssystems in enger Abstimmung und Zusammenarbeit erfolgte. Die Erfahrungen bei Vertragsverhandlungen und Implementierung von Alma sind Gegenstand des folgenden Berichtes. N2 - As regards implementing new library technology, the Berlin University libraries have been working closely together for more than 20 years. It was the case for the implementation of the legacy system Aleph 500, the linking system SFX, the digital library MetaLib and the library portal Primo, and therefore it was a matter of course to continue the close cooperation during the implementation of the new cloud-based library system, too. The experience gained during the contract negotiations and the implementation project, and lessons learned are the focus of this report. Y1 - 2018 U6 - https://doi.org/10.1515/abitech-2018-2002 VL - 38 IS - 2 SP - 128 EP - 141 ER - TY - THES A1 - Elijazyfer, Ziena T1 - Längenbeschränkte Teilgraphenbildung zur Maut-Kontrollstreckenoptimierung Y1 - 2018 ER - TY - THES A1 - Schreck, Vanessa T1 - Algorithmic Analysis of the Graph Segmentation Problem Y1 - 2018 ER - TY - JOUR A1 - Abbas, Aennes A1 - Schneider, Ilona A1 - Bollmann, Anna A1 - Funke, Jan A1 - Oehlmann, Jörg A1 - Prasse, Carsten A1 - Schulte-Oehlmann, Ulrike A1 - Seitz, Wolfram A1 - Ternes, Thomas A1 - Weber, Marcus A1 - Wesely, Henning A1 - Wagner, Martin T1 - What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays JF - Water Research N2 - The assessment of water quality is crucial for safeguarding drinking water resources and ecosystem integrity. To this end, sample preparation and extraction is critically important, especially when investigating emerging contaminants and the toxicity of water samples. As extraction methods are rarely optimised for bioassays but rather adopted from chemical analysis, this may result in a misrepresentation of the actual toxicity. In this study, surface water, groundwater, hospital and municipal wastewater were used to characterise the impacts of common sample preparation techniques (acidification, filtration and solid phase extraction (SPE)) on the outcomes of eleven in vitro bioassays. The latter covered endocrine activity (reporter gene assays for estrogen, androgen, aryl-hydrocarbon, retinoic acid, retinoid X, vitamin D, thyroid receptor), mutagenicity (Ames fluctuation test), genotoxicity (umu test) and cytotoxicity. Water samples extracted using different SPE sorbents (Oasis HLB, Supelco ENVI-Carb+, Telos C18/ENV) at acidic and neutral pH were compared for their performance in recovering biological effects. Acidification, commonly used for stabilisation, significantly altered the endocrine activity and toxicity of most (waste)water samples. Sample filtration did not affect the majority of endpoints but in certain cases affected the (anti-)estrogenic and dioxin-like activities. SPE extracts (10.4 × final concentration), including WWTP effluents, induced significant endocrine effects that were not detected in aqueous samples (0.63 × final concentration), such as estrogenic, (anti-)androgenic and dioxin-like activities. When ranking the SPE methods using multivariate Pareto optimisation an extraction with Telos C18/ENV at pH 7 was most effective in recovering toxicity. At the same time, these extracts were highly cytotoxic masking the endpoint under investigation. Compared to that, extraction at pH 2.5 enriched less cytotoxicity. In summary, our study demonstrates that sample preparation and extraction critically affect the outcome of bioassays when assessing the toxicity of water samples. Depending on the water matrix and the bioassay, these methods need to be optimised to accurately assess water quality. Y1 - 2019 U6 - https://doi.org/10.1016/j.watres.2018.12.049 VL - 152 SP - 47 EP - 60 ER - TY - THES A1 - Villatoro, José T1 - A combined approach for the analysis of biomolecules using IR-MALDI ion mobility spectrometry and molecular dynamics simulations of peptide ions in the gas phase Y1 - 2018 ER - TY - THES A1 - Klimm, Martina T1 - New Strategies in Conformation Dynamics Y1 - 2018 ER - TY - THES A1 - Quer, Jannes T1 - Importance Sampling for metastable dynamical systems in molecular dynamics Y1 - 2018 ER - TY - THES A1 - Reuter, Bernhard T1 - Generalisierte Markov-Modellierung von Nichtgleichgewichtssystemen - Simulation und Modellierung der Amyloid-beta(1-40)-Konformationsdynamik unter Mikrowelleneinfluss Y1 - 2018 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Winkler, Michael T1 - Structure-driven fix-and-propagate heuristics for mixed integer programming JF - Mathematical Programming Computation N2 - Primal heuristics play an important role in the solving of mixed integer programs (MIPs). They often provide good feasible solutions early and help to reduce the time needed to prove optimality. In this paper, we present a scheme for start heuristics that can be executed without previous knowledge of an LP solution or a previously found integer feasible solution. It uses global structures available within MIP solvers to iteratively fix integer variables and propagate these fixings. Thereby, fixings are determined based on the predicted impact they have on the subsequent domain propagation. If sufficiently many variables can be fixed that way, the resulting problem is solved first as an LP, and then as an auxiliary MIP if the rounded LP solution does not provide a feasible solution already. We present three primal heuristics that use this scheme based on different global structures. Our computational experiments on standard MIP test sets show that the proposed heuristics find solutions for about 60 % of the instances and by this, help to improve several performance measures for MIP solvers, including the primal integral and the average solving time. Y1 - 2019 U6 - https://doi.org/10.1007/s12532-019-00159-1 VL - 11 IS - 4 SP - 675 EP - 702 PB - Springer CY - Berlin Heidelberg ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection JF - Clinical Microbiology and Infection Y1 - 2018 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 IS - 06/18 SP - 1 EP - 1 ER - TY - JOUR A1 - Mireles, Victor A1 - Conrad, Tim T1 - Reusable building blocks in biological systems JF - Journal of the Royal Society Interface N2 - One of the most widely recognized features of biological systems is their modularity. The modules that constitute biological systems are said to be redeployed and combined across several conditions, thus acting as building blocks. In this work, we analyse to what extent are these building blocks reusable as compared with those found in randomized versions of a system. We develop a notion of decompositions of systems into phenotypic building blocks, which allows them to overlap while maximizing the number of times a building block is reused across several conditions. Different biological systems present building blocks whose reusability ranges from single use (e.g. condition specific) to constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of building block sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity. Y1 - 2018 U6 - https://doi.org/10.1098/rsif.2018.0595 VL - 15 IS - 149 SP - 1 EP - 10 ER - TY - JOUR A1 - Ma, Xiaolin A1 - Conrad, Tim A1 - Alchikh, Maren A1 - Reiche, J. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review JF - Medical Virology N2 - Studies have shown that the predictive value of “clinical diagnoses” of influenza and other respiratory viral infections is low, especially in children. In routine care, pediatricians often resort to clinical diagnoses, even in the absence of robust evidence‐based criteria. We used a dual approach to identify clinical characteristics that may help to differentiate infections with common pathogens including influenza, respiratory syncytial virus, adenovirus, metapneumovirus, rhinovirus, bocavirus‐1, coronaviruses, or parainfluenza virus: (a) systematic review and meta‐analysis of 47 clinical studies published in Medline (June 1996 to March 2017, PROSPERO registration number: CRD42017059557) comprising 49 858 individuals and (b) data‐driven analysis of an inception cohort of 6073 children with ILI (aged 0‐18 years, 56% male, December 2009 to March 2015) examined at the point of care in addition to blinded PCR testing. We determined pooled odds ratios for the literature analysis and compared these to odds ratios based on the clinical cohort dataset. This combined analysis suggested significant associations between influenza and fever or headache, as well as between respiratory syncytial virus infection and cough, dyspnea, and wheezing. Similarly, literature and cohort data agreed on significant associations between HMPV infection and cough, as well as adenovirus infection and fever. Importantly, none of the abovementioned features were unique to any particular pathogen but were also observed in association with other respiratory viruses. In summary, our “real‐world” dataset confirmed published literature trends, but no individual feature allows any particular type of viral infection to be ruled in or ruled out. For the time being, laboratory confirmation remains essential. More research is needed to develop scientifically validated decision models to inform best practice guidelines and targeted diagnostic algorithms. Y1 - 2018 U6 - https://doi.org/10.1002/rmv.1997 VL - 28 IS - 5 SP - 1 EP - 12 ER - TY - GEN ED - Borndörfer, Ralf ED - Storandt, Sabine T1 - Proceedings of the 18th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems N2 - Running and optimizing transportation systems give rise to very complex and large-scale optimization problems requiring innovative solution techniques and ideas from mathematical optimization, theoretical computer science, and operations research. Since 2000, the series of Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS) workshops brings together researchers and practitioners who are interested in all aspects of algorithmic methods and models for transportation optimization and provides a forum for the exchange and dissemination of new ideas and techniques. The scope of ATMOS comprises all modes of transportation. The 18th ATMOS workshop (ATMOS’18) was held in connection with ALGO’18 and hosted by Aalto University in Helsinki, Finland, on August 23–24, 2018. Topics of interest were all optimization problems for passenger and freight transport, including, but not limited to, demand forecasting, models for user behavior, design of pricing systems, infrastructure planning, multi-modal transport optimization, mobile applications for transport, congestion modelling and reduction, line planning, timetable generation, routing and platform assignment, vehicle scheduling, route planning, crew and duty scheduling, rostering, delay management, routing in road networks, traffic guidance, and electro mobility. Of particular interest were papers applying and advancing techniques like graph and network algorithms, combinatorial optimization, mathematical programming, approximation algorithms, methods for the integration of planning stages, stochastic and robust optimization, online and real-time algorithms, algorithmic game theory, heuristics for real-world instances, and simulation tools. There were twenty-nine submissions from eighteen countries. All of them were reviewed by at least three referees in ninety-one reviews, among them five external ones, and judged on their originality, technical quality, and relevance to the topics of the workshop. Based on the reviews, the program committee selected sixteen submissions to be presented at the workshop (acceptance rate: 55%), which are collected in this volume in the order in which they were presented. Together, they quite impressively demonstrate the range of applicability of algorithmic optimization to transportation problems in a wide sense. In addition, Dennis Huisman kindly agreed to complement the program with an invited talk on Railway Disruption Management: State-of-the-art in practice and new research directions. Based on the reviews, Ralf Borndörfer, Marika Karbstein, Christian Liebchen, and Niels Lindner won the Best Paper Award of ATMOS’18 with their paper A simple way to compute the number of vehicles that Are required to operate a periodic timetable. In addition, we awarded Tomas Lidén the Best VGI Paper Award of ATMOS’18 for his paper Reformulations for railway traffic and maintenance planning. We would like to thank the members of the Steering Committee of ATMOS for giving us the opportunity to serve as Program Chairs of ATMOS’18, all the authors who submitted papers, Dennis Huisman for accepting our invitation to present an invited talk, the members of the Program Committee and the additional reviewers for their valuable work in selecting the papers appearing in this volume, our sponsors MODAL, TomTom, and VGIscience for their support of the prizes, and the local organizers for hosting the workshop as part of ALGO’18. We acknowledge the use of the EasyChair system for the great help in managing the submission and review processes, and Schloss Dagstuhl for publishing the proceedings of ATMOS’18 in its OASIcs series. Y1 - 2018 SN - ISBN 978-3-95977-096-5 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2018.0 PB - Dagstuhl Publishing, Saarbrücken/Wadern, Germany ER - TY - JOUR A1 - Villatoro, José A1 - Weber, Marcus A1 - Zühlke, Martin A1 - Lehmann, Andreas A1 - Zechiowski, Karl A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd A1 - Kreuzer, Oliver T1 - Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations JF - International Journal of Mass Spectrometry N2 - Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540–3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). Y1 - 2019 U6 - https://doi.org/10.1016/j.ijms.2018.10.036 VL - 436 SP - 108 EP - 117 ER - TY - JOUR A1 - Reidelbach, Marco A1 - Weber, Marcus A1 - Imhof, Petra T1 - Prediction of perturbed proton transfer networks JF - PLoS ONE N2 - The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80%, while important network properties are maintained in most predictions. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1371/journal.pone.0207718 VL - 13 IS - 12 SP - e0207718 EP - e0207718 ER - TY - THES A1 - Nöckel, Celine T1 - Bidirectional A* Search on Time-Dependent Airway Networks N2 - This thesis deals with a new algorithm for finding Shortest Paths on Airway Networks. It is about a Bidirectional A* Search, a Greedy algorithm exploring a network from two sides instead of one. We will use it to solve the so-called 'Horizontal Flight Trajectory Problem', where one searches for an aircraft trajectory between two airports of minimal costs on an Airway Network. The given network will be modeled as a directed graph and in order to reflect reality we concentrate on the dynamic version. Here a timedependent cost function for all arcs is integrated, that shall represent the winds blowing. This way we model the Horizontal Flight Trajectory Problem mathematically as a Time-Dependent Shortest Path Problem. The basic algorithm idea derives from the algorithm presented in 'Bidirectional A* Search on Time-Dependent Road Networks' [1], where a similar setting is elaborated for road networks. The algorithm procedure bears on a modified generalization of Dijkstra's algorithm, made bidirectional and improved in several aspects. As for the backwards search the arrival times are not known in advance, the reversed graph it occurs on has to be weighted by a lower bound. Contrary to the static case the forwards search still has to go on, when they 'meet' in one node. In the static case, the shortest path would have been found at this point. For road networks the TDSPP is well-studied, for airway networks cannot be found as much in literature. In order to test efficiency, we implement Dijkstra's algorithm, unidirectional A* Search and Bidirectional A* Search. We draw up how potential functions for the static case could look like and that with a suitable potential A* Search with works approx. 7 times faster than Dijkstra in the dynamic case. Our computations lead also to the result, that the unidirectional A* Search works even better on the network than our new bidirectional approach does. On average it labels fewer nodes and also yields 1,7 times faster to the solutions. For assessing the efficiency of the different algorithms we compare the running times and to exclude processor characteristics we consider also the set labels relative to the labels on the resulting optimal path. In addition, we present examples of routes visually and explain shortly why there appear local differences regarding performance of A* Search and Bidirectional A* Search. Y1 - 2018 ER - TY - THES A1 - Mett, Fabian T1 - Über die optimale Platzierung von Ladestationen für Elektrobusse N2 - In dieser Arbeit wird die Platzierung von Ladestationen für Elektrobusse untersucht. Dabei soll für eine Menge an gegebenen Linien eine Menge an Ladestationen gefunden werden, sodass jede Linie mit Nutzung der Ladestationen befahren werden kann und gleichzeitig die Kosten minimal sind. Zunächst wird der Fall betrachtet, dass die Batterie an jeder Station komplett vollgeladen werden könnte. Dieses Problem stellt sich als NP-schwer heraus. Für einige einfachere Fällewerden zudem Algorithmen entwickelt und untersucht. Anschließend wird der Fall einer unbegrenzt großen Batterie betrachtet, wobei an jeder Station derselbe Wert geladen werden kann. Auch dieses Problem ist NP-schwer. Erneut werden Algorithmen zur Lösung vereinfachter Problemstellungen gegeben und analysiert. Wird zudem angenommen, an jeder Station würde ein individueller Wert geladen, so ist das Problem schon für nur eine einzige Linie NP-schwer. Dennoch werden zwei exakte und ein approximierender Algorithmus entwickelt. Schließlich wird eine Batteriekapazität hinzugefügt und die zuvor entwickelten Algorithmen werden entsprechend angepasst. Für die abschließende Problemdefinition werden verschiedene Batteriegrößen betrachtet und es werden zwei gemischt-ganzzahlige Programme aufgestellt. Anhand von existierenden Buslinien aus Berlin werden diese untersucht. Dabei stellt sich heraus, dass die Batteriekosten einen deutlich größeren Teil der Kosten ausmachen als die Ladestationen. Zudem sollten kleinere Batterien statt größerer und mehr Ladestationen genutzt werden. Y1 - 2018 ER - TY - THES A1 - Krug, Matthias T1 - Analysis of the Shortest Path Problem with Piecewise Constant Crossing Costs Y1 - 2018 ER - TY - THES A1 - Husemann, Christoph T1 - Multimodales Routing mit Leihfahrradsystemen am Beispiel Berlins N2 - The aim of multimodal routing is to extract the best integrated journey of multiple transportation networks. The integration of bike rental networks is challenging particularly with respect to recognizing a valid path dependent on real-time availability of bike boarding and alighting places. In this work a common model for station-based bike rental networks extended with boarding possibilities for free floating bikes is presented. Moreover a new model for alighting inside a free floating area is introduced. In addition, a prototype of multimodal routing with a bike rental network in Berlin is developed by extending the OpenTripPlanner software. Due to recent public dispute about bike rental networks in Berlin, an examination about speed-up potential of an integrated bike rental network in the public transit of Berlin is provided. Y1 - 2018 ER - TY - THES A1 - Vornberger, Leo T1 - Approximation von Windkomponenten in der Luftfahrt durch lineare Interpolation N2 - Das Wind-Interpolation-Problem (WIP) ist ein bisher selten diskutiertes Problem der Flugplanungsoptimierung, bei dem es darum geht, Wind-Komponenten auf einer Luftstraße zu approximieren. Anhand von Winddaten, die vektoriell an den Gitterpunkten eines den Globus umspannenden Gitters vorliegen, soll bestimmt werden, wie viel Wind entlang der Luftstraße und quer zu ihr weht. Thema dieser Arbeit ist ein Spezialfall des WIP, nämlich das statische WIP auf einer Planfläche (SWIPP). Dazu wird zuerst ein Algorithmus besprochen, der das SWIPP zwar löst, aber einem Ansatz zugrunde liegt, der bei genauerem Hinsehen nicht sinnvoll erscheint: hier wird Wind zwischen vier Punkten interpoliert, wozu es keine triviale Methode gibt. Ähnlich zu diesem Algorithmus, der heute als State-of-the-Art gilt, wird als Ergebnis dieser Arbeit ein neuer Algorithmus vorgestellt, der das SWIPP akkurater und schneller löst. Hier wird deutlich seltener auf die Interpolation zwischen vier Punkten zurückgegriffen - stattdessen wird fast immer linear zwischen zwei Punkten interpoliert. Die Algorithmen zum Lösen des SWIPP werden auf ihre Genauigkeit, asymptotische Laufzeit und Geschwindigkeit untersucht und verglichen. Als Testareal dienen zum einen echte Wetterdaten sowie das Luftstraßennetz, das die Erde umspannt, und zum anderen ein eigens generiertes Windfeld und fiktive Luftstraßen. Es wird gezeigt, dass der hier vorgestellte Algorithmus die State-of-the-Art-Variante in allen genannten Aspekten übertrifft. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71570 ER - TY - THES A1 - Akil, Fatima T1 - Lineare Gleichungssysteme modulo T N2 - Mit dem Voranschreiten der Technologie erhalten die öffentlichen Verkehrsmittel eine größere Bedeutung. Die Beförderung mehrerer Personen eröffnet der Gesellschaft viele Möglichkeiten, unter Anderem den Vorteil der Zeitersparnis. Die Dauer des Verkehrswegs mit öffentlichen Verkehrsmitteln ist häufig geringer, als die mit individuellen Verkehrsmitteln. Jedes öffentliche Transportmittel ist mit einem Fahrplan versehen. Dieser bietet Passagieren, die öffentliche Verkehrsmittel öfter nutzen, eine Strukturierung und Planung ihrer Zeit. Dabei lassen sich Taktfahrpläne aufgrund ihres periodischen Verhaltens leicht einprägen. Dieses periodische Verhalten ist durch mathematische Modellierungen darstellbar. Das persönliche Nutzverhalten vieler Bürger im Personenverkehr ist auf die öffentlichen Verkehrsmittel beschränkt. Diese beinhalten im Gegensatz zum individuellen Verkehrsmittel eine Wartezeit. Dabei stellt sich die Frage, ob man anhand mathematischer Modelle diese Wartezeit minimieren kann. Eine bekannte mathematische Modellierung dieses Problems ist das Periodic Event Scheduling Problem (PESP). Die optimale Planung eines periodischen Taktfahrplanes steht im Vordergrund. Während ich dieses Problem betrachtet habe, wurde ich auf das Rechnen mit linearen Gleichungssystemen modulo T aufmerksam. Bei periodischen Taktfahrplänen wird ein einheitliches zeitliches Muster, welches sich nach T Minuten wiederholt, betrachtet. Das dabei zu betrachtende Lösungsproblem eröffnet ein Teilgebiet der Mathematik, welches bislang nicht im Vordergrund stand: Das Lösen linearer Gleichungen modulo T, wobei T für die Zeit in Minuten steht und somit 60 ist. Da 60 keine Primzahl ist, kann – wie im Laufe der Arbeit präsentiert – das lineare Gleichungssystem nicht mehr über einen Körper gelöst werden. Lineare Gleichungssysteme werden nun über Nicht-Körpern betrachtet. Die Literatur weist sowohl im deutschsprachigem als auch im englischsprachigen Raum wenig Umfang bezüglich linearer Gleichungssysteme über Nicht-Körper auf. Der Bestand an Fachliteratur bezüglich den Themen lineare diophantische Gleichungssysteme, Hermite- Normalform und Smith-Normalform ist zurzeit gering, dennoch erreichbar, beispielsweise in [1], welches in dieser Bachelorarbeit genutzt wurde. Insbesondere wurde ich bei der Suche nach geeigneter Literatur zu linearen Gleichungssystemen über Restklassenringe, die keinen Körper bilden, nicht fündig. Dabei recherchierte ich sowohl in den Universitätsbibliotheken als auch in webbasierenden Suchmaschinen. Aufgrund dem geringen Bestand an Fachliteratur in diesem Kontext, war ich gezwungen, an vielen Stellen eigene logische Verknüpfungen zu konzipieren und zu beweisen. Dies brachte viele Schwierigkeiten mit sich, die mit bestmöglichem Verständnis bearbeitet wurden. Abseits der Zugänglichkeit der Literatur, finde ich es sehr überraschend, dass sich viele Professoren der Mathematik mit diesem Themenbereich nicht beschäftigten. Insbesondere gingen von den Dozenten, die ich um Literaturempfehlung bat, kein Werk aus. Damit wurde das Thema "Lineare Gleichungssysteme Modulo T" einerseits eine große Herausforderung, andererseits eine große Motivation, da ich mit dieser Bachelorarbeit vielen Interessenten der Mathematik als Sekundärliteratur dienen kann. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71560 ER - TY - THES A1 - Wyczik, Christopher T1 - Optimierung von Deployment- und Umgebungs-Integrität durch ein dezentrales Konfigurationsrepository auf Basis einer Blockchain N2 - Viele Firmen nutzen für ihre eigenen Softwareentwicklungen verschiedene Server mit unterschiedlichen Konfigurationen. Manche Server werden dazu eingestzt das Verhalten einer Software in einer bestimmten Umgebung zu testen und andere dienen zur Bereitstellung der Software für den Endnutzer. Hierbei ist es wichtig, dass die Konfiguration der Server regelmäßig überprüft wird. Eine solche Sicherstellung der Deployment- und Umgebungs-Integrität wird meistens durch eine Mitarbeiter der Firma oder durch einen externen Dienstleister erbracht. D.h. die Firma muss sich auf die Zuverlässigkeit eines Mitarbeiters oder einer externen Dienstleistung verlassen, bie zunehmender Komplexität ist sie sogar abhängig. Das Ziel dieser Masterarbeit ist es, zu untersuchen, ob die Sicherstellung der Deployment- und Umgebungs-Integrität durch automatisierte kryptografische Beweise, anstelle externer Dienstleistungen oder anderer Mitarbeiter, gewährleistet werden kann. Als Anwendungsfall dient die Toll Collect GmbH. Im ersten Teil dieser Arbeit wird das Matheamtische Modell einer Blockchain erläutert. die Blockchain wurde erstmals in einem Dokument, welches unter dem Pseudonym Satoshi Nakamoto veröffentlicht wurde, beschrieben. Die erste große Anwendungen der Blockchain ist das dezentrale Zahlungssystem Bitcoin. Im zweiten Teil dieser Arbeit wird die Softwareimplementierung vorgestellt, welche im Rahmen dieser Arbeit entstanden ist. Mithilfe dieses Programms kann die Deployment- und Umgebungs-Integrität durch eine heirführ entwickelte Blockchainlösung dezentralisiert werden. Es wird außerdem der Übergang vom Mathematischen Modell zur Implementierung gezeigt. Y1 - 2018 ER - TY - THES A1 - Oleynikova, Ekaterina T1 - Mathematical optimization of joint order batching and picker routing problems N2 - In this thesis we study order picking optimization problems for a two-blocks rectangle warehouse layout. We present combinatorial formulations and linear programming models based on the Steiner graph representation for order batching, picker routing, and joint order batching and picker routing problems. A special case of the latter is considered. This case assumes that each order contains exactly one item and each item can be picked from different possible locations in a warehouse. The underlying optimization problem is called joint multi-location order batching and picker routing problem (JMLOBPRP). Since having only one-item orders turns the JMLOBPRP into a special case of a capacitated vehicle routing problem, we suggest to implement algorithmic approaches for those to solve the JMLOBPRP. In particular, we define the JMLOBPRP as a generalization of the resource constrained assignment problem, for which a regional search method exists. The intention of the thesis is to investigate how a relaxation of the JMLOBPRP, a so-called group assignment problem (GrAP), can be solved following the ideas of regional search. We present a mathematical model of the GrAP and prove that it is NP-hard. Furthermore, we propose a novel heuristic algorithm for the GrAP. We call this method a network search algorithm, as it is based on a Lagrangian relaxation of the GrAP, which is solved by the network simplex method. On each its iteration network search examines a solution region suggested by the network simplex algorithm and improves the incumbent solution. Numerical experiments are conducted to assess a performance of the network search method. We create more realistic problem instances. The proposed algorithm is compared to the integer optimal solution of the GrAP and optimal fractional solution of its linear relaxation. Both computed using the commercial linear solver Gurobi. Our experiments show that the developed network search algorithm leads to the hight-quality solution within a short computing time. The results obtained testing large problem instances which cannot be solved by Gurobi within a reasonable computing time, show that the network search method provides a solution approach which can be used in practice. Y1 - 2018 ER - TY - THES A1 - Jeschke, Björn-Marcel T1 - Alternativen zum Dijkstra Algorithmus in der (Nah-) Verkehrsoptimierung N2 - In dieser Arbeit betrachten wir das Problem, für den Fahrplan eines (Nah-) Verkehrsnetzes schnellste Wege zu berechnen. Da die Verkehrsmittel zu unterschiedlichen Zeiten von den einzelnen Haltestellen/Bahnhöfen abfahren, kann das Problem nicht ohne Weiteres mit einem „statischen“ Graphen modelliert werden. Es gibt zwei unterschiedliche Ansätze für dieses zeitabhängige Problem: Erstens können die verschiedenen An-/Abfahrtereignisse an einem Halt durch „Kopien“ dargestellt werden, das ist das zeit-expandierte Modell. Zweitens können die Gewichte der Kanten zeitabhängig sein, das ist das zeitabhängige Modell. Wir untersuchen in dieser Arbeit, wie der „klassische“ Dijkstra-Algorithmus und der A* Algorithmus mit einer geeigneten Heuristik im Vergleich abschneiden. Die gewählte Heuristik ist der Abstand zum Zielknoten, wenn die Abfahrtszeiten ignoriert werden. Nach unseren Untersuchungen zeigt sich, dass der A* Algorithmus dem Dijkstra-Algorithmus weit überlegen ist für genügend große Nahverkehrsnetze. Wir testen anhand der echten Verkehrsnetze von Berlin und Aachen. Unsere Berechnungen zeigen, dass die gewählte Heuristik besonders gut ist für Start- und Zielknoten, welche unabhängig von ihrer Distanz nur 1–2 verschiedene mögliche kürzeste Pfade für alle Zeitschritte haben. Dort ist der A* Algorithmus bis zu 20-mal schneller. Dies kommt aber nicht häufig in unseren Testinstanzen vor. Die einzelnen Laufzeitvergleich zeigen, dass der A* Algorithmus durchschnittlich 7-mal so schnell ist wie der Dikstra-Algorithmus. Y1 - 2017 ER - TY - THES A1 - Wirsching, Marie T1 - Der Einfluss von Langzahlarithmetik auf das Gewichtsraumpolyeder in mehrkriterieller Optimierung N2 - Die Arbeit befasst sich mit einem gewichtsraumbasierten Algorithmus, der ganzzahlige und lineare Optimierungsprobleme mit mehreren Zielfunktionen löst und die Menge der unterstützt nicht dominierten Punkte ermittelt. Die dabei erzeugten Gewichtsraumpolyeder sind das entscheidende Mittel, um die gesuchte Lösungsmenge zu bestimmen. Aus softwaretechnischer Sicht sind numerische Ungenauigkeiten potentielle Fehlerquellen, die sich negativ auf das Endergebnis auswirken. Aus diesem Grund untersuchen wir anhand von Zuweisungs- und Rucksackinstanzen mit 3 Zielfunktionen, inwieweit der Gebrauch von Langzahlarithmetik die Gewichtsraumpolyeder und die damit verbundene Menge der unterstützt nicht dominierten Punkte beeinflusst. Y1 - 2018 ER - TY - THES A1 - Euler, Ricardo T1 - The Bienstock Zuckerberg Algorithm for the Rolling Stock Rotation Problem N2 - The design of rolling stock rotations is an important task in large-scale railway planning. This so-called rolling stock rotation problem (RSRP) is usually tackled using an integer programming approach. Markus Reuther did so in his dissertation [15] for the ICE railway network of DB ("Deutsche Bahn"). Due to the size of the network and the complexity of further technical requirements, the resulting integer problems tend to become very large and computationally involved. In this thesis, we tackle the linear programming relaxation of the RSRP integer program. We will do so by applying a modified version of an algorithm recently proposed by Dan Bienstock and Mark Zuckerberg [2] for the precedence constrained production scheduling problem that arises in open pit mine scheduling. This problem contains a large number of "easy" constraints and a relatively small number of "hard" constraints. We will see that a similar problem structure can also be found in the RSRP. The Bienstock-Zuckerberg algorithm relies on applying Lagrangian relaxation to the hard constraints as well as on partitioning the variable set. We propose three different partition schemes which try to exploit the specific problem structure of the RSRP. Furthermore, we will discuss the influence of primal degeneracy on the algorithm's performance, as well as possible merits of perturbating the right-hand side of the constraint matrix. We provide computational results to assess the performance of those approaches. Y1 - 2018 ER - TY - GEN A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs N2 - To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE constrained optimization. In order to develop an efficient fully time-parallel algorithm we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a non-linear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches. T3 - ZIB-Report - 19-04 KW - PDE-constrained optimization KW - parallel-in-time methods KW - PFASST Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71490 SN - 1438-0064 ER - TY - JOUR A1 - Gupta, Pooja A1 - Peter, Sarah A1 - Jung, Markus A1 - Lewin, Astrid A1 - Hemmrich-Stanisak, Georg A1 - Franke, Andre A1 - von Kleist, Max A1 - Schütte, Christof A1 - Einspanier, Ralf A1 - Sharbati, Soroush A1 - zur Bruegge, Jennifer T1 - Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections JF - Scientific Reports in Nature N2 - Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-018-38141-x VL - 9 ER - TY - JOUR A1 - Shao, Borong A1 - Bjaanaes, Maria A1 - Helland, Aslaug A1 - Schütte, Christof A1 - Conrad, Tim T1 - EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma JF - PLOS ONE N2 - Various feature selection algorithms have been proposed to identify cancer prognostic biomarkers. In recent years, however, their reproducibility is criticized. The performance of feature selection algorithms is shown to be affected by the datasets, underlying networks and evaluation metrics. One of the causes is the curse of dimensionality, which makes it hard to select the features that generalize well on independent data. Even the integration of biological networks does not mitigate this issue because the networks are large and many of their components are not relevant for the phenotype of interest. With the availability of multi-omics data, integrative approaches are being developed to build more robust predictive models. In this scenario, the higher data dimensions create greater challenges. We proposed a phenotype relevant network-based feature selection (PRNFS) framework and demonstrated its advantages in lung cancer prognosis prediction. We constructed cancer prognosis relevant networks based on epithelial mesenchymal transition (EMT) and integrated them with different types of omics data for feature selection. With less than 2.5% of the total dimensionality, we obtained EMT prognostic signatures that achieved remarkable prediction performance (average AUC values above 0.8), very significant sample stratifications, and meaningful biological interpretations. In addition to finding EMT signatures from different omics data levels, we combined these single-omics signatures into multi-omics signatures, which improved sample stratifications significantly. Both single- and multi-omics EMT signatures were tested on independent multi-omics lung cancer datasets and significant sample stratifications were obtained. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0204186 VL - 14 IS - 1 ER - TY - JOUR A1 - Kersting, Hans A1 - Sullivan, T. J. A1 - Hennig, Philipp T1 - Convergence rates of Gaussian ODE filters JF - Statistics and Computing Y1 - 2020 U6 - https://doi.org/10.1007/s11222-020-09972-4 VL - 30 SP - 1791 EP - 1816 PB - Springer CY - Statistics and Computing ER - TY - GEN A1 - Oates, Chris A1 - Cockayne, Jon A1 - Prangle, Dennis A1 - Sullivan, T. J. A1 - Girolami, Mark ED - Hickernell, F. J. ED - Kritzer, P. T1 - Optimality criteria for probabilistic numerical methods T2 - Multivariate Algorithms and Information-Based Complexity N2 - It is well understood that Bayesian decision theory and average case analysis are essentially identical. However, if one is interested in performing uncertainty quantification for a numerical task, it can be argued that the decision-theoretic framework is neither appropriate nor sufficient. To this end, we consider an alternative optimality criterion from Bayesian experimental design and study its implied optimal information in the numerical context. This information is demonstrated to differ, in general, from the information that would be used in an average-case-optimal numerical method. The explicit connection to Bayesian experimental design suggests several distinct regimes in which optimal probabilistic numerical methods can be developed. Y1 - 2020 U6 - https://doi.org/10.1515/9783110635461-005 VL - 27 SP - 65 EP - 88 PB - De Gruyter ER - TY - JOUR A1 - Oates, Chris A1 - Sullivan, T. J. T1 - A modern retrospective on probabilistic numerics JF - Statistics and Computing N2 - This article attempts to place the emergence of probabilistic numerics as a mathematical-statistical research field within its historical context and to explore how its gradual development can be related to modern formal treatments and applications. We highlight in particular the parallel contributions of Sul'din and Larkin in the 1960s and how their pioneering early ideas have reached a degree of maturity in the intervening period, mediated by paradigms such as average-case analysis and information-based complexity. We provide a subjective assessment of the state of research in probabilistic numerics and highlight some difficulties to be addressed by future works. Y1 - 2019 U6 - https://doi.org/10.1007/s11222-019-09902-z VL - 29 IS - 6 SP - 1335 EP - 1351 ER - TY - GEN A1 - Tack, Alexander A1 - Zachow, Stefan T1 - Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - Volumetry of the cartilage of the knee, as needed for the assessment of knee osteoarthritis (KOA), is typically performed in a tedious and subjective process. We present an automated segmentation-based method for the quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data as well as cartilage volumetry readings given by clinical experts for 1378 subjects. It was shown that 3D CNNs can be employed for cartilage volumetry with an accuracy similar to expert volumetry readings. In future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as assessment of KOA progression via longitudinal analysis. T3 - ZIB-Report - 19-05 KW - Deep Learning KW - imaging biomarker KW - radiomics KW - cartilage morphometry KW - volume assessment Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71439 SN - 1438-0064 ER - TY - JOUR A1 - Wilson, Jon A1 - Gutsche, Philipp A1 - Herrmann, Sven A1 - Burger, Sven A1 - McPeak, Kevin T1 - Correlation of circular differential optical absorption with geometric chirality in plasmonic meta-atoms JF - Opt. Express Y1 - 2019 U6 - https://doi.org/10.1364/OE.27.005097 VL - 27 SP - 5097 ER - TY - THES A1 - Deppisch, Daniel T1 - Advancing the Heterogeneous Active Messages Approach Y1 - 2019 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Schulz, Christof A1 - Weider, Steffen T1 - The Rolling Stock Rotation Planning Problem under Revenue Considerations N2 - In many railway undertakings a railway timetable is offered that is valid for a longer period of time. At DB Fernverkehr AG, one of our industrial partners, this results in a summer and a winter timetable. For both of these timetables rotation plans, i.e., a detailed plan of railway vehicle movements is constructed as a template for this period. Sometimes there are be periods where you know for sure that vehicle capacities are not sufficient to cover all trips of the timetable or to transport all passenger of the trips. Reasons for that could be a heavy increase of passenger flow, a heavy decrease of vehicle availability, impacts from nature, or even strikes of some employees. In such events the rolling stock rotations have to be adapted. Optimization methods are particularly valuable in such situations in order to maintain a best possible level of service or to maximize the expected revenue using the resources that are still available. In most cases found in the literature, a rescheduling based on a timetable update is done, followed by the construction of new rotations that reward the recovery of parts of the obsolete rotations. We consider a different, novel, and more integrated approach. The idea is to guide the cancellation of the trips or reconfiguration of the vehicle composition used to operate a trip of the timetable by the rotation planning process, which is based on the mixed integer programming approach presented in Reuther (2017). The goal is to minimize the operating costs while cancelling or operating a trip with an insufficient vehicle configuration in sense of passenger capacities inflicts opportunity costs and loss of revenue, which are based on an estimation of the expected number of passengers. The performance of the algorithms presented in two case studies, including real world scenarios from DB Fernverkehr AG and a railway operator in North America. T3 - ZIB-Report - 19-01 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71339 SN - 1438-0064 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Schulz, Christof A1 - Weider, Steffen T1 - The Rolling Stock Rotation Planning Problem under Revenue Considerations T2 - Proceedings of the Rail Transport Demand Management Conference N2 - In many railway undertakings a railway timetable is offered that is valid for a longer period of time. At DB Fernverkehr AG, one of our industrial partners, this results in a summer and a winter timetable. For both of these timetables rotation plans, i.e., a detailed plan of railway vehicle movements is constructed as a template for this period. Sometimes there are be periods where you know for sure that vehicle capacities are not sufficient to cover all trips of the timetable or to transport all passenger of the trips. Reasons for that could be a heavy increase of passenger flow, a heavy decrease of vehicle availability, impacts from nature, or even strikes of some employees. In such events the rolling stock rotations have to be adapted. Optimization methods are particularly valuable in such situations in order to maintain a best possible level of service or to maximize the expected revenue using the resources that are still available. In most cases found in the literature, a rescheduling based on a timetable update is done, followed by the construction of new rotations that reward the recovery of parts of the obsolete rotations. We consider a different, novel, and more integrated approach. The idea is to guide the cancellation of the trips or reconfiguration of the vehicle composition used to operate a trip of the timetable by the rotation planning process, which is based on the mixed integer programming approach presented in Reuther (2017). The goal is to minimize the operating costs while cancelling or operating a trip with an insufficient vehicle configuration in sense of passenger capacities inflicts opportunity costs and loss of revenue, which are based on an estimation of the expected number of passengers. The performance of the algorithms presented in two case studies, including real world scenarios from DB Fernverkehr AG and a railway operator in North America. Y1 - 2018 ER - TY - CHAP A1 - Klindt, Marco T1 - Implications of perceived preservation levels T2 - Proceedings of iPres – 15th International Conference on Digital Preservation / Boston, MA, USA / September 24 – 27, 2018 N2 - This paper describes and explores the concept of perceived preservation levels and their implications. Perceived preservation levels are a way to communicate preservation policies, options and actions to the various stakeholders in digital preservation a digital preservation system is capable and able of. While explicitly assigned or stated preservation levels are promises to adhere to a certain set of policies and decisions, it may be hard to impossible for a best effort preservation service to fulfill these expectations. Perceived preservation levels combine different outcomes from preservation actions with preservation options and available resources to convey a holistic view of the archive’s worflow and decision states. A preservation system providing information about current states of digital objects puts the data producers in a position to reassure themselves of the trustworthiness of the archive without the need of formal certification. This openness has implications not only for the trust relationship between producer and archive but provides the opportunity to constantly reassess the archive’s decisions and priorities from the outside. Y1 - 2018 U6 - https://doi.org/10.17605/OSF.IO/M6QA5 VL - 15 ER - TY - GEN A1 - Schneck, Jakob A1 - Weiser, Martin A1 - Wende, Florian T1 - Impact of mixed precision and storage layout on additive Schwarz smoothers N2 - The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth- bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage. T3 - ZIB-Report - 18-62 KW - higher order finite elements KW - mixed precision KW - overlapping Schwarz smoother Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71305 SN - 1438-0064 ER - TY - JOUR A1 - Ozel, Mehmet Neset A1 - Kulkarni, Abhishek A1 - Hasan, Amr A1 - Brummer, Josephine A1 - Moldenhauer, Marian A1 - Daumann, Ilsa-Maria A1 - Wolfenberg, Heike A1 - Dercksen, Vincent J. A1 - Kiral, Ferdi Ridvan A1 - Weiser, Martin A1 - Prohaska, Steffen A1 - von Kleist, Max A1 - Hiesinger, Peter Robin T1 - Serial synapse formation through filopodial competition for synaptic seeding factors JF - Developmental Cell N2 - Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses. Y1 - 2019 U6 - https://doi.org/10.1016/j.devcel.2019.06.014 VL - 50 IS - 4 SP - 447 EP - 461 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Hviid, Stubbe A1 - Jorda, Laurent A1 - Keller, Horst Uwe A1 - Kührt, Ekkehard T1 - Comet 67P/Churyumov-Gerasimenko rotation changes derived from sublimation induced torques JF - Astronomy & Astrophysics N2 - Context. The change of the rotation period and the orientation of the rotation axis of comet 67P/Churyumov-Gerasimenko (67P/C-G) is deducible from images taken by the scientific imaging instruments on-board the Rosetta mission with high precision. Non gravitational forces are a natural explanation for these data. Aims. We describe observed changes for the orientation of the rotation axis and the rotation period of 67P/C-G. For these changes we give an explanation based on a sublimation model with a best-fit for the surface active fraction (model P). Torque effects of periodically changing gas emissions on the surface are considered. Methods. We solve the equation of state for the angular momentum in the inertial and the body- fixed frames and provide an analytic theory of the rotation changes in terms of Fourier coefficients, generally applicable to periodically forced rigid body dynamics. Results. The torque induced changes of the rotation state constrain the physical properties of the surface, the sublimation rate and the local active fraction of the surface. Conclusions. We determine a distribution of the local surface active fraction in agreement with the rotation properties, period and orientation, of 67P/C-G. The torque movement confirms that the sublimation increases faster than the insolation towards perihelion. The derived relatively uniform activity pattern is discussed in terms of related surface features. Y1 - 2019 U6 - https://doi.org/10.1051/0004-6361/201834349 VL - 630 SP - A3 ER - TY - JOUR A1 - Rodríguez, Mirta A1 - Kramer, Tobias T1 - Machine Learning of Two-Dimensional Spectroscopic Data JF - Chemical Physics N2 - Two-dimensional electronic spectroscopy has become one of the main experimental tools for analyzing the dynamics of excitonic energy transfer in large molecular complexes. Simplified theoretical models are usually employed to extract model parameters from the experimental spectral data. Here we show that computationally expensive but exact theoretical methods encoded into a neural network can be used to extract model parameters and infer structural information such as dipole orientation from two dimensional electronic spectra (2DES) or reversely, to produce 2DES from model parameters. We propose to use machine learning as a tool to predict unknown parameters in the models underlying recorded spectra and as a way to encode computationally expensive numerical methods into efficient prediction tools. We showcase the use of a trained neural network to efficiently compute disordered averaged spectra and demonstrate that disorder averaging has non-trivial effects for polarization controlled 2DES. Y1 - 2019 U6 - https://doi.org/10.1016/j.chemphys.2019.01.002 VL - 520 SP - 52 EP - 60 ER - TY - THES A1 - Gidey, Henok Hagos T1 - Automated Hip Knee Ankle Angle Determination using Convolutional Neural Networks N2 - Advanced osteoarthritis is a leading cause of knee replacement and loss of functionality. Early detection of risk factors plays an important role in the application of preventive measures. One of the risk factors is the leg alignment which influences the speed of knee cartilage degradation. The ’gold standard’ measurement of leg alignment is done by determining the Hip Knee Ankle (HKA) angle from full lower limb radiographs. Convolutional Neural Networks (CNNs) have gained popularity recently in computer vision. In this thesis we developed methods using CNNs to determine HKA angles from full lower limb radiographs. We trained the CNNs using data from the Osteoarthritis Initiative (OAI). We evaluated our method’s performance by evaluating its agreement to experts measurement and its reliability. Our best performing method shows excellent agreement and reliability levels. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71263 ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Schmidt genannt Waldschmidt, Daniel A1 - Tesch, Alexander T1 - The Price of Fixed Assignments in Stochastic Extensible Bin Packing T2 - WAOA 2018: Approximation and Online Algorithms N2 - We consider the stochastic extensible bin packing problem (SEBP) in which n items of stochastic size are packed into m bins of unit capacity. In contrast to the classical bin packing problem, the number of bins is fixed and they can be extended at extra cost. This problem plays an important role in stochastic environments such as in surgery scheduling: Patients must be assigned to operating rooms beforehand, such that the regular capacity is fully utilized while the amount of overtime is as small as possible. This paper focuses on essential ratios between different classes of policies: First, we consider the price of non-splittability, in which we compare the optimal non-anticipatory policy against the optimal fractional assignment policy. We show that this ratio has a tight upper bound of 2. Moreover, we develop an analysis of a fixed assignment variant of the LEPT rule yielding a tight approximation ratio of (1+e−1)≈1.368 under a reasonable assumption on the distributions of job durations. Furthermore, we prove that the price of fixed assignments, related to the benefit of adaptivity, which describes the loss when restricting to fixed assignment policies, is within the same factor. This shows that in some sense, LEPT is the best fixed assignment policy we can hope for. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-030-04693-4_20 VL - 11312 SP - 327 EP - 347 ER - TY - CHAP A1 - Tack, Alexander A1 - Zachow, Stefan T1 - Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative T2 - IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) N2 - Volumetry of cartilage of the knee is needed for knee osteoarthritis (KOA) assessment. It is typically performed manually in a tedious and subjective process. We developed a method for an automated, segmentation-based quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data and cartilage volumetry readings performed by clinical experts for 1378 subjects provided by the Osteoarthritis Initiative. It was shown that 3D CNNs are able to achieve volume measures comparable to the magnitude of variation between expert readings and the real in vivo situation. In the future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as longitudinal analysis of KOA progression. Y1 - 2019 U6 - https://doi.org/10.1109/ISBI.2019.8759201 SP - 40 EP - 43 ER - TY - GEN A1 - Berthold, Timo A1 - Stuckey, Peter A1 - Witzig, Jakob T1 - Local Rapid Learning for Integer Programs N2 - Conflict learning algorithms are an important component of modern MIP and CP solvers. But strong conflict information is typically gained by depth-first search. While this is the natural mode for CP solving, it is not for MIP solving. Rapid Learning is a hybrid CP/MIP approach where CP search is applied at the root to learn information to support the remaining MIP solve. This has been demonstrated to be beneficial for binary programs. In this paper, we extend the idea of Rapid Learning to integer programs, where not all variables are restricted to the domain {0, 1}, and rather than just running a rapid CP search at the root, we will apply it repeatedly at local search nodes within the MIP search tree. To do so efficiently, we present six heuristic criteria to predict the chance for local Rapid Learning to be successful. Our computational experiments indicate that our extended Rapid Learning algorithm significantly speeds up MIP search and is particularly beneficial on highly dual degenerate problems. T3 - ZIB-Report - 18-56 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71190 SN - 1438-0064 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo A1 - Heinz, Stefan T1 - A Status Report on Conflict Analysis in Mixed Integer Nonlinear Programming N2 - Mixed integer nonlinear programs (MINLPs) are arguably among the hardest optimization problems, with a wide range of applications. MINLP solvers that are based on linear relaxations and spatial branching work similar as mixed integer programming (MIP) solvers in the sense that they are based on a branch-and-cut algorithm, enhanced by various heuristics, domain propagation, and presolving techniques. However, the analysis of infeasible subproblems, which is an important component of most major MIP solvers, has been hardly studied in the context of MINLPs. There are two main approaches for infeasibility analysis in MIP solvers: conflict graph analysis, which originates from artificial intelligence and constraint programming, and dual ray analysis. The main contribution of this short paper is twofold. Firstly, we present the first computational study regarding the impact of dual ray analysis on convex and nonconvex MINLPs. In that context, we introduce a modified generation of infeasibility proofs that incorporates linearization cuts that are only locally valid. Secondly, we describe an extension of conflict analysis that works directly with the nonlinear relaxation of convex MINLPs instead of considering a linear relaxation. This is work-in-progress, and this short paper is meant to present first theoretical considerations without a computational study for that part. T3 - ZIB-Report - 18-57 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71170 SN - 1438-0064 ER - TY - CHAP A1 - Hendel, Gregor A1 - Miltenberger, Matthias A1 - Witzig, Jakob T1 - Adaptive Algorithmic Behavior for Solving Mixed Integer Programs Using Bandit Algorithms T2 - OR 2018: International Conference on Operations Research N2 - State-of-the-art solvers for mixed integer programs (MIP) govern a variety of algorithmic components. Ideally, the solver adaptively learns to concentrate its computational budget on those components that perform well on a particular problem, especially if they are time consuming. We focus on three such algorithms, namely the classes of large neighborhood search and diving heuristics as well as Simplex pricing strategies. For each class we propose a selection strategy that is updated based on the observed runtime behavior, aiming to ultimately select only the best algorithms for a given instance. We review several common strategies for such a selection scenario under uncertainty, also known as Multi Armed Bandit Problem. In order to apply those bandit strategies, we carefully design reward functions to rank and compare each individual heuristic or pricing algorithm within its respective class. Finally, we discuss the computational benefits of using the proposed adaptive selection within the SCIP Optimization Suite on publicly available MIP instances. Y1 - 2018 ER - TY - GEN A1 - Hendel, Gregor T1 - Adaptive Large Neighborhood Search for Mixed Integer Programming N2 - Large Neighborhood Search (LNS) heuristics are among the most powerful but also most expensive heuristics for mixed integer programs (MIP). Ideally, a solver learns adaptively which LNS heuristics work best for the MIP problem at hand in order to concentrate its limited computational budget. To this end, this work introduces Adaptive Large Neighborhood Search (ALNS) for MIP, a primal heuristic that acts a framework for eight popular LNS heuristics such as Local Branching and Relaxation Induced Neighborhood Search (RINS). We distinguish the available LNS heuristics by their individual search domains, which we call neighborhoods. The decision which neighborhood should be executed is guided by selection strategies for the multi armed bandit problem, a related optimization problem during which suitable actions have to be chosen to maximize a reward function. In this paper, we propose an LNS-specific reward function to learn to distinguish between the available neighborhoods based on successful calls and failures. A second, algorithmic enhancement is a generic variable fixing priorization, which ALNS employs to adjust the subproblem complexity as needed. This is particularly useful for some neighborhoods which do not fix variables by themselves. The proposed primal heuristic has been implemented within the MIP solver SCIP. An extensive computational study is conducted to compare different LNS strategies within our ALNS framework on a large set of publicly available MIP instances from the MIPLIB and Coral benchmark sets. The results of this simulation are used to calibrate the parameters of the bandit selection strategies. A second computational experiment shows the computational benefits of the proposed ALNS framework within the MIP solver SCIP. T3 - ZIB-Report - 18-60 KW - mixed integer programming KW - primal heuristics KW - large neighborhood search KW - multi armed bandit problem Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71167 SN - 1438-0064 ER - TY - JOUR A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - Numerical Investigation of Light Emission from Quantum Dots Embedded into On-Chip, Low Index Contrast Optical Waveguides JF - Phys. Status Solidi B Y1 - 2019 U6 - https://doi.org/10.1002/pssb.201800437 VL - 256 SP - 1800437 ER - TY - GEN A1 - Beckenbach, Isabel A1 - Hatzel, Meike A1 - Wiederrecht, Sebastian T1 - The Tight Cut Decomposition of Matching Covered Uniformable Hypergraphs N2 - The perfect matching polytope, i.e. the convex hull of (incidence vectors of) perfect matchings of a graph is used in many combinatorial algorithms. Kotzig, Lovász and Plummer developed a decomposition theory for graphs with perfect matchings and their corresponding polytopes known as the tight cut decomposition which breaks down every graph into a number of indecomposable graphs, so called bricks. For many properties that are of interest on graphs with perfect matchings, including the description of the perfect matching polytope, it suffices to consider these bricks. A key result by Lovász on the tight cut decomposition is that the list of bricks obtained is the same independent of the choice of tight cuts made during the tight cut decomposition procedure. This implies that finding a tight cut decomposition is polynomial time equivalent to finding a single tight cut. We generalise the notions of a tight cut, a tight cut contraction and a tight cut decomposition to hypergraphs. By providing an example, we show that the outcome of the tight cut decomposition on general hypergraphs is no longer unique. However, we are able to prove that the uniqueness of the tight cut decomposition is preserved on a slight generalisation of uniform hypergraphs. Moreover, we show how the tight cut decomposition leads to a decomposition of the perfect matching polytope of uniformable hypergraphs and that the recognition problem for tight cuts in uniformable hypergraphs is polynomial time solvable. T3 - ZIB-Report - 18-61 KW - uniform hypergraphs KW - perfect matchings KW - tight cuts Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71149 SN - 1438-0064 ER - TY - CHAP A1 - Anderson, Lovis A1 - Hiller, Benjamin T1 - A Sweep-Plane Algorithm for the Computation of the Volume of a Union of Polytopes T2 - Operations Research Proceedings 2018 N2 - Optimization models often feature disjunctions of polytopes as submodels. Such a disjunctive set is initially at best) relaxed to its convex hull, which is then refined by branching. To measure the error of the convex relaxation, the (relative) difference between the volume of the convex hull and the volume of the disjunctive set may be used. This requires a method to compute the volume of the disjunctive set. We propose a revised variant of an old algorithm by Bieri and Nef (1983) for this purpose. The algorithm uses a sweep-plane to incrementally calculate the volume of the disjunctive set as a function of the offset parameter of the sweep-plane. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-18500-8_12 VL - Operations Research Proceedings ER - TY - GEN A1 - Serrano, Felipe T1 - Intersection cuts for factorable MINLP N2 - Given a factorable function f, we propose a procedure that constructs a concave underestimor of f that is tight at a given point. These underestimators can be used to generate intersection cuts. A peculiarity of these underestimators is that they do not rely on a bounded domain. We propose a strengthening procedure for the intersection cuts that exploits the bounds of the domain. Finally, we propose an extension of monoidal strengthening to take advantage of the integrality of the non-basic variables. T3 - ZIB-Report - 18-59 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71105 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Building Optimal Steiner Trees on Supercomputers by using up to 43,000 Cores N2 - SCIP-JACK is a customized, branch-and-cut based solver for Steiner tree and related problems. ug [SCIP-JACK, MPI] extends SCIP-JACK to a massively par- allel solver by using the Ubiquity Generator (UG) framework. ug [SCIP-JACK, MPI] was the only solver that could run on a distributed environment at the (latest) 11th DIMACS Challenge in 2014. Furthermore, it could solve three well-known open instances and updated 14 best known solutions to instances from the bench- mark libary STEINLIB. After the DIMACS Challenge, SCIP-JACK has been con- siderably improved. However, the improvements were not reflected on ug [SCIP- JACK, MPI]. This paper describes an updated version of ug [SCIP-JACK, MPI], especially branching on constrains and a customized racing ramp-up. Furthermore, the different stages of the solution process on a supercomputer are described in detail. We also show the latest results on open instances from the STEINLIB. T3 - ZIB-Report - 18-58 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71118 SN - 1438-0064 ER - TY - JOUR A1 - Klus, Stefan A1 - Bittracher, Andreas A1 - Schuster, Ingmar A1 - Schütte, Christof T1 - A kernel-based approach to molecular conformation analysis JF - Journal of Chemical Physics N2 - We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for analyzing dynamical systems in order to identify conformation dynamics based on molecular dynamics simulation data. We show that many of the prominent methods like Markov State Models, EDMD, and TICA can be regarded as special cases of this approach and that new efficient algorithms can be constructed based on this derivation. The results of these new powerful methods will be illustrated with several examples, in particular the alanine dipeptide and the protein NTL9. Y1 - 2018 U6 - https://doi.org/10.1063/1.5063533 VL - 149 IS - 24 ER - TY - JOUR A1 - Dell’Amico, M. A1 - Hadjidimitriou, Natalia Selini A1 - Koch, Thorsten A1 - Petkovic, Milena T1 - Forecasting Natural Gas Flows in Large Networks JF - Machine Learning, Optimization, and Big Data. MOD 2017. N2 - Natural gas is the cleanest fossil fuel since it emits the lowest amount of other remains after being burned. Over the years, natural gas usage has increased significantly. Accurate forecasting is crucial for maintaining gas supplies, transportation and network stability. This paper presents two methodologies to identify the optimal configuration o parameters of a Neural Network (NN) to forecast the next 24 h of gas flow for each node of a large gas network. In particular the first one applies a Design Of Experiments (DOE) to obtain a quick initial solution. An orthogonal design, consisting of 18 experiments selected among a total of 4.374 combinations of seven parameters (training algorithm, transfer function, regularization, learning rate, lags, and epochs), is used. The best result is selected as initial solution of an extended experiment for which the Simulated Annealing is run to find the optimal design among 89.100 possible combinations of parameters. The second technique is based on the application of Genetic Algorithm for the selection of the optimal parameters of a recurrent neural network for time series forecast. GA was applied with binary representation of potential solutions, where subsets of bits in the bit string represent different values for several parameters of the recurrent neural network. We tested these methods on three municipal nodes, using one year and half of hourly gas flow to train the network and 60 days for testing. Our results clearly show that the presented methodologies bring promising results in terms of optimal configuration of parameters and forecast error. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/978-3-319-72926-8_14 VL - Lecture Notes in Computer Science IS - vol 10710 SP - 158 EP - 171 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Erratum: Equivalence of weak and strong modes of measures on topological vector spaces (2018 Inverse Problems 34 115013) JF - Inverse Problems Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aae55b VL - 34 IS - 12 SP - 129601 ER - TY - JOUR A1 - Lalanne, P. A1 - Yan, W. A1 - Gras, A. A1 - Sauvan, C. A1 - Hugonin, J.-P. A1 - Besbes, M. A1 - Demésy, G. A1 - Truong, M. D. A1 - Gralak, B. A1 - Zolla, F. A1 - Nicolet, A. A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Zimmerling, J. A1 - Remis, R. A1 - Urbach, H. Paul A1 - Liu, H. T. A1 - Weiss, T. T1 - Quasinormal mode solvers for resonators with dispersive materials JF - J. Opt. Soc. Am. A Y1 - 2019 U6 - https://doi.org/10.1364/JOSAA.36.000686 VL - 36 SP - 686 ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - A Riesz-projection-based method for nonlinear eigenvalue problems JF - J. Comput. Phys. Y1 - 2020 U6 - https://doi.org/10.1016/j.jcp.2020.109678 VL - 419 SP - 109678 ER - TY - JOUR A1 - Al Hajj, Hassan A1 - Sahu, Manish A1 - Lamard, Mathieu A1 - Conze, Pierre-Henri A1 - Roychowdhury, Soumali A1 - Hu, Xiaowei A1 - Marsalkaite, Gabija A1 - Zisimopoulos, Odysseas A1 - Dedmari, Muneer Ahmad A1 - Zhao, Fenqiang A1 - Prellberg, Jonas A1 - Galdran, Adrian A1 - Araujo, Teresa A1 - Vo, Duc My A1 - Panda, Chandan A1 - Dahiya, Navdeep A1 - Kondo, Satoshi A1 - Bian, Zhengbing A1 - Bialopetravicius, Jonas A1 - Qiu, Chenghui A1 - Dill, Sabrina A1 - Mukhopadyay, Anirban A1 - Costa, Pedro A1 - Aresta, Guilherme A1 - Ramamurthy, Senthil A1 - Lee, Sang-Woong A1 - Campilho, Aurelio A1 - Zachow, Stefan A1 - Xia, Shunren A1 - Conjeti, Sailesh A1 - Armaitis, Jogundas A1 - Heng, Pheng-Ann A1 - Vahdat, Arash A1 - Cochener, Beatrice A1 - Quellec, Gwenole T1 - CATARACTS: Challenge on Automatic Tool Annotation for cataRACT Surgery JF - Medical Image Analysis N2 - Surgical tool detection is attracting increasing attention from the medical image analysis community. The goal generally is not to precisely locate tools in images, but rather to indicate which tools are being used by the surgeon at each instant. The main motivation for annotating tool usage is to design efficient solutions for surgical workflow analysis, with potential applications in report generation, surgical training and even real-time decision support. Most existing tool annotation algorithms focus on laparoscopic surgeries. However, with 19 million interventions per year, the most common surgical procedure in the world is cataract surgery. The CATARACTS challenge was organized in 2017 to evaluate tool annotation algorithms in the specific context of cataract surgery. It relies on more than nine hours of videos, from 50 cataract surgeries, in which the presence of 21 surgical tools was manually annotated by two experts. With 14 participating teams, this challenge can be considered a success. As might be expected, the submitted solutions are based on deep learning. This paper thoroughly evaluates these solutions: in particular, the quality of their annotations are compared to that of human interpretations. Next, lessons learnt from the differential analysis of these solutions are discussed. We expect that they will guide the design of efficient surgery monitoring tools in the near future. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.008 N1 - Best paper award - Computer Graphics Night 2020 (TU Darmstadt) VL - 52 IS - 2 SP - 24 EP - 41 PB - Elsevier ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Reduction-based exact solution of prize-collecting Steiner tree problems T3 - ZIB-Report - 18-55 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70958 SN - 1438-0064 ER - TY - JOUR A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Medical Image Analysis N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The shape models and neural networks employed are trained using data of the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets of the SKI10 challenge. For the first time, an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We made the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation. In conclusion, combining statistical anatomical knowledge via SSMs with the localized classification via CNNs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.009 VL - 52 IS - 2 SP - 109 EP - 118 ER - TY - JOUR A1 - Peitz, Sebastian A1 - Gräler, Manuel A1 - Henke, Christian A1 - Hessel-von Molo, Mirko A1 - Dellnitz, Michael A1 - Trächtler, Ansgar T1 - Multiobjective Model Predictive Control of an Industrial Laundry JF - Procedia Technology N2 - In a wide range of applications, it is desirable to optimally control a system with respect to concurrent, potentially competing goals. This gives rise to a multiobjective optimal control problem where, instead of computing a single optimal solution, the set of optimal compromises, the so-called Pareto set, has to be approximated. When it is not possible to compute the entire control trajectory in advance, for instance due to uncertainties or unforeseeable events, model predictive control methods can be applied to control the system during operation in real time. In this article, we present an algorithm for the solution of multiobjective model predictive control problems. In an offline scenario, it can be used to compute the entire set of optimal compromises whereas in a real time scenario, one optimal compromise is computed according to an operator’s preference. The results are illustrated using the example of an industrial laundry. A logistics model of the laundry is developed and then utilized in the optimization routine. Results are presented for an offline as well as an online scenario Y1 - 2016 IS - 26 SP - 483 EP - 490 ER - TY - GEN A1 - Nägel, Arne A1 - Deuflhard, Peter A1 - Wittum, Gabriel T1 - Efficient Stiff Integration of Density Driven Flow Problems N2 - The paper investigates the efficient use of a linearly implicit stiff integrator for the numerical solution of density driven flow problems. Upon choosing a one-step method of extrapolation type (code LIMEX), the use of full Jacobians and reduced approximations are discussed. Numerical experiments include nonlinear density flow problems such as diffusion from a salt dome (2D), a (modified) Elder problem (3D), the saltpool benchmark (3D) and a real life salt dome problem (2D). The arising linear equations are solved using either a multigrid preconditioner from the software package UG4 or the sparse matrix solver SuperLU. T3 - ZIB-Report - 18-54 KW - stiff integration for PDEs KW - linearly implicit Euler discretization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70891 SN - 1438-0064 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Surface localization of gas sources on comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data JF - Monthly Notices of the Royal Astronomical Society N2 - We reconstruct the temporal evolution of the source distribution for the four major gas species H2O, CO2, CO, and O2 on the surface of comet 67P/Churyumov-Gerasimenko during its 2015 apparition. The analysis applies an inverse coma model and fits to data between August 6th 2014 and September 5th 2016 measured with the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS). The spatial distribution of gas sources with their temporal variation allows one to construct surface maps for gas emissions and to evaluate integrated productions rates. For all species peak production rates and integrated productions rates per orbit are evaluated separately for the northern and the southern hemisphere. The nine most active emitting areas on the comet’s surface are defined and their correlation to emissions for each of the species is discussed. Y1 - 2018 U6 - https://doi.org/10.1093/mnras/sty3103 VL - 483 SP - 852 EP - 861 PB - Monthly Notices of the Royal Astronomical Society ER - TY - GEN A1 - Borndörfer, Ralf A1 - Egerer, Ascan A1 - Karbstein, Marika A1 - Messerschmidt, Ralf A1 - Perez, Marc A1 - Pfisterer, Steven A1 - Strauß, Petra T1 - Kombilösung: Optimierung des Liniennetzes in Karlsruhe N2 - Wir beschreiben die Optimierung des Nahverkehrsnetzes der Stadt Karlsruhe im Zusammmenhang mit den Baumaßnahmen der sogenannten Kombilösung. T3 - ZIB-Report - 18-45 KW - ÖPNV KW - Linienplanung Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69677 SN - 1438-0064 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Combining NP-Hard Reduction Techniques and Strong Heuristics in an Exact Algorithm for the Maximum-Weight Connected Subgraph Problem JF - SIAM Journal on Optimization N2 - Borne out of a surprising variety of practical applications, the maximum-weight connected subgraph problem has attracted considerable interest during the past years. This interest has not only led to notable research on theoretical properties, but has also brought about several (exact) solvers-with steadily increasing performance. Continuing along this path, the following article introduces several new algorithms such as reduction techniques and heuristics and describes their integration into an exact solver. The new methods are evaluated with respect to both their theoretical and practical properties. Notably, the new exact framework allows to solve common problem instances from the literature faster than all previous approaches. Moreover, one large-scale benchmark instance from the 11th DIMACS Challenge can be solved for the first time to optimality and the primal-dual gap for two other ones can be significantly reduced. Y1 - 2019 U6 - https://doi.org/10.1137/17M1145963 VL - 29 IS - 1 SP - 369 EP - 398 PB - Society for Industrial and Applied Mathematics ER - TY - CHAP A1 - Jäger, Klaus A1 - Manley, Phillip A1 - Eisenhauer, David A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Light management with sinusoidal nanotextures T2 - Light, Energy and the Environment 2018 Y1 - 2018 U6 - https://doi.org/10.1364/OSE.2018.OT5C.5 SP - OT5C.5 ER - TY - JOUR A1 - Hoffmann, Rene A1 - Lemanis, Robert A1 - Wulff, Lena A1 - Zachow, Stefan A1 - Lukeneder, Alexander A1 - Klug, Christian A1 - Keupp, Helmut T1 - Traumatic events in the life of the deep-sea cephalopod mollusc, the coleoid Spirula spirula JF - ScienceDirect: Deep Sea Research Part I - Oceanographic Research N2 - Here, we report on different types of shell pathologies of the enigmatic deep-sea (mesopelagic) cephalopod Spirula spirula. For the first time, we apply non-invasive imaging methods to: document trauma-induced changes in shell shapes, reconstruct the different causes and effects of these pathologies, unravel the etiology, and attempt to quantify the efficiency of the buoyancy apparatus. We have analysed 2D and 3D shell parameters from eleven shells collected as beach findings from the Canary Islands (Gran Canaria and Fuerteventura), West-Australia, and the Maldives. All shells were scanned with a nanotom-m computer tomograph. Seven shells were likely injured by predator attacks: fishes, cephalopods or crustaceans, one specimen was infested by an endoparasite (potentially Digenea) and one shell shows signs of inflammation and one shell shows large fluctuations of chamber volumes without any signs of pathology. These fluctuations are potential indicators of a stressed environment. Pathological shells represent the most deviant morphologies of a single species and can therefore be regarded as morphological end-members. The changes in the shell volume / chamber volume ratio were assessed in order to evaluate the functional tolerance of the buoyancy apparatus showing that these had little effect. Y1 - 2018 U6 - https://doi.org/10.1016/j.dsr.2018.10.007 VL - 142 IS - 12 SP - 127 EP - 144 ER - TY - THES A1 - Steininger, Lennart T1 - Atomarer Datenzugriff auf verteilten persistenten Arbeitsspeicher N2 - Nicht flüchtiger Arbeitsspeicher bzw. Non-volatile Random Access Memory oder auch Persistent Memory befindet sich im frühen Markteintritt. Diese Art von Speicher nimmt eine Stellung zwischen bisherigem flüchtigen Arbeitsspeicher (Memory) und bisherigem Permanentspeicher (Storage) ein. Im Zusammenspiel mit verteilten Algorithmen und Systemen sowie dem Zugriff auf entfernte Speicherbereiche durch die Netzwerkinterfaces per Remote Direct Memory Access sind die Konzepte zum Umgang mit Durability und allen einhergehenden Herausforderungen bisher nicht ausgereift. Diese Arbeit untersucht, wie sich in Rechnernetzen mit persistentem Speicher und möglichst passivem Zugriff auf entfernten Speicher performante verteilte Systeme implementieren lassen. Es werden Anforderungen und Voraussetzungen eines solchen Systems bestimmt und daraufhin Lösungsmöglichkeiten aufgezeigt, wie sich diese Anforderungen mit Nutzung nicht flüchtigen Arbeitsspeichers umsetzen lassen. Die notwendigen Eigenschaften der Hard- und Software sowie der eingesetzten Netzwerkprotokolle werden beschrieben. Y1 - 2018 ER - TY - CHAP A1 - Schmidtke, Robert A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - From Application to Disk: Tracing I/O Through the Big Data Stack T2 - High Performance Computing ISC High Performance 2018 International Workshops, Frankfurt/Main, Germany, June 24 - 28, 2018, Revised Selected Papers, Workshop on Performance and Scalability of Storage Systems (WOPSSS) N2 - Typical applications in data science consume, process and produce large amounts of data, making disk I/O one of the dominating — and thus worthwhile optimizing — factors of their overall performance. Distributed processing frameworks, such as Hadoop, Flink and Spark, hide a lot of complexity from the programmer when they parallelize these applications across a compute cluster. This exacerbates reasoning about I/O of both the application and the framework, through the distributed file system, such as HDFS, down to the local file systems. We present SFS (Statistics File System), a modular framework to trace each I/O request issued by the application and any JVM-based big data framework involved, mapping these requests to actual disk I/O. This allows detection of inefficient I/O patterns, both by the applications and the underlying frameworks, and builds the basis for improving I/O scheduling in the big data software stack. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-030-02465-9_6 SP - 89 EP - 102 ER - TY - CHAP A1 - Renken, Malte A1 - Ahmadi, Amin A1 - Borndörfer, Ralf A1 - Sahin, Guvenc A1 - Schlechte, Thomas T1 - Demand-Driven Line Planning with Selfish Routing T2 - Operations Research Proceedings 2017 N2 - Bus rapid transit systems in developing and newly industrialized countries are often operated at the limits of passenger capacity. In particular, demand during morning and afternoon peaks is hardly or even not covered with available line plans. In order to develop demand-driven line plans, we use two mathematical models in the form of integer programming problem formulations. While the actual demand data is specified with origin-destination pairs, the arc-based model considers the demand over the arcs derived from the origin-destination demand. In order to test the accuracy of the models in terms of demand satisfaction, we simulate the optimal solutions and compare number of transfers and travel times. We also question the effect of a selfish route choice behavior which in theory results in a Braess-like paradox by increasing the number of transfers when system capacity is increased with additional lines. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_91 SP - 687 EP - 692 PB - Springer International Publishing ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Liebchen, Christian A1 - Lindner, Niels T1 - A Simple Way to Compute the Number of Vehicles That Are Required to Operate a Periodic Timetable T2 - 18th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2018) N2 - We consider the following planning problem in public transportation: Given a periodic timetable, how many vehicles are required to operate it? In [9], for this sequential approach, it is proposed to first expand the periodic timetable over time, and then answer the above question by solving a flow-based aperiodic optimization problem. In this contribution we propose to keep the compact periodic representation of the timetable and simply solve a particular perfect matching problem. For practical networks, it is very much likely that the matching problem decomposes into several connected components. Our key observation is that there is no need to change any turnaround decision for the vehicles of a line during the day, as long as the timetable stays exactly the same. Y1 - 2018 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2018.16 VL - 65 SP - 16:1 EP - 16:15 ER - TY - GEN A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Modeling Checkpoint Schedules for Concurrent HPC Applications T2 - CoSaS 2018 International Symposium on Computational Science at Scale Y1 - 2018 ER - TY - JOUR A1 - Donati, Luca A1 - Heida, Martin A1 - Keller, Bettina G. A1 - Weber, Marcus T1 - Estimation of the infinitesimal generator by square-root approximation JF - J. Phys.: Condens. Matter N2 - In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is—from a mathematical point of view—an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi tessellation, then the transition rates between adjacent cells is approximated by the geometric average of the Boltzmann weights of the Voronoi cells. This method demonstrates that there is a direct relation between the potential energy surface of molecular structures and the transition rates of conformational changes. We will show also that this approximation is correct and converges to the generator of the Smoluchowski equation in the limit of infinitely small Voronoi cells. We present results for a two dimensional diffusion process and alanine dipeptide as a high-dimensional system. Y1 - 2018 U6 - https://doi.org/10.1088/1361-648X/aadfc8 VL - 30 IS - 42 SP - 425201 EP - 425201 ER - TY - JOUR A1 - Manley, Phillip A1 - Abdi, Fatwa F. A1 - Berglund, Sean P. A1 - Islam, A. T. M. Nazmul A1 - Burger, Sven A1 - van de Krol, Roel A1 - Schmid, Martina T1 - Absorption Enhancement for Ultra-Thin Solar Fuel Devices with Plasmonic Gratings JF - ACS Appl. Energy Mater. Y1 - 2018 U6 - https://doi.org/10.1021/acsaem.8b01070 VL - 1 SP - 5810 ER - TY - CHAP A1 - Knötel, David A1 - Becker, Carola A1 - Scholtz, Gerhard A1 - Baum, Daniel T1 - Global and Local Mesh Morphing for Complex Biological Objects from microCT Data T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations. Y1 - 2018 U6 - https://doi.org/10.2312/vcbm.20181243 SP - 179 EP - 183 CY - Granada, Spain ER - TY - GEN A1 - Knötel, David A1 - Becker, Carola A1 - Scholtz, Gerhard A1 - Baum, Daniel T1 - Global and Local Mesh Morphing for Complex Biological Objects from microCT Data N2 - We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations. T3 - ZIB-Report - 18-53 KW - Mesh interpolation KW - Geometry processing KW - microCT Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70618 SN - 1438-0064 ER - TY - GEN A1 - Ito, Satoshi A1 - Shinano, Yuji T1 - Calculation of clinch and elimination numbers for sports leagues with multiple tiebreaking criteria N2 - The clinch (elimination) number is a minimal number of future wins (losses) needed to clinch (to be eliminated from) a specified place in a sports league. Several optimization models and computational results are shown in this paper for calculating clinch and elimination numbers in the presence of predefined multiple tiebreaking criteria. The main subject of this paper is to provide a general algorithmic framework based on integer programming with utilizing possibly multilayered upper and lower bounds. T3 - ZIB-Report - 18-51 KW - Sports league KW - Round-robin tournament KW - Tiebreaking criteria KW - Clinch number KW - Elimination number KW - Combinatorial optimization KW - Integer programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70591 SN - 1438-0064 ER - TY - JOUR A1 - Lange, Alexander A1 - Schwieger, Robert A1 - Plöntzke, Julia A1 - Schäfer, Stefan A1 - Röblitz, Susanna T1 - Follicular competition in cows: the selection of dominant follicles as a synergistic effect JF - Journal of Mathematical Biology N2 - The reproductive cycle of mono-ovulatory species such as cows or humans is known to show two or more waves of follicular growth and decline between two successive ovulations. Within each wave, there is one dominant follicle escorted by subordinate follicles of varying number. Under the surge of the luteinizing hormone a growing dominant follicle ovulates. Rarely the number of ovulating follicles exceeds one. In the biological literature, the change of hormonal concentrations and individually varying numbers of follicular receptors are made responsible for the selection of exactly one dominant follicle, yet a clear cause has not been identified. In this paper, we suggest a synergistic explanation based on competition, formulated by a parsimoniously defined system of ordinary differential equations (ODEs) that quantifies the time evolution of multiple follicles and their competitive interaction during one wave. Not discriminating between follicles, growth and decline are given by fixed rates. Competition is introduced via a growth-suppressing term, equally supported by all follicles. We prove that the number of dominant follicles is determined exclusively by the ratio of follicular growth and competition. This number turns out to be independent of the number of subordinate follicles. The asymptotic behavior of the corresponding dynamical system is investigated rigorously, where we demonstrate that the ω-limit set only contains fixed points. When also including follicular decline, our ODEs perfectly resemble ultrasound data of bovine follicles. Implications for the involved but not explicitly modeled hormones are discussed. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/s00285-018-1284-0 ER - TY - JOUR A1 - Schwieger, Robert A1 - Siebert, Heike A1 - Röblitz, Susanna T1 - Correspondence of Trap Spaces in Different Models of Bioregulatory Networks JF - SIAM Journal on Applied Dynamical Systems N2 - Mathematical models for bioregulatory networks can be based on different formalisms, depending on the quality of available data and the research question to be answered. Discrete boolean models can be constructed based on qualitative data, which are frequently available. On the other hand, continuous models in terms of ordinary differential equations (ODEs) can incorporate time-series data and give more detailed insight into the dynamics of the underlying system. A few years ago, a method based on multivariate polynomial interpolation and Hill functions has been developed for an automatic conversion of boolean models to systems of ordinary differential equations. This method is frequently used by modellers in systems biology today, but there are only a few results available about the conservation of mathematical structures and properties across the formalisms. Here, we consider subsets of the phase space where some components stay fixed, called trap spaces, and demonstrate how boolean trap spaces can be linked to invariant sets in the continuous state space. This knowledge is of practical relevance since finding trap spaces in the boolean setting, which is relatively easy, allows for the construction of reduced ODE models. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1137/17M1155302 VL - 17 IS - 2 SP - 1742 EP - 1765 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Euler, Ricardo A1 - Karbstein, Marika A1 - Mett, Fabian T1 - Ein mathematisches Modell zur Beschreibung von Preissystemen im öV N2 - Dieses Dokument fasst den Stand der mathematischen Modellierung von Preissystemen des öV mittels eines am ZIB entwickelten Tarifgraphenmodells zusammen. Damit sind sehr einfache und konzise Beschreibungen von Tarifstrukturen möglich, die sich algorithmisch behandeln lassen: Durch das zeitgleiche Tracken eines Pfades im Routinggraphen im Tarifgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Wir beschreiben zunächst das Konzept. Die konkrete Realisierung wird im Folgenden beispielhaft an den Tarifsystemen der Verkehrsverbünde Warnow, MDV, Vogtland, Bremen/Niedersachsen, Berlin/Brandenburg und Mittelsachsen erläutert. Anschließend folgen Überlegungen zur konkreten Implementierung von Kurzstrecken-Tarifen und zur Behandlung des Verbundübergriffs. T3 - ZIB-Report - 18-47 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70564 SN - 1438-0064 ER - TY - JOUR A1 - Sunkara, Vikram T1 - Algebraic Expressions of Conditional Expectations in Gene Regulatory Networks JF - Journal of Mathematical Biology N2 - Gene Regulatory Networks are powerful models for describing the mechanisms and dynamics inside a cell. These networks are generally large in dimension and seldom yield analytical formulations. It was shown that studying the conditional expectations between dimensions (vertices or species) of a network could lead to drastic dimension reduction. These conditional expectations were classically given by solving equations of motions derived from the Chemical Master Equation. In this paper we deviate from this convention and take an Algebraic approach instead. That is, we explore the consequences of conditional expectations being described by a polynomial function. There are two main results in this work. Firstly: if the conditional expectation can be described by a polynomial function, then coefficients of this polynomial function can be reconstructed using the classical moments. And secondly: there are dimensions in Gene Regulatory Networks which inherently have conditional expectations with algebraic forms. We demonstrate through examples, that the theory derived in this work can be used to develop new and effective numerical schemes for forward simulation and parameter inference. The algebraic line of investigation of conditional expectations has considerable scope to be applied to many different aspects of Gene Regulatory Networks; this paper serves as a preliminary commentary in this direction. T3 - ZIB-Report - 18-52 KW - Markov Chains KW - Chemical Master Equations KW - Dimension Reduction Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70526 SN - 1438-0064 IS - 79 SP - 1779 EP - 1829 PB - Journal of Mathematical Biology ER - TY - CHAP A1 - Dennstedt, Anne A1 - Gaslain, Fabrice A1 - Bartsch, Marion A1 - Guipont, Vincent A1 - Maurel, Vincent T1 - Crack Morphology in a Columnar Thermal Barrier Coating System N2 - Ceramic layers are used as thermal barrier coatings (TBCs) on metallic substrates. During thermal transients, the thermal expansion mismatch between coating and substrate drives failure of the TBC mainly by interfacial cracking. Laser Shock Adhesion Test (LASAT) provides stresses at the ceramic/metal interface enabling controlled interfacial cracking. For achieving a clear understanding of the influence of local morphology on interfacial toughness, this study aims at characterizing the 3D morphology of a crack at the interface between metal and an EB-PVD TBC having a columnar structure. Cracks were produced by LASAT and documented further in SE and BSE image stacks collected simultaneously during subsequent slice and view operations using a focus ion beam (FIB) and a scanning electron microscope (FIB slice & view). The segmented 3D data gives clear understanding of the columnar structure of the ceramic and of the interaction between the crack and the TBC microstructure. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69385 ER - TY - CHAP A1 - Manley, Phillip A1 - Jäger, Klaus A1 - Tockhorn, Philipp A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Optimization of nanostructured high efficiency perovskite/c-Si tandem solar cells via numerical simulation T2 - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2321240 VL - 10731 SP - 107310B ER - TY - CHAP A1 - Werdehausen, Daniel A1 - Staude, Isabelle A1 - Burger, Sven A1 - Petschulat, Jörg A1 - Scharf, Toralf A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Using effective medium theories to design tailored nanocomposite materials for optical systems T2 - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2320525 VL - 10745 SP - 107450H ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Soltwisch, Victor A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Rockstuhl, Carsten T1 - Benchmarking five global optimization approaches for nano-optical shape optimization and parameter reconstruction JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.9b00706 VL - 6 SP - 2726 ER - TY - JOUR A1 - Kewes, Günter A1 - Binkowski, Felix A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Benson, Oliver T1 - Heuristic Modeling of Strong Coupling in Plasmonic Resonators JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.8b00766 VL - 5 SP - 4089 ER - TY - GEN A1 - Radons, Manuel A1 - Lehmann, Lutz A1 - Streubel, Tom A1 - Griewank, Andreas T1 - An Open Newton Method for Piecewise Smooth Systems N2 - Recent research has shown that piecewise smooth (PS) functions can be approximated by piecewise linear functions with second order error in the distance to a given reference point. A semismooth Newton type algorithm based on successive application of these piecewise linearizations was subsequently developed for the solution of PS equation systems. For local bijectivity of the linearization at a root, a radius of quadratic convergence was explicitly calculated in terms of local Lipschitz constants of the underlying PS function. In the present work we relax the criterium of local bijectivity of the linearization to local openness. For this purpose a weak implicit function theorem is proved via local mapping degree theory. It is shown that there exist PS functions f:IR^2 --> IR^2 satisfying the weaker criterium where every neighborhood of the root of f contains a point x such that all elements of the Clarke Jacobian at x are singular. In such neighborhoods the steps of classical semismooth Newton are not defined, which establishes the new method as an independent algorithm. To further clarify the relation between a PS function and its piecewise linearization, several statements about structure correspondences between the two are proved. Moreover, the influence of the specific representation of the local piecewise linear models on the robustness of our method is studied. An example application from cardiovascular mathematics is given. T3 - ZIB-Report - 18-43 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70418 SN - 1438-0064 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Spectral Clustering for Non-Reversible Markov Chains JF - Computational and Applied Mathematics N2 - Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e., generalized PCCA), since it includes the case of non-reversible processes. We also apply the method to real-world eye-tracking data. KW - Spectral clustering KW - Markov chain KW - Non-reversible KW - Schur decomposition KW - GenPCCA Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/s40314-018-0697-0 VL - 37 IS - 5 SP - 6376 EP - 6391 ER - TY - JOUR A1 - Apprich, Christian A1 - Dieterich, Annegret A1 - Höllig, Klaus A1 - Nava-Yazdani, Esfandiar T1 - Cubic spline approximation of a circle with maximal smoothness and accuracy JF - Computer Aided Geometric Design N2 - We construct cubic spline approximations of a circle which are four times continuously differentiable and converge with order six. Y1 - 2017 U6 - https://doi.org/10.1016/j.cagd.2017.05.001 VL - 56 SP - 1 EP - 3 PB - Elsevier B.V. ER - TY - CHAP A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Coconu, Liviu A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - An 1834 mediterranean garden in Berlin – engaged from 2004, 2018, 2032, and 2202 T2 - PerDis ’18 – 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as “italienisches Kunststück” (Italian legerdemain) by Peter Joseph Lenné. The park was originally realized on the grounds of Schloss Sanssouci in Potsdam, Germany. The installation centered on highly detailed renderings of hundreds of plants projected upon a panoramic display. Interactivity was expressed with a tangible interface which (while presently dated) we believe remains without near-precedent then or since. We present the installation (experienced by roughly 20,000 visitors), focusing on the interaction aspects. We introduce new book and table/door-format mockups. Drawing upon a heuristic of the scientist-philosopher Freeman Dyson, we consider grounded future prospect variations in the contexts of 2018, 2032, and 2202. We see this exercise as prospectively generalizing to a variety of similar and widely diverse application domains. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3205894 SP - no. 12 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Coconu, Liviu A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - A smartphone-based tangible interaction approach for landscape visualization. T2 - PerDis ’18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - The use of tangible interfaces for navigation of landscape scenery – for example, lost places re-created in 3D – has been pursued and articulated as a promising, impactful application of interactive visualization. In this demonstration, we present a modern, low-cost implementation of a previously-realized multimodal gallery installation. Our demonstration centers upon the versatile usage of a smartphone for sensing, navigating, and (optionally) displaying element on a physical surface in tandem with a larger, more immersive display. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3210707 SP - no. 23 PB - ACM CY - New York, NY, USA ER - TY - GEN A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-Dimensional Reconstruction and Quantification of Dislocation Substructures from Transmission Electron Microscopy Stereo-Pairs N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 % and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. T3 - ZIB-Report - 18-50 KW - dislocation, diffraction contrast, scanning transmission electron microscopy, stereoscopy, visualization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70339 SN - 1438-0064 ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Checkpoint Scheduling for Shared Usage of Burst-Buffers in Supercomputers T2 - Proceedings of the 47th International Conference on Parallel Processing Companion; SRMPDS 2018: The 14th International Workshop on Scheduling and Resource Management for Parallel and Distributed Systems N2 - User-defined and system-level checkpointing have contrary properties. While user-defined checkpoints are smaller and simpler to recover, system-level checkpointing better knows the global system's state and parameters like the expected mean time to failure (MTTF) per node. Both approaches lead to non-optimal checkpoint time, intervals, sizes, or I/O bandwidth when concurrent checkpoints conflict and compete for it. We combine user-defined and system-level checkpointing to exploit the benefits and avoid the drawbacks of each other. Thus, applications frequently offer to create checkpoints. The system accepts such offers according to the current status and implied costs to recalculate from the last checkpoint or denies them, i.e., immediately lets continue the application without checkpoint creation. To support this approach, we develop economic models for multi-application checkpointing on shared I/O resources that are dedicated for checkpointing (e.g. burst-buffers) by defining an appropriate goal function and solving a global optimization problem. Using our models, the checkpoints of applications on a supercomputer are scheduled to effectively use the available I/O bandwidth and minimize the failure overhead (checkpoint creations plus recalculations). Our simulations show an overall reduction in failure overhead of all nodes of up to 30% for a typical supercomputer workload (HLRN). We can also derive the most cost effective burst-buffer bandwidth for a given node's MTTF and application workload. Y1 - 2018 U6 - https://doi.org/10.1145/3229710.3229755 SP - 44:1 EP - 44:10 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - Chvátal’s Conjecture Holds for Ground Sets of Seven Elements N2 - We establish a general computational framework for Chvátal’s conjecture based on exact rational integer programming. As a result we prove Chvátal’s conjecture holds for all downsets whose union of sets contains seven elements or less. The computational proof relies on an exact branch-and-bound certificate that allows for elementary verification and is independent of the integer programming solver used. T3 - ZIB-Report - 18-49 KW - extremal combinatorics KW - exact rational integer programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70240 SN - 1438-0064 ER - TY - GEN A1 - Fackeldey, Konstantin A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Spectral Clustering for Non-reversible Markov Chains N2 - Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g. the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e. Generalized PCCA), since it includes the case of non reversible processes. We also apply the method to real world eye tracking data. T3 - ZIB-Report - 18-48 KW - spectral clustering KW - Markov chain KW - Schur decomposition KW - non-reversible Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70218 SN - 1438-0064 ER - TY - JOUR A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics JF - SIAM J. Multiscale Model. Simul. N2 - We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one. Y1 - 2018 U6 - https://doi.org/10.1137/17M1146403 VL - 16 IS - 4 SP - 1455 EP - 1485 PB - SIAM ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf T1 - Hall’s and Kőnig’s theorem in graphs and hypergraphs JF - Discrete Mathematics N2 - We investigate the relation between Hall’s theorem and Kőnig’s theorem in graphs and hypergraphs. In particular, we characterize the graphs satisfying a deficiency version of Hall’s theorem, thereby showing that this class strictly contains all Kőnig–Egerváry graphs. Furthermore, we give a generalization of Hall’s theorem to normal hypergraphs. Y1 - 2018 U6 - https://doi.org/10.1016/j.disc.2018.06.013 VL - 341 IS - 10 SP - 2753 EP - 2761 ER - TY - THES A1 - Mattrisch, Lisa T1 - Optimization of a Master Surgery Schedule N2 - During the past years hospitals saw themselves confronted with increasing economical pressure (WB06, p. V). Therefore, optimizing the general operational procedures has gained in importance. The revenue of a hospital depends on the kinds and quantity of treatments performed and on the effcient use and utilization of the corresponding resources. About 25 − 50% of the treatment costs of a patient needing surgery incurs in the operating rooms (WB06, p. 58). Hence skillful management of the operating rooms can have a large impact on the overall revenue of a hospital. Belien and Demeulemeester (BD07) describe the planning of operating room (OR) schedules as a multi-stage process. In the first stage OR time is allocated to the hospitals specialties and capacities and resources are adjusted. In the second stage a master surgery schedule (MSS) is developed, that is a timetable for D days that specifies the amount of OR time assigned to the specialties on every individual day. After D days this schedule will be repeated without any changes. Hence, developing an MSS is a long-term problem. Finally, specialties will schedule specific surgeries within their assigned OR time. In this work we will focus on the development of the MSS that maximizes the revenue of the hospital. Our main focus will be to ensure that the capacities of the downstream resources, i.e. the bed capacities in the ICU and ward, will not be exceeded. Additionally, we hope that our formulation of the problem will lead to a leveled bed demand without significant peaks. We will incorporate the uncertainty of patient demand and case mix in our model. There have been several approaches on this subject, for example in (Fü15) and (BD07) and this work is in part in� uenced by these advances. KW - Master Surgery Scheduling KW - Conic Programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69996 ER - TY - CHAP A1 - Mancini, Toni A1 - Mari, Federico A1 - Massini, Annalisa A1 - Melatti, Igor A1 - Salvo, Ivano A1 - Sinisi, Stefano A1 - Tronci, Enrico A1 - Ehrig, Rainald A1 - Röblitz, Susanna A1 - Leeners, Brigitte T1 - Computing Personalised Treatments through In Silico Clinical Trials. A Case Study on Downregulation in Assisted Reproduction T2 - Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion, Workshop of the Federated Logic Conference 2018 (FLoC 2018), Oxford N2 - In Silico Clinical Trials (ISCT), i.e., clinical experimental campaigns carried out by means of computer simulations, hold the promise to decrease time and cost for the safety and efficacy assessment of pharmacological treatments, reduce the need for animal and human testing, and enable precision medicine. In this paper we present a case study aiming at quantifying, by means of a multi-arm ISCT supervised by intelligent search, the potential impact of precision medicine approaches on a real pharmacological treatment, namely the downregulation phase of a complex clinical protocol for assisted reproduction. Y1 - 2018 U6 - https://doi.org/10.29007/g864 SP - 1 EP - 16 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative (Supplementary Material) T2 - Medical Image Analysis N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The shape models and neural networks employed are trained using data of the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets of the SKI10 challenge. For the first time, an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We made the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation. In conclusion, combining statistical anatomical knowledge via SSMs with the localized classification via CNNs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. Y1 - 2019 U6 - https://doi.org/10.12752/4.ATEZ.1.0 N1 - OAI-ZIB dataset VL - 52 IS - 2 SP - 109 EP - 118 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Staude, Isabelle A1 - Burger, Sven A1 - Petschulat, Jörg A1 - Scharf, Toralf A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Design rules for customizable optical materials based on nanocomposites JF - Opt. Mater. Express Y1 - 2018 U6 - https://doi.org/10.1364/OME.8.003456 VL - 8 SP - 3456 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Blanco, Marco A1 - Sauvage, Thibaut T1 - The Cone of Flow Matrices: Approximation Hierarchies and Applications JF - Networks N2 - Let G be a directed acyclic graph with n arcs, a source s and a sink t. We introduce the cone K of flow matrices, which is a polyhedral cone generated by the matrices $\vec{1}_P\vec{1}_P^T\in\RR^{n\times n}$, where $\vec{1}_P\in\RR^n$ is the incidence vector of the (s,t)-path P. We show that several hard flow (or path) optimization problems, that cannot be solved by using the standard arc-representation of a flow, reduce to a linear optimization problem over $\mathcal{K}$. This cone is intractable: we prove that the membership problem associated to $\mathcal{K}$ is NP-complete. However, the affine hull of this cone admits a nice description, and we give an algorithm which computes in polynomial-time the decomposition of a matrix $X\in \operatorname{span} \mathcal{K}$ as a linear combination of some $\vec{1}_P\vec{1}_P^T$'s. Then, we provide two convergent approximation hierarchies, one of them based on a completely positive representation of~K. We illustrate this approach by computing bounds for the quadratic shortest path problem, as well as a maximum flow problem with pairwise arc-capacities. Y1 - 2018 U6 - https://doi.org/10.1002/net.21820 VL - 72 IS - 1 SP - 128 EP - 150 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan A1 - Zschiedrich, Lin T1 - Decomposition of scattered electromagnetic fields into vector spherical wave functions on surfaces with general shapes JF - Phys. Rev. B Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevB.99.045406 VL - 99 SP - 045406 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Lantzsch, Ina A1 - Lindow, Norbert A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Müller-Reichert, Thomas T1 - A switch in microtubule orientation during C. elegans meiosis JF - Current Biology N2 - In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.07.012 SN - 0960-9822 ER - TY - GEN A1 - Redemann, Stefanie A1 - Lantzsch, Ina A1 - Lindow, Norbert A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Müller-Reichert, Thomas T1 - A switch in microtubule orientation during C. elegans meiosis N2 - In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes. T3 - ZIB-Report - 18-34 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69855 SN - 1438-0064 ER - TY - JOUR A1 - Becker, Christiane A1 - Burger, Sven A1 - Barth, Carlo A1 - Manley, Phillip A1 - Jäger, Klaus A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Chabera, Pavel A1 - Chen, Junsheng A1 - Zheng, Kaibo A1 - Pullerits, Tönu T1 - Nanophotonic enhanced two-photon excited photoluminescence of perovskite quantum dots JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.8b01199 VL - 5 SP - 4668 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Santiago, Xavier Garcia A1 - Schneider, Philipp-Immanuel A1 - McPeak, Kevin A1 - Nieto-Vesperinas, Manuel A1 - Burger, Sven T1 - Role of Geometric Shape in Chiral Optics JF - Symmetry Y1 - 2020 U6 - https://doi.org/10.3390/sym12010158 VL - 12 SP - 158 ER - TY - GEN A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph A1 - Sullivan, T. J. T1 - A Shape Trajectories Approach to Longitudinal Statistical Analysis N2 - For Kendall’s shape space we determine analytically Jacobi fields and parallel transport, and compute geodesic regression. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and reduce the computational expense by several orders of magnitude. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As application example we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative. Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data only. T3 - ZIB-Report - 18-42 KW - shape space, shape trajectories, geodesic regression, longitudinal analysis, osteoarthritis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69759 SN - 1438-0064 ER - TY - GEN A1 - Becker, Kai-Helge A1 - Hiller, Benjamin T1 - ASTS Orientations on Undirected Graphs: Structural analysis and enumeration N2 - All feasible flows in potential-driven networks induce an orientation on the undirected graph underlying the network. Clearly, these orientations must satisfy two conditions: they are acyclic and there are no "dead ends" in the network, i.e. each source requires outgoing flows, each sink requires incoming flows, and each transhipment vertex requires both an incoming and an outgoing flow. In this paper we will call orientations that satisfy these conditions acyclic source-transhipment-sink orientations (ASTS-orientation) and study their structure. In particular, we characterize graphs that allow for such an orientation, describe a way to enumerate all possible ASTS-orientations of a given graph, present an algorithm to simplify and decompose a graph before such an enumeration and shed light on the role of zero flows in the context of ASTS-orientations. T3 - ZIB-Report - 18-31 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69632 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Becker, Kai-Helge T1 - Improving relaxations for potential-driven network flow problems via acyclic flow orientations N2 - The class of potential-driven network flow problems provides important models for a range of infrastructure networks. For real-world applications, they need to be combined with integer models for switching certain network elements, giving rise to hard-to-solve MINLPs. We observe that on large-scale real-world meshed networks the usually employed relaxations are rather weak due to cycles in the network. We propose acyclic flow orientations as a combinatorial relaxation of feasible solutions of potential-driven flow problems and show how they can be used to strengthen existing relaxations. First computational results indicate that the strengthend model is much tighter than the original relaxation, thus promising a computational advantage. T3 - ZIB-Report - 18-30 KW - potential-driven network flows KW - acyclic orientations KW - flow orientations KW - MINLPs Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69622 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika A1 - Lindner, Niels T1 - Separation of Cycle Inequalities in Periodic Timetabling N2 - Cycle inequalities play an important role in the polyhedral study of the periodic timetabling problem. We give the first pseudo-polynomial time separation algo- rithm for cycle inequalities, and we give a rigorous proof for the pseudo-polynomial time separability of the change-cycle inequalities. Moreover, we provide several NP-completeness results, indicating that pseudo-polynomial time is best possible. The efficiency of these cutting planes is demonstrated on real-world instances of the periodic timetabling problem. T3 - ZIB-Report - 18-16 KW - Periodic timetabling KW - Cycle inequality KW - Change-cycle inequality Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69746 SN - 1438-0064 ER - TY - GEN A1 - Lenz, Ralf A1 - Becker, Kai-Helge T1 - Optimization of Capacity Expansion in Potential-driven Networks including Multiple Looping - A comparison of modelling approaches N2 - In commodity transport networks such as natural gas, hydrogen and water networks, flows arise from nonlinear potential differences between the nodes, which can be represented by so-called "potential-driven" network models. When operators of these networks face increasing demand or the need to handle more diverse transport situations, they regularly seek to expand the capacity of their network by building new pipelines parallel to existing ones ("looping"). The paper introduces a new mixed-integer non-linear programming (MINLP) model and a new non-linear programming (NLP) model and compares these with existing models for the looping problem and related problems in the literature, both theoretically and experimentally. On this basis, we give recommendations about the circumstances under which a certain model should be used. In particular, it turns out that one of our novel models outperforms the existing models. Moreover, the paper is the first to include the practically relevant option that a particular pipeline may be looped several times. T3 - ZIB-Report - 18-44 KW - OR in energy KW - Network expansion KW - MINLP Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69726 SN - 1438-0064 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization. Y1 - 2019 U6 - https://doi.org/10.1109/TVCG.2018.2864507 VL - 25 IS - 1 SP - 967 EP - 976 ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures N2 - The analysis and visualization of nucleic acids (RNA and DNA) play an increasingly important role due to the growing number of known 3-dimensional structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. For the first time, we present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization. T3 - ZIB-Report - 18-33 KW - ribonucleic acids KW - DNA KW - RNA KW - secondary & tertiary structures KW - interactive rendering KW - ray casting KW - brushing & linking Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69704 SN - 1438-0064 ER - TY - CHAP A1 - Malureanu, Radu A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivinskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei A1 - Mørk, Jesper A1 - Gregersen, Niels T1 - Which Computational Methods Are Good for Analyzing Large Photonic Crystal Membrane Cavities? T2 - 20th International Conference on Transparent Optical Networks (ICTON) Y1 - 2018 U6 - https://doi.org/10.1109/ICTON.2018.8473951 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Liebchen, Christian A1 - Lindner, Niels T1 - A Simple Way to Compute the Number of Vehicles That Are Required to Operate a Periodic Timetable N2 - We consider the following planning problem in public transportation: Given a periodic timetable, how many vehicles are required to operate it? In [9], for this sequential approach, it is proposed to first expand the periodic timetable over time, and then answer the above question by solving a flow-based aperiodic optimization problem. In this contribution we propose to keep the compact periodic representation of the timetable and simply solve a particular perfect matching problem. For practical networks, it is very much likely that the matching problem decomposes into several connected components. Our key observation is that there is no need to change any turnaround decision for the vehicles of a line during the day, as long as the timetable stays exactly the same. T3 - ZIB-Report - 18-38 KW - Vehicle scheduling KW - Periodic timetabling KW - Bipartite matching Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69688 SN - 1438-0064 ER - TY - GEN A1 - Koch, Thorsten A1 - Ceynowa, Klaus A1 - Söllner, Konstanze A1 - Christof, Jürgen A1 - Bertelmann, Roland T1 - DeepGreen – Open Access Transformation Etablierung und Weiterentwicklung rechtssicherer Workflows zur effizienten Umsetzung von Open-Access-Komponenten in Lizenzvereinbarungen für wissenschaftliche Publikationen N2 - Für den geforderten – und von der Deutschen Forschungsgemeinschaft (DFG) geförderten – Open-Access-Transformationsprozess der deutschen, wissenschaftlichen Publikationslandschaft braucht es neue Formen der Zusammenarbeit zwischen Wissenschaft und Verlagen. Bereits seit 2011 wurden mit Unterstützung seitens der DFG in Deutschland die sogenannten Allianz-Lizenzen zwischen Bibliotheken und Verlagen verhandelt, in denen weitreichende Rechte hinsichtlich der Open-Access-Archivierung verankert sind: Autorinnen und Autoren aber auch die sie vertretenden Einrichtungen dürfen Artikel, die in lizenzierten Zeitschriften erschienen sind, ohne oder mit nur kurzer Embargofrist in geeigneten Repositorien ihrer Wahl frei zugänglich machen. Aufbauend auf diese Open-Access-Komponenten zeigt das DFG-geförderte Projekt „DeepGreen“ ein mögliches neues Modell der Zusammenarbeit mit Verlagen auf: DeepGreen setzt auf die automatisierte Verteilung von Artikeldaten von Verlagen an Repositorien und will disziplinübergreifend einen Großteil jener wissenschaftlichen Publikationen aus Fachzeitschriften, die unter lizenzrechtlichen Kontexten frei zugänglich online gehen dürften, auch tatsächlich online abrufbar machen. Erprobte DeepGreen von 2016 bis Ende 2017 prototypisch die Machbarkeit der Zielstellung, will das Projekt in der zweiten Projektphase (2018-2020) den (möglichst stark) automatisierten Workflow gemeinsam mit Verlagen, berechtigten Bibliotheken und anderen Einrichtungen etablieren. Technischer Baustein ist eine zentrale, intermediäre Datenverteilstation, die die automatische und rechtssichere Ablieferung von Metadaten inklusive der Volltexte aus Verlagshand direkt an dazu berechtigte institutionelle Repositorien gewährleistet. Erreicht werden soll ein bundesweiter Service, der auf verbindlichen Absprachen mit Verlagen und Bibliotheken fußt und (zunächst) die Bedingungen der Allianz-Lizenzen umsetzt. Gleichzeitig wird die Übertragbarkeit des DeepGreen-Ansatzes auf weitere Lizenzkontexte (FID-Lizenzen, Konsortiallizenzen, Gold-Open-Access-Vereinbarungen) geprüft. Eine zusätzliche Ausbaustufe stellt die Überlegung zur automatisierten Ablieferung an Fachrepositorien und Forschungsinformationssysteme dar, die ebenfalls geplant wird. Das nationale Projektkonsortium besteht aus den zwei Bibliotheksverbünden Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) und Bibliotheksverbund Bayern (BVB), zwei Universitätsbibliotheken, der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) und der Technische Universität Berlin (TU Berlin), zusätzlich der Bayerischen Staatsbibliothek (BSB) und einer außeruniversitären Forschungseinrichtung - dem Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum (GFZ). Das Folgeprojekt beginnt am 01. August 2018. Hier vorliegend finden Sie den Projektantrag zum Nachlesen. T3 - ZIB-Report - 18-39 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69612 SN - 1438-0064 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Barner, Christoph A1 - Borndörfer, Ralf A1 - Grima, Mickaël A1 - Seeling, Mathes A1 - Spies, Claudia A1 - Wernecke, Klaus T1 - Robust Allocation of Operating Rooms: a Cutting Plane Approach to handle Lognormal Case Durations JF - European Journal of Operational Research N2 - The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. We formulate this problem as a parallel machines scheduling problem, in which job durations follow a lognormal distribution, and a fixed assignment of jobs to machines must be computed. We propose a cutting-plane approach to solve the robust counterpart of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations that identifies worst-case scenarios and generates cut inequalities. The main result of this article uses Hilbert's projective geometry to prove the convergence of this procedure under mild conditions. We also propose two exact solution methods for a similar problem, but with a polyhedral uncertainty set, for which only approximation approaches were known. Our model can be extended to balance the load over several planning periods in a rolling horizon. We present extensive numerical experiments for instances based on real data from a major hospital in Berlin. In particular, we find that: (i) our approach performs well compared to a previous model that ignored the distribution of case durations; (ii) compared to an alternative stochastic programming approach, robust optimization yields solutions that are more robust against uncertainty, at a small price in terms of average cost; (iii) the \emph{longest expected processing time first} (LEPT) heuristic performs well and efficiently protects against extreme scenarios, but only if a good prediction model for the durations is available. Finally, we draw a number of managerial implications from these observations. Y1 - 2018 U6 - https://doi.org/10.1016/j.ejor.2018.05.022 VL - 271 IS - 2 SP - 420 EP - 435 ER - TY - GEN A1 - Hendel, Gregor A1 - Miltenberger, Matthias A1 - Witzig, Jakob T1 - Adaptive Algorithmic Behavior for Solving Mixed Integer Programs Using Bandit Algorithms N2 - State-of-the-art solvers for mixed integer programs (MIP) govern a variety of algorithmic components. Ideally, the solver adaptively learns to concentrate its computational budget on those components that perform well on a particular problem, especially if they are time consuming. We focus on three such algorithms, namely the classes of large neighborhood search and diving heuristics as well as Simplex pricing strategies. For each class we propose a selection strategy that is updated based on the observed runtime behavior, aiming to ultimately select only the best algorithms for a given instance. We review several common strategies for such a selection scenario under uncertainty, also known as Multi Armed Bandit Problem. In order to apply those bandit strategies, we carefully design reward functions to rank and compare each individual heuristic or pricing algorithm within its respective class. Finally, we discuss the computational benefits of using the proposed adaptive selection within the \scip Optimization Suite on publicly available MIP instances. T3 - ZIB-Report - 18-36 KW - mixed integer programming KW - primal heuristics KW - multi armed bandit Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69563 SN - 1438-0064 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Helfmann, Luzie A1 - Zonker, Johannes A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach JF - EPJ Data Science N2 - Human mobility always had a great influence on the spreading of cultural, social and technological ideas. Developing realistic models that allow for a better understanding, prediction and control of such coupled processes has gained a lot of attention in recent years. However, the modeling of spreading processes that happened in ancient times faces the additional challenge that available knowledge and data is often limited and sparse. In this paper, we present a new agent-based model for the spreading of innovations in the ancient world that is governed by human movements. Our model considers the diffusion of innovations on a spatial network that is changing in time, as the agents are changing their positions. Additionally, we propose a novel stochastic simulation approach to produce spatio-temporal realizations of the spreading process that are instructive for studying its dynamical properties and exploring how different influences affect its speed and spatial evolution. Y1 - 2018 U6 - https://doi.org/10.1140/epjds/s13688-018-0153-9 VL - 7 IS - 1 PB - EPJ Data Science ET - EPJ Data Science ER - TY - GEN A1 - Anderson, Lovis A1 - Hiller, Benjamin T1 - A Sweep-Plane Algorithm for the Computation of the Volume of a Union of Polytopes N2 - Optimization models often feature disjunctions of polytopes as submodels. Such a disjunctive set is initially (at best) relaxed to its convex hull, which is then refined by branching. To measure the error of the convex relaxation, the (relative) difference between the volume of the convex hull and the volume of the disjunctive set may be used. This requires a method to compute the volume of the disjunctive set. Naively, this can be done via inclusion/exclusion and leveraging the existing code for the volume of polytopes. However, this is often inefficient. We propose a revised variant of an old algorithm by Bieri and Nef (1983) for this purpose. The algorithm uses a sweep-plane to incrementally calculate the volume of the disjunctive set as a function of the offset parameter of the sweep-plane. T3 - ZIB-Report - 18-37 KW - Disjunctive Programming KW - Volume Algorithm KW - Union of Polytopes Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69489 SN - 1438-0064 ER - TY - GEN A1 - Schweiger, Jonas T1 - Exploiting structure in non-convex quadratic optimization N2 - The amazing success of computational mathematical optimization over the last decades has been driven more by insights into mathematical structures than by the advance of computing technology. In this vein, we address applications, where nonconvexity in the model poses principal difficulties. This paper summarizes the dissertation of Jonas Schweiger for the occasion of the GOR dissertation award 2018. We focus on the work on non-convex quadratic programs and show how problem specific structure can be used to obtain tight relaxations and speed up Branch&Bound methods. Both a classic general QP and the Pooling Problem as an important practical application serve as showcases. T3 - ZIB-Report - 18-35 KW - Nonconvexity KW - Quadratic Programming KW - Relaxations KW - Cutting Planes KW - Standard Quadratic Programming KW - Pooling Problem Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69476 SN - 1438-0064 ER - TY - JOUR A1 - Peters-Kottig, Wolfgang T1 - Anwendung von OPUS für Forschungsdaten – das Beispiel eines außeruniversitären Forschungsinstituts JF - o-bib. Das offene Bibliotheksjournal N2 - OPUS wurde als Dokumentenserver konzipiert und ursprünglich nicht für den Nachweis von Forschungsdaten angelegt. Mit vergleichsweise geringem Aufwand können dennoch Forschungsdaten als Supplementary Material zu Zeitschriftenbeiträgen publiziert werden. Auch reine Forschungsdatenpublikationen können via OPUS veröffentlicht werden, selbst wenn die gegenwärtig auf Textpublikationen zugeschnittene Metadatenerfassung weniger gut für die Beschreibung reiner Forschungsdaten geeignet ist. Ein Unterschied zu anderen Systemen und Anwendungsszenarien besteht in der Beschränkung, großvolumige Daten nicht innerhalb von OPUS selbst vorzuhalten. Der für das institutionelle Repository des Zuse-Instituts Berlin konzipierte pragmatische Lösungsansatz ist in OPUS ohne zusätzliche Programmierung umsetzbar und skaliert für beliebig große Forschungsdatensätze. Y1 - 2018 U6 - https://doi.org/10.5282/o-bib/2018h2s79-91 VL - 5 IS - 2 SP - 79 EP - 91 ER - TY - JOUR A1 - Manley, Phillip A1 - Song, Min A1 - Burger, Sven A1 - Schmid, Martina T1 - Efficient determination of bespoke optically active nanoparticle distributions JF - J. Opt. Y1 - 2018 U6 - https://doi.org/10.1088/2040-8986/aad114 VL - 20 SP - 085003 ER - TY - JOUR A1 - Dibak, Manuel A1 - J. del Razo, Mauricio A1 - De Sancho, David A1 - Schütte, Christof A1 - Noé, Frank T1 - MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations JF - Journal of Chemical Physics N2 - Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B <--> C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported. Y1 - 2018 U6 - https://doi.org/10.1063/1.5020294 VL - 148 IS - 214107 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms JF - Journal of Statistical Physics N2 - In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these nonequilibrium theorems using mathematical arguments, therefore enabling further investigations in the mathematical community. On the numerical side, variance reduction approaches such as importance sampling method are studied in order to compute free energy differences based on Jarzynski's equality. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-019-02286-4 VL - 175 IS - 6 SP - 1214 EP - 1261 ER - TY - CHAP A1 - Lindow, Norbert A1 - Redemann, Stefanie A1 - Brünig, Florian A1 - Fabig, Gunar A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Quantification of three-dimensional spindle architecture T2 - Methods in Cell Biology Part B N2 - Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms. Y1 - 2018 U6 - https://doi.org/10.1016/bs.mcb.2018.03.012 SN - 0091-679X VL - 145 SP - 45 EP - 64 PB - Academic Press ER - TY - GEN A1 - Gleixner, Ambros A1 - Bastubbe, Michael A1 - Eifler, Leon A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schlösser, Franziska A1 - Schubert, Christoph A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Viernickel, Jan Merlin A1 - Walter, Matthias A1 - Wegscheider, Fabian A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 6.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 6.0 of the SCIP Optimization Suite. Besides performance improvements of the MIP and MINLP core achieved by new primal heuristics and a new selection criterion for cutting planes, one focus of this release are decomposition algorithms. Both SCIP and the automatic decomposition solver GCG now include advanced functionality for performing Benders’ decomposition in a generic framework. GCG’s detection loop for structured matrices and the coordination of pricing routines for Dantzig-Wolfe decomposition has been significantly revised for greater flexibility. Two SCIP extensions have been added to solve the recursive circle packing problem by a problem-specific column generation scheme and to demonstrate the use of the new Benders’ framework for stochastic capacitated facility location. Last, not least, the report presents updates and additions to the other components and extensions of the SCIP Optimization Suite: the LP solver SoPlex, the modeling language Zimpl, the parallelization framework UG, the Steiner tree solver SCIP-Jack, and the mixed-integer semidefinite programming solver SCIP-SDP. T3 - ZIB-Report - 18-26 KW - constraint integer programming KW - linear programming KW - mixed-integer linear programming KW - mixed-integer nonlinear programming KW - optimization solver KW - branch-and-cut KW - branch-and-price KW - column generation framework KW - parallelization KW - mixed-integer semidefinite programming KW - Steiner tree optimization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69361 SN - 1438-0064 ER - TY - CHAP A1 - Teymur, Onur A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Calderhead, Ben T1 - Implicit probabilistic integrators for ODEs T2 - Advances in Neural Information Processing Systems 31 (NIPS 2018) Y1 - 2018 UR - http://papers.nips.cc/paper/7955-implicit-probabilistic-integrators-for-odes ER - TY - GEN A1 - Tesch, Alexander T1 - Improving Energetic Propagations for Cumulative Scheduling N2 - We consider the Cumulative Scheduling Problem (CuSP) in which a set of $n$ jobs must be scheduled according to release dates, due dates and cumulative resource constraints. In constraint programming, the CuSP is modeled as the cumulative constraint. Among the most common propagation algorithms for the CuSP there is energetic reasoning (Baptiste et al., 1999) with a complexity of O(n^3) and edge-finding (Vilim, 2009) with O(kn log n) where k <= n is the number of different resource demands. We consider the complete versions of the propagators that perform all deductions in one call of the algorithm. In this paper, we introduce the energetic edge-finding rule that is a generalization of both energetic reasoning and edge-finding. Our main result is a complete energetic edge-finding algorithm with a complexity of O(n^2 log n) which improves upon the complexity of energetic reasoning. Moreover, we show that a relaxation of energetic edge-finding with a complexity of O(n^2) subsumes edge-finding while performing stronger propagations from energetic reasoning. A further result shows that energetic edge-finding reaches its fixpoint in strongly polynomial time. Our main insight is that energetic schedules can be interpreted as a single machine scheduling problem from which we deduce a monotonicity property that is exploited in the algorithms. Hence, our algorithms improve upon the strength and the complexity of energetic reasoning and edge-finding whose complexity status seemed widely untouchable for the last decades. T3 - ZIB-Report - 18-29 KW - Cumulative Scheduling KW - Constraint Programming KW - Propagation Algorithm Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69331 SN - 1438-0064 ER - TY - JOUR A1 - Reuter, Bernhard A1 - Weber, Marcus A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Garcia, Martin E. T1 - Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field JF - Journal of Chemical Theory and Computation N2 - Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems. To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid β (1−40) peptide, periodically driven by an oscillating electric field. Y1 - 2018 U6 - https://doi.org/10.1021/acs.jctc.8b00079 VL - 14 IS - 7 SP - 3579 EP - 3594 ER - TY - CHAP A1 - Tesch, Alexander T1 - Improving Energetic Propagations for Cumulative Scheduling T2 - Principles and Practice of Constraint Programming (CP 2018) N2 - We consider the Cumulative Scheduling Problem (CuSP) in which a set of $n$ jobs must be scheduled according to release dates, due dates and cumulative resource constraints. In constraint programming, the CuSP is modeled as the cumulative constraint. Among the most common propagation algorithms for the CuSP there is energetic reasoning (Baptiste et al., 1999) with a complexity of O(n^3) and edge-finding (Vilim, 2009) with O(kn log n) where k <= n is the number of different resource demands. We consider the complete versions of the propagators that perform all deductions in one call of the algorithm. In this paper, we introduce the energetic edge-finding rule that is a generalization of both energetic reasoning and edge-finding. Our main result is a complete energetic edge-finding algorithm with a complexity of O(n^2 log n) which improves upon the complexity of energetic reasoning. Moreover, we show that a relaxation of energetic edge-finding with a complexity of O(n^2) subsumes edge-finding while performing stronger propagations from energetic reasoning. A further result shows that energetic edge-finding reaches its fixpoint in strongly polynomial time. Our main insight is that energetic schedules can be interpreted as a single machine scheduling problem from which we deduce a monotonicity property that is exploited in the algorithms. Hence, our algorithms improve upon the strength and the complexity of energetic reasoning and edge-finding whose complexity status seemed widely untouchable for the last decades. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69321 ER - TY - CHAP A1 - Scheffler, Daniel A1 - Sips, Mike A1 - Behling, Robert A1 - Dransch, Doris A1 - Eggert, Daniel A1 - Fajerski, Jan A1 - Freytag, Johann-Christoph A1 - Griffiths, Patrick A1 - Hollstein, André A1 - Hostert, Patrick A1 - Köthur, Patrick A1 - Peters, Mathias A1 - Pflugmacher, Dirk A1 - Rabe, Andreas A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Segel, Karl T1 - Geomultisens – a common automatic processing and analysis system for multi-sensor satellite data T2 - Advancing Horizons for Land Cover Services Entering the Big Data Era, Second joint Workshop of the EARSeL Special Interest Group on Land Use & Land Cover and the NASA LCLUC Program Y1 - 2016 SP - 18 EP - 19 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Bartz, Gerald T1 - The Graph Segmentation Problem T2 - INOC 2017 – 8th International Network Optimization Conference N2 - We investigate a graph theoretical problem arising in the automatic billing of a network toll. Given a network and a family of user paths, we study the graph segmentation problem (GSP) to cover parts of the user paths by a set of disjoint segments. The GSP is shown to be NP-hard but for special cases it can be solved in polynomial time. We also show that the marginal utility of a segment is bounded. Computational results for real-world instances show that in practice the problem is more amenable than the theoretic bounds suggest. Y1 - 2018 VL - 64 SP - 35 EP - 44 ER - TY - CHAP A1 - Schwartz, Stephan A1 - Borndörfer, Ralf A1 - Balestrieri, Leonardo T1 - On Finding Subpaths With High Demand T2 - Operations Research Proceedings 2017 N2 - We study the problem of finding subpaths with high demand in a given network that is traversed by several users. The demand of a subpath is the number of users who completely cover this subpath during their trip. Especially with large instances, an efficient algorithm for computing all subpaths' demands is necessary. We introduce a path-graph to prevent multiple generations of the same subpath and give a recursive approach to compute the demands of all subpaths. Our runtime analysis shows, that the presented approach compares very well against the theoretical minimum runtime. Y1 - 2018 SP - 355 EP - 360 PB - Springer International Publishing ER - TY - GEN A1 - Schwartz, Stephan A1 - Balestrieri, Leonardo A1 - Borndörfer, Ralf T1 - On Finding Subpaths With High Demand N2 - We study the problem of finding subpaths with high demand in a given network that is traversed by several users. The demand of a subpath is the number of users who completely cover this subpath during their trip. Especially with large instances, an efficient algorithm for computing all subpaths' demands is necessary. We introduce a path-graph to prevent multiple generations of the same subpath and give a recursive approach to compute the demands of all subpaths. Our runtime analysis shows, that the presented approach compares very well against the theoretical minimum runtime. T3 - ZIB-Report - 18-27 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69280 SN - 1438-0064 ER - TY - CHAP A1 - Krämer, Martin A1 - Maggioni, Marta A1 - Tycowicz, Christoph von A1 - Brisson, Nick A1 - Zachow, Stefan A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - Ultra-short echo-time (UTE) imaging of the knee with curved surface reconstruction-based extraction of the patellar tendon T2 - ISMRM (International Society for Magnetic Resonance in Medicine), 26th Annual Meeting 2018, Paris, France N2 - Due to very short T2 relaxation times, imaging of tendons is typically performed using ultra-short echo-time (UTE) acquisition techniques. In this work, we combined an echo-train shifted multi-echo 3D UTE imaging sequence with a 3D curved surface reconstruction to virtually extract the patellar tendon from an acquired 3D UTE dataset. Based on the analysis of the acquired multi-echo data, a T2* relaxation time parameter map was calculated and interpolated to the curved surface of the patellar tendon. Y1 - 2018 ER - TY - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis T2 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data N2 - In molecular structure analysis and visualization, the molecule’s atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius’, that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely. Y1 - 2018 SN - 978-3-03868-061-1 U6 - https://doi.org/10.2312/molva.20181101 PB - The Eurographics Association ER - TY - CHAP A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Kramer, Tobias A1 - Steinke, Thomas T1 - DM-HEOM: A Portable and Scalable Solver-Framework for the Hierarchical Equations of Motion T2 - 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018) N2 - Computing the Hierarchical Equations of Motion (HEOM) is by itself a challenging problem, and so is writing portable production code that runs efficiently on a variety of architectures while scaling from PCs to supercomputers. We combined both challenges to push the boundaries of simulating quantum systems, and to evaluate and improve methodologies for scientific software engineering. Our contributions are threefold: We present the first distributed memory implementation of the HEOM method (DM-HEOM), we describe an interdisciplinary development workflow, and we provide guidelines and experiences for designing distributed, performance-portable HPC applications with MPI-3, OpenCL and other state-of-the-art programming models. We evaluated the resulting code on multi- and many-core CPUs as well as GPUs, and demonstrate scalability on a Cray XC40 supercomputer for the PS I molecular light harvesting complex. Y1 - 2018 SN - 978-1-5386-5555-9 U6 - https://doi.org/10.1109/IPDPSW.2018.00149 N1 - Best Paper Award SP - 947 EP - 956 ER - TY - GEN A1 - Scheffler, Daniel A1 - Sips, Mike A1 - Behling, Robert A1 - Dransch, Doris A1 - Eggert, Daniel A1 - Fajerski, Jan A1 - Freytag, Johann-Christoph A1 - Griffiths, Patrick A1 - Hollstein, André A1 - Hostert, Patrick A1 - Köthur, Patrick A1 - Peters, Mathias A1 - Pflugmacher, Dirk A1 - Rabe, Andreas A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Segel, Karl T1 - GeoMultiSens – Scalable Multisensoral Analysis of Satellite Remote Sensing Data T2 - ESA Living Planet Symposium, EO Open Science Posters Y1 - 2016 ER - TY - GEN A1 - Seblany, Feda A1 - Homberg, Ulrike A1 - Vincens, Eric A1 - Winkler, Paul A1 - Witt, Karl Josef T1 - Merging criteria for defining pores and constrictions in numerical packing of spheres N2 - The void space of granular materials is generally divided into larger local volumes denoted as pores and throats connecting pores. The smallest section in a throat is usually denoted as constriction. A correct description of pores and constrictions may help to understand the processes related to the transport of fluid or fine particles through granular materials, or to build models of imbibition for unsaturated granular media. In the case of numerical granular materials involving packings of spheres, different methods can be used to compute the pore space properties. However, these methods generally induce an over-segmentation of the pore network and a merging step is usually applied to mitigate such undesirable artifacts even if a precise delineation of a pore is somewhat subjective. This study provides a comparison between different merging criteria for pores in packing of spheres and a discussion about their implication on both the pore size distribution and the constriction size distribution of the material. A correspondence between these merging techniques is eventually proposed as a guide for the user. T3 - ZIB-Report - 18-25 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69158 SN - 1438-0064 ER - TY - JOUR A1 - Seblany, Feda A1 - Homberg, Ulrike A1 - Vincens, Eric A1 - Winkler, Paul A1 - Witt, Karl Josef T1 - Merging criteria for defining pores and constrictions in numerical packing of spheres JF - Granular Matter N2 - The void space of granular materials is generally divided into larger local volumes denoted as pores and throats connecting pores. The smallest section in a throat is usually denoted as constriction. A correct description of pores and constrictions may help to understand the processes related to the transport of fluid or fine particles through granular materials, or to build models of imbibition for unsaturated granular media. In the case of numerical granular materials involving packings of spheres, different methods can be used to compute the pore space properties. However, these methods generally induce an over-segmentation of the pore network and a merging step is usually applied to mitigate such undesirable artifacts even if a precise delineation of a pore is somewhat subjective. This study provides a comparison between different merging criteria for pores in packing of spheres and a discussion about their implication on both the pore size distribution and the constriction size distribution of the material. A correspondence between these merging techniques is eventually proposed as a guide for the user. Y1 - 2018 U6 - https://doi.org/10.1007/s10035-018-0808-z SN - 1434-5021 SN - 1434-7636 VL - 20 IS - 37 PB - Springer Berlin Heidelberg ER - TY - GEN A1 - Sahu, Manish A1 - Dill, Sabrina A1 - Mukhopadyay, Anirban A1 - Zachow, Stefan T1 - Surgical Tool Presence Detection for Cataract Procedures N2 - This article outlines the submission to the CATARACTS challenge for automatic tool presence detection [1]. Our approach for this multi-label classification problem comprises labelset-based sampling, a CNN architecture and temporal smothing as described in [3], which we call ZIB-Res-TS. T3 - ZIB-Report - 18-28 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69110 SN - 1438-0064 ER - TY - CHAP A1 - Grewe, Carl Martin A1 - le Roux, Gabriel A1 - Pilz, Sven-Kristofer A1 - Zachow, Stefan T1 - Spotting the Details: The Various Facets of Facial Expressions T2 - IEEE International Conference on Automatic Face and Gesture Recognition Y1 - 2018 U6 - https://doi.org/10.1109/FG.2018.00049 SP - 286 EP - 293 ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Polthier, Konrad T1 - De Casteljau's Algotithm on Manifolds JF - Computer Aided Geometric Design N2 - This paper proposes a generalization of the ordinary de Casteljau algorithm to manifold-valued data including an important special case which uses the exponential map of a symmetric space or Riemannian manifold. We investigate some basic properties of the corresponding Bézier curves and present applications to curve design on polyhedra and implicit surfaces as well as motion of rigid body and positive definite matrices. Moreover, we apply our approach to construct canal and developable surfaces. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69096 VL - 30 IS - 7 SP - 722 EP - 732 PB - CAGD ER - TY - THES A1 - Breitbach, Paula T1 - Molecular Binding Kinetics of CYP P450 by Using the Infinitesimal Generator Approach Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69076 ER - TY - JOUR A1 - Seibert, Felix A1 - Peters, Mathias A1 - Schintke, Florian T1 - Improving I/O Performance Through Colocating Interrelated Input Data and Near-Optimal Load Balancing JF - Proceedings of the IPDPSW; Fourth IEEE International Workshop on High-Performance Big Data, Deep Learning, and Cloud Computing (HPBDC) N2 - Most distributed file systems assign new files to storage servers randomly. While working well in some situations, this does not help to optimize the input performance for most MapReduce computations’ data access patterns. In this work, we consider an access pattern where input files are partitioned into groups of heterogeneous size. Each group is accessed by exactly one process. We design and implement a data placement strategy that places these file groups together on the same storage server. This colocation approach is combined with near-optimal storage load balancing. To do so, we use a classical scheduling approximation algorithm to solve the NP hard group assignment problem. We argue that local processing is not only beneficial because of reduced network traffic, but especially because it imposes an even resource schedule. Our experiments, based on the parallel processing of remote sensing images, reveal an enormous reduction of network traffic and up to 39 % faster input read times. Further, simulations show that our approximate assignments limit storage server imbalances to less than 5 % above the theoretical minimum, in contrast to more than 85 % with random assignment. Y1 - 2018 U6 - https://doi.org/10.1109/IPDPSW.2018.00081 N1 - Best Paper Award VL - 2018 SP - 448 EP - 457 ER - TY - JOUR A1 - Weber, Marcus T1 - Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung JF - KA Korrespondenz Abwasser, Abfall Y1 - 2018 ER - TY - JOUR A1 - Spahn, Viola A1 - Del Vecchio, Giovanna A1 - Rodriguez-Gaztelumendi, Antonio A1 - Temp, Julia A1 - Labuz, Dominika A1 - Kloner, Michael A1 - Reidelbach, Marco A1 - Machelska, Halina A1 - Weber, Marcus A1 - Stein, Christoph T1 - Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist JF - Scientific Reports N2 - Novel pain killers without adverse effects are urgently needed. Y1 - 2018 VL - 8 SP - 8965 PB - Springer Nature ER - TY - JOUR A1 - Wagner, Sabine A1 - Zapata, Carlos A1 - Wan, Wei A1 - Gawlitza, Kornelia A1 - Weber, Marcus A1 - Rurack, Knut T1 - Role of Counterions in Molecularly Imprinted Polymers for Anionic Species JF - Langmuir N2 - Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-L/D-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme–substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development. Y1 - 2018 U6 - https://doi.org/10.1021/acs.langmuir.8b00500 VL - 34 IS - 23 SP - 6963 EP - 6975 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Zschiedrich, Lin A1 - Weiser, Martin A1 - Burger, Sven T1 - Solving inverse problems appearing in design and metrology of diffractive optical elements by using Bayesian optimization JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2315468 VL - 10694 SP - 1069407 ER - TY - THES A1 - Kammeyer, Alexander T1 - Radix sort for massively parallel hardware: a multi-GPU implementation N2 - Computers, servers and supercomputers with more than one GPU become more and more common. To fully utilize such systems the application needs to be aware of the additional GPUs. E.g., computational workload needs to be distributed across the GPUs. Along with that goes data movement as well as communication. Recently, NVIDIA introduced new features, Unified Memory and Cooperative Groups, that enable programmers to extend their applications with multi-GPU capabilities. In this thesis the aforementioned features are presented in detail and evaluated in the context of the GPU molecular dynamics simulation HAL's MD package on the latest NVIDIA GPU architecture Pascal. A hotspot analysis with the NVIDIA Visual Profiler identified the radix sort as a major hotspot within HAL's MD package. This thesis presents an approach towards a multi-GPU implementation of radix sort. The individual kernels are analysed and an implementation is discussed. Then, the radix sort is transformed into a multi-GPU implementation kernel per kernel. For each step the individual runtime measurements and bottlenecks are presented to analyse the approach. A general sequence diagram of the implementation shows how the individual parts interact with each other. The outlook discusses the further development of HAL's MD package, especially the force computation for multi-GPU which has not been covered in this thesis. N2 - Computer, Server und Supercomputer mit mehr als einer GPU sind immer häufiger zu finden. Um solche Systeme komplett ausnutzen zu können, müssen Anwendung für die Verwendung mehrerer GPUs angepasst werden. Z.B. müssen die Berechnungen zwischen den GPUs verteilt werden. Damit einher gehen die Kommunikation zwischen den GPUs sowie der Austausch der Daten. Mit Unified Memory und Cooperative Groups hat NVIDIA zwei neue Funktionen vorgestellt, damit Programmierer ihre Anwendungen einfach an Multi-GPU Systeme anpassen können. Im Rahmen dieser Arbeit werden die oben genannten Funktionen im Detail vorgestellt und anhand der Molekulardynamiksimulation HAL's MD package auf der neuesten NVIDIA GPU Architektur Pascal evaluiert. Eine Hotspot Analyse von HAL's MD package mit dem NVIDIA Visual Profiler hat den Radix Sort als einen großen Hotspot identifiziert. Daher stellt diese Arbeit eine Multi-GPU Implementierung für Radix Sort vor. Dabei werden die einzelnen Kernel Schritt für Schritt vorgestellt und ihre Implementierung, insbesondere Laufzeiten und Probleme bei der Umsetzung, im Detail diskutiert. Ein Sequenzdiagramm der einzelnen Teile von Radix Sort zeigt dabei, wie die einzelnen Teile in der Multi-GPU Implementierung zusammenarbeiten. Abschließend wird, ausgehend von den Ergebnissen, die zukünftige Entwicklung von HAL's MD package unter besonderen Berücksichtigung einer vollständigen Multi-GPU Molekulardynamiksimulation betrachtet. Y1 - 2018 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reimers, Jeffrey R. A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Yin, Shiwei T1 - Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM JF - Chemical Physics N2 - We analyze the exciton dynamics in PhotosystemI from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Foerster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results. Y1 - 2018 U6 - https://doi.org/10.1016/j.chemphys.2018.05.028 VL - 515 SP - 262 EP - 271 PB - Elsevier B.V. ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM) JF - Journal of Computational Chemistry N2 - Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes. Y1 - 2018 U6 - https://doi.org/doi:10.1002/jcc.25354 VL - 39 IS - 22 SP - 1779 EP - 1794 PB - Wiley Periodicals, Inc. ER - TY - GEN A1 - Streubel, Tom A1 - Tischendorf, Caren A1 - Griewank, Andreas T1 - Piecewise Polynomial Taylor Expansions – The Generalization of Faà di Bruno’s Formula N2 - We present an extension of Taylor’s theorem towards nonsmooth evalua- tion procedures incorporating absolute value operaions. Evaluations procedures are computer programs of mathematical functions in closed form expression and al- low a different treatment of smooth operations and calls to the absolute value value function. The well known classical Theorem of Taylor defines polynomial approx- imation of sufficiently smooth functions and is widely used for the derivation and analysis of numerical integrators for systems of ordinary differential or differential algebraic equations, for the construction of solvers for the continuous nonlinear op- timization of finite dimensional objective functions and for root solving of nonlinear systems of equations. The herein provided proof is construtive and allow efficiently designed algorithms for the execution and computation of generalized piecewise polynomial expansions. As a demonstration we will derive a k-step method on the basis of polynomial interpolation and the proposed generalized expansions. T3 - ZIB-Report - 18-24 KW - generalized Taylor expansion KW - implicit generation of splines KW - nonsmooth integration of differential algebraic equations (DAE and ODE) KW - multistep methods KW - generalized hermite interpolation KW - algorithmic piecewise differentiation (AD and APD) KW - evaluation procedures KW - treating absolute values (abs, max and min) Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68859 SN - 1438-0064 ER - TY - JOUR A1 - Abebe, Muluneh G. A1 - Abass, Aimi A1 - Gomard, Guillaume A1 - Zschiedrich, Lin A1 - Lemmer, Uli A1 - Richards, Bryce S. A1 - Rockstuhl, Carsten A1 - Paetzold, Ulrich W. T1 - Rigorous wave-optical treatment of photon recycling in thermodynamics of photovoltaics: Perovskite thin-film solar cells JF - Phys. Rev. B Y1 - 2018 U6 - https://doi.org/10.1103/PhysRevB.98.075141 VL - 98 SP - 075141 ER - TY - JOUR A1 - Jäger, Klaus A1 - Manley, Phillip A1 - Chen, Duote A1 - Tockhorn, Philipp A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Antireflective nanotextures for monolithic perovskite-silicon tandem solar cells JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2306142 VL - 10688 SP - 106880A ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Binkowski, Felix A1 - Gutsche, Philipp A1 - Höhne, Theresa A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Light Management for Engineering Luminescence in Nanoscale Environments By Numerical Optimization T2 - The Electrochemical Society, Meeting Abstracts Y1 - 2018 U6 - https://doi.org/10.1149/MA2018-01/16/1164 SN - 2151-2043 VL - 16 SP - 1164 ER - TY - CHAP A1 - Gregersen, Niels A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Ivinskaya, Aliaksandra A1 - Lavrinenko, Andrei A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Häyrynen, Teppo A1 - Mørk, Jesper T1 - Benchmarking state-of-the-art optical simulation methods for analyzing large nanophotonic structures T2 - XXVI International Workshop on Optical Wave & Waveguide Theory and Numerical Modelling, Proceedings Y1 - 2018 SN - 978-3-921823-98-9 SP - 9 ER - TY - CHAP A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Santiago, Xavier Garcia A1 - Burger, Sven T1 - Optimization of quantum optical devices with machine learning T2 - XXVI International Workshop on Optical Wave & Waveguide Theory and Numerical Modelling, Proceedings Y1 - 2018 SN - 978-3-921823-98-9 SP - 6 ER - TY - CHAP A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Analysis of light-matter interaction of optical sources with dispersive nanoresonators via contour integration T2 - XXVI International Workshop on Optical Wave & Waveguide Theory and Numerical Modelling, Proceedings Y1 - 2018 SN - 978-3-921823-98-9 SP - 40 ER - TY - JOUR A1 - Höhne, Theresa A1 - Zschiedrich, Lin A1 - Haghighi, Nasibeh A1 - Lott, James A. A1 - Burger, Sven T1 - Validation of quasi-normal modes and of constant-flux modes for computing fundamental resonances of VCSELs JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2307200 VL - 10682 SP - 106821U ER - TY - JOUR A1 - Gregersen, Niels A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivinskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei T1 - Benchmarking state-of-the-art numerical simulation techniques for analyzing large photonic crystal membrane line defect cavities JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2304338 VL - 10672 SP - 106721C ER - TY - JOUR A1 - Castagna, Natascia A1 - Morel, Jacques A1 - Testa, Luc A1 - Burger, Sven T1 - Modelling of standard and specialty fibre-based systems using finite element methods JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2307372 VL - 10683 SP - 1068336 ER - TY - JOUR A1 - Shpak, Maksim A1 - Burger, Sven A1 - Byman, Ville A1 - Saastamoinen, Kimmo A1 - Haapalainen, Mertsi A1 - Lassila, Antti T1 - Online measurement of optical fibre geometry during manufacturing JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2314762 VL - 10683 SP - 1068318 ER - TY - THES A1 - von Lindheim, Johannes T1 - On Intrinsic Dimension Estimation and Minimal Diffusion Maps Embeddings of Point Clouds Y1 - 2018 UR - http://www.zib.de/ext-data/manifold-learning/ ER - TY - GEN A1 - Ralphs, Ted A1 - Shinano, Yuji A1 - Berthold, Timo A1 - Koch, Thorsten ED - Hamadi, Youssef T1 - Parallel Solvers for Mixed Integer Linear Optimization T2 - Handbook of Parallel Constraint Reasoning Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-63516-3_8 SP - 283 EP - 336 PB - Springer Nature ER - TY - CHAP A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative T2 - Medical Imaging with Deep Learning N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging, that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The method is evaluated on data of the MICCAI grand challenge "Segmentation of Knee Images 2010". For the first time an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy. In conclusion, combining of anatomical knowledge using SSMs with localized classification via CNNs results in a state-of-the-art segmentation method. Y1 - 2018 ER - TY - GEN A1 - Ciccotti, Giovanni A1 - Ferrario, Mauro A1 - Schütte, Christof T1 - Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? T2 - Special Issue: Understanding Molecular Dynamics via Stochastic Processes, Entropy Y1 - 2018 U6 - https://doi.org/10.3390/e20050348 VL - 20 IS - 5 ER - TY - GEN A1 - Hasenfelder, Richard A1 - Lehmann, Lutz A1 - Radons, Manuel A1 - Streubel, Tom A1 - Strohm, Christian A1 - Griewank, Andreas T1 - Computational aspects of the Generalized Trapezoidal Rule N2 - In this article we analyze a generalized trapezoidal rule for initial value problems with piecewise smooth right hand side F:IR^n -> IR^n. When applied to such a problem, the classical trapezoidal rule suffers from a loss of accuracy if the solution trajectory intersects a non-differentiability of F. In such a situation the investigated generalized trapezoidal rule achieves a higher convergence order than the classical method. While the asymptotic behavior of the generalized method was investigated in a previous work, in the present article we develop the algorithmic structure for efficient implementation strategies and estimate the actual computational cost of the latter. Moreover, energy preservation of the generalized trapezoidal rule is proved for Hamiltonian systems with piecewise linear right hand side. T3 - ZIB-Report - 18-23 KW - Algorithmic Differentiation KW - Automatic Differentiation KW - Lipschitz Continuity KW - Piecewise Linearization KW - Nonsmooth KW - Trapezoidal Rule KW - Implementation KW - Computational Cost Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68615 SN - 1438-0064 ER - TY - JOUR A1 - Srocka, Nicole A1 - Musiał, Anna A1 - Schneider, Philipp-Immanuel A1 - Mrowiński, Paweł A1 - Holewa, Paweł A1 - Burger, Sven A1 - Quandt, David A1 - Strittmatter, André A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Sęk, Grzegorz T1 - Enhanced photon-extraction efficiency from InGaAs/GaAs quantum dots in deterministic photonic structures at 1.3 μm fabricated by in-situ electron-beam lithography JF - AIP Adv. Y1 - 2018 U6 - https://doi.org/10.1063/1.5038137 VL - 8 SP - 085205 ER - TY - JOUR A1 - Spötter, Andreas A1 - Gupta, Pooja A1 - Nürnberg, A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica) N2 - Honey bees are exposed to a number of damaging pathogens and parasites. The most destructive among them, affecting mainly the brood, is Varroa destructor. A promising approach to prevent its spread is to breed for Varroa‐tolerant honey bees. A trait that has been shown to provide significant resistance against the Varroa mite is hygienic behaviour, a behavioural response of honey bee workers to brood diseases in general. This study reports the development of a 44K SNP assay, specifically designed for the analysis of hygienic behaviour of individual worker bees (Apis mellifera carnica) directed against V. destructor. Initially, 70 000 SNPs chosen from a large set of SNPs published by the Honey Bee Genome Project were validated for their suitability in the analysis of the Varroa resistance trait ‘uncapping of Varroa‐infested brood’. This was achieved by genotyping of pooled DNA samples of trait bearers and two trait‐negative controls using next‐generation sequencing. Approximately 36 000 of these validated SNPs and another 8000 SNPs not validated in this study were selected for the construction of a SNP assay. This assay will be employed in following experiments to analyse individualized DNA samples in order to identify quantitative trait loci (QTL) involved in the control of the investigated trait and to evaluate and possibly confirm QTL found in other studies. However, this assay is not just suitable to study Varroa tolerance, it is as well applicable to analyse any other trait in honey bees. In addition, because of its high density, this assay provides access into genomic selection with respect to several traits considered in honey bee breeding. It will become publicly available via AROS Applied Biotechnology AS, Aarhus, Denmark, before the end of the year 2011. Y1 - 2012 U6 - https://doi.org/10.1111/j.1755-0998.2011.03106.x VL - 12 IS - 2 SP - 323 EP - 332 ER - TY - JOUR A1 - Weiser, Martin A1 - Freytag, Yvonne A1 - Erdmann, Bodo A1 - Hubig, Michael A1 - Mall, Gita T1 - Optimal Design of Experiments for Estimating the Time of Death in Forensic Medicine JF - Inverse Problems N2 - Estimation of time of death based on a single measurement of body core temperature is a standard procedure in forensic medicine. Mechanistic models using simulation of heat transport promise higher accuracy than established phenomenological models in particular in nonstandard situations, but involve many not exactly known physical parameters. Identifying both time of death and physical parameters from multiple temperature measurements is one possibility to reduce the uncertainty significantly. In this paper, we consider the inverse problem in a Bayesian setting and perform both local and sampling-based uncertainty quantification, where proper orthogonal decomposition is used as model reduction for fast solution of the forward model. Based on the local uncertainty quantification, optimal design of experiments is performed in order to minimize the uncertainty in the time of death estimate for a given number of measurements. For reasons of practicability, temperature acquisition points are selected from a set of candidates in different spatial and temporal locations. Applied to a real corpse model, a significant accuracy improvement is obtained already with a small number of measurements. Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aae7a5 VL - 34 IS - 12 SP - 125005 ER - TY - GEN A1 - Tesch, Alexander T1 - A Polyhedral Study of Event-Based Models for the Resource-Constrained Project Scheduling Problem N2 - We consider event-based Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP) that represent an alternative to the common time-indexed model (DDT) of Pritsker et al. (1969) for the case where the underlying time horizon is large or job processing times are subject to huge variations. In contrast to the time-indexed model, the size of event-based models does not depend on the time horizon. For two event-based formulations OOE and SEE of Koné et al. (2011) we present new valid inequalities that dominate the original formulation. Additionally, we introduce a new event-based model: the Interval Event-Based Model (IEE). We deduce linear transformations between all three models that yield the strict domination order IEE > SEE > OOE for their linear programming (LP) relaxations, meaning that IEE has the strongest linear relaxation among the event-based models. We further show that the popular DDT formulation can be retrieved from IEE by certain polyhedral operations, thus giving a unifying view on a complete branch of MIP formulations for the RCPSP. In addition, we analyze the computational performance of all presented models on test instances of the PSPLIB (Kolisch and Sprecher 1997). T3 - ZIB-Report - 17-79 KW - Scheduling KW - Mixed-Integer Programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68485 SN - 1438-0064waoa ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis N2 - In molecular structure analysis and visualization, the molecule’s atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius’, that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely. T3 - ZIB-Report - 18-18 KW - molecular dynamics KW - atomic radii KW - cavity analysis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68468 SN - 1438-0064 ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Blanco, Marco A1 - Sauvage, Thibaut T1 - Approximation Hierarchies for the cone of flow matrices T2 - INOC 2017 – 8th International Network Optimization Conference N2 - Let $G$ be a directed acyclic graph with $n$ arcs, a source $s$ and a sink $t$. We introduce the cone $K$ of flow matrices, which is a polyhedral cone generated by the matrices $1_P 1_P^T \in R^{n\times n}$, where $1_P\in R^n$ is the incidence vector of the $(s,t)$-path $P$. Several combinatorial problems reduce to a linear optimization problem over $K$. This cone is intractable, but we provide two convergent approximation hierarchies, one of them based on a completely positive representation of $K$. We illustrate this approach by computing bounds for a maximum flow problem with pairwise arc-capacities. Y1 - 2018 U6 - https://doi.org/10.1016/j.endm.2018.02.002 VL - 64 SP - 275 EP - 284 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Blanco, Marco A1 - Sauvage, Thibaut T1 - Approximation Hierarchies for the cone of flow matrices N2 - Let $G$ be a directed acyclic graph with $n$ arcs, a source $s$ and a sink $t$. We introduce the cone $K$ of flow matrices, which is a polyhedral cone generated by the matrices $1_P 1_P^T \in R^{n\times n}$, where $1_P\in R^n$ is the incidence vector of the $(s,t)$-path $P$. Several combinatorial problems reduce to a linear optimization problem over $K$. This cone is intractable, but we provide two convergent approximation hierarchies, one of them based on a completely positive representation of $K$. We illustrate this approach by computing bounds for a maximum flow problem with pairwise arc-capacities. T3 - ZIB-Report - 18-20 KW - Flows in graphs KW - Approximation hierarchies KW - Copositive programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68424 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Schmidt genannt Waldschmidt, Daniel A1 - Tesch, Alexander T1 - The Price of Fixed Assignments in Stochastic Extensible Bin Packing N2 - We consider the stochastic extensible bin packing problem (SEBP) in which $n$ items of stochastic size are packed into $m$ bins of unit capacity. In contrast to the classical bin packing problem, bins can be extended at extra cost. This problem plays an important role in stochastic environments such as in surgery scheduling: Patients must be assigned to operating rooms beforehand, such that the regular capacity is fully utilized while the amount of overtime is as small as possible. This paper focuses on essential ratios between different classes of policies: First, we consider the price of non-splittability, in which we compare the optimal non-anticipatory policy against the optimal fractional assignment policy. We show that this ratio has a tight upper bound of $2$. Moreover, we develop an analysis of a fixed assignment variant of the LEPT rule yielding a tight approximation ratio of $1+1/e \approx 1.368$ under a reasonable assumption on the distributions of job durations. Furthermore, we prove that the price of fixed assignments, which describes the loss when restricting to fixed assignment policies, is within the same factor. This shows that in some sense, LEPT is the best fixed assignment policy we can hope for. T3 - ZIB-Report - 18-19 KW - Approximation Algorithms KW - Stochastic Scheduling KW - Extensible Bin Packing Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68415 SN - 1438-0064 ER - TY - THES A1 - Herter, Felix T1 - Supervised Classification of Microtubule Ends: An Evaluation of Machine Learning Approaches N2 - Aim of this thesis was to evaluate the performance of three popular machine learning methods – decision trees, support vector machines, and neural networks – on a supervised image classification task from the domain of cell biology. Specifically, the task was to classify microtubule ends in electron tomography images as open or closed. Microtubules are filamentous macromolecules of the cytoskeleton. Distribution of their end types is of interest to cell biologists as it allows to analyze microtubule nucleation sites. Currently classification is done manually by domain experts, which is a difficult task due to the low signal-to-noise ratio and the abundance of microtubules in a single cell. Automating this tedious and error prone task would be beneficial to both efficiency and consistency. Images of microtubule ends were obtained from electron tomography reconstructions of mitotic spindles. As ground truth data for training and testing four independent expert classifications for the same samples from different tomograms were used. Image information around microtubule ends was extracted in various formats for further processing. For all classifiers we considered how the performance varies when different preprocessing techniques (per-feature and per-image standardization) are applied. or decision trees and support vector machines we also evaluated the effect of training on a) imbalanced versus under- and over-sampled data and b) image-based vs feature-based input for specifically designed features. The results show that for decision trees and support vector machines classification on features outperforms classification on images. Both methods give most equalized per-class accuracies when the training data was undersampled and when preprocessed with per-image standardization prior to features extraction. Neural networks gave the best results when no preprocessing was applied. The final decision tree, support vector machine, and neural network obtained accuracies on the test set for (open,closed ) samples of (62%, 72%), (66%, 70%), and (61%, 78%) respectively, when considering all samples where at least one expert assigned a label. Restricting the test set to samples with at least three agreeing expert labels raised these to (78%, 84%), (74%, 92%), and (82%, 88%). It can be observed that many samples misclassified by the algorithms were also difficult to classify for the experts. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68395 ER - TY - GEN A1 - Schwieger, Robert A1 - Siebert, Heike A1 - Röblitz, Susanna T1 - Correspondence of Trap Spaces in Different Models of Bioregulatory Networks N2 - Mathematical models for bioregulatory networks can be based on different formalisms, depending on the quality of available data and the research question to be answered. Discrete boolean models can be constructed based on qualitative data, which are frequently available. On the other hand, continuous models in terms of ordinary differential equations (ODEs) can incorporate time-series data and give more detailed insight into the dynamics of the underlying system. A few years ago, a method based on multivariate polynomial interpolation and Hill functions has been developed for an automatic conversion of boolean models to systems of ordinary differential equations. This method is frequently used by modellers in systems biology today, but there are only a few results available about the conservation of mathematical structures and properties across the formalisms. Here, we consider subsets of the phase space where some components stay fixed, called trap spaces, and demonstrate how boolean trap spaces can be linked to invariant sets in the continuous state space. This knowledge is of practical relevance since finding trap spaces in the boolean setting, which is relatively easy, allows for the construction of reduced ODE models. T3 - ZIB-Report - 18-10 KW - dynamical systems KW - trap spaces KW - attractors KW - invariant sets KW - ordinary differential equations KW - Boolean networks Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67121 SN - 1438-0064 ER - TY - JOUR A1 - Barth, Carlo A1 - Becker, Christiane T1 - Machine learning classification for field distributions of photonic modes JF - Commun. Phys. Y1 - 2018 U6 - https://doi.org/10.1038/s42005-018-0060-1 VL - 1 SP - 58 ER - TY - GEN A1 - Georges, Alexander A1 - Gleixner, Ambros A1 - Gojic, Gorana A1 - Gottwald, Robert Lion A1 - Haley, David A1 - Hendel, Gregor A1 - Matejczyk, Bartlomiej T1 - Feature-Based Algorithm Selection for Mixed Integer Programming N2 - Mixed integer programming is a versatile and valuable optimization tool. However, solving specific problem instances can be computationally demanding even for cutting-edge solvers. Such long running times are often significantly reduced by an appropriate change of the solver's parameters. In this paper we investigate "algorithm selection", the task of choosing among a set of algorithms the ones that are likely to perform best for a particular instance. In our case, we treat different parameter settings of the MIP solver SCIP as different algorithms to choose from. Two peculiarities of the MIP solving process have our special attention. We address the well-known problem of performance variability by using multiple random seeds. Besides solving time, primal dual integrals are recorded as a second performance measure in order to distinguish solvers that timed out. We collected feature and performance data for a large set of publicly available MIP instances. The algorithm selection problem is addressed by several popular, feature-based methods, which have been partly extended for our purpose. Finally, an analysis of the feature space and performance results of the selected algorithms are presented. T3 - ZIB-Report - 18-17 KW - algorithm selection KW - mixed integer programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68362 SN - 1438-0064 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Data-flow scheduling for a scalable FLESnet JF - CBM Progress Report 2017 Y1 - 2018 SN - 978-3-9815227-5-4 U6 - https://doi.org/10.15120/GSI-2018-00485 SP - 130 EP - 131 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Mett, Fabian A1 - Nardin, Antonella A1 - Pulaj, Jonad T1 - Integrating LP-guided variable fixing with MIP heuristics in the robust design of hybrid wired-wireless FTTx access networks JF - Applied Soft Computing N2 - This study investigates how to model and solve the problem of optimally designing FTTx telecommunications access networks integrating wired and wireless technologies, while taking into account the uncertainty of wireless signal propagation. We propose an original robust optimization model for the related robust 3-architecture Connected Facility Location problem, which includes additional variables and constraints to model wireless signal coverage represented through signal-to-interference ratios. Since the resulting robust problem can prove very challenging even for a modern state-of-the art optimization solver, we propose to solve it by an original primal heuristic that combines a probabilistic variable fixing procedure, guided by peculiar Linear Programming relaxations, with a Mixed Integer Programming heuristic, based on an exact very large neighborhood search. A numerical study carried out on a set of realistic instances show that our heuristic can find solutions of much higher quality than a state-of-the-art solver. Y1 - 2017 U6 - https://doi.org/10.1016/j.asoc.2017.07.018 VL - 61 SP - 1074 EP - 1087 ER - TY - THES A1 - Reuther, Markus T1 - Mathematical Optimization of Rolling Stock Rotations N2 - We show how to optimize rolling stock rotations that are required for the operation of a passenger timetable. The underlying mathematical ptimization problem is called rolling stock rotation problem (RSRP) and the leitmotiv of the thesis is RotOR, i.e., a highly integrated optimization algorithm for the RSRP. RotOR is used by DB Fernverkehr AG (DBF) in order to optimize intercity express (ICE) rotations for the European high-speed network. In this application, RSRPs have to be solved which (A) require many different aspects to be simultaneously considered, (B) are typically of large scale, and (C) include constraints that have a difficult combinatorial structure. This thesis suggests answers to these issues via the following concepts. (A) The main model, which RotOR uses, relies on a hypergraph. The hypergraph provides an easy way to model manifold industrial railway requirements in great detail. This includes well known vehicle composition requirements as well as relatively unexplored regularity stipulations. At the same time, the hypergraph directly leads to a mixed-integer programming (MIP) model for the RSRP. (B) The main algorithmic ingredient to solve industrial instances of the RSRP is a coarse-to-fine (C2F) column generation procedure. In this approach, the hypergraph is layered into coarse and fine layers that distinguish different levels of detail of the RSRP. The coarse layers are algorithmically utilized while pricing fine columns until proven optimality. Initially, the C2F approach is presented in terms of pure linear programming in order to provide an interface for other applications. (C) Rolling stock rotations have to comply to resource constraints in order to ensure, e.g., enough maintenance inspections along the rotations. These constraints are computationally hard, but are well known in the literature on the vehicle routing problem (VRP). We define an interface problem in order to bridge between the RSRP and the VRP and derive a straightforward algorithmic concept, namely regional search (RS), from their common features and, moreover, differences. Our RS algorithms show promising results for classical VRPs and RSRPs. In the first part of the thesis we present these concepts, which encompass its main mathematical contribution. The second part explains all modeling and solving components of RotOR that turn out to be essential in its industrial application. The thesis concludes with a solution to a complex re-optimization RSRP that RotOR has computed successfully for DBF. In this application all ICE vehicles of the ICE-W fleets of DBF had to be redirected past a construction site on a high-speed line in the heart of Germany. Y1 - 2017 UR - https://depositonce.tu-berlin.de/handle/11303/6309 ER - TY - GEN A1 - Hiller, Benjamin A1 - Saitenmacher, René A1 - Walther, Tom T1 - Analysis of operating modes of complex compressor stations N2 - We consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. In particular, we propose a refined model that allows to precompute tighter relaxations for each operation mode. These relaxations may be used to strengthen the compressor station submodels in gas network optimization problems. We provide a procedure to obtain the refined model from the input data for the original model. This procedure is based on a nontrivial reduction of the graph representing the gas flow through the compressor station in an operation mode. T3 - ZIB-Report - 17-65 KW - bound tightening KW - flow patterns KW - model reformulation KW - multi-way compressor station Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68179 SN - 1438-0064 ER - TY - THES A1 - Barth, Carlo T1 - Analysis of photonic crystals for interaction with near-surface emitters Y1 - 2018 U6 - https://doi.org/10.14279/depositonce-6880 ER - TY - JOUR A1 - Weber, Tobias A1 - Sager, Sebastian A1 - Gleixner, Ambros T1 - Solving Quadratic Programs to High Precision using Scaled Iterative Refinement JF - Mathematical Programming Computation N2 - Quadratic optimization problems (QPs) are ubiquitous, and solution algorithms have matured to a reliable technology. However, the precision of solutions is usually limited due to the underlying floating-point operations. This may cause inconveniences when solutions are used for rigorous reasoning. We contribute on three levels to overcome this issue. First, we present a novel refinement algorithm to solve QPs to arbitrary precision. It iteratively solves refined QPs, assuming a floating-point QP solver oracle. We prove linear convergence of residuals and primal errors. Second, we provide an efficient implementation, based on SoPlex and qpOASES that is publicly available in source code. Third, we give precise reference solutions for the Maros and Mészáros benchmark library. Y1 - 2019 U6 - https://doi.org/10.1007/s12532-019-00154-6 VL - 11 SP - 421 EP - 455 PB - Springer Berlin Heidelberg ER - TY - GEN A1 - Weber, Tobias A1 - Sager, Sebastian A1 - Gleixner, Ambros T1 - Solving Quadratic Programs to High Precision using Scaled Iterative Refinement N2 - Quadratic optimization problems (QPs) are ubiquitous, and solution algorithms have matured to a reliable technology. However, the precision of solutions is usually limited due to the underlying floating-point operations. This may cause inconveniences when solutions are used for rigorous reasoning. We contribute on three levels to overcome this issue. First, we present a novel refinement algorithm to solve QPs to arbitrary precision. It iteratively solves refined QPs, assuming a floating-point QP solver oracle. We prove linear convergence of residuals and primal errors. Second, we provide an efficient implementation, based on SoPlex and qpOASES that is publicly available in source code. Third, we give precise reference solutions for the Maros and Mészáros benchmark library. T3 - ZIB-Report - 18-04 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68152 SN - 1438-0064 ER - TY - JOUR A1 - Löchner, Franz A1 - Fedotova, Anna A1 - Liu, Sheng A1 - Keeler, Gordon A1 - Peake, Gregory A1 - Saravi, Sina A1 - Shcherbakov, Maxim A1 - Burger, Sven A1 - Fedyanin, Andrey A1 - Brener, Igal A1 - Pertsch, Thomas A1 - Setzpfandt, Frank A1 - Staude, Isabelle T1 - Polarization-Dependent Second Harmonic Diffraction from Resonant GaAs Metasurfaces JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.7b01533 VL - 5 SP - 1786 ER - TY - JOUR A1 - Sullivan, T. J. T1 - Well-posed Bayesian inverse problems and heavy-tailed stable quasi-Banach space priors JF - Inverse Problems and Imaging Y1 - 2017 U6 - https://doi.org/10.3934/ipi.2017040 VL - 11 IS - 5 SP - 857 EP - 874 ER - TY - CHAP A1 - Sullivan, T. J. T1 - Well-posedness of Bayesian inverse problems in quasi-Banach spaces with stable priors T2 - 88th Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM), Weimar 2017 Y1 - 2017 U6 - https://doi.org/10.1002/pamm.201710402 VL - 17 IS - 1 SP - 871 EP - 874 ER - TY - JOUR A1 - Kork, F. A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 SN - 0959-2962 VL - 73 IS - 6 SP - 711 EP - 718 ER - TY - JOUR A1 - Marzban, Forough A1 - Conrad, Tim A1 - Marban, Pouria A1 - Sodoudi, Sahar T1 - Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany JF - International Journal of Advanced Remote Sensing and GIS N2 - Air temperature (Tair or T2m) is an important climatological variable for forest biosphere processes and climate change research. Due to the low density and the uneven distribution of weather stations, traditional ground-based observations cannot accurately capture the spatial distribution of Tair. In this study, Tair in Berlin is estimated during the day and night time over six land cover/land use (LC/LU) types by satellite remote sensing data over a large domain and a relatively long period (7 years). Aqua and Terra MODIS (Moderate Resolution Imaging Spectroradiometer) data and meteorological data for the period from 2007 to 2013 were collected to estimate Tair. Twelve environmental variables (land surface temperature (LST), normalized difference vegetation index (NDVI), Julian day, latitude, longitude, Emissivity31, Emissivity32, altitude, albedo, wind speed, wind direction and air pressure) were selected as predictors. Moreover, a comparison between LST from MODIS Terra and Aqua with daytime and night time air temperatures (Tday, Tnight) was done respectively and in addition, the spatial variability of LST and Tair relationship by applying a varying window size on the MODIS LST grid was examined. An analysis of the relationship between the observed Tair and the spatially averaged remotely sensed LST, indicated that 3 × 3 and 1 × 1 pixel size was the optimal window size for the statistical model estimating Tair from MODIS data during the day and night time, respectively. Three supervised learning methods (Adaptive Neuro Fuzzy Inference system (ANFIS), Artificial Neural Network (ANN) and Support vector machine (SVR)) were used to estimate Tair during the day and night time, and their performances were validated by cross-validation for each LC/LU. Moreover, tuning the hyper parameters of some models like SVR and ANN were investigated. For tuning the hyper parameters of SVR, Simulated Annealing (SA) was applied (SA-SVR model) and a multiple-layer feed-forward (MLF) neural networks with three layers and different nodes in hidden layers are used with Levenber-Marquardt back-propagation (LM-BP), in order to achieve higher accuracy in the estimation of Tair. Results indicated that the ANN model achieved better accuracy (RMSE= 2.16°C, MAE = 1.69°C, R2 = 0.95) than SA_SVR model (RMSE= 2.50°C, MAE = 1.92°C, R2 = 0.91) and ANFIS model (RMSE= 2.88°C, MAE= 2.2°C, R2 = 0.89) over six LC/LU during the day and night time. The Q-Q diagram of SA-SVR, ANFIS and NN show that all three models slightly tended to underestimate and overestimate the extreme and low temperatures for all LC/LU classes during the day and night time. The weak performance in the extreme and low temperatures are a consequence of the small number of data in these temperatures. These satisfactory results indicate that this approach is proper for estimating air temperature and spatial window size is an important factor that should be considered in the estimation of air temperature. KW - ANFIS KW - ANN KW - Cross-validation KW - MODIS KW - Simulated annealing KW - SVR Y1 - 2018 U6 - https://doi.org/10.23953/cloud.ijarsg.337 VL - 7 IS - 1 SP - 2478 EP - 2517 ER - TY - JOUR A1 - Jayrannejad, Fahrnaz A1 - Conrad, Tim T1 - Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining JF - Springer Lecture Notes in Artificial Intelligence N2 - Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set. Y1 - 2017 ER - TY - JOUR A1 - Shao, Borong A1 - Cannistraci, Carlo Vittorio A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data JF - Genomics and Computational Biology N2 - Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type. Y1 - 2017 U6 - https://doi.org/10.18547/gcb.2017.vol3.iss3.e57 VL - 3 IS - 3 SP - e57 ER - TY - JOUR A1 - Rath, Barbara A1 - Conrad, Tim A1 - Myles, Puja A1 - Alchikh, Maren A1 - Ma, Xiaolin A1 - Hoppe, Christian A1 - Tief, Franziska A1 - Chen, Xi A1 - Obermeier, Patrick A1 - Kisler, Bron A1 - Schweiger, Brunhilde T1 - Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials JF - Expert Review of Anti-infective Therapy N2 - Introduction: Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0–18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level. KW - Disease severity KW - influenza-like illness KW - influenza KW - respiratory syncytial virus KW - human metapneumovirus KW - human rhinovirus KW - adenovirus KW - seasonality KW - antivirals KW - clinical trials Y1 - 2017 U6 - https://doi.org/10.1080/14787210.2017.1295847 VL - 15 IS - 6 SP - 545 EP - 568 ER - TY - GEN A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative (Supplementary Material) N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. Y1 - 2018 U6 - https://doi.org/10.12752/4.TMZ.1.0 N1 - Supplementary data to reproduce results from the related publication, including convolutional neural networks' weights. ER - TY - GEN A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. T3 - ZIB-Report - 18-15 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68038 SN - 1438-0064 VL - 26 IS - 5 SP - 680 EP - 688 ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Matsuyama, Kei A1 - Boos, Karin A1 - Färber, Claudia A1 - Kahl, Wolf-Achim A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Soriano, Carmen A1 - Stock, Stuart R. T1 - Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data N2 - During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources. T3 - ZIB-Report - 18-14 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67982 SN - 1438-0064 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Matsuyama, Kei A1 - Boos, Karin A1 - Färber, Claudia A1 - Kahl, Wolf-Achim A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Soriano, Carmen A1 - Stock, Stuart R. T1 - Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data JF - Computers and Geosciences N2 - During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources. Y1 - 2018 U6 - https://doi.org/10.1016/j.cageo.2018.03.007 VL - 115 SP - 75 EP - 87 ER - TY - JOUR A1 - Jin, Eugene Jennifer A1 - Kiral, Ferdi Ridvan A1 - Ozel, Mehmet Neset A1 - Burchardt, Lara Sophie A1 - Osterland, Marc A1 - Epstein, Daniel A1 - Wolfenberg, Heike A1 - Prohaska, Steffen A1 - Hiesinger, Peter Robin T1 - Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals JF - Current Biology N2 - Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains. We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ‘‘hub’’ compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent, whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.02.032 VL - 28 IS - 7 SP - 1027 EP - 1038.e4 ER - TY - CHAP A1 - Schienle, Adam ED - Kliewer, Natalia ED - Ehmke, Jan Fabian ED - Borndörfer, Ralf T1 - Solving the Time-Dependent Shortest Path Problem Using Super-Optimal Wind T2 - Operations Research Proceedings 2017 N2 - Planning efficient routes fast becomes ever more important, especially in the context of aircraft trajectories. As time-dependent wind conditions factor into the shortest path query, we use an artificial wind vector called Super-Optimal Wind as a means of creating a suitable potential function for the A* algorithm, thus speeding up the query. We assess the quality of Super-Optimal Wind both theoretically and computationally, and use Super-Optimal Wind in a real-world instance. Y1 - 2018 PB - Springer CY - Cham ER - TY - JOUR A1 - Oeltze-Jaffra, Steffen A1 - Meuschke, Monique A1 - Neugebauer, Mathias A1 - Saalfeld, Sylvia A1 - Lawonn, Kai A1 - Janiga, Gabor A1 - Hege, Hans-Christian A1 - Zachow, Stefan A1 - Preim, Bernhard T1 - Generation and Visual Exploration of Medical Flow Data: Survey, Research Trends, and Future Challenges JF - Computer Graphics Forum N2 - Simulations and measurements of blood and air flow inside the human circulatory and respiratory system play an increasingly important role in personalized medicine for prevention, diagnosis, and treatment of diseases. This survey focuses on three main application areas. (1) Computational Fluid Dynamics (CFD) simulations of blood flow in cerebral aneurysms assist in predicting the outcome of this pathologic process and of therapeutic interventions. (2) CFD simulations of nasal airflow allow for investigating the effects of obstructions and deformities and provide therapy decision support. (3) 4D Phase-Contrast (4D PC) Magnetic Resonance Imaging (MRI) of aortic hemodynamics supports the diagnosis of various vascular and valve pathologies as well as their treatment. An investigation of the complex and often dynamic simulation and measurement data requires the coupling of sophisticated visualization, interaction, and data analysis techniques. In this paper, we survey the large body of work that has been conducted within this realm. We extend previous surveys by incorporating nasal airflow, addressing the joint investigation of blood flow and vessel wall properties, and providing a more fine-granular taxonomy of the existing techniques. From the survey, we extract major research trends and identify open problems and future challenges. The survey is intended for researchers interested in medical flow but also more general, in the combined visualization of physiology and anatomy, the extraction of features from flow field data and feature-based visualization, the visual comparison of different simulation results, and the interactive visual analysis of the flow field and derived characteristics. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13394 VL - 38 IS - 1 SP - 87 EP - 125 PB - Wiley ER - TY - GEN A1 - Luedtke, James A1 - D'Ambrosio, Claudia A1 - Linderoth, Jeff A1 - Schweiger, Jonas T1 - Strong Convex Nonlinear Relaxations of the Pooling Problem: Extreme Points N2 - We investigate new convex relaxations for the pooling problem, a classic nonconvex production planning problem in which products are mixed in intermediate pools in order to meet quality targets at their destinations. In this technical report, we characterize the extreme points of the convex hull of our non-convex set, and show that they are not finite, i.e., the convex hull is not polyhedral. This analysis was used to derive valid nonlinear convex inequalities and show that, for a specific case, they characterize the convex hull of our set. The new valid inequalities and computational results are presented in ZIB Report 18-12. T3 - ZIB-Report - 18-13 KW - Pooling Problem KW - Relaxation KW - Extreme Points Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67801 SN - 1438-0064 ER - TY - GEN A1 - Luedtke, James A1 - D'Ambrosio, Claudia A1 - Linderoth, Jeff A1 - Schweiger, Jonas T1 - Strong Convex Nonlinear Relaxations of the Pooling Problem N2 - We investigate new convex relaxations for the pooling problem, a classic nonconvex production planning problem in which input materials are mixed in intermediate pools, with the outputs of these pools further mixed to make output products meeting given attribute percentage requirements. Our relaxations are derived by considering a set which arises from the formulation by considering a single product, a single attibute, and a single pool. The convex hull of the resulting nonconvex set is not polyhedral. We derive valid linear and convex nonlinear inequalities for the convex hull, and demonstrate that different subsets of these inequalities define the convex hull of the nonconvex set in three cases determined by the parameters of the set. Computational results on literature instances and newly created larger test instances demonstrate that the inequalities can significantly strengthen the convex relaxation of the pq-formulation of the pooling problem, which is the relaxation known to have the strongest bound. T3 - ZIB-Report - 18-12 KW - Pooling Problem KW - Relaxation KW - Valid Inequalities Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67824 SN - 1438-0064 ER - TY - GEN A1 - Grewe, Carl Martin A1 - Le Roux, Gabriel A1 - Pilz, Sven-Kristofer A1 - Zachow, Stefan T1 - Spotting the Details: The Various Facets of Facial Expressions N2 - 3D Morphable Models (MM) are a popular tool for analysis and synthesis of facial expressions. They represent plausible variations in facial shape and appearance within a low-dimensional parameter space. Fitted to a face scan, the model's parameters compactly encode its expression patterns. This expression code can be used, for instance, as a feature in automatic facial expression recognition. For accurate classification, an MM that can adequately represent the various characteristic facets and variants of each expression is necessary. Currently available MMs are limited in the diversity of expression patterns. We present a novel high-quality Facial Expression Morphable Model built from a large-scale face database as a tool for expression analysis and synthesis. Establishment of accurate dense correspondence, up to finest skin features, enables a detailed statistical analysis of facial expressions. Various characteristic shape patterns are identified for each expression. The results of our analysis give rise to a new facial expression code. We demonstrate the advantages of such a code for the automatic recognition of expressions, and compare the accuracy of our classifier to state-of-the-art. T3 - ZIB-Report - 18-06 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67696 SN - 1438-0064 ER - TY - CHAP A1 - Papazov, Chavdar A1 - Hege, Hans-Christian T1 - Blue-noise Optimized Point Sets Based on Procrustes Analysis T2 - SIGGRAPH Asia 2017 Technical Briefs Y1 - 2017 U6 - https://doi.org/10.1145/3145749.3149442 SP - 20:1 EP - 20:4 ER - TY - CHAP A1 - Beckenbach, Isabel ED - Kliewer, Natalia ED - Ehmke, Jan Fabian ED - Borndörfer, Ralf T1 - A Hypergraph Network Simplex Algorithm T2 - Operations Research Proceedings 2017 N2 - We describe a network simplex algorithm for the minimum cost flow problem on graph-based hypergraphs which are directed hypergraphs of a particular form occurring in railway rotation planning. The algorithm is based on work of Cambini, Gallo, and Scutellà who developed a hypergraphic generalization of the network simplex algorithm. Their main theoretical result is the characterization of basis matrices. We give a similar characterization for graph-based hypergraphs and show that some operations of the simplex algorithm can be done combinatorially by exploiting the underlying digraph structure. Y1 - 2018 VL - Operations Research Proceedings 2017 SP - 309 EP - 316 PB - Springer CY - Cham ER - TY - THES A1 - Durmaz, Vedat T1 - Atomistic Binding Free Energy Estimations for Biological Host–Guest Systems N2 - Accurate quantifications of protein–ligand binding affinities by means of in silico methods increasingly gain importance in various scientific branches including toxicology and pharmacology. In silico techniques not only are generally less demanding than laboratory experiments regarding time as well as cost, in particular, if binding assays or synthesis protocols need to be developed in advance. At times, they also provide the only access to risk assessments on novel chemical compounds arising from biotic or abiotic degradation of anthropogenic substances. However, despite the continuous technological and algorithmic progress over the past decades, binding free energy estimations through molecular dynamics simulations still pose an enormous computational challenge owed to the mathematical complexity of solvated macromolecular systems often consisting of hundreds of thousands of atoms. The goals of this thesis can roughly be divided into two categories dealing with different aspects of host–guest binding quantification. On the one side algorithmic strategies for a comprehensive exploration and decomposition of conformational space in conjunction with an automated selection of representative molecular geometries and binding poses have been elaborated providing initial structures for free energy calculations. In light of the dreaded trapping problem typically associated with molecular dynamics simulations, the focus was laid on a particularly systematic generation of representatives covering a broad range of physically accessible molecular conformations and interaction modes. On the other side and ensuing from these input geometries, binding affinity models based on the linear interaction energy (LIE) method have been developed for a couple of (bio)molecular systems. The applications included a successful prediction of the liquid-chromatographic elution order as well as retention times of highly similar hexabromocyclododecane (HBCD) stereoisomers, a novel empirical LIE–QSAR hybrid binding affinity model related to the human estrogen receptor α (ERα), and, finally, the (eco)toxicological prioritization of transformation products originating from the antibiotic sulfamethoxazole with respect to their binding affinities to the bacterial enzyme dihydropteroate synthase. Altogether, a fully automated approach to binding mode and affinity estimation has been presented that is content with an arbitrary geometry of a small molecule under observation and a spatial vector specifying the binding site of a potential target molecule. According to our studies, it is superior to conventional docking and thermodynamic average methods and primarily suggesting binding free energy calculation on the basis of several heavily distinct complex geometries. Both chromatographic retention times of HBCD and binding affinities to ERα yielded squared coefficients of correlation with experimental results significantly higher than 0.8. Approximately 85 % (100 %) of predicted receptor–ligand binding modes deviated less than 1.53 Å (2.05 Å) from available crystallographic structures. KW - molecular modelling KW - molecular dynamics KW - molecular simulation KW - binding affinity KW - prediction KW - free energy KW - receptor ligand KW - retention time KW - liquid chromatography Y1 - 2016 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000103765 PB - FU Dissertationen Online ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Breuer, Matthias A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schade, Stanley A1 - Schlechte, Thomas T1 - Timetable Sparsification by Rolling Stock Rotation Optimization T2 - Operations Research 2017 N2 - Rolling stock optimization is a task that naturally arises by operating a railway system. It could be seen with different level of details. From a strategic perspective to have a rough plan which types of fleets to be bought to a more operational perspective to decide which coaches have to be maintained first. This paper presents a new approach to deal with rolling stock optimisation in case of a (long term) strike. Instead of constructing a completely new timetable for the strike period, we propose a mixed integer programming model that is able to choose appropriate trips from a given timetable to construct efficient tours of railway vehicles covering an optimized subset of trips, in terms of deadhead kilometers and importance of the trips. The decision which trip is preferred over the other is made by a simple evaluation method that is deduced from the network and trip defining data. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_96 SP - 723 EP - 728 PB - Springer International Publishing ER - TY - JOUR A1 - Gotzes, Uwe A1 - Gotzes, Claudia T1 - The Jeep Problem: A Flexible MIP Formulation JF - Journal of Nepal Mathematical Society N2 - This article deals with the Jeep Problem (also known as Desert Crossing Problem), which reads as follows: An unlimited supply of fuel is available at one edge of a desert, but there is no source on the desert itself. A vehicle can carry enough fuel to go a certain distance, and it can built up its own refuelling stations. What is the minimum amount of fuel the vehicle will require in order to cross the desert? Under these mild conditions this question is answered since the 1940s. But what is the answer if the caches are restricted to certain areas or if the fuel consumption does not depend linearly on the distance travelled? To answer these and similar questions we develop and solve a flexible mixed-integer programming (MIP) model for the classical problem and enhance it with new further aspects of practical relevance. Y1 - 2018 SN - 2616-0161 VL - 1 SP - 11 EP - 17 ER - TY - GEN A1 - Weber, Marcus A1 - Durmaz, Vedat A1 - Sabri, Peggy A1 - Reidelbach, Marco T1 - Supplementary simulation data for Science Manuscript ai8636 N2 - The simulation data has been produced by Vedat Durmaz, Peggy Sabri and Marco Reidelbach inside the "Computational Molecular Design" Group headed by Marcus Weber at Zuse-Institut Berlin, Takustr. 7, D-14195 Berlin, Germany. The file contains classical simulation data for different fentanyl derivates in the MOR binding pocket at different pHs. It also includes instruction files for quantum-chemical pKa-value estimations and a description of how we derived the pKa-values from the Gaussian09 log-files. Y1 - 2017 U6 - https://doi.org/10.12752/5.MWB.1.0 N1 - GROMACS trajectories and GAUSSIAN files of MOR and fentanyl derivates ER - TY - GEN A1 - Weber, Marcus T1 - Supplementary: Implications of PCCA+ in Molecular Simulation N2 - Matlab-software and data sets to recapitulate the presented results in M. Weber: Implications of PCCA+ in Molecular Simulation. Computation, 6(1):20, 2018. Y1 - 2018 N1 - This data set includes one folder per published figure. The folders contain all needed resources to recapitulate the presented results. ER - TY - THES A1 - Pulaj, Jonad T1 - Cutting Planes for Union-Closed Families N2 - Frankl’s (union-closed sets) conjecture states that for any nonempty finite union-closed (UC) family of distinct sets there exists an element in at least half of the sets. Poonen’s Theorem characterizes the existence of weights which determine whether a given UC family ensures Frankl’s conjecture holds for all UC families which contain it. The weight systems are nontrivial to identify for a given UC family, and methods to determine such weight systems have led to several other open questions and conjectures regarding structures in UC families. We design a cutting-plane method that computes the explicit weights which imply the existence conditions of Poonen’s Theorem using computational integer programming coupled with redundant verification routines that ensure correctness. We find over one hundred previously unknown families of sets which ensure Frankl’s conjecture holds for all families that contain any of them. This improves significantly on all previous results of the kind. Our framework allows us to answer several open questions and conjectures regarding structural properties of UC families, including proving the 3-sets conjecture of Morris from 2006 which characterizes the minimum number of 3-sets that ensure Frankl’s conjecture holds for all families that contain them. Furthermore, our method provides a general algorithmic road-map for improving other known results and uncovering structures in UC families. Y1 - 2017 UR - https://depositonce.tu-berlin.de//handle/11303/7258 ER - TY - CHAP A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - SCIP-Jack—a solver for STP and variants with parallelization extensions: An update T2 - Operations Research Proceedings 2017 N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. Although the different Steiner tree problem variants are usually strongly related, solution approaches employed so far have been prevalently problem-specific. Against this backdrop, the solver SCIP-Jack was created as a general-purpose framework that can be used to solve the classical Steiner tree problem and 11 of its variants. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. Furthermore, SCIP-Jack includes various newly developed algorithmic components such as preprocessing routines and heuristics. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. After the introduction of SCIP-Jack at the 2014 DIMACS Challenge on Steiner problems, the overall performance of the solver has considerably improved. This article provides an overview on the current state. Y1 - 2018 SP - 191 EP - 196 ER - TY - THES A1 - Schubert, Christoph T1 - Multi-Level Lookahead Branching Y1 - 2017 ER - TY - THES A1 - Wischlinsky, William T1 - Feasibility-based bound tightening via linear programming Y1 - 2017 ER - TY - JOUR A1 - Furini, Fabio A1 - Traversi, Emiliano A1 - Belotti, Pietro A1 - Frangioni, Antonio A1 - Gleixner, Ambros A1 - Gould, Nick A1 - Liberti, Leo A1 - Lodi, Andrea A1 - Misener, Ruth A1 - Mittelmann, Hans A1 - Sahinidis, Nikolaos V. A1 - Vigerske, Stefan A1 - Wiegele, Angelika T1 - QPLIB: A Library of Quadratic Programming Instances JF - Mathematical Programming Computation N2 - This paper describes a new instance library for Quadratic Programming (QP), i.e., the family of continuous and (mixed)-integer optimization problems where the objective function, the constrains, or both are quadratic. QP is a very diverse class of problems, comprising sub-classes of problems ranging from trivial to undecidable. This diversity is reflected in the variety of solution methods for QP, ranging from entirely combinatorial ones to completely continuous ones, including many for which both aspects are fundamental. Selecting a set of instances of QP that is at the same time not overwhelmingly onerous but sufficiently challenging for the many different interested communities is therefore important. We propose a simple taxonomy for QP instances that leads to a systematic problem selection mechanism. We then briefly survey the field of QP, giving an overview of theory, methods and solvers. Finally, we describe how the library was put together, and detail its final contents. Y1 - 2019 U6 - https://doi.org/10.1007/s12532-018-0147-4 VL - 11 IS - 2 SP - 237 EP - 265 ER - TY - CHAP A1 - Cheung, Kevin K. H. A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Verifying Integer Programming Results T2 - F. Eisenbrand and J. Koenemann, eds., Integer Programming and Combinatorial Optimization: 19th International Conference, IPCO 2017 N2 - Software for mixed-integer linear programming can return incorrect results for a number of reasons, one being the use of inexact floating-point arithmetic. Even solvers that employ exact arithmetic may suffer from programming or algorithmic errors, motivating the desire for a way to produce independently verifiable certificates of claimed results. Due to the complex nature of state-of-the-art MIP solution algorithms, the ideal form of such a certificate is not entirely clear. This paper proposes such a certificate format designed with simplicity in mind, which is composed of a list of statements that can be sequentially verified using a limited number of inference rules. We present a supplementary verification tool for compressing and checking these certificates independently of how they were created. We report computational results on a selection of MIP instances from the literature. To this end, we have extended the exact rational version of the MIP solver SCIP to produce such certificates. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-59250-3_13 VL - 10328 SP - 148 EP - 160 ER - TY - JOUR A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin A1 - Gottwald, Robert Lion A1 - Grösser, Stefan T1 - Using white-box nonlinear optimization methods in system dynamics policy improvement JF - System Dynamics Review N2 - We present a new strategy for the direct optimization of the values of policy functions. This approach is particularly well suited to model actors with a global perspective on the system and relies heavily on modern mathematical white-box optimization methods. We demonstrate our strategy on two classical models: market growth and World2. Each model is first transformed into an optimization problem by defining how the actor can influence the models' dynamics and by choosing objective functions to measure improvements. To improve comparability between different runs, we also introduce a comparison measure for possible interventions. We solve the optimization problems, discuss the resulting policies and compare them to the existing results from the literature. In particular, we present a run of the World2 model which significantly improves the published “towards a global equilibrium” run with equal cost of intervention. Y1 - 2017 U6 - https://doi.org/10.1002/sdr.1583 VL - 33 IS - 2 SP - 138 EP - 168 ER - TY - CHAP A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Cao, Karl-Kien A1 - Cebulla, Felix A1 - Fiand, Frederik A1 - Gils, Hans Christian A1 - Gleixner, Ambros A1 - Khabi, Dmitry A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Wetzel, Manuel T1 - Optimizing Large-Scale Linear Energy System Problems with Block Diagonal Structure by Using Parallel Interior-Point Methods T2 - Operations Research Proceedings 2017 N2 - Current linear energy system models (ESM) acquiring to provide sufficient detail and reliability frequently bring along problems of both high intricacy and increasing scale. Unfortunately, the size and complexity of these problems often prove to be intractable even for commercial state-of-the-art linear programming solvers. This article describes an interdisciplinary approach to exploit the intrinsic structure of these large-scale linear problems to be able to solve them on massively parallel high-performance computers. A key aspect are extensions to the parallel interior-point solver PIPS-IPM originally developed for stochastic optimization problems. Furthermore, a newly developed GAMS interface to the solver as well as some GAMS language extensions to model block-structured problems will be described. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_85 SP - 641 EP - 647 PB - Springer International Publishing ER - TY - CHAP A1 - Schade, Stanley A1 - Schlechte, Thomas A1 - Witzig, Jakob T1 - Structure-based Decomposition for Pattern-Detection for Railway Timetables T2 - Operations Research Proceedings 2017 N2 - We consider the problem of pattern detection in large scale railway timetables. This problem arises in rolling stock optimization planning in order to identify invariant sections of the timetable for which a cyclic rotation plan is adequate. We propose a dual reduction technique which leads to an decomposition and enumeration method. Computational results for real world instances demonstrate that the method is able to produce optimal solutions as fast as standard MIP solvers. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_95 SP - 715 EP - 721 PB - Springer International Publishing ER - TY - JOUR A1 - Maher, Stephen J. A1 - Desaulniers, Guy A1 - Soumis, Francois T1 - The daily tail assignment problem under operational uncertainty using look-ahead maintenance constraints JF - European Journal of Operational Research N2 - The tail assignment problem is a critical part of the airline planning process that assigns specific aircraft to sequences of flights, called lines-of-flight, to satisfy operational constraints. The aim of this paper is to develop an operationally flexible method, based upon the one-day routes business model, to compute tail assignments that satisfy short-range—within the next three days—aircraft maintenance requirements. While maintenance plans commonly span multiple days, the methods used to compute tail assignments for the given plans can be overly complex and provide little recourse in the event of schedule perturbations. The presented approach addresses operational uncertainty by using solutions from the one-day routes aircraft maintenance routing approach as input. The daily tail assignment problem is solved with an objective to satisfy maintenance requirements explicitly for the current day and implicitly for the subsequent two days. A computational study will be performed to assess the performance of exact and heuristic solution algorithms that modify the input lines-of-flight to reduce maintenance misalignments. The daily tail assignment problem and the developed algorithms are demonstrated to compute solutions that effectively satisfy maintenance requirements when evaluated using input data collected from three different airlines. Y1 - 2018 U6 - https://doi.org/10.1016/j.ejor.2017.06.041 VL - 264 IS - 2 SP - 534 EP - 547 ER - TY - JOUR A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Osteoarthritis and Cartilage N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. Y1 - 2018 U6 - https://doi.org/10.1016/j.joca.2018.02.907 VL - 26 IS - 5 SP - 680 EP - 688 ER - TY - GEN A1 - Hiller, Benjamin A1 - Walther, Tom T1 - Improving branching for disjunctive polyhedral models using approximate convex decompositions N2 - Disjunctive sets arise in a variety of optimization models and much esearch has been devoted to obtain strong relaxations for them. This paper focuses on the evaluation of the relaxation during the branch-and-bound search process. We argue that the branching possibilities (\ie binary variables) of the usual formulations are unsuitable to obtain strong bounds early in the search process as they do not capture the overall shape of the the entire disjunctive set. To analyze and exploit the shape of the disjunctive set we propose to compute a hierarchy of approximate convex decompositions and show how to extend the known formulations to obtain improved branching behavior. T3 - ZIB-Report - 17-68 KW - approximate convex decomposition KW - branch-and-bound KW - convex hull reformulation KW - disjunctive set Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67462 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Walther, Tom T1 - Modelling compressor stations in gas networks N2 - Gas networks are an important application area for optimization. When considering long-range transmission, compressor stations play a crucial role in these applications. The purpose of this report is to collect and systematize the models used for compressor stations in the literature. The emphasis is on recent work on simple yet accurate polyhedral models that may replace more simplified traditional models without increasing model complexity. The report also describes an extension of the compressor station data available in GasLib (http://gaslib.zib.de/) with the parameters of these models. T3 - ZIB-Report - 17-67 KW - MINLP model KW - compressor station KW - gas compressor modeling KW - nonlinear model KW - polyhedral model Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67443 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Koch, Thorsten A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Schweiger, Jonas T1 - A System to Evaluate Gas Network Capacities: Concepts and Implementation N2 - In 2005 the European Union liberalized the gas market with a disruptive change and decoupled trading of natural gas from its transport. The gas is now transported by independent so-called transmissions system operators or TSOs. The market model established by the European Union views the gas transmission network as a black box, providing shippers (gas traders and consumers) the opportunity to transport gas from any entry to any exit. TSOs are required to offer the maximum possible capacities at each entry and exit such that any resulting gas flow can be realized by the network. The revenue from selling these capacities more than one billion Euro in Germany alone, but overestimating the capacity might compromise the security of supply. Therefore, evaluating the available transport capacities is extremely important to the TSOs. This is a report on a large project in mathematical optimization, set out to develop a new toolset for evaluating gas network capacities. The goals and the challenges as they occurred in the project are described, as well as the developments and design decisions taken to meet the requirements. T3 - ZIB-Report - 18-11 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67438 SN - 1438-0064 N1 - An earlier version of this report is available as ZR 17-03 at https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/6193. ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Nakamura, Ryo A1 - Wakui, Tetsuya A1 - Shinano, Yuji T1 - Evaluation of Performance Robustness of a Gas Turbine Cogeneration Plant Based on a Mixed-Integer Linear Model T2 - ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition N2 - In designing energy supply systems, designers are requested to rationally determine equipment types, capacities, and numbers in consideration of equipment operational strategies corresponding to seasonal and hourly variations in energy demands. However, energy demands have some uncertainty at the design stage, and the energy demands which become certain at the operation stage may differ from those estimated at the design stage. Therefore, designers should consider that energy demands have some uncertainty, evaluate the performance robustness against the uncertainty, and design the systems to heighten the robustness. Especially, this issue is important for cogeneration plants, because their performances depend significantly on both heat and power demands. Although robust optimal design methods of energy supply systems under uncertain energy demands were developed, all of them are based on linear models for energy supply systems. However, it is still a hard challenge to develop a robust optimal design method even based on a mixed-integer linear model. At the first step for this challenge, in this paper, a method of evaluating the performance robustness of energy supply systems under uncertain energy demands is proposed based on a mixed-integer linear model. This problem is formulated as a bilevel mixed-integer linear programming one, and a sequential solution method is applied to solve it approximately by discretizing uncertain energy demands within their intervals. In addition, a hierarchical optimization method in consideration of the hierarchical relationship between design and operation variables is applied to solve large scale problems efficiently. Through a case study on a gas turbine cogeneration plant for district energy supply, the validity and effectiveness of the proposed method and features of the performance robustness of the plant are clarified. Y1 - 2016 U6 - https://doi.org/doi:10.1115/GT2016-56217 VL - 3 SP - 1 EP - 9 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Multiobjective Optimal Design of a Gas Turbine Cogeneration Plant by a Revised Hierarchical Optimization Method T2 - ASME Turbo Expo 2017: Turbomachinery Technical Conference and Exposition N2 - To attain the highest performance of energy supply systems, it is necessary to rationally determine design specifications in consideration of operational strategies corresponding to energy demands. Mixed-integer linear programming (MILP) approaches have been applied widely to such optimal design problems. A MILP method utilizing the hierarchical relationship between design and operation variables have been proposed to solve them efficiently. However, it cannot necessarily be effective to multi-objective optimal design problems because of the existence of a large number of competing design candidates. In this paper, the hierarchical MILP method is revised from the viewpoint of computation efficiency so that it can be applied practically to multi-objective optimal design problems. At the lower level, the order of the optimal operation problems to be solved is changed based on incumbents obtained previously to increase a lower bound for the optimal value of the combined objective function and reduce the number of the optimal operation problems to be solved. At the upper level, a lower bound for the optimal value of the combined objective function is incorporated into the solution method to reduce the number of the design candidates to be generated. This revised hierarchical MILP method is applied to a multiobjective optimal design of a gas turbine cogeneration plant, and its validity and effectiveness are clarified. Y1 - 2017 U6 - https://doi.org/doi:10.1115/GT2017-64296 VL - 3 SP - 1 EP - 14 ER - TY - JOUR A1 - Shinano, Yuji A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - FiberSCIP - A shared memory parallelization of SCIP JF - INFORMS Journal on Computing N2 - Recently, parallel computing environments have become significantly popular. In order to obtain the benefit of using parallel computing environments, we have to deploy our programs for these effectively. This paper focuses on a parallelization of SCIP (Solving Constraint Integer Programs), which is a mixed-integer linear programming solver and constraint integer programming framework available in source code. There is a parallel extension of SCIP named ParaSCIP, which parallelizes SCIP on massively parallel distributed memory computing environments. This paper describes FiberSCIP, which is yet another parallel extension of SCIP to utilize multi-threaded parallel computation on shared memory computing environments, and has the following contributions: First, we present the basic concept of having two parallel extensions, and the relationship between them and the parallelization framework provided by UG (Ubiquity Generator), including an implementation of deterministic parallelization. Second, we discuss the difficulties in achieving a good performance that utilizes all resources on an actual computing environment, and the difficulties of performance evaluation of the parallel solvers. Third, we present a way to evaluate the performance of new algorithms and parameter settings of the parallel extensions. Finally, we demonstrate the current performance of FiberSCIP for solving mixed-integer linear programs (MIPs) and mixed-integer nonlinear programs (MINLPs) in parallel. Y1 - 2018 U6 - https://doi.org/10.1287/ijoc.2017.0762 VL - 30 IS - 1 SP - 11 EP - 30 ER - TY - JOUR A1 - Shinano, Yuji A1 - Berthold, Timo A1 - Heinz, Stefan T1 - ParaXpress: An Experimental Extension of the FICO Xpress-Optimizer to Solve Hard MIPs on Supercomputers JF - Optimization Methods & Software N2 - The Ubiquity Generator (UG) is a general framework for the external parallelization of mixed integer programming (MIP) solvers. In this paper, we present ParaXpress, a distributed memory parallelization of the powerful commercial MIP solver FICO Xpress. Besides sheer performance, an important feature of Xpress is that it provides an internal parallelization for shared memory systems. When aiming for a best possible performance of ParaXpress on a supercomputer, the question arises how to balance the internal Xpress parallelization and the external parallelization by UG against each other. We provide computational experiments to address this question and we show computational results for running ParaXpress on a Top500 supercomputer, using up to 43,344 cores in parallel. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2018.1428602 VL - 33 IS - 3 SP - 530 EP - 539 ER - TY - CHAP A1 - Shinano, Yuji T1 - The Ubiquity Generator Framework: 7 Years of Progress in Parallelizing Branch-and-Bound T2 - Operations Research Proceedings 2017 N2 - Mixed integer linear programming (MIP) is a general form to model combinatorial optimization problems and has many industrial applications. The performance of MIP solvers has improved tremendously in the last two decades and these solvers have been used to solve many real-word problems. However, against the backdrop of modern computer technology, parallelization is of pivotal importance. In this way, ParaSCIP is the most successful parallel MIP solver in terms of solving previously unsolvable instances from the well-known benchmark instance set MIPLIB by using supercomputers. It solved two instances from MIPLIB2003 and 12 from MIPLIB2010 for the first time to optimality by using up to 80,000 cores on supercomputers. ParaSCIP has been developed by using the Ubiquity Generator (UG) framework, which is a general software package to parallelize any state-of-the-art branch-and-bound based solver. This paper discusses 7 years of progress in parallelizing branch-and-bound solvers with UG. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_20 SP - 143 EP - 149 PB - Springer International Publishing ER - TY - JOUR A1 - Dierkes, Thomas T1 - Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert? JF - ABI Technik N2 - Thomas Dierkes ist promovierter Mathematiker und als Entwickler beim Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) am Zuse-Institut Berlin (ZIB) tätig. Er arbeitet dort an der Entwicklung einer „Datendrehscheibe“ für die Umsetzung der Open-Access-Komponente in Allianz-Lizenzen. Er beantwortet die aktuelle Abi Technikfrage: „Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert?“ Y1 - 2017 U6 - https://doi.org/10.1515/abitech-2017-0051 VL - 37 IS - 3 SP - 237 ER - TY - CHAP A1 - Gottwald, Robert Lion A1 - Maher, Stephen J. A1 - Shinano, Yuji T1 - Distributed Domain Propagation T2 - 16th International Symposium on Experimental Algorithms (SEA 2017) N2 - Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite its simplicity, portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after the domain of a variable has been reduced. In this paper we introduce distributed domain propagation, a technique that shares bound tightenings across solvers to trigger further domain propagations. We investigate its impact in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions, they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers. Y1 - 2017 U6 - https://doi.org/10.4230/LIPIcs.SEA.2017.6 VL - 75 SP - 6:1 EP - 6:11 ER - TY - CHAP A1 - Streubel, Tom A1 - Strohm, Christian A1 - Trunschke, Philipp A1 - Tischendorf, Caren T1 - Generic Construction and Efficient Evaluation of Network DAEs and Their Derivatives in the Context of Gas Networks T2 - Operations Research Proceedings 2017 N2 - We present a concept that provides an efficient description of differential-algebraic equations (DAEs) describing flow networks which provides the DAE function f and their Jacobians in an automatized way such that the sparsity pattern of the Jacobians is determined before their evaluation and previously determined values of f can be exploited. The user only has to provide the network topology and local function descriptions for each network element. The approach uses automatic differentiation (AD) and is adapted to switching element functions via the abs-normal-form (ANF). KW - compressed sparse row format KW - algorithmic differentiation KW - abs-normal form KW - piecewise linear tangent approximation KW - piecewise smooth Y1 - 2018 SN - 978-3-319-89920-6 U6 - https://doi.org/10.1007/978-3-319-89920-6_83 SP - 627 EP - 632 PB - Springer International Publishing ER - TY - JOUR A1 - Hiller, Benjamin A1 - Koch, Thorsten A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Schweiger, Jonas T1 - A System to Evaluate Gas Network Capacities: Concepts and Implementation JF - European Journal of Operational Research N2 - In 2005 the European Union liberalized the gas market with a disruptive change and decoupled trading of natural gas from its transport. The gas is now trans- ported by independent so-called transmissions system operators or TSOs. The market model established by the European Union views the gas transmission network as a black box, providing shippers (gas traders and consumers) the opportunity to transport gas from any entry to any exit. TSOs are required to offer the maximum possible capacities at each entry and exit such that any resulting gas flow can be realized by the network. The revenue from selling these capacities more than one billion Euro in Germany alone, but overestimating the capacity might compromise the security of supply. Therefore, evaluating the available transport capacities is extremely important to the TSOs. This is a report on a large project in mathematical optimization, set out to develop a new toolset for evaluating gas network capacities. The goals and the challenges as they occurred in the project are described, as well as the developments and design decisions taken to meet the requirements. Y1 - 2018 VL - 270 IS - 3 SP - 797 EP - 808 ER - TY - CHAP A1 - Gamrath, Gerald A1 - Schubert, Christoph T1 - Measuring the impact of branching rules for mixed-integer programming T2 - Operations Research Proceedings 2017 N2 - Branching rules are an integral component of the branch-and-bound algorithm typically used to solve mixed-integer programs and subject to intense research. Different approaches for branching are typically compared based on the solving time as well as the size of the branch-and-bound tree needed to prove optimality. The latter, however, has some flaws when it comes to sophisticated branching rules that do not only try to take a good branching decision, but have additional side-effects. We propose a new measure for the quality of a branching rule that distinguishes tree size reductions obtained by better branching decisions from those obtained by such side-effects. It is evaluated for common branching rules providing new insights in the importance of strong branching. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_23 SP - 165 EP - 170 PB - Springer International Publishing ER - TY - THES A1 - Clausecker, Robert T1 - Notes on the Construction of Tablebases Y1 - 2017 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Pabisiak, Jakub A1 - Perez-Gea, Ana Cristina A1 - Julian, Nicolas A1 - Hon, Sean A1 - Burger, Sven T1 - Efficient finite-element-based numerical modelling of large sub-wavelength patterned optical structures JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2292438 VL - 10542 SP - 105421G ER - TY - GEN A1 - Weiser, Martin A1 - Freytag, Yvonne A1 - Erdmann, Bodo A1 - Hubig, Michael A1 - Mall, Gita T1 - Optimal Design of Experiments for Estimating the Time of Death in Forensic Medicine N2 - Estimation of time of death based on a single measurement of body core temperature is a standard procedure in forensic medicine. Mechanistic models using simulation of heat transport promise higher accuracy than established phenomenological models in particular in nonstandard situations, but involve many not exactly known physical parameters. Identifying both time of death and physical parameters from multiple temperature measurements is one possibility to reduce the uncertainty significantly. In this paper, we consider the inverse problem in a Bayesian setting and perform both local and sampling-based uncertainty quantification, where proper orthogonal decomposition is used as model reduction for fast solution of the forward model. Based on the local uncertainty quantification, optimal design of experiments is performed in order to minimize the uncertainty in the time of death estimate for a given number of measurements. For reasons of practicability, temperature acquisition points are selected from a set of candidates in different spatial and temporal locations. Applied to a real corpse model, a significant accuracy improvement is obtained already with a small number of measurements. T3 - ZIB-Report - 18-08 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67247 SN - 1438-0064 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Nieto-Vesperinas, Manuel T1 - Optical Chirality of Time-Harmonic Wavefields for Classification of Scatterers JF - Sci. Rep. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-27496-w VL - 8 SP - 9416 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Schneider, Philipp-Immanuel A1 - Burger, Sven A1 - Nieto-Vesperinas, Manuel T1 - Chiral scatterers designed by Bayesian optimization JF - J. Phys.: Conf. Ser. Y1 - 2018 U6 - https://doi.org/10.1088/1742-6596/963/1/012004 VL - 963 SP - 012004 ER - TY - CHAP A1 - Hennings, Felix T1 - Benefits and Limitations of Simplified Transient Gas Flow Formulations T2 - Operations Research Proceedings 2017 N2 - Although intensively studied in recent years, the optimization of the transient (time-dependent) control of large real-world gas networks is still out of reach for current state-of-the-art approaches. For this reason, we present further simplifications of the commonly used model, which lead to a linear description of the gas flow on pipelines. In an empirical analysis of real-world data, we investigate the properties of the involved quantities and evaluate the errors made by our simplification. Y1 - 2018 UR - https://link.springer.com/chapter/10.1007/978-3-319-89920-6_32 U6 - https://doi.org/10.1007/978-3-319-89920-6_32 VL - Operations Research Proceedings SP - 231 EP - 237 PB - Springer, Cham ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Schneider, Philipp-Immanuel A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Shape design of a reflecting surface using Bayesian Optimization JF - J. Phys.: Conf. Ser. Y1 - 2018 U6 - https://doi.org/10.1088/1742-6596/963/1/012003 VL - 963 SP - 012003 ER - TY - CHAP A1 - Hoppmann, Kai A1 - Schwarz, Robert T1 - Finding Maximum Minimum Cost Flows to Evaluate Gas Network Capacities T2 - Operations Research Proceedings 2017 N2 - In this article we consider the following problem arising in the context of scenario generation to evaluate the transport capacity of gas networks: In the Uncapacitated Maximum Minimum Cost Flow Problem (UMMCF) we are given a flow network where each arc has an associated nonnegative length and infinite capacity. Additionally, for each source and each sink a lower and an upper bound on its supply and demand are known, respectively. The goal is to find values for the supplies and demands respecting these bounds, such that the optimal value of the induced Minimum Cost Flow Problem is maximized, i.e., to determine a scenario with maximum transportmoment. In this article we propose two linear bilevel optimization models for UMMCF, introduce a greedy-style heuristic, and report on our first computational experiment. Y1 - 2018 SN - 978-3-319-89919-0 U6 - https://doi.org/10.1007/978-3-319-89920-6_46 SP - 339 EP - 346 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Zschiedrich, Lin A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - Numerical optimization of the extraction efficiency of a quantum-dot based single-photon emitter into a single-mode fiber JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.008479 VL - 26 SP - 8479 ER - TY - JOUR A1 - Weber, Marcus T1 - Implications of PCCA+ in Molecular Simulation JF - Computation N2 - Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ’bound’ vs. ’unbound’), although the process itself takes place in a continuous space. In this context, the formula chi=XA connects the micro-dynamics of the molecular system to its macro-dynamics. Chi can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences. Y1 - 2018 U6 - https://doi.org/10.3390/computation6010020 VL - 6 IS - 1 SP - 20 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Fuerstenau, Daniel A1 - Grabundzija, Ana A1 - Helfmann, Luzie A1 - Park, Martin A1 - Schier, Wolfram A1 - Schütt, Brigitta A1 - Schütte, Christof A1 - Weber, Marcus A1 - Wulkow, Niklas A1 - Zonker, Johannes T1 - Mathematical modeling of the spreading of innovations in the ancient world JF - eTopoi. Journal for Ancient Studies Y1 - 2018 U6 - https://doi.org/10.17171/4-7-1 SN - ISSN 2192-2608 VL - 7 ER - TY - GEN A1 - Seblany, Feda A1 - Homberg, Ulrike A1 - Vincens, Eric A1 - Winkler, Paul A1 - Witt, Karl Josef T1 - Merging criteria for the definition of a local pore and the CSD computation of granular materials T3 - ZIB-Report - 18-09 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67069 SN - 1438-0064 ER - TY - CHAP A1 - Seblany, Feda A1 - Homberg, Ulrike A1 - Vincens, Eric A1 - Winkler, Paul A1 - Witt, Karl Josef T1 - Merging criteria for the definition of a local pore and the CSD computation of granular materials T2 - Proceedings of the 25th meeting of the Working Group on Internal Erosion in embankment dams and their foundations Y1 - 2017 SN - 978-90-827468-1-5 | 978-90-827468-0-8 SP - 150 EP - 159 PB - Deltares CY - Delft, Netherlands ER - TY - JOUR A1 - Dibak, Manuel A1 - del Razo, Mauricio J. A1 - de Sancho, David A1 - Schütte, Christof A1 - Noé, Frank T1 - MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations JF - Journal of Chemical Physics N2 - Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported. Y1 - 2018 U6 - https://doi.org/10.1063/1.5020294 VL - 148 IS - 21 ER - TY - JOUR A1 - Koltai, Peter A1 - Wu, Hao A1 - Noé, Frank A1 - Schütte, Christof T1 - Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics JF - Computation Y1 - 2018 U6 - https://doi.org/10.3390/computation6010022 VL - 6 IS - 1 PB - MDPI CY - Basel, Switzerland ER - TY - GEN A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - Parallel-in-Time for Parabolic Optimal Control Problems Using PFASST BT - DD 2017. T2 - Domain Decomposition Methods in Science and Engineering XXIV N2 - In gradient-based methods for parabolic optimal control problems, it is necessary to solve both the state equation and a backward-in-time adjoint equation in each iteration of the optimization method. In order to facilitate fully parallel gradient-type and nonlinear conjugate gradient methods for the solution of such optimal control problems, we discuss the application of the parallel-in-time method PFASST to adjoint gradient computation. In addition to enabling time parallelism, PFASST provides high flexibility for handling nonlinear equations, as well as potential extra computational savings from reusing previous solutions in the optimization loop. The approach is demonstrated here for a model reaction-diffusion optimal control problem. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-93873-8_34 SP - 363 EP - 371 PB - Springer CY - Cham ER - TY - JOUR A1 - Schweiger, Jonas A1 - Liers, Frauke T1 - A Decomposition Approach for Optimal Gas Network Extension with a Finite Set of Demand Scenarios JF - Optimization and Engineering N2 - Today's gas markets demand more flexibility from the network operators which in turn have to invest into their network infrastructure. As these investments are very cost-intensive and long-living, network extensions should not only focus on a single bottleneck scenario, but should increase the flexibility to fulfill different demand scenarios. In this work, we formulate a model for the network extension problem for multiple demand scenarios and propose a scenario decomposition in order to solve the arising challenging optimization tasks. In fact, each subproblem consists of a mixed-integer nonlinear optimization problem (MINLP). Valid bounds on the objective value are derived even without solving the subproblems to optimality. Furthermore, we develop heuristics that prove capable of improving the initial solutions substantially. Results of computational experiments on realistic network topologies are presented. It turns out that our method is able to solve these challenging instances to optimality within a reasonable amount of time. Y1 - 2018 VL - 19 IS - 2 SP - 297 EP - 326 PB - Springer ER - TY - THES A1 - Schweiger, Jonas T1 - Exploiting structure in non-convex quadratic optimization and gas network planning under uncertainty N2 - The amazing success of computational mathematical optimization over the last decades has been driven more by insights into mathematical structures than by the advance of computing technology. In this vein, we address applications, where nonconvexity in the model and uncertainty in the data pose principal difficulties. The first part of the thesis deals with non-convex quadratic programs. Branch&Bound methods for this problem class depend on tight relaxations. We contribute in several ways: First, we establish a new way to handle missing linearization variables in the well-known Reformulation-Linearization-Technique (RLT). This is implemented into the commercial software CPLEX. Second, we study the optimization of a quadratic objective over the standard simplex or a knapsack constraint. These basic structures appear as part of many complex models. Exploiting connections to the maximum clique problem and RLT, we derive new valid inequalities. Using exact and heuristic separation methods, we demonstrate the impact of the new inequalities on the relaxation and the global optimization of these problems. Third, we strengthen the state-of-the-art relaxation for the pooling problem, a well-known non-convex quadratic problem, which is, for example, relevant in the petrochemical industry. We propose a novel relaxation that captures the essential non-convex structure of the problem but is small enough for an in-depth study. We provide a complete inner description in terms of the extreme points as well as an outer description in terms of inequalities defining its convex hull (which is not a polyhedron). We show that the resulting valid convex inequalities significantly strengthen the standard relaxation of the pooling problem. The second part of this thesis focuses on a common challenge in real world applications, namely, the uncertainty entailed in the input data. We study the extension of a gas transport network, e.g., from our project partner Open Grid Europe GmbH. For a single scenario this maps to a challenging non-convex MINLP. As the future transport patterns are highly uncertain, we propose a robust model to best prepare the network operator for an array of scenarios. We develop a custom decomposition approach that makes use of the hierarchical structure of network extensions and the loose coupling between the scenarios. The algorithm used the single-scenario problem as black-box subproblem allowing the generalization of our approach to problems with the same structure. The scenario-expanded version of this problem is out of reach for today's general-purpose MINLP solvers. Yet our approach provides primal and dual bounds for instances with up to 256 scenarios and solves many of them to optimality. Extensive computational studies show the impact of our work. N2 - Der bemerkenswerte Erfolg der angewandten mathematischen Optimierung in den letzten Dekaden ist mehr auf Einsichten in mathematische Strukturen zurückzuführen, als auf eine Steigerung der Rechenleistung. In diesem Sinne adressieren wir Anwendungen, in denen Nichtkonvexität und Unsicherheit in den Daten die Hauptschwierigkeiten darstellen. Der erste Teil dieser Arbeit beschäftigt sich mit nichtkonvexen quadratischen Optimierungsproblemen. Relaxierungen sind integraler Bestandteil von \BranchAndBound{}-Lösungsmethoden für diese Problemkategorie. Wir leisten folgende Beiträge: Erstens beschreiben wir eine neue Art fehlende Linearisierungsvariablen, in der so genannten Reformulation-Linearization-Technique (RLT), zu behandeln. Diese wird inzwischen in der kommerziellen Software CPLEX verwendet. Zweitens beschäftigen wir uns mit der Optimierung einer quadratischen Zielfunktion über die Standardsimplex oder einen so genannten Knapsack-Constraint. Solche grundlegenden Strukturen sind Teil vieler komplexer Modelle. Wir benutzen bekannte Verbindungen zum maximalen Cliquenproblem sowie zu RLT, um neue gültige Ungleichungen herzuleiten, die die Relaxierung verstärken. Drittens beschäftigen wir uns mit dem Pooling Problem, das z.B. in der Erdölindustrie relevant ist. Wie leiten eine neue Relaxierung her, die die wesentliche nicht-konvexe Struktur des Problems erfasst, aber klein genug für eine grundlegende Untersuchung ist. Wir geben eine innere Beschreibung in Form der Extrempunkte, sowie eine äußere Beschreibung in Form von Ungleichungen, die die konvexe Hülle (welche im Allgemeinen kein Polyeder ist) beschreiben, an. Wir zeigen, dass neuen die Ungleichungen die Relaxierung des Pooling Problems erheblich verstärken. Der zweite Teil der Arbeit befasst sich mit einer weiteren Herausforderung in realen Anwendungen, nämlich Unsicherheit in den Eingabedaten. Konkret untersuchen wir die Optimierung des Ausbaus eines Gastransportnetzes, wie z.B. von unserem Projektpartner Open Grid Europe GmbH. Dieses Problem ist bereits bei gegebenen Eingabedaten ein schweres nicht-konvexes gemischt-ganzzahliges Optimierungsproblem. Da zukünftige Nutzungsmuster des Netzes mit großer Unsicherheit behaftet sind, beschreiben wir ein robustes Modell, um den Netzbetreiber gegen verschiedene Szenarien abzusichern. Wir entwickeln einen speziellen Dekompositionsalgorithmus unter Berücksichtigung der hierarchischen Struktur der Ausbauten und der schwachen Kopplung zwischen den Szenarien. Unser Ansatz liefert primale und duale Schranken für Instanzen mit bis zu 256 Szenarien und löst viele beweisbar optimal. Umfangreiche Rechnungen bestätigen die Effizient der vorgestellten Methoden. KW - Nonconvexity KW - Uncertainty KW - Quadratic Programming KW - Relaxations KW - Cutting Planes KW - Standard Quadratic Programming KW - Pooling Problem KW - Gas Network Planning KW - Robust Optimization KW - Decomposition KW - Computations Y1 - 2017 UR - http://dx.doi.org/10.14279/depositonce-6015 ER - TY - JOUR A1 - Lang, Annemarie A1 - Volkamer, Andrea A1 - Behm, Laura A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Schneider, Marlon A1 - Geris, Lisbet A1 - Wichard, Joerg A1 - Buttgereit, Frank T1 - In silico Methods - Computational Alternatives to Animal Testing JF - ALTEX N2 - A seminar and interactive workshop on “In silico Methods – Computational Alternatives to Animal Testing” was held in Berlin, Germany, organized by Annemarie Lang, Frank Butt- gereit and Andrea Volkamer at the Charité-Universitätsmedizin Berlin, on August 17-18, 2017. During the half-day seminar, the variety and applications of in silico methods as alternatives to animal testing were presented with room for scientific discus- sions with experts from academia, industry and the German fed- eral ministry (Fig. 1). Talks on computational systems biology were followed by detailed information on predictive toxicology in order to display the diversity of in silico methods and the potential to embrace them in current approaches (Hartung and Hoffmann, 2009; Luechtefeld and Hartung, 2017). The follow- ing interactive one-day Design Thinking Workshop was aimed at experts, interested researchers and PhD-students interested in the use of in silico as alternative methods to promote the 3Rs (Fig. 2). Forty participants took part in the seminar while the workshop was restricted to sixteen participants. Y1 - 2018 U6 - https://doi.org/10.14573/altex.1712031 VL - 35 IS - 1 SP - 126 EP - 128 ER - TY - JOUR A1 - Gilg, Brady A1 - Klug, Torsten A1 - Martienssen, Rosemarie A1 - Paat, Joseph A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Seymen, Senan A1 - Tesch, Alexander T1 - Conflict-free railway track assignment at depots JF - Journal of Rail Transport Planning & Management N2 - Managing rolling stock with no passengers aboard is a critical component of railway operations. One aspect of managing rolling stock is to park the rolling stock on a given set of tracks at the end of a day or service. Depending on the parking assignment, shunting may be required in order for a parked train to depart or for an incoming train to park. Given a collection of tracks M and a collection of trains T with a fixed arrival-departure timetable, the train assignment problem (TAP) is to determine the maximum number of trains from T that can be parked on M according to the timetable and without the use of shunting. Hence, efficiently solving the TAP allows to quickly compute feasible parking schedules that do not require further shunting adjustments. In this paper, we show that the TAP is NP-hard and present two integer programming models for solving the TAP. We compare both models on a theoretical level. Moreover, to our knowledge, we consider the first approach that integrates track lengths along with the three most common types of parking tracks FIFO, LIFO and FREE tracks in a common model. Furthermore, to optimize against uncertainty in the arrival times of the trains we extend our models by stochastic and robust modeling techniques. We conclude by giving computational results for both models, observing that they perform well on real timetables. Y1 - 2018 U6 - https://doi.org/10.1016/j.jrtpm.2017.12.004 ER - TY - CHAP A1 - Klug, Torsten T1 - Freight Train Routing T2 - Handbook of Optimization in the Railway Industry N2 - This chapter is about strategic routing of freight trains in railway transportation networks with mixed traffic. A good utilization of a railway transportation network is important since in contrast to road and air traffic the routing through railway networks is more challenging and the extension of capacities is expensive and a long-term projects. Therefore, an optimized routing of freight trains have a great potential to exploit remaining capacity since the routing has fewer restrictions compared to passenger trains. In this chapter we describe the freight train routing problem in full detail and present a mixed-integer formulation. Wo focus on a strategic level that take into account the actual immutable passenger traffic. We conclude the chapter with a case study for the German railway network. Y1 - 2018 SN - 978-3-319-72152-1 U6 - https://doi.org/10.1007/978-3-319-72153-8 VL - 268 SP - 73 EP - 92 PB - Springer International Publishing ER - TY - CHAP A1 - Caimi, Gabrio A1 - Fischer, Frank A1 - Schlechte, Thomas T1 - Railway Track Allocation T2 - Handbook of Optimization in the Railway Industry N2 - This chapter addresses the classical task to decide which train runs on which track in a railway network. In this context a track allocation defines the precise routing of trains through a railway network, which usually has only a limited capacity. Moreover, the departure and arrival times at the visited stations of each train must simultaneously meet several operational and safety requirements. The problem to find the 'best possible' allocation for all trains is called the track allocation problem (TTP). Railway systems can be modeled on a very detailed scale covering the behavior of individual trains and the safety system to a large extent. However, those microscopic models are too big and not scalable to large networks, which make them inappropriate for mathematical optimization on a network wide level. Hence, most network optimization approaches consider simplified, so called macroscopic, models. In the first part we take a look at the challenge to construct a reliable and condensed macroscopic model for the associated microscopic model and to facilitate the transition between both models of different scale. In the main part we focus on the optimization problem for macroscopic models of the railway system. Based on classical graph-theoretical tools the track allocation problem is formulated to determine conflict-free paths in corresponding time-expanded graphs. We present standard integer programming model formulations for the track allocation problem that model resource or block conflicts in terms of packing constraints. In addition, we discuss the role of maximal clique inequalities and the concept of configuration networks. We will also present classical decomposition approaches like Lagrangian relaxation and bundle methods. Furthermore, we will discuss recently developed techniques, e.g., dynamic graph generation. Finally, we will discuss the status quo and show a vision of mathematical optimization to support real world track allocation, i.e. integrated train routing and scheduling, in a data-dominated and digitized railway future. Y1 - 2018 SN - 978-3-319-72152-1 U6 - https://doi.org/https://doi.org/10.1007/978-3-319-72153-8 VL - 268 SP - 141 EP - 160 PB - Springer International Publishing ER - TY - CHAP A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Optimization of Rolling Stock Rotations T2 - Handbook of Optimization in the Railway Industry N2 - This chapter shows a successful approach how to model and optimize rolling stock rotations that are required for the operation of a passenger timetable. The underlying mathematical optimization problem is described in detail and solved by RotOR, i.e., a complex optimization algorithm based on linear programming and combinatorial methods. RotOR is used by DB Fernverkehr AG (DBF) in order to optimize intercity express (ICE) rotations for the European high-speed network. We focus on main modeling and solving components, i.e. a hypergraph model and a coarse-to-fine column generation approach. Finally, the chapter concludes with a complex industrial re-optimization application showing the effectiveness of the approach for real world challenges. Y1 - 2018 SN - 978-3-319-72152-1 U6 - https://doi.org/https://doi.org/10.1007/978-3-319-72153-8 VL - 268 SP - 213 EP - 241 PB - Springer International Publishing ER - TY - CHAP A1 - Müller, Jan A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Maierhofer, Christiane T1 - Thermografie mit optimierter Anregung für die quantitative Untersuchung von Delaminationen in kohlenstofffaserverstärkten Kunststoffen T2 - NDT.net Proc. DGZfP 2017 N2 - Da kohlenstofffaserverstärkte Kunststoffe (CFK) in anspruchsvollen sicherheitsrelevanten Einsatzgebieten wie im Automobilbau und in der Luftfahrt eingesetzt werden, besteht ein zunehmender Bedarf an zerstörungsfreien Prüfmethoden. Ziel ist die Gewährleistung der Sicherheit und Zuverlässigkeit der eingesetzten Bauteile. Aktive Thermografieverfahren ermöglichen die effiziente Prüfung großer Flächen mit hoher Auflösung in wenigen Arbeitsschritten. Ein wichtiges Teilgebiet der Prüfungen ist die Ortung und Charakterisierung von Delaminationen, die sowohl bereits in der Fertigung als auch während der Nutzung eines Bauteils auftreten können, und dessen strukturelle Integrität schwächen. ;In diesem Beitrag werden CFK-Strukturen mit künstlichen und natürlichen Delaminationen mit Hilfe unterschiedlich zeitlich modulierter Strahlungsquellen experimentell untersucht. Verwendet werden dabei Anregungen mit Blitzlampen und mit frequenzmodulierten Halogenlampen. Mittels Filterfunktionen im Zeit- und Frequenzbereich wird das Kontrast-zu-Rausch-Verhältnis (CNR) der detektierten Fehlstellen optimiert. Verglichen werden anschließend die Nachweisempfindlichkeit, das CNR und die Ortsauflösung der zu charakterisierenden Delaminationen für die unterschiedlichen Anregungs- und Auswertungstechniken. Ergänzt werden die Experimente durch numerische Simulationen des dreidimensionalen Wärmetransportes. Y1 - 2017 ER - TY - THES A1 - Wulkow, Niklas T1 - Modelling the Spread of Innovations by a Markov Process in a Bayesian Framework Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66869 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Koltai, Péter A1 - Klus, Stefan A1 - Banisch, Ralf A1 - Dellnitz, Michael A1 - Schütte, Christof T1 - Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics JF - Jounal of Nonlinear Science N2 - We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics. Y1 - 2018 U6 - https://doi.org/10.1007/s00332-017-9415-0 VL - 28 IS - 2 SP - 471 EP - 512 ER - TY - GEN A1 - Grewe, Carl Martin A1 - Zachow, Stefan ED - Doll, Nikola ED - Bredekamp, Horst ED - Schäffner, Wolfgang T1 - Face to Face-Interface T2 - +ultra. Knowledge & Gestaltung Y1 - 2017 SP - 320 EP - 321 PB - Seemann Henschel ER - TY - GEN A1 - Grewe, Carl Martin A1 - Schreiber, Lisa ED - Doll, Nikola ED - Bredekamp, Horst ED - Schäffner, Wolfgang T1 - Digital Image Archive. The Archiving and Coding of Emotions T2 - +ultra. Knowledge & Gestaltung Y1 - 2017 SP - 281 EP - 286 PB - Seemann Henschel ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Nikolay, Niko A1 - Benson, Oliver A1 - Kewes, Günter A1 - Burger, Sven T1 - Riesz-projection-based theory of light-matter interaction in dispersive nanoresonators JF - Phys. Rev. A Y1 - 2018 U6 - https://doi.org/10.1103/PhysRevA.98.043806 VL - 98 SP - 043806 ER - TY - CHAP A1 - Klindt, Marco T1 - PDF/A considered harmful for digital preservation T2 - Proceedings of iPres – 14th International Conference on Digital Preservation / Kyoto, Japan / September 25 – 29, 2017 N2 - Today, the Portable Document Format (PDF) is the prevalent file format for the exchange of fixed content electronic documents for publication, research, and dissemination work in the academic and cultural heritage domains. Therefore it is not surprising that PDF/A is perceived to be an archival format suitable for digital archiving workflows. This paper gives a rather short overview about the history and technical complexity of the format, its benefits, shortcomings and potential pitfalls in the area of digital preservation with respect to aspects of accessibility and reusability of the information content of PDF/A. Several potential problems within the creation, preservation, and dissemination contexts are identified that may create problems for present and future content users. It also discusses some of the risks inherent to PDF/A for parts of the preservation community and suggests possible strategies to mitigate problems that might prevent future human or machine-based usability of the data and information stored within digital archives. Y1 - 2017 UR - https://phaidra.univie.ac.at/o:931063 VL - 14 ER - TY - JOUR A1 - Willie, Bettina M. A1 - Pap, Thomas A1 - Perka, Carsten A1 - Schmidt, Carsten Oliver A1 - Eckstein, Felix A1 - Arampatzis, Adamantios A1 - Hege, Hans-Christian A1 - Madry, Henning A1 - Vortkamp, Andrea A1 - Duda, Georg T1 - OVERLOAD of joints and its role in osteoarthritis - Towards understanding and preventing progression of primary osteoarthritis JF - Zeitschrift für Rheumatologie N2 - Intact joints are necessary for skeletal function and mobility in daily life. A healthy musculoskeletal system is the basis for a functional cardiovascular system as well as an intact immune system. Locomotion, physiotherapy, and various forms of patient activity are essential clinical therapies used in the treatment of neurodegeneration, stroke, diabetes, and cancer. Mobility is substantially impaired with degeneration of joints and, in advanced stages, nighttime pain and sleep disturbance are particularly cumbersome. Osteoarthritis (OA) is also known as degenerative joint disease. OA involves structural and compositional changes in the articular cartilage, as well as in the calcified cartilage, subchondral cortical bone, subchondral cancellous bone, meniscus, joint capsular tissue, and synovium; which eventually lead to degeneration of these tissues comprising synovial joints. Y1 - 2015 U6 - https://doi.org/10.1007/s00393-014-1561-2 VL - 76 IS - Suppl. 1 SP - 1 EP - 4 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Gross, Markus A1 - Theisel, Holger T1 - Progressive Monte Carlo rendering of atmospheric flow features across scales JF - Physical Review Fluids N2 - To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere. This paper is associated with a poster winner of a 2016 APS/DFD Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion. The original poster is available from the Gallery of Fluid Motion, https://doi.org/10.1103/APS.DFD.2016.GFM.P0030 Y1 - 2017 U6 - https://doi.org/10.1103/PhysRevFluids.2.090502 VL - 2 SP - 09050-1 EP - 09050-3 ER - TY - CHAP A1 - Sakurai, Daisuke A1 - Hege, Hans-Christian A1 - Kuhn, Alexander A1 - Rust, Henning A1 - Kern, Bastian A1 - Breitkopf, Tom-Lukas T1 - An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences T2 - Proceedings of 2017 IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV) N2 - In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features - which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66685 SP - 96 EP - 97 ER - TY - JOUR A1 - Klus, Stefan A1 - Schuster, Ingmar A1 - Muandet, Krikamol T1 - Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces JF - Journal of Machine Learning Research N2 - Transfer operators such as the Perron-Frobenius or Koopman operator play an important role in the global analysis of complex dynamical systems. The eigenfunctions of these operators can be used to detect metastable sets, to project the dynamics onto the dominant slow processes, or to separate superimposed signals. We extend transfer operator theory to reproducing kernel Hilbert spaces and show that these operators are related to Hilbert space representations of conditional distributions, known as conditional mean embeddings in the machine learning community. Moreover, numerical methods to compute empirical estimates of these embeddings are akin to data-driven methods for the approximation of transfer operators such as extended dynamic mode decomposition and its variants. In fact, most of the existing methods can be derived from our framework, providing a unifying view on the approximation of transfer operators. One main benefit of the presented kernel-based approaches is that these methods can be applied to any domain where a similarity measure given by a kernel is available. We illustrate the results with the aid of guiding examples and highlight potential applications in molecular dynamics as well as video and text data analysis. Y1 - 2017 ER - TY - CHAP A1 - Schuster, Ingmar A1 - Strathmann, Heiko A1 - Paige, Brooks A1 - Sejdinovic, Dino T1 - Kernel Sequential Monte Carlo T2 - Joint European Conference on Machine Learning and Knowledge Discovery in Databases N2 - We propose kernel sequential Monte Carlo (KSMC), a framework for sampling from static target densities. KSMC is a family of sequential Monte Carlo algorithms that are based on building emulator models of the current particle system in a reproducing kernel Hilbert space. We here focus on modelling nonlinear covariance structure and gradients of the target. The emulator's geometry is adaptively updated and subsequently used to inform local proposals. Unlike in adaptive Markov chain Monte Carlo, continuous adaptation does not compromise convergence of the sampler. KSMC combines the strengths of sequental Monte Carlo and kernel methods: superior performance for multimodal targets and the ability to estimate model evidence as compared to Markov chain Monte Carlo, and the emulator's ability to represent targets that exhibit high degrees of nonlinearity. As KSMC does not require access to target gradients, it is particularly applicable on targets whose gradients are unknown or prohibitively expensive. We describe necessary tuning details and demonstrate the benefits of the the proposed methodology on a series of challenging synthetic and real-world examples. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-71249-9_24 SP - 390 EP - 409 ER - TY - JOUR A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death JF - Heat and Mass Transfer N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. Y1 - 2018 U6 - https://doi.org/10.1007/s00231-018-2324-4 VL - 54 IS - 9 SP - 2815 EP - 2826 PB - Springer ER - TY - JOUR A1 - Tierney, Nicholas J. A1 - Mira, Antonietta A1 - Reinhold, J. Jost A1 - Weiser, Martin A1 - Burkart, Roman A1 - Benvenuti, Claudio A1 - Auricchio, Angelo T1 - Novel relocation methods for automatic external defibrillator improve out-of-hospital cardiac arrest coverage under limited resources JF - Resuscitation N2 - Background Mathematical optimisation models have recently been applied to identify ideal Automatic External Defibrillator (AED) locations that maximise coverage of Out of Hospital Cardiac Arrest (OHCA). However, these fixed location models cannot relocate existing AEDs in a flexible way, and have nearly exclusively been applied to urban regions. We developed a flexible location model for AEDs, compared its performance to existing fixed location and population models, and explored how these perform across urban and rural regions. Methods Optimisation techniques were applied to AED deployment and OHCA coverage was assessed. A total of 2802 geolocated OHCAs occurred in Canton Ticino, Switzerland, from January 1st 2005 to December 31st 2015. Results There were 719 AEDs in Canton Ticino. 635 (23%) OHCA events occurred within 100m of an AED, with 306 (31%) in urban, and 329 (18%) in rural areas. Median distance from OHCA events to the nearest AED was 224m (168m urban vs. 269m rural). Flexible location models performed better than fixed location and population models, with the cost to deploy 20 new AEDs instead relocating 171 existing AEDs to new locations, improving OHCA coverage to 38%, compared to 26% using fixed models, and 24% with the population based model. Conclusions Optimisation models for AEDs placement are superior to population models and should be strongly considered by communities when selecting areas for AED deployment. Compared to other models, flexible location models increase overall OHCA coverage, and decreases the distance to nearby AEDs, even in rural areas, while saving significant financial resources. Y1 - 2018 U6 - https://doi.org/10.1016/j.resuscitation.2018.01.055 IS - 125 SP - 83 EP - 89 ER - TY - JOUR A1 - Schrade, Katharina A1 - Tröger, Jessica A1 - Eldashan, Adeep A1 - Zühlke, Kerstin A1 - Abdul Azees, Kamal R. A1 - Elkins, Jonathan M. A1 - Neuenschwander, Martin A1 - Oder, Andreas A1 - Elkewedi, Mohamed A1 - Jaksch, Sarah A1 - Andrae, Karsten A1 - Li, Jinliang A1 - Fernandes, Jaoa A1 - Müller, Paul Markus A1 - Grunwald, Stephan A1 - Marino, Stephen F. A1 - Vukicevic, Tanja A1 - Eichhorst, Jenny A1 - Wiesner, Burkhard A1 - Weber, Marcus A1 - Kapiloff, Michael A1 - Rocks, Oliver A1 - Daumke, Oliver A1 - Wieland, Thomas A1 - Knapp, Stefan A1 - von Kries, Jens Peter A1 - Klussmann, Enno T1 - An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells JF - PLOS ONE N2 - Stimulation of renal collecting duct principal cells with antidiuretic hormone (arginine-vasopressin, AVP) results in inhibition of the small GTPase RhoA and the enrichment of the water channel aquaporin-2 (AQP2) in the plasma membrane. The membrane insertion facilitates water reabsorption from primary urine and fine-tuning of body water homeostasis. Rho guanine nucleotide exchange factors (GEFs) interact with RhoA, catalyze the exchange of GDP for GTP and thereby activate the GTPase. However, GEFs involved in the control of AQP2 in renal principal cells are unknown. The A-kinase anchoring protein, AKAP-Lbc, possesses GEF activity, specifically activates RhoA, and is expressed in primary renal inner medullary collecting duct principal (IMCD) cells. Through screening of 18,431 small molecules and synthesis of a focused library around one of the hits, we identified an inhibitor of the interaction of AKAP-Lbc and RhoA. This molecule, Scaff10-8, bound to RhoA, inhibited the AKAP-Lbc-mediated RhoA activation but did not interfere with RhoA activation through other GEFs or activities of other members of the Rho family of small GTPases, Rac1 and Cdc42. Scaff10-8 promoted the redistribution of AQP2 from intracellular vesicles to the periphery of IMCD cells. Thus, our data demonstrate an involvement of AKAP-Lbc-mediated RhoA activation in the control of AQP2 trafficking. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0191423 VL - 13 IS - 1 SP - e0191423 EP - e0191423 ER - TY - JOUR A1 - Schuster, Ingmar A1 - Constantine, Paul A1 - Sullivan, T. J. T1 - Exact active subspace Metropolis–Hastings, with applications to the Lorenz-96 system N2 - We consider the application of active subspaces to inform a Metropolis-Hastings algorithm, thereby aggressively reducing the computational dimension of the sampling problem. We show that the original formulation, as proposed by Constantine, Kent, and Bui-Thanh (SIAM J. Sci. Comput., 38(5):A2779-A2805, 2016), possesses asymptotic bias. Using pseudo-marginal arguments, we develop an asymptotically unbiased variant. Our algorithm is applied to a synthetic multimodal target distribution as well as a Bayesian formulation of a parameter inference problem for a Lorenz-96 system. Y1 - 2017 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Equivalence of weak and strong modes of measures on topological vector spaces JF - Inverse Problems N2 - Modes of a probability measure on an infinite-dimensional Banach space X are often defined by maximising the small-radius limit of the ratio of measures of norm balls. Helin and Burger weakened the definition of such modes by considering only balls with centres in proper subspaces of X, and posed the question of when this restricted notion coincides with the unrestricted one. We generalise these definitions to modes of arbitrary measures on topological vector spaces, defined by arbitrary bounded, convex, neighbourhoods of the origin. We show that a coincident limiting ratios condition is a necessary and sufficient condition for the equivalence of these two types of modes, and show that the coincident limiting ratios condition is satisfied in a wide range of topological vector spaces. Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aadef2 VL - 34 IS - 11 SP - 115013 ER - TY - JOUR A1 - Schäfer, Florian A1 - Sullivan, T. J. A1 - Owhadi, Houman T1 - Compression, inversion, and approximate PCA of dense kernel matrices at near-linear computational complexity JF - Multiscale Modeling and Simulation Y1 - 2021 U6 - https://doi.org/10.1137/19M129526X VL - 19 IS - 2 SP - 688 EP - 730 ER - TY - CHAP A1 - Cockayne, Jon A1 - Oates, Chris A1 - Sullivan, T. J. A1 - Girolami, Mark T1 - Probabilistic Numerical Methods for PDE-constrained Bayesian Inverse Problems T2 - Proceedings of the 36th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering N2 - This paper develops meshless methods for probabilistically describing discretisation error in the numerical solution of partial differential equations. This construction enables the solution of Bayesian inverse problems while accounting for the impact of the discretisation of the forward problem. In particular, this drives statistical inferences to be more conservative in the presence of significant solver error. Theoretical results are presented describing rates of convergence for the posteriors in both the forward and inverse problems. This method is tested on a challenging inverse problem with a nonlinear forward model Y1 - 2017 U6 - https://doi.org/10.1063/1.4985359 VL - 1853 SP - 060001-1 EP - 060001-8 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Stuart, Andrew T1 - Strong convergence rates of probabilistic integrators for ordinary differential equations JF - Statistics and Computing N2 - Probabilistic integration of a continuous dynamical system is a way of systematically introducing model error, at scales no larger than errors inroduced by standard numerical discretisation, in order to enable thorough exploration of possible responses of the system to inputs. It is thus a potentially useful approach in a number of applications such as forward uncertainty quantification, inverse problems, and data assimilation. We extend the convergence analysis of probabilistic integrators for deterministic ordinary differential equations, as proposed by Conrad et al.\ (\textit{Stat.\ Comput.}, 2016), to establish mean-square convergence in the uniform norm on discrete- or continuous-time solutions under relaxed regularity assumptions on the driving vector fields and their induced flows. Specifically, we show that randomised high-order integrators for globally Lipschitz flows and randomised Euler integrators for dissipative vector fields with polynomially-bounded local Lipschitz constants all have the same mean-square convergence rate as their deterministic counterparts, provided that the variance of the integration noise is not of higher order than the corresponding deterministic integrator. Y1 - 2019 U6 - https://doi.org/10.1007/s11222-019-09898-6 VL - 29 IS - 6 SP - 1265 EP - 1283 ER - TY - GEN A1 - Lindow, Norbert A1 - Redemann, Stefanie A1 - Fabig, Gunar A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Quantification of Three-Dimensional Spindle Architecture N2 - Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. Three-dimensional reconstruction of microtubules, however, is only the first step towards biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms. T3 - ZIB-Report - 18-07 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66562 SN - 1438-0064 ER - TY - THES A1 - Sikorski, Alexander T1 - An Information-Theoretic Empirical Bayes Method and its Application to a Systems Biology Model N2 - This thesis covers the development and application of an empirical Bayes method to the problem of parameter estimation in systems biology. The goal was to provide a general and practical solution to the Bayesian inverse problem in the case of high dimensional parameter spaces making use of present cohort-data. We show that the maximum penalized likelihood estimator (MPLE) with information penalty is based on natural, information-theoretic considerations and admits the desirable property of transformation invariance. Due to its concavity, the objective function is computationally feasible and its mesh-free Monte-Carlo approximation enables its application to high-dimensional problems eluding the curse of dimensionality. We furthermore show how to apply the developed methods to a real world problem by the means of Markov chain Monte-Carlo sampling (MCMC), affirming its proficiency in a practical scenario. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65098 ER - TY - JOUR A1 - Schmidtke, Robert A1 - Erleben, Kenny T1 - Chunked Bounding Volume Hierarchies for Fast Digital Prototyping using Volumetric Meshes JF - IEEE Transactions on Visualization and Computer Graphics N2 - We present a novel approach to using Bounding Volume Hierarchies (BVHs) for collision detection of volumetric meshes for digital prototyping based on accurate simulation. In general, volumetric meshes contain more primitives than surface meshes, which in turn means larger BVHs. To manage these larger BVHs, we propose an algorithm for splitting meshes into smaller chunks with a limited-size BVH each. Limited-height BVHs make guided, all-pairs testing of two chunked meshes well-suited for GPU implementation. This is because the dynamically generated work during BVH traversal becomes bounded. Chunking is simple to implement compared to dynamic load balancing methods and can result in an overall two orders of magnitude speedup on GPUs. This indicates that dynamic load balancing may not be a well suited scheme for the GPU. The overall application timings showed that data transfers were not the bottleneck. Instead, the conversion to and from OpenCL friendly data structures was causing serious performance impediments. Still, a simple OpenMP acceleration of the conversion allowed the GPU solution to beat the CPU solution by 20%. We demonstrate our results using rigid and deformable body scenes of varying complexities on a variety of GPUs. Y1 - 2018 U6 - https://doi.org/10.1109/TVCG.2017.2784441 SN - 1941-0506 VL - 24 IS - 12 SP - 3044 EP - 3057 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko JF - Advances in Physics: X N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. Y1 - 2018 U6 - https://doi.org/10.1080/23746149.2017.1404436 VL - 3 IS - 1 SP - 1404436 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Zaslansky, Paul A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material) N2 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens. Y1 - 2017 U6 - https://doi.org/10.12752/4.DKN.1.0 N1 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. ER - TY - JOUR A1 - Chen, Duote A1 - Manley, Phillip A1 - Tockhorn, Philipp A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane A1 - Jäger, Klaus T1 - Nanophotonic Light Management for Perovskite-Silicon Tandem Solar Cells JF - J. Photonics Energy Y1 - 2018 U6 - https://doi.org/10.1117/1.JPE.8.022601 VL - 8 SP - 022601 ER - TY - THES A1 - Eifler, Leon T1 - Mixed-Integer Programming for Clustering in Non-reversible Markov Processes N2 - The topic of this thesis is the examination of an optimization model which stems from the clustering process of non-reversible markov processes. We introduce the cycle clustering problem und formulate it as a mixed integer program (MIP). We prove that this problem is N P-hard and discuss polytopal aspects such as facets and dimension. The focus of this thesis is the development of solving methods for this clustering problem. We develop problem specific primal heuristics, as well as separation methods and an approximation algorithm. These techniques are implemented in practice as an application for the MIP solver SCIP. Our computational experiments show that these solving methods result in an average speedup of ×4 compared to generic solvers and that our application is able to solve more instances to optimality within the given time limit of one hour. KW - Markov State Models KW - NESS KW - Non-reversible Markov Processes KW - Mixed-Integer Programming Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66486 ER - TY - JOUR A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Müller, Anne A1 - Kolbe, Katharina A1 - Boden, Sophia A1 - Fessele, Claudia A1 - Lindhorst, Thisbe A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH JF - Marcomolecular Bioscience Y1 - 2017 U6 - https://doi.org/10.1002/mabi.201700198 VL - 17 IS - 12 SP - 1700198 ER - TY - JOUR A1 - Villatoro, Jose A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Riedel, Jens A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry JF - Analytical and Bioanalytical Chemistry Y1 - 2016 U6 - https://doi.org/10.1007/s00216-016-9739-x VL - 408 IS - 23 SP - 6259 EP - 6268 ER - TY - JOUR A1 - Lorenz, Philipp A1 - Wolf, Frederik A1 - Braun, Jonas A1 - Djurdjevac Conrad, Natasa A1 - Hövel, Philipp T1 - Capturing the Dynamics of Hashtag-Communities JF - International Workshop on Complex Networks and their Applications Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-72150-7_33 SP - 401 EP - 413 ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa T1 - Cycle-flow-based module detection in directed recurrence networks JF - EPL (Europhysics Letters) Y1 - 2014 U6 - https://doi.org/10.1209/0295-5075/108/68008 VL - 108 IS - 6 ER - TY - THES A1 - Djurdjevac Conrad, Natasa T1 - Methods for analyzing complex networks using random walker Y1 - 2012 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - SCIP-Jack—a solver for STP and variants with parallelization extensions: An update N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. Although the different Steiner tree problem variants are usually strongly related, solution approaches employed so far have been prevalently problem-specific. Against this backdrop, the solver SCIP-Jack was created as a general-purpose framework that can be used to solve the classical Steiner tree problem and 11 of its variants. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. Furthermore, SCIP-Jack includes various newly developed algorithmic components such as preprocessing routines and heuristics. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. After the introduction of SCIP-Jack at the 2014 DIMACS Challenge on Steiner problems, the overall performance of the solver has considerably improved. This article provides an overview on the current state. T3 - ZIB-Report - 18-05 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66416 SN - 1438-0064 ER - TY - CHAP A1 - Abebe, Muluneh G. A1 - Gomard, Guillaume A1 - Zschiedrich, Lin A1 - Rockstuhl, Carsten A1 - Paetzold, Ulrich W. A1 - Abass, Aimi T1 - Thermodynamics of Photon Recycling in Four Terminal Perovskite/si Tandem Solar Cells T2 - Optical Nanostructures and Advanced Materials for Photovoltaics Y1 - 2017 U6 - https://doi.org/10.1364/PV.2017.PM4A.2 SP - PM4A.2 ER - TY - GEN A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. T3 - ZIB-Report - 17-78 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66338 SN - 1438-0064 ER - TY - GEN A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Teckentrup, Aretha T1 - Random forward models and log-likelihoods in Bayesian inverse problems T2 - SIAM/ASA Journal on Uncertainty Quantification N2 - We consider the use of randomised forward models and log-likelihoods within the Bayesian approach to inverse problems. Such random approximations to the exact forward model or log-likelihood arise naturally when a computationally expensive model is approximated using a cheaper stochastic surrogate, as in Gaussian process emulation (kriging), or in the field of probabilistic numerical methods. We show that the Hellinger distance between the exact and approximate Bayesian posteriors is bounded by moments of the difference between the true and approximate log-likelihoods. Example applications of these stability results are given for randomised misfit models in large data applications and the probabilistic solution of ordinary differential equations. T3 - ZIB-Report - 18-03 KW - Bayesian inverse problem KW - random likelihood KW - surrogate model KW - posterior consistency KW - probabilistic numerics KW - uncertainty quantification KW - randomised misfit Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66324 SN - 1438-0064 VL - 6 IS - 4 SP - 1600 EP - 1629 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Heller, Markus O. T1 - On intrinsic equivalences of the finite helical axis, the instantaneous helical axis, and the SARA approach. A mathematical perspective. JF - Journal of Biomechanics Y1 - 2019 U6 - https://doi.org/10.1016/j.jbiomech.2018.12.034 VL - 84 SP - 4 EP - 10 ER - TY - JOUR A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage JF - PLOS ONE N2 - Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0188018 ER - TY - GEN A1 - Gleixner, Ambros A1 - Eifler, Leon A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gemander, Patrick A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Viernickel, Jan Merlin A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 5.0 N2 - This article describes new features and enhanced algorithms made available in version 5.0 of the SCIP Optimization Suite. In its central component, the constraint integer programming solver SCIP, remarkable performance improvements have been achieved for solving mixed-integer linear and nonlinear programs. On MIPs, SCIP 5.0 is about 41 % faster than SCIP 4.0 and over twice as fast on instances that take at least 100 seconds to solve. For MINLP, SCIP 5.0 is about 17 % faster overall and 23 % faster on instances that take at least 100 seconds to solve. This boost is due to algorithmic advances in several parts of the solver such as cutting plane generation and management, a new adaptive coordination of large neighborhood search heuristics, symmetry handling, and strengthened McCormick relaxations for bilinear terms in MINLPs. Besides discussing the theoretical background and the implementational aspects of these developments, the report describes recent additions for the other software packages connected to SCIP, in particular for the LP solver SoPlex, the Steiner tree solver SCIP-Jack, the MISDP solver SCIP-SDP, and the parallelization framework UG. T3 - ZIB-Report - 17-61 KW - constraint integer programming KW - linear programming KW - mixed-integer linear programming KW - mixed-integer nonlinear programming KW - optimization solver KW - branch-and-cut KW - branch-and-price KW - column generation framework KW - parallelization KW - mixed-integer semidefinite programming KW - Steiner tree optimization Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66297 SN - 1438-0064 ER - TY - JOUR A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Lehmann, Lutz A1 - Radons, Manuel A1 - Hasenfelder, Richard T1 - Piecewise linear secant approximation via algorithmic piecewise differentiation JF - Optimization Methods and Software N2 - It is shown how piecewise differentiable functions F : IR^n -> IR^m that are defined by evaluation programmes can be approximated locally by a piecewise linear model based on a pair of sample points \check x and \hat x. We show that the discrepancy between function and model at any point x is of the bilinear order O(||x - \check x||*||x - \hat x||). As an application of the piecewise linearization procedure we devise a generalized Newton's method based on successive piecewise linearization and prove for it sufficient conditions for convergence and convergence rates equalling those of semismooth Newton. We conclude with the derivation of formulas for the numerically stable implementation of the aforedeveloped piecewise linearization methods. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2017.1387256 VL - 33 IS - 4-6 SP - 1108 EP - 1126 PB - Taylor & Francis ER - TY - JOUR A1 - Griewank, Andreas A1 - Hasenfelder, Richard A1 - Radons, Manuel A1 - Lehmann, Lutz A1 - Streubel, Tom T1 - Integrating Lipschitzian dynamical systems using piecewise algorithmic differentiation JF - Optimization Methods and Software N2 - In this article we analyse a generalized trapezoidal rule for initial value problems with piecewise smooth right-hand side F : IR^n -> IR^n based on a generalization of algorithmic differentiation. When applied to such a problem, the classical trapezoidal rule suffers from a loss of accuracy if the solution trajectory intersects a nondifferentiability of F. The advantage of the proposed generalized trapezoidal rule is threefold: Firstly, we can achieve a higher convergence order than with the classical method. Moreover, the method is energy preserving for piecewise linear Hamiltonian systems. Finally, in analogy to the classical case we derive a third-order interpolation polynomial for the numerical trajectory. In the smooth case, the generalized rule reduces to the classical one. Hence, it is a proper extension of the classical theory. An error estimator is given and numerical results are presented. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1378653 VL - 33 SP - 1089 EP - 1107 PB - Taylor & Francis ER - TY - GEN A1 - Benner, Peter A1 - Grundel, Sara A1 - Himpe, Christian A1 - Huck, Christoph A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - Gas Network Benchmark Models N2 - The simulation of gas transportation networks becomes increasingly more important as its use-cases broadens to more complex applications. Classically, the purpose of the gas network was the transportation of predominantly natural gas from a supplier to the consumer for long-term scheduled volumes. With the rise of renewable energy sources, gas-fired power plants are often chosen to compensate for the fluctuating nature of the renewables, due to their on-demand power generation capability. Such an only short-term plannable supply and demand setting requires sophisticated simulations of the gas network prior to the dispatch to ensure the supply of all customers for a range of possible scenarios and to prevent damages to the gas network. In this work we describe the modelling of gas networks and present benchmark systems to test implementations and compare new or extended models. T3 - ZIB-Report - 17-73 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66274 SN - 1438-0064 ER - TY - GEN A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume T1 - Approximate and exact D-optimal designs for $2^k$ factorial experiments for Generalized Linear Models via SOCP N2 - We propose (Mixed Integer) Second Order Cone Programming formulations to find approximate and exact $D-$optimal designs for $2^k$ factorial experiments for Generalized Linear Models (GLMs). Locally optimal designs are addressed with Second Order Cone Programming (SOCP) and Mixed Integer Second Order Cone Programming (MISOCP) formulations. The formulations are extended for scenarios of parametric uncertainty employing the Bayesian framework for \emph{log det} $D-$optimality criterion. A quasi Monte-Carlo sampling procedure based on the Hammersley sequence is used for integrating the optimality criterion in the parametric region. The problems are solved in \texttt{GAMS} environment using \texttt{CPLEX} solver. We demonstrate the application of the algorithm with the logistic, probit and complementary log-log models and consider full and fractional factorial designs. T3 - ZIB-Report - 18-02 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66256 SN - 1438-0064 ER - TY - JOUR A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume A1 - Wong, Weng Kee T1 - An algorithm based on Semidefinite Programming for finding minimax optimal designs JF - Computational Statistics & Data Analysis Y1 - 2018 U6 - https://doi.org/10.1016/j.csda.2017.09.008 VL - 119 SP - 99 EP - 117 ER - TY - GEN A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume A1 - Wong, Weng Kee T1 - An algorithm based on Semidefinite Programming for finding minimax optimal designs N2 - An algorithm based on a delayed constraint generation method for solving semi-infinite programs for constructing minimax optimal designs for nonlinear models is proposed. The outer optimization level of the minimax optimization problem is solved using a semidefinite programming based approach that requires the design space be discretized. A nonlinear programming solver is then used to solve the inner program to determine the combination of the parameters that yields the worst-case value of the design criterion. The proposed algorithm is applied to find minimax optimal designs for the logistic model, the flexible 4-parameter Hill homoscedastic model and the general nth order consecutive reaction model, and shows that it (i) produces designs that compare well with minimax $D-$optimal designs obtained from semi-infinite programming method in the literature; (ii) can be applied to semidefinite representable optimality criteria, that include the common A-, E-,G-, I- and D-optimality criteria; (iii) can tackle design problems with arbitrary linear constraints on the weights; and (iv) is fast and relatively easy to use. T3 - ZIB-Report - 18-01 KW - Cutting plane algorithm KW - Design efficiency KW - Equivalence theorem KW - Model-based optimal design KW - Nonlinear programming Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66249 SN - 1438-0064 ER - TY - CHAP A1 - Noack, Matthias T1 - OpenCL in Scientific High Performance Computing: The Good, the Bad, and the Ugly T2 - Proceedings of the 5th International Workshop on OpenCL N2 - For writing a new scientific application, portability across existing and future hardware should be the major design goal, as there is a multitude of different compute devices, and programme codes typically outlive systems by far. Unlike other programming models that address parallelism or heterogeneity, OpenCL does provide practical portability across a wide range of HPC-relevant architectures. Other than that, it has a range of further advantages like being a library-only implementation, and using runtime kernel-compilation. We present experiences with utilising OpenCL alongside C++, MPI, and CMake in two real-world scientific codes. Our targets are a Cray XC40 supercomputer with multi- and many-core (Xeon Phi) CPUs, as well as multiple smaller systems with Nvidia and AMD GPUs. We shed light on practical issues arising in such a scenario, like the interaction between OpenCL and MPI, discuss solutions, and point out current limitations of OpenCL in the domain of scientific HPC from an application developer's and user's point of view. Y1 - 2017 U6 - https://doi.org/10.1145/3078155.3078170 SP - 12:1 EP - 12:3 ER - TY - GEN A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Cao, Karl-Kien A1 - Cebulla, Felix A1 - Fiand, Frederik A1 - Gils, Hans Christian A1 - Gleixner, Ambros A1 - Khabi, Dmitry A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Wetzel, Manuel T1 - Optimizing Large-Scale Linear Energy System Problems with Block Diagonal Structure by Using Parallel Interior-Point Methods N2 - Current linear energy system models (ESM) acquiring to provide sufficient detail and reliability frequently bring along problems of both high intricacy and increasing scale. Unfortunately, the size and complexity of these problems often prove to be intractable even for commercial state-of-the-art linear programming solvers. This article describes an interdisciplinary approach to exploit the intrinsic structure of these large-scale linear problems to be able to solve them on massively parallel high-performance computers. A key aspect are extensions to the parallel interior-point solver PIPS-IPM originally developed for stochastic optimization problems. Furthermore, a newly developed GAMS interface to the solver as well as some GAMS language extensions to model block-structured problems will be described. T3 - ZIB-Report - 17-75 KW - energy system models KW - interior-point methods KW - high-performance computing Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66183 SN - 1438-0064 ER - TY - GEN A1 - Bittracher, Andreas A1 - Banisch, Ralf A1 - Schütte, Christof T1 - Data-driven Computation of Molecular Reaction Coordinates N2 - The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, the authors identified a condition under which such reaction coordinates exist - the existence of a so-called transition manifold - and proposed a numerical method for their point-wise computation that relies on short bursts of MD simulations. This article represents an extension of the method towards practical applicability in computational chemistry. It describes an alternative computational scheme that instead relies on more commonly available types of simulation data, such as single long molecular trajectories, or the push-forward of arbitrary canonically-distributed point clouds. It is based on a Galerkin approximation of the transition manifold reaction coordinates, that can be tuned to individual requirements by the choice of the Galerkin ansatz functions. Moreover, we propose a ready-to-implement variant of the new scheme, that computes data-fitted, mesh-free ansatz functions directly from the available simulation data. The efficacy of the new method is demonstrated on a realistic peptide system. T3 - ZIB-Report - 17-77 KW - reaction coordinate KW - coarse graining KW - transition manifold KW - transfer operator KW - Galerkin method KW - meshfree basis KW - data-driven Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66179 SN - 1438-0064 ER - TY - JOUR A1 - Cockayne, Jon A1 - Oates, Chris A1 - Sullivan, T. J. A1 - Girolami, Mark T1 - Bayesian Probabilistic Numerical Methods JF - SIAM Review N2 - Over forty years ago average-case error was proposed in the applied mathematics literature as an alternative criterion with which to assess numerical methods. In contrast to worst-case error, this criterion relies on the construction of a probability measure over candidate numerical tasks, and numerical methods are assessed based on their average performance over those tasks with respect to the measure. This paper goes further and establishes Bayesian probabilistic numerical methods as solutions to certain inverse problems based upon the numerical task within the Bayesian framework. This allows us to establish general conditions under which Bayesian probabilistic numerical methods are well defined, encompassing both the non-linear and non-Gaussian context. For general computation, a numerical approximation scheme is proposed and its asymptotic convergence established. The theoretical development is extended to pipelines of computation, wherein probabilistic numerical methods are composed to solve more challenging numerical tasks. The contribution highlights an important research frontier at the interface of numerical analysis and uncertainty quantification, and a challenging industrial application is presented. Y1 - 2019 U6 - https://doi.org/10.1137/17M1139357 VL - 61 IS - 4 SP - 756 EP - 789 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - On accurate simulations of thin-film solar cells with a thick glass superstrate JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.000A99 VL - 26 SP - A99 ER - TY - GEN A1 - Witzig, Jakob T1 - Conflict Driven Diving for Mixed Integer Programming N2 - The analysis of infeasibility plays an important role in solving satisfiability problems (SAT) and mixed integer programs (MIPs). In mixed integer programming, this procedure is called conflict analysis. So far, modern MIP solvers use conflict analysis only for propagation and improving the dual bound, i.e., fathoming nodes that cannot contain feasible solutions. In this short paper, we present a new approach which uses conflict information to improve the primal bound during a MIP solve. To derive new improving primal solutions we use a conflict driven diving heuristic called conflict diving that uses the information obtained by conflict analysis. Conflict diving pursues a twofold strategy. By using conflict information the new diving approach is guided into parts of the search space that are usually not explored by other diving heuristics. At the same time, conflict diving has a fail-fast-strategy to reduce the time spent if it cannot find a new primal solution. As a byproduct, additional valid conflict constraints can be derived, from which a MIP solver can gain benefit to improve the dual bound as well. To show the added-value of conflict diving within a MIP solver, conflict diving has been implemented within the non-commercial MIP solver SCIP. Experiments are carried out on general MIP instances from standard public test sets, like MIPLIB2010 or Cor@l. T3 - ZIB-Report - 17-69 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66116 SN - 1438-0064 ER - TY - JOUR A1 - Schnauber, Peter A1 - Schall, Johannes A1 - Bounouar, Samir A1 - Höhne, Theresa A1 - Park, Suk-In A1 - Ryu, Geun-Hwan A1 - Heindel, Tobias A1 - Burger, Sven A1 - Song, Jin-Dong A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Deterministic integration of quantum dots into on-chip multi-mode interference beamsplitters using in-situ electron beam lithography JF - Nano Lett. Y1 - 2018 U6 - https://doi.org/10.1021/acs.nanolett.7b05218 VL - 18 SP - 2336 ER - TY - THES A1 - Zänker, Martin T1 - Estimating Human Face Reflectance from Single-Shot Multiview Data Y1 - 2017 ER - TY - THES A1 - le Roux, Gabriel T1 - Development and Evaluation of Algorithms for 3D Facial Motion Estimation from Stereo Videos Y1 - 2017 ER - TY - GEN A1 - Fackeldey, Konstantin A1 - Koltai, Péter A1 - Névir, Peter A1 - Rust, Henning A1 - Schild, Axel A1 - Weber, Marcus T1 - From Metastable to Coherent Sets - time-discretization schemes N2 - Given a time-dependent stochastic process with trajectories x(t) in a space $\Omega$, there may be sets such that the corresponding trajectories only very rarely cross the boundaries of these sets. We can analyze such a process in terms of metastability or coherence. Metastable sets M are defined in space $M\subset\Omega$, coherent sets $M(t)\subset\Omega$ are defined in space and time. Hence, if we extend the space by the time-variable t, coherent sets are metastable sets in $\Omega\times[0,\infty]$. This relation can be exploited, because there already exist spectral algorithms for the identification of metastable sets. In this article we show that these well-established spectral algorithms (like PCCA+) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-timediscretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application. T3 - ZIB-Report - 17-74 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66074 SN - 1438-0064 ER - TY - GEN A1 - Joachimsky, Robert A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung früher Gonarthrose N2 - Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein häufiges Krankheitsbild unter älteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder geschädigter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfläche erhöhen und so der teilweise oder vollständige Gelenkersatz hinausgezögert oder vermieden werden. In dieser Arbeit präsentieren wir eine Planungssoftware für die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgewählt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. Für jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern Rückmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterstützt somit als Entscheidungshilfe die behandelnden Ärzte bei der patientenspezifischen Spacerauswahl. T3 - ZIB-Report - 17-72 KW - Osteoarthrose KW - Kniegelenk KW - Medizinische Planung KW - Visualisierung Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66064 SN - 1438-0064 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. T3 - ZIB-Report - 17-71 KW - Knee Arthroplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66052 SN - 1438-0064 ER - TY - GEN A1 - Deuflhard, Peter T1 - The Grand Four N2 - This paper gives a concise synopsis and some new insights concerning four affine invariant globalizations of the local Newton method. The invariance classes include: affine covariance, affine contravariance, affine conjugacy, and affine similarity. In view of algorithmic robustness, each of these classes of algorithms is particularly suitable for some corresponding problem class. T3 - ZIB-Report - 17-70 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66038 SN - 1438-0064 ER - TY - GEN A1 - Binkowski, Felix T1 - On the convergence behavior of spectral deferred correction methods for convection-diffusion equations N2 - Spectral deferred correction (SDC) Methoden, vorgestellt von Dutt, Greengard und Rokhlin in [1], sind iterative Verfahren zur numerischen Lösung von Anfangswertproblemen für gewöhnliche Differentialgleichungen. Wenn diese Methoden konvergieren, dann wird unter Verwendung von Zeitschrittverfahren niedriger Ordnung eine Kollokationslösung berechnet. Die Lösung von steifen Anfangswertproblemen ist eine relevante Problemstellung in der numerischen Mathematik. SDC-Methoden, speziell für steife Probleme, werden von Martin Weiser in [2] konstruiert. Die Theorie und die Experimente beziehen sich dabei auf Probleme, die aus räumlich semidiskretisierten Reaktions-Diffusions-Gleichungen entstehen. In dieser Arbeit werden die Ansätze aus [2] auf Konvektions-Diffusions-Gleichungen angewendet und das resultierende Konvergenzverhalten von SDC-Methoden untersucht. Basierend auf einem einfachen Konvektions-Diffusions-Operator, dessen spektrale Eigenschaften umfassend studiert werden, wird ein Schema zur Verbesserung dieses Verhaltens entwickelt. Numerische Experimente zeigen, dass eine Verbesserung der in [1] eingeführten SDC-Methoden möglich ist. Die Untersuchungen ergeben weiterhin, dass das auch für komplexere Konvektions-Diffusions-Probleme gilt. [1] Alok Dutt, Leslie Greengard, und Vladimir Rokhlin. “Spectral deferred correction methods for ordinary differential equations.” In: BIT 40.2 (2000), pp. 241–266. [2] Martin Weiser. “Faster SDC convergence on non-equidistant grids by DIRK sweeps.” In: BIT 55.4 (2015), pp. 1219–1241. T3 - ZIB-Report - 17-53 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66016 SN - 1438-0064 ER - TY - THES A1 - Reddy, Gutha Vaishnavi T1 - Automatic Classification of 3D MRI data using Deep Convolutional Neural Networks N2 - The chronic disease of Osteoarthritis of the knee that causes pain and discomfort in the knee is associated with the degradation of the joint between the tibia and the femur. The degeneration of this joint is attributed partially to the damage of the meniscus of the knee which forms an important part of the knee joint. Magnetic Resonance Imaging (MRI) is used to diagnose such a kind of osteoarthritis by identifying the degeneration of the knee meniscus. A computer aided diagnostic system that aims to assist a doctor in decision making regarding such a diagnosis can expedite the very diagnosis. Diagnostic decision making for medical imaging falls into the category of classification for a computer vision task. Very Deep Convolutional Networks have been central to the largest advances in computer vision, in recent years. This work entails application of such convolutional networks for the purpose of recognizing a meniscus tear in MRI images as attempting a step towards developing a computer aided diagnosis system for osteoarthritis. Consequently, state-of-the-art pre-trained image recognition networks namely Alexnet, Inceptionv3, VGG and Resnet and Xception were trained on MRI data of the knee meniscus to see if they work for the task of recognizing a tear. A comparison of their classification performance on MRI data was done. The best performing model was the fine-tuned InceptionV3 network which achieved an accuracy close to 60% for classifying 600 patients based on presence of a tear or not. Y1 - 2017 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Breuer, Matthias A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schade, Stanley A1 - Schlechte, Thomas T1 - Timetable Sparsification by Rolling Stock Rotation Optimization N2 - Rolling stock optimization is a task that naturally arises by operating a railway system. It could be seen with different level of details. From a strategic perspective to have a rough plan which types of fleets to be bought to a more operational perspective to decide which coaches have to be maintained first. This paper presents a new approach to deal with rolling stock optimisation in case of a (long term) strike. Instead of constructing a completely new timetable for the strike period, we propose a mixed integer programming model that is able to choose appropriate trips from a given timetable to construct efficient tours of railway vehicles covering an optimized subset of trips, in terms of deadhead kilometers and importance of the trips. The decision which trip is preferred over the other is made by a simple evaluation method that is deduced from the network and trip defining data. T3 - ZIB-Report - 17-63 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65948 SN - 1438-0064 ER - TY - JOUR A1 - Quer, Jannes A1 - Donati, Luca A1 - Keller, Bettina A1 - Weber, Marcus T1 - An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates JF - SIAM Journal on Scientific Computing N2 - In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities. Y1 - 2018 U6 - https://doi.org/10.1137/17m1124772 VL - 40 IS - 2 SP - A653 EP - A670 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage N2 - Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours. T3 - ZIB-Report - 17-62 KW - micro-CT KW - image segmentation KW - 2D distance map KW - hierarchical watershed KW - stingray KW - tesserae KW - biological tilings KW - Amira Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65785 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: theory and algorithms JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19110626 VL - 19 IS - 11 ER - TY - JOUR A1 - Schmidt, Martin A1 - Assmann, Denis A1 - Burlacu, Robert A1 - Humpola, Jesco A1 - Joormann, Imke A1 - Kanelakis, Nikolaos A1 - Koch, Thorsten A1 - Oucherif, Djamal A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Sirvent, Matthias T1 - GasLib – A Library of Gas Network Instances JF - Data Y1 - 2017 U6 - https://doi.org/10.3390/data2040040 VL - 2 IS - 4 ER - TY - JOUR A1 - Koch, Thorsten T1 - The ZIMPL modeling language JF - Optima Y1 - 2017 UR - http://www.mathopt.org/Optima-Issues/optima103.pdf VL - 103 SP - 8 EP - 9 ER - TY - GEN A1 - Clausecker, Robert T1 - Notes on the Construction of Pattern Databases N2 - This report aims to explain and extend pattern databases as a tool in finding optimal solutions to combination puzzles. Using sliding tile puzzles as an example, an overview over techniques to construct and use pattern databases is given, analysed, and extended. As novel results, zero aware additive pattern databases and PDB catalogues are introduced. This report originally appeared as a bachelor thesis at Humboldt University of Berlin under the title Notes on the Construction of Tablebases. T3 - ZIB-Report - 17-59 KW - pattern-database 15-puzzle 24-puzzle ida* heuristic-search pdb-catalogue zpdb Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65586 SN - 1438-0064 ER - TY - GEN A1 - Walther, Tom A1 - Hiller, Benjamin A1 - Saitenmacher, René T1 - Polyhedral 3D Models for compressors in gas networks N2 - Compressor machines are crucial elements in a gas transmission network, required to compensate for the pressure loss caused by friction in the pipes. Modelling all physical and technical details of a compressor machine involves a large amount of nonlinearity, which makes it hard to use such models in the optimization of large-scale gas networks. In this paper, we are going to describe a modelling approach for the operating range of a compressor machine, starting from a physical reference model and resulting in a polyhedral representation in the 3D space of mass flow throughput as well as in- and outlet pressure. T3 - ZIB-Report - 17-66 KW - gas compressor modeling, polyhedral model, accuracy, z factor Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65864 SN - 1438-0064 ER - TY - THES A1 - Skrzypczak, Jan T1 - Weakening Paxos Consensus Sequences for Commutative Commands N2 - Consensus (agreement on a value) is regarded as a fundamental primitive in the design of fault tolerant distributed systems. A well-known solution to the consensus problem is Paxos. Extensions of the Paxos algorithm make it possible to reach agreement on a sequence of commands which can then be applied on a replicated state. However, concurrently proposed commands can create conflicts that must be resolved by ordering them. This thesis delivers an in-depth description of a Paxos-based algorithm to establish such command sequences, called Paxos Round Based Register (PRBR). In contrast to conventional approaches like Multi-Paxos, PRBR can manage multiple command sequences independently. Furthermore, each sequence is established in-place, which eliminates the need for managing multiple Paxos instances. PRBR is extended as part of this thesis to exploit the commutativity of concurrently proposed commands. As a result, conflict potential can be greatly reduced which increases the number of commands that can be handled by PRBR. This is shown for a number of workloads in an experimental evaluation. KW - Paxos KW - Consensus Y1 - 2017 ER - TY - JOUR A1 - Berthold, Timo A1 - Hendel, Gregor A1 - Koch, Thorsten T1 - From feasibility to improvement to proof: three phases of solving mixed-integer programs JF - Optimization Methods and Software N2 - Modern mixed-integer programming (MIP) solvers employ dozens of auxiliary algorithmic components to support the branch-and-bound search in finding and improving primal solutions and in strengthening the dual bound. Typically, all components are tuned to minimize the average running time to prove optimality. In this article, we take a different look at the run of a MIP solver. We argue that the solution process consists of three distinct phases, namely achieving feasibility, improving the incumbent solution, and proving optimality. We first show that the entire solving process can be improved by adapting the search strategy with respect to the phase-specific aims using different control tunings. Afterwards, we provide criteria to predict the transition between the individual phases and evaluate the performance impact of altering the algorithmic behaviour of the non-commercial MIP solver Scip at the predicted phase transition points. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2017.1392519 VL - 33 IS - 3 SP - 499 EP - 517 PB - Taylor & Francis ER - TY - GEN A1 - Skrzypczak, Jan T1 - Weakening Paxos Consensus Sequences for Commutative Commands N2 - Consensus (agreement on a value) is regarded as a fundamental primitive in the design of fault tolerant distributed systems. A well-known solution to the consensus problem is Paxos. Extensions of the Paxos algorithm make it possible to reach agreement on a sequence of commands which can then be applied on a replicated state. However, concurrently proposed commands can create conflicts that must be resolved by ordering them. This thesis delivers an in-depth description of a Paxos-based algorithm to establish such command sequences, called Paxos Round Based Register (PRBR). In contrast to conventional approaches like Multi-Paxos, PRBR can manage multiple command sequences independently. Furthermore, each sequence is established in-place, which eliminates the need for managing multiple Paxos instances. PRBR is extended as part of this thesis to exploit the commutativity of concurrently proposed commands. As a result, conflict potential can be greatly reduced which increases the number of commands that can be handled by PRBR. This is shown for a number of workloads in an experimental evaluation. T3 - ZIB-Report - 17-64 KW - Consensus KW - Paxos Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65741 SN - 1438-0064 ER - TY - CHAP A1 - Gregersen, Niels A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Ivinskaya, Aliaksandra A1 - Lavrinenko, Andrei A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Häyrynen, Teppo A1 - Merk, Jesper T1 - Comparison of five numerical methods for computing quality factors and resonance wavelengths in photonic crystal membrane cavities T2 - CLEO/Europe-EQEC Y1 - 2017 U6 - https://doi.org/10.1109/CLEOE-EQEC.2017.8087750 ER - TY - GEN A1 - Shinano, Yuji T1 - The Ubiquity Generator Framework: 7 Years of Progress in Parallelizing Branch-and-Bound N2 - Mixed integer linear programming (MIP) is a general form to model combinatorial optimization problems and has many industrial applications. The performance of MIP solvers has improved tremendously in the last two decades and these solvers have been used to solve many real-word problems. However, against the backdrop of modern computer technology, parallelization is of pivotal importance. In this way, ParaSCIP is the most successful parallel MIP solver in terms of solving previously unsolvable instances from the well-known benchmark instance set MIPLIB by using supercomputers. It solved two instances from MIPLIB2003 and 12 from MIPLIB2010 for the first time to optimality by using up to 80,000 cores on supercomputers. ParaSCIP has been developed by using the Ubiquity Generator (UG) framework, which is a general software package to parallelize any state-of-the-art branch-and-bound based solver. This paper discusses 7 years of progress in parallelizing branch-and-bound solvers with UG. T3 - ZIB-Report - 17-60 KW - Parallelization, Branch-and-bound, Mixed Integer Programming, UG, ParaSCIP, FiberSCIP, ParaXpress, FiberXpress, SCIP-Jack Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65545 SN - 1438-0064 ER - TY - GEN A1 - Munguia, Lluis-Miquel A1 - Oxberry, Geoffrey A1 - Rajan, Deepak A1 - Shinano, Yuji T1 - Parallel PIPS-SBB: Multi-Level Parallelism For Stochastic Mixed-Integer Programs N2 - PIPS-SBB is a distributed-memory parallel solver with a scalable data distribution paradigm. It is designed to solve MIPs with a dual-block angular structure, which is characteristic of deterministic-equivalent Stochastic Mixed-Integer Programs (SMIPs). In this paper, we present two different parallelizations of Branch & Bound (B&B), implementing both as extensions of PIPS-SBB, thus adding an additional layer of parallelism. In the first of the proposed frameworks, PIPS-PSBB, the coordination and load-balancing of the different optimization workers is done in a decentralized fashion. This new framework is designed to ensure all available cores are processing the most promising parts of the B&B tree. The second, ug[PIPS-SBB,MPI], is a parallel implementation using the Ubiquity Generator (UG), a universal framework for parallelizing B&B tree search that has been successfully applied to other MIP solvers. We show the effects of leveraging multiple levels of parallelism in potentially improving scaling performance beyond thousands of cores. T3 - ZIB-Report - 17-58 KW - PIPS-SBB, UG, Parallel Branch and Bound Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65517 SN - 1438-0064 IS - ZIB-Report 17-58 ER - TY - CHAP A1 - Schmidt, Frank ED - Piprek, Joachim T1 - Photonics T2 - Handbook of Optoelectronic Device Modeling and Simulation Y1 - 2017 SN - 9781498749381 PB - CRC Press ER - TY - JOUR A1 - Gul, Raheem A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Mathematical modeling and sensitivity analysis of arterial anastomosis in arm arteries JF - Applied Mathematical Modelling Y1 - 2016 U6 - https://doi.org/10.1016/j.apm.2016.03.041 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Objective priors in the empirical Bayes framework JF - Scandinavian Journal of Statistics N2 - When dealing with Bayesian inference the choice of the prior often remains a debatable question. Empirical Bayes methods offer a data-driven solution to this problem by estimating the prior itself from an ensemble of data. In the nonparametric case, the maximum likelihood estimate is known to overfit the data, an issue that is commonly tackled by regularization. However, the majority of regularizations are ad hoc choices which lack invariance under reparametrization of the model and result in inconsistent estimates for equivalent models. We introduce a nonparametric, transformation-invariant estimator for the prior distribution. Being defined in terms of the missing information similar to the reference prior, it can be seen as an extension of the latter to the data-driven setting. This implies a natural interpretation as a trade-off between choosing the least informative prior and incorporating the information provided by the data, a symbiosis between the objective and empirical Bayes methodologies. Y1 - 2021 U6 - https://doi.org/10.1111/sjos.12485 VL - 48 IS - 4 SP - 1212 EP - 1233 PB - Wiley Online Library ER - TY - JOUR A1 - Akbari Shandiz, Mohsen A1 - Boulos, Paul A1 - Sævarsson, Stefan A1 - Ramm, Heiko A1 - Fu, Chun Kit A1 - Miller, Stephen A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Changes in Knee Shape and Geometry Resulting from Total Knee Arthroplasty JF - Journal of Engineering in Medicine N2 - Changes in knee shape and geometry resulting from total knee arthroplasty can affect patients in numerous important ways: pain, function, stability, range of motion, and kinematics. Quantitative data concerning these changes have not been previously available, to our knowledge, yet are essential to understand individual experiences of total knee arthroplasty and thereby improve outcomes for all patients. The limiting factor has been the challenge of accurately measuring these changes. Our study objective was to develop a conceptual framework and analysis method to investigate changes in knee shape and geometry, and prospectively apply it to a sample total knee arthroplasty population. Using clinically available computed tomography and radiography imaging systems, the three-dimensional knee shape and geometry of nine patients (eight varus and one valgus) were compared before and after total knee arthroplasty. All patients had largely good outcomes after their total knee arthroplasty. Knee shape changed both visually and numerically. On average, the distal condyles were slightly higher medially and lower laterally (range: +4.5 mm to −4.4 mm), the posterior condyles extended farther out medially but not laterally (range: +1.8 to −6.4 mm), patellofemoral distance increased throughout flexion by 1.8–3.5 mm, and patellar thickness alone increased by 2.9 mm (range: 0.7–5.2 mm). External femoral rotation differed preop and postop. Joint line distance, taking cartilage into account, changed by +0.7 to −1.5 mm on average throughout flexion. Important differences in shape and geometry were seen between pre-total knee arthroplasty and post-total knee arthroplasty knees. While this is qualitatively known, this is the first study to report it quantitatively, an important precursor to identifying the reasons for the poor outcome of some patients. Using the developed protocol and visualization techniques to compare patients with good versus poor clinical outcomes could lead to changes in implant design, implant selection, component positioning, and surgical technique. Recommendations based on this sample population are provided. Intraoperative and postoperative feedback could ultimately improve patient satisfaction. Y1 - 2018 UR - http://journals.sagepub.com/eprint/ZVgNrNESA9EjIcaFWSjb/full U6 - https://doi.org/10.1177/0954411917743274 VL - 232 IS - 1 SP - 67 EP - 79 ER - TY - JOUR A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Effective dynamics along given reaction coordinates, and reaction rate theory JF - Faraday Discussions Y1 - 2016 U6 - https://doi.org/10.1039/C6FD00147E IS - 195 SP - 365 EP - 394 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Reliable approximation of long relaxation timescales in molecular dynamics JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19070367 VL - 19 IS - 7 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Generalized preprocessing techniques for Steiner tree and maximum-weight connected subgraph problems N2 - This article introduces new preprocessing techniques for the Steiner tree problem in graphs and one of its most popular relatives, the maximum-weight connected subgraph problem. Several of the techniques generalize previous results from the literature. The correctness of the new methods is shown, but also their NP-hardness is demonstrated. Despite this pessimistic worst-case complexity, several relaxations are discussed that are expected to allow for a strong practical efficiency of these techniques in strengthening both exact and heuristic solving approaches. T3 - ZIB-Report - 17-57 KW - Steiner tree KW - maximum-weight connected subgraph Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65439 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Winkler, Michael T1 - Structure-driven fix-and-propagate heuristics for mixed integer programming N2 - Primal heuristics play an important role in the solving of mixed integer programs (MIPs). They often provide good feasible solutions early in the solving process and help to solve instances to optimality faster. In this paper, we present a scheme for primal start heuristics that can be executed without previous knowledge of an LP solution or a previously found integer feasible solution. It uses global structures available within MIP solvers to iteratively fix integer variables and propagate these fixings. Thereby, fixings are determined based on the predicted impact they have on the subsequent domain propagation. If sufficiently many variables can be fixed that way, the resulting problem is solved as an LP and the solution is rounded. If the rounded solution did not provide a feasible solution already, a sub-MIP is solved for the neighborhood defined by the variable fixings performed in the first phase. The global structures help to define a neighborhood that is with high probability significantly easier to process while (hopefully) still containing good feasible solutions. We present three primal heuristics that use this scheme based on different global structures. Our computational experiments on standard MIP test sets show that the proposed heuristics find solutions for about three out of five instances and therewith help to improve several performance measures for MIP solvers, including the primal integral and the average solving time. T3 - ZIB-Report - 17-56 KW - mixed-integer programming KW - primal heuristics KW - fix-and-propagate KW - large neighborhood search KW - domain propagation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65387 SN - 1438-0064 ER - TY - GEN A1 - Papazov, Chavdar A1 - Hege, Hans-Christian T1 - Blue-noise Optimized Point Sets Based on Procrustes Analysis N2 - In this paper, we propose a new method for optimizing the blue noise characteristics of point sets. It is based on Procrustes analysis, a technique for adjusting shapes to each other by applying optimal elements of an appropriate transformation group. We adapt this technique to the problem at hand and introduce a very simple, efficient and provably convergent point set optimizer. T3 - ZIB-Report - 17-55 KW - blue-noise KW - point set optimization KW - triangulation KW - Procrustes analysis Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65356 SN - 1438-0064 ER - TY - CHAP A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. KW - Total Knee Arthoplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65339 VL - 16 SP - 24 EP - 30 ER - TY - CHAP A1 - Joachimsky, Robert A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung früher Gonarthrose T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein häufiges Krankheitsbild unter älteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder geschädigter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfläche erhöhen und so der teilweise oder vollständige Gelenkersatz hinausgezögert oder vermieden werden. In dieser Arbeit präsentieren wir eine Planungssoftware für die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgewählt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. Für jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern Rückmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterstützt somit als Entscheidungshilfe die behandelnden Ärzte bei der patientenspezifischen Spacerauswahl. KW - Osteoarthrose KW - Kniegelenk KW - Medizinische Planung KW - Visualisierung Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65321 VL - 16 SP - 106 EP - 111 ER - TY - GEN T1 - Open Access als strategische Leitlinie des KOBV N2 - Open Access ist Grundlage und Voraussetzung für die Nachnutzbarkeit, Transparenz und freie Zugänglichkeit zu wissenschaftlichen Informationen, Forschungsergebnissen und Daten des kulturellen Erbes. Mit Bezug auf die vom Senat Berlin 2015 verabschiedete Open-Access-Strategie empfiehlt der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) seinen Bibliotheken praktische Maßnahmen zur Umsetzung von Open Access in den eigenen Einrichtungen und benennt Maßnahmen der KOBV-Zentrale zur Unterstützung seiner Mitgliedsbibliotheken im Zuge dieses Transformationsprozesses. T3 - ZIB-Report - 17-54 KW - Open Access, Maßnahmen, Empfehlungen Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65303 SN - 1438-0064 ER - TY - JOUR A1 - Berg, Mascha A1 - Plöntzke, Julia A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - A dynamic model to simulate potassium balance in dairy cows JF - Journal of Dairy Science N2 - High-performing dairy cows require a particular composition of nutritional ingredients, adapted to their individual requirements and depending on their production status. The optimal dimensioning of minerals in the diet, one being potassium, is indispensable for the prevention of imbalances. Potassium balance in cows is the result of potassium intake, distribution in the organism, and excretion, and it is closely related to glucose and electrolyte metabolism. In this paper, we present a dynamical model for potassium balance in lactating and nonlactating dairy cows based on ordinary differential equations. Parameter values were obtained from clinical trial data and from the literature. To verify the consistency of the model, we present simulation outcomes for 3 different scenarios: potassium balance in (1) nonlactating cows with varying feed intake, (2) nonlactating cows with varying potassium fraction in the diet, and (3) lactating cows with varying milk production levels. The results give insights into the short- and long-term potassium metabolism, providing an important step toward the understanding of the potassium network, the design of prophylactic feed additives, and possible treatment strategies. Y1 - 2017 U6 - https://doi.org/10.3168/jds.2016-12443 VL - 100 IS - 12 SP - 9799 EP - 9814 ER - TY - THES A1 - Makarenko, Oleksandra T1 - Square Root Approximation und statistische Umgewichtungstechnik für das Faltungsverhalten von Polymerbürsten Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65283 ER - TY - THES A1 - Frech, Ralf T1 - Das Konzept der Flussdichte und sein Bezug zur Bohmschen Mechanik Y1 - 2014 ER - TY - THES A1 - Tumescheit, Charlotte T1 - Using Birkhoff-von Neumann und Sinkhorn Algorithm to Find Dominating Cycles Y1 - 2014 ER - TY - THES A1 - Schöpke, Jessica T1 - Korrelation für lineare und nichtlineare Zusammenhänge Y1 - 2015 ER - TY - THES A1 - Solleder, Marthe T1 - Molecular Dynamics Simulations : What is the Effect of a Spin Probe on the Drug Loading of a Nanocarrier Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65239 ER - TY - THES A1 - Grever, Andreas T1 - Estimating Missing Entries of a Partial Mean First Passage Time Matrix Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65228 ER - TY - THES A1 - Röhm, Jonas T1 - Non-Negative Matrix Factorization for Raman Data Spectral Analysis Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65217 ER - TY - THES A1 - Röhl, Susanne T1 - Computing the minimal rebinding effect for nonreversible processes Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65203 ER - TY - THES A1 - Brust, Lisa T1 - Moleküldynamik-Simulation via eines Faltungsansatzes im Potential Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65198 ER - TY - GEN A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Nieto-Vesperinas, Manuel T1 - Fundamentals and Applications of an Optical Theorem for Chiral Optical Fields T2 - 4th International Conference on Optical Angular Momentum N2 - The helicity of light is of great interest in both fundamental research and in applications such as dichroism spectroscopy. Its time-harmonic formulation is directly proportional to the density of optical chirality. Recently, both an helicity optical theorem (HOT) and a chirality conservation law (CCL) have been formulated for arbitrary scatterers taking into account an underlying continuity equation of this quantity. We summarize these two equivalent fundamental laws and analyze their potential applications. Y1 - 2017 ER - TY - GEN A1 - Gutsche, Philipp A1 - Nieto-Vesperinas, Manuel A1 - Mäusle, Raquel A1 - Burger, Sven T1 - Chiral Nanophotonics: Theory and Simulation T2 - Doctoral Summer School on Nanophotonics and Metamaterials, ITMO University N2 - The interaction of light and chiral matter is subject of recent research both in fundamental science and applications. Among these are the helicity of electromagnetic fields described with the optical chirality density and emitters sensitive to circular polarization employed in quantum communications. In the weak coupling regime of chiral emitters, we analyze the conversion of chirality which can be regarded as an analogue to absorption of energy describing the change of circular polarization of the incident field. This enables the tailoring of chiral near-fields close to metamaterials, e.g. composed of gold helices, and gives insights into extinction measurements such as circular dichroism. We show relation of the weak and strong coupling regime. The latter can be modelled with cross electric-magnetic polarizabilities or with effective chiral materials, i.e. bi-anisotropic media. Accordingly, we motivate the necessity for rigorous numerical simulations to accurately describe chiral light-matter interaction. Y1 - 2017 ER - TY - JOUR A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivanskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei A1 - Mork, Jesper A1 - Gregersen, Niels T1 - Benchmarking five numerical simulation techniques for computing resonance wavelengths and quality factors in photonic crystal membrane line defect cavities JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.011366 VL - 26 SP - 11366 ER - TY - CHAP A1 - Noack, Matthias A1 - Wende, Florian A1 - Zitzlsberger, Georg A1 - Klemm, Michael A1 - Steinke, Thomas T1 - KART - A Runtime Compilation Library for Improving HPC Application Performance T2 - High Performance Computing: ISC High Performance 2017 International Workshops, DRBSD, ExaComm, HCPM, HPC-IODC, IWOPH, IXPUG, P^3MA, VHPC, Visualization at Scale, WOPSSS, Frankfurt, Germany, June 18-22, 2017, Revised Selected Papers N2 - The effectiveness of ahead-of-time compiler optimization heavily depends on the amount of available information at compile time. Input-specific information that is only available at runtime cannot be used, although it often determines loop counts, branching predicates and paths, as well as memory-access patterns. It can also be crucial for generating efficient SIMD-vectorized code. This is especially relevant for the many-core architectures paving the way to exascale computing, which are more sensitive to code-optimization. We explore the design-space for using input-specific information at compile-time and present KART, a C++ library solution that allows developers tocompile, link, and execute code (e.g., C, C++ , Fortran) at application runtime. Besides mere runtime compilation of performance-critical code, KART can be used to instantiate the same code multiple times using different inputs, compilers, and options. Other techniques like auto-tuning and code-generation can be integrated into a KART-enabled application instead of being scripted around it. We evaluate runtimes and compilation costs for different synthetic kernels, and show the effectiveness for two real-world applications, HEOM and a WSM6 proxy. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-67630-2_29 N1 - Best Paper Award VL - 10524 SP - 389 EP - 403 PB - Springer International Publishing ER - TY - JOUR A1 - Moldenhauer, Marian A1 - Weiser, Martin A1 - Zachow, Stefan T1 - Adaptive Algorithms for Optimal Hip Implant Positioning JF - PAMM N2 - In an aging society where the number of joint replacements rises, it is important to also increase the longevity of implants. In particular hip implants have a lifetime of at most 15 years. This derives primarily from pain due to implant migration, wear, inflammation, and dislocation, which is affected by the positioning of the implant during the surgery. Current joint replacement practice uses 2D software tools and relies on the experience of surgeons. Especially the 2D tools fail to take the patients’ natural range of motion as well as stress distribution in the 3D joint induced by different daily motions into account. Optimizing the hip joint implant position for all possible parametrized motions under the constraint of a contact problem is prohibitively expensive as there are too many motions and every position change demands a recalculation of the contact problem. For the reduction of the computational effort, we use adaptive refinement on the parameter domain coupled with the interpolation method of Kriging. A coarse initial grid is to be locally refined using goal-oriented error estimation, reducing locally high variances. This approach will be combined with multi-grid optimization such that numerical errors are reduced. Y1 - 2017 U6 - https://doi.org/10.1002/pamm.201710071 VL - 17 IS - 1 SP - 203 EP - 204 ER - TY - JOUR A1 - Knoop, Helge A1 - Gronemeier, Tobias A1 - Sühring, Matthias A1 - Steinbach, Peter A1 - Noack, Matthias A1 - Wende, Florian A1 - Steinke, Thomas A1 - Knigge, Christoph A1 - Raasch, Siegfried A1 - Ketelsen, Klaus T1 - Porting the MPI-parallelized LES model PALM to multi-GPU systems and many integrated core processors: an experience report JF - International Journal of Computational Science and Engineering. Special Issue on: Novel Strategies for Programming Accelerators N2 - The computational power and availability of graphics processing units (GPUs), such as the Nvidia Tesla, and Many Integrated Core (MIC) processors, such as the Intel Xeon Phi, on high performance computing (HPC) systems is rapidly evolving. However, HPC applications need to be ported to take advantage of such hardware. This paper is a report on our experience of porting the MPI+OpenMP parallelised large-eddy simulation model (PALM) to multi-GPU as well as to MIC processor environments using the directive-based high level programming paradigm OpenACC and OpenMP, respectively. PALM is a Fortran-based computational fluid dynamics software package, used for the simulation of atmospheric and oceanic boundary layers to answer questions linked to fundamental atmospheric turbulence research, urban modelling, aircraft safety and cloud physics. Development of PALM started in 1997, the project currently entails 140 kLOC and is used on HPC farms of up to 43,200 cores. The main challenges we faced during the porting process are the size and complexity of the PALM code base, its inconsistent modularisation and the complete lack of a unit-test suite. We report the methods used to identify performance issues as well as our experiences with state-of-the-art profiling tools. Moreover, we outline the required porting steps in order to properly execute our code on GPUs and MIC processors, describe the problems and bottlenecks that we encountered during the porting process, and present separate performance tests for both architectures. These performance tests, however, do not provide any benchmark information that compares the performance of the ported code between the two architectures. Y1 - 2017 PB - Inderscience ET - Special Issue on: Novel Strategies for Programming Accelerators ER - TY - CHAP A1 - Wende, Florian A1 - Marsman, Martijn A1 - Zhao, Zhengji A1 - Kim, Jeongnim T1 - Porting VASP from MPI to MPI+OpenMP [SIMD] T2 - Scaling OpenMP for Exascale Performance and Portability - 13th International Workshop on OpenMP, IWOMP 2017, Stony Brook, NY, USA, September 20-22, 2017 N2 - We describe for the VASP application (a widely used electronic structure code written in FORTRAN) the transition from an MPI-only to a hybrid code base leveraging the three relevant levels of parallelism to be addressed when optimizing for an effective execution on modern computer platforms: multiprocessing, multithreading and SIMD vectorization. To achieve code portability, we draw on MPI parallelization together with OpenMP threading and SIMD constructs. Combining the latter can be challenging in complex code bases. Optimization targets are combining multithreading and vectorization in different calling contexts as well as whole function vectorization. In addition to outlining design decisions made throughout the code transformation process, we will demonstrate the effectiveness of the code adaptations using different compilers (GNU, Intel) and target platforms (CPU, Intel Xeon Phi (KNL)). Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-65578-9_8 VL - 8766 SP - 107 EP - 122 ER - TY - CHAP A1 - Zhao, Zhengji A1 - Marsman, Martijn A1 - Wende, Florian A1 - Kim, Jeongnim T1 - Performance of Hybrid MPI/OpenMP VASP on Cray XC40 Based on Intel Knights Landing Many Integrated Core Architecture N2 - With the recent installation of Cori, a Cray XC40 system with Intel Xeon Phi Knights Landing (KNL) many integrated core (MIC) architecture, NERSC is transitioning from the multi-core to the more energy-efficient many-core era. The developers of VASP, a widely used materials science code, have adopted MPI/OpenMP parallelism to better exploit the increased on-node parallelism, wider vector units, and the high bandwidth on-package memory (MCDRAM) of KNL. To achieve optimal performance, KNL specifics relevant for the build, boot and run time setup must be explored. In this paper, we present the performance analysis of representative VASP workloads on Cori, focusing on the effects of the compilers, libraries, and boot/run time options such as the NUMA/MCDRAM modes, Hyper-Threading, huge pages, core specialization, and thread scaling. The paper is intended to serve as a KNL performance guide for VASP users, but it will also benefit other KNL users. Y1 - 2017 N1 - Availability: https://cug.org/conference-proceedings ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Bujotzek, Alexander T1 - Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach T2 - Progress in Industrial Mathematics at ECMI 2012 N2 - In this article a method to improve the precision of the classical molecular dynamics force field by solving an approximation problem with scattered quantum mechanical data is presented. This novel technique is based on two steps. In the first step a partition of unity scheme is used for partitioning the state space by meshfree basis functions. As a consequence the potential can be localized for each basis function. In a second step, for one state in each meshfree basis function, the precise QM-based charges are computed. These local QM-based charges are then used, to optimize the local potential function. The performance of this method is shown for the alanine tripeptide. Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-05365-3_42 VL - 19 SP - 309 EP - 313 ER - TY - THES A1 - Binkowski, Felix T1 - On the convergence behavior of spectral deferred correction methods for convection-diffusion equations N2 - Spectral deferred correction (SDC) Methoden, vorgestellt von Dutt, Greengard und Rokhlin in [1], sind iterative Verfahren zur numerischen Lösung von Anfangswertproblemen für gewöhnliche Differentialgleichungen. Wenn diese Methoden konvergieren, dann wird unter Verwendung von Zeitschrittverfahren niedriger Ordnung eine Kollokationslösung berechnet. Die Lösung von steifen Anfangswertproblemen ist eine relevante Problemstellung in der numerischen Mathematik. SDC-Methoden, speziell für steife Probleme, werden von Martin Weiser in [2] konstruiert. Die Theorie und die Experimente beziehen sich dabei auf Probleme, die aus räumlich semidiskretisierten Reaktions-Diffusions-Gleichungen entstehen. In dieser Arbeit werden die Ansätze aus [2] auf Konvektions-Diffusions-Gleichungen angewendet und das resultierende Konvergenzverhalten von SDC-Methoden untersucht. Basierend auf einem einfachen Konvektions-Diffusions-Operator, dessen spektrale Eigenschaften umfassend studiert werden, wird ein Schema zur Verbesserung dieses Verhaltens entwickelt. Numerische Experimente zeigen, dass eine Verbesserung der in [1] eingeführten SDC-Methoden möglich ist. Die Untersuchungen ergeben weiterhin, dass das auch für komplexere Konvektions-Diffusions-Probleme gilt. [1] Alok Dutt, Leslie Greengard, und Vladimir Rokhlin. “Spectral deferred correction methods for ordinary differential equations.” In: BIT 40.2 (2000), pp. 241–266. [2] Martin Weiser. “Faster SDC convergence on non-equidistant grids by DIRK sweeps.” In: BIT 55.4 (2015), pp. 1219–1241. Y1 - 2017 ER - TY - THES A1 - Fischer, Lisa T1 - On the convergence of inexact time parallel time integration Y1 - 2017 ER - TY - THES A1 - Freytag, Yvonne T1 - Optimal Experimental Design to Estimate the Time of Death in a Bayesian Context N2 - This thesis is devoted to the interdisciplinary work between mathematicians and forensic experts: the modeling of the human body cooling process after death laying the foundation for the estimation of the time of death. An inverse problem needs to be solved. In this thesis the inverse problem computes the time of death given the measured body temperature and the Forward Model that simulates the body cooling process. The Forward Model is based on the heat equation established by Fourier. This differential equation is numerically solved by the discretization over space by the Finite Element Method and the discretization over time by the Implicit Euler Method. The applications in this thesis demand a fast computation time. A model reduction is achieved by the Proper Orthogonal Decomposition in combination with the Galerkin Method. For reasons of simplification the computations and the measurements are restricted to a cylindrical phantom that is made out of homogeneous polyethylene. The estimate of the time of death is accompanied by an uncertainty. The inverse problem is incorporated by Bayesian inference to interpret the quality of the estimate and the effciency of the experiment. The uncertainty of the estimate of the time of death is minimized by approaching the Optimal Design of the Experiment. An objective function measures the certainty of the data and lays the foundation of the optimization problem. Solving the optimization problem is successfully done by relaxing the complex discrete NP-hard problem and applying a gradient-based method. The results of this thesis clearly show that the design of an experiment has a great in- uence on the outcome of the quality of the estimate. The comparison of the estimate and its properties based on different designs and conditions reveals the effciency of the Design of Experiment in the context of the estimation of the time of death. Y1 - 2017 ER - TY - GEN A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: Theory and algorithms N2 - The article surveys and extends variational formulations of the thermodynamic free energy and discusses their information-theoretic content from the perspective of mathematical statistics. We revisit the well-known Jarzynski equality for nonequilibrium free energy sampling within the framework of importance sampling and Girsanov change-of-measure transformations. The implications of the different variational formulations for designing efficient stochastic optimization and nonequilibrium simulation algorithms for computing free energies are discussed and illustrated. T3 - ZIB-Report - 17-52 KW - Importance sampling KW - Donsker-Varadhan principle KW - thermodynamic free energy KW - nonequilibrium molecular dynamics KW - stochastic approximation KW - cross-entropy method Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65045 SN - 1438-0064 ER - TY - JOUR A1 - Fischer, Lisa A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy data compression reduces communication time in hybrid time-parallel integrators JF - Comput. Vis. Sci. N2 - Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups. Y1 - 2018 U6 - https://doi.org/10.1007/s00791-018-0293-2 VL - 19 IS - 1 SP - 19 EP - 30 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems JF - The Journal of Chemical Physics N2 - Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations. Y1 - 2017 U6 - https://doi.org/10.1063/1.4986560 VL - 147 IS - 11 SP - 114115-1 EP - 114115-18 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan T1 - Measuring the electromagnetic chirality of 2D arrays under normal illumination JF - Opt. Lett. Y1 - 2017 U6 - https://doi.org/10.1364/OL.42.004075 VL - 42 SP - 4075 ER - TY - JOUR A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Saleh, Lanja A1 - Spanhaus, K. A1 - Schippert, Cordula A1 - Zhang, Y. A1 - Hengartner, M. P. T1 - Lack of association between female hormone levels and visuospatial working memory, divided attention and cognitive bias across two consecutive menstrual cycles JF - Front. Behav. Neurosci. Y1 - 2017 U6 - https://doi.org/10.3389/fnbeh.2017.00120 ER - TY - GEN A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - Parallel-in-Time for Parabolic Optimal Control Problems Using PFASST N2 - In gradient-based methods for parabolic optimal control problems, it is necessary to solve both the state equation and a backward-in-time adjoint equation in each iteration of the optimization method. In order to facilitate fully parallel gradient-type and nonlinear conjugate gradient methods for the solution of such optimal control problems, we discuss the application of the parallel-in-time method PFASST to adjoint gradient computation. In addition to enabling time parallelism, PFASST provides high flexibility for handling nonlinear equations, as well as potential extra computational savings from reusing previous solutions in the optimization loop. The approach is demonstrated here for a model reaction-diffusion optimal control problem. T3 - ZIB-Report - 17-51 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64989 SN - 1438-0064 ER - TY - CHAP A1 - Fischer, Frank A1 - Grimm, Boris A1 - Klug, Torsten A1 - Schlechte, Thomas T1 - A Re-optimization Approach for Train Dispatching T2 - Operations Research Proceedings 2016 N2 - The Train Dispatching Problem (TDP) is to schedule trains through a network in a cost optimal way. Due to disturbances during operation existing track allocations often have to be re-scheduled and integrated into the timetable. This has to be done in seconds and with minimal timetable changes to guarantee smooth and conflict free operation. We present an integrated modeling approach for the re-optimization task using Mixed Integer Programming. Finally, we provide computational results for scenarios provided by the INFORMS RAS Problem Soling Competition 2012. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-55702-1_85 SP - 645 EP - 651 ER - TY - CHAP A1 - Schwartz, Stephan A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Designing Inspector Rosters with Optimal Strategies T2 - Operations Research Proceedings 2016 N2 - We consider the problem of enforcing a toll on a transportation network with limited inspection resources. We formulate a game theoretic model to optimize the allocation of the inspectors, taking the reaction of the network users into account. The model includes several important aspects for practical operation of the control strategy, such as duty types for the inspectors. In contrast to an existing formulation using flows to describe the users' strategies we choose a path formulation and identify dominated user strategies to significantly reduce the problem size. Computational results suggest that our approach is better suited for practical instances. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-55702-1_30 SP - 217 EP - 223 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Arslan, Oytun A1 - Elijazyfer, Ziena A1 - Güler, Hakan A1 - Renken, Malte A1 - Sahin, Guvenc A1 - Schlechte, Thomas T1 - Line Planning on Path Networks with Application to the Istanbul Metrobüs T2 - Operations Research Proceedings 2016 N2 - Bus rapid transit systems in developing and newly industrialized countries often consist of a trunk with a path topology. On this trunk, several overlapping lines are operated which provide direct connections. The demand varies heavily over the day, with morning and afternoon peaks typically in reverse directions. We propose an integer programming model for this problem, derive a structural property of line plans in the static (or single period) ``unimodal demand'' case, and consider approaches to the solution of the multi-period version that rely on clustering the demand into peak and off-peak service periods. An application to the Metrobüs system of Istanbul is discussed. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-55702-1_32 SP - 235 EP - 241 ER - TY - CHAP A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Kaier, Anton A1 - Maristany de las Casas, Pedro A1 - Schlechte, Thomas A1 - Schlobach, Swen ED - D'Angelo, Gianlorenzo ED - Dollevoet, Twan T1 - Cost Projection Methods for the Shortest Path Problem with Crossing Costs T2 - 17th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2017) N2 - Real world routing problems, e.g., in the airline industry or in public and rail transit, can feature complex non-linear cost functions. An important case are costs for crossing regions, such as countries or fare zones. We introduce the shortest path problem with crossing costs (SPPCC) to address such situations; it generalizes the classical shortest path problem and variants such as the resource constrained shortest path problem and the minimum label path problem. Motivated by an application in flight trajectory optimization with overflight costs, we focus on the case in which the crossing costs of a region depend only on the nodes used to enter or exit it. We propose an exact Two-Layer-Dijkstra Algorithm as well as a novel cost-projection linearization technique that approximates crossing costs by shadow costs on individual arcs, thus reducing the SPPCC to a standard shortest path problem. We evaluate all algorithms’ performance on real-world flight trajectory optimization instances, obtaining very good à posteriori error bounds. Y1 - 2017 VL - 59 ER - TY - CHAP A1 - Fischer, Frank A1 - Schlechte, Thomas ED - D'Angelo, Gianlorenzo ED - Dollevoet, Twan T1 - Strong Relaxations for the Train Timetabling Problem using Connected Configurations T2 - 17th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2017) N2 - The task of the train timetabling problem or track allocation problem is to find conflict free schedules for a set of trains with predefined routes in a railway network. Especially for non-periodic instances models based on time expanded networks are often used. Unfortunately, the linear programming relaxation of these models is often extremely weak because these models do not describe combinatorial relations like overtaking possibilities very well. In this paper we extend the model by so called connected configuration subproblems. These subproblems perfectly describe feasible schedules of a small subset of trains (2-3) on consecutive track segments. In a Lagrangian relaxation approach we solve several of these subproblems together in order to produce solutions which consist of combinatorially compatible schedules along the track segments. The computational results on a mostly single track corridor taken from the INFORMS RAS Problem Solving Competition 2012 data indicate that our new solution approach is rather strong. Indeed, for this instance the solution of the Lagrangian relaxation is already integral. Y1 - 2017 SN - 978-3-95977-042-2 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2017.11 VL - 59 ER - TY - CHAP A1 - Novitsky, Andrey A1 - Rosenkrantz de Lasson, Jakob A1 - Hagedorn Frandsen, Lars A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivinskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei A1 - Mørk, Jesper A1 - Gregersen, Niels T1 - Comparison of five computational methods for computing Q factors in photonic crystal membrane cavities T2 - 19th International Conference on Transparent Optical Networks (ICTON) Y1 - 2017 U6 - https://doi.org/10.1109/ICTON.2017.8024813 ER - TY - GEN A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics N2 - We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one. T3 - ZIB-Report - 17-49 KW - Markov state model KW - non-equilibrium molecular dynamics KW - two timescale master equation KW - non-stationary forcing KW - metastability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64868 SN - 1438-0064 ER - TY - JOUR A1 - von Tycowicz, Christoph A1 - Ambellan, Felix A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - An Efficient Riemannian Statistical Shape Model using Differential Coordinates JF - Medical Image Analysis N2 - We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidean structure. A key advantage of our framework is that statistics in a manifold shape space becomes numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidean approach in terms of shape-based classification of morphological disorders. Y1 - 2018 U6 - https://doi.org/10.1016/j.media.2017.09.004 VL - 43 IS - 1 SP - 1 EP - 9 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Eisenhauer, David A1 - Chen, Duote A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Optical simulations of advanced light management for liquid-phase crystallized silicon thin-film solar cells JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2273994 VL - 10356 SP - 103560F ER - TY - CHAP A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank T1 - New Generation of Vertical-Cavity Surface-Emitting Lasers for Optical Interconnects T2 - Future Trends in Microelectronics: Journey into the Unknown Y1 - 2016 U6 - https://doi.org/10.1002/9781119069225.ch3-5 PB - John Wiley & Sons ER - TY - GEN A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Kaier, Anton A1 - Maristany de las Casas, Pedro A1 - Schlechte, Thomas A1 - Schlobach, Swen T1 - Cost Projection Methods for the Shortest Path Problem with Crossing Costs N2 - Real world routing problems, e.g., in the airline industry or in public and rail transit, can feature complex non-linear cost functions. An important case are costs for crossing regions, such as countries or fare zones. We introduce the shortest path problem with crossing costs (SPPCC) to address such situations; it generalizes the classical shortest path problem and variants such as the resource constrained shortest path problem and the minimum label path problem. Motivated by an application in flight trajectory optimization with overflight costs, we focus on the case in which the crossing costs of a region depend only on the nodes used to enter or exit it. We propose an exact Two-Layer-Dijkstra Algorithm as well as a novel cost-projection linearization technique that approximates crossing costs by shadow costs on individual arcs, thus reducing the SPPCC to a standard shortest path problem. We evaluate all algorithms’ performance on real-world flight trajectory optimization instances, obtaining very good à posteriori error bounds. T3 - ZIB-Report - 17-48 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64817 SN - 1438-0064 ER - TY - JOUR A1 - Hoffmann, René A1 - Lemanis, Robert A1 - Falkenberg, Janina A1 - Schneider, Steffen A1 - Wesendonk, Hendrik A1 - Zachow, Stefan T1 - Integrating 2D and 3D shell morphology to disentangle the palaeobiology of ammonoids: A virtual approach JF - Palaeontology N2 - We demonstrate, based on data derived from computed tomography, that integrating 2D and 3D morphological data of ammonoid shells represent an important new approach to disentangle the palaeobiology of ammonoids. Characterization of ammonite morphology has long been constrained to 2D data and only a few studies collect ontogenetic data in 180° steps. We combine this traditional approach with 3D data collected from high-resolution nano-computed tomography. For this approach, ontogenetic morphological data of the hollow shell of a juvenile ammonite Kosmoceras (Jurassic, Callovian) is collected. 2D data is collected in 10° steps and show significant changes in shell morphology. Preserved hollow spines show multiple mineralized membranes never reported before, representing temporal changes of the ammonoid mantle tissue. 3D data show that chamber volumes do not always increase exponentially, as was generally assumed, but may represent a proxy for life events, e.g. stress phases. Furthermore, chamber volume cannot be simply derived from septal spacing in forms comparable to Kosmoceras. Vogel numbers, a 3D parameter for chamber shape, of Kosmoceras are similar to other ammonoids (Arnsbergites, Amauroceras) and modern cephalopods (Nautilus, Spirula). Two methods to virtually document the suture line ontogeny, used to document phylogenetic relationships of larger taxonomic entities, were applied for the first time and seem a promising alternative to hand drawings. The curvature of the chamber surfaces increases during ontogeny due to increasing strength of ornamentation and septal complexity. As increasing curvature may allow for faster handling of cameral liquid, it could compensate for decreasing SA/V ratios through ontogeny. Y1 - 2017 UR - http://dx.doi.org/10.1111/pala.12328 U6 - https://doi.org/10.1111/pala.12328 VL - 61 IS - 1 SP - 89 EP - 104 ER - TY - GEN A1 - Berg, Mascha A1 - Plöntzke, Julia A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - A dynamic model to simulate potassium balance in dairy cows. N2 - High performing dairy cows require a particular composition of nutritional ingredients, adapted to their individual requirements and depending on their production status. The optimal dimensioning of minerals in the diet, one of them being potassium, is indispensable for the prevention of imbalances. The potassium balance in cows is the result of potassium intake, distribution in the organism, and excretion, it is closely related with the glucose and electrolyte metabolism. In this paper, we present a dynamical model for the potassium balance in lactating and non-lactating dairy cows based on ordinary differential equations. Parameter values are obtained from clinical trial data and from the literature. To verify the consistency of the model, we present simulation outcomes for three different scenarios: potassium balance in (i) non-lactating cows with varying feed intake, (ii) non-lactating cows with varying potassium fraction in the diet, and (iii) lactating cows with varying milk production levels. The results give insights into the short and long term potassium metabolism, providing an important step towards the understanding of the potassium network, the design of prophylactic feed additives, and possible treatment strategies. T3 - ZIB-Report - 17-47 KW - cow, potassium, model, ode Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64756 SN - 1438-0064 ER - TY - CHAP A1 - Gregersen, Niels A1 - Rosenkrantz de Lasson, Jakob A1 - Hagedorn Frandsen, Lars A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei A1 - Moerk, Jesper A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivinskaya, Aliaksandra A1 - Gutsche, Philipp A1 - Burger, Sven T1 - Benchmarking five computational methods for analyzing large photonic crystal membrane cavities T2 - Numerical Simulation of Optoelectronic Devices (NUSOD) Y1 - 2017 U6 - https://doi.org/10.1109/NUSOD.2017.8010005 SP - 89 ER - TY - GEN A1 - Fischer, Frank A1 - Schlechte, Thomas T1 - Strong Relaxations for the Train Timetabling Problem using Connected Configurations N2 - The task of the train timetabling problem or track allocation problem is to find conflict free schedules for a set of trains with predefined routes in a railway network. Especially for non-periodic instances models based on time expanded networks are often used. Unfortunately, the linear programming relaxation of these models is often extremely weak because these models do not describe combinatorial relations like overtaking possibilities very well. In this paper we extend the model by so called connected configuration subproblems. These subproblems perfectly describe feasible schedules of a small subset of trains (2-3) on consecutive track segments. In a Lagrangian relaxation approach we solve several of these subproblems together in order to produce solutions which consist of combinatorially compatible schedules along the track segments. The computational results on a mostly single track corridor taken from the INFORMS RAS Problem Solving Competition 2012 data indicate that our new solution approach is rather strong. Indeed, for this instance the solution of the Lagrangian relaxation is already integral. T3 - ZIB-Report - 17-46 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64743 SN - 1438-0064 ER - TY - CHAP A1 - Tesch, Alexander T1 - Improved Compact Models for the Resource-Constrained Project Scheduling Problem T2 - Operations Research Proceedings 2016 N2 - In this article, we study compact Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP). Compared to the classical time-indexed formulation, the size of compact models is strongly polynomial in the number of jobs. In addition to two compact models from the literature, we propose a new compact model. We can show that all three compact models are equivalent by successive linear transformations. For their LP-relaxations, however, we state a full inclusion hierarchy where our new model dominates the previous models in terms of polyhedral strength. Moreover, we reveal a polyhedral relationship to the common time-indexed model. Furthermore, a general class of valid cutting planes for the compact models is introduced and finally all models are evaluated by computational experiments. Y1 - 2017 SP - 25 EP - 30 ER - TY - GEN A1 - Gamrath, Gerald A1 - Schubert, Christoph T1 - Measuring the impact of branching rules for mixed-integer programming N2 - Branching rules are an integral component of the branch-and-bound algorithm typically used to solve mixed-integer programs and subject to intense research. Different approaches for branching are typically compared based on the solving time as well as the size of the branch-and-bound tree needed to prove optimality. The latter, however, has some flaws when it comes to sophisticated branching rules that do not only try to take a good branching decision, but have additional side-effects. We propose a new measure for the quality of a branching rule that distinguishes tree size reductions obtained by better branching decisions from those obtained by such side-effects. It is evaluated for common branching rules providing new insights in the importance of strong branching. T3 - ZIB-Report - 17-34 KW - mixed-integer programming KW - branch-and-bound KW - branching rule KW - strong branching Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64722 SN - 1438-0064 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Weiser, Martin A1 - Santiago, Xavier Garcia A1 - Zschiedrich, Lin A1 - Bodermann, Bernd A1 - Burger, Sven T1 - Quantifying parameter uncertainties in optical scatterometry using Bayesian inversion N2 - We present a Newton-like method to solve inverse problems and to quantify parameter uncertainties. We apply the method to parameter reconstruction in optical scatterometry, where we take into account a priori information and measurement uncertainties using a Bayesian approach. Further, we discuss the influence of numerical accuracy on the reconstruction result. T3 - ZIB-Report - 17-37 KW - computational metrology KW - optical metrology KW - computational lithography KW - nanolithography KW - finite- element methods KW - nanooptics Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64704 SN - 1438-0064 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Combining NP-Hard Reduction Techniques and Strong Heuristics in an Exact Algorithm for the Maximum-Weight Connected Subgraph Problem N2 - Borne out of a surprising variety of practical applications, the maximum-weight connected subgraph problem has attracted considerable interest during the past years. This interest has not only led to notable research on theoretical properties, but has also brought about several (exact) solvers-with steadily increasing performance. Continuing along this path, the following article introduces several new algorithms such as reduction techniques and heuristics and describes their integration into an exact solver. The new methods are evaluated with respect to both their theoretical and practical properties. Notably, the new exact framework allows to solve common problem instances from the literature faster than all previous approaches. Moreover, one large-scale benchmark instance from the 11th DIMACS Challenge can be solved for the first time to optimality and the primal-dual gap for two other ones can be significantly reduced. T3 - ZIB-Report - 17-45 KW - maximum-weight connected subgraph Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64699 SN - 1438-0064 ER - TY - CHAP A1 - Miltenberger, Matthias A1 - Ralphs, Ted A1 - Steffy, Daniel T1 - Exploring the Numerics of Branch-and-Cut for Mixed Integer Linear Optimization T2 - Operations Research Proceedings 2017 N2 - We investigate how the numerical properties of the LP relaxations evolve throughout the solution procedure in a solver employing the branch-and-cut algorithm. The long-term goal of this work is to determine whether the effect on the numerical conditioning of the LP relaxations resulting from the branching and cutting operations can be effectively predicted and whether such predictions can be used to make better algorithmic choices. In a first step towards this goal, we discuss here the numerical behavior of an existing solver in order to determine whether our intuitive understanding of this behavior is correct. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6 SP - 151 EP - 157 PB - Springer International Publishing ER - TY - GEN A1 - Miltenberger, Matthias A1 - Ralphs, Ted A1 - Steffy, Daniel T1 - Exploring the Numerics of Branch-and-Cut for Mixed Integer Linear Optimization T2 - Operations Research Proceedings 2017 N2 - We investigate how the numerical properties of the LP relaxations evolve throughout the solution procedure in a solver employing the branch-and-cut algorithm. The long-term goal of this work is to determine whether the effect on the numerical conditioning of the LP relaxations resulting from the branching and cutting operations can be effectively predicted and whether such predictions can be used to make better algorithmic choices. In a first step towards this goal, we discuss here the numerical behavior of an existing solver in order to determine whether our intuitive understanding of this behavior is correct. T3 - ZIB-Report - 17-43 KW - Mixed Integer Programming KW - Linear Programming KW - Algorithm Analysis Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64645 SN - 1438-0064 ER - TY - GEN A1 - Griewank, Andreas A1 - Hasenfelder, Richard A1 - Radons, Manuel A1 - Lehmann, Lutz A1 - Streubel, Tom T1 - Integrating Lipschitzian Dynamical Systems using Piecewise Algorithmic Differentiation N2 - In this article we analyze a generalized trapezoidal rule for initial value problems with piecewise smooth right hand side \(F:R^n \to R^n\) based on a generalization of algorithmic differentiation. When applied to such a problem, the classical trapezoidal rule suffers from a loss of accuracy if the solution trajectory intersects a nondifferentiability of \(F\). The advantage of the proposed generalized trapezoidal rule is threefold: Firstly, we can achieve a higher convergence order than with the classical method. Moreover, the method is energy preserving for piecewise linear Hamiltonian systems. Finally, in analogy to the classical case we derive a third order interpolation polynomial for the numerical trajectory. In the smooth case the generalized rule reduces to the classical one. Hence, it is a proper extension of the classical theory. An error estimator is given and numerical results are presented. T3 - ZIB-Report - 17-44 KW - Automatic Differentiation KW - Lipschitz Continuity KW - Piecewise Linearization KW - Nonsmooth KW - Trapezoidal Rule KW - Energy Preservation KW - Dense Output Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64639 SN - 1438-0064 ER - TY - JOUR A1 - Barth, Carlo A1 - Roder, Sebastian A1 - Brodoceanu, Daniel A1 - Kraus, Tobias A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Increased fluorescence of PbS quantum dots in photonic crystals by excitation enhancement JF - Appl. Phys. Lett. Y1 - 2017 U6 - https://doi.org/10.1063/1.4995229 VL - 111 SP - 031111 ER - TY - GEN A1 - Schade, Stanley A1 - Schlechte, Thomas A1 - Witzig, Jakob T1 - Structure-based Decomposition for Pattern-Detection for Railway Timetables N2 - We consider the problem of pattern detection in large scale railway timetables. This problem arises in rolling stock optimization planning in order to identify invariant sections of the timetable for which a cyclic rotation plan is adequate. We propose a dual reduction technique which leads to an decomposition and enumeration method. Computational results for real world instances demonstrate that the method is able to produce optimal solutions as fast as standard MIP solvers. T3 - ZIB-Report - 17-40 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64525 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Perregaard, Michael A1 - Mészáros, Csaba T1 - Four good reasons to use an Interior Point solver within a MIP solver N2 - "Interior point algorithms are a good choice for solving pure LPs or QPs, but when you solve MIPs, all you need is a dual simplex." This is the common conception which disregards that an interior point solution provides some unique structural insight into the problem at hand. In this paper, we will discuss some of the benefits that an interior point solver brings to the solution of difficult MIPs within FICO Xpress. This includes many different components of the MIP solver such as branching variable selection, primal heuristics, preprocessing, and of course the solution of the LP relaxation. T3 - ZIB-Report - 17-42 KW - mixed integer programming KW - interior point algorithm KW - Newton barrier method KW - analytic center Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64599 SN - 1438-0064 ER - TY - GEN A1 - Hennings, Felix T1 - Benefits and Limitations of Simplified Transient Gas Flow Formulations N2 - Although intensively studied in recent years, the optimization of the transient (time-dependent) control of large real-world gas networks is still out of reach for current state-of-the-art approaches. For this reason, we present further simplifications of the commonly used model, which lead to a linear description of the gas flow on pipelines. In an empirical analysis of real-world data, we investigate the properties of the involved quantities and evaluate the errors made by our simplification. T3 - ZIB-Report - 17-39 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64570 SN - 1438-0064 ER - TY - GEN A1 - Streubel, Tom A1 - Strohm, Christian A1 - Trunschke, Philipp A1 - Tischendorf, Caren T1 - Generic Construction and Efficient Evaluation of Network DAEs and Their Derivatives in the Context of Gas Networks N2 - We present a concept that provides an efficient description of differential-algebraic equations (DAEs) describing flow networks which provides the DAE function f and their Jacobians in an automatized way such that the sparsity pattern of the Jacobians is determined before their evaluation and previously determined values of f can be exploited. The user only has to provide the network topology and local function descriptions for each network element. The approach uses automatic differentiation (AD) and is adapted to switching element functions via the abs-normal-form (ANF). T3 - ZIB-Report - 17-41 KW - compressed sparse row format KW - algorithmic differentiation KW - abs-normal form KW - piecewise linear tangent approximation KW - piecewise smooth Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64582 SN - 1438-0064 ER - TY - GEN A1 - Renken, Malte A1 - Ahmadi, Amin A1 - Borndörfer, Ralf A1 - Sahin, Guvenc A1 - Schlechte, Thomas T1 - Demand-Driven Line Planning with Selfish Routing N2 - Bus rapid transit systems in developing and newly industrialized countries are often operated at the limits of passenger capacity. In particular, demand during morning and afternoon peaks is hardly or even not covered with available line plans. In order to develop demand-driven line plans, we use two mathematical models in the form of integer programming problem formulations. While the actual demand data is specified with origin-destination pairs, the arc-based model considers the demand over the arcs derived from the origin-destination demand. In order to test the accuracy of the models in terms of demand satisfaction, we simulate the optimal solutions and compare number of transfers and travel times. We also question the effect of a selfish route choice behavior which in theory results in a Braess-like paradox by increasing the number of transfers when system capacity is increased with additional lines. T3 - ZIB-Report - 17-38 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64547 SN - 1438-0064 ER - TY - GEN A1 - Beckenbach, Isabel T1 - A Hypergraph Network Simplex Algorithm N2 - We describe a network simplex algorithm for the minimum cost flow problem on graph-based hypergraphs which are directed hypergraphs of a particular form occurring in railway rotation planning. The algorithm is based on work of Cambini, Gallo, and Scutellà who developed a hypergraphic generalization of the network simplex algorithm. Their main theoretical result is the characterization of basis matrices. We give a similar characterization for graph-based hypergraphs and show that some operations of the simplex algorithm can be done combinatorially by exploiting the underlying digraph structure. T3 - ZIB-Report - 17-36 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64539 SN - 1438-0064 ER - TY - CHAP A1 - Müller, Benjamin A1 - Kuhlmann, Renke A1 - Vigerske, Stefan T1 - On the performance of NLP solvers within global MINLP solvers T2 - Operations Research Proceedings 2017 N2 - Solving mixed-integer nonlinear programs (MINLPs) to global optimality efficiently requires fast solvers for continuous sub-problems. These appear in, e.g., primal heuristics, convex relaxations, and bound tightening methods. Two of the best performing algorithms for these sub-problems are Sequential Quadratic Programming (SQP) and Interior Point Methods. In this paper we study the impact of different SQP and Interior Point implementations on important MINLP solver components that solve a sequence of similar NLPs. We use the constraint integer programming framework SCIP for our computational studies. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-319-89920-6_84 SP - 633 EP - 639 PB - Springer International Publishing ER - TY - GEN A1 - Müller, Benjamin A1 - Kuhlmann, Renke A1 - Vigerske, Stefan T1 - On the performance of NLP solvers within global MINLP solvers N2 - Solving mixed-integer nonlinear programs (MINLPs) to global optimality efficiently requires fast solvers for continuous sub-problems. These appear in, e.g., primal heuristics, convex relaxations, and bound tightening methods. Two of the best performing algorithms for these sub-problems are Sequential Quadratic Programming (SQP) and Interior Point Methods. In this paper we study the impact of different SQP and Interior Point implementations on important MINLP solver components that solve a sequence of similar NLPs. We use the constraint integer programming framework SCIP for our computational studies. T3 - ZIB-Report - 17-35 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64504 SN - 1438-0064 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Maher, Stephen A1 - Müller, Benjamin A1 - Pedroso, João Pedro T1 - Price-and-verify: a new algorithm for recursive circle packing using Dantzig–Wolfe decomposition JF - Annals of Operations Research N2 - Packing rings into a minimum number of rectangles is an optimization problem which appears naturally in the logistics operations of the tube industry. It encompasses two major difficulties, namely the positioning of rings in rectangles and the recursive packing of rings into other rings. This problem is known as the Recursive Circle Packing Problem (RCPP). We present the first dedicated method for solving RCPP that provides strong dual bounds based on an exact Dantzig–Wolfe reformulation of a nonconvex mixed-integer nonlinear programming formulation. The key idea of this reformulation is to break symmetry on each recursion level by enumerating one-level packings, i.e., packings of circles into other circles, and by dynamically generating packings of circles into rectangles. We use column generation techniques to design a “price-and-verify” algorithm that solves this reformulation to global optimality. Extensive computational experiments on a large test set show that our method not only computes tight dual bounds, but often produces primal solutions better than those computed by heuristics from the literature. Y1 - 2018 U6 - https://doi.org/10.1007/s10479-018-3115-5 VL - 284 IS - 2 SP - 527 EP - 555 PB - Springer US ER - TY - GEN A1 - Wolf, Thomas A1 - Amadi, Chimaobi T1 - Rational Solutions of Underdetermined Polynomial Equations N2 - In this paper we report on an application of computer algebra in which mathematical puzzles are generated of a type that had been widely used in mathematics contests by a large number of participants worldwide. The algorithmic aspect of our work provides a method to compute rational solutions of single polynomial equations that are typically large with 10^2 ... 10^5 terms and that are heavily underdetermined. It was possible to obtain this functionality by adding a number of new modules for a new type of splitting of equations to the existing package CRACK that is normally used to solve polynomial algebraic and differential systems of equations. T3 - ZIB-Report - 17-33 KW - underdetermined polynomial systems, rational solutions, computer algebra, recreational mathematics Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64488 SN - 1438-0064 ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Scheidweiler, Robert T1 - Perfect f-Matchings and f-Factors in Hypergraphs - A Combinatorial Approach JF - Discrete Mathematics N2 - We prove characterizations of the existence of perfect f-matchings in uniform mengerian and perfect hypergraphs. Moreover, we investigate the f-factor problem in balanced hypergraphs. For uniform balanced hypergraphs we prove two existence theorems with purely combinatorial arguments, whereas for non-uniform balanced hypergraphs we show that the f-factor problem is NP-hard. Y1 - 2017 U6 - https://doi.org/10.1016/j.disc.2017.05.005 VL - 340 IS - 10 SP - 2499 EP - 2506 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Global optimization of complex optical structures using Bayesian optimization based on Gaussian processes JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2270609 VL - 10335 SP - 103350O ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Weiser, Martin A1 - Santiago, Xavier Garcia A1 - Zschiedrich, Lin A1 - Bodermann, Bernd A1 - Burger, Sven T1 - Quantifying parameter uncertainties in optical scatterometry using Bayesian inversion JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2270596 VL - 10330 SP - 1033004 ER - TY - JOUR A1 - Benn, Andreas A1 - Hiepen, Christian A1 - Osterland, Marc A1 - Schütte, Christof A1 - Zwijsen, An A1 - Knaus, Petra T1 - Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence JF - FASEB Journal N2 - Before the onset of sprouting angiogenesis, the endothelium is prepatterned for the positioning of tip and stalk cells. Both cell identities are not static, as endothelial cells (ECs) constantly compete for the tip cell position in a dynamic fashion. Here, we show that both bone morphogenetic protein (BMP) 2 and BMP6 are proangiogenic in vitro and ex vivo and that the BMP type I receptors, activin receptor-like kinase (ALK)3 and ALK2, play crucial and distinct roles in this process. BMP2 activates the expression of tip cell–associated genes, such as DLL4 (delta-like ligand 4) and KDR (kinase insert domain receptor), and p38-heat shock protein 27 (HSP27)–dependent cell migration, thereby generating tip cell competence. Whereas BMP6 also triggers collective cell migration via the p38-HSP27 signaling axis, BMP6 induces in addition SMAD1/5 signaling, thereby promoting the expression of stalk cell–associated genes, such as HES1 (hairy and enhancer of split 1) and FLT1 (fms-like tyrosine kinase 1). Specifically, ALK3 is required for sprouting from HUVEC spheroids, whereas ALK2 represses sprout formation. We demonstrate that expression levels and respective complex formation of BMP type I receptors in ECs determine stalk vs. tip cell identity, thus contributing to endothelial plasticity during sprouting angiogenesis. As antiangiogenic monotherapies that target the VEGF or ALK1 pathways have not fulfilled efficacy objectives in clinical trials, the selective targeting of the ALK2/3 pathways may be an attractive new approach. Y1 - 2017 U6 - https://doi.org/10.1096/fj.201700193RR VL - 31 IS - 11 SP - 4720 EP - 4733 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Blanco, Marco A1 - Sauvage, Thibaut T1 - The Cone of Flow Matrices: Approximation Hierarchies and Applications N2 - Let G be a directed acyclic graph with n arcs, a source s and a sink t. We introduce the cone K of flow matrices, which is a polyhedral cone generated by the matrices $\vec{1}_P\vec{1}_P^T\in\RR^{n\times n}$, where $\vec{1}_P\in\RR^n$ is the incidence vector of the (s,t)-path P. We show that several hard flow (or path) optimization problems, that cannot be solved by using the standard arc-representation of a flow, reduce to a linear optimization problem over $\mathcal{K}$. This cone is intractable: we prove that the membership problem associated to $\mathcal{K}$ is NP-complete. However, the affine hull of this cone admits a nice description, and we give an algorithm which computes in polynomial-time the decomposition of a matrix $X\in \operatorname{span} \mathcal{K}$ as a linear combination of some $\vec{1}_P\vec{1}_P^T$'s. Then, we provide two convergent approximation hierarchies, one of them based on a completely positive representation of~K. We illustrate this approach by computing bounds for the quadratic shortest path problem, as well as a maximum flow problem with pairwise arc-capacities. T3 - ZIB-Report - 17-32 KW - Flows in graphs KW - Approximation Hierarchies KW - Copositive Programming KW - Semidefinite Programming Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64399 SN - 1438-0064 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schade, Stanley A1 - Schlechte, Thomas T1 - A Propagation Approach to Acyclic Rolling Stock Rotation Optimization T2 - Proceedings of the IAROR conference RailLille N2 - The rolling stock, i.e., railway vehicles, are one of the key ingredients of a running railway system. As it is well known, the offer of a railway company to their customers, i.e., the railway timetable, changes from time to time. Typical reasons for that are different timetables associated with different seasons, maintenance periods or holidays. Therefore, the regular lifetime of a timetable is split into (more or less) irregular periods where parts of the timetable are changed. In order to operate a railway timetable most railway companies set up sequences that define the operation of timetabled trips by a single physical railway vehicle called (rolling stock) rotations. Not surprisingly, the individual parts of a timetable also affect the rotations. More precisely, each of the parts brings up an acyclic rolling stock rotation problem with start and end conditions associated with the beginning and ending of the corresponding period. In this paper, we propose a propagation approach to deal with large planning horizons that are composed of many timetables with shorter individual lifetimes. The approach is based on an integer linear programming formulation that propagates rolling stock rotations through the irregular parts of the timetable while taking a large variety of operational requirements into account. This approach is implemented within the rolling stock rotation optimization framework ROTOR used by DB Fernverkehr AG, one of the leading railway operators in Europe. Computational results for real world scenarios are presented to evaluate the approach. Y1 - 2017 ER - TY - CHAP A1 - Coutinho, Jose A1 - Stillwell, Mark A1 - Argyraki, Katerina A1 - Ioannidis, George A1 - Iordache, Anca A1 - Kleineweber, Christoph A1 - Koliousis, Alexandros A1 - McGlone, John A1 - Pierre, Guillaume A1 - Ragusa, Carmelo A1 - Sanders, Peter A1 - Schütt, Thorsten A1 - Yu, Teng A1 - Wolf, Alexander T1 - The HARNESS Platform: A Hardware- and Network-Enhanced Software System for Cloud Computing T2 - Software Architecture for Big Data and the Cloud Y1 - 2017 SN - 9780128054673 SP - 323 EP - 351 PB - Morgan Kaufmann ER - TY - GEN T1 - Annual Report 2016 T3 - Jahresbericht - 2016 KW - Jahresbericht Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64339 SN - 0934-5892 VL - 2016 ER - TY - CHAP A1 - Schade, Stanley A1 - Borndörfer, Ralf A1 - Breuer, Matthias A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Siebeneicher, Patrick T1 - Pattern Detection For Large-Scale Railway Timetables T2 - Proceedings of the IAROR conference RailLille N2 - We consider railway timetables of our industrial partner DB Fernverkehr AG that operates the ICE high speed trains in the long-distance passenger railway network of Germany. Such a timetable covers a whole year with 364 days and, typically, includes more than 45,000 trips. A rolling stock rotation plan is not created for the whole timetable at once. Instead the timetable is divided into regular invariant sections and irregular deviations (e.g. for public holidays). A separate rotation plan with a weekly period can then be provided for each of the different sections of the timetable. We present an algorithmic approach to automatically recognize these sections. Together with the supplementing visualisation of the timetable this method has shown to be very relevant for our industrial partner. Y1 - 2017 ER - TY - JOUR A1 - Wilson, David A1 - Anglin, Carolyn A1 - Ambellan, Felix A1 - Grewe, Carl Martin A1 - Tack, Alexander A1 - Lamecker, Hans A1 - Dunbar, Michael A1 - Zachow, Stefan T1 - Validation of three-dimensional models of the distal femur created from surgical navigation point cloud data for intraoperative and postoperative analysis of total knee arthroplasty JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: Despite the success of total knee arthroplasty there continues to be a significant proportion of patients who are dissatisfied. One explanation may be a shape mismatch between pre and post-operative distal femurs. The purpose of this study was to investigate a method to match a statistical shape model (SSM) to intra-operatively acquired point cloud data from a surgical navigation system, and to validate it against the pre-operative magnetic resonance imaging (MRI) data from the same patients. Methods: A total of 10 patients who underwent navigated total knee arthroplasty also had an MRI scan less than 2 months pre-operatively. The standard surgical protocol was followed which included partial digitization of the distal femur. Two different methods were employed to fit the SSM to the digitized point cloud data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). The available MRI data were manually segmented and the reconstructed three-dimensional surfaces used as ground truth against which the statistical shape model fit was compared. Results: For both approaches, the difference between the statistical shape model-generated femur and the surface generated from MRI segmentation averaged less than 1.7 mm, with maximum errors occurring in less clinically important areas. Conclusion: The results demonstrated good correspondence with the distal femoral morphology even in cases of sparse data sets. Application of this technique will allow for measurement of mismatch between pre and post-operative femurs retrospectively on any case done using the surgical navigation system and could be integrated into the surgical navigation unit to provide real-time feedback. Y1 - 2017 UR - https://link.springer.com/content/pdf/10.1007%2Fs11548-017-1630-5.pdf U6 - https://doi.org/10.1007/s11548-017-1630-5 VL - 12 IS - 12 SP - 2097 EP - 2105 PB - Springer ER - TY - JOUR A1 - Hengartner, Michael A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Saleh, Lanja A1 - Spanaus, Katharina A1 - Schippert, Cordula A1 - Zhang, Yuanyuan A1 - Leeners, Brigitte T1 - Negative affect is unrelated to fluctuations in hormone levels across the menstrual cycle: evidence from a multisite observational study across two successive cycles JF - Journal of Psychosomatic Research Y1 - 2017 U6 - https://doi.org/10.1016/j.jpsychores.2017.05.018 VL - 99 SP - 21 EP - 27 ER - TY - GEN A1 - Quer, Jannes A1 - Lie, Han Cheng T1 - Some connections between importance sampling and enhanced sampling methods in molecular dynamics N2 - Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Schütte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling. T3 - ZIB-Report - 17-30 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64289 SN - 1438-0064 ER - TY - CHAP A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Flatken, Markus A1 - Hege, Hans-Christian A1 - Hotz, Ingrid T1 - Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions T2 - Topological Methods in Data Analysis and Visualization IV Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-44684-4_2 SP - 35 EP - 50 PB - Springer CY - Cham, Schweiz ER - TY - GEN A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Hybrid Models for Chemical Reaction Networks: Multiscale Theory and Application to Gene Regulatory Systems N2 - Well-mixed stochastic chemical kinetics are properly modelled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows to express various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. T3 - ZIB-Report - 17-29 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64264 ER - TY - JOUR A1 - Quer, Jannes A1 - Lie, Han Cheng T1 - Some connections between importance sampling and enhanced sampling methods in molecular dynamics JF - Journal of Chemical Physics N2 - Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Schütte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling. Y1 - 2017 ER - TY - JOUR A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data JF - Biomedical Physics & Engineering Express N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. Y1 - 2017 U6 - https://doi.org/10.1088/2057-1976/aa7611 VL - 3 IS - 3 PB - IOP Publishing ER - TY - CHAP A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Accurate optical simulations of periodic nanostructures on a thick glass substrate T2 - 29th Workshop on Quantum Solar Energy Conversion - (QUANTSOL) Y1 - 2017 ER - TY - GEN A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies N2 - Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 2 comparison cohort was used to translate MACC1 qRT- PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus 100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100% versus 90%, respectively). In the pooled dataset, 6.5% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17% higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100% and 96%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy. T3 - ZIB-Report - 17-28 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64184 SN - 1438-0064 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Baumgart, Johannes A1 - Lindow, Norbert A1 - Shelley, Michael A1 - Nazockdast, Ehssan A1 - Kratz, Andrea A1 - Prohaska, Steffen A1 - Brugués, Jan A1 - Fürthauer, Sebastian A1 - Müller-Reichert, Thomas T1 - C. elegans chromosomes connect to centrosomes by anchoring into the spindle network JF - Nature Communications N2 - The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15288 VL - 8 IS - 15288 ER - TY - CHAP A1 - Baum, Daniel A1 - Mahlow, Kristin A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Müller, Johannes A1 - Hege, Hans-Christian T1 - The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis) T2 - Abstract in DigitalSpecimen 2014 N2 - Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term ‘surface-based morphometrics’. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called ‘surface paths’, might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique. Y1 - 2014 ER - TY - JOUR A1 - Vigerske, Stefan A1 - Gleixner, Ambros T1 - SCIP: Global Optimization of Mixed-Integer Nonlinear Programs in a Branch-and-Cut Framework JF - Optimization Methods & Software N2 - This paper describes the extensions that were added to the constraint integer programming framework SCIP in order to enable it to solve convex and nonconvex mixed-integer nonlinear programs (MINLPs) to global optimality. SCIP implements a spatial branch-and-bound algorithm based on a linear outer-approximation, which is computed by convex over- and underestimation of nonconvex functions. An expression graph representation of nonlinear constraints allows for bound tightening, structure analysis, and reformulation. Primal heuristics are employed throughout the solving process to find feasible solutions early. We provide insights into the performance impact of individual MINLP solver components via a detailed computational study over a large and heterogeneous test set. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1335312 VL - 33 IS - 3 SP - 563 EP - 593 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Umsteigen ohne Warten T2 - HEUREKA 2017 N2 - Wir stellen einen mathematischen Optimierungsansatz zur Berechnung von periodischen Taktfahrplänen vor, bei dem die Umsteigezeiten unter Berücksichtigung des Passagierverhaltens minimiert werden. Wir untersuchen damit den Einfluss wichtiger Systemparameter und Verhaltensmuster auf die Beförderungsqualität. Y1 - 2017 ER - TY - CHAP A1 - Witzig, Jakob A1 - Berthold, Timo A1 - Heinz, Stefan T1 - Experiments with Conflict Analysis in Mixed Integer Programming T2 - Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2017 N2 - The analysis of infeasible subproblems plays an import role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications obtained by domain propagation that led to infeasibility. The result of the analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. The dual LP solution provides a set of multipliers that can be used to generate a single new globally valid linear constraint. The main contribution of this short paper is an empirical evaluation of two ways to combine both approaches. Experiments are carried out on general MIP instances from standard public test sets such as Miplib2010; the presented algorithms have been implemented within the non-commercial MIP solver SCIP. Moreover, we present a pool-based approach to manage conflicts which addresses the way a MIP solver traverses the search tree better than aging strategies known from SAT solving. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-59776-8_17 VL - 10335 SP - 211 EP - 222 PB - Springer ER - TY - CHAP A1 - Mangalgiri, Gauri A1 - Šiškins, Makars A1 - Arslanova, Alina A1 - Hammerschmidt, Martin A1 - Manley, Phillip A1 - Riedel, Wiebke A1 - Schmid, Martina T1 - Highly Transmittive Broadband Dielectric Nanoholes T2 - CLEO Y1 - 2017 U6 - https://doi.org/10.1364/CLEO_AT.2017.JTu5A.117 SP - JTu5A.117 ER - TY - THES A1 - Schienle, Adam T1 - Shortest Paths on Airway Networks Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64047 ER - TY - GEN A1 - Beckenbach, Isabel A1 - Peis, Britta A1 - Schaudt, Oliver A1 - Scheidweiler, Robert T1 - A Combinatorial Proof of a König-type Theorem for Unimodular Hypergraphs N2 - We state purely combinatorial proofs for König- and Hall-type theorems for a wide class of combinatorial optimization problems. Our methods rely on relaxations of the matching and vertex cover problem and, moreover, on the strong coloring properties admitted by bipartite graphs and their generalizations. T3 - ZIB-Report - 17-27 KW - Packing KW - Covering KW - Total Unimodularity KW - König's Theorem KW - Factors Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64017 SN - 1438-0064 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. T3 - ZIB-Report - 17-26 KW - trabecular structures KW - image-based analysis KW - additive manufacturing KW - printability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64004 SN - 1438-0064 ER - TY - GEN A1 - Fischer, Lisa A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy data compression reduces communication time in hybrid time-parallel integrators N2 - Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups. T3 - ZIB-Report - 17-25 KW - parallel-in-time integration KW - hybrid parareal KW - convergence KW - lossy compression KW - MPI Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63961 SN - 1438-0064 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - GenPCCA -- Markov State Models for Non-Equilibrium Steady States JF - Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29 Y1 - 2017 U6 - https://doi.org/10.20347/WIAS.REPORT.29 SP - 70 EP - 80 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Niknejad, Amir A1 - Weber, Marcus T1 - Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation JF - Special Matrices Y1 - 2017 U6 - https://doi.org/10.1515/spma-2017-0006 IS - 5/1 SP - 73 EP - 81 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schade, Stanley A1 - Schlechte, Thomas T1 - A Propagation Approach to Acyclic Rolling Stock Rotation Optimization N2 - The rolling stock, i.e., railway vehicles, are one of the key ingredients of a running railway system. As it is well known, the offer of a railway company to their customers, i.e., the railway timetable, changes from time to time. Typical reasons for that are different timetables associated with different seasons, maintenance periods or holidays. Therefore, the regular lifetime of a timetable is split into (more or less) irregular periods where parts of the timetable are changed. In order to operate a railway timetable most railway companies set up sequences that define the operation of timetabled trips by a single physical railway vehicle called (rolling stock) rotations. Not surprisingly, the individual parts of a timetable also affect the rotations. More precisely, each of the parts brings up an acyclic rolling stock rotation problem with start and end conditions associated with the beginning and ending of the corresponding period. In this paper, we propose a propagation approach to deal with large planning horizons that are composed of many timetables with shorter individual lifetimes. The approach is based on an integer linear programming formulation that propagates rolling stock rotations through the irregular parts of the timetable while taking a large variety of operational requirements into account. This approach is implemented within the rolling stock rotation optimization framework ROTOR used by DB Fernverkehr AG, one of the leading railway operators in Europe. Computational results for real world scenarios are presented to evaluate the approach. T3 - ZIB-Report - 17-24 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63930 SN - 1438-0064 ER - TY - JOUR A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies JF - Annals of Oncology N2 - Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 2 comparison cohort was used to translate MACC1 qRT-PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus 100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100% versus 90%, respectively). In the pooled dataset, 6.5% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17% higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100% and 96%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy. Y1 - 2017 U6 - https://doi.org/10.1093/annonc/mdx207 VL - 28 IS - 8 SP - 1869 EP - 1875 ER - TY - JOUR A1 - Brüning, Jan A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Numerical Analysis of Nasal Breathing - A Pilot Study JF - Facial Plastic Surgery N2 - Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose’s total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work’s aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal. Y1 - 2017 U6 - https://doi.org/doi:10.1055/s-0037-1603789 VL - 33 IS - 4 SP - 388 EP - 395 ER - TY - GEN A1 - Lange, Alexander A1 - Schwieger, Robert A1 - Plöntzke, Julia A1 - Schäfer, Stefan A1 - Röblitz, Susanna T1 - Follicular competition: the selection of dominant follicles as a synergistic effect N2 - The estrous cycle of mono-ovulatory species such as cows or humans, is known to show two or more waves of follicular growth and decline between two successive ovulations. Within each wave, there is one dominant follicle escorted by subordinate follicles of varying number. Under the surge of the luteinizing hormone a growing dominant follicle ovulates. Rarely the number of ovulating follicles exceeds one. In the biological literature, the change of hormonal concentrations and individually varying numbers of follicular receptors are made responsible for the selection of exactly one dominant follicle, yet a clear cause has not been identified. In this paper, we suggest a synergistic explanation based on competition, formulated by a parsimoniously defined system of ordinary differential equations (ODEs) that quantifies the time evolution of multiple follicles and their competitive interaction during one wave. Not discriminating between follicles, growth and decline are given by fixed rates. Competition is introduced via a growth-suppressing term, equally supported by all follicles. We prove that the number of dominant follicles is determined exclusively by the ratio of follicular growth and competition. This number turns out to be independent of the number of subordinate follicles. The asymptotic behavior of the corresponding dynamical system is investigated rigorously, where we demonstrate that the omega-limit set only contains fixed points. When also including follicular decline, our ODEs perfectly resemble ultrasound data of bovine follicles. Implications for the involved but not explicitly modeled hormones are discussed. T3 - ZIB-Report - 17-21 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63863 SN - 1438-0064 ER - TY - CHAP A1 - Gilg, Brady A1 - Klug, Torsten A1 - Martienssen, Rosemarie A1 - Paat, Joseph A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Seymen, Sinan A1 - Tesch, Alexander T1 - Conflict-Free Railway Track Assignment at Depots T2 - Proceedings of the IAROR conference RailLille N2 - Managing rolling stock with no passengers aboard is a critical component of railway operations. In particular, one problem is to park the rolling stock on a given set of tracks at the end of a day or service. Depending on the parking assignment, shunting may be required in order for a parked train to depart or for an incoming train to park. Given a collection of tracks M and a collection of trains T with fixed arrival-departure timetable, the train assignment problem (TAP) is to determine the maximum number of trains from T that can be parked on M according to the timetable and without the use of shunting. Hence, efficiently solving the TAP allows to quickly compute feasible parking schedules that do not require further shunting adjustments. In this paper, we present two integer programming models for solving the TAP. To our knowledge, this is the first integrated approach that considers track lengths along with the three most common types of parking tracks. We compare these models on a theoretical level. We also prove that a decision version of the TAP is NP-complete, justifying the use of integer programming techniques. Using stochastic and robust modelling techniques, both models produce parking assignments that are optimized and robust according to random train delays. We conclude with computational results for both models, observing that they perform well on real timetables. Y1 - 2017 ER - TY - GEN A1 - Gilg, Brady A1 - Klug, Torsten A1 - Martienssen, Rosemarie A1 - Paat, Joseph A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Seymen, Sinan A1 - Tesch, Alexander T1 - Conflict-Free Railway Track Assignment at Depots N2 - Managing rolling stock with no passengers aboard is a critical component of railway operations. In particular, one problem is to park the rolling stock on a given set of tracks at the end of a day or service. Depending on the parking assignment, shunting may be required in order for a parked train to depart or for an incoming train to park. Given a collection of tracks M and a collection of trains T with fixed arrival-departure timetable, the train assignment problem (TAP) is to determine the maximum number of trains from T that can be parked on M according to the timetable and without the use of shunting. Hence, efficiently solving the TAP allows to quickly compute feasible parking schedules that do not require further shunting adjustments. In this paper, we present two integer programming models for solving the TAP. To our knowledge, this is the first integrated approach that considers track lengths along with the three most common types of parking tracks. We compare these models on a theoretical level. We also prove that a decision version of the TAP is NP-complete, justifying the use of integer programming techniques. Using stochastic and robust modelling techniques, both models produce parking assignments that are optimized and robust according to random train delays. We conclude with computational results for both models, observing that they perform well on real timetables. T3 - ZIB-Report - 17-23 KW - Depot Planning KW - Railway Track Assignment Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63843 SN - 1438-0064 ER - TY - GEN A1 - Bittracher, Andreas A1 - Koltai, Péter A1 - Klus, Stefan A1 - Banisch, Ralf A1 - Dellnitz, Michael A1 - Schütte, Christof T1 - Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics N2 - We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics. T3 - ZIB-Report - 17-22 KW - metastability KW - slow dynamics KW - effective dynamics KW - transition manifold KW - embedding KW - transfer operator KW - reaction coordinate Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63822 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. From that we identify the most crucial parameters to measure or estimate, and obtain a local uncertainty quantifcation for the ToD. T3 - ZIB-Report - 17-18 KW - forensic medicine KW - determination of time of death KW - heat transfer equation KW - sensitivity i.r.t. thermal parameters KW - sensitivity i.r.t. geometric resolution Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63818 SN - 1438-0064 ER - TY - THES A1 - Vega, Iliusi T1 - Reconstruction and analysis of the state space for the identification of dynamical states in real-world time-series Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000104520-1 ER - TY - THES A1 - Sriwattanaworachai, Nisara T1 - Spectral approach to metastability of non-reversible complex processes Y1 - 2016 ER - TY - THES A1 - Lie, Han Cheng T1 - On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101680-4 ER - TY - THES A1 - Gul, Raheem T1 - Mathematical Modeling and Sensitivity Analysis of Lumped­ Parameter Model of the Human Cardiovascular System Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101271-2 ER - TY - THES A1 - Daragmeh, Adman T1 - Model Order Reduction of Linear Control Systems: Comparison of Balance Truncation and Singular Perturbation Approximation with Application to Optimal Control Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102586-2 ER - TY - THES A1 - Badowski, Tomasz T1 - Adaptive importance sampling via minimization of estimators of cross-entropy, mean square and inefficiency constants Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102823-3 ER - TY - THES A1 - Agarwal, Animesh T1 - Path Integral Techniques in Molecular Dynamics Simulations of Open Boundary Systems Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000103020-4 ER - TY - GEN A1 - Zhang, Wei A1 - Schütte, Christof T1 - Reliable approximation of long relaxation timescales in molecular dynamics N2 - Many interesting rare events in molecular systems like ligand association, protein folding or con- formational changes happen on timescales that often are not accessible by direct numerical simulation. Therefore rare event approximation approaches like interface sampling, Markov state model building or advanced reaction coordinate based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches: How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so they also allow for understanding deep connections between the different approaches. T3 - ZIB-Report - 17-19 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63718 SN - 1438-0064 ER - TY - THES A1 - Conrad, Tim T1 - Metabolic Pathways Y1 - 2004 UR - http://publications.imp.fu-berlin.de/10/ ER - TY - JOUR A1 - Conrad, Tim T1 - New Appraches for Visualizing and Analyzing Metabolic Pathways JF - Proceedings of the Second Australian Undergraduate Students? Computing Conference N2 - Visualizing of metabolic pathways (or networks) has been done by many differentapproaches. In this work, we implemented and tested existing graph layout algorithms, and present a new approach to lay-out medium size metabolic pathways (500-20,000 vertices) by implementing and combining three well known graph lay-out algorithms (high dimension embedding, spring-embedder preprocessing, spring-embedder), through 3D space density analysis facilitated by the Octree technique. For the analysis of the results of metabolic pathways simulations we present two new techniques: rstly, a powerful technique to visualize pathways simulation data was created to unveil and understand concentration ows through metabolic pathways. This was achieved by mapping the color encoded concentration value of every substance from each time step of the simulation to its graphical representation in the layout. By combining all resulting images (from each time step) and displaying them as a movie, many characteristics such as subnetworks, alternative routes through the network, and differences between a modied pathway and its unmodied version can be revealed. Secondly, a new method to detect co-regulated substances in metabolic pathways and to recognize differences between two versions of a pathway, was established. To do this, we transformed the simulation data into a row-based representation, color-coded these rows, and reordered them with respect to similarity by using a Genetic Algorithm variant. From the arising discrete 2-dimensional matrix consisting of concentration values, a continuous 2-dimensional fourier row function was computed. This function can be used to measure properties, such as similarities in a pathway between time steps, or substances, or to detect and evaluate differences between modied versions of the same pathway. Y1 - 2004 ER - TY - JOUR A1 - Conrad, Tim A1 - Rath, Barbara A1 - Tief, Franziska A1 - Karsch, K. A1 - Muehlhans, S. A1 - Obermeier, Patrick A1 - Adamou, E. A1 - Chen, X. A1 - Seeber, L. A1 - Peiser, Ch. A1 - Hoppe, Christian A1 - von Kleist, Max A1 - Schweiger, Brunhilde T1 - Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir JF - Infectious Disorders - Drug Targets Y1 - 2013 VL - 13 IS - 1 SP - 25 EP - 33 ER - TY - JOUR A1 - Conrad, Tim A1 - Shao, Borong T1 - Are NoSQL data stores useful for bioinformatics researchers? JF - International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC) Y1 - 2015 U6 - https://doi.org/10.17762/ijritcc2321-8169.1503176 VL - 3 IS - 3 SP - 1704 EP - 1708 ER - TY - JOUR A1 - Conrad, Tim A1 - Lenga, Matthias T1 - Non-convex regularization for supervised learning JF - Technical Report Y1 - 2015 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Döpking, Sandra A1 - Burger, Sven A1 - Matera, Sebastian T1 - Field Heterogeneities and their Impact on Photocatalysis: Combining optical and kinetic Monte Carlo Simulations on the Nanoscale N2 - Gaining insights into the working principles of photocatalysts on an atomic scale is a challenging task. The obviously high complexity of the reaction mechanism involving photo-excited electrons and holes is one reason. Another complicating aspect is that the electromagnetic field, driving photocatalysis, is not homogeneous on a nanoscale level for particle based catalysts as it is influenced by the particle’s shape and size. We present a simple model, inspired by the CO2 reduction on titania anatase, which addresses the impact of these heterogeneities on the photocatalytic kinetics by combining kinetic Monte Carlo with electromagnetic wave simulations. We find that average activity and especially efficiency might differ significantly between different particles. Moreover, we find sizable variation of the catalytic activity on a single facet of a nanocrystal. Besides this quantitative heterogeneity, the coverage situation in general changes laterally on this facet and we observe a concomitant change of the rate-determining steps. This heterogeneity on all levels of photocatalytic activity is masked in experimental studies, where only the spatially averaged activity can be addressed. Microkinetic models based on experimental findings might therefore not represent the true micro- scopic behavior, and mechanistic conclusion drawn from these need to be handled with care. T3 - ZIB-Report - 17-20 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63690 SN - 1438-0064 ER - TY - JOUR A1 - Gupta, Pooja A1 - Conrad, Tim A1 - Spötter, Andreas A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Simulating a base population in honey bee for molecular genetic studies JF - Genetics Selection Evolution N2 - Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding values estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has distinct genetic and reproductive biology characteristics. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee.  Results: Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) ?2 statistics for Hardy- Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion: We developed a software program that takes into account the genetic and reproductive biology characteristics specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html Y1 - 2012 U6 - https://doi.org/10.1186/1297-9686-44-14 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Nuoffer, Jean-Marc A1 - Ceglarek, Uta A1 - Kase, Julia A1 - Witzigmann, Helmut A1 - Thiery, Joachim A1 - Fiedler, Georg Martin T1 - Serum amino acid profiles and their alterations in colorectal cancer JF - Metabolomics N2 - Mass spectrometry-based serum metabolic profiling is a promising tool to analyse complex cancer associated metabolic alterations, which may broaden our pathophysiological understanding of the disease and may function as a source of new cancer-associated biomarkers. Highly standardized serum samples of patients suffering from colon cancer (n = 59) and controls (n = 58) were collected at the University Hospital Leipzig. We based our investigations on amino acid screening profiles using electrospray tandem-mass spectrometry. Metabolic profiles were evaluated using the Analyst 1.4.2 software. General, comparative and equivalence statistics were performed by R 2.12.2. 11 out of 26 serum amino acid concentrations were significantly different between colorectal cancer patients and healthy controls. We found a model including CEA, glycine, and tyrosine as best discriminating and superior to CEA alone with an AUROC of 0.878 (95\% CI 0.815?0.941). Our serum metabolic profiling in colon cancer revealed multiple significant disease-associated alterations in the amino acid profile with promising diagnostic power. Further large-scale studies are necessary to elucidate the potential of our model also to discriminate between cancer and potential differential diagnoses. In conclusion, serum glycine and tyrosine in combination with CEA are superior to CEA for the discrimination between colorectal cancer patients and controls. Y1 - 2012 U6 - https://doi.org/10.1007/s11306-011-0357-5 ER - TY - JOUR A1 - Conrad, Tim A1 - Bruckner, Sharon A1 - Kayser, Bastian T1 - Finding Modules in Networks with Non-modular Regions JF - Lecture Notes in Computer Science (Proceedings of SEA 2013) N2 - Most network clustering methods share the assumption that the network can be completely decomposed into modules, that is, every node belongs to (usually exactly one) module. Forcing this constraint can lead to misidentification of modules where none exist, while the true modules are drowned out in the noise, as has been observed e.g. for protein interaction networks. We thus propose a clustering model where networks contain both a modular region consisting of nodes that can be partitioned into modules, and a transition region containing nodes that lie between or outside modules. We propose two scores based on spectral properties to determine how well a network fits this model. We then evaluate three (partially adapted) clustering algorithms from the literature on random networks that fit our model, based on the scores and comparison to the ground truth. This allows to pinpoint the types of networks for which the different algorithms perform well. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38527-8_18 VL - 7933 SP - 188 EP - 199 ER - TY - JOUR A1 - Gupta, Pooja A1 - Reinsch, Norbert A1 - Spötter, Andreas A1 - Conrad, Tim A1 - Bienefeld, Kaspar T1 - Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera) JF - BMC Genetics Y1 - 2013 U6 - https://doi.org/10.1186/1471-2156-14-36 VL - 14 IS - 36 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Ceglarek, Uta A1 - Weinert, P. A1 - Nakas, C.T. A1 - Nuoffer, Jean-Marc A1 - Kase, Julia A1 - Witzigmann, Helmut A1 - Thiery, Joachim A1 - Fiedler, Georg Martin T1 - Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma JF - Metabolomics N2 - Background: Metabolomics as one of the most rapidly growing technologies in the ?-omics?field denotes the comprehensive analysis of low molecular-weight compounds and their pathways. Cancer-specific alterations of the metabolome can be detected by high-throughput massspectrometric metabolite profiling and serve as a considerable source of new markers for the early differentiation of malignant diseases as well as their distinction from benign states. However, a comprehensive framework for the statistical evaluation of marker panels in a multi-class setting has not yet been established. Methods: We collected serum samples of 40 pancreatic carcinoma patients, 40 controls, and 23 pancreatitis patients according to standard protocols and generated amino acid profiles by routine mass-spectrometry. In an intrinsic three-class bioinformatic approach we compared these profiles, evaluated their selectivity and computed multi-marker panels combined with the conventional tumor marker CA 19-9. Additionally, we tested for non-inferiority and superiority to determine the diagnostic surplus value of our multi-metabolite marker panels.  Results: Compared to CA 19-9 alone, the combined amino acid-based metabolite panel had a superior selectivity for the discrimination of healthy controls, pancreatitis, and pancreatic carcinoma patients [Volume under ROC surface (VUS) = 0.891 (95\% CI 0.794 - 0.968)]. Conclusions: We combined highly standardized samples, a three-class study design, a highthroughput mass-spectrometric technique, and a comprehensive bioinformatic framework to identify metabolite panels selective for all three groups in a single approach. Our results suggest that metabolomic profiling necessitates appropriate evaluation strategies and ?despite all its current limitations? can deliver marker panels with high selectivity even in multi-class settings. Y1 - 2013 U6 - https://doi.org/10.1007/s11306-012-0476-7 VL - 9 IS - 3 SP - 677 EP - 687 ER - TY - JOUR A1 - Conrad, Tim A1 - Wallmeyer, Leonie A1 - Rams, Mona A1 - Börno, Stefan A1 - Timmermann, Bernd A1 - Hedtrich, Sarah T1 - Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach JF - Technical Report Y1 - 2015 ER - TY - JOUR A1 - Conrad, Tim A1 - Mireles, Victor T1 - Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrics JF - Procedia Computer Science N2 - Given a set of n binary data points, a widely used technique is to group its features into k clusters. In the case where n {\ensuremath{<}} k, the question of how overlapping are the clusters becomes of interest. In this paper we approach the question through matrix decomposition, and relate the degree of overlap with the sparsity of one of the resulting matrices. We present analytical results regarding bounds on this sparsity, and a heuristic to estimate the minimum amount of overlap that an exact grouping of features into k clusters must have. As shown below, adding new data will not alter this minimum amount of overlap. Y1 - 2015 U6 - https://doi.org/10.1016/j.procs.2015.05.500 VL - 51 SP - 2967 EP - 2971 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Cameron--Martin theorems for sequences of Cauchy-distributed random variables JF - arXiv N2 - Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences. Y1 - 2016 SP - 1608.03784 ER - TY - JOUR A1 - Conrad, Tim A1 - Karsch, K. A1 - Obermeier, Patrick A1 - Seeber, L. A1 - Chen, X. A1 - Tief, Franziska A1 - Muehlhans, S. A1 - Hoppe, Christian A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Rath, Barbara T1 - Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children JF - The Pediatric Infectious Disease Journal Y1 - 2015 VL - 34 IS - 10 ER - TY - THES A1 - Saitenmacher, René T1 - Combinatorial Models of Compressor Stations in Gas Networks N2 - I consider models of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. In particular, my aim is to identify from a set of operation modes those that are infeasible or redundant. For this, I investigate optimization and network reduction based procedures. Ultimately, these procedures may be employed for data preprocessing in the context of gas network optimization. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63522 ER - TY - JOUR A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On Markov state models for non-equilibrium molecular dynamics JF - The Journal of Chemical Physics Y1 - 2016 U6 - https://doi.org/10.1063/1.4966157 N1 - 2016 Editor's Choice of The Journal of Chemical Physics VL - 145 IS - 174103 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Transformations for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem to SAP JF - Journal of Computational Mathematics N2 - Transformations of Steiner tree problem variants have been frequently discussed in the literature. Besides allowing to easily transfer complexity results, they constitute a central pillar of exact state-of-the-art solvers for well-known variants such as the Steiner tree problem in graphs. In this paper transformations for both the prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem to the Steiner arborescence problem are introduced for the first time. Furthermore, we demonstrate the considerable implications for practical solving approaches, including the computation of strong upper and lower bounds. Y1 - 2018 U6 - https://doi.org/10.4208/jcm.1709-m2017-0002 VL - 36 IS - 3 SP - 459 EP - 468 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Maher, Stephen J. T1 - Reduction Techniques for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem JF - Networks N2 - The concept of reduction has frequently distinguished itself as a pivotal ingredient of exact solving approaches for the Steiner tree problem in graphs. In this paper we broaden the focus and consider reduction techniques for three Steiner problem variants that have been extensively discussed in the literature and entail various practical applications: The prize-collecting Steiner tree problem, the rooted prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem. By introducing and subsequently deploying numerous new reduction methods, we are able to drastically decrease the size of a large number of benchmark instances, already solving more than 90 percent of them to optimality. Furthermore, we demonstrate the impact of these techniques on exact solving, using the example of the state-of-the-art Steiner problem solver SCIP-Jack. Y1 - 2019 U6 - https://doi.org/10.1002/net.21857 VL - 73 SP - 206 EP - 233 PB - Wiley ET - 2 ER - TY - GEN A1 - Schade, Stanley A1 - Borndörfer, Ralf A1 - Breuer, Matthias A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Siebeneicher, Patrick T1 - Pattern Detection For Large-Scale Railway Timetables N2 - We consider railway timetables of our industrial partner DB Fernverkehr AG that operates the ICE high speed trains in the long-distance passenger railway network of Germany. Such a timetable covers a whole year with 364 days and, typically, includes more than 45,000 trips. A rolling stock rotation plan is not created for the whole timetable at once. Instead the timetable is divided into regular invariant sections and irregular deviations (e.g. for public holidays). A separate rotation plan with a weekly period can then be provided for each of the different sections of the timetable. We present an algorithmic approach to automatically recognize these sections. Together with the supplementing visualisation of the timetable this method has shown to be very relevant for our industrial partner. T3 - ZIB-Report - 17-17 KW - railway timetables KW - visualization KW - pattern detection Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63390 SN - 1438-0064 ER - TY - JOUR A1 - Kadow, Christopher A1 - Illing, Sebastian A1 - Kunst, Oliver A1 - Rust, Henning A1 - Pohlmann, Holger A1 - Müller, Wolfgang A. A1 - Cubasch, Ulrich T1 - Evaluation of forecasts by accuracy and spread in the MiKlip decadal climate prediction system JF - Meteorologische Zeitschrift N2 - We present the evaluation of temperature and precipitation forecasts obtained with the MiKlip decadal climate prediction system. These decadal hindcast experiments are verified with respect to the accuracy of the ensemble mean and the ensemble spread as a representative for the forecast uncertainty. The skill assessment follows the verification framework already used by the decadal prediction community, but enhanced with additional evaluation techniques like the logarithmic ensemble spread score. The core of the MiKlip system is the coupled Max Planck Institute Earth System Model. An ensemble of 10 members is initialized annually with ocean and atmosphere reanalyses of the European Centre for Medium-Range Weather Forecasts. For assessing the effect of the initialization, we compare these predictions to uninitialized climate projections with the same model system. Initialization improves the accuracy of temperature and precipitation forecasts in year 1, particularly in the Pacific region. The ensemble spread well represents the forecast uncertainty in lead year 1, except in the tropics. This estimate of prediction skill creates confidence in the respective 2014 forecasts, which depict less precipitation in the tropics and a warming almost everywhere. However, large cooling patterns appear in the Northern Hemisphere, the Pacific South America and the Southern Ocean. Forecasts for 2015 to 2022 show even warmer temperatures than for 2014, especially over the continents. The evaluation of lead years 2 to 9 for temperature shows skill globally with the exception of the eastern Pacific. The ensemble spread can again be used as an estimate of the forecast uncertainty in many regions: It improves over the tropics compared to lead year 1. Due to a reduction of the conditional bias, the decadal predictions of the initialized system gain skill in the accuracy compared to the uninitialized simulations in the lead years 2 to 9. Furthermore, we show that increasing the ensemble size improves the MiKlip decadal climate prediction system for all lead years. Y1 - 2016 U6 - https://doi.org/10.1127/metz/2015/0639 VL - 25 IS - 6 SP - 631 EP - 643 ER - TY - JOUR A1 - Obermeier, Patrick A1 - Muehlhans, S. A1 - Hoppe, Christian A1 - Karsch, K. A1 - Tief, Franziska A1 - Seeber, L. A1 - Chen, X. A1 - Conrad, Tim A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Rath, Barbara T1 - Enabling Precision Medicine With Digital Case Classification at the Point-of-Care JF - EBioMedicine N2 - Infectious and inflammatory diseases of the central nervous system are difficult to identify early. Case definitions for aseptic meningitis, encephalitis, myelitis, and acute disseminated encephalomyelitis (ADEM) are available, but rarely put to use. The VACC-Tool (Vienna Vaccine Safety Initiative Automated Case Classification-Tool) is a mobile application enabling immediate case ascertainment based on consensus criteria at the point-of-care. The VACC-Tool was validated in a quality management program in collaboration with the Robert-Koch-Institute. Results were compared to ICD-10 coding and retrospective analysis of electronic health records using the same case criteria. Of 68,921 patients attending the emergency room in 10/2010-06/2013, 11,575 were hospitalized, with 521 eligible patients (mean age: 7.6 years) entering the quality management program. Using the VACC-Tool at the point-of-care, 180/521 cases were classified successfully and 194/521 ruled out with certainty. Of the 180 confirmed cases, 116 had been missed by ICD-10 coding, 38 misclassified. By retrospective application of the same case criteria, 33 cases were missed. Encephalitis and ADEM cases were most likely missed or misclassified. The VACC-Tool enables physicians to ask the right questions at the right time, thereby classifying cases consistently and accurately, facilitating translational research. Future applications will alert physicians when additional diagnostic procedures are required. Y1 - 2016 U6 - https://doi.org/10.1016/j.ebiom.2016.01.008 VL - 4 SP - 191 EP - 196 ER - TY - JOUR A1 - Tief, Franziska A1 - Hoppe, Christian A1 - Seeber, L. A1 - Obermeier, Patrick A1 - Chen, X. A1 - Karsch, K. A1 - Muehlhans, S. A1 - Adamou, E. A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Adam, T. A1 - Rath, Barbara T1 - An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use JF - Antiviral Therapy N2 - BACKGROUND: Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality. METHODS: In the context of a perennial quality management (QM) programme at the Charit{\'e} Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charit{\'e} Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness. RESULTS: Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55\% male, mean age 3.2 years, range 0-18, 19\% {\ensuremath{>}}5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35\%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90\%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20\%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P{\ensuremath{<}}0.01) with an incremental cost-effectiveness ratio of -99.55?. CONCLUSIONS: Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI. Y1 - 2016 U6 - https://doi.org/10.3851/IMP3034 VL - 21 SP - 413 EP - 424 ER - TY - CHAP A1 - Shao, Borong A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction T2 - Lecture Notes in Computer Science (LNCS) N2 - Feature selection technique is often applied in identifying cancer prognosis biomarkers. However, many feature selection methods are prone to over-fitting or poor biological interpretation when applied on biological high-dimensional data. Network-based feature selection and data integration approaches are proposed to identify more robust biomarkers. We conducted experiments to investigate the advantages of the two approaches using epithelial mesenchymal transition regulatory network, which is demonstrated as highly relevant to cancer prognosis. We obtained data from The Cancer Genome Atlas. Prognosis prediction was made using Support Vector Machine. Under our experimental settings, the results showed that network-based features gave significantly more accurate predictions than individual molecular features, and features selected from integrated data (RNA-Seq and micro-RNA data) gave significantly more accurate predictions than features selected from single source data (RNA-Seq data). Our study indicated that biological network-based feature transformation and data integration are two useful approaches to identify robust cancer biomarkers. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-31744-1_13 VL - 9656 SP - 1235 EP - 146 ER - TY - JOUR A1 - Hoppe, Christian A1 - Obermeier, Patrick A1 - Mehlhans, S. A1 - Alchikh, Maren A1 - Seeber, L. A1 - Tief, Franziska A1 - Karsch, K. A1 - Chen, X. A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Conrad, Tim T1 - Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study JF - Drug Safety N2 - Regulatory authorities often receive poorly structured safety reports requiring considerable effort to investigate potential adverse events post hoc. Automated question-and-answer systems may help to improve the overall quality of safety information transmitted to pharmacovigilance agencies. This paper explores the use of the VACC-Tool (ViVI Automated Case Classification Tool) 2.0, a mobile application enabling physicians to classify clinical cases according to 14 pre-defined case definitions for neuroinflammatory adverse events (NIAE) and in full compliance with data standards issued by the Clinical Data Interchange Standards Consortium. METHODS: The validation of the VACC-Tool 2.0 (beta-version) was conducted in the context of a unique quality management program for children with suspected NIAE in collaboration with the Robert Koch Institute in Berlin, Germany. The VACC-Tool was used for instant case classification and for longitudinal follow-up throughout the course of hospitalization. Results were compared to International Classification of Diseases , Tenth Revision (ICD-10) codes assigned in the emergency department (ED). RESULTS: From 07/2013 to 10/2014, a total of 34,368 patients were seen in the ED, and 5243 patients were hospitalized; 243 of these were admitted for suspected NIAE (mean age: 8.5 years), thus participating in the quality management program. Using the VACC-Tool in the ED, 209 cases were classified successfully, 69 \% of which had been missed or miscoded in the ED reports. Longitudinal follow-up with the VACC-Tool identified additional NIAE. CONCLUSION: Mobile applications are taking data standards to the point of care, enabling clinicians to ascertain potential adverse events in the ED setting and during inpatient follow-up. Compliance with Clinical Data Interchange Standards Consortium (CDISC) data standards facilitates data interoperability according to regulatory requirements. Y1 - 2016 U6 - https://doi.org/10.1007/s40264-016-0437-6 VL - 39 IS - 10 SP - 977 EP - 988 ER - TY - JOUR A1 - Mireles, Victor A1 - Conrad, Tim T1 - Decomposing biological systems into reusable modules reveals characteristic module size distributions N2 - One of the widely recognized features of biological systems is their modularity. The modules that comprise biological systems are said to be redeployed and combined across several conditions. In this work, we analyze to what extent are these modules indeed reusable as compared to randomized versions of a system. We develop a notion of modular decompositions of systems that allows for modules to overlap while maximizing the number of times a module is reused across several conditions. Different biological systems present modules whose reusability ranges from the condition specific to the constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of module sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity. Y1 - 2016 ER - TY - JOUR A1 - Conrad, Tim A1 - You, Xintian T1 - Acfs: accurate circRNA identification and quantification from NGS data JF - Nature Scientific Reports N2 - Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology. Y1 - 2016 U6 - https://doi.org/10.1038/srep38820 VL - 6 ER - TY - THES A1 - Schuh, Hannah T1 - Identification of Anisotropies in Welding Seams Using Ultrasound Measurements Y1 - 2016 ER - TY - GEN A1 - Amrhein, Kilian A1 - Hasler, Tim A1 - Klindt, Marco A1 - Oltmanns, Elias A1 - Peters-Kottig, Wolfgang T1 - Digitale Langzeitarchivierung: Mustervorlage für Übernahmevereinbarungen, Version 2 N2 - Digitale Langzeitarchivierung erfolgt auf Grundlage verbindlicher Regelungen zwischen Langzeitarchiv und Datengeber. Detaillierte organisatorische und technische Bedingungen für Datenübernahmen werden dabei in Absprache zwischen den Kooperationspartnern in einer Übernahmevereinbarung festgehalten. Im Rahmen der Entwicklung des Langzeitarchivs EWIG am Zuse Institute Berlin ist die hier dokumentierte zweite Version der Mustervorlage für Übernahmevereinbarungen entstanden. Das Submission Manifest wurde in aktualisierter Version 1.3 eingefügt, es erfolgten sprachliche Präzisierungen, und die Beispiele möglicher Verzeichnisstrukturen für Transferpakete wurden erneuert. T3 - ZIB-Report - 17-15 KW - digital preservation KW - submission agreement Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63245 SN - 1438-0064 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields JF - Computer Graphics Forum Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12914 N1 - By mistake the fourth author Hans-Christian Hege has been ommitted in the journal publication VL - 35 IS - 3 SP - 381 EP - 390 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. T3 - ZIB-Report - 17-16 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63239 SN - 1438-0064 ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Hege, Hans-Christian A1 - Weiser, Martin T1 - Using sparse kernels to design computer experiments with tunable precision T2 - 22nd Intern. Conf. on Computational Statistics - COMPSTAT 2016, Oviedo, Spain, 23-26 August 2016, Proceedings ISBN 978-90-73592-36-0 Y1 - 2016 SP - 397 EP - 408 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Saitenmacher, René A1 - Walther, Tom T1 - Analysis of operating modes of complex compressor stations T2 - Proceedings of Operations Research 2016 N2 - We consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. In particular, we propose a refined model that allows to precompute tighter relaxations for each operation mode. These relaxations may be used to strengthen the compressor station submodels in gas network optimization problems. We provide a procedure to obtain the refined model from the input data for the original model. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-55702-1_34 SP - 251 EP - 257 ER - TY - THES A1 - Lindow, Norbert T1 - Visual Analysis of Atomic Structures Based on the Hard-Sphere Model N2 - Visualization and Analysis of atomic compositions is essential to understand the structure and functionality of molecules. There exist versatile areas of applications, from fundamental researches in biophysics and materials science to drug development in pharmaceutics. For most applications, the hard-sphere model is the most often used molecular model. Although the model is a quite simple approximation of reality, it enables investigating important physical properties in a purely geometrical manner. Furthermore, large data sets with thousands up to millions of atoms can be visualized and analyzed. In addition to an adequate and efficient visualization of the data, the extraction of important structures plays a major role. For the investigation of biomolecules, such as proteins, especially the analysis of cavities and their dynamics is of high interest. Substrates can bind in cavities, thereby inducing changes in the function of the protein. Another example is the transport of substrates through membrane proteins by the dynamics of the cavities. For both, the visualization as well as the analysis of cavities, the following contributions will be presented in this thesis: 1. The rendering of smooth molecular surfaces for the analysis of cavities is accelerated and visually improved, which allows showing dynamic proteins. On the other hand, techniques are proposed to interactively render large static biological structures and inorganic materials up to atomic resolution for the first time. 2. A Voronoi-based method is presented to extract molecular cavities. The procedure comes with a high geometrical accuracy by a comparatively fast computation time. Additionally, new methods are presented to visualize and highlight the cavities within the molecular structure. In a further step, the techniques are extended for dynamic molecular data to trace cavities over time and visualize topological changes. 3. To further improve the accuracy of the approaches mentioned above, a new molecular surface model is presented that shows the accessibility of a substrate. For the first time, the structure and dynamics of the substrate as hard-sphere model is considered for the accessibility computation. In addition to the definition of the surface, an efficient algorithm for its computation is proposed, which additionally allows extracting cavities. The presented algorithms are demonstrated on different molecular data sets. The data sets are either the result of physical or biological experiments or molecular dynamics simulations. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63190 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Seasonal changes of the volatile density in the coma and on the surface of comet 67P/Churyumov-Gerasimenko JF - Monthly Notices of the Royal Astronomical Society N2 - Starting from several monthly data sets of Rosetta’s COmetary Pressure Sensor we reconstruct the gas density in the coma around comet 67P/Churyumov-Gerasimenko. The underlying inverse gas model is constructed by fitting ten thousands of measurements to thousands of potential gas sources distributed across the entire nucleus surface. The ensuing self-consistent solution for the entire coma density and surface activity reproduces the temporal and spatial variations seen in the data for monthly periods with Pearson correlation coefficients of 0.93 and higher. For different seasonal illumination conditions before and after perihelion we observe a systematic shift of gas sources on the nucleus. Y1 - 2017 U6 - https://doi.org/10.1093/mnras/stx866 VL - 469 SP - S20 EP - S28 ER - TY - CHAP A1 - Lange, Alexander T1 - A mathematical framework for predicting lifestyles of viral pathogens T2 - Modelling Biological Evolution 2017: Developing Novel Approaches Y1 - 2017 ER - TY - CHAP A1 - Dean, Mason N. A1 - Seidel, R. A1 - Knötel, David A1 - Lyons, K. A1 - Baum, Daniel A1 - Weaver, James C. A1 - Fratzl, Peter T1 - To build a shark: 3D tiling laws of tessellated cartilage T2 - Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA N2 - The endoskeleton of sharks and rays (elasmobranchs) is comprised of a cartilaginous core, covered by thousands of mineralized tiles, called tesserae. Characterizing the relationship between tesseral morphometrics, skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. We integrate material property, histology, electron microscopy and synchrotron and laboratory µCT scans of skeletal elements from an ontogenetic series of round stingray Urobatis halleri, to gain insights into the generation and maintenance of a natural tessellated system. Using a custom-made semiautomatic segmentation algorithm, we present the first quantitative and 3d description of tesserae across whole skeletal elements. The tessellation is not interlocking or regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick- or disc-shaped tesserae are found in planar/flatter areas. Comparison of the tessellation across ontogeny, shows that in younger animals, the forming tesseral network is less densely packed, appearing as a covering of separate, poorly mineralized islands that grow together with age to form a complete surface. Some gaps in the tessellation are localized to specific regions in all samples, indicating they are real features, perhaps either regions of delayed mineralization or of tendon insertion. We will use the structure of elasmobranch skeletons as a road map for understanding shark and ray skeletal mechanics, but also to extract fundamental engineering principles for tiled composite materials. Y1 - 2016 UR - https://academic.oup.com/icb/article-pdf/56/suppl_1/e1/9102603/icw002.pdf VL - 56 (suppl 1) ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies JF - Computer Graphics Forum N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. Y1 - 2017 U6 - https://doi.org/10.1111/cgf.13191 VL - 36 IS - 3 SP - 329 EP - 339 PB - Wiley ER - TY - JOUR A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Jäger, Klaus A1 - Chen, Duote A1 - Shargaieva, Oleksandra A1 - Sonntag, Paul A1 - Armkreutz, Daniel A1 - Rech, Bernd A1 - Becker, Christiane T1 - Smooth anti-reflective three-dimensional textures for liquid phase crystallized silicon thin-film solar cells on glass JF - Sci. Rep. Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-02874-y VL - 7 SP - 2658 ER - TY - JOUR A1 - Eisenhauer, David A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Rech, Bernd A1 - Becker, Christiane T1 - Optical Properties of Smooth Anti-reflective Three-dimensional Textures for Silicon Thin-film Solar Cells JF - Energy Procedia Y1 - 2016 U6 - https://doi.org/10.1016/j.egypro.2016.11.314 VL - 102 SP - 27 EP - 35 ER - TY - GEN A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. T3 - ZIB-Report - 17-06 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63053 SN - 1438-0064 ER - TY - THES A1 - Manley, Phillip T1 - Simulation of Plasmonic Nanoparticles in Thin Film Solar Cells Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102531-2 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000102531 ER - TY - CHAP A1 - Kuhn, Alexander A1 - Hege, Hans-Christian T1 - Object-based visualization and evaluation of cloud-resolving simulations T2 - Book of Abstracts, SCCS 2017 – Scaling Cascades in Complex Systems, Mar 27-29, 2017, Berlin, Germany N2 - Recent advances in high-resolution, cloud resolving simulation models pose several challenges towards respective analysis methodologies. To enable efficient comparison and validation of such models efficient, scalable, and informative diagnostic procedures are mandatory. In this talk, an object-based evaluation scheme based on the notion of scalar field topology will be presented. The presentation will cover the application of topological clustering procedures for object identification, tracking, and the retrieval of object-based statistics. The pro-posed methodology is shown to enable an advanced in-depth evaluation and visualization of high cloud-resolving models. Using a newly developed large-scale high-resolution model (i.e., HD(CP)2 ICON), it will be demonstrated that the presented procedures are applicable to assess the model performance compared to measurements (e.g., radar, satellite) and standard operational models (COSMO) at different domains and spatial scales. Y1 - 2017 ER - TY - CHAP A1 - Arlt, Tobias A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hilger, Andre A1 - Mahnke, Ingo A1 - Hege, Hans-Christian A1 - Lepper, Verena A1 - Siopi, Tzulia A1 - Mahnke, Heinz.Eberhard T1 - Virtual Access to Hidden Texts – Study of Ancient Papyri T2 - Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany N2 - When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text. Y1 - 2016 ER - TY - GEN A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Gross, Markus A1 - Theisel, Holger T1 - Progressive Monte-Carlo Rendering of Atmospheric Flow Features Across Scales T2 - 69th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 20-22, 2016, Portland, OR, USA. N2 - To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere. Y1 - 2016 U6 - https://doi.org/10.1103/APS.DFD.2016.GFM.P0030 ER - TY - JOUR A1 - Kozlíková, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art Revisited JF - Computer Graphics Forum N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.13072 VL - 36 IS - 8 SP - 178 EP - 204 ER - TY - THES A1 - Teuchert, Andreas T1 - Degeneriertheit im Simplexverfahren Y1 - 2017 ER - TY - THES A1 - Roessig, Ansgar T1 - Formulations and algorithms for the USCCSP Y1 - 2016 ER - TY - JOUR A1 - Ablyazimov, T. A1 - Abuhoza, A. A1 - Adak, R. P. A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - et al., T1 - Challenges in QCD matter physics – The scientific programme of the Compressed Baryonic Matter experiment at FAIR JF - The European Physical Journal A Y1 - 2017 U6 - https://doi.org/10.1140/epja/i2017-12248-y N1 - This paper has 587 authors. For the complete list of authors use the DOI, please. ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Supporting various interconnects in FLESnet using Libfabric JF - CBM Progress Report 2016 Y1 - 2017 UR - https://repository.gsi.de/record/201318 SN - 978-3-9815227-4-7 SP - 159 EP - 160 ER - TY - THES A1 - Gottwald, Robert Lion T1 - Experiments with Concurrency and Heuristics in SCIP Y1 - 2016 ER - TY - THES A1 - Viernickel, Jan Merlin T1 - Abschätzung der Suchbaumgröße und Laufzeit für Branch-and-Bound Algorithmen Y1 - 2016 ER - TY - GEN A1 - Tesch, Alexander T1 - Improved Compact Models for the Resource-Constrained Project Scheduling Problem N2 - In this article, we study compact Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP). Compared to the classical time-indexed formulation, the size of compact models is strongly polynomial in the number of jobs. In addition to two compact models from the literature, we propose a new compact model. We can show that all three compact models are equivalent by successive linear transformations. For their LP-relaxations, however, we state a full inclusion hierarchy where our new model dominates the previous models in terms of polyhedral strength. Moreover, we reveal a polyhedral relationship to the common time-indexed model. Furthermore, a general class of valid cutting planes for the compact models is introduced and finally all models are evaluated by computational experiments. T3 - ZIB-Report - 16-76 KW - Scheduling Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62891 SN - 1438-0064 ER - TY - THES A1 - Pilz, Sven-Kristofer T1 - Multi-View Reconstruction based on Mesh Photo-Consistency Optimization KW - Multi-View Reconstruction KW - Photo-Consistency Optimization Y1 - 2016 ER - TY - THES A1 - Auch, Simón T1 - Realtime Action Unit detection Y1 - 2016 ER - TY - CHAP A1 - Müller, Jan A1 - Götschel, Sebastian A1 - Maierhofer, Christiane A1 - Weiser, Martin T1 - Determining the material parameters for the reconstruction of defects in carbon fiber reinforced polymers from data measured by flash thermography T2 - AIP Conference Proceedings Y1 - 2017 U6 - https://doi.org/10.1063/1.4974671 VL - 1806 ER - TY - CHAP A1 - Götschel, Sebastian A1 - Maierhofer, Christiane A1 - Müller, Jan A1 - Rothbart, Nick A1 - Weiser, Martin T1 - Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites T2 - Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016) Y1 - 2016 UR - https://www.wcndt2016.com/portals/wcndt/bb/Th4C4.pdf ER - TY - CHAP A1 - Götschel, Sebastian A1 - Höhne, Christian A1 - Kolkoori, Sanjeevareddy A1 - Mitzscherling, Steffen A1 - Prager, Jens A1 - Weiser, Martin T1 - Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing T2 - Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016) Y1 - 2016 UR - https://www.wcndt2016.com/portals/wcndt/bb/Fr1H4.pdf ER - TY - CHAP A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin T1 - Global and Local Optimal Control of a Resource Utilization Problem T2 - Proceedings of the 33rd International Conference of the System Dynamics Society N2 - System Dynamic models describe physical, technical, economical, or social systems using differential and algebraic equations. In their purest form, these models are intended to describe the evolution of a system from a given initial state. In many applications, it is possible to intervene with the system in order to obtain a desired dynamic or a certain outcome in the end. On the mathematical side, this leads to control problems, where aside from the simulation one has to find optimal intervention functions over time that maximize a specific objective function. Using a dynamical model for the utilization of a natural nonrenewable resource of Behrens as a demonstrator example, we present two main mathematical solution strategies. They are distinguished by the quality certificate on their respective solution: one leads to proven local optimal solution, and the other technique yields proven global optimal solutions. We present implementational and numerical issues, and a comparison of both methods. Y1 - 2015 ER - TY - JOUR A1 - Seidel, Ronald A1 - Blumer, Michael A1 - Zaslansky, Paul A1 - Knötel, David A1 - Huber, Daniel R. A1 - Weaver, James C. A1 - Fratzl, Peter A1 - Omelon, Sidney A1 - Bertinetti, Luca A1 - Dean, Mason N. T1 - Ultrastructural, material and crystallographic description of endophytic masses – a possible damage response in shark and ray tessellated calcified cartilage JF - Journal of Structural Biology N2 - The cartilaginous endoskeletons of Elasmobranchs (sharks and rays) are reinforced superficially by minute, mineralized tiles, called tesserae. Unlike the bony skeletons of other vertebrates, elasmobranch skeletons have limited healing capability and their tissues’ mechanisms for avoiding damage or managing it when it does occur are largely unknown. Here we describe an aberrant type of mineralized elasmobranch skeletal tissue called endophytic masses (EPMs), which grow into the uncalcified cartilage of the skeleton, but exhibit a strikingly different morphology compared to tesserae and other elasmobranch calcified tissues. We use biological and materials characterization techniques, including computed tomography, electron and light microscopy, x-ray and Raman spectroscopy and histology to characterize the morphology, ultrastructure and chemical composition of tesserae-associated EPMs in different elasmobranch species. EPMs appear to develop between and in intimate association with tesserae, but lack the lines of periodic growth and varying mineral density characteristic of tesserae. EPMs are mineral-dominated (high mineral and low organic content), comprised of birefringent bundles of large monetite or brushite crystals aligned end to end in long strings. Both Unusual skeletal mineralization in elasmobranchs tesserae and EPMs appear to develop in a type-2 collagen-based matrix, but in contrast to tesserae, all chondrocytes embedded or in contact with EPMs are dead and mineralized. The differences outlined between EPMs and tesserae demonstrate them to be distinct tissues. We discuss several possible reasons for EPM development, including tissue reinforcement, repair, and disruptions of mineralization processes, within the context of elasmobranch skeletal biology as well as descriptions of damage responses of other vertebrate mineralized tissues. Y1 - 2017 U6 - https://doi.org/10.1016/j.jsb.2017.03.004 ER - TY - JOUR A1 - Heinze, Rieke A1 - Dipankar, Anurag A1 - Henken, Cintia Carbajal A1 - Moseley, Christopher A1 - Sourdeval, Odran A1 - Trömel, Silke A1 - Xie, Xinxin A1 - Adamidis, Panos A1 - Ament, Felix A1 - Baars, Holger A1 - Barthlott, Christian A1 - Behrendt, Andreas A1 - Blahak, Ulrich A1 - Bley, Sebastian A1 - Brdar, Slavko A1 - Brueck, Matthias A1 - Crewell, Susanne A1 - Deneke, Hartwig A1 - Di Girolamo, Paolo A1 - Evaristo, Raquel A1 - Fischer, Jürgen A1 - Frank, Christopher A1 - Friederichs, Petra A1 - Göcke, Tobias A1 - Gorges, Ksenia A1 - Hande, Luke A1 - Hanke, Moritz A1 - Hansen, Akio A1 - Hege, Hans-Christian A1 - Hose, Corinna A1 - Jahns, Thomas A1 - Kalthoff, Norbert A1 - Klocke, Daniel A1 - Kneifel, Stefan A1 - Knippertz, Peter A1 - Kuhn, Alexander A1 - van Laar, Thriza A1 - Macke, Andreas A1 - Maurer, Vera A1 - Mayer, Bernhard A1 - Meyer, Catrin I. A1 - Muppa, Shravan K. A1 - Neggers, Roeland A. J. A1 - Orlandi, Emiliano A1 - Pantillon, Florian A1 - Pospichal, Bernhard A1 - Röber, Niklas A1 - Scheck, Leonhard A1 - Seifert, Axel A1 - Seifert, Patric A1 - Senf, Fabian A1 - Siligam, Pavan A1 - Simmer, Clemens A1 - Steinke, Sandra A1 - Stevens, Bjorn A1 - Wapler, Kathrin A1 - Weniger, Michael A1 - Wulfmeyer, Volker A1 - Zängl, Günther A1 - Zhang, Dan A1 - Quaas, Johannes T1 - Large-eddy simulations over Germany using ICON: a comprehensive evaluation JF - Quarterly Journal of the Royal Meteorological Society N2 - Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model. Y1 - 2017 U6 - https://doi.org/10.1002/qj.2947 VL - 143 IS - 702 SP - 69 EP - 100 ER - TY - CHAP A1 - Coconu, Liviu A1 - Hege, Hans-Christian T1 - devEyes: Tangible Devices on Augmented Passive Surfaces T2 - TEI '17 Proceedings of the Eleventh International Conference on Tangible, Embedded, and Embodied Interaction, Yokohama, Japan, March 20 - 23, 2017 N2 - We present a novel approach to turn smartphones/ tablets into tangible near-surface devices with augmented reality (AR) capability on virtually any passive surface, like desks, tables and wallboards. A low-cost optoelectronic add-on for the device back camera enables position tracking on an almost invisible printable fiducial marker grid. This approach is promising in terms of adoption potential because it can be used anywhere with existing devices, requires no dedicated hardware installations and is applicable to a broad range of real-world applications. Y1 - 2017 U6 - https://doi.org/10.1145/3024969.3025065 SP - 409 EP - 411 ER - TY - CHAP A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing N2 - Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo–based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values. Y1 - 2017 U6 - https://doi.org/10.1117/12.2252359 VL - 10064 SP - 1006416 EP - 1006416-8 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Koltai, Peter A1 - Wu, Hao A1 - Kevrekidis, Ioannis A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-driven model reduction and transfer operator approximation JF - Journal of Nonlinear Science Y1 - 2018 UR - https://link.springer.com/article/10.1007/s00332-017-9437-7 U6 - https://doi.org/10.1007/s00332-017-9437-7 VL - 28 IS - 3 SP - 985 EP - 1010 ER - TY - GEN A1 - Gupta, Pooja A1 - Gramatke, Annika A1 - Einspanier, Ralf A1 - Schütte, Christof A1 - von Kleist, Max A1 - Sharbati, Jutta T1 - In silicio cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements N2 - Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence’s real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50% inhibitory concentration IC_{50} on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC_{50} values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA’s in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master. T3 - ZIB-Report - 17-08 KW - Real-time cell analyzer KW - Toxicity KW - Mathematical modeling KW - IC_{50} Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62666 SN - 1438-0064 ER - TY - JOUR A1 - Huttary, Rudolf A1 - Goubergrits, Leonid A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling JF - Computers in Biology and Medicine Y1 - 2017 U6 - https://doi.org/10.1016/j.compbiomed.2017.05.021 VL - 87 SP - 104 EP - 123 ER - TY - JOUR A1 - von Kleist, Max A1 - Schütte, Christof A1 - Zhang, Wei T1 - Statistical analysis of the first passage path ensemble of jump processes JF - Journal of Statistical Physics N2 - The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-017-1949-x VL - 170 SP - 809 EP - 843 ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin A1 - Schütte, Christof T1 - Set-Free Markov State Model Building JF - Journal of Chemical Physics Y1 - 2017 U6 - https://doi.org/10.1063/1.4978501 VL - 146 IS - 12 ER - TY - JOUR A1 - Klus, Stefan A1 - Gelß, Patrick A1 - Peitz, Sebastian A1 - Schütte, Christof T1 - Tensor-based dynamic mode decomposition JF - Nonlinearity Y1 - 2018 U6 - https://doi.org/10.1088/1361-6544/aabc8f VL - 31 IS - 7 PB - IOP Publishing Ltd & London Mathematical Society ER - TY - JOUR A1 - Gupta, Pooja A1 - Gramatke, Annika A1 - Einspanier, Ralf A1 - Schütte, Christof A1 - von Kleist, Max A1 - Sharbati, Jutta T1 - In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements JF - Toxicology in Vitro N2 - Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence’s real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50% inhibitory concentration IC50 on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC50 values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA’s in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master. KW - Real-time cell analyzer KW - Toxicity KW - Mathematical modeling Y1 - 2017 SN - 1438-0064 VL - 41 SP - 179 EP - 188 ER - TY - JOUR A1 - Rüdrich, S. A1 - Sarich, Marco A1 - Schütte, Christof T1 - Utilizing hitting times for finding metastable sets in non-reversible Markov chains JF - Journal of Comp. Dynamics Y1 - 2017 ER - TY - JOUR A1 - Orgis, Thomas A1 - Läuter, Matthias A1 - Handorf, Dörthe A1 - Dethloff, Klaus T1 - Baroclinic waves on the β plane using low-order Discontinuous Galerkin discretisation JF - Journal of Computational Physics N2 - A classic Discontinuous Galerkin Method with low-order polynomials and explicit as well as semi-implicit time-stepping is applied to an atmospheric model employing the Euler equations on the β plane. The method, which was initially proposed without regard for the source terms and their balance with the pressure gradient that dominates atmospheric dynamics, needs to be adapted to be able to keep the combined geostrophic and hydrostatic balance in three spatial dimensions. This is achieved inside the discretisation through a polynomial mapping of both source and flux terms without imposing filters between time steps. After introduction and verification of this balancing, the realistic development of barotropic and baroclinic waves in the model is demonstrated, including the formation of a retrograde Rossby wave pattern. A prerequesite is the numerical solution of the thermal wind equation to construct geostrophically balanced initial states in z coordinates with arbitrary prescribed zonal wind profile, offering a new set of test cases for atmospheric models employing z coordinates. The resulting simulations demonstrate that the balanced low-order Discontinous Galerkin discretisation with polynomial degrees down to k=1 can be a viable option for atmospheric modelling. Y1 - 2017 U6 - https://doi.org/10.1016/j.jcp.2017.03.029 VL - 339 SP - 461 EP - 481 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Leichtle, Alexander Benedikt A1 - Vybiral, Jan A1 - Kytyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinfomatics N2 - Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust against noise and outliers, while the identified feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA),based on thet heory of compressed sensing that allows us to identify a minimal discriminating set of features from mass spectrometry data-sets. We show (1) how our method performs on artificial and real-world data-sets, (2) that its performance is competitive with standard (and widely used) algorithms for analyzing proteomics data, and (3) that it is robust against random and systematic noise. We further demonstrate the applicability of our algorithm to two previously published clinical data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 ER - TY - JOUR A1 - Vega, Iliusi A1 - Schütte, Christof A1 - Conrad, Tim T1 - Finding metastable states in real-world time series with recurrence networks JF - Physica A: Statistical Mechanics and its Applications N2 - In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we introduce a way to set the embedding parameters used to reconstruct the state space from the time series. We set them as the ones giving the maximum Shannon entropy of the diagonal line length distribution for the first simultaneous minima of recurrence rate and Shannon entropy. To identify metastable states, as well as the transitions between them, we use a soft partitioning algorithm for module finding which is specifically developed for the case in which a system shows metastability. We illustrate our method with a complex time series example. Finally, we show the robustness of our method for identifying metastable states. Our results suggest that our method is robust for identifying metastable states in complex time series, even when introducing considerable levels of noise and missing data points. Y1 - 2016 U6 - https://doi.org/10.1016/j.physa.2015.10.041 VL - 445 SP - 1 EP - 17 ER - TY - JOUR A1 - Gelß, Patrick A1 - Matera, Sebastian A1 - Schütte, Christof T1 - Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model JF - Journal of Computational Physics N2 - In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased Y1 - 2016 U6 - https://doi.org/10.1016/j.jcp.2016.03.025 VL - 314 SP - 489 EP - 502 ER - TY - JOUR A1 - Suinesiaputra, Avan A1 - Albin, Pierre A1 - Alba, Xenia A1 - Alessandrini, Martino A1 - Allen, Jack A1 - Bai, Wenjia A1 - Cimen, Serkan A1 - Claes, Peter A1 - Cowan, Brett A1 - D'hooge, Jan A1 - Duchateau, Nicolas A1 - Ehrhardt, Jan A1 - Frangi, Alejandro A1 - Gooya, Ali A1 - Grau, Vicente A1 - Lekadir, Karim A1 - Lu, Allen A1 - Mukhopadhyay, Anirban A1 - Oksuz, Ilkay A1 - Parajuli, Nripesh A1 - Pennec, Xavier A1 - Pereanez, Marco A1 - Pinto, Catarina A1 - Piras, Paolo A1 - Rohe, Marc-Michael A1 - Rueckert, Daniel A1 - Saring, Dennis A1 - Sermesant, Maxime A1 - Siddiqi, Kaleem A1 - Tabassian, Mahdi A1 - Teresi, Lusiano A1 - Tsaftaris, Sotirios A1 - Wilms, Matthias A1 - Young, Alistair A1 - Zhang, Xingyu A1 - Medrano-Gracia, Pau T1 - Statistical shape modeling of the left ventricle: myocardial infarct classification challenge JF - IEEE Journal of Biomedical and Health Informatics N2 - Statistical shape modeling is a powerful tool for visualizing and quantifying geometric and functional patterns of the heart. After myocardial infarction (MI), the left ventricle typically remodels in response to physiological challenges. Several methods have been proposed in the literature to describe statistical shape changes. Which method best characterizes left ventricular remodeling after MI is an open research question. A better descriptor of remodeling is expected to provide a more accurate evaluation of disease status in MI patients. We therefore designed a challenge to test shape characterization in MI given a set of three-dimensional left ventricular surface points. The training set comprised 100 MI patients, and 100 asymptomatic volunteers (AV). The challenge was initiated in 2015 at the Statistical Atlases and Computational Models of the Heart workshop, in conjunction with the MICCAI conference. The training set with labels was provided to participants, who were asked to submit the likelihood of MI from a different (validation) set of 200 cases (100 AV and 100 MI). Sensitivity, specificity, accuracy and area under the receiver operating characteristic curve were used as the outcome measures. The goals of this challenge were to (1) establish a common dataset for evaluating statistical shape modeling algorithms in MI, and (2) test whether statistical shape modeling provides additional information characterizing MI patients over standard clinical measures. Eleven groups with a wide variety of classification and feature extraction approaches participated in this challenge. All methods achieved excellent classification results with accuracy ranges from 0.83 to 0.98. The areas under the receiver operating characteristic curves were all above 0.90. Four methods showed significantly higher performance than standard clinical measures. The dataset and software for evaluation are available from the Cardiac Atlas Project website1. Y1 - 2017 U6 - https://doi.org/10.1109/JBHI.2017.2652449 IS - 99 ER - TY - JOUR A1 - Klus, Stefan A1 - Koltai, Peter A1 - Schütte, Christof T1 - On the numerical approximation of the Perron-Frobenius and Koopman operator JF - Journal of Computational Dynamics N2 - Information about the behavior of dynamical systems can often be obtained by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with a dynamical system. Examples of such operators are the Perron-Frobenius and the Koopman operator. In this paper, we will review di� fferent methods that have been developed over the last decades to compute � infinite-dimensional approximations of these in� finite-dimensional operators - in particular Ulam's method and Extended Dynamic Mode Decomposition (EDMD) - and highlight the similarities and di� fferences between these approaches. The results will be illustrated using simple stochastic di� fferential equations and molecular dynamics examples. Y1 - 2016 U6 - https://doi.org/10.3934/jcd.2016003 VL - 3 IS - 1 SP - 51 EP - 77 ER - TY - GEN A1 - Freytag, Yvonne T1 - Optimal Experimental Design to Estimate the Time of Death in a Bayesian Context N2 - This thesis is devoted to the interdisciplinary work between mathematicians and forensic experts: the modeling of the human body cooling process after death laying the foundation for the estimation of the time of death. An inverse problem needs to be solved. In this thesis the inverse problem computes the time of death given the measured body temperature and the Forward Model that simulates the body cooling process. The Forward Model is based on the heat equation established by Fourier. This differential equation is numerically solved by the discretization over space by the Finite Element Method and the discretization over time by the Implicit Euler Method. The applications in this thesis demand a fast computation time. A model reduction is achieved by the Proper Orthogonal Decomposition in combination with the Galerkin Method. For reasons of simplification the computations and the measurements are restricted to a cylindrical phantom that is made out of homogeneous polyethylene. The estimate of the time of death is accompanied by an uncertainty. The inverse problem is incorporated by Bayesian inference to interpret the quality of the estimate and the effciency of the experiment. The uncertainty of the estimate of the time of death is minimized by approaching the Optimal Design of the Experiment. An objective function measures the certainty of the data and lays the foundation of the optimization problem. Solving the optimization problem is successfully done by relaxing the complex discrete NP-hard problem and applying a gradient-based method. The results of this thesis clearly show that the design of an experiment has a great in- uence on the outcome of the quality of the estimate. The comparison of the estimate and its properties based on different designs and conditions reveals the effciency of the Design of Experiment in the context of the estimation of the time of death. T3 - ZIB-Report - 17-14 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62475 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Model reduction algorithms for optimal control and importance sampling of diffusions JF - Nonlinearity N2 - We propose numerical algorithms for solving optimal control and importance sampling problems based on simplified models. The algorithms combine model reduction techniques for multiscale diffusions and stochastic optimization tools, with the aim of reducing the original, possibly high-dimensional problem to a lower dimensional representation of the dynamics, in which only a few relevant degrees of freedom are controlled or biased. Specifically, we study situations in which either a reaction coordinate onto which the dynamics can be projected is known, or situations in which the dynamics shows strongly localized behavior in the small noise regime. No explicit assumptions about small parameters or scale separation have to be made. We illustrate the approach with simple, but paradigmatic numerical examples. Y1 - 2016 U6 - https://doi.org/10.1088/0951-7715/29/8/2298 VL - 29 IS - 8 SP - 2298 EP - 2326 ER - TY - JOUR A1 - Klus, Stefan A1 - Schütte, Christof T1 - Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator JF - Journal of Computational Dynamics N2 - The global behavior of dynamical systems can be studied by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with the system. Two important operators which are frequently used to gain insight into the system's behavior are the Perron-Frobenius operator and the Koopman operator. Due to the curse of dimensionality, computing the eigenfunctions of high-dimensional systems is in general infeasible. We will propose a tensor-based reformulation of two numerical methods for computing finite-dimensional approximations of the aforementioned infinite-dimensional operators, namely Ulam's method and Extended Dynamic Mode Decomposition (EDMD). The aim of the tensor formulation is to approximate the eigenfunctions by low-rank tensors, potentially resulting in a significant reduction of the time and memory required to solve the resulting eigenvalue problems, provided that such a low-rank tensor decomposition exists. Typically, not all variables of a high-dimensional dynamical system contribute equally to the system's behavior, often the dynamics can be decomposed into slow and fast processes, which is also reflected in the eigenfunctions. Thus, the weak coupling between different variables might be approximated by low-rank tensor cores. We will illustrate the efficiency of the tensor-based formulation of Ulam's method and EDMD using simple stochastic differential equations. Y1 - 2016 U6 - https://doi.org/10.3934/jcd.2016007 VL - 3 IS - 2 SP - 139 EP - 161 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Szengel, Angelika A1 - Zachow, Stefan T1 - Addressing multi-label imbalance problem of Surgical Tool Detection using CNN JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: A fully automated surgical tool detection framework is proposed for endoscopic video streams. State-of-the-art surgical tool detection methods rely on supervised one-vs-all or multi-class classification techniques, completely ignoring the co-occurrence relationship of the tools and the associated class imbalance. Methods: In this paper, we formulate tool detection as a multi-label classification task where tool co-occurrences are treated as separate classes. In addition, imbalance on tool co-occurrences is analyzed and stratification techniques are employed to address the imbalance during Convolutional Neural Network (CNN) training. Moreover, temporal smoothing is introduced as an online post-processing step to enhance run time prediction. Results: Quantitative analysis is performed on the M2CAI16 tool detection dataset to highlight the importance of stratification, temporal smoothing and the overall framework for tool detection. Conclusion: The analysis on tool imbalance, backed by the empirical results indicates the need and superiority of the proposed framework over state-of-the-art techniques. Y1 - 2017 UR - https://link.springer.com/article/10.1007/s11548-017-1565-x U6 - https://doi.org/10.1007/s11548-017-1565-x N1 - Selected for final oral presentation VL - 12 IS - 6 SP - 1013 EP - 1020 PB - Springer ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodriguez, Mirta T1 - Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria JF - Scientific Reports N2 - Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. From our calculation one can infer the coupling of the antenna chlorosome with the environment and the coupling between the chlorosome and the Fenna-Matthews-Olson complex. We show that environment assisted transport between the subunits is the required mechanism to reproduce the experimental two-dimensional electronic spectra. Y1 - 2017 U6 - https://doi.org/10.1038/srep45245 VL - 7 SP - 45245 ER - TY - THES A1 - Burtscher, Felicia T1 - Algorithmic approaches to the change-point problem for ovulation detection in the human menstrual cycle Y1 - 2016 ER - TY - THES A1 - Günther, Matthias T1 - Implementation and verification of methods for the validation of knee joint kinematics KW - Biomechanics Y1 - 2014 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Quasi-invariance of countable products of Cauchy measures under non-unitary dilations JF - Electronic Communications in Probability Y1 - 2018 U6 - https://doi.org/10.1214/18-ECP113 VL - 23 IS - 8 SP - 1 EP - 6 ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Porikli, Fatih A1 - Bhandarkar, Suchendra T1 - Detection and Characterization of Intrinsic Symmetry of 3D Shapes T2 - Proceedings of IEEE International Conference on Pattern Recognition N2 - A comprehensive framework for detection and characterization of partial intrinsic symmetry over 3D shapes is proposed. To identify prominent symmetric regions which overlap in space and vary in form, the proposed framework is decoupled into a Correspondence Space Voting (CSV) procedure followed by a Transformation Space Mapping (TSM) procedure. In the CSV procedure, significant symmetries are first detected by identifying surface point pairs on the input shape that exhibit local similarity in terms of their intrinsic geometry while simultaneously maintaining an intrinsic distance structure at a global level. To allow detection of potentially overlapping symmetric shape regions, a global intrinsic distance-based voting scheme is employed to ensure the inclusion of only those point pairs that exhibit significant intrinsic symmetry. In the TSM procedure, the Functional Map framework is employed to generate the final map of symmetries between point pairs. The TSM procedure ensures the retrieval of the underlying dense correspondence map throughout the 3D shape that follows a particular symmetry. The TSM procedure is also shown to result in the formulation of a metric symmetry space where each point in the space represents a specific symmetry transformation and the distance between points represents the complexity between the corresponding transformations. Experimental results show that the proposed framework can successfully analyze complex 3D shapes that possess rich symmetries. Y1 - 2016 ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Morillo, Oscar A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Robust and Accurate Appearance Models Based on Joint Dictionary Learning Data from the Osteoarthritis Initiative T2 - Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016 N2 - Deformable model-based approaches to 3D image segmentation have been shown to be highly successful. Such methodology requires an appearance model that drives the deformation of a geometric model to the image data. Appearance models are usually either created heuristically or through supervised learning. Heuristic methods have been shown to work effectively in many applications but are hard to transfer from one application (imaging modality/anatomical structure) to another. On the contrary, supervised learning approaches can learn patterns from a collection of annotated training data. In this work, we show that the supervised joint dictionary learning technique is capable of overcoming the traditional drawbacks of the heuristic approaches. Our evaluation based on two different applications (liver/CT and knee/MR) reveals that our approach generates appearance models, which can be used effectively and efficiently in a deformable model-based segmentation framework. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-47118-1_4 VL - 9993 SP - 25 EP - 33 ER - TY - JOUR A1 - Mukhopadhyay, Anirban A1 - Bhandarkar, Suchendra T1 - Biharmonic Density Estimate - a scale space descriptor for 3D deformable surfaces JF - Pattern Analysis and Application Y1 - 2017 U6 - https://doi.org/10.1007/s10044-017-0610-2 SP - 1 EP - 13 ER - TY - CHAP A1 - Mukhopadhyay, Anirban T1 - Total Variation Random Forest: Fully automatic MRI segmentation in congenital heart disease T2 - RAMBO 2016, HVSMR 2016: Reconstruction, Segmentation, and Analysis of Medical Images Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-52280-7_17 VL - LNCS 10129 SP - 165 EP - 171 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER - TY - CHAP A1 - Kaplan, Bernhard A1 - Buchmann, Jens A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017 N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. Y1 - 2017 U6 - https://doi.org/10.1117/12.2251945 VL - 10064 SP - 100645J EP - 100645J-13 ER - TY - GEN A1 - Kaplan, Bernhard A1 - Laufer, Jan A1 - Prohaska, Steffen A1 - Buchmann, Jens T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. T3 - ZIB-Report - 17-04 KW - quantitative photoacoustic tomography KW - model-based inversion KW - oxygen saturation KW - chromophore concentration KW - photoacoustic imaging KW - Monte Carlo methods for light transport KW - boundary conditions KW - coordinate search Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62318 SN - 1438-0064 ER - TY - GEN A1 - Ralphs, Ted A1 - Shinano, Yuji A1 - Berthold, Timo A1 - Koch, Thorsten T1 - Parallel Solvers for Mixed Integer Linear Programming N2 - In this article, we introduce parallel mixed integer linear programming (MILP) solvers. MILP solving algorithms have been improved tremendously in the last two decades. Currently, commercial MILP solvers are known as a strong optimization tool. Parallel MILP solver development has started in 1990s. However, since the improvements of solving algorithms have much impact to solve MILP problems than application of parallel computing, there were not many visible successes. With the spread of multi-core CPUs, current state-of-the-art MILP solvers have parallel implementations and researches to apply parallelism in the solving algorithm also getting popular. We summarize current existing parallel MILP solver architectures. T3 - ZIB-Report - 16-74 KW - parallel computing KW - integer programming KW - branch-and-bound KW - supercomputing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62239 SN - 1438-0064 ER - TY - GEN A1 - Chrapary, Hagen A1 - Dalitz, Wolfgang A1 - Neun, Winfried A1 - Sperber, Wolfram T1 - Design, concepts, and state of the art of the swMATH service N2 - In this paper, the concepts and design for an efficient information service for mathematical software and further mathematical research data are presented. The publication-based approach and the Web-based approach are the main building blocks of the service and will be discussed. Heuristic methods are used for identification, extraction, and ranking of information about software and other mathematical research data. The methods provide not only information about the research data but also link software and mathematical research data to the scientific context. T3 - ZIB-Report - 17-11 KW - software information, software citation, mathematical research data Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62263 SN - 1438-0064 ER - TY - JOUR A1 - Ritter, Zully A1 - Belavy, Daniel A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo bone remodeling rates determination and compressive stiffness variations before, during 60 days bed rest and two years follow up: a micro-FE-analysis from HR-pQCT measurements of the Berlin bed rest study-2 JF - Acta Astronautica KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2017 U6 - https://doi.org/10.1016/j.actaastro.2016.12.002 VL - 132 SP - 67 EP - 77 ER - TY - JOUR A1 - Zander, Thomas A1 - Dreischarf, Marcel A1 - Timm, Anne-Katrin A1 - Baumann, Wolfgang A1 - Schmidt, Hendrik T1 - Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study JF - Journal of Biomechanics KW - finite element modelling KW - lumbar spine KW - sensitivity analysis KW - model validation KW - coefficient of determination Y1 - 2016 U6 - https://doi.org/10.1016/j.jbiomech.2016.12.014 VL - 53 SP - 185 EP - 190 ER - TY - CHAP A1 - Ritter, Zully A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo tibial compressive stiffness variations after HR-pQCT measurements of 60 days immobility during the Berlin bed rest study II using μfinite element analysis T2 - 6th World Congress of Biomechanics (WCB 2010), August 1-6, 2010 Singapore: In Conjunction with 14th International Conference on Biomedical Engineering (ICBME) and 5th Asia Pacific Conference on Biomechanics (APBiomech) KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-14515-5_209 VL - 31 SP - 823 EP - 826 ER - TY - GEN A1 - Weber, Marcus T1 - Eigenvalues of non-reversible Markov chains – A case study N2 - Finite reversible Markov chains are characterized by a transition matrix P that has real eigenvalues and pi-orthogonal eigenvectors, where pi is the stationary distribution of P. This means, that a transition matrix with complex eigenvalues corresponds to a non-reversible Markov chain. This observation leads to the question, whether the imaginary part of that eigendecomposition corresponds to or indicates the “pattern” of the nonreversibility. This article shows that the direct relation between imaginary parts of eigendecompositions and the non-reversibility of a transition matrix is not given. It is proposed to apply the Schur decomposition of P instead of the eigendecomposition in order to characterize its nonreversibility. T3 - ZIB-Report - 17-13 KW - non-reversible KW - transition matrix KW - detailed balance Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62191 SN - 1438-0064 ER - TY - JOUR A1 - Kreisbeck, Christoph A1 - Kramer, Tobias A1 - Molina, Rafael T1 - Time-dependent wave packet simulations of transport through Aharanov–Bohm rings with an embedded quantum dot JF - Journal of Physics: Condensed Matter N2 - We have performed time-dependent wave packet simulations of realistic Aharonov-Bohm (AB) devices with a quantum dot embedded in one of the arms of the interferometer. The AB ring can function as a measurement device for the intrinsic transmission phase through the quantum dot, however, care has to be taken in analyzing the influence of scattering processes in the junctions of the interferometer arms. We consider a harmonic quantum dot and show how the Darwin–Fock spectrum emerges as a unique pattern in the interference fringes of the AB oscillations. Y1 - 2017 U6 - https://doi.org/10.1088/1361-648X/aa605d VL - 29 IS - 15 SP - 155301 ER - TY - GEN A1 - Maher, Stephen J. A1 - Fischer, Tobias A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schenker, Sebastian A1 - Schwarz, Robert A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Weninger, Dieter A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 4.0 N2 - The SCIP Optimization Suite is a powerful collection of optimization software that consists of the branch-cut-and-price framework and mixed-integer programming solver SCIP, the linear programming solver SoPlex, the modeling language Zimpl, the parallelization framework UG, and the generic branch-cut-and-price solver GCG. Additionally, it features the extensions SCIP-Jack for solving Steiner tree problems, PolySCIP for solving multi-objective problems, and SCIP-SDP for solving mixed-integer semidefinite programs. The SCIP Optimization Suite has been continuously developed and has now reached version 4.0. The goal of this report is to present the recent changes to the collection. We not only describe the theoretical basis, but focus on implementation aspects and their computational consequences. T3 - ZIB-Report - 17-12 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62170 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus A1 - Fackeldey, Konstantin A1 - Schütte, Christof T1 - Set-free Markov State Building N2 - Molecular dynamics (MD) simulations face challenging problems since the timescales of interest often are much longer than what is possible to simulate and even if sufficiently long simulation are possible the complex nature of the resulting simulation data makes interpretation difficult. Markov State Models (MSMs) help to overcome these problems by making experimentally relevant timescales accessible via coarse grained representations that also allows for convenient interpretation. However, standard set-based MSMs exhibit some caveats limiting their approximation quality and statistical significance. One of the main caveats results from the fact that typical MD trajectories repeatedly re-cross the boundary between the sets used to build the MSM which causes statistical bias in estimating the transition probabilities between these sets. In this article, we present a set-free approach to MSM building utilizing smooth overlapping ansatz functions instead of sets and an adaptive refinement approach. This kind of meshless discretization helps to overcome the recrossing problem and yields an adaptive refinement procedure that allows to improve the quality of the model while exploring state space and inserting new ansatz functions into the MSM. T3 - ZIB-Report - 17-10 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62167 SN - 1438-0064 ER - TY - JOUR A1 - Spahn, Viola A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Rodriguez-Gaztelumendi, Antonio A1 - Massaly, N. A1 - Temp, Julia A1 - Durmaz, Vedat A1 - Sabri, P. A1 - Reidelbach, Marco A1 - Machelska, Halina A1 - Weber, Marcus A1 - Stein, Christoph T1 - A nontoxic pain killer designed by modeling of pathological receptor conformations JF - Science Y1 - 2017 U6 - https://doi.org/10.1126/science.aai8636 VL - 355 IS - 6328 SP - 966 EP - 969 ER - TY - GEN A1 - Quer, Jannes A1 - Donati, Luca A1 - Keller, Bettina A1 - Weber, Marcus T1 - An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates N2 - In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities. T3 - ZIB-Report - 17-09 KW - Adaptive Importance Sampling KW - Molecular Dynamics KW - Metastability KW - Variance Reduction KW - Non Equilibrium Sampling KW - Metadynamics KW - Girsanov Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62075 SN - 1438-0064 ER - TY - CHAP A1 - Tesch, Alexander T1 - A Nearly Exact Propagation Algorithm for Energetic Reasoning in O(n^2 log n) T2 - Principles and Practice of Constraint Programming (CP 2016) N2 - In constraint programming, energetic reasoning constitutes a powerful start time propagation rule for cumulative scheduling problems (CuSP). In this paper, we first present an improved time interval checking algorithm that is derived from a polyhedral model. In a second step, we extend this algorithm to an energetic reasoning propagation algorithm with complexity O(n^2 log n) where n denotes the number of jobs. The key idea is based on a new sweep line subroutine that efficiently evaluates the relevant time intervals for all jobs. In particular, our algorithm yields at least one possible energetic reasoning propagation for each job. Finally, we show that on the vast number of relevant time intervals our approach yields the maximum possible propagation according to the energetic reasoning rule. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-44953-1_32 VL - 22 SP - 493 EP - 519 ER - TY - GEN A1 - Gleixner, Ambros A1 - Maher, Stephen J. A1 - Müller, Benjamin A1 - Pedroso, João Pedro T1 - Exact Methods for Recursive Circle Packing N2 - Packing rings into a minimum number of rectangles is an optimization problem which appears naturally in the logistics operations of the tube industry. It encompasses two major difficulties, namely the positioning of rings in rectangles and the recursive packing of rings into other rings. This problem is known as the Recursive Circle Packing Problem (RCPP). We present the first dedicated method for solving RCPP that provides strong dual bounds based on an exact Dantzig–Wolfe reformulation of a nonconvex mixed-integer nonlinear programming formulation. The key idea of this reformulation is to break symmetry on each recursion level by enumerating one-level packings, i.e., packings of circles into other circles, and by dynamically generating packings of circles into rectangles. We use column generation techniques to design a “price-and-verify” algorithm that solves this reformulation to global optimality. Extensive computational experiments on a large test set show that our method not only computes tight dual bounds, but often produces primal solutions better than those computed by heuristics from the literature. T3 - ZIB-Report - 17-07 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62039 ER - TY - JOUR A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration JF - Advanced Healthcare Materials N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. Y1 - 2017 U6 - https://doi.org/10.1002/adhm.201601244 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Umsteigen ohne Warten N2 - Wir stellen einen mathematischen Optimierungsansatz zur Berechnung von periodischen Taktfahrplänen vor, bei dem die Umsteigezeiten unter Berücksichtigung des Passagierverhaltens minimiert werden. Wir untersuchen damit den Einfluss wichtiger Systemparameter und Verhaltensmuster auf die Beförderungsqualität. T3 - ZIB-Report - 17-05 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62006 SN - 1438-0064 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Kropp, Jörg-R. A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Ledentsov, Jr., Nikolay T1 - Resonant cavity light–emitting diodes based on dielectric passive cavity structures JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2253089 VL - 10124 SP - 101240O ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds JF - Medical Image Analysis N2 - The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. Y1 - 2017 UR - http://www.sciencedirect.com/science/article/pii/S1361841517300233 U6 - https://doi.org/10.1016/j.media.2017.02.005 VL - 38 SP - 77 EP - 89 ER - TY - JOUR A1 - Weiser, Martin A1 - Ghosh, Sunayana T1 - Theoretically optimal inexact SDC methods JF - Communications in Applied Mathematics and Computational Science N2 - In several inital value problems with particularly expensive right hand side evaluation or implicit step computation, there is a trade-off between accuracy and computational effort. We consider inexact spectral deferred correction (SDC) methods for solving such initial value problems. SDC methods are interpreted as fixed point iterations and, due to their corrective iterative nature, allow to exploit the accuracy-work-tradeoff for a reduction of the total computational effort. On one hand we derive error models bounding the total error in terms of the evaluation errors. On the other hand, we define work models describing the computational effort in terms of the evaluation accuracy. Combining both, a theoretically optimal local tolerance selection is worked out by minimizing the total work subject to achieving the requested tolerance. The properties of optimal local tolerances and the predicted efficiency gain compared to simpler heuristics, and a reasonable practical performance, are illustrated on simple numerical examples. Y1 - 2018 U6 - https://doi.org/10.2140/camcos.2018.13.53 IS - 13-1 SP - 53 EP - 86 ER - TY - GEN A1 - Hiller, Benjamin A1 - Koch, Thorsten A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Schweiger, Jonas T1 - A System to Evaluate Gas Network Capacities: Concepts and Implementation N2 - Since 2005, the gas market in the European Union is liberalized and the trading of natural gas is decoupled from its transport. The transport is done by so-called transmissions system operators or TSOs. The market model established by the European Union views the gas transmission network as a black box, providing shippers (gas traders and consumers) the opportunity to transport gas from any entry to any exit. TSOs are required to offer maximum independent capacities at each entry and exit such that the resulting gas flows can be realized by the network without compromising security of supply. Therefore, evaluating the available transport capacities is extremely important to the TSOs. This paper gives an overview of the toolset for evaluating gas network capacities that has been developed within the ForNe project, a joint research project of seven research partners initiated by Open Grid Europe, Germany's biggest TSO. While most of the relevant mathematics is described in the book "Evaluating Gas Network Capacities", this article sketches the system as a whole, describes some developments that have taken place recently, and gives some details about the current implementation. T3 - ZIB-Report - 17-03 KW - operations research in energy KW - gas network optimization KW - entry-exit model KW - freely allocable capacity KW - large-scale mixed-integer nonlinear programming Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61931 SN - 1438-0064 N1 - A revised and extended version is available as ZIB-Report 18-11. ER - TY - JOUR A1 - Kickhöfer, Benjamin A1 - Kern, Julia T1 - Pricing local emission exposure of road traffic: An agent-based approach JF - Transportation Research Part D: Transport and Environment N2 - This paper proposes a new approach to iteratively calculate local air pollution exposure tolls in large-scale urban settings by taking the exposure times and locations of individuals into consideration. It explicitly avoids detailed air pollution concentration calculations and is therefore characterized by little data requirements, reasonable computation times for iterative calculations, and open-source compatibility. In a first step, the paper shows how to derive time-dependent vehicle-specific exposure tolls in an agent-based model. It closes the circle from the polluting entity, to the receiving entity, to damage costs, to tolls, and back to the behavioral change of the polluting entity. In a second step, the approach is applied to a large-scale real-world scenario of the Munich metropolitan area in Germany. Changes in emission levels, exposure costs, and user benefits are calculated. These figures are compared to a flat emission toll, and to a regulatory measure (a speed reduction in the inner city), respectively. The results indicate that the flat emission toll reduces overall emissions more significantly than the exposure toll, but its exposure cost reductions are rather small. For the exposure toll, overall emissions increase for freight traffic which implies a potential conflict between pricing schemes to optimize local emission exposure and others to abate climate change. Regarding the mitigation of exposure costs caused by urban travelers, the regulatory measure is found to be an effective strategy, but it implies losses in user benefits. Y1 - 2015 U6 - https://doi.org/10.1016/j.trd.2015.04.019 VL - 37 SP - 14 EP - 28 ER - TY - CHAP A1 - Schenker, Sebastian A1 - Vierhaus, Ingmar A1 - Borndörfer, Ralf A1 - Fügenschuh, Armin A1 - Skutella, Martin ED - Stark, Rainer ED - Seliger, Günther ED - Bonvoisin, Jérémy T1 - Optimisation Methods in Sustainable Manufacturing BT - Challenges, Solutions and Implementation Perspectives T2 - Sustainable Manufacturing N2 - Sustainable manufacturing is driven by the insight that the focus on the economic dimension in current businesses and lifestyles has to be broadened to cover all three pillars of sustainability: economic development, social development, and environmental protection. Y1 - 2017 SN - 978-3-319-48514-0 U6 - https://doi.org/10.1007/978-3-319-48514-0_15 SP - 239 EP - 253 PB - Springer International Publishing ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Template-based Re-optimization of Rolling Stock Rotations JF - Public Transport N2 - Rolling stock, i.e., the set of railway vehicles, is among the most expensive and limited assets of a railway company and must be used efficiently. We consider in this paper the re-optimization problem to recover from unforeseen disruptions. We propose a template concept that allows to recover cost minimal rolling stock rotations from reference rotations under a large variety of operational requirements. To this end, connection templates as well as rotation templates are introduced and their application within a rolling stock rotation planning model is discussed. We present an implementation within the rolling stock rotation optimization framework rotor and computational results for scenarios provided by DB Fernverkehr AG, one of the leading railway operators in Europe. Y1 - 2017 U6 - https://doi.org/10.1007/s12469-017-0152-4 SP - 1 EP - 19 PB - Springer ER - TY - JOUR A1 - Chrapary, Hagen A1 - Dalitz, Wolfgang A1 - Sperber, Wolfram T1 - swMATH - Challenges, Next Steps, and Outlook JF - CICM-WS-WIP 2016, Workshop and Work in Progress Papers at CICM 2016 N2 - swMATH is currently one of the most comprehensive specialized information services and search engines for Mathematical SoftWare (MSW). It was the intention of the project to support the user community by providing infor- mation about MSW and searching relevant MSW. Currently swMATH lists infor- mation of more than 13,000 items and 120,000 publications which refer to MSW. Maintaining and updating of the service is mainly done automatically, the num- ber of requests is permanently increasing. This sounds like a perfect solution. But swMATH is only a first step to a powerful information system on mathematical research data. This talk addresses some open problems for the further develop- ment of the swMATH service. It is shown that some problems for swMATH lead to central questions for the information management of mathematical research data, especially for MSW. This contains an extended content analysis of MSW, versioning and citation standard of MSW, a typing of the swMATH resources and the presentation of context information and high-quality control within the swMATH service. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1785-8 VL - Vol-1785 SP - 107 EP - 116 ER - TY - GEN A1 - Baum, Daniel A1 - Lindow, Norbert A1 - Hege, Hans-Christian A1 - Lepper, Verena A1 - Siopi, Tzulia A1 - Kutz, Frank A1 - Mahlow, Kristin A1 - Mahnke, Heinz-Eberhard T1 - Revealing hidden text in rolled and folded papyri N2 - Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds. T3 - ZIB-Report - 17-02 KW - unfolding, papyri, computed tomography Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61826 SN - 1438-0064 ER - TY - JOUR A1 - Baum, Daniel A1 - Lindow, Norbert A1 - Hege, Hans-Christian A1 - Lepper, Verena A1 - Siopi, Tzulia A1 - Kutz, Frank A1 - Mahlow, Kristin A1 - Mahnke, Heinz-Eberhard T1 - Revealing hidden text in rolled and folded papyri JF - Applied Physics A N2 - Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds. Y1 - 2017 U6 - https://doi.org/10.1007/s00339-017-0808-6 VL - 123 IS - 3 SP - 171 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Weber, Marcus A1 - Zhang, Wei T1 - Importance sampling in path space for diffusion processes with slow-fast variables JF - Probability Theory and Related Fields N2 - Importance sampling is a widely used technique to reduce the variance of a Monte Carlo estimator by an appropriate change of measure. In this work, we study importance sampling in the framework of diffusion process and consider the change of measure which is realized by adding a control force to the original dynamics. For certain exponential type expectation, the corresponding control force of the optimal change of measure leads to a zero-variance estimator and is related to the solution of a Hamilton–Jacobi–Bellmann equation. We focus on certain diffusions with both slow and fast variables, and the main result is that we obtain an upper bound of the relative error for the importance sampling estimators with control obtained from the limiting dynamics. We demonstrate our approximation strategy with an illustrative numerical example. Y1 - 2017 UR - http://rdcu.be/oA51 U6 - https://doi.org/10.1007/s00440-017-0755-3 N1 - If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative SP - 1 EP - 52 ER - TY - GEN A1 - Franck, Hildegard A1 - Lohrum, Stefan A1 - Polojannis, Jannis T1 - Automatisierte Fernleihe im KOBV - Handbuch für Bibliotheken - 5. Auflage N2 - Im Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) wird für die automatisierte Fernleihe der Zentrale-Fernleihserver (ZFL-Server) der Firma SISIS eingesetzt. Die Software ist in der KOBV-Zentrale installiert. Der ZFL-Server dient im KOBV sowohl für die Bestellung von Monographien als auch für die Bestellung von Aufsatzkopien aus Zeitschriften und Monographien. Prinzipiell gibt es zwei Verfahren, mit denen sich Bibliotheken an der automatisierten Fernleihe beteiligen können: das E-Mail-Verfahren und das SLNP-Verfahren. Auf beide wird im Handbuch eingegangen. Die automatisierte Fernleihe wurde im KOBV eingeführt, um die Fernleihe für die Benutzer zu be­schleunigen, das Verfahren für die Bibliotheksmitarbeiter zu vereinfachen und den Arbeitsaufwand zu reduzieren. Sie basiert darauf, dass eine Bestellung anhand eines gefundenen Treffers ausgelöst wird – d.h. die bibliographischen Daten sind bereits verifiziert und in einem Katalog nachgewiesen. Anschließend werden die Bestellungen über den ZFL-Server automatisch ausgeführt und verwaltet – sowohl in der regionalen KOBV-Fernleihe als auch in der verbundübergreifenden Fernleihe mit den deutschen Bibliotheksverbünden. Der ZFL-Server besteht aus verschiedenen technischen Komponen­ten. Eine dieser Komponenten ist das Bibliothekskonto, eine Internetanwendung, in der die Bestell­verwaltung des ZFL-Servers für die Bibliotheksbediensteten transparent abläuft. Dazu hat jede Biblio­thek im Bibliothekskonto eine eigene, Passwort-geschützte Dienstoberfläche. Seit Juli 2016 wird im Bibliothekskonto eine neu konzipierte Leitwegsteuerung basierend auf dem KOBV-Portal und dem Fernleihindex, der die deutschen Verbunddatenbanken enthält, eingesetzt. T3 - ZIB-Report - 17-01 KW - Automatisierte Fernleihe Bibliotheksverbund KW - KOBV-Fernleihe KW - Online-Fernleihe KW - Verbundübergreifende Fernleihe KW - ZFL-Server Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61766 SN - 1438-0064 ER - TY - THES A1 - Dillmann, Johannes T1 - Implementierung und Evaluation von Erasure Coding im verteilten Dateisystem XtreemFS Y1 - 2017 ER - TY - THES A1 - Fischer, Jens T1 - Evaluating the Scalability of Scalaris Y1 - 2016 ER - TY - JOUR A1 - Lohrum, Stefan A1 - Kratzer, Mathias A1 - Risch, Uwe A1 - Thiessen, Peter T1 - Zum Stand des Projektes "Cloudbasierte Infrastruktur für Bibliotheksdaten" (CIB) JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 2016 U6 - https://doi.org/10.3196/1864295016635627 VL - Jahrgang 63 IS - Heft 5-6 SP - 250 EP - 257 ER - TY - JOUR A1 - Rusch, Beate A1 - Albrecht, Rita A1 - Meßmer, Gabriele A1 - Thiessen, Peter T1 - Katalogisierung in der Datenwolke JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 2016 U6 - https://doi.org/10.3196/1864295016635631 VL - Jahrgang 63 IS - Heft 5-6 SP - 258 EP - 264 ER - TY - THES A1 - Gamrath, Gerwin T1 - A Coarse-to-Fine Approach for the Workforce Scheduling of Teams N2 - We present a coarse-to-fine column generation approach for the workforce scheduling of teams. In addition we present a price-and-branch approach and a new hypergraph formulation for a specific workforce team problem, called the Toll Enforcement Problem. KW - Scheduling KW - Rostering KW - Coarse-to-Fine KW - Coarse KW - Toll Control KW - Workforce Y1 - 2016 ER - TY - GEN A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Lehmann, Lutz A1 - Hasenfelder, Richard A1 - Radons, Manuel T1 - Piecewise linear secant approximation via Algorithmic Piecewise Differentiation N2 - It is shown how piecewise differentiable functions \(F: R^n → R^m\) that are defined by evaluation programs can be approximated locally by a piecewise linear model based on a pair of sample points x̌ and x̂. We show that the discrepancy between function and model at any point x is of the bilinear order O(||x − x̌|| ||x − x̂||). This is a little surprising since x ∈ R^n may vary over the whole Euclidean space, and we utilize only two function samples F̌ = F(x̌) and F̂ = F(x̂), as well as the intermediates computed during their evaluation. As an application of the piecewise linearization procedure we devise a generalized Newton’s method based on successive piecewise linearization and prove for it sufficient conditions for convergence and convergence rates equaling those of semismooth Newton. We conclude with the derivation of formulas for the numerically stable implementation of the aforedeveloped piecewise linearization methods. T3 - ZIB-Report - 16-54 KW - Automatic differentiation KW - Computational graph KW - Lipschitz continuity KW - Generalized Hermite interpolation KW - ADOL-C Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61642 SN - 1438-0064 ER - TY - GEN A1 - Rusch, Beate A1 - Putnings, Markus ED - Brintzinger, Klaus-Rainer ED - Hohoff, Ulrich ED - Scholle, Ulrike ED - Stäcker, Thomas ED - Steenweg, Helge ED - Wiesenmüller, Heidrun T1 - DeepGreen - Entwicklung eines rechtssicheren Workflows zur effizienten Umsetzung der Open-Access-Komponente in den Allianz-Lizenzen für die Wissenschaft T2 - o-bib. Das offene Bibliotheksjournal / herausgegeben vom VDB, 4/2016 N2 - Die Grundsätze für den Erwerb überregionaler Lizenzen, die von der Deutschen Forschungsgemeinschaft(DFG) gefördert werden (sog. Allianz-Lizenzen), beinhalten spezifische Regelungen zum Open Access. Damit wird DFG-seitig sichergestellt, dass bei Abschluss von Allianz-Verträgen die inkludierten Inhalte sowohl von Autoren als auch von den lizenznehmenden Einrichtungen unter vorteilhafteren Konditionen gegenüber den üblichen Self Archiving Policies (z.B. Verlagsversion, verkürzte Embargofrist) in Repositorien archiviert und veröffentlicht werden dürfen. Die Erfahrung der seit 2011 getätigten Allianz-Abschlüsse zeigt allerdings, dass der Kreis berechtigter Autorinnen und Autoren und Institutionen eigenständig kaum Gebrauch von ihren hierdurch erhaltenen Open-Access-Rechten macht. Entsprechend liegt ein großer Schatz wissenschaftlicher Literatur bei den Verlagen, der noch zu heben ist. Das bewilligte DFG-Projekt DeepGreen (Ausschreibung „Open-Access-Transformation“ von 2014) zielt darauf ab, die vereinbarten Open-Access-Konditionen der Allianz-Lizenzen auf technischer Ebene komfortabel auszugestalten und, wenn möglich, zu automatisieren, so dass nicht mehr Autorinnen und Autoren oder die hierzu berechtigten Bibliotheken die Publikationen manuell in Open-Access-Repositorien einpflegen müssen, sondern die Verlage selbst zyklisch über definierte Schnittstellen abliefern. Dazu bauen die Projektpartner (Universitätsbibliothek Erlangen-Nürnberg, Universitätsbibliothek TU Berlin, Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum, Bayerische Staatsbibliothek München sowie die Verbünde Bibliotheksverbund Bayern und KooperativerBibliotheksverbund Berlin-Brandenburg) ein Dark Archive namens DeepGreen auf, in das teilnehmende Allianz-Lizenz-Verlage Publikationen und Metadaten einspeisen. DeepGreen soll im Anschluss als Datendrehscheibe für berechtigte Open-Access-Repositorien dienen. Als Pilotpartner konnten die Verlage Karger und SAGE gewonnen werden. Der vorliegende Aufsatz stellt das Projekt und den aktuellen Stand der Arbeiten vor. Y1 - 2016 U6 - https://doi.org/10.5282/o-bib/2016H4S110-119 VL - 4/2016 SP - 110 EP - 118 PB - VDB - Verein Deutscher Bibliothekarinnen und Bibliothekare e.V. ER - TY - GEN A1 - Berthold, Timo A1 - Hendel, Gregor A1 - Koch, Thorsten T1 - The Three Phases of MIP Solving N2 - Modern MIP solvers employ dozens of auxiliary algorithmic components to support the branch-and-bound search in finding and improving primal solutions and in strengthening the dual bound. Typically, all components are tuned to minimize the average running time to prove optimality. In this article, we take a different look at the run of a MIP solver. We argue that the solution process consists of three different phases, namely achieving feasibility, improving the incumbent solution, and proving optimality. We first show that the entire solving process can be improved by adapting the search strategy with respect to the phase-specific aims using different control tunings. Afterwards, we provide criteria to predict the transition between the individual phases and evaluate the performance impact of altering the algorithmic behavior of the MIP solver SCIP at the predicted phase transition points. T3 - ZIB-Report - 16-78 KW - optimization software KW - mixed-integer programming KW - branch-and-bound KW - adaptive search behavior KW - optimality prediction Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61607 SN - 1438-0064 ER - TY - JOUR A1 - Tesch, Alexander T1 - Kompakte MIP Modelle für das Ressourcenbeschränkte Projektplanungsproblem JF - OR News Y1 - 2016 VL - 58 SP - 19 EP - 21 ER - TY - GEN A1 - Lenz, Ralf A1 - Schwarz, Robert T1 - Optimal Looping of Pipelines in Gas Networks N2 - In this paper, we compare several approaches for the problem of gas network expansions using loops, that is, to build new pipelines in parallel to existing ones. We present different model formulations for the problem of continuous loop expansions as well as discrete loop expansions. We then analyze problem properties, such as the structure and convexity of the underlying feasible regions. The paper concludes with a computational study comparing the continuous and the discrete formulations. T3 - ZIB-Report - 16-67 KW - Mixed Integer Nonlinear Programming KW - Gas Network Applications KW - Expansion Planning Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61564 SN - 1438-0064 ER - TY - GEN A1 - Hennig, Kai A1 - Schwarz, Robert T1 - Using Bilevel Optimization to find Severe Transport Situations in Gas Transmission Networks N2 - In the context of gas transmission in decoupled entry-exit systems, many approaches to determine the network capacity are based on the evaluation of realistic and severe transport situations. In this paper, we review the Reference Point Method, which is an algorithm used in practice to generate a set of scenarios using the so-called transport moment as a measure for severity. We introduce a new algorithm for finding severe transport situations that considers an actual routing of the flow through the network and is designed to handle issues arising from cyclic structures in a more dynamical manner. Further, in order to better approximate the physics of gas, an alternative, potential based flow formulation is proposed. The report concludes with a case study based on data from the benchmark library GasLib. T3 - ZIB-Report - 16-68 KW - bilevel optimization KW - gas networks KW - network flow Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61519 SN - 1438-0064 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodriguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems JF - Journal of Physical Chemistry B N2 - Time-resolved spectroscopy provides the main tool for analyzing the dynamics of excitonic energy transfer in light-harvesting complexes. To infer time-scales and effective coupling parameters from experimental data requires to develop numerical exact theoretical models. The finite duration of the laser-molecule interactions and the reorganization process during the exciton migration affect the location and strength of spectroscopic signals. We show that the non-perturbative hierarchical equations of motion (HEOM) method captures these processes in a model exciton system, including the charge transfer state. Y1 - 2017 U6 - https://doi.org/10.1021/acs.jpcb.6b09858 VL - 121 SP - 463 EP - 470 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Optimization of Handouts for Rolling Stock Rotations Visualization N2 - A railway operator creates (rolling stock) rotations in order to have a precise master plan for the operation of a timetable by railway vehicles. A rotation is considered as a cycle that multiply traverses a set of operational days while covering trips of the timetable. As it is well known, the proper creation of rolling stock rotations by, e.g., optimization algorithms is challenging and still a topical research subject. Nevertheless, we study a completely different but strongly related question in this paper, i.e.: How to visualize a rotation? For this purpose, we introduce a basic handout concept, which directly leads to the visualization, i.e., handout of a rotation. In our industrial application at DB Fernverkehr AG, the handout is exactly as important as the rotation itself. Moreover, it turns out that also other European railway operators use exactly the same methodology (but not terminology). Since a rotation can have many handouts of different quality, we show how to compute optimal ones through an integer program (IP) by standard software. In addition, a construction as well as an improvement heuristic are presented. Our computational results show that the heuristics are a very reliable standalone approach to quickly find near-optimal and even optimal handouts. The efficiency of the heuristics is shown via a computational comparison to the IP approach. T3 - ZIB-Report - ZR-16-73 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61430 SN - 1438-0064 ER - TY - GEN A1 - Gottwald, Robert Lion A1 - Maher, Stephen J. A1 - Shinano, Yuji T1 - Distributed domain propagation N2 - Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite it's simplicity portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after a variables domain has been reduced. This paper investigates the impact of distributed domain propagation in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers. T3 - ZIB-Report - 16-71 KW - mixed integer programming KW - parallelization KW - domain propagation KW - portfolio solvers Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61380 SN - 1438-0064 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Schade, Stanley T1 - Regularity patterns for rolling stock rotation optimization T2 - 8th International Conference on Applied Operational Research, Proceedings N2 - The operation of railways gives rise to many fundamental optimization problems. One of these problems is to cover a given set of timetabled trips by a set of rolling stock rotations. This is well known as the Rolling Stock Rotation Problem (RSRP). Most approaches in the literature focus primarily on modeling and minimizing the operational costs. However, an essential aspect for the industrial application is mostly neglected. As the RSRP follows timetabling and line planning, where periodicity is a highly desired property, it is also desired to carry over periodic structures to rolling stock rotations and following operations. We call this complex requirement regularity. Regularity turns out to be of essential interest, especially in the industrial scenarios that we tackle in cooperation with DB Fernverkehr AG. Moreover, regularity in the context of the RSRP has not been investigated thoroughly in the literature so far. We introduce three regularity patterns to tackle this requirement, namely regular trips, regular turns, and regular handouts. We present a two-stage approach in order to optimize all three regularity patterns. At first, we integrate regularity patterns into an integer programming approach for the minimization of the operational cost of rolling stock rotations. Afterwards regular handouts are computed. These handouts present the rotations of the first stage in the most regular way. Our computational results (i.e., rolling stock rotations evaluated by planners of DB Fernverkehr AG) show that the three regularity patterns and our concept are a valuable and, moreover, an essential contribution to rolling stock rotation optimization. Y1 - 2016 VL - 8 SP - 28 EP - 32 ER - TY - GEN A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Pedroso, João Pedro A1 - Rehfeldt, Daniel A1 - Schwarz, Robert A1 - Serrano, Felipe T1 - PySCIPOpt: Mathematical Programming in Python with the SCIP Optimization Suite N2 - SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP. T3 - ZIB-Report - 16-64 KW - SCIP, Mathematical optimization, Python, Modeling Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61348 SN - 1438-0064 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Hoffmann, René T1 - Comparative cephalopod shell strength and the role of septum morphology on stress distribution JF - PeerJ N2 - The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio used to characterize septal morphology in the septal strength index and in calculations of tensile strength of nacre are likely insufficient. A better understanding of the material properties of cephalopod nacre may allow the estimation of maximum depth limits of shelled cephalopods through finite element analysis. Y1 - 2016 U6 - https://doi.org/10.7717/peerj.2434 VL - 4 SP - e2434 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Pumberger, Matthias A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Influence of pelvic tilt on functional acetabular orientation JF - Technology and Health Care Y1 - 2016 U6 - https://doi.org/10.3233/THC-161281 VL - 25 IS - 3 SP - 557 EP - 565 PB - IOS Press ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods for Prior Estimation in Systems Medicine N2 - One of the main goals of mathematical modelling in systems medicine related to medical applications is to obtain patient-specific parameterizations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Therefore, before applying Bayes’ rule separately to the data of each patient (which is typically performed using a non-informative prior), it is meaningful to use empirical Bayes methods in order to construct an informative prior from all available data. We compare the performance of four priors - a non-informative prior and priors chosen by nonparametric maximum likelihood estimation (NPMLE), by maximum penalized lilelihood estimation (MPLE) and by doubly-smoothed maximum likelihood estimation (DS-MLE) - by applying them to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling. T3 - ZIB-Report - 16-57 KW - Parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modelling KW - NPMLE KW - MPLE KW - DS-MLE KW - EM algorithm KW - Jeffreys prior KW - reference prior KW - hyperparameter KW - hyperprior KW - principle of maximum entropy Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61307 SN - 1438-0064 ER - TY - GEN A1 - Schenker, Sebastian A1 - Borndörfer, Ralf A1 - Skutella, Martin T1 - A novel partitioning of the set of non-dominated points N2 - We consider a novel partitioning of the set of non-dominated points for general multi-objective integer programs with $k$ objectives. The set of non-dominated points is partitioned into a set of non-dominated points whose efficient solutions are also efficient for some restricted subproblem with one less objective; the second partition comprises the non-dominated points whose efficient solutions are inefficient for any of the restricted subproblems. We show that the first partition has the nice property that it yields finite rectangular boxes in which the points of the second partition are located. T3 - ZIB-Report - 16-55 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61286 SN - 1438-0064 ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods, Reference Priors, Cross Entropy and the EM Algorithm N2 - When estimating a probability density within the empirical Bayes framework, the non-parametric maximum likelihood estimate (NPMLE) usually tends to overfit the data. This issue is usually taken care of by regularization - a penalization term is subtracted from the marginal log-likelihood before the maximization step, so that the estimate favors smooth solutions, resulting in the so-called maximum penalized likelihood estimation (MPLE). The majority of penalizations currently in use are rather arbitrary brute-force solutions, which lack invariance under transformation of the parameters(reparametrization) and measurements. This contradicts the principle that, if the underlying model has several equivalent formulations, the methods of inductive inference should lead to consistent results. Motivated by this principle and using an information-theoretic point of view, we suggest an entropy-based penalization term that guarantees this kind of invariance. The resulting density estimate can be seen as a generalization of reference priors. Using the reference prior as a hyperprior, on the other hand, is argued to be a poor choice for regularization. We also present an insightful connection between the NPMLE, the cross entropy and the principle of minimum discrimination information suggesting another method of inference that contains the doubly-smoothed maximum likelihood estimation as a special case. T3 - ZIB-Report - 16-56 KW - parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modeling KW - hyperparameter KW - hyperprior KW - EM algorithm KW - NPMLE KW - MPLE KW - DS-MLE KW - principle of maximum entropy KW - cross entropy KW - minimum discrimination information KW - reference prior KW - Jeffreys prior Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61230 SN - 1438-0064 ER - TY - GEN A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Kaier, Anton A1 - Schlechte, Thomas A1 - Schlobach, Swen T1 - The Shortest Path Problem with Crossing Costs N2 - We introduce the shortest path problem with crossing costs (SPPCC), a shortest path problem in a directed graph, in which the objective function is the sum of arc weights and crossing costs. The former are independently paid for each arc used by the path, the latter need to be paid every time the path intersects certain sets of arcs, which we call regions. The SPPCC generalizes not only the classical shortest path problem but also variants such as the resource constrained shortest path problem and the minimum label path problem. We use the SPPCC to model the flight trajectory optimization problem with overflight costs. In this paper, we provide a comprehensive analysis of the problem. In particular, we identify efficient exact and approximation algorithms for the cases that are most relevant in practice. T3 - ZIB-Report - 16-70 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61240 SN - 1438-0064 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Klug, Torsten A1 - Lamorgese, Leonardo A1 - Mannino, Carlo A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Recent success stories on integrated optimization of railway systems JF - Transportation Research Part C: Emerging Technologies N2 - Planning and operating railway transportation systems is an extremely hard task due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. Because of that, however, mathematical models and optimization techniques can result in large gains for both railway customers and operators, e.g., in terms of cost reductions or service quality improvements. In the last years a large and growing group of researchers in the OR community have devoted their attention to this domain developing mathematical models and optimization approaches to tackle many of the relevant problems in the railway planning process. However, there is still a gap to bridge between theory and practice (e.g. Cacchiani et al., 2014; Borndörfer et al., 2010), with a few notable exceptions. In this paper we address three individual success stories, namely, long-term freight train routing (part I), mid-term rolling stock rotation planning (part II), and real-time train dispatching (part III). In each case, we describe real-life, successful implementations. We will discuss the individual problem setting, survey the optimization literature, and focus on particular aspects addressed by the mathematical models. We demonstrate on concrete applications how mathematical optimization can support railway planning and operations. This gives proof that mathematical optimization can support the planning of railway resources. Thus, mathematical models and optimization can lead to a greater efficiency of railway operations and will serve as a powerful and innovative tool to meet recent challenges of the railway industry. Y1 - 2017 U6 - https://doi.org/10.1016/j.trc.2016.11.015 VL - 74 IS - 1 SP - 196 EP - 211 ER - TY - GEN A1 - Müller, Anja A1 - Rusch, Beate T1 - Was in der Zwischenzeit geschah – vier Jahre und 49 Digitalisierungsprojekte später: Förderprogramm Digitalisierung und Servicestelle Digitalisierung Berlin (digiS) 2012 bis 2016 T2 - Föderale Vielfalt – Globale Vernetzung. Strategien der Bundesländer für das kulturelle Erbe in der digitalen Welt. Y1 - 2016 U6 - https://doi.org/10.15460/ddb.2.168 PB - Deutsche Digitale Bibliothek ER - TY - GEN A1 - Tycowicz, Christoph von A1 - Ambellan, Felix A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - A Riemannian Statistical Shape Model using Differential Coordinates N2 - We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidian structure. A key advantage of our framework is that statistics in a manifold shape space become numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidian approach in terms of shape-based classification of morphological disorders. T3 - ZIB-Report - 16-69 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61175 UR - https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/6485 SN - 1438-0064 ER - TY - GEN A1 - Wilson, Jon A1 - Herrmann, Sven A1 - Gutsche, Philipp A1 - Burger, Sven A1 - McPeak, Kevin T1 - The Chiral Coefficient: Rapid Optimization of Broadband Plasmonic Chirality T2 - 2016 MRS Fall Meeting & Exhibit Y1 - 2016 ER - TY - GEN A1 - Schwartz, Stephan A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Designing Inspector Rosters with Optimal Strategies N2 - We consider the problem of enforcing a toll on a transportation network with limited inspection resources. We formulate a game theoretic model to optimize the allocation of the inspectors, taking the reaction of the network users into account. The model includes several important aspects for practical operation of the control strategy, such as duty types for the inspectors. In contrast to an existing formulation using flows to describe the users' strategies we choose a path formulation and identify dominated user strategies to significantly reduce the problem size. Computational results suggest that our approach is better suited for practical instances. T3 - ZIB-Report - 16-65 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61123 SN - 1438-0064 ER - TY - JOUR A1 - Landau, Itamar D. A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sompolinsky, Haim T1 - The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks JF - Neuron N2 - Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.10.027 VL - 92 IS - 5 SP - 1106 EP - 1121 ER - TY - GEN A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Kniasew, Dimitri A1 - Schlögel, Dominik A1 - Martin, Alexander A1 - Weninger, Dieter T1 - Tackling Industrial-Scale Supply Chain Problems by Mixed-Integer Programming N2 - SAP's decision support systems for optimized supply network planning rely on mixed-integer programming as the core engine to compute optimal or near-optimal solutions. The modeling flexibility and the optimality guarantees provided by mixed-integer programming greatly aid the design of a robust and future-proof decision support system for a large and diverse customer base. In this paper we describe our coordinated efforts to ensure that the performance of the underlying solution algorithms matches the complexity of the large supply chain problems and tight time limits encountered in practice. T3 - ZIB-Report - 16-45 KW - supply chain management, supply network optimization, mixed-integer linear programming, primal heuristics, numerical stability, large-scale optimization Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61107 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Saitenmacher, René A1 - Walther, Tom T1 - Analysis of operating modes of complex compressor stations N2 - We consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. In particular, we propose a refined model that allows to precompute tighter relaxations for each operation mode. These relaxations may be used to strengthen the compressor station submodels in gas network optimization problems. We provide a procedure to obtain the refined model from the input data for the original model. T3 - ZIB-Report - 16-61 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61092 SN - 1438-0064 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo A1 - Heinz, Stefan T1 - Experiments with Conflict Analysis in Mixed Integer Programming N2 - The analysis of infeasible subproblems plays an import role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications obtained by domain propagation that led to infeasibility. The result of the analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. The dual LP solution provides a set of multipliers that can be used to generate a single new globally valid linear constraint. The main contribution of this short paper is an empirical evaluation of two ways to combine both approaches. Experiments are carried out on general MIP instances from standard public test sets such as Miplib2010; the presented algorithms have been implemented within the non-commercial MIP solver SCIP. Moreover, we present a pool-based approach to manage conflicts which addresses the way a MIP solver traverses the search tree better than aging strategies known from SAT solving. T3 - ZIB-Report - 16-63 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61087 SN - 1438-0064 ER - TY - GEN A1 - Cheung, Kevin K. H. A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Verifying Integer Programming Results N2 - Software for mixed-integer linear programming can return incorrect results for a number of reasons, one being the use of inexact floating-point arithmetic. Even solvers that employ exact arithmetic may suffer from programming or algorithmic errors, motivating the desire for a way to produce independently verifiable certificates of claimed results. Due to the complex nature of state-of-the-art MILP solution algorithms, the ideal form of such a certificate is not entirely clear. This paper proposes such a certificate format, illustrating its capabilities and structure through examples. The certificate format is designed with simplicity in mind and is composed of a list of statements that can be sequentially verified using a limited number of simple yet powerful inference rules. We present a supplementary verification tool for compressing and checking these certificates independently of how they were created. We report computational results on a selection of mixed-integer linear programming instances from the literature. To this end, we have extended the exact rational version of the MIP solver SCIP to produce such certificates. T3 - ZIB-Report - 16-58 KW - correctness, verification, proof, certificate, optimality, infeasibility, mixed-integer linear programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61044 SN - 1438-0064 ER - TY - CHAP A1 - Gutsche, Philipp A1 - Mäusle, Raquel A1 - Burger, Sven T1 - Tailoring local optical chirality in helical metamaterials T2 - 2016 10th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics Y1 - 2016 U6 - https://doi.org/10.1109/MetaMaterials.2016.7746440 SP - 73 EP - 75 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Mäusle, Raquel A1 - Burger, Sven T1 - Locally Enhanced and Tunable Optical Chirality in Helical Metamaterials JF - Photonics Y1 - 2016 U6 - https://doi.org/10.3390/photonics3040060 VL - 3 SP - 60 ER - TY - GEN A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest. We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. T3 - ZIB-Report - 16-60 KW - reaction-diffusion KW - stochastic chemical kinetics KW - chemical master equation Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60999 SN - 1438-0064 ER - TY - GEN A1 - Winkelmann, Stefanie T1 - Markov Control with Rare State Observation: Average Optimality N2 - This paper investigates the criterion of long-term average costs for a Markov decision process (MDP) which is not permanently observable. Each observation of the process produces a fixed amount of \textit{information costs} which enter the considered performance criterion and preclude from arbitrarily frequent state testing. Choosing the \textit{rare} observation times is part of the control procedure. In contrast to the theory of partially observable Markov decision processes, we consider an arbitrary continuous-time Markov process on a finite state space without further restrictions on the dynamics or the type of interaction. Based on the original Markov control theory, we redefine the control model and the average cost criterion for the setting of information costs. We analyze the constant of average costs for the case of ergodic dynamics and present an optimality equation which characterizes the optimal choice of control actions and observation times. For this purpose, we construct an equivalent freely observable MDP and translate the well-known results from the original theory to the new setting. T3 - ZIB-Report - 16-59 KW - Markov decision process KW - partial observability KW - average optimality KW - information costs Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60981 SN - 1438-0064 ER - TY - JOUR A1 - Duwal, Sulav A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings JF - PloS Computational Biology N2 - An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pcbi.1004200 VL - 11 IS - 4 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling JF - Journal of Chemical Physics N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest.We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. Y1 - 2016 U6 - https://doi.org/10.1063/1.4971163 VL - 145 IS - 21 ER - TY - JOUR A1 - Winkelmann, Stefanie T1 - Markov Control with Rare State Observation: Average Optimality JF - Markov Processes and Related Fields N2 - This paper investigates the criterion of long-term average costs for a Markov decision process (MDP) which is not permanently observable. Each observation of the process produces a fixed amount of information costs which enter the considered performance criterion and preclude from arbitrarily frequent state testing. Choosing the rare observation times is part of the control procedure. In contrast to the theory of partially observable Markov decision processes, we consider an arbitrary continuous-time Markov process on a finite state space without further restrictions on the dynamics or the type of interaction. Based on the original Markov control theory, we redefine the control model and the average cost criterion for the setting of information costs. We analyze the constant of average costs for the case of ergodic dynamics and present an optimality equation which characterizes the optimal choice of control actions and observation times. For this purpose, we construct an equivalent freely observable MDP and translate the well-known results from the original theory to the new setting. Y1 - 2017 VL - 23 SP - 1 EP - 34 ER - TY - GEN A1 - Omari, Mohamed A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Röblitz, Susanna T1 - Modelling of glucose-insulin metabolism and its effect on the estrous cycle in bovine T2 - Annual Meeting of the Population Approach Group in Europe Y1 - 2016 ER - TY - CHAP A1 - Lange, Alexander A1 - Plöntzke, Julia A1 - Schäfer, Stefan A1 - Röblitz, Susanna T1 - Follicular maturation in cows: mathematical models and data T2 - 10. European Conference on Mathematical and Theoretical Biology Y1 - 2016 ER - TY - JOUR A1 - Bauer, Gernot A1 - Gribova, Nadezhda A1 - Lange, Alexander A1 - Holm, Christian A1 - Gross, Joachim T1 - Three-body effects in triplets of capped gold nanocrystals JF - Molecular Physics Y1 - 2017 U6 - https://doi.org/10.1080/00268976.2016.1213909 VL - 115 SP - 1031 EP - 1040 ER - TY - JOUR A1 - Lange, Alexander T1 - Reconstruction of disease transmission rates: applications to measles, dengue, and influenza JF - Journal of Theoretical Biology Y1 - 2016 U6 - https://doi.org/10.1016/j.jtbi.2016.04.017 VL - 400 SP - 138 EP - 153 ER - TY - CHAP A1 - Chrapary, Hagen A1 - Ren, Yue T1 - The Software Portal swMATH: A State of the Art Report and Next Steps T2 - Mathematical Software - ICMS 2016, 5th International Conference Berlin, Germany, July 11-14, 2016 Proceedings Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42432-3_49 SP - 397 EP - 402 ER - TY - CHAP A1 - Shinano, Yuji A1 - Berthold, Timo A1 - Heinz, Stefan T1 - A First Implementation of ParaXpress: Combining Internal and External Parallelization to Solve MIPs on Supercomputers T2 - Mathematical Software - ICMS 2016, 5th International Conference Berlin, Germany, July 11-14, 2016 Proceedings Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42432-3_38 SP - 308 EP - 316 ER - TY - CHAP A1 - Berthold, Timo A1 - Farmer, James A1 - Heinz, Stefan A1 - Perregaard, Michael T1 - Parallelization of the FICO Xpress-Optimizer T2 - Mathematical Software - ICMS 2016, 5th International Conference Berlin, Germany, July 11-14, 2016 Proceedings Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42432-3_31 SP - 251 EP - 258 ER - TY - CHAP A1 - Wu, Cheng-Lung A1 - Maher, Stephen J. T1 - Airline scheduling and disruption management T2 - L. Budd, S. Ison, eds., Air transportation management: an international perspective Y1 - 2017 SN - 9781472451064 SP - 151 EP - 167 PB - Routledge CY - New York ER - TY - BOOK A1 - Greuel, Martin A1 - Koch, Thorsten A1 - Paule, Peter A1 - Sommese, Andrew T1 - Mathematical Software - ICMS 2016, 5th Int. Conf. Berlin, Germany, July 11-14, 2016, Proceedings T3 - Lecture Notes in Computer Science (LNCS) Y1 - 2016 SN - 978-3-319-42431-6 U6 - https://doi.org/10.1007/978-3-319-42432-3 VL - 9725 PB - Springer ER - TY - CHAP A1 - Gutsche, Philipp A1 - Mäusle, Raquel A1 - Burger, Sven T1 - Circular polarization phenomena in chiral nano-optical devices T2 - Light, Energy and the Environment 2016 Y1 - 2016 U6 - https://doi.org/10.1364/FTS.2016.JW4A.4 SP - JW4A.4 ER - TY - CHAP A1 - Jäger, Klaus A1 - Hammerschmidt, Martin A1 - Köppel, Grit A1 - Burger, Sven A1 - Becker, Christiane T1 - On Accurate Simulations of Thin-Film Solar Cells With a Thick Glass Superstrate T2 - Light, Energy and the Environment 2016 Y1 - 2016 U6 - https://doi.org/10.1364/PV.2016.PM3B.5 SP - PM3B.5 ER - TY - CHAP A1 - Krzikalla, Olaf A1 - Wende, Florian A1 - Höhnerbach, Markus T1 - Dynamic SIMD Vector Lane Scheduling T2 - High Performance Computing, ISC High Performance 2016 International Workshops, ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P^3MA, VHPC, WOPSSS N2 - A classical technique to vectorize code that contains control flow is a control-flow to data-flow conversion. In that approach statements are augmented with masks that denote whether a given vector lane participates in the statement’s execution or idles. If the scheduling of work to vector lanes is performed statically, then some of the vector lanes will run idle in case of control flow divergences or varying work intensities across the loop iterations. With an increasing number of vector lanes, the likelihood of divergences or heavily unbalanced work assignments increases and static scheduling leads to a poor resource utilization. In this paper, we investigate different approaches to dynamic SIMD vector lane scheduling using the Mandelbrot set algorithm as a test case. To overcome the limitations of static scheduling, idle vector lanes are assigned work items dynamically, thereby minimizing per-lane idle cycles. Our evaluation on the Knights Corner and Knights Landing platform shows, that our approaches can lead to considerable performance gains over a static work assignment. By using the AVX-512 vector compress and expand instruction, we are able to further improve the scheduling. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-46079-6_25 VL - 9945 SP - 354 EP - 365 ER - TY - CHAP A1 - Grewe, Carl Martin A1 - Schreiber, Lisa T1 - Digitale Bildarchive. Archivierung und Codierung der Gefühle T2 - +ultra gestaltung schafft wissen Y1 - 2016 SN - 978-3-86502-378-0 SP - 285 EP - 290 PB - Seemann Henschel ER - TY - CHAP A1 - Grewe, Carl Martin A1 - Zachow, Stefan T1 - Fully Automated and Highly Accurate Dense Correspondence for Facial Surfaces T2 - Computer Vision – ECCV 2016 Workshops N2 - We present a novel framework for fully automated and highly accurate determination of facial landmarks and dense correspondence, e.g. a topologically identical mesh of arbitrary resolution, across the entire surface of 3D face models. For robustness and reliability of the proposed approach, we are combining 2D landmark detectors and 3D statistical shape priors with a variational matching method. Instead of matching faces in the spatial domain only, we employ image registration to align the 2D parametrization of the facial surface to a planar template we call the Unified Facial Parameter Domain (ufpd). This allows us to simultaneously match salient photometric and geometric facial features using robust image similarity measures while reasonably constraining geometric distortion in regions with less significant features. We demonstrate the accuracy of the dense correspondence established by our framework on the BU3DFE database with 2500 facial surfaces and show, that our framework outperforms current state-of-the-art methods with respect to the fully automated location of facial landmarks. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-48881-3_38 VL - 9914 SP - 552 EP - 568 PB - Springer International Publishing ER - TY - GEN A1 - Schwartz, Stephan A1 - Borndörfer, Ralf A1 - Bartz, Gerald T1 - The Graph Segmentation Problem N2 - We investigate a graph theoretical problem arising in the automatic billing of a network toll. Given a network and a family of user paths, we study the graph segmentation problem (GSP) to cover parts of the user paths by a set of disjoint segments. The GSP is shown to be NP-hard but for special cases it can be solved in polynomial time. We also show that the marginal utility of a segment is bounded. Computational results for real-world instances show that in practice the problem is more amenable than the theoretic bounds suggest. T3 - ZIB-Report - 16-53 KW - toll billing KW - graph segmentation KW - combinatorial optimization Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60750 SN - 1438-0064 ER - TY - GEN A1 - Noack, Matthias A1 - Wende, Florian A1 - Zitzlsberger, Georg A1 - Klemm, Michael A1 - Steinke, Thomas T1 - KART – A Runtime Compilation Library for Improving HPC Application Performance N2 - The effectiveness of ahead-of-time compiler optimization heavily depends on the amount of available information at compile time. Input-specific information that is only available at runtime cannot be used, although it often determines loop counts, branching predicates and paths, as well as memory-access patterns. It can also be crucial for generating efficient SIMD-vectorized code. This is especially relevant for the many-core architectures paving the way to exascale computing, which are more sensitive to code-optimization. We explore the design-space for using input-specific information at compile-time and present KART, a C++ library solution that allows developers to compile, link, and execute code (e.g., C, C++ , Fortran) at application runtime. Besides mere runtime compilation of performance-critical code, KART can be used to instantiate the same code multiple times using different inputs, compilers, and options. Other techniques like auto-tuning and code-generation can be integrated into a KART-enabled application instead of being scripted around it. We evaluate runtimes and compilation costs for different synthetic kernels, and show the effectiveness for two real-world applications, HEOM and a WSM6 proxy. T3 - ZIB-Report - 16-48 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60730 SN - 1438-0064 ER - TY - GEN A1 - Rusch, Beate A1 - Bertelmann, Roland A1 - Pampel, Heinz A1 - Aust, Pamela A1 - Helbig, Kerstin A1 - Müller, Anja Doreen A1 - Conrad-Rempel, Steffi A1 - Weihe, Signe A1 - Dierkes, Thomas A1 - Kuhlen, Rainer A1 - Schobert, Dagmar A1 - Voigt, Michaela A1 - Klimpel, Paul A1 - Riesenweber, Christina A1 - Kennecke, Andreas A1 - Kowalak, Mario A1 - Schlegel, Birgit A1 - Taubert, Niels A1 - Hübner, Andreas A1 - Mruck, Katja T1 - KOBV-Sonderedition zur International Open Access Week 2016 „Open in Action“ N2 - An der internationalen Open-Access-Woche 2016 vom 24.-28. Oktober war der KOBV erstmalig mit einem Online „Publishing Event“ beteiligt. An fünf aufeinanderfolgenden Tagen erschien täglich eine Sonderausgabe des KOBV-Newsletters zu ausgewählten Open-Access-Themen. Die einzelnen Beiträge sind in dieser Sonderedition als Online-Reader zusammengestellt. Der aktuelle Diskussionsstand zum jeweiligen Thema wird von Expertinnen und Experten in kurzen Übersichtsartikeln vorgestellt und mit Praxistipps ergänzt. Zielgruppe sind vor allem Bibliothekare und Bibliothekarinnen, die sich einen schnellen Überblick zu Open Access verschaffen wollen. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60708 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse Data JF - arXiv N2 - The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods. Y1 - 2016 SP - 1602.08425v1 ER - TY - GEN A1 - Weiser, Martin A1 - Ghosh, Sunayana T1 - Theoretically optimal inexact SDC methods N2 - In several inital value problems with particularly expensive right hand side computation, there is a trade-off between accuracy and computational effort in evaluating the right hand sides. We consider inexact spectral deferred correction (SDC) methods for solving such non-stiff initial value problems. SDC methods are interpreted as fixed point iterations and, due to their corrective iterative nature, allow to exploit the accuracy-work-tradeoff for a reduction of the total computational effort. On one hand we derive an error model bounding the total error in terms of the right hand side evaluation errors. On the other hand, we define work models describing the computational effort in terms of the evaluation accuracy. Combining both, a theoretically optimal tolerance selection is worked out by minimizing the total work subject to achieving the requested tolerance. T3 - ZIB-Report - 16-52 KW - Spectral deferred correction, initial value problems, error propagation, adaptive control of tolerances Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53140 SN - 1438-0064 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika A1 - Löbel, Fabian T1 - The Modulo Network Simplex with Integrated Passenger Routing T2 - Operations Research Proceedings 2016 N2 - Periodic timetabling is an important strategic planning problem in public transport. The task is to determine periodic arrival and departure times of the lines in a given network, minimizing the travel time of the passengers. We extend the modulo network simplex method, a well-established heuristic for the periodic timetabling problem, by integrating a passenger (re)routing step into the pivot operations. Computations on real-world networks show that we can indeed find timetables with much shorter total travel time, when we take the passengers' travel paths into consideration. Y1 - 2016 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack – A solver for STP and variants with parallelization extensions JF - Mathematical Programming Computation N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. Y1 - 2017 U6 - https://doi.org/10.1007/s12532-016-0114-x VL - 9 IS - 2 SP - 231 EP - 296 ER - TY - GEN A1 - Pulaj, Jonad T1 - Cutting Planes for Families Implying Frankl's Conjecture N2 - We find previously unknown families which imply Frankl’s conjecture using an algorithmic framework. The conjecture states that for any non-empty union-closed (or Frankl) family there exists an element in at least half of the sets. Poonen’s Theorem characterizes the existence of weights which determine whether a given Frankl family implies the conjecture for all Frankl families which contain it. A Frankl family is Non–Frankl-Complete (Non–FC), if it does not imply the conjecture in its elements for some Frankl family that contains it. We design a cutting-plane method that computes the explicit weights which imply the existence conditions of Poonen’s Theorem. This method allows us to find a counterexample to a ten-year-old conjecture by R. Morris about the structure of generators for Non–FC-families. T3 - ZIB-Report - 16-51 KW - extremal combinatorics, extremal set theory, cutting plane, exact integer programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60626 SN - 1438-0064 ER - TY - CHAP A1 - Wende, Florian A1 - Noack, Matthias A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Zitzlsberger, Georg A1 - Newburn, Chris J. ED - Dutot, Pierre-Francois ED - Trystram, Denis T1 - Portable SIMD Performance with OpenMP* 4.x Compiler Directives N2 - Effective vectorization is becoming increasingly important for high performance and energy efficiency on processors with wide SIMD units. Compilers often require programmers to identify opportunities for vectorization, using directives to disprove data dependences. The OpenMP 4.x SIMD directives strive to provide portability. We investigate the ability of current compilers (GNU, Clang, and Intel) to generate SIMD code for microbenchmarks that cover common patterns in scientific codes and for two kernels from the VASP and the MOM5/ERGOM application. We explore coding strategies for improving SIMD performance across different compilers and platforms (Intel® Xeon® processor and Intel® Xeon Phi™ (co)processor). We compare OpenMP* 4.x SIMD vectorization with and without vector data types against SIMD intrinsics and C++ SIMD types. Our experiments show that in many cases portable performance can be achieved. All microbenchmarks are available as open source as a reference for programmers and compiler experts to enhance SIMD code generation. Y1 - 2016 SN - 978-3-319-43659-3 U6 - https://doi.org/10.1007/978-3-319-43659-3_20 VL - Euro-Par 2016: Parallel Processing: 22nd International Conference on Parallel and Distributed Computing PB - Springer International Publishing ER - TY - JOUR A1 - Villatoro, José A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Weber, Marcus A1 - Riedel, Jens A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector JF - International Journal for Ion Mobility Spectrometry Y1 - 2016 U6 - https://doi.org/10.1007/s12127-016-0208-1 IS - 19/4 SP - 197 EP - 297 ER - TY - GEN A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Burger, Sven A1 - Gutsche, Philipp A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Sigmund, Ole A1 - Mork, Jesper A1 - Gregersen, Niels T1 - Comparison of four computational methods for computing Q factors and resonance wavelengths in photonic crystal membrane cavities T2 - Proceedings of the 7th International Conference on Metamaterials, Photonic Crystals and Plasmonics Y1 - 2016 UR - http://jakobrdl.dk/presentationfiles/2016/META16Poster_Niels_July2016.pdf ER - TY - THES A1 - Sali, Adrian T1 - Coupling of Monodomain and Eikonal Models for Cardiac Electrophysiology N2 - The primary goal of this paper is to study the coupling of monodomain and eikonal models for the numerical simulation of cardiac electrophysiology. Eikonal models are nonlinear elliptic equations describing the excitation time of the cardiac tissue. They are often used as very fast approximations for monodomain or bidomain models - parabolic reaction-diffusion systems describing the excitation wavefront in terms of ionic currents. The excitation front is a thin region with high gradients, whereas excitation times vary over larger domains. Hence, eikonal equations can be solved on much coarser grids than monodomain equations. Moreover, as eikonal models are not time-dependent, no time integration is needed. Eikonal models are derived from monodomain models making additional assumptions and using certain approximations. While generally the approximation is rather good, several specific situations are not well captured by eikonal models. We consider coupling the two models, i.e. using the monodomain model in regions where more accurate results or the shape of the wavefront are needed, and the eikonal model in the remaining parts of the domain, where the excitation time is sufficient. Restricting the monodomain simulation to a small subdomain reduces the computational effort considerably. Numerical methods for the simulation of the individual models are presented, with the finite element method as the main ingredient. Coupling conditions as well as algorithms for implementing the coupling are explained. The approximation quality and efficiency of the coupled model is illustrated on simple geometries using an Aliev-Panfilov membrane model. Y1 - 2016 ER - TY - GEN A1 - Sali, Adrian T1 - Coupling of Monodomain and Eikonal Models for Cardiac Electrophysiology N2 - The primary goal of this paper is to study the coupling of monodomain and eikonal models for the numerical simulation of cardiac electrophysiology. Eikonal models are nonlinear elliptic equations describing the excitation time of the cardiac tissue. They are often used as very fast approximations for monodomain or bidomain models - parabolic reaction-diffusion systems describing the excitation wavefront in terms of ionic currents. The excitation front is a thin region with high gradients, whereas excitation times vary over larger domains. Hence, eikonal equations can be solved on much coarser grids than monodomain equations. Moreover, as eikonal models are not time-dependent, no time integration is needed. Eikonal models are derived from monodomain models making additional assumptions and using certain approximations. While generally the approximation is rather good, several specific situations are not well captured by eikonal models. We consider coupling the two models, i.e. using the monodomain model in regions where more accurate results or the shape of the wavefront are needed, and the eikonal model in the remaining parts of the domain, where the excitation time is sufficient. Restricting the monodomain simulation to a small subdomain reduces the computational effort considerably. Numerical methods for the simulation of the individual models are presented, with the finite element method as the main ingredient. Coupling conditions as well as algorithms for implementing the coupling are explained. The approximation quality and efficiency of the coupled model is illustrated on simple geometries using an Aliev-Panfilov membrane model. T3 - ZIB-Report - 16-50 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60508 SN - 1438-0064 ER - TY - GEN A1 - Fischer, Frank A1 - Grimm, Boris A1 - Klug, Torsten A1 - Schlechte, Thomas T1 - A Re-optimization Approach for Train Dispatching N2 - The Train Dispatching Problem (TDP) is to schedule trains through a network in a cost optimal way. Due to disturbances during operation existing track allocations often have to be re-scheduled and integrated into the timetable. This has to be done in seconds and with minimal timetable changes to guarantee smooth and conflict free operation. We present an integrated modeling approach for the re-optimization task using Mixed Integer Programming. Finally, we provide computational results for scenarios provided by the INFORMS RAS Problem Soling Competition 2012. T3 - ZIB-Report - 16-49 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60493 SN - 1438-0064 ER - TY - GEN A1 - Dean, Mason N. A1 - Hosny, Ahmed A1 - Seidel, Ronald A1 - Baum, Daniel T1 - Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth T2 - Poster, Tomography for Scientific Advancement symposium (ToScA) Y1 - 2016 ER - TY - CHAP A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Pedroso, João Pedro A1 - Rehfeldt, Daniel A1 - Schwarz, Robert A1 - Serrano, Felipe T1 - PySCIPOpt: Mathematical Programming in Python with the SCIP Optimization Suite T2 - Mathematical Software – ICMS 2016 N2 - SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42432-3_37 VL - 9725 SP - 301 EP - 307 PB - Springer ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Maher, Stephen J. T1 - Reduction Techniques for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem N2 - The concept of reduction has frequently distinguished itself as a pivotal ingredient of exact solving approaches for the Steiner tree problem in graphs. In this paper we broaden the focus and consider reduction techniques for three Steiner problem variants that have been extensively discussed in the literature and entail various practical applications: The prize-collecting Steiner tree problem, the rooted prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem. By introducing and subsequently deploying numerous new reduction methods, we are able to drastically decrease the size of a large number of benchmark instances, already solving more than 90 percent of them to optimality. Furthermore, we demonstrate the impact of these techniques on exact solving, using the example of the state-of-the-art Steiner problem solver SCIP-Jack. T3 - ZIB-Report - 16-47 KW - Steiner tree problems KW - reduction techniques KW - prize-collecting Steiner tree problem KW - maximum-weight connected subgraph problem Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60420 SN - 1438-0064 ER - TY - GEN A1 - Becker, Pascal-Nicolas A1 - Bertelmann, Roland A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Heidrich, Regina A1 - Höhnow, Tobias A1 - Kassube, Michael A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Landes, Lilian A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schobert, Dagmar A1 - Schwab, Oliver A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Stoyanova, Tonka A1 - Vierkant, Paul T1 - Questionnaire for effective exchange of bibliographic metadata – current status of publishing houses N2 - The project DeepGreen aims to realise better usage of green open access publication rights with regard to Alliance Licenses in Germany (https://www.nationallizenzen.de/open-access). Together with publishers who offer Alliance Licenses and authorized libraries, the project group intends to develop a prototype of a nearly fully automated workflow that covers the delivery of data from the publishers, including the article full texts, as well as the process of loading data into the institutional repositories of licensees. Further information about the project can be found within ZIB-Report 15-58, urn:nbn:de:0297-zib-56799. In order to become acquainted with publishers’ processes for exchanging documents and metadata, the project group developed a questionnaire for an online survey. The publishing of this questionnaire is intended to demonstrate relevant aspects of the issue (e. g. methods of data exchange, protocols and interfaces) and to foster reuse of valuable questionnaire elements. The XML-file can be reused as a template, the PDF-file reproduces the original survey layout. KW - Open Access KW - Open Access KW - Questionnaire Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60419 N1 - This work is in the public domain: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. https://creativecommons.org/publicdomain/zero/1.0/ ER - TY - GEN A1 - Achterberg, Tobias A1 - Bixby, Robert E. A1 - Gu, Zonghao A1 - Rothberg, Edward A1 - Weninger, Dieter T1 - Presolve Reductions in Mixed Integer Programming N2 - Mixed integer programming has become a very powerful tool for modeling and solving real-world planning and scheduling problems, with the breadth of applications appearing to be almost unlimited. A critical component in the solution of these mixed-integer programs is a set of routines commonly referred to as presolve. Presolve can be viewed as a collection of preprocessing techniques that reduce the size of and, more importantly, improve the ``strength'' of the given model formulation, that is, the degree to which the constraints of the formulation accurately describe the underlying polyhedron of integer-feasible solutions. As our computational results will show, presolve is a key factor in the speed with which we can solve mixed-integer programs, and is often the difference between a model being intractable and solvable, in some cases easily solvable. In this paper we describe the presolve functionality in the Gurobi commercial mixed-integer programming code. This includes an overview, or taxonomy of the different methods that are employed, as well as more-detailed descriptions of several of the techniques, with some of them appearing, to our knowledge, for the first time in the literature. T3 - ZIB-Report - 16-44 KW - integer programming KW - presolving KW - Gurobi Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60370 SN - 1438-0064 ER - TY - GEN A1 - Tesch, Alexander T1 - Exact Energetic Reasoning in O(n^2 log^2 n) N2 - In this paper, we address the Energetic Reasoning propagation rule for the Cumulative Scheduling Problem (CuSP). An energetic reasoning propagation algorithm is called exact, if it computes the maximum possible energetic reasoning propagation for all the jobs. The currently best known exact energetic reasoning algorithm has complexity O(n^3). In this paper, we present a new exact energetic reasoning propagation algorithm with improved complexity of O(n^2 \log^2 n). T3 - ZIB-Report - 16-46 KW - Cumulative Scheduling KW - Energetic Reasoning KW - Sweep Line KW - Constraint Programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60367 SN - 1438-0064 N1 - Preprint Version ER - TY - GEN A1 - Witzig, Jakob A1 - Beckenbach, Isabel A1 - Eifler, Leon A1 - Fackeldey, Konstantin A1 - Gleixner, Ambros A1 - Grever, Andreas A1 - Weber, Marcus T1 - Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes N2 - In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst. T3 - ZIB-Report - 16-39 KW - Non-reversible Markov Processes KW - NESS KW - Mixed-Integer Programming KW - Markov State Models Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60353 SN - 1438-0064 ER - TY - CHAP A1 - Igde, Sinaida A1 - Wölk, Hendrik A1 - Röblitz, Susanna A1 - Reidelbach, Marco A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC T2 - Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015 N2 - Multivalent sugar/protein interactions are well-known to proceed through different binding modes 1-5 which in turn can be described by their binding kinetics 3-5. This study provides additional insight into the association and dissociation reaction rates of complex multivalent sugar/protein interactions. Binding kinetics of recently introduced multivalent precision glycomacromolecules 6-8 to Concanavalin A (Con A) were studied by " kinetic Isothermal Titration Calorimetry " (kinITC) 9-11. The effect of multivalency is evaluated by comparing rate constants of glycomacromolecules obtaining the same and different valency of mannose ligands and by variation of the overall backbone properties, such as hydrophilic/ hydrophoboc. In addition, binding kinetics were studied using different conformations of Con A (homodimer vs.-tetramer) and thus a different protein valency. Our results show that precision glycomacromolecule/Con A binding proceeds non-cooperatively. Further, association and dissociation rates are mainly described by intermolecular complex formation. Together with the so-called functional valency, we can discriminate between " bound " and " unbound " states for macroscopic on-and off-rates, even for such complex glycooligomer/protein systems. By comparing e.g. a mono-to a divalent glycomacromolecule for their binding to dimeric Con A, we see a lower dissociation rate for the latter. As both bind monovalently to Con A, this is a strong indication for a statistical rebinding event. Further, there is a strong dependence of multivalent binding kinetics on the ligand density of glycomacromolecules as well as the Con A conformation and thus the overall on-and off-rates. Y1 - 2015 ER - TY - CHAP A1 - Schade, Stanley A1 - Strehler, Martin ED - Goerigk, Marc ED - Werneck, Renato T1 - The Maximum Flow Problem for Oriented Flows T2 - 16th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2016) N2 - In several applications of network flows, additional constraints have to be considered. In this paper, we study flows, where the flow particles have an orientation. For example, cargo containers with doors only on one side and train coaches with 1st and 2nd class compartments have such an orientation. If the end position has a mandatory orientation, not every path from source to sink is feasible for routing or additional transposition maneuvers have to be made. As a result, a source-sink path may visit a certain vertex several times. We describe structural properties of optimal solutions, determine the computational complexity, and present an approach for approximating such flows. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0030-drops-65318 UR - http://drops.dagstuhl.de/opus/volltexte/2016/6531 SN - 978-3-95977-021-7 SN - 2190-6807 N1 - Keywords: network flow with orientation, graph expansion, approximation, container logistics, train routing VL - 54 SP - 1 EP - 13 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika A1 - Löbel, Fabian T1 - The Modulo Network Simplex with Integrated Passenger Routing N2 - Periodic timetabling is an important strategic planning problem in public transport. The task is to determine periodic arrival and departure times of the lines in a given network, minimizing the travel time of the passengers. We extend the modulo network simplex method, a well-established heuristic for the periodic timetabling problem, by integrating a passenger (re)routing step into the pivot operations. Computations on real-world networks show that we can indeed find timetables with much shorter total travel time, when we take the passengers' travel paths into consideration. T3 - ZIB-Report - 16-43 KW - periodic timetabling, modulo network simplex, passenger routing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60319 SN - 1438-0064 ER - TY - JOUR A1 - Witzig, Jakob A1 - Beckenbach, Isabel A1 - Eifler, Leon A1 - Fackeldey, Konstantin A1 - Gleixner, Ambros A1 - Grever, Andreas A1 - Weber, Marcus T1 - Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes JF - Multiscale Modeling and Simulation N2 - In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst. KW - Markov State Models KW - NESS KW - Non-reversible Markov Processes KW - Mixed-Integer Programming Y1 - 2018 U6 - https://doi.org/10.1137/16M1091162 SN - 1438-0064 VL - 16 IS - 1 SP - 248 EP - 265 ER - TY - CHAP A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Kaier, Anton A1 - Schienle, Adam A1 - Schlechte, Thomas A1 - Schlobach, Swen ED - Marc, Goerigk T1 - Solving Time Dependent Shortest Path Problems on Airway Networks Using Super-Optimal Wind T2 - 16th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2016) N2 - We study the Flight Planning Problem for a single aircraft, which deals with finding a path of minimal travel time in an airway network. Flight time along arcs is affected by wind speed and direction, which are functions of time. We consider three variants of the problem, which can be modeled as, respectively, a classical shortest path problem in a metric space, a time-dependent shortest path problem with piecewise linear travel time functions, and a time-dependent shortest path problem with piecewise differentiable travel time functions. The shortest path problem and its time-dependent variant have been extensively studied, in particular, for road networks. Airway networks, however, have different characteristics: the average node degree is higher and shortest paths usually have only few arcs. We propose A* algorithms for each of the problem variants. In particular, for the third problem, we introduce an application-specific "super-optimal wind" potential function that overestimates optimal wind conditions on each arc, and establish a linear error bound. We compare the performance of our methods with the standard Dijkstra algorithm and the Contraction Hierarchies (CHs) algorithm. Our computational results on real world instances show that CHs do not perform as well as on road networks. On the other hand, A* guided by our potentials yields very good results. In particular, for the case of piecewise linear travel time functions, we achieve query times about 15 times shorter than CHs. Y1 - 2016 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2016.12 VL - 54 ER - TY - CHAP A1 - Hoppmann, Heide T1 - An Extended Formulation for the Line Planning Problem T2 - Operations Research Proceedings 2015 N2 - In this paper we present a novel extended formulation for the line planning problem that is based on what we call “configurations” of lines and frequencies. Configurations account for all possible options to provide a required transportation capacity on an infrastructure edge. The proposed configuration model is strong in the sense that it implies several facet-defining inequalities for the standard model: set cover, symmetric band, MIR, and multicover inequalities. These theoretical findings can be confirmed in computational results. Further, we show how this concept can be generalized to define configurations for subsets of edges; the generalized model implies additional inequalities from the line planning literature. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42902-1_2 SP - 11 EP - 17 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Separation of Cycle Inequalities for the Periodic Timetabling Problem T2 - 24th Annual European Symposium on Algorithms (ESA 2016) N2 - Cycle inequalities play an important role in the polyhedral study of the periodic timetabling problem. We give the first pseudo-polynomial time separation algorithm for cycle inequalities, and we give a rigorous proof for the pseudo-polynomial time separability of the change-cycle inequalities. The efficiency of these cutting planes is demonstrated on real-world instances of the periodic timetabling problem. Y1 - 2016 U6 - https://doi.org/10.4230/LIPIcs.ESA.2016.21 VL - 57 ER - TY - JOUR A1 - Humpola, Jesco A1 - Serrano, Felipe T1 - Sufficient pruning conditions for MINLP in gas network design JF - EURO Journal on Computational Optimization N2 - One-quarter of Europe’s energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euros per kilometer the extension of the European pipeline network is already a multi-billion Euro business. Therefore, automatic planning tools that support the decision process are desired. We model the topology optimization problem in gas networks by a mixed-integer nonlinear program (MINLP). This gives rise to a so-called active transmission problem, a continuous nonlinear non-convex feasibility problem which emerges from the MINLP model by fixing all integral variables. We offer novel sufficient conditions for proving the infeasibility of this active transmission problem. These conditions can be expressed in the form of a mixed-integer program (MILP), i.e., the infeasibility of a non-convex continuous nonlinear program (NLP) can be certified by solving an MILP. This result provides an efficient pruning procedure in a branch-and-bound algorithm. Our computational results demonstrate a substantial speedup for the necessary computations. Y1 - 2017 U6 - https://doi.org/10.1007/s13675-016-0077-8 VL - 5 IS - 1-2 SP - 239 EP - 261 PB - Springer Berlin Heidelberg ER - TY - GEN A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Cameron--Martin theorems for sequences of Cauchy-distributed random variables N2 - Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences. T3 - ZIB-Report - 16-40 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60230 SN - 1438-0064 ER - TY - THES A1 - Tesch, Alexander T1 - Compact MIP Models for the Resource-Constrained Project Scheduling Problem N2 - In the Resource-Constrained Project Scheduling Problem (RCPSP) a set of jobs is planned subject to resource- and precedence constraints. The objective is to minimize the makespan, that is the time when all jobs have been completed. There exist several Mixed-Integer-Programming (MIP) models in order to solve the problem. Most common models are based on time-discretization. In this case, the scheduling horizon is split into unit size intervals and each job gets assigned a unique starting interval. The drawback of time-discrete models is the computational intractability for large scheduling horizons or fine discretizations. In this connection, this thesis deals with compact MIP models where the model size is independent of the scheduling horizon. In addition to two compact models from the literature, we present two new compact models. We investigate their induced polyhedra and deduce an inclusion hierarchy via linear transformations. Moreover, we give a combinatorial interpretation of these transformations. Furthermore, we study a class of valid cutting planes for the compact models, which are known as cover inequalities. In order to strengthen these cutting planes we introduce a lifting algorithm that is independent of the model size. Subsequently, we examine lower bounds for the RCPSP from linear programming. Based on a linear transformation, we reveal a connection between two approaches from the literature. For one model we generate strong cutting planes that are obtained from a primal-dual relation between the models. Two cutting plane algorithms are derived. Likewise, we show that similar cutting planes can be transferred to the compact MIP models. Our models have been implemented, tested and evaluated on the instances of the PSPLIB problem library. KW - Resource-Constrained Project Scheduling KW - Compact MIP Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60208 ER - TY - GEN A1 - Krone, Michael A1 - Kozlikova, Barbora A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Parulek, Julius A1 - Hege, Hans-Christian A1 - Viola, Ivan T1 - Visual Analysis of Biomolecular Cavities: State of the Art N2 - In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field. T3 - ZIB-Report - 16-42 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60193 SN - 1438-0064 ER - TY - JOUR A1 - Abass, Aimi A1 - Gutsche, Philipp A1 - Maes, Bjorn A1 - Rockstuhl, Carsten A1 - Martins, Emiliano R T1 - Insights into directional scattering: from coupled dipoles to asymmetric dimer nanoantennas JF - Opt. Express N2 - Strong and directionally specific forward scattering from optical nanoantennas is of utmost importance for various applications in the broader context of photovoltaics and integrated light sources. Here, we outline a simple yet powerful design principle to perceive a nanoantenna that provides directional scattering into a higher index substrate based on the interference of multiple electric dipoles. A structural implementation of the electric dipole distribution is possible using plasmonic nanoparticles with a fairly simple geometry, i.e. two coupled rectangular nanoparticles, forming a dimer, on top of a substrate. The key to achieve directionality is to choose a sufficiently large size for the nanoparticles. This promotes the excitation of vertical electric dipole moments due to the bi-anisotropy of the nanoantenna. In turn, asymmetric scattering is obtained by ensuring the appropriate phase relation between the vertical electric dipole moments. The scattering strength and angular spread for an optimized nanoantenna can be shown to be broadband and robust against changes in the incidence angle. The scattering directionality is maintained even for an array configuration of the dimer. It only requires the preferred scattering direction of the isolated nanoantenna not to be prohibited by interference. Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.019638 VL - 24 IS - 17 SP - 19638 EP - 19650 ER - TY - GEN A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack – A solver for STP and variants with parallelization extensions N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. T3 - ZIB-Report - 16-41 KW - Steiner tree problem KW - SCIP-Jack KW - Steiner tree variants KW - maximum-weight connected subgraph KW - prize-collecting Steiner tree Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60170 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Arslan, Oytun A1 - Elijazyfer, Ziena A1 - Güler, Hakan A1 - Renken, Malte A1 - Sahin, Güvenc A1 - Schlechte, Thomas T1 - Line Planning on Path Networks with Application to the Istanbul Metrobüs N2 - Bus rapid transit systems in developing and newly industrialized countries often consist of a trunk with a path topology. On this trunk, several overlapping lines are operated which provide direct connections. The demand varies heavily over the day, with morning and afternoon peaks typically in reverse directions. We propose an integer programming model for this problem, derive a structural property of line plans in the static (or single period) ``unimodal demand'' case, and consider approaches to the solution of the multi-period version that rely on clustering the demand into peak and off-peak service periods. An application to the Metrobüs system of Istanbul is discussed. T3 - ZIB-Report - 16-38 KW - line planning KW - unimodal demand Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60119 SN - 1438-0064 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Passenger routing for periodic timetable optimization BT - Planning and Operations JF - Public Transport N2 - The task of periodic timetabling is to determine trip arrival and departure times in a public transport system such that travel and transfer times are minimized. This paper investigates periodic timetabling models with integrated passenger routing. We show that different routing models can have a huge influence on the quality of the entire system: Whatever metric is applied, the performance ratios of timetables w.r.t. different routing models can be arbitrarily large. Computations on a real-world instance for the city of Wuppertal substantiate the theoretical findings. These results indicate the existence of untapped optimization potentials that can be used to improve the efficiency of public transport systems by integrating passenger routing. Y1 - 2016 U6 - https://doi.org/10.1007/s12469-016-0132-0 PB - Springer-Verlag Berlin Heidelberg ER - TY - THES A1 - Lieser, Philippe T1 - Ende-zu-Ende Verschlüsselung in XtreemFS Y1 - 2016 ER - TY - GEN A1 - Nielsen, Adam T1 - The Monte Carlo Computation Error of Transition Probabilities N2 - In many applications one is interested to compute transition probabilities of a Markov chain. This can be achieved by using Monte Carlo methods with local or global sampling points. In this article, we analyze the error by the difference in the $L^2$ norm between the true transition probabilities and the approximation achieved through a Monte Carlo method. We give a formula for the error for Markov chains with locally computed sampling points. Further, in the case of reversible Markov chains, we will deduce a formula for the error when sampling points are computed globally. We will see that in both cases the error itself can be approximated with Monte Carlo methods. As a consequence of the result, we will derive surprising properties of reversible Markov chains. T3 - ZIB-Report - 16-37 KW - Reversible Markov chain KW - Monte Carlo methods KW - Computation error KW - Measurable state space KW - Markov operator Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59933 SN - 1438-0064 ER - TY - JOUR A1 - Nielsen, Adam T1 - The Monte Carlo Computation Error of Transition Probabilities JF - Statistics & Probability Letters N2 - In many applications one is interested to compute transition probabilities of a Markov chain. This can be achieved by using Monte Carlo methods with local or global sampling points. In this article, we analyze the error by the difference in the $L^2$ norm between the true transition probabilities and the approximation achieved through a Monte Carlo method. We give a formula for the error for Markov chains with locally computed sampling points. Further, in the case of reversible Markov chains, we will deduce a formula for the error when sampling points are computed globally. We will see that in both cases the error itself can be approximated with Monte Carlo methods. As a consequence of the result, we will derive surprising properties of reversible Markov chains. Y1 - 2016 U6 - https://doi.org/10.1016/j.spl.2016.06.011 VL - 118 SP - 163 EP - 170 PB - Elsevier ER - TY - CHAP A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - 3D Reconstruction, Visualization and Quantification of Dislocations from Transmission Electron Microscopy Stereo-Pairs T2 - Microscopy and Microanalysis 2016, July 24-28 Columbus, Ohio Y1 - 2016 UR - https://www.microscopy.org/MandM/2016/program/abstracts/PDP-57.pdf ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schenker, Sebastian A1 - Skutella, Martin A1 - Strunk, Timo ED - Greuel, G.-M. ED - Koch, Thorsten ED - Paule, Peter ED - Sommese, Andrew T1 - PolySCIP T2 - Mathematical Software – ICMS 2016, 5th International Conference, Berlin, Germany, July 11-14, 2016, Proceedings N2 - PolySCIP is a new solver for multi-criteria integer and multi-criteria linear programs handling an arbitrary number of objectives. It is available as an official part of the non-commercial constraint integer programming framework SCIP. It utilizes a lifted weight space approach to compute the set of supported extreme non-dominated points and unbounded non-dominated rays, respectively. The algorithmic approach can be summarized as follows: At the beginning an arbitrary non-dominated point is computed (or it is determined that there is none) and a weight space polyhedron created. In every next iteration a vertex of the weight space polyhedron is selected whose entries give rise to a single-objective optimization problem via a combination of the original objectives. If the ptimization of this single-objective problem yields a new non-dominated point, the weight space polyhedron is updated. Otherwise another vertex of the weight space polyhedron is investigated. The algorithm finishes when all vertices of the weight space polyhedron have been investigated. The file format of PolySCIP is based on the widely used MPS format and allows a simple generation of multi-criteria models via an algebraic modelling language. Y1 - 2016 SN - 978-3-319-42431-6 U6 - https://doi.org/10.1007/978-3-319-42432-3_32 VL - 9725 SP - 259 EP - 264 PB - Springer International Publishing ET - Mathematical Software – ICMS 2016 ER - TY - THES A1 - Hammerschmidt, Martin T1 - Optical simulation of complex nanostructured solar cells with a reduced basis method N2 - Simulations of optical processes and complex nanostructured devices have become omnipresent in recent years in several fields of current research and industrial applications, not limited to the field of photovoltaics. Devices or processes are optimized with respect to a certain objective where the underlying physical processes are described by partial differential equations. In photovoltaics and photonics electromagnetic fields are investigated which are governed by Maxwell’s equations. In this thesis a reduced basis method for the solution of the parameter dependent electromagnetic scattering problem with arbitrary parameters is developed. The method is developed with the specific challenges arising in optical simulations of thin-film silicon solar cells in mind. These are large in domain size and have a complex three-dimensional structure, making optimization tasks infeasible if high-accuracy of the electromagnetic field solution is required. The application of the empirical interpolation methods allows to expand an arbitrary parameter dependence affinely. Thus not only geometries, but also material tensors and source fields can be parameterized. Additionally, the required non-linear post-processing steps of the electromagnetic field to derive energy fluxes or volume absorption are addressed. The reduced basis method allows to reduce the computational costs by orders of magnitude compared to efficient finite element solvers. In addition, an efficient tailored domain decomposition algorithm is presented to model incoherent layers or illuminations in optical systems efficiently. This is of particular interest for solar cells in superstrate configuration where the absorber is illuminated through a glass substrate. The developed methods are employed in application examples taken from collaborations with experimentalists active in the joint lab “BerOSE” (Berlin Joint Lab for Optical Simulations for Energy Research). The optical model of a thin-film silicon multi-junction with incoherent light-trapping is characterized in great detail. The computational gains through hybrid, hp adaptive finite elements are studied and the incoherent domain decomposition algorithm is applied to model a more realistic light-trapping by the glass substrate. The numerical examples of a hexagonal nano-hole array and multi-junction silicon solar cell with a tunable intermediate reflector layer show that the reduced basis method is well suited as a forward solver for modeling and optimization tasks arising in photovoltaics and photonics. Reduced models for illumination and geometric parameters are built providing up to five orders of magnitude savings in computational costs. Resonance phenomena present in the nano-hole array example are detected and the model adapts itself automatically. KW - reduced basis method; model reduction; electromagnetics; photonics; solar cells; nanooptics; Maxwells equations; incoherence Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102429-1 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000102429 ER - TY - JOUR A1 - Soltwisch, Victor A1 - Haase, Anton A1 - Wernecke, Jan A1 - Probst, Jürgen A1 - Schoengen, Max A1 - Burger, Sven A1 - Krumrey, Michael A1 - Scholze, Frank T1 - Correlated diffuse x-ray scattering from periodically nanostructured surfaces JF - Phys. Rev. B Y1 - 2016 U6 - https://doi.org/10.1103/PhysRevB.94.035419 VL - 94 SP - 035419 ER - TY - CHAP A1 - Schäfer, Stefan A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Mathematical Modelling of Follicular Maturation in Cows and Women T2 - 49. Jahrestagung der Physiologie und Pathologie der Fortpflanzung und gleichzeitig 41. Veterinär-Humanmedizinische Gemeinschaftstagung 2016, Leipzig. Y1 - 2016 ER - TY - JOUR A1 - Reimers, Jeffrey R. A1 - Biczysko, Malgorzata A1 - Bruce, Douglas A1 - Coker, David F. A1 - Frankcombe, Terry J. A1 - Hashimoto, Hideki A1 - Hauer, Jürgen A1 - Jankowiak, Ryszard A1 - Kramer, Tobias A1 - Linnanto, Juha A1 - Mamedov, Fikret A1 - Müh, Frank A1 - Rätsep, Margus A1 - Renger, Thomas A1 - Styring, Stenbjörn A1 - Wan, Jian A1 - Wang, Zhuan A1 - Wang-Otomo, Zheng-Yu A1 - Weng, Yu-Xiang A1 - Yang, Chunhong A1 - Zhang, Jian-Ping A1 - Freiberg, Arvi A1 - Krausz, Elmars T1 - Challenges facing an understanding of the nature of low-energy excited states in photosynthesis JF - BBA Bioenergetics N2 - While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding. Y1 - 2016 U6 - https://doi.org/10.1016/j.bbabio.2016.06.010 VL - 1857 IS - 9 SP - 1627 EP - 1640 ER - TY - JOUR A1 - Dunlop, Jason A1 - Apanaskevich, Dmitry A1 - Lehmann, Jens A1 - Hoffmann, Rene A1 - Fusseis, Florian A1 - Ehlke, Moritz A1 - Zachow, Stefan A1 - Xiao, Xianghui T1 - Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus JF - BMC Evolutionary Biology N2 - Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases. Y1 - 2016 U6 - https://doi.org/10.1186/s12862-016-0777-y VL - 16 IS - 1 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Transformations for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem to SAP N2 - Transformations of Steiner tree problem variants have been frequently discussed in the literature. Besides allowing to easily transfer complexity results, they constitute a central pillar of exact state-of-the-art solvers for well-known variants such as the Steiner tree problem in graphs. In this paper transformations for both the prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem to the Steiner arborescence problem are introduced for the first time. Furthermore, we demonstrate the considerable implications for practical solving approaches, including the computation of strong upper and lower bounds. T3 - ZIB-Report - 16-36 KW - graph transformation KW - Steiner tree problems KW - prize-collecting Steiner tree problem KW - maximum-weight connected subgraph problem Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59777 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2015 T3 - Jahresbericht - 2015 KW - Jahresbericht Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59748 SN - 0934-5892 VL - 2015 ER - TY - GEN A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Effective Dynamics Along Given Reaction Coordinates, and Reaction Rate Theory N2 - In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the ”equation-free” approach and the ”heterogeneous multiscale method” can be seen as special cases of our approach. T3 - ZIB-Report - 16-35 KW - Ergodic diffusion KW - reaction coordinate KW - effective dynamics KW - model reduction KW - equation-free KW - heterogeneous multiscale method Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59706 SN - 1438-0064 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Berthold, Timo A1 - Müller, Benjamin A1 - Weltge, Stefan T1 - Three Enhancements for Optimization-Based Bound Tightening JF - Journal of Global Optimization N2 - Optimization-based bound tightening (OBBT) is one of the most effective procedures to reduce variable domains of nonconvex mixed-integer nonlinear programs (MINLPs). At the same time it is one of the most expensive bound tightening procedures, since it solves auxiliary linear programs (LPs)—up to twice the number of variables many. The main goal of this paper is to discuss algorithmic techniques for an efficient implementation of OBBT. Most state-of-the-art MINLP solvers apply some restricted version of OBBT and it seems to be common belief that OBBT is beneficial if only one is able to keep its computational cost under control. To this end, we introduce three techniques to increase the efficiency of OBBT: filtering strategies to reduce the number of solved LPs, ordering heuristics to exploit simplex warm starts, and the generation of Lagrangian variable bounds (LVBs). The propagation of LVBs during tree search is a fast approximation to OBBT without the need to solve auxiliary LPs. We conduct extensive computational experiments on MINLPLib2. Our results indicate that OBBT is most beneficial on hard instances, for which we observe a speedup of 17% to 19% on average. Most importantly, more instances can be solved when using OBBT. Y1 - 2017 U6 - https://doi.org/10.1007/s10898-016-0450-4 VL - 67 IS - 4 SP - 731 EP - 757 ER - TY - JOUR A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases JF - Neuron N2 - Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.06.012 VL - 91 IS - 2 SP - 293 EP - 311 ER - TY - GEN A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases N2 - Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish. T3 - ZIB-Report - 16-34 KW - neuroinformatics KW - NBLAST KW - neuron similarity KW - cell type KW - clustering Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59672 SN - 1438-0064 ER - TY - JOUR A1 - Krone, Michael A1 - Kozlíková, Barbora A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Parulek, Julius A1 - Hege, Hans-Christian A1 - Viola, Ivan T1 - Visual Analysis of Biomolecular Cavities: State of the Art JF - Computer Graphics Forum N2 - In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12928 SN - 1467-8659 VL - 35 IS - 3 SP - 527 EP - 551 ER - TY - JOUR A1 - Kramer, Tobias A1 - Kreisbeck, Christoph A1 - Riha, Christian A1 - Chiatti, Olivio A1 - Buchholz, Sven A1 - Wieck, Andreas A1 - Reuter, Dirk A1 - Fischer, Saskia T1 - Thermal energy and charge currents in multi-terminal nanorings JF - AIP Advances N2 - We study in experiment and theory thermal energy and charge transfer close to the quantum limit in a ballistic nanodevice, consisting of multiply connected one-dimensional electron waveguides. The fabricated device is based on an AlGaAs/GaAs heterostructure and is covered by a global top-gate to steer the thermal energy and charge transfer in the presence of a temperature gradient, which is established by a heating current. The estimate of the heat transfer by means of thermal noise measurements shows the device acting as a switch for charge and thermal energy transfer. The wave-packet simulations are based on the multi-terminal Landauer-Büttiker approach and confirm the experimental finding of a mode-dependent redistribution of the thermal energy current, if a scatterer breaks the device symmetry. Y1 - 2016 U6 - https://doi.org/10.1063/1.4953812 VL - 6 SP - 065306 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Hege, Hans-Christian A1 - Weiser, Martin T1 - Using sparse kernels to design computer experiments with tunable precision N2 - Statistical methods to design computer experiments usually rely on a Gaussian process (GP) surrogate model, and typically aim at selecting design points (combinations of algorithmic and model parameters) that minimize the average prediction variance, or maximize the prediction accuracy for the hyperparameters of the GP surrogate. In many applications, experiments have a tunable precision, in the sense that one software parameter controls the tradeoff between accuracy and computing time (e.g., mesh size in FEM simulations or number of Monte-Carlo samples). We formulate the problem of allocating a budget of computing time over a finite set of candidate points for the goals mentioned above. This is a continuous optimization problem, which is moreover convex whenever the tradeoff function accuracy vs. computing time is concave. On the other hand, using non-concave weight functions can help to identify sparse designs. In addition, using sparse kernel approximations drastically reduce the cost per iteration of the multiplicative weights updates that can be used to solve this problem. T3 - ZIB-Report - 16-33 KW - Optimal design of computer experiments KW - Sparse kernels KW - Gaussian Process Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59605 SN - 1438-0064 ER - TY - CHAP A1 - Baum, Daniel A1 - Titschack, Jürgen T1 - Cavity and Pore Segmentation in 3D Images with Ambient Occlusion T2 - EuroVis 2016 - Short Papers Y1 - 2016 U6 - https://doi.org/10.2312/eurovisshort.20161171 PB - The Eurographics Association ER - TY - JOUR A1 - Titschack, Jürgen A1 - Fink, Hiske G. A1 - Baum, Daniel A1 - Wienberg, Claudia A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Mediterranean cold-water corals - an important regional carbonate factory? JF - The Depositional Record Y1 - 2016 U6 - https://doi.org/10.1002/dep2.14 VL - 2 IS - 1 SP - 74 EP - 96 ER - TY - GEN A1 - Becker, Pascal-Nicolas A1 - Bertelmann, Roland A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Heidrich, Regina A1 - Höhnow, Tobias A1 - Kassube, Michael A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Landes, Lilian A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schobert, Dagmar A1 - Schwab, Oliver A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Stoyanova, Tonka A1 - Vierkant, Paul T1 - DeepGreen – Metadata Schema for the exchange of publications between publishers and open access repositories. Version 1.1. June 2016 N2 - In 2011, important priorities were set to realize green publications in the open access movement in Germany. With financial support from the German Research Foundation (DFG), libraries negotiated Alliance licenses with publishers that guarantee extensive open access rights. Authors of institutions, that have therewith access to licensed journals, can freely publish their articles immediately or after a short embargo period in a repository of their choice. However, authors hesitantly use these open access rights. Also libraries – as managers of institutional and subject based repositories and thus legitimated representatives for the authors – only rarely make use of these rights. The aim of DeepGreen is to make the majority of those publications available online. Together with publishers of the Alliance licenses, the project consortium wants to develop a nearly fully automated workflow that covers both the delivery of data, including the full texts, of the publishers, as well as the data transformation to the necessary import formats and the loading process into the repositories. An intermediate “publication router” will serve as a distribution platform. The DeepGreen metadata schema contains metadata properties describing a wide range of deliverable bibliographic metadata from the Alliance license publishers (most common standards are JATS and CrossRef XML) as well as its compliance with technical, quality and metadata standards of the repositories. The schema includes required metadata elements and optional properties providing additional information.The metadata schema is aligned to the OCLC repository best practices (“Best Practices for CONTENTdm and other OAI-PMH compliant repositories: creating sharable metadata”, URL: http://www.oclc.org/content/dam/support/wcdigitalcollectiongateway/MetadataBestPractices.pdf). The current version of the schema is subject to changes as the functional requirements and workflow practices are evolving during the project experiences and prototype production. T3 - ZIB-Report - 16-32 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59580 SN - 1438-0064 N1 - This work is in the public domain: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. https://creativecommons.org/publicdomain/zero/1.0/ ER - TY - JOUR A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Erdmann, Bodo A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Heinrich, Andreas A1 - Güttler, Felix Victor A1 - Teichgräber, Ulf A1 - Mall, Gita T1 - Automatic CT-based finite element model generation for temperature-based death time estimation: feasibility study and sensitivity analysis JF - International Journal of Legal Medicine N2 - Temperature based death time estimation is based either on simple phenomenological models of corpse cooling or on detailed physical heat transfer models. The latter are much more complex, but allow a higher accuracy of death time estimation as in principle all relevant cooling mechanisms can be taken into account. Here, a complete work flow for finite element based cooling simulation models is presented. The following steps are demonstrated on CT-phantoms: • CT-scan • Segmentation of the CT images for thermodynamically relevant features of individual geometries • Conversion of the segmentation result into a Finite Element (FE) simulation model • Computation of the model cooling curve • Calculation of the cooling time For the first time in FE-based cooling time estimation the steps from the CT image over segmentation to FE model generation are semi-automatically performed. The cooling time calculation results are compared to cooling measurements performed on the phantoms under controlled conditions. In this context, the method is validated using different CTphantoms. Some of the CT phantoms thermodynamic material parameters had to be experimentally determined via independent experiments. Moreover the impact of geometry and material parameter uncertainties on the estimated cooling time is investigated by a sensitivity analysis. KW - temperature based death time estimation KW - finite element method KW - CT segmentation KW - sensitivity analysis Y1 - 2017 U6 - https://doi.org/doi:10.1007/s00414-016-1523-0 VL - 131 IS - 3 SP - 699 EP - 712 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Schwartz, Stephan T1 - An Extended Network Interdiction Problem for Optimal Toll Control T2 - INOC 2015 – 7th International Network Optimization Conference N2 - We study an extension of the shortest path network interdiction problem and present a novel real-world application in this area. We consider the problem of determining optimal locations for toll control stations on the arcs of a transportation network. We handle the fact that drivers can avoid control stations on parallel secondary roads. The problem is formulated as a mixed integer program and solved using Benders decomposition. We present experimental results for the application of our models to German motorways. Y1 - 2016 U6 - https://doi.org/10.1016/j.endm.2016.03.040 VL - 52 SP - 301 EP - 308 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Harman, Radoslav T1 - Computing exact D-optimal designs by mixed integer second-order cone programming JF - The Annals of Statistics N2 - Let the design of an experiment be represented by an $s-$dimensional vector $w$ of weights with nonnegative components. Let the quality of $w$ for the estimation of the parameters of the statistical model be measured by the criterion of $D-$optimality, defined as the $m$th root of the determinant of the information matrix $M(w)=\sum_{i=1}^s w_i A_i A_i^T$, where $A_i$,$i=1,\ldots,s$ are known matrices with $m$ rows. In this paper, we show that the criterion of $D-$optimality is second-order cone representable. As a result, the method of second-order cone programming can be used to compute an approximate $D-$optimal design with any system of linear constraints on the vector of weights. More importantly, the proposed characterization allows us to compute an exact $D-$optimal design, which is possible thanks to high-quality branch-and-cut solvers specialized to solve mixed integer second-order cone programming problems. Our results extend to the case of the criterion of $D_K-$optimality, which measures the quality of $w$ for the estimation of a linear parameter subsystem defined by a full-rank coefficient matrix $K$. We prove that some other widely used criteria are also second-order cone representable, for instance, the criteria of $A-$, $A_K$-, $G-$ and $I-$optimality. We present several numerical examples demonstrating the efficiency and general applicability of the proposed method. We show that in many cases the mixed integer second-order cone programming approach allows us to find a provably optimal exact design, while the standard heuristics systematically miss the optimum. Y1 - 2015 U6 - https://doi.org/10.1214/15-AOS1339 VL - 43 IS - 5 SP - 2198 EP - 2224 ER - TY - CHAP A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume A1 - Oliveira, Nuno M.C. T1 - A Robust Minimax Semidefinite Programming Formulation for Optimal Design of Experiments for Model Parametrization T2 - 12th International Symposium on Process Systems Engineering and 25th European Symposium on Computer Aided Process Engineering N2 - Model-based optimal design of experiments (M-bODE) is a crucial step in model parametrization since it encloses a framework that maximizes the amount of information extracted from a battery of lab experiments. We address the design of M-bODE for dynamic models considering a continuous representation of the design. We use Semidefinite Programming (SDP) to derive robust minmax formulations for nonlinear models, and extend the formulations to other criteria. The approaches are demonstrated for a CSTR where a two-step reaction occurs. Y1 - 2015 U6 - https://doi.org/10.1016/B978-0-444-63578-5.50146-8 VL - 37 SP - 905 EP - 910 ER - TY - GEN A1 - Cockayne, Jon A1 - Oates, Chris A1 - Sullivan, T. J. A1 - Girolami, Mark T1 - Probabilistic Meshless Methods for Partial Differential Equations and Bayesian Inverse Problems N2 - This paper develops a class of meshless methods that are well-suited to statistical inverse problems involving partial differential equations (PDEs). The methods discussed in this paper view the forcing term in the PDE as a random field that induces a probability distribution over the residual error of a symmetric collocation method. This construction enables the solution of challenging inverse problems while accounting, in a rigorous way, for the impact of the discretisation of the forward problem. In particular, this confers robustness to failure of meshless methods, with statistical inferences driven to be more conservative in the presence of significant solver error. In addition, (i) a principled learning-theoretic approach to minimise the impact of solver error is developed, and (ii) the challenging setting of inverse problems with a non-linear forward model is considered. The method is applied to parameter inference problems in which non-negligible solver error must be accounted for in order to draw valid statistical conclusions. T3 - ZIB-Report - 16-31 KW - Probabilistic Numerics KW - Partial Differential Equations KW - Inverse Problems KW - Meshless Methods KW - Gaussian Processes KW - Pseudo-Marginal MCMC Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59513 SN - 1438-0064 ER - TY - GEN A1 - Brandt, Christopher A1 - Tycowicz, Christoph von A1 - Hildebrandt, Klaus T1 - Geometric Flows of Curves in Shape Space for Processing Motion of Deformable Objects N2 - We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in R^n to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear “Bézier curves” by executing de Casteljau’s algorithm in shape space. T3 - ZIB-Report - 16-29 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59504 SN - 1438-0064 ER - TY - THES A1 - Kammeyer, Alexander T1 - Evaluierung autovektorisierender Compiler anhand von Schleifenklassen N2 - Modern CPU architectures require the use of vector instructions to fully exploit the available performance. State-of-the art compilers offer means to automatically vectorize program code. In this thesis these compilers are assessed on test cases and their capabilities to auto\-{}vectorize are evaluated to show strengths and weaknesses of the compilers. Run time measurements and vectorizations are compared to another and recommendations depending on the use case are presented. N2 - Moderne CPU-Architekturen erfordern die Verwendung von Vektorinstruktionen, um die vorhandene Leistung vollständig auszuschöpfen. Aktuelle Compiler bieten Möglichkeiten zur automatischen Vektorisierung von Programmcode. Im Rahmen dieser Arbeit werden an Testfällen verschiedene Compiler auf ihre Fähigkeiten zur Autovektorisierung getestet und evaluiert, um Stärken und Schwächen der jeweiligen Compiler aufzuzeigen. Es werden Laufzeitergebnisse und Vektorisierungsvermögen miteinander verglichen und eine Empfehlung in Abhängigkeit des jeweiligen Anwendungsfalls gegeben. Y1 - 2016 ER - TY - GEN A1 - Amrhein, Kilian A1 - Hasler, Tim A1 - Klindt, Marco A1 - Oltmanns, Elias A1 - Peters-Kottig, Wolfgang T1 - Digitale Langzeitarchivierung: Mustervorlage für Übernahmevereinbarungen N2 - Digitale Langzeitarchivierung erfolgt auf Grundlage verbindlicher Regelungen zwischen Langzeitarchiv und Datengeber. Detaillierte organisatorische und technische Bedingungen für Datenübernahmen werden dabei in Absprache zwischen den Kooperationspartnern in einer Übernahmevereinbarung festgehalten. Im Rahmen der Entwicklung des Langzeitarchivs EWIG am Zuse Institute Berlin ist die hier dokumentierte Mustervorlage für Übernahmevereinbarungen entstanden. T3 - ZIB-Report - 16-27 KW - digital preservation KW - submission agreement KW - digitale Langzeitarchivierung KW - KOBV KW - digiS Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59452 SN - 1438-0064 ER - TY - CHAP A1 - Wende, Florian A1 - Marsman, Martijn A1 - Steinke, Thomas T1 - On Enhancing 3D-FFT Performance in VASP T2 - CUG Proceedings Y1 - 2016 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/Churyumov-Gerasimenko JF - The Astrophysical Journal Letters N2 - The Rosetta probe around comet 67P/Churyumov–Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localized emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case; the neck region of the bi-lobed nucleus of 67P is an example of the latter case. The conjunction of multiple sources, in addition to dust released from all other sunlit areas, results in a high correlation coefficient (~0.8) of the predictions with observations during a complete diurnal rotation period of 67P. Y1 - 2016 U6 - https://doi.org/10.3847/2041-8205/823/1/L11 VL - 823 IS - 1 SP - L11 ER - TY - GEN A1 - Sullivan, T. J. T1 - Well-posed Bayesian inverse problems and heavy-tailed stable Banach space priors N2 - This article extends the framework of Bayesian inverse problems in infinite-dimensional parameter spaces, as advocated by Stuart (Acta Numer. 19:451–559, 2010) and others, to the case of a heavy-tailed prior measure in the family of stable distributions, such as an infinite-dimensional Cauchy distribution, for which polynomial moments are infinite or undefined. It is shown that analogues of the Karhunen–Loève expansion for square-integrable random variables can be used to sample such measures. Furthermore, under weaker regularity assumptions than those used to date, the Bayesian posterior measure is shown to depend Lipschitz continuously in the Hellinger metric upon perturbations of the misfit function and observed data. T3 - ZIB-Report - 16-30 KW - Bayesian inverse problems KW - heavy-tailed distribution KW - Karhunen–Loève expansion KW - stable distribution KW - uncertainty quantification KW - well-posedness Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59422 SN - 1438-0064 ER - TY - CHAP A1 - Schmidtke, Robert A1 - Laubender, Guido A1 - Steinke, Thomas T1 - Big Data Analytics on Cray XC Series DataWarp using Hadoop, Spark and Flink T2 - CUG Proceedings Y1 - 2016 ER - TY - GEN A1 - Vigerske, Stefan A1 - Gleixner, Ambros T1 - SCIP: Global Optimization of Mixed-Integer Nonlinear Programs in a Branch-and-Cut Framework N2 - This paper describes the extensions that were added to the constraint integer programming framework SCIP in order to enable it to solve convex and nonconvex mixed-integer nonlinear programs (MINLPs) to global optimality. SCIP implements a spatial branch-and-bound algorithm based on a linear outer-approximation, which is computed by convex over- and underestimation of nonconvex functions. An expression graph representation of nonlinear constraints allows for bound tightening, structure analysis, and reformulation. Primal heuristics are employed throughout the solving process to find feasible solutions early. We provide insights into the performance impact of individual MINLP solver components via a detailed computational study over a large and heterogeneous test set. T3 - ZIB-Report - 16-24 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59377 SN - 1438-0064 ER - TY - GEN A1 - Tesch, Alexander T1 - A Nearly Exact Propagation Algorithm for Energetic Reasoning in O(n^2 log n) N2 - In constraint programming, energetic reasoning constitutes a powerful start time propagation rule for cumulative scheduling problems (CuSP). In this paper, we first present an improved time interval checking algorithm that is derived from a polyhedral model. In a second step, we extend this algorithm to an energetic reasoning propagation algorithm with complexity O(n^2 log n) where n denotes the number of jobs. The key idea is based on a new sweep line subroutine that efficiently evaluates the relevant time intervals for all jobs. In particular, our algorithm yields at least one possible energetic reasoning propagation for each job. Finally, we show that on the vast number of relevant time intervals our approach yields the maximum possible propagation according to the energetic reasoning rule. T3 - ZIB-Report - 16-25 KW - Cumulative Scheduling KW - Energetic Reasoning KW - Sweep Line Algorithm Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59332 SN - 1438-0064 ER - TY - THES A1 - Wenzel, Ron T1 - On the In-Flight Rest Assignment Problem N2 - The airplane has changed the world in a tremendous way. Efficient scheduling of airmen and aircrafts is of considerable importance for cost-effectiveness of compa- nies. Attentiveness of flight crew members is vital as fatigue can lead to severe accidents. Therefore, duty times of flight crews are strictly limited. Long distance flights may be difficult to schedule with only one set of crew members. Furthermore, pertu- bations of the schedules may entail exchanging the entire crew, which confounds multiday schedules. A new EU regulation introduced in-flight rest: a schedule may extend pilots’ duty times if they rest for a certain time in designated crew compart- ments provided aboard airplanes. Of course they have to be replaced in that period of time. This thesis examines the in-flight rest assignment problem, which is the decision problem whether a given schedule allows for all crew members to take their compul- sory rest. The problem can be seen as multimachine scheduling problem. Efficient algorithms for special cases were developed and an alternative approach for entire hard cases is discussed. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59328 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Sinusoidal gratings for optimized light management in c-Si thin-film solar cells JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2225459 VL - 9898 SP - 989808 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Balzer, Felix A1 - Borndörfer, Ralf A1 - Spies, Claudia A1 - von Dincklage, Falk T1 - Makespan and Tardiness in Activity Networks with Lognormal Activity Durations N2 - We propose an algorithm to approximate the distribution of the completion time (makespan) and the tardiness costs of a project, when durations are lognormally distributed. This problem arises naturally for the optimization of surgery scheduling, where it is very common to assume lognormal procedure times. We present an analogous of Clark's formulas to compute the moments of the maximum of a set of lognormal variables. Then, we use moment matching formulas to approximate the earliest starting time of each activity of the project by a shifted lognormal variable. This approach can be seen as a lognormal variant of a state-of-the-art method used for the statistical static timing analysis (SSTA) of digital circuits. We carried out numerical experiments with instances based on real data from the application to surgery scheduling. We obtained very promising results, especially for the approximation of the mean overtime in operating rooms, for which our algorithm yields results of a similar quality to Monte-Carlo simulations requiring an amount of computing time several orders of magnitude larger. T3 - ZIB-Report - 16-23 KW - scheduling KW - activity network KW - lognormal distribution Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59290 SN - 1438-0064 ER - TY - JOUR A1 - Barth, Carlo A1 - Probst, Jürgen A1 - Herrmann, Sven A1 - Hammerschmidt, Martin A1 - Becker, Christiane T1 - Numerical characterization of symmetry properties for photonic crystals with hexagonal lattice JF - Proc. SPIE N2 - We present a numerical method to characterize the symmetry properties of photonic crystal (PhC) modes based on field distributions, which themselves can be obtained numerically. These properties can be used to forecast specific features of the optical response of such systems, e.g. which modes are allowed to couple to external radiation fields. We use 2D PhCs with a hexagonal lattice of holes in dielectric as an example and apply our technique to reproduce results from analytical considerations. Further, the method is extended to fully vectorial problems in view of 3D PhCs and PhC slabs, its functionality is demonstrated using test cases and, finally, we provide an efficient implementation. The technique can thus readily be applied to output data of all band structure computation methods or even be embedded – gaining additional information about the mode symmetry. Y1 - 2016 U6 - https://doi.org/10.1117/12.2227094 VL - 9885 SP - 988506 ER - TY - JOUR A1 - Barth, Carlo A1 - Burger, Sven A1 - Becker, Christiane T1 - Symmetry-Dependency of Anticrossing Phenomena in Slab-Type Photonic Crystals JF - Opt. Express Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.010931 VL - 24 SP - 10931 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko N2 - We compute trajectories of dust grains starting from a homogeneous surface activity-profile on a irregularly shaped cometary nucleus. Despite the initially homogeneous dust distribution a collimation in jet-like structures becomes visible. The fine structure is caused by concave topographical features with similar bundles of normal vectors. The model incorporates accurately determined gravitational forces, rotation of the nucleus, and gas-dust interaction. Jet-like dust structures are obtained for a wide range of gas-dust interactions. For the comet 67P/Churyumov-Gerasimenko, we derive the global dust distribution around the nucleus and find several areas of agreement between the homogeneous dust emission model and the Rosetta observation of dust jets, including velocity-dependent bending of trajectories. Y1 - 2015 ER - TY - GEN A1 - Kramer, Tobias A1 - Noack, Matthias T1 - On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/Churyumov-Gerasimenko. N2 - The Rosetta probe around comet 67P/Churyumov-Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localised emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case, the neck region of the bilobed nucleus of 67P for the latter one. The conjunction of multiple sources in addition to dust released from all other sunlit areas results in a high correlation coefficient (∼0.8) of the predictions with observations during a complete diurnal rotation period of 67P. T3 - ZIB-Report - 16-26 KW - comet KW - 67p Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59225 SN - 1438-0064 ER - TY - CHAP A1 - Jäger, Klaus A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane ED - European Society for Quantum Solar Energy Conversion, T1 - Sinusoidal Nanotextures for Enhanced Light Management in Thin-Film Solar Cells T2 - 28th Workshop on Quantum Solar Energy Conversion - (QUANTSOL) Y1 - 2016 ER - TY - GEN A1 - Hahn, Helene ED - digiS - Servicestelle Digitalisierung Berlin, T1 - Kooperativ in die digitale Zeit - wie öffentliche Kulturinstitutionen Cultural Commons fördern N2 - Viele Kulturinstitutionen nutzen bereits die Möglichkeiten, die ihnen die Digitalisierung und das Internet bieten. Bestände werden digitalisiert und digital aufbereitet, ganze Kunstgattungen gibt es bereits digital. Im heutigen 21. Jahrhundert existieren viele Kultureinrichtungen, wie Museen, Archive und Bibliotheken, bereits seit 100 Jahren oder länger. Doch was ist notwendig, um Institutionen, die vor der Erfindung des Fernsehens etabliert wurden, in der heutigen von Technologien bestimmten Welt bei ihren gesellschaftlichen Aufgaben zu unterstützen? Der vorliegende Text gibt eine Einführung in offene Kulturdaten und zeigt Möglichkeiten auf, wie Kultureinrichtungen von der offenen Bereitstellung ihrer digitalen Bestände profitieren und durch neue Kooperationen kulturinteressierte Menschen stärker an sich binden können. Es wird erklärt, was die Cultural Commons ausmacht und wie Kulturinstitutionen bei der Öffnung ihrer Daten vorgehen können. Um den gesellschaftlichen und institutionellen Wert frei nutzbarer Sammlungsbestände zu verdeutlichen, werden realisierte Projekte basierend auf offenen Kulturdaten im lokalen und internationalen Kontext vorgestellt. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59131 ER - TY - GEN A1 - Baum, Daniel A1 - Titschack, Jürgen T1 - Cavity and Pore Segmentation in 3D Images with Ambient Occlusion N2 - Many natural objects contain pores and cavities that are filled with the same material that also surrounds the object. When such objects are imaged using, for example, computed tomography, the pores and cavities cannot be distinguished from the surrounding material by considering gray values and texture properties of the image. In this case, morphological operations are often used to fill the inner region. This is efficient, if the pore and cavity structures are small compared to the overall size of the object and if the object’s shape is mainly convex. If this is not the case, the segmentation might be very difficult and may result in a lot of noise. We propose the usage of ambient occlusion for the segmentation of pores and cavities. One nice property of ambient occlusion is that it generates smooth scalar fields. Due to this smoothness property, a segmentation based on those fields will result in smooth boundaries at the pore and cavity openings. This is often desired, particularly when dealing with natural objects. T3 - ZIB-Report - 16-17 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59151 SN - 1438-0064 ER - TY - THES A1 - Tack, Alexander T1 - Gruppenweise Registrierung zur robusten Bewegungsfeldschätzung in artefaktbehafteten 4D-CT-Bilddaten N2 - Das Ziel der Strahlentherapie ist, eine möglichst hohe Dosis in den Tumor zu applizieren und zeitgleich die Strahlenexposition des Normalgewebes zu minimieren. Insbesondere bei thorakalen und abdominalen Tumoren treten aufgrund der Atmung während der Bestrahlung große, komplexe und patientenspezifisch unterschiedliche Bewegungen der Gewebe auf. Um den Einfluss dieser Bewegung auf die i.d.R. statisch geplante Dosisverteilung abzuschätzen, können unter Verwendung der nicht-linearen Bildregistrierung anhand von 3D-CT-Aufnahmen eines Atmungszyklus - also 4D-CT-Daten - zunächst die Bewegungsfelder für die strahlentherapeutisch relevanten Strukturen, beispielsweise für die Lunge, berechnet werden. Diese Informationen bilden die Grundlage für sogenannte 4D-Dosisberechnungs- oder Dosisakkumulationsverfahren. Deren Genauigkeit hängt aber wesentlich von der Genauigkeit der Bewegungsfeldschätzung ab. Klassisch erfolgt die Berechnung der Bewegungsfelder mittels paarweiser Bildregistrierung, womit für die Berechnung des Bewegungsfeldes zwischen zwei Bildern im Allgemeinen eine sehr hohe Genauigkeit erreicht wird. Auch für CT-Bilder, die Bewegungsartefakte, wie beispielsweise doppelte oder unvollständige Strukturen, enthalten, wird unter Verwendung der paarweisen Bildregistrierung im Kontext der Registrierung eine exakte Abbildung der anatomischen Strukturen zwischen den beiden Bildern erreicht. Dabei erfolgt aber eine physiologisch unplausible Anpassung der Felder an die Artefakte. Bei Verwendung der paarweisen Bildregistrierung müssen weiterhin für einen Atemzyklus die Voxel-Trajektorien aus Bewegungsfeldern zwischen mehreren dreidimensionalen Bildern zusammengesetzt werden. Durch Bewegungsartefakte entsprechen diese Trajektorien dann teilweise keiner natürlichen Bewegung der anatomischen Strukturen. Diese Ungenauigkeit stellt in der klinischen Anwendung ein Problem dar; dies gilt umso mehr, wenn Bewegungsartefakte im Bereich eines Tumors vorliegen. Im Gegensatz zu der paarweisen Registrierung kann mit der gruppenweisen Registrierung das Problem der durch Bewegungsartefakte hervorgerufenen ungenauen Abbildung der physiologischen Gegebenheiten dadurch reduziert werden, dass im Registrierungsprozess Bildinformationen aller Bilder, also in diesem Kontext der CT-Daten zu unterschiedlichen Atemphasen, gleichzeitig genutzt werden. Es kann bereits im Registrierungsprozess eine zeitliche Glattheit der Voxel-Trajektorien gefordert werden. In dieser Arbeit wird eine Methode zur B-Spline-basierten zeitlich regularisierten gruppenweisen Registrierung entwickelt. Die Genauigkeit der entwickelten Methode wird für frei zugängliche klinische Datensätze landmarkenbasiert evaluiert. Dabei wird mit dem Target Registration Error (TRE) die durchschnittliche dreidimensionale euklidische Distanz zwischen den korrespondierenden Landmarken nach Transformation der Landmarken bezeichnet. Eine Genauigkeit in der Größenordnung von aktuellen paarweisen Registrierungen verdeutlicht die Qualität des vorgestellten Registrierungs-Algorithmus. Anschließend werden die Vorteile der gruppenweisen Registrierung durch Experimente an einem Lungenphantom und an manipulierten, artefaktbehafteten klinischen 4D-CT-Bilddaten demonstriert. Dabei werden unter Verwendung der gruppenweisen Registrierung im Vergleich zu der paarweisen Registrierung glattere Trajektorien berechnet, die der realen Bewegung der anatomischen Strukturen stärker entsprechen. Für die Patientendaten wird außerdem anhand von automatisch detektierten Landmarken der TRE ausgewertet. Der TRE verschlechterte sich für die paarweise Bildregistrierung unter Vorliegen von Bewegungsartefakten von durchschnittlich 1,30 mm auf 3,94 mm. Auch hier zeigte sich für die gruppenweise Registrierung die Robustheit gegenüber Bewegungsartefakten und der TRE verschlechterte sich nur geringfügig von 1,45 mm auf 1,71 mm. KW - Gruppenweise Registrierung KW - 4D-CT Y1 - 2015 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Gleixner, Ambros T1 - Towards an accurate solution of wireless network design problems T2 - Cerulli R., Fujishige S., Mahjoub A. (eds) Combinatorial Optimization. ISCO 2016 N2 - The optimal design of wireless networks has been widely studied in the literature and many optimization models have been proposed over the years. However, most models directly include the signal-to-interference ratios representing service coverage conditions. This leads to mixed-integer linear programs with constraint matrices containing tiny coefficients that vary widely in their order of magnitude. These formulations are known to be challenging even for state-of-the-art solvers: the standard numerical precision supported by these solvers is usually not sufficient to reliably guarantee feasible solutions. Service coverage errors are thus commonly present. Though these numerical issues are known and become evident even for small-sized instances, just a very limited number of papers has tried to tackle them, by mainly investigating alternative non-compact formulations in which the sources of numerical instabilities are eliminated. In this work, we explore a new approach by investigating how recent advances in exact solution algorithms for linear and mixed-integer programs over the rational numbers can be applied to analyze and tackle the numerical difficulties arising in wireless network design models. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-45587-7_12 SP - 135 EP - 147 ER - TY - GEN A1 - Beckenbach, Isabel A1 - Scheidweiler, Robert T1 - Perfect f-Matchings and f-Factors in Hypergraphs - A Combinatorial Approach N2 - We prove characterizations of the existence of perfect f-matchings in uniform mengerian and perfect hypergraphs. Moreover, we investigate the f-factor problem in balanced hypergraphs. For uniform balanced hypergraphs we prove two existence theorems with purely combinatorial arguments, whereas for non-uniform balanced hypergraphs we show that the f-factor problem is NP-hard. T3 - ZIB-Report - 16-22 KW - perfect f-matchings in hypergraphs KW - f-factors in hypergraphs KW - mengerian hypergraph KW - balanced hypergraph KW - perfect hypergraph KW - Hall's Theorem Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59071 SN - 1438-0064 ER - TY - GEN A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields N2 - Traditionally, Lagrangian fields such as finite-time Lyapunov exponents (FTLE) are precomputed on a discrete grid and are ray casted afterwards. This, however, introduces both grid discretization errors and sampling errors during ray marching. In this work, we apply a progressive, view-dependent Monte Carlo-based approach for the visualization of such Lagrangian fields in time-dependent flows. Our ap- proach avoids grid discretization and ray marching errors completely, is consistent, and has a low memory consumption. The system provides noisy previews that con- verge over time to an accurate high-quality visualization. Compared to traditional approaches, the proposed system avoids explicitly predefined fieldline seeding structures, and uses a Monte Carlo sampling strategy named Woodcock tracking to distribute samples along the view ray. An acceleration of this sampling strategy requires local upper bounds for the FTLE values, which we progressively acquire during the rendering. Our approach is tailored for high-quality visualizations of complex FTLE fields and is guaranteed to faithfully represent detailed ridge surface structures as indicators for Lagrangian coherent structures (LCS). We demonstrate the effectiveness of our approach by using a set of analytic test cases and real-world numerical simulations. T3 - ZIB-Report - 16-21 KW - Picture/Image Generation, Display algorithms, Three-Dimensional Graphics and Realism, Raytracing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59054 SN - 1438-0064 N1 - By mistake the fourth author Hans-Christian Hege has been ommitted in the journal publication ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Gleixner, Ambros T1 - Towards an accurate solution of wireless network design problems N2 - The optimal design of wireless networks has been widely studied in the literature and many optimization models have been proposed over the years. However, most models directly include the signal-to-interference ratios representing service coverage conditions. This leads to mixed-integer linear programs with constraint matrices containing tiny coefficients that vary widely in their order of magnitude. These formulations are known to be challenging even for state-of-the-art solvers: the standard numerical precision supported by these solvers is usually not sufficient to reliably guarantee feasible solutions. Service coverage errors are thus commonly present. Though these numerical issues are known and become evident even for small-sized instances, just a very limited number of papers has tried to tackle them, by mainly investigating alternative non-compact formulations in which the sources of numerical instabilities are eliminated. In this work, we explore a new approach by investigating how recent advances in exact solution algorithms for linear and mixed-integer programs over the rational numbers can be applied to analyze and tackle the numerical difficulties arising in wireless network design models. T3 - ZIB-Report - 16-12 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59010 SN - 1438-0064 ER - TY - THES A1 - Schöpke, Jessica T1 - Korrelation für lineare und nichtlineare Zusammenhänge Y1 - 2015 ER - TY - THES A1 - Lange, Christoph T1 - Approximating and Clustering Markov Chains via Kullback-Leibler-Divergence Y1 - 2015 ER - TY - THES A1 - Zwingel, Oliver T1 - Die Cross-Entropy-Methode für stochastische Optimierungsprobleme Y1 - 2015 ER - TY - THES A1 - Mett, Fabian T1 - The Connected Facility Location Problem Y1 - 2015 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Felici, Giovanni A1 - Lacalandra, Fabrizio T1 - Multiband Robust Optimization for optimal energy offering under price uncertainty T2 - Proc. of ROADEF 2016 N2 - We consider the problem of a price-taker generating company that wants to select energy offering strategies for its generation units, to maximize the profit while considering the uncertainty of market price. First, we review central references available in literature about the use of Robust Optimization (RO) for price-uncertain energy offering, pointing out how they can expose to the risk of suboptimal and even infeasible offering. We then propose a new RO method for energy offering that overcomes all the limits of other RO methods. We show the effectiveness of the new method on realistic instances provided by our industrial partners, getting very high increases in profit. Our method is based on Multiband Robustness (MR - Büsing, D'Andreagiovanni, 2012), an RO model that refines the classical RO model by Bertsimas and Sim, while maintaining its computational tractability and accessibility. MR is essentially based on the use of histogram-like uncertainty sets, which result particularly suitable to represent empirical distributions commonly available in uncertain real-world optimization problems. Y1 - 2016 ER - TY - JOUR A1 - Leitner, Markus A1 - Ljubic, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - ILP heuristics and a new exact method for bi-objective 0/1 ILPs: Application to FTTx-network design JF - Computers & Operations Research Y1 - 2016 U6 - https://doi.org/10.1016/j.cor.2016.02.006 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Mett, Fabian A1 - Pulaj, Jonad T1 - An (MI)LP-based Primal Heuristic for 3-Architecture Connected Facility Location in Urban Access Network Design T2 - EvoApplications: European Conference on the Applications of Evolutionary Computation. Applications of Evolutionary Computation. 19th European Conference, EvoApplications 2016, Porto, Portugal, March 30 -- April 1, 2016, Proceedings, Part I N2 - We investigate the 3-architecture Connected Facility Location Problem arising in the design of urban telecommunication access networks integrating wired and wireless technologies. We propose an original optimization model for the problem that includes additional variables and constraints to take into account wireless signal coverage represented through signal-to-interference ratios. Since the problem can prove very challenging even for modern state-of-the art optimization solvers, we propose to solve it by an original primal heuristic that combines a probabilistic fixing procedure, guided by peculiar Linear Programming relaxations, with an exact MIP heuristic, based on a very large neighborhood search. Computational experiments on a set of realistic instances show that our heuristic can find solutions associated with much lower optimality gaps than a state-of-the-art solver. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-31204-0_19 VL - 9597 SP - 283 EP - 298 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - Generation of multiple best solutions in multiobjective optimal design of energy supply systems T2 - Proceedings of the 15th International Conference on Power Engineering. ICOPE 2015 N2 - Optimization approaches based on the mixed-integer linear programming (MILP) have been utilized to design energy supply systems. In this paper, an MILP method utilizing the hierarchical relationship between design and operation is extended to search not only the optimal solution but also suboptimal ones which follow the optimal one without any omissions, what are called K-best solutions, efficiently in a multiobjective optimal design problem. At the upper level, the values of design variables for the K-best solutions are searched by the branch and bound method. At the lower level, the values of operation variables are optimized independently at each period by the branch and bound method under the values of design variables given tentatively. Incumbents for the K-best solutions and an upper bound for all the values of the objective function for the K-best solutions are renewed if necessary between both the levels. This method is implemented into a commercial MILP solver. A practical case study on the multiobjective optimal design of a cogeneration system is conducted, and the validity and effectiveness of the method are clarified. Y1 - 2015 U6 - https://doi.org/10.1299/jsmeicope.2015.12._ICOPE-15-_56 ER - TY - CHAP A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael T1 - Solving Open MIP Instances with ParaSCIP on Supercomputers using up to 80,000 Cores T2 - Proc. of 30th IEEE International Parallel & Distributed Processing Symposium N2 - This paper describes how we solved 12 previously unsolved mixed-integer program- ming (MIP) instances from the MIPLIB benchmark sets. To achieve these results we used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper we describe the basic parallelization mechanism of ParaSCIP, improvements of the dynamic load balancing and novel techniques to exploit the power of parallelization for MIP solving. We give a detailed overview of computing times and statistics for solving open MIPLIB instances. Y1 - 2016 U6 - https://doi.org/10.1109/IPDPS.2016.56 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Iterative Refinement for Linear Programming JF - INFORMS Journal on Computing N2 - We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the objective function, right-hand side, and variable bounds. Exact computation is used to compute and store the exact representation of the transformed problems, while numeric computation is used for solving LPs. At all steps of the algorithm the LP bases encountered in the transformed problems correspond directly to LP bases in the original problem description. We show that this algorithm is effective in practice for computing extended precision solutions and that it leads to a direct improvement of the best known methods for solving LPs exactly over the rational numbers. Our implementation is publically available as an extension of the academic LP solver SoPlex. Y1 - 2016 U6 - https://doi.org/10.1287/ijoc.2016.0692 VL - 28 IS - 3 SP - 449 EP - 464 ER - TY - CHAP A1 - Hendel, Gregor T1 - Exploiting Solving Phases for Mixed-Integer Programs T2 - Operations Research Proceedings 2015 N2 - Modern MIP solving software incorporates dozens of auxiliary algorithmic components for supporting the branch-and-bound search in finding and improving solutions and in strengthening the relaxation. Intuitively, a dynamic solving strategy with an appropriate emphasis on different solving components and strategies is desirable during the search process. We propose an adaptive solver behavior that dynamically reacts on transitions between the three typical phases of a MIP solving process: The first phase objective is to find a feasible solution. During the second phase, a sequence of incumbent solutions gets constructed until the incumbent is eventually optimal. Proving optimality is the central objective of the remaining third phase. Based on the MIP-solver SCIP, we demonstrate the usefulness of the phase concept both with an exact recognition of the optimality of a solution, and provide heuristic alternatives to make use of the concept in practice. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42902-1_1 SP - 3 EP - 9 ER - TY - THES A1 - Wyczisk, Christopher T1 - Portfoliooptimierung mittels mathematischer Optimierung Y1 - 2016 ER - TY - THES A1 - Gleixner, Ambros T1 - Exact and Fast Algorithms for Mixed-Integer Nonlinear Programming N2 - Mixed-integer nonlinear programming (MINLP) comprises the broad class of finite-dimensional mathematical optimization problems from mixed-integer linear programming and global optimization. The combination of the two disciplines allows us to construct more accurate models of real-world systems, while at the same time it increases the algorithmic challenges that come with solving them. This thesis presents new methods that improve the numerical reliability and the computational performance of global MINLP solvers. Since state-of-the-art algorithms for nonconvex MINLP fundamentally rely on solving linear programming (LP) relaxations, we address numerical accuracy directly for LP by means of LP iterative refinement: a new algorithm to solve linear programs to arbitrarily high levels of precision. The thesis is supplemented by an exact extension of the LP solver SoPlex, which proves on average 1.85 to 3 times faster than current state-of-the-art software for solving general linear programs exactly over the rational numbers. These methods can be generalized to quadratic programming. We study their application to numerically difficult multiscale LP models for metabolic networks in systems biology. To improve the computational performance of LP-based MINLP solvers, we show how the expensive, but effective, bound-tightening technique called optimization-based bound tightening can be approximated more efficiently via feasibility-based bound tightening. The resulting implementation increases the number of instances that can be solved and reduces the average running time of the MINLP solver SCIP by 17-19% on hard mixed-integer nonlinear programs. Last, we present branching rules that exploit the presence of nonlinear integer variables, i.e., variables both contained in nonlinear terms and required to be integral. The new branching rules prefer integer variables when performing spatial branching, and favor variables in nonlinear terms when resolving integer infeasibility. They reduce the average running time of SCIP by 17% on affected instances. Most importantly, all of the new methods enable us to solve problems which could not be solved before, either due to their numerical complexity or because of limited computing resources. Y1 - 2015 UR - http://dx.doi.org/10.14279/depositonce-4938 SN - 978-3-8325-4190-3 PB - Logos Verlag Berlin ER - TY - THES A1 - Gupta, Pooja T1 - Integrating high-density marker information into the genetic evaluation of the honey bee Y1 - 2013 ER - TY - THES A1 - Krenz, Konstantin T1 - How likely is it that one’s standing on a ridge? Probabilistic Ridges in Gaussian Random Fields N2 - A method is developed for computing the local probability for the presence of a ridge in a Gaussian Random field. KW - Uncertainty quantification, Gaussian random fields, ridge, feature detection Y1 - 2016 ER - TY - THES A1 - Meier, Annett T1 - Monte-Carlo-Verfahren zur Niedrig-Rang Approximation Y1 - 2015 ER - TY - THES A1 - Röhl, Susanne T1 - Kondition des Eigenwertproblems von Markov-Ketten Y1 - 2015 ER - TY - JOUR A1 - Brandt, Christopher A1 - Tycowicz, Christoph von A1 - Hildebrandt, Klaus T1 - Geometric Flows of Curves in Shape Space for Processing Motion of Deformable Objects JF - Computer Graphics Forum N2 - We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in Rn to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear Bézier curves by executing de Casteljau's algorithm in shape space. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12832 VL - 35 IS - 2 ER - TY - CHAP A1 - Schewe, Lars A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Pfetsch, Marc T1 - Mathematical optimization for evaluating gas network capacities T2 - Evaluating Gas Network Capacities Y1 - 2015 SN - 9781611973686 SP - 87 EP - 102 PB - Society for Industrial and Applied Mathematics ER - TY - CHAP A1 - Bargmann, Dagmar A1 - Ebbers, Mirko A1 - Heinecke, Nina A1 - Koch, Thorsten A1 - Kühl, Veronika A1 - Pelzer, Antje A1 - Pfetsch, Marc A1 - Rövekamp, Jessica A1 - Spreckelsen, Klaus T1 - State-of-the-art in evaluating gas network capacities T2 - Evaluating Gas Network Capacities Y1 - 2015 SN - 9781611973686 SP - 65 EP - 84 PB - Society for Industrial and Applied Mathematics ER - TY - CHAP A1 - Koch, Thorsten A1 - Pfetsch, Marc A1 - Rövekamp, Jessica T1 - Introduction T2 - Evaluating Gas Network Capacities Y1 - 2015 SN - 9781611973686 SP - 3 EP - 16 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Krebek, von, Larissa K. S. A1 - Achazi, Andreas J. A1 - Solleder, Marthe A1 - Weber, Marcus A1 - Paulus, Beate A1 - Schalley, Christoph A. T1 - Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements JF - Chem. Eur. J. Y1 - 2016 U6 - https://doi.org/10.1002/chem.201603098 N1 - Has been announced under the title: Cooperativity in Multivalent Binding: A Detailed Experimental and Theoretical Thermochemical Study of Divalent Crown Ether-Ammonium Complexes VL - 22 IS - 43 SP - 15475 EP - 15484 ER - TY - JOUR A1 - Domschke, Pia A1 - Groß, Martin A1 - Hante, Falk M. A1 - Hiller, Benjamin A1 - Schewe, Lars A1 - Schmidt, Martin T1 - Mathematische Modellierung, Simulation und Optimierung von Gastransportnetzwerken JF - gwf - Gas+Energie Y1 - 2015 VL - 156 IS - 11 SP - 880 EP - 885 ER - TY - BOOK A1 - Weiser, Martin T1 - Inside Finite Elements N2 - All relevant implementation aspects of finite element methods are discussed in this book. The focus is on algorithms and data structures as well as on their concrete implementation. Theory is covered as far as it gives insight into the construction of algorithms.Throughout the exercises a complete FE-solver for scalar 2D problems will be implemented in Matlab/Octave. Y1 - 2016 PB - De Gruyter ER - TY - GEN A1 - Bojarovski, Stefan A1 - Hege, Hans-Christian A1 - Lie, Han Cheng A1 - Weber, Marcus T1 - Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales T2 - Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany N2 - Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models. Y1 - 2015 ER - TY - THES A1 - Nielsen, Adam T1 - Computation Schemes for Transfer Operators Y1 - 2016 ER - TY - THES A1 - Sikorski, Alexander T1 - PCCA+ and Its Application to Spatial Time Series Clustering Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58769 ER - TY - CHAP A1 - Jácome, Leonardo Agudo A1 - Eggeler, Gunter A1 - Pöthkow, Kai A1 - Paetsch, Olaf A1 - Hege, Hans-Christian T1 - Three-Dimensional Characterization of Superdislocation Interactions in the High Temperature and Low Stress Creep Regime of Ni-Base Superalloy Single Crystals T2 - Proceedings of CREEP 2015 – 13th International Conference on Creep and Fracture of Engineering Materials and Structures, May 31 – June 4, 2015, Toulouse, France N2 - Monocrystaline Ni-base superalloys are the material of choice for first row blades in jet engine gas turbines. Using a novel visualization tool for 3D reconstruction and visualization of dislocation line segments from stereo-pairs of scanning transmission electron microscopies, the superdislocation substructures in Ni-base superalloy LEK 94 (crept to ε = 26%) are characterized. Probable scenarios are discussed, how these dislocation substructures form. Y1 - 2015 SP - 16 EP - 17 ER - TY - GEN A1 - Sieber, Moritz A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Paschereit, C. Oliver A1 - Oberleithner, Kilian T1 - A Graphical Representation of the Spectral Proper Orthogonal Decomposition T2 - 68th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 22-24, 2015, Boston, MA, USA. N2 - We consider the spectral proper orthogonal decomposition (SPOD) for experimental data of a turbulent swirling jet. This newly introduced method combines the advantages of spectral methods, such as Fourier decomposition or dynamic mode decomposition, with the energy-ranked proper orthogonal decomposition (POD). This poster visualizes how the modal energy spectrum transitions from the spectral purity of Fourier space to the sparsity of POD space. The transition is achieved by changing a single parameter – the width of the SPOD filter. Each dot in the 3D space corresponds to an SPOD mode pair, where the size and color indicates its spectral coherence. What we notice is that neither the Fourier nor the POD spectrum achieves a clear separation of the dynamic phenomena. Scanning through the graph from the front plane (Fourier) to the back plane (POD), we observe how three highly coherent SPOD modes emerge from the dispersed Fourier spectrum and later branch out into numerous POD modes. The spatial properties of these three individual SPOD modes are displayed in the back of the graph using line integral convolution colored by vorticity. The first two modes correspond to single-helical global instabilities that are well known for these flows. Their coexistence, however, has not been observed until now. The third mode is of double- helical shape and has not been observed so far. For this considered data set and many others, the SPOD is superior in identification of coherent structures in turbulent flows. Hopefully, it gives access to new fluid dynamic phenomena and enriches the available methods. Y1 - 2015 ER - TY - JOUR A1 - Willie, Bettina M. A1 - Pap, Thomas A1 - Perka, Carsten A1 - Schmidt, Carsten Oliver A1 - Eckstein, Felix A1 - Arampatzis, Adamantios A1 - Hege, Hans-Christian A1 - Madry, Henning A1 - Vortkamp, Andrea A1 - Duda, Georg T1 - OVERLOAD – Rolle der Gelenküberlastung in der primären Arthrose – Die Krankheitsprogression verstehen und vermeiden JF - Zeitschrift für Rheumatologie N2 - Intakte Gelenke sind eine Voraussetzung für das Funktionieren des Skeletts und die Mobilität im Lebensalltag. Ein gesunder Bewegungsapparat ist die Grundlage für die Funktionsfähigkeit des Herz-Kreislauf-Systems wie auch der Immunabwehr. Bewegungs- und Physiotherapie sowie verschiedene Formen der Patientenaktivität stellen essenzielle klinische Ansätze in der Behandlung von neurodegenerativen Erkrankungen, Schlaganfall, Diabetes und Krebs dar. Kommt es zu degenerativen Veränderungen von Gelenken, bedeutet dies eine wesentliche Beeinträchtigung der Mobilität. Nächtliche Schmerzen und Schlafstörungen treten in fortgeschrittenen Stadien auf und sind besonders belastend. Arthrose wird auch als degenerative Gelenkerkrankung bezeichnet. Sie geht mit Veränderungen in der Struktur und Zusammensetzung des Gelenkknorpels wie auch des verkalkten Knorpels, der subchondralen Kortikalis, der subchondralen Spongiosa, des Meniskus, der Gelenkkapsel und der Synovialis einher, was schließlich zur Degeneration dieser Gewebe führt, aus denen sich die Synovialgelenke zusammensetzen. Y1 - 2015 U6 - https://doi.org/10.1007/s00393-014-1561-2 VL - 74 SP - 618 EP - 621 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Osman, Jan A1 - Mevert, Ricardo A1 - Kertzscher, Ulrich A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Turbulence in blood damage modeling JF - The International Journal of Artificial Organs N2 - Purpose: To account for the impact of turbulence in blood damage modeling, a novel approach based on the generation of instantaneous flow fields from RANS simulations is proposed. Methods: Turbulent flow in a bileaflet mechanical heart valve was simulated using RANS-based (SST k-ω) flow solver using FLUENT 14.5. The calculated Reynolds shear stress (RSS) field is transformed into a set of divergence-free random vector fields representing turbulent velocity fluctuations using procedural noise functions. To consider the random path of the blood cells, instantaneous flow fields were computed for each time step by summation of RSS-based divergence-free random and mean velocity fields. Using those instantaneous flow fields, instantaneous pathlines and corresponding point-wise instantaneous shear stresses were calculated. For a comparison, averaged pathlines based on mean velocity field and respective viscous shear stresses together with RSS values were calculated. Finally, the blood damage index (hemolysis) was integrated along the averaged and instantaneous pathlines using a power law approach and then compared. Results: Using RSS in blood damage modeling without a correction factor overestimates damaging stress and thus the blood damage (hemolysis). Blood damage histograms based on both presented approaches differ. Conclusions: A novel approach to calculate blood damage without using RSS as a damaging parameter is established. The results of our numerical experiment support the hypothesis that the use of RSS as a damaging parameter should be avoided. Y1 - 2016 U6 - https://doi.org/10.5301/ijao.5000476 VL - 39 IS - 4 SP - 147 EP - 210 ER - TY - JOUR A1 - Hermann, Gunter A1 - Pohl, Vincent A1 - Tremblay, Jean Christophe A1 - Paulus, Beate A1 - Hege, Hans-Christian A1 - Schild, Axel T1 - ORBKIT – A modular Python toolbox for cross-platform post-processing of quantum chemical wavefunction data JF - Journal of Computational Chemistry N2 - ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wave function, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT offers routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. Y1 - 2016 U6 - https://doi.org/10.1002/jcc.24358 VL - 37 IS - 16 SP - 1511 EP - 1520 ER - TY - GEN A1 - Mukhopadhyay, Anirban A1 - Kumar, Arun A1 - Bhandarkar, Suchendra T1 - Joint Geometric Graph Embedding for Partial Shape Matching in Images T2 - IEEE Winter Conference on Applications of Computer Vision N2 - A novel multi-criteria optimization framework for matching of partially visible shapes in multiple images using joint geometric graph embedding is proposed. The proposed framework achieves matching of partial shapes in images that exhibit extreme variations in scale, orientation, viewpoint and illumination and also instances of occlusion; conditions which render impractical the use of global contour-based descriptors or local pixel-level features for shape matching. The proposed technique is based on optimization of the embedding distances of geometric features obtained from the eigenspectrum of the joint image graph, coupled with regularization over values of the mean pixel intensity or histogram of oriented gradients. It is shown to obtain successfully the correspondences denoting partial shape similarities as well as correspondences between feature points in the images. A new benchmark dataset is proposed which contains disparate image pairs with extremely challenging variations in viewing conditions when compared to an existing dataset [18]. The proposed technique is shown to significantly outperform several state-of-the-art partial shape matching techniques on both datasets. Y1 - 2016 SP - 1 EP - 9 PB - IEEE ET - IEEE Winter Conference on Applications of Computer Vision (WACV) ER - TY - THES A1 - Sahu, Manish T1 - Instrument Gesture Recognition and Tracking for Effective Control of Laparoscopic Tracking and Guidance Device Y1 - 2016 ER - TY - GEN A1 - Grewe, Carl Martin T1 - 3D Digital Morphology of Human Faces T2 - Anthropologie der Wahrnehmung. Marsilius-Sommerakademie Heidelberg, 14.-20. September Y1 - 2015 ER - TY - JOUR A1 - Fournier, David A1 - Palidwor, Gareth A. A1 - Shcherbinin, Sergey A1 - Szengel, Angelika A1 - Schaefer, Martin H. A1 - Perez-Iratxeta, Carol A1 - Andrade-Navarro, Miguel A. T1 - Functional and Genomic Analyses of Alpha-Solenoid Proteins JF - PLoS ONE Journal N2 - Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0079894 ER - TY - CHAP A1 - Tack, Alexander A1 - Kobayashi, Yuske A1 - Gauer, Tobias A1 - Schlaefer, Alexander A1 - Werner, René T1 - Groupwise Registration for Robust Motion Field Estimation in Artifact-Affected 4D CT Images T2 - ICART: Imaging and Computer Assistance in Radiation Therapy: A workshop held on Friday 9th October as part of MICCAI 2015 in Munich, Germany. MICCAI workshop. 2015. N2 - Precise voxel trajectory estimation in 4D CT images is a prerequisite for reliable dose accumulation during 4D treatment planning. 4D CT image data is, however, often affected by motion artifacts and applying standard pairwise registration to such data sets bears the risk of aligning anatomical structures to artifacts – with physiologically unrealistic trajectories being the consequence. In this work, the potential of a novel non-linear hybrid intensity- and feature-based groupwise registration method for robust motion field estimation in artifact-affected 4D CT image data is investigated. The overall registration performance is evaluated on the DIR-lab datasets; Its robustness if applied to artifact-affected data sets is analyzed using clinically acquired data sets with and without artifacts. The proposed registration approach achieves an accuracy comparable to the state-of-the-art (subvoxel accuracy), but smoother voxel trajectories compared to pairwise registration. Even more important: it maintained accuracy and trajectory smoothness in the presence of image artifacts – in contrast to standard pairwise registration, which yields higher landmark-based registration errors and a loss of trajectory smoothness when applied to artifact-affected data sets. Y1 - 2015 SP - 18 EP - 25 ER - TY - GEN A1 - Tack, Alexander A1 - Kobayashi, Yuske A1 - Gauer, Tobias A1 - Schlaefer, Alexander A1 - Werner, René T1 - Bewegungsfeldschätzung in artefaktbehafteten 4D-CT-Bilddaten: Vergleich von paar- und gruppenweiser Registrierung T2 - 21st Annual Meeting of the German-Society-for-Radiation-Oncology N2 - In der Strahlentherapie von Lungentumoren kann mittels Dosisakkumulation der Einfluss von Atembewegungen auf statisch geplante Dosisverteilungen abgeschätzt werden. Grundlage sind 4D-CT-Daten des Patienten, aus denen mittels nicht-linearer Bildregistrierung eine Sequenz von Bewegungsfeldern berechnet wird. Typischerweise werden Methoden der paarweisen Bildregistrierung eingesetzt, d.h. konsekutiv zwei Atemphasen aufeinander registriert. Hierbei erfolgt i.d.R. eine physiologisch nicht plausible Anpassung der Felder an CT-Bewegungsartefakte. Gruppenweise Registrierungsansätze berücksichtigen hingegen gleichzeitig sämtliche Bilddaten des 4D-CT-Scans und ermöglichen die Integration von zeitlichen Konsistenzbetrachtungen. In diesem Beitrag wird der potentielle Vorteil der gruppen- im Vergleich zur paarweisen Registrierung in artefaktbehafteten 4D-CT-Daten untersucht. Y1 - 2015 U6 - https://doi.org/10.1007/s00066-015-0847-x VL - Supplement 1 SP - 65 EP - 65 PB - Springer CY - Strahlentherapie und Onkologie ET - 191 ER - TY - JOUR A1 - Sahu, Manish A1 - Moerman, Daniil A1 - Mewes, Philip A1 - Mountney, Peter A1 - Rose, Georg T1 - Instrument State Recognition and Tracking for Effective Control of Robotized Laparoscopic Systems JF - International Journal of Mechanical Engineering and Robotics Research N2 - Surgical robots are an important component for delivering advanced paradigm shifting technology such as image guided surgery and navigation. However, for robotic systems to be readily adopted into the operating room they must be easy and convenient to control and facilitate a smooth surgical workflow. In minimally invasive surgery, the laparoscope may be held by a robot but controlling and moving the laparoscope remains challenging. It is disruptive to the workflow for the surgeon to put down the tools to move the robot in particular for solo surgery approaches. This paper proposes a novel approach for naturally controlling the robot mounted laparoscope’s position by detecting a surgical grasping tool and recognizing if its state is open or close. This approach does not require markers or fiducials and uses a machine learning framework for tool and state recognition which exploits naturally occurring visual cues. Furthermore a virtual user interface on the laparoscopic image is proposed that uses the surgical tool as a pointing device to overcome common problems in depth perception. Instrument detection and state recognition are evaluated on in-vivo and ex-vivo porcine datasets. To demonstrate the practical surgical application and real time performance the system is validated in a simulated surgical environment. Y1 - 2016 U6 - https://doi.org/10.18178/ijmerr.5.1.33-38 VL - 5 IS - 1 SP - 33 EP - 38 ER - TY - CHAP A1 - Saleh, Salah A1 - Sahu, Manish A1 - Zafar, Zuhair A1 - Berns, Karsten T1 - A Multimodal Nonverbal Human-robot Communication System T2 - VI International Conference on Computational Bioengineering N2 - Socially interactive robot needs the same behaviors and capabilities of human to be accepted as a member in human society. The environment, in which this robot should operate, is the human daily life. The interaction capabilities of current robots are still limited due to complex inter-human interaction system. Humans usually use different types of verbal and nonverbal cues in their communication. Facial expression and head movement are good examples of nonverbal cues used in feedback. This paper presents a biological inspired system for Human-Robot Interaction (HRI). This system is based on the interactive model of inter-human communication proposed by Schramm. In this model, the robot and its interaction partner can be send and receive information at the same time. For example, if the robot is talking, it also perceive the feedback of the human via his/her nonverbal cues. In this work, we are focusing on recognizing the facial expression of human. The proposed facial expression recognition technique is based on machine learning. Multi SVMs have been used to recognize the six basic emotions in addition to the neutral expression. This technique uses only the depth information, acquired by Kinect, of human face. Y1 - 2015 ER - TY - CHAP A1 - Oksuz, Ilkay A1 - Mukhopadhyay, Anirban A1 - Bevilacqua, Marco A1 - Dharmakumar, Rohan A1 - Tsaftaris, Sotirios T1 - Dictionary Learning Based Image Descriptor for Myocardial Registration of CP-BOLD MR T2 - Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015 N2 - Cardiac Phase-resolved Blood Oxygen-Level-Dependent (CP- BOLD) MRI is a new contrast agent- and stress-free imaging technique for the assessment of myocardial ischemia at rest. The precise registration among the cardiac phases in this cine type acquisition is essential for automating the analysis of images of this technique, since it can potentially lead to better specificity of ischemia detection. However, inconsistency in myocardial intensity patterns and the changes in myocardial shape due to the heart’s motion lead to low registration performance for state- of-the-art methods. This low accuracy can be explained by the lack of distinguishable features in CP-BOLD and inappropriate metric defini- tions in current intensity-based registration frameworks. In this paper, the sparse representations, which are defined by a discriminative dictionary learning approach for source and target images, are used to improve myocardial registration. This method combines appearance with Gabor and HOG features in a dictionary learning framework to sparsely represent features in a low dimensional space. The sum of squared differences of these distinctive sparse representations are used to define a similarity term in the registration framework. The proposed descriptor is validated on a challenging dataset of CP-BOLD MR and standard CINE MR acquired in baseline and ischemic condition across 10 canines. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-24571-3_25 VL - 9350 SP - 205 EP - 213 PB - Springer ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Oksuz, Ilkay A1 - Bevilacqua, Marco A1 - Dharmakumar, Rohan A1 - Tsaftaris, Sotirios T1 - Unsupervised myocardial segmentation for cardiac MRI T2 - Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015 N2 - Though unsupervised segmentation was a de-facto standard for cardiac MRI segmentation early on, recently cardiac MRI segmentation literature has favored fully supervised techniques such as Dictionary Learning and Atlas-based techniques. But, the benefits of unsupervised techniques e.g., no need for large amount of training data and better potential of handling variability in anatomy and image contrast, is more evident with emerging cardiac MR modalities. For example, CP-BOLD is a new MRI technique that has been shown to detect ischemia without any contrast at stress but also at rest conditions. Although CP-BOLD looks similar to standard CINE, changes in myocardial intensity patterns and shape across cardiac phases, due to the heart’s motion, BOLD effect and artifacts affect the underlying mechanisms of fully supervised segmentation techniques resulting in a significant drop in segmentation accuracy. In this paper, we present a fully unsupervised technique for segmenting myocardium from the background in both standard CINE MR and CP-BOLD MR. We combine appearance with motion information (obtained via Optical Flow) in a dictionary learning framework to sparsely represent important features in a low dimensional space and separate myocardium from background accordingly. Our fully automated method learns background-only models and one class classifier provides myocardial segmentation. The advantages of the proposed technique are demonstrated on a dataset containing CP-BOLD MR and standard CINE MR image sequences acquired in baseline and ischemic condition across 10 canine subjects, where our method outperforms state-of-the-art supervised segmentation techniques in CP-BOLD MR and performs at-par for standard CINE MR. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-24574-4_2 VL - LNCS 9351 SP - 12 EP - 20 ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Oksuz, Ilkay A1 - Bevilacqua, Marco A1 - Dharmakumar, Rohan A1 - Tsaftaris, Sotirios T1 - Data-Driven Feature Learning for Myocardial Segmentation of CP-BOLD MRI T2 - Functional Imaging and Modeling of the Heart N2 - Cardiac Phase-resolved Blood Oxygen-Level-Dependent (CP- BOLD) MR is capable of diagnosing an ongoing ischemia by detecting changes in myocardial intensity patterns at rest without any contrast and stress agents. Visualizing and detecting these changes require significant post-processing, including myocardial segmentation for isolating the myocardium. But, changes in myocardial intensity pattern and myocardial shape due to the heart’s motion challenge automated standard CINE MR myocardial segmentation techniques resulting in a significant drop of segmentation accuracy. We hypothesize that the main reason behind this phenomenon is the lack of discernible features. In this paper, a multi scale discriminative dictionary learning approach is proposed for supervised learning and sparse representation of the myocardium, to improve the myocardial feature selection. The technique is validated on a challenging dataset of CP-BOLD MR and standard CINE MR acquired in baseline and ischemic condition across 10 canine subjects. The proposed method significantly outperforms standard cardiac segmentation techniques, including segmentation via registration, level sets and supervised methods for myocardial segmentation. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-20309-6_22 VL - 9126 SP - 189 EP - 197 PB - Springer ER - TY - GEN A1 - Sagnol, Guillaume A1 - Barner, Christoph A1 - Borndörfer, Ralf A1 - Grima, Mickaël A1 - Seeling, Matthes A1 - Spies, Claudia A1 - Wernecke, Klaus T1 - Robust Allocation of Operating Rooms: a Cutting Plane Approach to handle Lognormal Case Durations N2 - The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. We formulate this problem as a parallel machines scheduling problem, in which job durations follow a lognormal distribution, and a fixed assignment of jobs to machines must be computed. We propose a cutting-plane approach to solve the robust counterpart of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations that identifies worst-case scenarios and generates cut inequalities. The main result of this article uses Hilbert's projective geometry to prove the convergence of this procedure under mild conditions. We also propose two exact solution methods for a similar problem, but with a polyhedral uncertainty set, for which only approximation approaches were known. Our model can be extended to balance the load over several planning periods in a rolling horizon. We present extensive numerical experiments for instances based on real data from a major hospital in Berlin. In particular, we find that: (i) our approach performs well compared to a previous model that ignored the distribution of case durations; (ii) compared to an alternative stochastic programming approach, robust optimization yields solutions that are more robust against uncertainty, at a small price in terms of average cost; (iii) the \emph{longest expected processing time first} (LEPT) heuristic performs well and efficiently protects against extreme scenarios, but only if a good prediction model for the durations is available. Finally, we draw a number of managerial implications from these observations. T3 - ZIB-Report - 16-18 KW - robust optimization KW - lognormal duration KW - Hilbert's projective metric Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58502 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Borndörfer, Ralf A1 - Grima, Mickaël A1 - Seeling, Matthes A1 - Spies, Claudia T1 - Robust Allocation of Operating Rooms with Lognormal case Durations N2 - The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. In this article, we formulate this problem as a job shop scheduling problem, in which the job durations follow a lognormal distribution. We propose to use a cutting-plane approach to solve a robust version of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations to solve the subproblems that identify worst-case scenarios and generate cut inequalities. The procedure is illustrated with numerical experiments based on real data from a major hospital in Berlin. T3 - ZIB-Report - 16-16 KW - robust optimization KW - lognormal duration KW - Hilbert's projective metric Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58497 UR - http://www.pms2016.com/congreso/ficha.en.html SN - 1438-0064 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - Optimization of energy supply systems by MILP branch and bound method in consideration of hierarchical relationship between design and operation JF - Energy Conversion and Management N2 - To attain the highest performance of energy supply systems, it is necessary to rationally determine types, capacities, and numbers of equipment in consideration of their operational strategies corresponding to seasonal and hourly variations in energy demands. In the combinatorial optimization method based on the mixed-integer linear programming (MILP), integer variables are used to express the selection, numbers, and on/off status of operation of equipment, and the number of these variables increases with those of equipment and periods for variations in energy demands, and affects the computation efficiency significantly. In this paper, a MILP method utilizing the hierarchical relationship between design and operation variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized independently at each period by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function to be minimized are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2015 U6 - https://doi.org/10.1016/j.enconman.2014.12.020 VL - 92 SP - 92 EP - 104 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Shinano, Yuji T1 - MILP Approaches to Optimal Design and Operation of Distributed Energy Systems T2 - Optimization in the Real World N2 - Energy field is one of the practical areas to which optimization can contribute significantly. In this chapter, the application of mixed-integer linear programming (MILP) approaches to optimal design and operation of distributed energy systems is described. First, the optimal design and operation problems are defined, and relevant previous work is reviewed. Then, an MILP method utilizing the hierarchical relationship between design and operation variables is presented. In the optimal design problem, integer variables are used to express the types, capacities, numbers, operation modes, and on/off states of operation of equipment, and the number of these variables increases with those of equipment and periods for variations in energy demands, and affects the computation efficiency significantly. The presented method can change the enumeration tree for the branching and bounding procedures, and can search the optimal solution very efficiently. Finally, future work in relation to this method is described. Y1 - 2015 SN - 978-4-431-55419-6 U6 - https://doi.org/10.1007/978-4-431-55420-2_9 VL - Volume 13 SP - 157 EP - 176 PB - Springer ER - TY - THES A1 - Bärhold, Robert T1 - Konzipierung und Implementierung eines Quota-Protokolls in objektbasierten Dateisystemen N2 - Verteilte Dateisysteme, wie sie unter anderem in Cloud-Umgebungen eingesetzt werden, werden häufig von verschiedenen Anwendern und Anwendungen zeitgleich verwendet. Da diese Ressourcen in Cloud-Umgebungen gemietet sind, muss sichergestellt werden, dass ein Kunde nur die Ressourcen verwenden kann, für die er bezahlt hat. Andernfalls könnten andere Kunden beeinträchtigt werden. Solch eine Obergrenze wird auch als Quota bezeichnet. Speziell für objektbasierte Dateisysteme, bei denen die Metadaten einer Datei von den Dateiinhalten getrennt gespeichert und verwaltet werden, erfordert die Forcierung einer Quota ein verteiltes Protokoll. Im Rahmen der vorliegenden Arbeit wurde ein Quota-Protokoll für objektbasierte Dateisysteme entwickelt und implementiert. Bei einer aktiven Quota wird zunächst ein Teil des Speicherplatzes für eine bestimmte Datei blockiert, der als Voucher bezeichnet wird. Anschließend wird dem Client die maximale Dateigröße in signierter Form zugewiesen. Sie ergibt sich aus der Summe der bisherigen Dateigröße und allen erstellten Vouchers. Durch diesen Ansatz können die Speicherserver bei jedem Zugriff lokal prüfen, ob der Schreibzugriff die maximale Dateigröße überschreiten würde. Reicht diese nicht aus, muss ein zusätzlicher Voucher erstellt werden, sofern noch Speicherplatz verfügbar ist. Nicht verbrauchter Speicherplatz wird am Ende wieder freigegeben. Zusätzlich unterstützt das Protokoll die Verteilung der Inhalte einer Datei auf mehrere Server (Striping) sowie Sparse-Dateien, bei denen beliebige Bereiche der Datei leer bleiben. Die Implementierung erfolgte im objektbasierten Dateisystem XtreemFS. Dabei wurden spezielle Funktionen von XtreemFS, wie die Dateireplikation, mit einbezogen. In einer abschließenden Evaluation wurde der Einfluss des implementierten Quota- Protokolls bezüglich der Performanz von XtreemFS untersucht. Dabei zeigte sich zunächst, dass bei einer aktiven Quota die Performanz beim Schreiben großer Daten- mengen abhängig von der eingestellten Voucher-Größe ist. Ist diese zu niedrig gewählt, so muss der Client seine maximale Dateigröße durch zusätzliche Anfragen beim Metada- tenserver erhöhen, was die Performanz negativ beeinträchtigt. Bei einer Voucher-Größe von 100 MiB wurde beim Schreiben einer 10 GiB-Datei ein Performanzverlust von unter 2% gemessen, verglichen mit dem Entwicklungsstand ohne implementiertes Quota- Protokoll. Bei der Erstellung mehrerer 64 KiB-Dateien wurde aufgrund zusätzlicher Nachrichten ein Verlust von rund 8% gemessen. KW - Quota KW - Protokoll KW - Verteiltes Dateisystem Y1 - 2016 ER - TY - CHAP A1 - Karbstein, Marika T1 - Integrated Line Planning and Passenger Routing: Connectivity and Transfers T2 - Operations Research Proceedings 2014 N2 - The integrated line planning and passenger routing problem is an important planning problem in service design of public transport. A major challenge is the treatment of transfers. A main property of a line system is its connectivity. In this paper we show that analysing the connecvitiy aspect of a line plan gives a new idea to handle the transfer aspect of the line planning problem. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-28697-6_37 SP - 263 EP - 269 ER - TY - GEN A1 - Götschel, Sebastian A1 - Höhne, Christian A1 - Kolkoori, Sanjeevareddy A1 - Mitzscherling, Steffen A1 - Prager, Jens A1 - Weiser, Martin T1 - Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing N2 - The application of advanced imaging techniques for the ultrasonic inspection of inhomogeneous anisotropic materials like austenitic and dissimilar welds requires information about acoustic wave propagation through the material, in particular travel times between two points in the material. Forward ray tracing is a popular approach to determine traveling paths and arrival times but is ill suited for inverse problems since a large number of rays have to be computed in order to arrive at prescribed end points. In this contribution we discuss boundary value problems for acoustic rays, where the ray path between two given points is determined by solving the eikonal equation. The implementation of such a two point boundary value ray tracer for sound field simulations through an austenitic weld is described and its efficiency as well as the obtained results are compared to those of a forward ray tracer. The results are validated by comparison with experimental results and commercially available UT simulation tools. As an application, we discuss an implementation of the method for SAFT (Synthetic Aperture Focusing Technique) reconstruction. The ray tracer calculates the required travel time through the anisotropic columnar grain structure of the austenitic weld. There, the formulation of ray tracing as a boundary value problem allows a straightforward derivation of the ray path from a given transducer position to any pixel in the reconstruction area and reduces the computational cost considerably. T3 - ZIB-Report - 16-14 KW - ray tracing KW - ODE boundary value problems KW - ultrasonics KW - nondestructive testing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58386 UR - https://www.wcndt2016.com/portals/wcndt/bb/Fr1H4.pdf SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Maierhofer, Christiane A1 - Müller, Jan P. A1 - Rothbart, Nick A1 - Weiser, Martin T1 - Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites N2 - Carbon-fiber reinforced composites are becoming more and more important in the production of light-weight structures, e.g., in the automotive and aerospace industry. Thermography is often used for non-destructive testing of these products, especially to detect delaminations between different layers of the composite. In this presentation, we aim at methods for defect reconstruction from thermographic measurements of such carbon-fiber reinforced composites. The reconstruction results shall not only allow to locate defects, but also give a quantitative characterization of the defect properties. We discuss the simulation of the measurement process using finite element methods, as well as the experimental validation on flat bottom holes. Especially in pulse thermography, thin boundary layers with steep temperature gradients occurring at the heated surface need to be resolved. Here we use the combination of a 1D analytical solution combined with numerical solution of the remaining defect equation. We use the simulations to identify material parameters from the measurements. Finally, fast heuristics for reconstructing defect geometries are applied to the acquired data, and compared for their accuracy and utility in detecting different defects like back surface defects or delaminations. T3 - ZIB-Report - 16-13 KW - thermography KW - inverse problems KW - parameter identification KW - geometry identification KW - nondestructive testing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58374 UR - https://www.wcndt2016.com/portals/wcndt/bb/Th4C4.pdf SN - 1438-0064 ER - TY - GEN A1 - Osterland, Marc A1 - Benn, Andreas A1 - Prohaska, Steffen A1 - Schütte, Christof T1 - Single Cell Tracking in Phase-Contrast Microscopy T2 - EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life N2 - In this work, we developed an automatic algorithm to analyze cell migration in chemotaxis assays, based on phase-contrast time-lapse microscopy. While manual approaches are still widely used in recent publications, our algorithm is able to track hundreds of single cells per frame. The extracted paths are analysed with traditional geometrical approaches as well as diffusion-driven Markov state models (MSM). Based on these models, a detailed view on spatial and temporal effects is possible. Using our new approach on experimental data, we are able to distinguish between directed migration (e.g. towards a VEGF gradient) and random migration without favored direction. A calculation of the committor probabilities reveals that cells of the whole image area are more likely to migrate directly towards the VEGF than away from it during the first four hours. However, in absence of a chemoattractant, cells migrate more likely to their nearest image border. These conclusions are supported by the spatial mean directions. In a next step, the cell-cell interaction during migration and the migration of cell clusters will be analyzed. Furthermore, we want to observe phenotypical changes during migration based on fluorescence microscopy and machine learning. The algorithm is part of a collaborative platform which brings the experimental expertise of scientists from life sciences and the analytical knowledge of computer scientists together. This platform is built using web-based technologies with a responsive real-time user interface. All data, including raw and metadata as well as the accompanying results, will be stored in a secure and scalable compute cluster. The compute cluster provides sufficient space and computational power for modern image-based experiments and their analyses. Specific versions of data and results can be tagged to keep immutable records for archival. Y1 - 2015 ER - TY - GEN A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Daviller, Guillaume A1 - Morzyński, Marek T1 - Acceleration feature points of unsteady shear flows N2 - A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2. T3 - ZIB-Report - 15-65 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58397 SN - 1438-0064 ER - TY - JOUR A1 - Spötter, Andreas A1 - Gupta, Pooja A1 - Mayer, Manfred A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera) JF - Journal of Heredity Y1 - 2016 VL - 107 IS - 3 SP - 220 EP - 227 ER - TY - JOUR A1 - Bienefeld, Kaspar A1 - Zautke, Fred A1 - Gupta, Pooja T1 - A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour – illustrated by the hygienic behaviour towards Varroa infestation JF - Journal of Apicultural Research Y1 - 2016 VL - 54(5) SP - 541 EP - 547 ER - TY - JOUR A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An affine covariant composite step method for optimization with PDEs as equality constraints JF - Optimization Methods and Software N2 - We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2016.1241783 VL - 32 IS - 5 SP - 1132 EP - 1161 ER - TY - JOUR A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Daviller, Guillaume A1 - Morzyński, Marek T1 - Acceleration feature points of unsteady shear flows JF - Archives of Mechanics N2 - A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2. Y1 - 2016 VL - 68 IS - 1 SP - 55 EP - 80 ER - TY - CHAP A1 - Engelke, Wito A1 - Kuhn, Alexander A1 - Flatken, Markus A1 - Chen, Fang A1 - Hege, Hans-Christian A1 - Gerndt, Andreas A1 - Hotz, Ingrid T1 - Atmospheric Impact of Volcano Eruptions T2 - Proceedings IEEE SciVis 2014 N2 - The analysis of data that captures volcanic eruptions and their atmospheric aftermath plays an important role for domain experts to gain a deeper understanding of the volcanic eruption and their consequences for atmosphere, climate and air traffic. Thereby, one major challenge is to extract and combine the essential information, which is spread over various, mostly sparse data sources. This requires a careful integration of each data set with its strength and limitations. The sparse, but more reliable measurement data is mainly used to calibrate the more dense simulation data. This work combines a collection of visualization approaches into an exploitative framework. The goal is to support the domain experts to build a complete picture of the situation. But it is also important to understand the individual data sources, the wealth of their information and the quality of the simulation results. All presented methods are designed for direct interaction with the data from different perspectives rather than the sole generation of some final images. Y1 - 2014 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimal duty rostering for toll enforcement inspectors JF - Annals of Operations Research N2 - We present the problem of planning mobile tours of inspectors on German motorways to enforce the payment of the toll for heavy good trucks. This is a special type of vehicle routing problem with the objective to conduct as good inspections as possible on the complete network. In addition, we developed a personalized crew rostering model, to schedule the crews of the tours. The planning of daily tours and the rostering are combined in a novel integrated approach and formulated as a complex and large scale Integer Program. The main focus of this paper extends our previous publications on how different requirements for the rostering can be modeled in detail. The second focus is on a bi-criteria analysis of the planning problem to find the balance between the control quality and the roster acceptance. Finally, computational results on real-world instances show the practicability of our method and how different input parameters influence the problem complexity. Y1 - 2016 U6 - https://doi.org/10.1007/s10479-016-2152-1 VL - 252(2) SP - 383 EP - 406 PB - Springer US ET - 252 ER - TY - GEN A1 - Seidel, Ronald A1 - Knötel, David A1 - Baum, Daniel A1 - Weaver, James C. A1 - Dean, Mason N. T1 - Material and structural characterization of mineralized elasmobranch cartilage – lessons in repeated tiling patterns in mechanically loaded 3D objects T2 - Poster, Tomography for Scientific Advancement symposium (ToScA), London, UK, September 1 - 3, 2014 N2 - Biological tissues achieve a wide range of properties and function, however with limited components. The organization of these constituent parts is a decisive factor in the impressive properties of biological materials, with tissues often exhibiting complex arrangements of hard and soft materials. The “tessellated” cartilage of the endoskeleton of sharks and rays, for example, is a natural composite of mineralized polygonal tiles (tesserae), collagen fiber bundles, and unmineralized cartilage, resulting in a material that is both flexible and strong, with optimal stiffness. The properties of the materials and the tiling geometry are vital to the growth and mechanics of the system, but had not been investigated due to the technical challenges involved. We use high-resolution materials characterization techniques (qBEI, µCT) to show that tesserae exhibit great variability in mineral density, supporting theories of accretive growth mechanisms. We present a developmental series of tesserae and outline the development of unique structural features that appear to function in load bearing and energy dissipation, with some structural features far exceeding cortical bone’s mineral content and tissue stiffness. To examine interactions among tesserae, we developed an advanced tiling-recognition-algorithm to semi-automatically detect and isolate individual tiles in microCT scans of tesseral mats. The method allows quantification of shape variation across a wide area, allowing localization of regions of high/low reinforcement or flexibility in the skeleton. The combination of our material characterization and visualization techniques allows the first quantitative 3d description of anatomy and material properties of tesserae and the organization of tesseral networks in elasmobranch mineralized cartilage, providing insight into form-function relationships of the repeating tiled pattern. We aim to combine detailed knowledge of intra-tesseral morphology and mineralization to model the relationships of tesseral shapes and skeletal surface curvature, to understand fundamental tiling laws important for complex, mechanically loaded 3d objects. Y1 - 2014 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Weaver, James C. A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays T2 - Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015 N2 - The cartilaginous endoskeletons of sharks and rays are covered by tiles of mineralized cartilage called tesserae that enclose areas of unmineralized cartilage. These tesselated layers are vital to the growth as well as the material properties of the skeleton, providing both flexibility and strength. An understanding of the principles behind the tiling of the mineralized layer requires a quantitative analysis of shark and ray skeletal tessellation. However, since a single skeletal element comprises several thousand tesserae, manual segmentation is infeasible. We developed an automated segmentation pipeline that, working from micro-CT data, allows quantification of all tesserae in a skeletal element in less than an hour. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. In micro-CT scans, tesserae usually appear as round or star-shaped plate-like tiles, wider than deep and connected by mineralized intertesseral joints. Based on these observations, we exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Utilizing a two-dimensional distance map that measures the distance in the plane of the mineralized layer only greatly improves the segmentation. We developed post-processing techniques to quickly correct segmentation errors in regions where tesseral shape differs from the assumed shape. Evaluation of our results is done qualitatively by visual comparison with raw datasets, and quantitatively by comparison to manual segmentations. Furthermore, we generate two-dimensional abstractions of the tiling network based on the neighborhood, allowing representation of complex, biological forms as simpler geometries. We apply our newly developed techniques to the analysis of the left and right hyomandibulae of four ages of stingray enabling the first quantitative analyses of the tesseral tiling structure, while clarifying how these patterns develop across ontogeny. Y1 - 2015 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Hosny, Ahmed A1 - Zaslansky, Paul A1 - Weaver, James C. A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays T2 - Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016 N2 - The endoskeletons of sharks and rays are composed of an unmineralized cartilaginous core, covered in an outer layer of mineralized tiles called tesserae. The tessellated layer is vital to the growth as well as the material properties of the skeletal element, providing both flexibility and strength. However, characterizing the relationship between tesseral size and shape, and skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. Using a custom-made semi-automatic segmentation algorithm, we present the first quantitative and three-dimensional description of tesserae in micro-CT scans of whole skeletal elements. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. We exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Additionally, we have developed post-processing techniques to quickly correct segmentation errors. Our data reveals that the tessellation is not regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick-or disc-shaped tesserae are found in planar areas. We apply our newly developed techniques on the left and right hyomandibula (skeletal elements supporting the jaws) from four different ages of a stingray species, to clarify how tiling patterns develop across ontogeny and differ within and between individuals. We evaluate the functional consequences of tesseral morphologies using finite element analysis and 3d-printing, for a better understanding of shark skeletal mechanics, but also to extract fundamental engineering design principles of tiling arrangements on load-bearing three-dimensional objects. Y1 - 2016 ER - TY - JOUR A1 - Knight, James C A1 - Tully, Philip J A1 - Kaplan, Bernhard A1 - Lansner, Anders A1 - Furber, Steve T1 - Large-scale simulations of plastic neural networks on neuromorphic hardware JF - Frontiers in Neuroanatomy N2 - SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Rather than using bespoke analog or digital hardware, the basic computational unit of a SpiNNaker system is a general-purpose ARM processor, allowing it to be programmed to simulate a wide variety of neuron and synapse models. This flexibility is particularly valuable in the study of biological plasticity phenomena. A recently proposed learning rule based on the Bayesian Confidence Propagation Neural Network (BCPNN) paradigm offers a generic framework for modeling the interaction of different plasticity mechanisms using spiking neurons. However, it can be computationally expensive to simulate large networks with BCPNN learning since it requires multiple state variables for each synapse, each of which needs to be updated every simulation time-step. We discuss the trade-offs in efficiency and accuracy involved in developing an event-based BCPNN implementation for SpiNNaker based on an analytical solution to the BCPNN equations, and detail the steps taken to fit this within the limited computational and memory resources of the SpiNNaker architecture. We demonstrate this learning rule by learning temporal sequences of neural activity within a recurrent attractor network which we simulate at scales of up to 2.0 × 10^4 neurons and 5.1 × 10^7 plastic synapses: the largest plastic neural network ever to be simulated on neuromorphic hardware. We also run a comparable simulation on a Cray XC-30 supercomputer system and find that, if it is to match the run-time of our SpiNNaker simulation, the super computer system uses approximately 45× more power. This suggests that cheaper, more power efficient neuromorphic systems are becoming useful discovery tools in the study of plasticity in large-scale brain models. Y1 - 2016 U6 - https://doi.org/10.3389/fnana.2016.00037 VL - 10:37 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for electromagnetic scattering problem: a case study for FinFETs JF - Optical and Quantum Electronics N2 - Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occurring e. g. in optical metrology. The reduced basis method pre- sented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources. Y1 - 2016 U6 - https://doi.org/10.1007/s11082-016-0530-1 VL - 48 SP - 250 ER - TY - GEN A1 - Gutsche, Philipp A1 - Läuter, Matthias A1 - Schmidt, Frank T1 - Parameter-dependent Parallel Block Sparse Arnoldi and Döhler Algorithms on Distributed Systems N2 - We summarize the basics and first results of the analyses within our ZIB Bridge Project and give an outlook on further studies broadening the usage of hardware acceleration within the Finite Element Method (FEM) based solution of Maxwell’s equations. T3 - ZIB-Report - 16-15 KW - Generalized Eigenvalue Problem KW - Many Integrated Core Coprocessor (MIC) KW - Finite Element Method Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58202 SN - 1438-0064 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures JF - Proc. SPIE N2 - Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell's equation. Highly accurate geometrical modelling and numerical accuracy at low computational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scattering at optical wavelengths of periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range. Y1 - 2016 U6 - https://doi.org/10.1117/12.2212367 VL - 9742 SP - 97420M ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Pomplun, Jan A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs JF - Proc. SPIE N2 - Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58187 VL - 9756 SP - 97561R ER - TY - CHAP A1 - Gupta, Pooja A1 - Krause, Carola A1 - Rikeit, Paul A1 - Röblitz, Susanna A1 - Knaus, Petra A1 - Schütte, Christof T1 - Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density T2 - 10th International BMP conference, 2014, Berlin, Germany Y1 - 2014 ER - TY - GEN A1 - Gupta, Pooja A1 - Röblitz, Susanna A1 - Krause, Carola A1 - Knaus, Petra A1 - Schütte, Christof T1 - Mathematical modeling of the Smad and Non-Smad BMP signaling pathways in context of cell density T2 - Computational Models in biology and medicine, 2013, Dresden, Germany Y1 - 2013 ER - TY - CHAP A1 - Bienefeld, Kaspar A1 - Spötter, Andreas A1 - Reinsch, Norbert A1 - Mayer, Manfred A1 - Gupta, Pooja T1 - A new approach for honeybee breeding - genomic selection T2 - 44th Apimondia International Apicultural congress, 2015. Daejeon, South Korea Y1 - 2015 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Ebell, Gino T1 - 3D Corrosion Detection in Time-dependent CT Images of Concrete T2 - DIR-2015 Proceedings N2 - In civil engineering, the corrosion of steel reinforcements in structural elements of concrete bares a risk of stability-reduction, mainly caused by the exposure to chlorides. 3D computed tomography (CT) reveals the inner structure of concrete and allows one to investigate the corrosion with non-destructive testing methods. To carry out such investigations, specimens with a large artificial crack and an embedded steel rebar have been manufactured. 3D CT images of those specimens were acquired in the original state. Subsequently three cycles of electrochemical pre-damaging together with CT imaging were applied. These time series have been evaluated by means of image processing algorithms to segment and quantify the corrosion products. Visualization of the results supports the understanding of how corrosion propagates into cracks and pores. Furthermore, pitting of structural elements can be seen without dismantling. In this work, several image processing and visualization techniques are presented that have turned out to be particularly effective for the visualization and segmentation of corrosion products. Their combination to a workflow for corrosion analysis is the main contribution of this work. Y1 - 2015 UR - http://www.ndt.net/events/DIR2015/app/content/Paper/36_Paetsch.pdf ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Fügenschuh, Armin A1 - Klug, Torsten A1 - Schang, Thilo A1 - Schlechte, Thomas A1 - Schülldorf, Hanno T1 - The Freight Train Routing Problem for Congested Railway Networks with Mixed Traffic JF - Transportation Science N2 - We consider the following freight train routing problem (FTRP). Given is a transportation network with fixed routes for passenger trains and a set of freight trains (requests), each defined by an origin and destination station pair. The objective is to calculate a feasible route for each freight train such that the sum of all expected delays and all running times is minimal. Previous research concentrated on microscopic train routings for junctions or inside major stations. Only recently approaches were developed to tackle larger corridors or even networks. We investigate the routing problem from a strategic perspective, calculating the routes in a macroscopic transportation network of Deutsche Bahn AG. In this context, macroscopic refers to an aggregation of complex and large real-world structures into fewer network elements. Moreover, the departure and arrival times of freight trains are approximated. The problem has a strategic character since it asks only for a coarse routing through the network without the precise timings. We provide a mixed-integer nonlinear programming (MINLP) formulation for the FTRP, which is a multicommodity flow model on a time-expanded graph with additional routing constraints. The model’s nonlinearities originate from an algebraic approximation of the delays of the trains on the arcs of the network by capacity restraint functions. The MINLP is reduced to a mixed-integer linear model (MILP) by piecewise linear approximation. The latter is solved by a state-of-the art MILP solver for various real-world test instances. Y1 - 2016 U6 - https://doi.org/10.1287/trsc.2015.0656 VL - 50 IS - 2 SP - 408 EP - 423 ER - TY - BOOK A1 - Sullivan, T. J. T1 - Introduction to Uncertainty Quantification Y1 - 2015 SN - 978-3-319-23394-9 U6 - https://doi.org/10.1007/978-3-319-23395-6 VL - 63 PB - Springer ER - TY - JOUR A1 - Owhadi, Houman A1 - Scovel, Clint A1 - Sullivan, T. J. T1 - On the Brittleness of Bayesian Inference JF - SIAM Review N2 - With the advent of high-performance computing, Bayesian methods are becoming increasingly popular tools for the quantification of uncertainty throughout science and industry. Since these methods can impact the making of sometimes critical decisions in increasingly complicated contexts, the sensitivity of their posterior conclusions with respect to the underlying models and prior beliefs is a pressing question to which there currently exist positive and negative answers. We report new results suggesting that, although Bayesian methods are robust when the number of possible outcomes is finite or when only a finite number of marginals of the data-generating distribution are unknown, they could be generically brittle when applied to continuous systems (and their discretizations) with finite information on the data-generating distribution. If closeness is defined in terms of the total variation (TV) metric or the matching of a finite system of generalized moments, then (1) two practitioners who use arbitrarily close models and observe the same (possibly arbitrarily large amount of) data may reach opposite conclusions; and (2) any given prior and model can be slightly perturbed to achieve any desired posterior conclusion. The mechanism causing brittleness/robustness suggests that learning and robustness are antagonistic requirements, which raises the possibility of a missing stability condition when using Bayesian inference in a continuous world under finite information. Y1 - 2015 U6 - https://doi.org/10.1137/130938633 VL - 57 IS - 4 SP - 566 EP - 582 ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals T2 - Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Kraków, Poland Y1 - 2015 ER - TY - THES A1 - Fackeldey, Konstantin T1 - Crossing the Scales in Structural Mechanics and Molecular Research Y1 - 2015 ER - TY - GEN A1 - Weitzmann, John H. A1 - Klimpel, Paul ED - digiS - Servicestelle Digitalisierung Berlin, T1 - Rechtliche Rahmenbedingungen für Digitalisierungsprojekte von Gedächtnisinstitutionen N2 - Kulturerbe- und Gedächtnisinstitutionen sammeln, bewahren, dokumentieren und vermitteln Zeugnisse und Objekte des kulturellen Erbes. Die Digitalisierung eröffnet für alle diese Handlungsfelder neue Möglichkeiten, aber gleichzeitig auch neue Herausforderungen. Diese berühren sowohl organisatorische und technische als auch rechtliche Aspekte. Gerade letztere sind oft mit schwer kalkulierbaren Risiken für die Kultureinrichtungen behaftet. Die vorliegende Handreichung, die von iRights im Auftrag von digiS erstellt wurde, soll eine Einführung für die Mitarbeiter der Kulturinstitutionen in die Themen Urheber- und Leistungsschutzrechte sein. Sie soll für rechtliche Risiken sensibilisieren und Handlungsspielräume aufzeigen. Die bisherige Version 1.1 aus dem letzten Jahr wurde nun überarbeitet. Y1 - 2015 U6 - https://doi.org/10.12752/2.0.002.2 ET - 2. geänderte Auflage ER - TY - CHAP A1 - Peters-Kottig, Wolfgang A1 - Hasler, Tim A1 - Amrhein, Kilian T1 - Langzeitarchivierung: Just SIP it - Übernahmevereinbarung zum Mitnehmen. T2 - 104. Deutscher Bibliothekartag in Nürnberg 2015 N2 - Das Thema digitale Langzeitarchivierung betrifft alle Einrichtungen, die Verantwortung für die langfristige Verfügbarkeit von Daten übernommen haben oder übernehmen werden. In dem Workshop werden die Teilnehmer anhand von mehreren konkreten Beispielen Schritt für Schritt durch den Prozess der Datenübernahme (Ingest) in ein Langzeitarchiv geführt. Die verwendeten Verfahren werden detailliert erläutert und diskutiert. Vorgestellt wird eine konkrete Vereinbarung, die für alle Sparten bzw. Disziplinen gelten kann und die den Übernahmeprozess von Daten für alle Beteiligten transparent beschreibt. Dieses generische Dokument kann auch von anderen Institutionen als Basisdokument zur Erstellung einer eigenen Policy eingesetzt werden. Durchaus erwünscht sind Anwendungsfälle der Teilnehmer, um die vorgestellten Verfahren daran nachzuvollziehen. Dadurch soll jeder in die Lage versetzt werden, die Inhalte des Workshops in die tägliche Praxis mitzunehmen. Der Workshop wird angeboten vom Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) und der Servicestelle Digitalisierung Berlin (digiS), die in enger Kooperation miteinander eine spartenübergreifende Langzeitarchivierungsinfrastruktur aufbauen. Er richtet sich an alle Mitarbeiter, die die digitale Langzeitarchivierung in ihren Institutionen organisieren. Grundlegende Kenntnisse des OAIS-Referenzmodells sind von Vorteil, technische Kenntnisse sind nicht erforderlich. Y1 - 2015 ER - TY - JOUR A1 - Heye, Katharina A1 - Becker, Dennis A1 - Lütke-Eversloh, Christian A1 - Durmaz, Vedat A1 - Ternes, Thomas A1 - Oetken, Matthias A1 - Oehlmann, Jörg T1 - Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test JF - Water Research N2 - The antiepileptic drug carbamazepine (CBZ) and its main metabolites carbamazepine-10,11-epoxide (EP-CBZ) and 10,11-dihydro-10,11-dihydroxy-carbamazepine (DiOH-CBZ) were chosen as test substances to assess chronic toxicity on the non-biting midge Chironomus riparius. All three substances were tested in a 40-day sediment full life cycle test (according to OECD 233) in which mortality, emergence, fertility, and clutch size were evaluated. In addition, these parameters were integrated into the population growth rate to reveal population relevant effects. With an LC50 of 0.203 mg/kg (time-weighted mean), the metabolite EP-CBZ was significantly more toxic than the parent substance CBZ (LC50: 1.11 mg/kg). Especially mortality, emergence, and fertility showed to be sensitive parameters under the exposure to CBZ and EP-CBZ. By using classical molecular dynamics (MD) simulations, the binding of CBZ to the ecdysone receptor was investigated as one possible mode of action but showed to be unlikely. The second metabolite DiOH-CBZ did not show any effects within the tested concentration rage (0.171 – 1.22 mg/kg). Even though CBZ was less toxic compared to EP-CBZ, CBZ is found in the environment at much higher concentrations and causes therefore a higher potential risk for sediment dwelling organisms compared to its metabolites. Nevertheless, the current study illustrates the importance of including commonly found metabolites into the risk assessment of parent substances. Y1 - 2016 VL - 98 SP - 19 EP - 27 ER - TY - GEN A1 - Fackeldey, Konstantin T1 - Challenges in Atomistic-to-Continuum Coupling T2 - ZIB Report N2 - This paper is concerned with the design, analysis, and implementation of concurrent coupling approaches where different (atomic and continuous) models are used simultaneously within a single simulation process. Thereby, several problems or pitfalls can happen, for example, the reflection of molecular movements at the “boundary” between the atomic and continuum regions which leads to an unphysical increase in energy in the atomic model. We investigate the problems with the aim of giving an introduction into this field and preventing errors for scientists starting their research towards multiscale methods. Y1 - 2010 U6 - https://doi.org/10.1155/2015/834517 VL - 2010 ET - 10-12 ER - TY - JOUR A1 - Durmaz, Vedat T1 - Markov model-based polymer assembly from force field-parameterized building blocks JF - Journal of Computer-Aided Molecular Design N2 - A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very workintensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantumchemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. Y1 - 2015 U6 - https://doi.org/10.1007/s10822-014-9817-0 VL - 29 SP - 225 EP - 232 ER - TY - CHAP A1 - Fajerski, J. A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Steinke, Thomas T1 - Fast In-Memory Checkpointing with POSIX API for Legacy Exascale-Applications T2 - SPPEXA Symposium 2016 Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-40528-5_19 ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Advanced computed tomography analyses of cold-water coral mound cores: new insights into mound formation processes T2 - Poster, 19th International Sedimentological Congress, Geneva, Switzerland, 2014, August 18 - 22 Y1 - 2014 ER - TY - CHAP A1 - Weinhold, Carsten A1 - Lackorzynski, Adam A1 - Bierbaum, Jan A1 - Küttler, Martin A1 - Planeta, Maksym A1 - Härtig, Hermann A1 - Shiloh, Amnon A1 - Levy, Ely A1 - Ben-Nun, Tal A1 - Barak, Amnon A1 - Steinke, Thomas A1 - Schütt, Thorsten A1 - Fajerski, Jan A1 - Reinefeld, Alexander A1 - Lieber, Matthias A1 - Nagel, Wolfgang T1 - FFMK: A Fast and Fault-tolerant Microkernel-based System for Exascale Computing T2 - SPPEXA Symposium 2016 Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-40528-5_18 ER - TY - JOUR A1 - Humpola, Jesco A1 - Joormann, Imke A1 - Oucherif, Djamal A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schwarz, Robert T1 - GasLib - A Library of Gas Network Instances JF - Optimization Online N2 - The development of mathematical simulation and optimization models and algorithms for solving gas transport problems is an active field of research. In order to test and compare these models and algorithms, gas network instances together with demand data are needed. The goal of GasLib is to provide a set of publicly available gas network instances that can be used by researchers in the field of gas transport. The advantages are that researchers save time by using these instances and that different models and algorithms can be compared on the same specified test sets. The library instances are encoded in an XML format. In this paper, we explain this format and present the instances that are available in the library. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57950 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Weber, Marcus A1 - Schütte, Christof T1 - Finding dominant structures of nonreversible Markov processes JF - Multiscale Modeling and Simulation Y1 - 2016 U6 - https://doi.org/10.1137/15M1032272 VL - 14 IS - 4 SP - 1319 EP - 1340 ER - TY - JOUR A1 - Lemanis, Robert A1 - Korn, Dieter A1 - Zachow, Stefan A1 - Rybacki, Erik A1 - Hoffmann, René T1 - The Evolution and Development of Cephalopod Chambers and Their Shape JF - PLOS ONE N2 - The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0151404 VL - 11 IS - 3 ER - TY - THES A1 - Weber, Britta T1 - Reconstruction of Microtubule Centerlines from Electron Tomograms N2 - The organization of the mitotic spindle, a structure that separates the chromosomes during cell division, is an active research topic in molecular cell biology. It is composed of microtubules, elongated tubular macromolecules with a diameter of 25 nm. The only volumetric imaging technique that is available to a wide community and provides the required resolution to capture details about microtubules is electron tomography. However, the automatic detection of microtubules in electron tomograms is a difficult task due to the low contrast of the data. Furthermore, thick samples have to be cut into 300 nm thin sections before electron tomography can be applied. Software for automatically segmentation and stitching of the microtubules are not available and therefore these tasks have to be performed manually. Unfortunately, manual segmentation is time consuming for large samples and manual stitching of the tomograms is often infeasible due to the lack of prominent features for registration. Conclusions drawn from electron tomographic data is currently mostly based on either small samples containing few microtubules or single sections of complex structures. Consequently, simple properties, such as the length of microtubules in the spindle or their number, are still unknown for most model organisms. In this thesis, we present methods for 1) an automatic segmentation of microtubule centerlines in electron tomograms, and 2) an automatic stitching of the lines extracted from serial sections. For the centerline segmentation, we use 3D template matching and exploit knowledge about shape of microtubules and microscopy artifacts to design the templates. For the registration of the lines, we present a way to model the orientation of lines as a mixture of Fisher-Mises distributions where we estimate transformation parameters with the expectation maximization algorithm. The final line matching problem is formulated in terms of a probabilistic graphical model. To find the correct correspondences of line ends, we use belief propagation. We handle the poor convergence properties of this algorithm by detecting ambiguous and conflicting assignments of lines automatically. An expert can then influence the final output of the algorithm by solving conflicts manually. A detailed error analysis on true biological data and assessment of the reliability of the results is the prerequisite for analyzing the resulting line representations of the microtubules. To this end, the developed workflow for segmenting and stitching of microtubule centerlines is evaluated on plasticembedded samples of C. elegans early embryos and of spindles from X. laevis egg extracts. Our results suggest that the output of the presented algorithms together with little manual correction is of sufficient quality to allow a detailed analysis of dense microtubule networks. Finally, we exemplarily show results for the centrosome of a C. elegans mitotic spindle. KW - microtubules KW - electron tomography KW - c.elegans KW - image processing KW - graphical model KW - gaussian mixture model KW - template matching Y1 - 2015 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000100915 ER - TY - THES A1 - Pöthkow, Kai T1 - Modeling, Quantification and Visualization of Probabilistic Features in Fields with Uncertainties N2 - Eine grundlegende Eigenschaft von naturwissenschaftlichen Daten ist, dass der wahre Wert einer Größe nicht beliebig genau bestimmbar ist. Es ist lediglich möglich, ihn durch Intervalle einzugrenzen oder die Unsicherheit durch eine Wahrscheinlichkeitsverteilung zu charakterisieren. Dies gilt für alle reellwertigen Daten, sowohl für Mess-, als auch für Simulationsergebnisse. Beispiele sind Messungen von grundlegenden physikalischen Größen wie Geschwindigkeit oder auch langfristige Temperaturvorhersagen, die durch Klimamodelle berechnet werden. Die Unsicherheit von Ergebnissen ist eine wichtige Information, die in Natur- und Ingenieurwissenschaften häufig durch Konfidenzintervalle in 1D-Plots und Tabellen angezeigt wird. Im Gegensatz dazu ist es bisher bei der Visualisierung von 2D- und 3D-Daten mithilfe von Standardmethoden meist unmöglich, die Datenunsicherheit zu repräsentieren. Diese Arbeit stellt wahrscheinlichkeitstheoretisch fundierte Methoden vor, die die Analyse und Visualisierung von Skalar-, Vektor- und Tensorfeldern mit Unsicherheiten ermöglichen. Der Fokus liegt dabei auf der Extraktion von raumzeitlichen geometrischen und topologischen Merkmalen aus den Feldern (z.B. Isokonturen und kritische Punkte). Wir nutzen parametrische und nichtparametrische Zufallsfelder, um Variabilität und räumliche Korrelation mathematisch zu modellieren. Die Wahrscheinlichkeitsverteilungen werden aus Ensemble-Datensätzen geschätzt, die mehrere Simulationsergebnisse (z.B. basierend auf variierenden Simulationsparametern) zusammenfassen. Wir untersuchen die Konditionszahlen von Merkmalsextraktionsmethoden, um die Sensitivität, d.h. die Verstärkung oder Abschwächung der Unsicherheit der Ergebnisse relativ zu Unsicherheiten in den Eingangsdaten abzuschätzen. Wir stellen einen allgemeiner Ansatz für die probabilistische Merkmalsextraktion vor, der die Basis für die Berechnung räumlicher Wahrscheinlichkeitsverteilungen von verschiedenen Merkmalen in Skalar-, Vektor- und Tensorfeldern bildet. In diesem Framework werden Wahrscheinlichkeiten für die Existenz von Merkmalen aus lokalen Randverteilungen und formalen Merkmalsdefinitionen berechnet. Numerisch können die Wahrscheinlichkeiten durch Monte-Carlo­-Integration bestimmt werden. Um den hohen Rechenaufwand dieses Ansatzes zu vermeiden, schlagen wir schnelle Berechnungsmethoden vor, wobei Merkmalswahrscheinlichkeiten näherungsweise mit Hilfe von Surrogatfunktionen bzw. Lookup-Tabellen geschätzt werden. Die vorgeschlagenen Methoden werden anhand von Daten aus Klima- und Biofluidmechaniksimulationen sowie aus der medizinischen Bildgebung qualitativ und quantitativ evaluiert. KW - uncertainty quantification KW - feature extraction KW - probability Y1 - 2015 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000099462?lang=en ER - TY - THES A1 - Schotte, Merlind T1 - Automatische Dickenbestimmung der mineralisierten Schicht in Skelettelementen von Knorpelfischen anhand von CT- Bilddaten N2 - Diese Bachelorarbeit beschäftigt sich mit der Entwicklung eines allgemeinen Verfahrens, welches die Dicke der mineralisierten Schicht von Haikieferelementen automatisch bestimmt. Dabei soll das Verfahren die Dicke näherungsweise im zweidimensionalen (2D) Raum sowie im dreidimensionalen (3D) Raum anhand von Computertomografie-Scans berechnen (im Folgenden als zweidimensionaler bzw. dreidimensionaler Fall bezeichnet). Es werden drei mögliche Verfahren eingeführt und im Anschluss auf ihre Verwendbarkeit analysiert. Für die Implementierung zur Dickenbestimmung wird der Kern der Rayburst Sampling Methode verwendet und im Weiteren für den 2D-Raum durch kleinere Optimierungen verbessert. Die Überprüfung der Genauigkeit des für den zweidimensionalen Fall entwickelten Programms erfolgt manuell. Für einen Vergleich im 3D-Raum wird ein zweites Verfahren programmiert, das auf der Berechnung der Isoflächen basiert. Diese Arbeit ist in den Bereich der angewandten Mathematik mit dem Schwerpunkt Informatik einzuordnen. Das entwickelte Programm wird im Anschluss Anwendung im Bereich der Biologie am Max-Planck-Institut für Grenzflächen- und Kolloidforschung Potsdam-Golm finden. Y1 - 2015 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Poulikakos, Lisa A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Time-harmonic optical chirality in inhomogeneous space JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2209551 VL - 9756 SP - 97560X ER - TY - GEN A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On metastability and Markov state models for non-stationary molecular dynamics BT - 2016 Editor's Choice of The Journal of Chemical Physics T2 - The Journal of Chemical Physics N2 - We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples. T3 - ZIB-Report - 16-11 KW - coherent set, KW - Markov state model KW - non-equilibrium molecular dynamics KW - metastability Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57869 SN - 1438-0064 VL - 174103 ET - 145 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Mehrgahrdt, Julika A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - The Cycle Embedding Problem T2 - Operations Research Proceedings 2014 N2 - Given two hypergraphs, representing a fine and a coarse "layer", and a cycle cover of the nodes of the coarse layer, the cycle embedding problem (CEP) asks for an embedding of the coarse cycles into the fine layer. The CEP is NP-hard for general hypergraphs, but it can be solved in polynomial time for graphs. We propose an integer rogramming formulation for the CEP that provides a complete escription of the CEP polytope for the graphical case. The CEP comes up in railway vehicle rotation scheduling. We present computational results for problem instances of DB Fernverkehr AG that justify a sequential coarse-first-fine-second planning approach. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-28697-6_65 SP - 465 EP - 472 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Gutsche, Philipp A1 - Schmidt, Frank T1 - Method for fast computation of angular light scattering spectra from 2D periodic arrays JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2219666 VL - 9778 SP - 977839 ER - TY - THES A1 - Rehfeldt, Daniel T1 - A Generic Approach to Solving the Steiner Tree Problem and Variants N2 - Spawned by practical applications, numerous variations of the classical Steiner tree problem in graphs have been studied during the last decades. Despite the strong relationship between the different variants, solution approaches employed so far have been prevalently problem-specific. In contrast, we pursue a general-purpose strategy resulting in a solver able to solve both the classical Steiner tree problem and ten of its variants without modification. These variants include well-known problems such as the prize-collecting Steiner tree problem, the maximum-weight connected subgraph problem or the rectilinear minimum Steiner tree problem. Bolstered by a variety of new methods, most notably reduction techniques, our solver is not only of unprecedented versatility, but furthermore competitive or even superior to specialized state-of-the-art programs for several Steiner problem variants. KW - Steiner Tree Problem KW - Steiner Tree Problem Variants Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57817 ER - TY - GEN A1 - Gleixner, Ambros A1 - Berthold, Timo A1 - Müller, Benjamin A1 - Weltge, Stefan T1 - Three Enhancements for Optimization-Based Bound Tightening N2 - Optimization-based bound tightening (OBBT) is one of the most effective procedures to reduce variable domains of nonconvex mixed-integer nonlinear programs (MINLPs). At the same time it is one of the most expensive bound tightening procedures, since it solves auxiliary linear programs (LPs)—up to twice the number of variables many. The main goal of this paper is to discuss algorithmic techniques for an efficient implementation of OBBT. Most state-of-the-art MINLP solvers apply some restricted version of OBBT and it seems to be common belief that OBBT is beneficial if only one is able to keep its computational cost under control. To this end, we introduce three techniques to increase the efficiency of OBBT: filtering strategies to reduce the number of solved LPs, ordering heuristics to exploit simplex warm starts, and the generation of Lagrangian variable bounds (LVBs). The propagation of LVBs during tree search is a fast approximation to OBBT without the need to solve auxiliary LPs. We conduct extensive computational experiments on MINLPLib2. Our results indicate that OBBT is most beneficial on hard instances, for which we observe a speedup of 17% to 19% on average. Most importantly, more instances can be solved when using OBBT. T3 - ZIB-Report - 15-16 KW - MINLP KW - optimization-based bound tightening KW - optimality-based bound tightening KW - OBBT KW - propagation KW - bound tightening Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57803 SN - 1438-0064 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank A1 - Ledentsov, Jr., Nikolay T1 - Direct visualization of the in-plane leakage of high-order transverse modes in vertical-cavity surface-emitting lasers mediated by oxide-aperture engineering JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2208909 VL - 9766 SP - 976608 ER - TY - JOUR A1 - Jäger, Klaus A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Simulations of sinusoidal nanotextures for coupling light into c-Si thin-film solar cells JF - Opt. Express Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.00A569 VL - 24 SP - A569 ER - TY - GEN A1 - Gamrath, Gerald A1 - Fischer, Tobias A1 - Gally, Tristan A1 - Gleixner, Ambros A1 - Hendel, Gregor A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schenker, Sebastian A1 - Schwarz, Robert A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Winkler, Michael A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 3.2 N2 - The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers. This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs. T3 - ZIB-Report - 15-60 KW - mixed-integer linear and nonlinear programming KW - MIP solver KW - MINLP solver KW - linear programming KW - LP solver KW - simplex method KW - modeling KW - parallel branch-and-bound KW - branch-cut-and-price framework KW - generic column generation KW - Steiner tree solver KW - multi-criteria optimization KW - mixed-integer semidefinite programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57675 SN - 1438-0064 ER - TY - GEN A1 - D'Andreagiovanni, Fabio T1 - Revisiting wireless network jamming by SIR-based considerations and Multiband Robust Optimization N2 - We revisit the mathematical models for wireless network jamming introduced by Commander et al. (2007,2008): we first point out the strong connections with classical wireless network design and then we propose a new model based on the explicit use of signal-to-interference quantities. Moreover, to ad- dress the uncertain nature of the jamming problem and tackle the peculiar right-hand-side (RHS) uncertainty of the corresponding model, we propose an original robust cutting-plane algorithm drawing inspiration from Multiband Robust Optimization. Finally, we assess the performance of the proposed cutting plane algorithm by experiments on realistic network instances. T3 - ZIB-Report - 15-12 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57728 SN - 1438-0064 N1 - Published in Optimization Letters 9 (8), 1495-1510, 2015 (First online: 24 December 2014). The final publication is available at Springer http://dx.doi.org/10.1007/s11590-014-0839-2. ER - TY - CHAP A1 - Cao, Karl-Kiên A1 - Gleixner, Ambros A1 - Miltenberger, Matthias T1 - Methoden zur Reduktion der Rechenzeit linearer Optimierungsmodelle in der Energiewirtschaft - Eine Performance-Analyse T2 - EnInnov 2016: 14. Symposium Energieinnovation 2016 N2 - Dieser Beitrag stellt mögliche Ansätze zur Reduktion der Rechenzeit von linearen Optimierungsproblemen mit energiewirtschaftlichem Anwendungshintergrund vor. Diese Ansätze bilden im Allgemeinen die Grundlage für konzeptionelle Strategien zur Beschleunigung von Energiesystemmodellen. Zu den einfachsten Beschleunigungsstrategien zählt die Verkleinerung der Modelldimensionen, was beispielsweise durch Ändern der zeitlichen, räumlichen oder technologischen Auflösung eines Energiesystemmodells erreicht werden kann. Diese Strategien sind zwar häufig ein Teil der Methodik in der Energiesystemanalyse, systematische Benchmarks zur Bewertung ihrer Effektivität werden jedoch meist nicht durchgeführt. Die vorliegende Arbeit adressiert genau diesen Sachverhalt. Hierzu werden Modellinstanzen des Modells REMix in verschiedenen Größenordnungen mittels einer Performance-Benchmark-Analyse untersucht. Die Ergebnisse legen zum einen den Schluss nahe, dass verkürzte Betrachtungszeiträume das größte Potential unter den hier analysierten Strategien zur Reduktion von Rechenzeit bieten. Zum anderen empfiehlt sich die Verwendung des Barrier-Lösungsverfahrens mit multiplen Threads unter Vernachlässigung des Cross-Over. Y1 - 2016 ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Prior estimation and Bayesian inference from large cohort data sets N2 - One of the main goals of mathematical modelling in systems biology related to medical applications is to obtain patient-specific parameterisations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Using these population data, we propose an iterative algorithm for contructing an informative prior distribution, which then serves as the basis for computing patient-specific posteriors and obtaining individual predictions. We demonsrate the performance of our method by applying it to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling. T3 - ZIB-Report - 16-09 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57475 SN - 1438-0064 ER - TY - CHAP A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf T1 - An Approximation Result for Matchings in Partitioned Hypergraphs T2 - Operations Research Proceedings 2014 N2 - We investigate the matching and perfect matching polytopes of hypergraphs having a special structure, which we call partitioned hypergraphs. We show that the integrality gap of the standard LP-relaxation is at most $2\sqrt{d}$ for partitioned hypergraphs with parts of size $\leq d$. Furthermore, we show that this bound cannot be improved to $\mathcal{O}(d^{0.5-\epsilon})$. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-28697-6_5 SP - 31 EP - 36 PB - Springer International Publishing ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Template based re-optimization of rolling stock rotations T2 - Proceedings of Conference on Advanced Systems in Public Transport 2015 (CASPT2015) N2 - Rolling stock, i.e., rail vehicles, are among the most expensive and limited assets of a railway company. They must be used efficiently applying optimization techniques. One important aspect is re-optimization, which is the topic that we consider in this paper. We propose a template concept that allows to compute cost minimal rolling stock rotations under a large variety of re-optimization requirements. Two examples, involving a connection template and a rotation template, are discussed. An implementation within the rolling stock rotation optimizer rotor and computational results for scenarios provided by DB Fernverkehr AG, one of the leading railway operators in Europe, are presented. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57539 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Reuther, Markus T1 - Regional Search for the Resource Constrained Assignment Problem T2 - 15th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2015) N2 - The resource constrained assignment problem (RCAP) is to find a minimal cost partition of the nodes of a directed graph into cycles such that a resource constraint is fulfilled. The RCAP has its roots in rolling stock rotation optimization where a railway timetable has to be covered by rotations, i.e., cycles. In that context, the resource constraint corresponds to maintenance constraints for rail vehicles. Moreover, the RCAP generalizes variants of the vehicle routing problem (VRP). The paper contributes an exact branch and bound algorithm for the RCAP and, primarily, a straightforward algorithmic concept that we call regional search (RS). As a symbiosis of a local and a global search algorithm, the result of an RS is a local optimum for a combinatorial optimization problem. In addition, the local optimum must be globally optimal as well if an instance of a problem relaxation is computed. In order to present the idea for a standardized setup we introduce an RS for binary programs. But the proper contribution of the paper is an RS that turns the Hungarian method into a powerful heuristic for the resource constrained assignment problem by utilizing the exact branch and bound. We present computational results for RCAP instances from an industrial cooperation with Deutsche Bahn Fernverkehr AG as well as for VRP instances from the literature. The results show that our RS provides a solution quality of 1.4 % average gap w.r.t. the best known solutions of a large test set. In addition, our branch and bound algorithm can solve many RCAP instances to proven optimality, e.g., almost all asymmetric traveling salesman and capacitated vehicle routing problems that we consider. Y1 - 2015 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2015.111 VL - 48 SP - 111 EP - 129 ER - TY - JOUR A1 - Hoppmann, Heide T1 - Linienplanung und Minimale Konfigurationen JF - OR News Y1 - 2015 VL - 55 SP - 22 EP - 23 ER - TY - CHAP A1 - Grötschel, Martin A1 - Borndörfer, Ralf T1 - Mathematik im Verkehr T2 - HEUREKA '14. Vorträge der Tagung am 2./3. April 2014 in Stuttgart N2 - Nach einem kurzen Abriss über die Bedeutung des Verkehrssektors als eine wichtige Schlüsseltechnologie im gesamten Verlauf der Menschheitsgeschichte skizzieren wir die Rolle der Mathematik für Verkehr und Transport. Wir spekulieren dann über zukünftige Entwicklungen, insbesondere im Bereich des öffentlichen Personenverkehrs, und begründen, dass die in diesem Bereich anstehenden Herausforderungen nur mit dem Einsatz mathematischer Methoden angemessen bewältigt werden können. Die demographischen Prozesse, die in verschiedenen Teilen der Welt unterschiedlich verlaufen, wie z.B. Überalterung in Europa oder dynamische Trends zu Megastädten in Entwicklungsländern, sich ändernde Lebens- und Produktionsverhältnisse, stark wachsender Bedarf nach Mobilität und enormes Anwachsen der Komplexität der Verkehrsplanung und -durchführung, machen einen verstärkten Zugriff auf mathematische Modellierung, Simulation und Optimierung notwendig. Diese Entwicklung stellt sowohl große Herausforderungen an die Mathematik, wo vielfach noch keine geeigneten Methoden vorhanden sind, als auch an die Praktiker im Bereich von Verkehr und Transport, die sich mit neuen Planungs- und Steuerungstechnologien befassen und diese effizient einsetzen müssen. Hier wird intensive Kooperation zwischen vielen beteiligten Akteuren gefragt sein. Y1 - 2014 SN - 978-3-86446-074-6 SP - 28 EP - 44 ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf A1 - Knoben, Loes A1 - Kretz, David A1 - Uetz, Marc J. T1 - The S-Bahn Challenge in Berlin JF - OR News Y1 - 2015 UR - https://gor.uni-paderborn.de/index.php?id=362 IS - 53 SP - 10 EP - 14 ER - TY - GEN A1 - Kuhn, Alexander A1 - Trömel, Silke T1 - Intercomparison Study of Cloud Feature Extraction and Tracking Algorithms BT - EGU General Assembly 2015, held 12-17 April, 2015 in Vienna, Austria T2 - Geophysical Research Abstracts, Vol 17 N2 - Clouds and precipitation systems are fundamental features in the global climate cycle and are one focus aspect of recent high resolution, cloud resolving simulations and measurement modalities. Highly resolved data sources allow for more precise methodologies to extract and track cloud features on different scales and enable novel evaluation tasks such as life-cycle tracking, feature-based statistics, and feature-based comparison of simulation and measurements. However, their complex dynamics and highly variable shape morphology makes extraction and tracking of clouds a challenging task with respect to stable and reliable algorithms. In this work we will present our efforts on establishing an community-wide inter-comparison study to provide an overview of state-of-the-art algorithms for cloud extraction and tracking. We propose a set of 2D and 3D benchmark data sets (from simulations and measurements) that are used as a common basis for comparison. In addition we describe a joint feature-based evaluation framework and provide an in depth analysis and comparison of those algorithms. The goal is to systematically compare and assess numerical extraction and tracking techniques for cloud features in meteorological data and provide a comprehensive overview of suitable application scenarios, describe current strengths and limitations, and derive statements about their variability for feature-based analysis tasks. Y1 - 2015 N1 - Oral presentation at EGU 2015 VL - 17 SP - ID 14128 ER - TY - CHAP A1 - Klug, Torsten A1 - Junosza-Szaniawski, Konstanty A1 - Kwasiborski, Slawomir A1 - Fügenschuh, Armin A1 - Schlechte, Thomas T1 - Fastest, Average and Quantile Schedule T2 - SOFSEM 2015: Theory and Practice of Computer Science N2 - We consider problems concerning the scheduling of a set of trains on a single track. For every pair of trains there is a minimum headway, which every train must wait before it enters the track after another train. The speed of each train is also given. Hence for every schedule - a sequence of trains - we may compute the time that is at least needed for all trains to travel along the track in the given order. We give the solution to three problems: the fastest schedule, the average schedule, and the problem of quantile schedules. The last problem is a question about the smallest upper bound on the time of a given fraction of all possible schedules. We show how these problems are related to the travelling salesman problem. We prove NP-completeness of the fastest schedule problem, NP-hardness of quantile of schedules problem, and polynomiality of the average schedule problem. We also describe some algorithms for all three problems. In the solution of the quantile problem we give an algorithm, based on a reverse search method, generating with polynomial delay all Eulerian multigraphs with the given degree sequence and a bound on the number of such multigraphs. A better bound is left as an open question. KW - scheduling KW - eulerian multigraphs Y1 - 2015 U6 - https://doi.org/10.1007/978-3-662-46078-8_17 SP - 201 EP - 216 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Heismann, Olga T1 - The hypergraph assignment problem JF - Discrete Optimization Y1 - 2015 U6 - https://doi.org/10.1016/j.disopt.2014.11.002 VL - 15 SP - 15 EP - 25 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Reduced basis method for the optimization of nano-photonic devices N2 - Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occuring e. g. in optical metrology. The reduced basis method presented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources. T3 - ZIB-Report - 16-10 KW - reduced basis method KW - model reduction KW - optical critical dimension metrology KW - electromagnetic field solver Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57556 SN - 1438-0064 ER - TY - THES A1 - Gamrath, Gerald T1 - Generic Branch-Cut-and-Price N2 - In this thesis, we present the theoretical background, implementational details and computational results concerning the generic branch-cut-and-price solver GCG. KW - mixed-integer programming KW - column generation KW - branch-and-price Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57543 ER - TY - CHAP A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Winkler, Michael T1 - Structure-Based Primal Heuristics for Mixed Integer Programming T2 - Optimization in the Real World N2 - Primal heuristics play an important role in the solving of mixed integer programs (MIPs). They help to reach optimality faster and provide good feasible solutions early in the solving process. In this paper, we present two new primal heuristics which take into account global structures available within MIP solvers to construct feasible solutions at the beginning of the solving process. These heuristics follow a large neighborhood search (LNS) approach and use global structures to define a neighborhood that is with high probability significantly easier to process while (hopefully) still containing good feasible solutions. The definition of the neighborhood is done by iteratively fixing variables and propagating these fixings. Thereby, fixings are determined based on the predicted impact they have on the subsequent domain propagation. The neighborhood is solved as a sub-MIP and solutions are transferred back to the original problem. Our computational experiments on standard MIP test sets show that the proposed heuristics find solutions for about every third instance and therewith help to improve the average solving time. Y1 - 2015 SN - 978-4-431-55419-6 U6 - https://doi.org/10.1007/978-4-431-55420-2_3 VL - 13 SP - 37 EP - 53 PB - Springer Japan ER - TY - CHAP A1 - Gamrath, Gerald A1 - Melchiori, Anna A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Salvagnin, Domenico T1 - Branching on Multi-aggregated Variables T2 - Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2015 N2 - In mixed-integer programming, the branching rule is a key component to a fast convergence of the branch-and-bound algorithm. The most common strategy is to branch on simple disjunctions that split the domain of a single integer variable into two disjoint intervals. Multi-aggregation is a presolving step that replaces variables by an affine linear sum of other variables, thereby reducing the problem size. While this simplification typically improves the performance of MIP solvers, it also restricts the degree of freedom in variable-based branching rules. We present a novel branching scheme that tries to overcome the above drawback by considering general disjunctions defined by multi-aggregated variables in addition to the standard disjunctions based on single variables. This natural idea results in a hybrid between variable- and constraint-based branching rules. Our implementation within the constraint integer programming framework SCIP incorporates this into a full strong branching rule and reduces the number of branch-and-bound nodes on a general test set of publicly available benchmark instances. For a specific class of problems, we show that the solving time decreases significantly. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-18008-3_10 VL - 9075 SP - 141 EP - 156 ER - TY - GEN A1 - Hoppmann, Heide T1 - An Extended Formulation for the Line Planning Problem N2 - In this paper we present a novel extended formulation for the line planning problem that is based on what we call “configurations” of lines and frequencies. Configurations account for all possible options to provide a required transportation capacity on an infrastructure edge. The proposed configuration model is strong in the sense that it implies several facet-defining inequalities for the standard model: set cover, symmetric band, MIR, and multicover inequalities. These theoretical findings can be confirmed in computational results. Further, we show how this concept can be generalized to define configurations for subsets of edges; the generalized model implies additional inequalities from the line planning literature. T3 - ZIB-Report - 16-08 KW - Line Planning, Extended Formulation, Public Transport Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57467 SN - 1438-0064 ER - TY - GEN A1 - Kozlikova, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets. T3 - ZIB-Report - 15-63 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57217 SN - 1438-0064 ER - TY - JOUR A1 - Berthold, Timo A1 - Hendel, Gregor T1 - Shift-and-Propagate JF - Journal of Heuristics N2 - In recent years, there has been a growing interest in the design of general purpose primal heuristics for use inside complete mixed integer programming solvers. Many of these heuristics rely on an optimal LP solution, which may take a significant amount of time to find. In this paper, we address this issue by introducing a pre-root primal heuristic that does not require a previously found LP solution. This heuristic, named Shift-and-Propagate , applies domain propagation techniques to quickly drive a variable assignment towards feasibility. Computational experiments indicate that this heuristic is a powerful supplement to existing rounding and propagation heuristics. Y1 - 2014 U6 - https://doi.org/10.1007/s10732-014-9271-0 VL - 21 IS - 1 SP - 73 EP - 106 ER - TY - THES A1 - Lubkoll, Lars T1 - An Optimal Control Approach to Implant Shape Design : Modeling, Analysis and Numerics N2 - Facial trauma or congenital malformation of bones of the skull may degrade both skeletal integrity as well as the esthetic appearance. For the attending surgeon a prediction of the esthetic outcome of a bone replacement or augmentation implant insertion is challenging. Therefore, it would be advantageous if we were able to compute an implant shape from a given desired outcome. This task presents the main focus of this thesis. Besides the development of a model for the implant shape design problem, this work is concerned with the efficient solution and optimization of realistic models. This includes recent material laws for different soft tissue types as well as complex geometries attained from medical image data. The implant shape design problem can be described as an optimal control problem with constraints given by the necessary optimality conditions in polyconvex hyperelasticity with nonlinear pressure-type boundary conditions. Important theoretical results, such as existence of solutions and higher regularity, are currently not available for such problems. Based on the existence result for polyconvex materials laws, existence of solutions of the nonconvex optimal control problem is proven for the case of a simpler Neumann boundary condition. Due to the “impossible convexity” and the high nonlinearity of hyperelastic material laws the numerical solution of the arising problems is difficult. In this regard, an affine covariant composite step method for nonconvex, equality constrained optimization is presented. The corresponding globalization strategy is based on the affine covariant Newton method for underdetermined systems and cubic regularization methods for unconstrained optimization problems. The linear systems arising from the discretization of constrained optimization problems are described by saddle point matrices. The efficient solution of these equality systems by conjugate gradient methods for convex and nonconvex problems is discussed. Moreover, an error estimator that fits into the affine covariant setting is presented. The presented composite step method was implemented in the C++ finite element library Kaskade 7. The performance of the algorithm is demonstrated on several examples. Next to simple optimization problems, with admissible set given through models of linear and nonlinear heat transfer, we give four examples with nonconvex, hyperelastic constraints. Y1 - 2015 UR - https://epub.uni-bayreuth.de/2522/ ER - TY - JOUR A1 - Wohlfeil, Benjamin A1 - Rademacher, Georg A1 - Stamatiadis, Christos A1 - Voigt, Karsten A1 - Zimmermann, Lars A1 - Petermann, Klaus T1 - A Two Dimensional Fiber Grating Coupler on SOI for Mode Division Multiplexing JF - IEEE Photon. Technol. Lett. Y1 - 2016 U6 - https://doi.org/10.1109/LPT.2016.2514712 VL - 28 SP - 1241 ER - TY - JOUR A1 - Fodor, Bálint A1 - Kozma, Peter A1 - Burger, Sven A1 - Fried, Miklos A1 - Petrik, Peter T1 - Effective medium approximation of ellipsometric response from random surface roughness simulated by finite-element method JF - Thin Solid Films Y1 - 2016 U6 - https://doi.org/10.1016/j.tsf.2016.01.054 VL - 617 SP - 20 ER - TY - GEN A1 - Gutsche, Philipp A1 - Poulikakos, Lisa A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Schmidt, Frank T1 - Optical chirality: conservation law in arbitrary space T2 - 606. WE-Heraeus-Seminar on Nanophotonics and Complex Spatial Modes of Light N2 - The introduction of the near-field quantity of optical chirality has emerged in various numerical and few experimental studies of local chirality enhancement due to its relation to the excitation rate of chiral molecules. This time-even pseudoscalar has been dismissed as being a higher-order version of helicity. Nevertheless, we revisit the derivation of the underlying conservation law and define optical chirality in media similar to. We identify the mechanism of chirality conversion by either inhomogeneous or anisotropic space to complement the conservation of optical chirality. The conservation law of optical chirality in arbitrary space enables the extension of the concept of polarization to the near-field where no distiniguished propagation direction of light is present. We show that the connection of electromagnetic energy and optical chirality provide the ability to define a circular polarization basis in time-harmonic near-field analysis. In order to illustrate our theory, we present electromagnetic field simulations of simple as well as more complex nanostructures. Results using the well-known far-field polarization concept are readily reproduced and extended from the point of view of chirality conversion. Y1 - 2016 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Pomplun, Jan A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs N2 - Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters. T3 - ZIB-Report - 16-06 KW - finite element method KW - rigorous optical modeling KW - photonic crystals KW - reduced basis method KW - parameter estimation KW - optical metrology Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57249 SN - 1438-0064 ER - TY - CHAP A1 - Fischer, Frank A1 - Schlechte, Thomas T1 - Comparing two dual relaxations of large scale train timetabling problems T2 - Proceedings of Conference on Advanced Systems in Public Transport 2015 N2 - Railway transportation and in particular train timetabling is one of the basic and source application areas of combinatorial optimization and integer programming. We will discuss two well established modeling techniques for the train timetabling problem. In this paper we focus on one major ingredient - the bounding by dual relaxations. We compare two classical dual relaxations of large scale time expanded train timetabling problems - the Lagrangean Dual and Lagrangean Decomposition. We discuss the convergence behavior and show limitations of the Lagrangean Decomposition approach for a configuration based model. We introduce a third dualization approach to overcome those limitations. Finally, we present promising preliminary computational experiments that show that our new approach indeed has superior convergence properties. Y1 - 2015 ER - TY - THES A1 - Schneck, Jakob T1 - Zielorientierte Fehlerschätzer für die Topologieoptimierung Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57303 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Swarat, Elmar A1 - Weider, Steffen T1 - Duty Rostering in Public Transport - Facing Preferences, Fairness, and Fatigue T2 - Proceedings of Conference on Advanced Systems in Public Transport 2015 (CASPT2015) N2 - Duty rostering problems occur in different application contexts and come in different flavors. They give rise to very large scale integer programs which ypically have lots of solutions and extremely fractional LP relaxations. In such a situation, heuristics can be a viable algorithmic choice. We propose an mprovement method of the Lin-Kernighan type for the solution of duty rostering problems. We illustrate its versatility and solution quality on three different applications in public transit, vehicle routing, and airline rostering with a focus on the management of preferences, fairness, and fatigue, respectively. Y1 - 2015 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Lamorgese, Leonardo A1 - Klug, Torsten A1 - Mannino, Carlo A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Recent Success Stories on Optimization of Railway Systems T2 - Proceedings of the IAROR conference RailTokyo N2 - Planning and operating railway transportation systems is an extremely hard task due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. Because of that, however, mathematical models and optimization techniques can result in large gains for both railway cus- tomers and operators, e.g., in terms of cost reductions or service quality improvements. In the last years a large and growing group of researchers in the OR community have devoted their attention to this domain devel- oping mathematical models and optimization approaches to tackle many of the relevant problems in the railway planning process. However, there is still a gap to bridge between theory and practice, with a few notable exceptions. In this paper we address three success stories, namely, long-term freight train routing (part I), mid-term rolling stock rotation planning (part II), and real-time train dispatching (part III). In each case, we describe real-life, successful implementations. We will dis- cuss the individual problem setting, survey the optimization literature, and focus on particular aspects addressed by the mathematical models. We demonstrate on concrete applications how mathematical optimization can support railway planning and operations. This gives proof that math- ematical optimization can support the planning of rolling stock resources. Thus, mathematical models and optimization can lead to a greater effi- ciency of railway operations and will serve as a powerful and innovative tool to meet recent challenges of the railway industry. Y1 - 2015 ER - TY - THES A1 - Spiegel, Christoph T1 - Approximating Primitive Integand Aircraft Performance N2 - A commercial aircraft cannot freely use the available airspace but instead has to stick to a three-dimensional network of segments similar to a car in a road network. In this network it faces several variable and interdependent costs in the form of travel time, fuel consumption and overflight charges. These are also highly dependent on other factors such as weather conditions, aircraft performance, take-off time and weight as well as the changing availability of elements in the graph. This is further complicated by the distinction of separate flight phases that challenge the standard notion of a graph with predetermined nodes and arcs. Therefore when trying to find either a distance, fuel, time or cost minimal trajectory for a specific aircraft between an origin and a destination airport, one faces a very complex shortest path problem in the airway network graph that even for strong implifications is often NP-hard. This thesis will focus on exploring the costs that occur in this graph and that are associated with the aircraft performance. Here we will rely on actual performance and weather data supplied by Lufthansa Systems AG in Frankfurt and analyze whether they meet the requirements necessary for common algorithms such as the First-in, First-out property. Since it is vital for any shortest path algorithm to have a fast and accurate way of determining the costs in the graph, we will face two problems regarding the calculation of aircraft performance during cruise as well as the calculation of the so-called air distance. So far these problems have been approached by the industry with rudimentary approximative methods. We will reformulate them as initial value problems and try to find good approximations using both general Runge-Kutta methods as well as a novel approach which relies on finding piecewise linear approximations of some primitive integrals in pre-processing. Computations will show that these approaches deliver fast and accurate results. Y1 - 2015 ER - TY - THES A1 - Brückner, Michael T1 - On the Shortest Path Problem with Pair Constraints N2 - This thesis investigates the shortest path problem with pair constraints or the pair constraint problem (PCP) for short. We consider two types of pair constraints, namely forbidden pairs and binding pairs consisting of two distinct vertices each. A path respects a forbidden pair if it uses at most one of the two vertices and it respects a binding pair (x,y) if it uses also y, if x is used. Within this thesis, we bring together and compare several formulations and variants of the pair constraint problem and their complexities. We also collect existing recursive algorithms and present their running times. Most of the presented contributions only consider forbidden pairs. We introduce a new recursive algorithm also handling binding pairs and prove its theoretical complexity of O(n^4). We implemented the algorithm and tested it on real-world instances provided by Lufthansa Systems AG. Therefore we needed to develop a heuristic translating the real-world data into an instance of the shortest path problem with pair constraints. This heuristic is presented as well as all computational results. In Chapter 4, we start investigating the associated polytope of an integer program formulation of the shortest path problem with pair constraints. For the case of one forbidden or binding pair, we find a complete linear description of the associated polytope. We prove that the number of facets grows exponentially in |V| even in these simple cases. However, separation is still possible in polynomial time. The complete linear description can be extended to the case of contiguously disjoint pairs. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57265 ER - TY - JOUR A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Brückner, Michael A1 - Hoang, Nam-Dung A1 - Schlechte, Thomas T1 - On the Path Avoiding Forbidden Pairs Polytope JF - Electronic Notes in Discrete Mathematics N2 - Given a directed, acyclic graph, a source and a sink node, and a set of forbidden pairs of arcs, the path avoiding forbidden pairs (PAFP) problem is to find a path that connects the source and sink nodes and contains at most one arc from each forbidden pair. The general version of the problem is NP-hard, but it becomes polynomially solvable for certain topological configurations of the pairs. We present the first polyhedral study of the PAFP problem. We introduce a new family of valid inequalities for the PAFP polytope and show that they are sufficient to provide a complete linear description in the special case where the forbidden pairs satisfy a disjointness property. Furthermore, we show that the number of facets of the PAFP polytope is exponential in the size of the graph, even for the case of a single forbidden pair. Y1 - 2015 U6 - https://doi.org/10.1016/j.endm.2015.07.057 VL - 50 SP - 343 EP - 348 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures T2 - Proc. SPIE N2 - Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell’s equation. Highly accurate geometrical modeling and numerical accuracy atcomputational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scatteringoptical wavelengths off periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range. T3 - ZIB-Report - 16-05 KW - reduced basis method KW - finite element method KW - rigorous optical modeling KW - reduced order models KW - electromagnetic field solver Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57239 SN - 1438-0064 VL - 9742 SP - 97420M ER - TY - JOUR A1 - Poulikakos, Lisa A1 - Gutsche, Philipp A1 - McPeak, Kevin A1 - Burger, Sven A1 - Niegemann, Jens A1 - Hafner, Christian A1 - Norris, David T1 - The Optical Chirality Flux as a Useful Far-Field Probe of Chiral Near Fields JF - ACS Photonics Y1 - 2016 U6 - https://doi.org/10.1021/acsphotonics.6b00201 VL - 3 SP - 1619 ER - TY - THES A1 - Dercksen, Vincent J. T1 - Visual computing techniques for the reconstruction and analysis of anatomically realistic neural networks N2 - To understand how the brain translates sensory input into behavior, one needs to identify, at the cellular level, the involved neural circuitry and the electrical signals it carries. This thesis describes methods and tools that enable neuroscientists to obtain important anatomical data, including neuron numbers and shapes, from 3D microscopy images. On this basis, tools have been developed to create and visually analyze anatomically realistic 3D models of neural networks: 1. An automatic segmentation method for determining the number and location of neuron cell bodies in 3D microscopy images. Application of this method yields a difference of merely ∼4% between automatically and manually counted cells, which is sufficiently accurate for application in large-scale counting experiments. 2. A method for the automatic alignment of 3D section volumes containing filamentous structures. To this end, an existing point-matching-based method has been adapted such that sections containing neuron and microtubule fragments could be successfully aligned. 3. The Filament Editor, a 3D proof-editing tool for visual verification and correction of automatically traced filaments. The usefulness of the Filament Editor is demonstrated by applying it in a validated neuron reconstruction pipeline to create 3D models of long-range and complex neuronal branches. 4. The tool NeuroNet, which is used to assemble an anatomical model of a neural network representing the rat barrel cortex (or subnetworks therein, e.g. individual cortical columns), based on reconstructed anatomical data, such as neuron distributions and 3D morphologies. The tool estimates synaptic connectivity between neurons based on structural overlap between axons and dendrites. 5. A framework for the interactive visual analysis of synaptic connectivity in such networks at multiple scales. It works from the level of neuron populations down to individual synapse positions on dendritic trees. It comprises the Cortical Column Connectivity Viewer, developed to analyze synaptic connections between neuron populations within and between cortical columns. The usefulness of these methods is demonstrated by applying them to reconstruct and analyze neural networks in the rat barrel cortex. Finally, I describe several applications of these methods and tools by neuroscientists, yielding significant biological findings regarding neuron anatomy and connectivity. KW - 3D reconstruction KW - image segmentation KW - neural network KW - neuron tracing KW - connectome Y1 - 2015 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000100938 ER - TY - JOUR A1 - Färber, Claudia A1 - Titschack, Jürgen A1 - Schönberg, Christine H. L. A1 - Ehrig, Karsten A1 - Boos, Karin A1 - Baum, Daniel A1 - Illerhaus, Bernd A1 - Asgaard, Ulla A1 - Bromley, Richard G. A1 - Freiwald, André A1 - Wisshak, Max T1 - Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography JF - Biogeosciences N2 - Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 % of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^−2 yr^−1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments. Y1 - 2016 U6 - https://doi.org/10.5194/bg-13-3461-2016 VL - 13 IS - 11 SP - 3461 EP - 3474 CY - http://www.biogeosciences.net/13/3461/2016/ ER - TY - BOOK ED - Lepper, Verena ED - Deuflhard, Peter ED - Markschies, Christoph T1 - Räume - Bilder - Kulturen Y1 - 2015 SN - 978-3-11-035993-0 PB - De Gruyter ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Lepper, Verena ED - Deuflhard, Peter ED - Markschies, Christoph T1 - Raumtiefe in Malerei und Computergrafik T2 - Räume - Bilder - Kulturen N2 - Einführung: Die Tiefenwirkung dreidimensionaler Räume in einem zweidimensionalen Bild einzufangen, ist ein Faszinosum nahezu aller Kulturen der Menschheitsgeschichte. Der vorliegende Aufsatz folgt den Spuren dieses Faszinosums, vergleichend in der Malerei und der mathematisierten Computergrafik. Die Entdeckung der Zentralperspektive in der italienischen Renaissance zeigt bereits den engen Zusammenhang von Malerei und Mathematik. Auf der Suche nach Maltechniken, mit denen Raumtiefe bildnerisch dargestellt werden kann, beginnen wir in Kap. 2 mit einem chronologischen Gang durch verschiedene Epochen der europäischen Malerei. Hieraus abgeleitete Prinzipien, soweit sie im Rechner realisierbar scheinen, stellen wir in Kap. 3 am Beispiel moderner Methoden der mathematischen Visualisierung vor. Y1 - 2015 SN - 978-3-11-035993-0 SP - 33 EP - 46 PB - Walter De Gruyter ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Mett, Fabian A1 - Pulaj, Jonad T1 - An (MI)LP-based Primal Heuristic for 3-Architecture Connected Facility Location in Urban Access Network Design N2 - We investigate the 3-architecture Connected Facility Location Problem arising in the design of urban telecommunication access networks integrating wired and wireless technologies. We propose an original optimization model for the problem that includes additional variables and constraints to take into account wireless signal coverage represented through signal-to-interference ratios. Since the problem can prove very challenging even for modern state-of-the art optimization solvers, we propose to solve it by an original primal heuristic that combines a probabilistic fixing procedure, guided by peculiar Linear Programming relaxations, with an exact MIP heuristic, based on a very large neighborhood search. Computational experiments on a set of realistic instances show that our heuristic can find solutions associated with much lower optimality gaps than a state-of-the-art solver. T3 - ZIB-Report - 15-62 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57139 SN - 1438-0064 ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Felici, Giovanni A1 - Lacalandra, Fabrizio T1 - Revisiting the use of Robust Optimization for optimal energy offering under price uncertainty N2 - We propose a new Robust Optimization method for the energy offering problem of a price-taker generating company that wants to build offering curves for its generation units, in order to maximize its profit while taking into account the uncertainty of market price. Our investigations have been motivated by a critique to another Robust Optimization method, which entails the solution of a sequence of robust optimization problems imposing full protection and defined over a sequence of nested subintervals of market prices: this method presents a number of issues that may severely limit its application and computational efficiency in practice and that may expose a company to the risk of presenting offering curves resulting into suboptimal or even infeasible accepted offers. To tackle all such issues, our method provides for solving one single robust counterpart, considering an intermediate level of protection between null and full protection, and to make energy offers at zero price, practically eliminating the risk of non-acceptance. Computational results on instances provided by our industrial partners show that our new method is able to grant a great improvement in profit. T3 - ZIB-Report - 15-61 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57128 SN - 1438-0064 N1 - Fabio D'Andreagiovanni is First Author ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Waas, Kerstin A1 - Weider, Steffen T1 - Integrated Optimization of Rolling Stock Rotations for Intercity Railways JF - Transportation Science N2 - This paper proposes a highly integrated solution approach for rolling stock planning problems in the context of long distance passenger traffic between cities. The main contributions are a generic hypergraph-based mixed-integer programming model for the considered rolling stock rotation problem and an integrated algorithm for its solution. The newly developed algorithm is able to handle a large spectrum of industrial railway requirements, such as vehicle composition, maintenance constraints, infrastructure capacities, and regularity aspects. We show that our approach has the power to produce rolling stock rotations that can be implemented in practice. In this way, the rolling stock rotations at the largest German long distance operator Deutsche Bahn Fernverkehr AG could be optimized by an automated system utilizing advanced mathematical programming techniques. Y1 - 2016 U6 - https://doi.org/10.1287/trsc.2015.0633 VL - 50 IS - 3 SP - 863 EP - 877 ER - TY - GEN A1 - Ehrig, Rainald A1 - Dierkes, Thomas A1 - Schäfer, Stefan A1 - Röblitz, Susanna A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Alimguzhin, Vadim A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian A1 - Leeners, Brigitte T1 - An Integrative Approach for Model Driven Computation of Treatments in Reproductive Medicine N2 - We present an overview of the current status of the European collaborative project PAEON. The challenge of PAEON is to provide specialists in reproduc- tive medicine with a computerised model of the menstrual cycle under normal and various pathological conditions, which will allow them to get further in- sight in fertility dynamics. This model also enables the simulation of treatment protocols, which were used within in vitro fertilization. By the definition of virtual patients through biologically admissible parametrizations our approach allows not only the evaluation of a given treatment strategy in silico, but also the design and optimization of such protocols. Once a protocol is formalized in the virtual hospital, the success can be controlled by a treatment execution monitor, which works then as a clinical decision support system. All these tools will be combined in a virtual hospital environment, enabling the access to the PAEON services through the web. T3 - ZIB-Report - 16-04 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57103 SN - 1438-0064 ER - TY - GEN A1 - Hendel, Gregor T1 - Exploiting Solving Phases for Mixed-Integer Programs N2 - Modern MIP solving software incorporates dozens of auxiliary algorithmic components for supporting the branch-and-bound search in finding and improving solutions and in strengthening the relaxation. Intuitively, a dynamic solving strategy with an appropriate emphasis on different solving components and strategies is desirable during the search process. We propose an adaptive solver behavior that dynamically reacts on transitions between the three typical phases of a MIP solving process: The first phase objective is to find a feasible solution. During the second phase, a sequence of incumbent solutions gets constructed until the incumbent is eventually optimal. Proving optimality is the central objective of the remaining third phase. Based on the MIP-solver SCIP, we demonstrate the usefulness of the phase concept both with an exact recognition of the optimality of a solution, and provide heuristic alternatives to make use of the concept in practice. T3 - ZIB-Report - 15-64 KW - Branch-and-Bound, Mixed-Integer Programming Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57098 SN - 1438-0064 ER - TY - CHAP A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael ED - IEEE, T1 - Solving Hard MIPLIP2003 Problems with ParaSCIP on Supercomputers: An Update T2 - IPDPSW'14 Proceedings of the 2014 IEEE, International Parallel & Distributed Processing Symposium Workshops Y1 - 2014 SN - 978-1-4799-4117-9 U6 - https://doi.org/10.1109/IPDPSW.2014.174 SP - 1552 EP - 1561 PB - IEEE Computer Society CY - Washington, DC, USA ER - TY - GEN A1 - Stötzel, Claudia A1 - Ehrig, Rainald A1 - Boer, H. Marike T. A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis N2 - Cows typically have different numbers of follicular waves during their hormonal cycle. Understanding the underlying regulations leads to insights into the reasons for declined fertility, a phenomenon that has been observed during the last decades. We present a systematic approach based on Fourier analysis to examine how parameter changes in a model of the bovine estrous cycle lead to different wave patterns. Even without any biological considerations, this allows to detect the responsible model parameters that control the type of periodicity of the solution, thus supporting experimental planning of animal scientists. T3 - ZIB-Report - 16-02 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57039 SN - 1438-0064 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank T1 - Direct Evidence of the Leaky Emission in Oxide-Confined Vertical Cavity Lasers JF - IEEE J. Quant. Electron. Y1 - 2016 U6 - https://doi.org/10.1109/JQE.2016.2518081 VL - 52 IS - 3 SP - 2400207 ER - TY - GEN A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Flatken, Markus A1 - Hege, Hans-Christian A1 - Hotz, Ingrid T1 - Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions N2 - Many scientific applications deal with data from a multitude of different sources, e.g., measurements, imaging and simulations. Each source provides an additional perspective on the phenomenon of interest, but also comes with specific limitations, e.g. regarding accuracy, spatial and temporal availability. Effectively combining and analyzing such multimodal and partially incomplete data of limited accuracy in an integrated way is challenging. In this work, we outline an approach for an integrated analysis and visualization of the atmospheric impact of volcano eruptions. The data sets comprise observation and imaging data from satellites as well as results from numerical particle simulations. To analyze the clouds from the volcano eruption in the spatiotemporal domain we apply topological methods. Extremal structures reveal structures in the data that support clustering and comparison. We further discuss the robustness of those methods with respect to different properties of the data and different parameter setups. Finally we outline open challenges for the effective integrated visualization using topological methods. T3 - ZIB-Report - 16-03 KW - multi-modal, intergrated data analysis, topology Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57043 SN - 1438-0064 ER - TY - GEN A1 - Willenbockel, Christian Tobias A1 - Schütte, Christof T1 - Variational Bayesian Inference and Model Selection for the Stochastic Block Model with Irrelevant Vertices N2 - Real World networks often exhibit a significant number of vertices which are sparsely and irregularly connected to other vertices in the network. For clustering theses networks with a model based algorithm, we propose the Stochastic Block Model with Irrelevant Vertices (SBMIV) for weighted net- works. We propose an original Variational Bayesian Expectation Maximiza- tion inference algorithm for the SBMIV which is an advanced version of our Blockloading algorithm for the Stochastic Block Model. We introduce a model selection criterion for the number of clusters of the SBMIV which is based on the lower variational bound of the model likelihood. We propose a fully Bayesian inference process, based on plausible informative priors, which is independent of other algorithms for preprocessing start values for the cluster assignment of vertices. Our inference methods allow for a multi level identification of irrelevant vertices which are hard to cluster reliably ac- cording to the SBM. We demonstrate that our methods improve on the normal Stochastic Block model by applying it to to Earthquake Networks which are an example of networks with a large number of sparsely and irregularly con- nected vertices. T3 - ZIB-Report - 16-01 KW - Clustering KW - Variational Bayes EM KW - Model Selection, KW - Stochastic Block Model KW - Networks KW - unsupervised classification KW - Noise Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57003 SN - 1438-0064 ER - TY - JOUR A1 - Grötschel, Martin T1 - Die IMU und ihr Sekretariat JF - Mitteilungen der DMV N2 - Was macht die International Mathematical Union (IMU) eigentlich, und wozu ist das IMU-Sekretariat da? ... Y1 - 2015 U6 - https://doi.org/10.1515/dmvm-2015-0012 VL - 23 IS - 1 SP - 24 EP - 29 ER - TY - BOOK A1 - Ehrig, Hartmut A1 - Ermel, Claudia A1 - Golas, Ulrike A1 - Hermann, Frank T1 - Graph and Model Transformation BT - General Framework and Applications N2 - This book is a comprehensive explanation of graph and model transformation. It contains a detailed introduction, including basic results and applications of the algebraic theory of graph transformations, and references to the historical context. Then in the main part the book contains detailed chapters on M-adhesive categories, M-adhesive transformation systems, and multi-amalgamated transformations, and model transformation based on triple graph grammars. In the final part of the book the authors examine application of the techniques in various domains, including chapters on case studies and tool support. The book will be of interest to researchers and practitioners in the areas of theoretical computer science, software engineering, concurrent and distributed systems, and visual modelling. Y1 - 2015 SN - 978-3-662-47979-7 U6 - https://doi.org/10.1007/978-3-662-47980-3 PB - Springer-Verlag Berlin Heidelberg ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Pelvic tilt compensates for increased acetabular anteversion JF - International Orthopaedics N2 - Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position. Y1 - 2015 U6 - https://doi.org/10.1007/s00264-015-2949-6 VL - 40 IS - 8 SP - 1571 EP - 1575 ER - TY - JOUR A1 - Zachow, Stefan A1 - Heppt, Werner T1 - The Facial Profile JF - Facial Plastic Surgery N2 - Facial appearance in our societies is often associated with notions of attractiveness, juvenileness, beauty, success, and so forth. Hence, the role of facial plastic surgery is highly interrelated to a patient's desire to feature many of these positively connoted attributes, which of course, are subject of different cultural perceptions or social trends. To judge about somebody's facial appearance, appropriate quantitative measures as well as methods to obtain and compare individual facial features are required. This special issue on facial profile is intended to provide an overview on how facial characteristics are surgically managed in an interdisciplinary way based on experience, instrumentation, and modern technology to obtain an aesthetic facial appearance with harmonious facial proportions. The facial profile will be discussed within the context of facial aesthetics. Latest concepts for capturing facial morphology in high speed and impressive detail are presented for quantitative analysis of even subtle changes, aging effects, or facial expressions. In addition, the perception of facial profiles is evaluated based on eye tracking technology. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1566132 VL - 31 IS - 5 SP - 419 EP - 420 ER - TY - CHAP A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Statistical Shape Modeling of Musculoskeletal Structures and Its Applications T2 - Computational Radiology for Orthopaedic Interventions N2 - Statistical shape models (SSM) describe the shape variability contained in a given population. They are able to describe large populations of complex shapes with few degrees of freedom. This makes them a useful tool for a variety of tasks that arise in computer-aided madicine. In this chapter we are going to explain the basic methodology of SSMs and present a variety of examples, where SSMs have been successfully applied. Y1 - 2016 SN - 978-3-319-23481-6 U6 - https://doi.org/10.1007/978-3-319-23482-3 VL - 23 SP - 1 EP - 23 PB - Springer ER - TY - JOUR A1 - Tuma, Christian A1 - Sauer, Joachim T1 - Quantum chemical ab initio prediction of proton exchange barriers between CH4 and different H-zeolites JF - The Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/10.1063/1.4923086 VL - 143 IS - 10 SP - 102810-1 EP - 102810-13 ER - TY - CHAP A1 - Kruber, Nico A1 - Lange, Maik A1 - Schintke, Florian T1 - Approximate Hash-Based Set Reconciliation for Distributed Replica Repair T2 - 2015 IEEE 34th International Symposium on Reliable Distributed Systems (SRDS) Y1 - 2015 U6 - https://doi.org/10.1109/SRDS.2015.30 SP - 166 EP - 175 PB - IEEE ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas A1 - Reinefeld, Alexander ED - Gray, A. ED - Smith, L. ED - Weiland, M. T1 - The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing T2 - Proceedings of the 3rd International Conference on Exascale Applications and Software, EASC 2015 Y1 - 2015 SN - 978 -0-9 926615 -1-9 SP - 13 EP - 18 PB - The University of Edinburgh ER - TY - JOUR A1 - Härtig, Hermann A1 - Matsuoka, Satoshi A1 - Mueller, Frank A1 - Reinefeld, Alexander T1 - Resilience in Exascale Computing (Dagstuhl Seminar 14402) JF - Dagstuhl Reports Y1 - 2015 U6 - https://doi.org/10.4230/DagRep.4.9.124 VL - 4 IS - 9 SP - 124 EP - 139 ER - TY - JOUR A1 - Schnauber, Peter A1 - Thoma, Alexander A1 - Heine, Christoph V. A1 - Schlehahn, Alexander A1 - Gantz, Liron A1 - Gschrey, Manuel A1 - Schmidt, Ronny A1 - Hopfmann, Caspar A1 - Wohlfeil, Benjamin A1 - Schulze, Jan-Hindrick A1 - Strittmatter, Andre A1 - Heindel, Tobias A1 - Rodt, Sven A1 - Woggon, Ulrike A1 - Gershoni, David A1 - Reitzenstein, Stephan T1 - Bright Single-Photon Sources Based on Anti-Reflection Coated Deterministic Quantum Dot Microlenses JF - Technologies Y1 - 2016 U6 - https://doi.org/10.3390/technologies4010001 VL - 4 IS - 1 SP - 1 ER - TY - GEN A1 - Pulaj, Jonad A1 - Raymond, Annie A1 - Theis, Dirk T1 - New Conjectures For Union-Closed Families N2 - The Frankl conjecture, also known as the union-closed sets conjecture, states that there exists an element in at least half of the sets of any (non-empty) union-closed family. From an optimization point of view, one could instead prove that 2a is an upper bound to the number of sets in a union-closed family with n elements where each element is in at most a sets, where a and n are non-negative integers. Formulating these problems as integer programs we observe that computed optimal values do not vary with n. We formalize these observations as conjectures, and show that they are not equivalent to the Frankl conjecture while still having wide-reaching implications if proven true. Finally, we partially prove the new conjectures and discuss possible approaches to solve them completely. T3 - ZIB-Report - 15-57 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56804 SN - 1438-0064 ER - TY - GEN A1 - Koch, Thorsten A1 - Griebel, Rolf A1 - Söllner, Konstanze A1 - Christof, Jürgen A1 - Bertelmann, Roland T1 - DeepGreen - Entwicklung eines rechtssicheren Workflows zur effizienten Umsetzung der Open-Access-Komponente in den Allianz-Lizenzen für die Wissenschaft N2 - In Deutschland wurden 2011 wichtige Akzente für die Umsetzung des Grünen Wegs der Open-Access-Bewegung gesetzt: Mit finanzieller Unterstützung der Deutschen Forschungsgemeinschaft (DFG) haben Bibliotheken sogenannte Allianz-Lizenzen mit Verlagen verhandelt, in denen weitreichende Rechte hinsichtlich der Open-Access-Archivierung verankert sind. Autorinnen und Autoren zugriffsberechtigter Einrichtungen können ihre Artikel, die in diesen lizenzierten Zeitschriften erschienen sind, ohne oder mit nur kurzer Embargofrist in geeigneten Repositorien ihrer Wahl frei zugänglich machen. Allerdings macht der Kreis berechtigter Autorinnen und Autoren nur sehr zögerlich von seinen Open-Access-Rechten Gebrauch. Auch die Bibliotheken – als Betreiber der Repositorien und damit Vertreter für die berechtigten Autorinnen und Autoren – nutzen dieses Recht nur unzureichend. Mit DeepGreen verfolgen die Antragssteller das Ziel, einen Großteil jener Publikationen, die unter den speziell im DFG-geförderten Kontext verhandelten Bedingungen grün online gehen dürften, auch tatsächlich online abrufbar zu machen. Im Rahmen des Projektes wird prototypisch mit Allianzverlagen und berechtigten Bibliotheken ein möglichst stark automatisierter Workflow entwickelt, in dem rechtssichere Verlagsdaten inklusive der Volltexte abgeliefert und von Repositorien eingespielt werden. Ein technischer Baustein ist dabei ein intermediäres Repositorium, das als Datenverteiler dient. Das nationale Projektkonsortium besteht aus den zwei Bibliotheksverbünden Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) und Bibliotheksverbund Bayern (BVB), den zwei Universitätsbibliotheken der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) und der Technische Universität Berlin (TU Berlin), zusätzlich die Bayerische Staatsbibliothek (BSB) und eine außeruniversitäre Forschungseinrichtung - das Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum (GFZ). Das Projekt startet zum 01. Januar 2016. Hier vorliegend finden Sie den Projektantrag zum Nachlesen. T3 - ZIB-Report - 15-58 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56799 SN - 1438-0064 ER - TY - JOUR A1 - Dierkes, Thomas T1 - Construction of ODE systems from time series data by a highly flexible modelling approach JF - ArXiv e-prints N2 - In this paper, a down-to-earth approach to purely data-based modelling of unknown dynamical systems is presented. Starting from a classical, explicit ODE formulation y=f(t,y) of a dynamical system, a method determining the unknown right-hand side f(t,y) from some trajectory data y_k(t_j), possibly very sparse, is given. As illustrative examples, a semi-standard predator-prey model is reconstructed from a data set describing the population numbers of hares and lynxes over a period of twenty years, and a simple damped pendulum system with a highly non-linear right-hand side is recovered from some artificial but very sparse data. Y1 - 2015 VL - math.NA 1512.03357 ER - TY - GEN A1 - Dierkes, Thomas T1 - Construction of ODE systems from time series data by a highly flexible modelling approach N2 - In this paper, a down-to-earth approach to purely data-based modelling of unknown dynamical systems is presented. Starting from a classical, explicit ODE formulation y=f(t,y) of a dynamical system, a method determining the unknown right-hand side f(t,y) from some trajectory data y_k(t_j), possibly very sparse, is given. As illustrative examples, a semi-standard predator-prey model is reconstructed from a data set describing the population numbers of hares and lynxes over a period of twenty years [1], and a simple damped pendulum system with a highly non-linear right-hand side is recovered from some artificial but very sparse data [2]. T3 - ZIB-Report - 15-59 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56768 SN - 1438-0064 ER - TY - CHAP A1 - Klindt, Marco A1 - Amrhein, Kilian T1 - One Core Preservation System for All your Data. No Exceptions! T2 - iPRES 2015 - Proceedings of the 12th International Conference on Preservation of Digital Objects N2 - In this paper, we describe an OAIS aligned data model and architectural design that enables us to archive digital infor- mation with a single core preservation workflow. The data model allows for normalization of metadata from widely var- ied domains to ingest and manage the submitted information utilizing only one generalized toolchain and be able to create access platforms that are tailored to designated data con- sumer communities. The design of the preservation system is not dependent on its components to continue to exist over its lifetime, as we anticipate changes both of technology and environment. The initial implementation depends mainly on the open-source tools Archivematica, Fedora/Islandora, and iRODS. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56639 UR - http://phaidra.univie.ac.at/o:429551 UR - http://hdl.handle.net/11353/10.429551 SP - 101 EP - 108 PB - School of Information and Library Science, University of North Carolina at Chapel Hill ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Passenger Routing for Periodic Timetable Optimization N2 - The task of periodic timetabling is to schedule the trips in a public transport system by determining arrival and departure times at every station such that travel and transfer times are minimized. To date, the optimization literature generally assumes that passengers do not respond to changes in the timetable, i.e., the passenger routes are fixed. This is unrealistic and ignores potentially valuable degrees of freedom. We investigate in this paper periodic timetabling models with integrated passenger routing. We show that different routing models have a huge influence on the quality of the entire system: Whatever metric is applied, the performance ratios of timetables w.r.t. to different routing models can be arbitrarily large. Computations on a real-world instance for the city of Wuppertal substantiate the theoretical findings. These results indicate the existence of untapped optimization potentials that can be used to improve the efficiency of public transport systems. T3 - ZIB-Report - 15-55 KW - Passenger routing KW - Periodic timetabling KW - Public transport Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56739 SN - 1438-0064 ER - TY - JOUR A1 - Zachow, Stefan T1 - Computational Planning in Facial Surgery JF - Facial Plastic Surgery N2 - This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564717 VL - 31 IS - 5 SP - 446 EP - 462 ER - TY - GEN A1 - Maher, Stephen J. A1 - Desaulniers, Guy A1 - Soumis, Francois T1 - The tail assignment problem with look-ahead maintenance constraints N2 - The tail assignment problem is a critical part of the airline planning process that assigns specific aircraft to sequences of flights, called lines-of-flight, to be operated the next day. The aim of this paper is to develop an operationally flexible tail assignment that satisfies short-range---within the next three days---aircraft maintenance requirements and performs the aircraft/flight gate assignment for each input line-of-flight. While maintenance plans commonly span multiple days, the related tail assignment problems can be overly complex and provide little recourse in the event of schedule perturbations. The presented approach addresses operational uncertainty by extending the one-day routes aircraft maintenance routing approach to satisfy maintenance requirements explicitly for the current day and implicitly for the subsequent two days. A mathematical model is presented that integrates the gate assignment and maintenance planning problems. To increase the satisfaction of maintenance requirements, an iterative algorithm is developed that modifies the fixed lines-of-flight provided as input to the tail assignment problem. The tail assignment problem and iterative algorithm are demonstrated to effectively satisfy maintenance requirements within appropriate run times using input data collected from three different airlines. T3 - ZIB-Report - 15-56 KW - Tail assignment KW - Column generation KW - Iterative algorithm Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56717 SN - 1438-0064 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Miltenberger, Matthias A1 - Weninger, Dieter T1 - Progress in presolving for mixed integer programming JF - Mathematical Programming Computation N2 - This paper describes three presolving techniques for solving mixed integer programming problems (MIPs) that were implemented in the academic MIP solver SCIP. The task of presolving is to reduce the problem size and strengthen the formulation, mainly by eliminating redundant information and exploiting problem structures. The first method fixes continuous singleton columns and extends results known from duality fixing. The second analyzes and exploits pairwise dominance relations between variables, whereas the third detects isolated subproblems and solves them independently. The performance of the presented techniques is demonstrated on two MIP test sets. One contains all benchmark instances from the last three MIPLIB versions, while the other consists of real-world supply chain management problems. The computational results show that the combination of all three presolving techniques almost halves the solving time for the considered supply chain management problems. For the MIPLIB instances we obtain a speedup of 20 % on affected instances while not degrading the performance on the remaining problems. Y1 - 2015 U6 - https://doi.org/10.1007/s12532-015-0083-5 VL - 7 IS - 4 SP - 367 EP - 398 ER - TY - CHAP A1 - Amrhein, Kilian A1 - Klindt, Marco T1 - Islandora as an access system for iRODS managed information packages T2 - 10th International Conference on Open Repositories (OR2015) N2 - Accessing information packages with Islandora is straight forward, albeit not so much when they reside within a federated data management environment. In our case, dissemination information packages live in the Fedora object store for immediate access. The archival information packages are stored safely in a hierarchical storage infrastructure managed by iRODS and are only accessible for administrative and preservation action purposes. We present a data model that supports both use cases utilizing just a single Islandora instance. To integrate with iRODS, we developed an Islandora module to display and deliver data and metadata from the storage location. This solution also allows us to extend the system with further preservation workflow actions that will be required in the future. Y1 - 2015 UR - http://program.or2015.net/default_041.html#paperID32 U6 - https://doi.org/10.12752/5665 ER - TY - GEN A1 - Weber, Marcus A1 - Quer, Jannes T1 - Estimating exit rates in rare event dynamical systems via extrapolation N2 - In this article we present a new idea for approximating exit rates for diffusion processes living in a craggy landscape. We are especially interested in the exit rates of a process living in a metastable regions. Due to the fact that Monte Carlo simulations perform quite poor and are very computational expensive in this setting we create several similar situations with a smoothed potential. For this we introduce a new parameter $\lambda \in [0,1]$ ($\lambda = 1$ very smoothed potential, $\lambda=0$ original potential) into the potential which controls the influence the smoothing. We then sample the exit rate for different parameters $\lambda$ the exit rate from a given region. Due to the fact that $\lambda$ is connected to the exit rate we can use this dependency to approximate the real exit rate. The method can be seen as something between hyperdynamics and temperature accelerated MC. T3 - ZIB-Report - 15-54 KW - rare event sampling, smoothing, membership functions, perturbed potential Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56622 SN - 1438-0064 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Schreiber, Lisa A1 - Zachow, Stefan T1 - Fast and Accurate Digital Morphometry of Facial Expressions JF - Facial Plastic Surgery Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564720 VL - 31 IS - 05 SP - 431 EP - 438 PB - Thieme Medical Publishers CY - New York ER - TY - CHAP A1 - Kozlikova, Barbora A1 - Krone, Michael A1 - Lindow, Norbert A1 - Falk, Martin A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art T2 - EuroVis 2015 STARS Proceedings N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures. Y1 - 2015 U6 - https://doi.org/10.2312/eurovisstar.20151112 SP - 61 EP - 81 ER - TY - JOUR A1 - Schäfer, Patrick T1 - Scalable time series classification JF - Data Mining and Knowledge Discovery N2 - Time series classification tries to mimic the human understanding of similarity. When it comes to long or larger time series datasets, state-of-the-art classifiers reach their limits because of unreasonably high training or testing times. One representative example is the 1-nearest-neighbor dynamic time warping classifier (1-NN DTW) that is commonly used as the benchmark to compare to. It has several shortcomings: it has a quadratic time complexity in the time series length and its accuracy degenerates in the presence of noise. To reduce the computational complexity, early abandoning techniques, cascading lower bounds, or recently, a nearest centroid classifier have been introduced. Still, classification times on datasets of a few thousand time series are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space classifier that is accurate, fast and robust to noise. We show that it is significantly more accurate than 1-NN DTW while being multiple orders of magnitude faster. Its low computational complexity combined with its good classification accuracy makes it relevant for use cases like long or large amounts of time series or real-time analytics. Y1 - 2015 U6 - https://doi.org/10.1007/s10618-015-0441-y SP - 1 EP - 26 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Influence of pH and sequence in peptide aggregation via molecular simulation JF - Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/https://doi.org/10.1063/1.4935707 VL - 143 IS - 24 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - Prevailing Dust-transport Directions on Comet 67P/Churyumov–Gerasimenko JF - The Astrophysical Journal Letters N2 - Dust transport and deposition behind larger boulders on the comet 67P/Churyumov–Gerasimenko (67P/C–G) have been observed by the Rosetta mission. We present a mechanism for dust-transport vectors based on a homogeneous surface activity model incorporating in detail the topography of 67P/C–G. The combination of gravitation, gas drag, and Coriolis force leads to specific dust transfer pathways, which for higher dust velocities fuel the near-nucleus coma. By distributing dust sources homogeneously across the whole cometary surface, we derive a global dust-transport map of 67P/C–G. The transport vectors are in agreement with the reported wind-tail directions in the Philae descent area. Y1 - 2015 U6 - https://doi.org/10.1088/2041-8205/813/2/L33 VL - 813 IS - 2 SP - L33 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Timetabling and Passenger Routing in Public Transport T2 - Proceedings of Conference on Advanced Systems in Public Transport 2015 (CASPT2015) N2 - The task of timetabling is to schedule the trips in a public transport system by determining periodic arrival and departure times at every station. The goal is to provide a service that is both attractive for passengers and can be operated economically. To date, timetable optimization is generally done with respect to fixed passenger routes, i.e., it is assumed that passengers do not respond to changes in the timetable. This is unrealistic and ignores potentially valuable degrees of freedom. We investigate in this paper periodic timetabling models with integrated passenger routing. We propose several models that differ in the allowed passenger paths and the objectives. We compare these models theoretically and report on computations on real-world instances for the city of Wuppertal. KW - Passenger routing KW - Periodic timetabling KW - Public transport Y1 - 2015 ER - TY - CHAP A1 - Thoma, Alexander A1 - Schnauber, Peter A1 - Gschrey, Manuel A1 - Schmidt, Ronny A1 - Wohlfeil, Benjamin A1 - Seifried, Marc A1 - Schulze, Jan-Hindrick A1 - Burger, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Rodt, Sven A1 - Heindel, Tobias A1 - Reitzenstein, Stephan T1 - Indistinguishable Photons from Deterministic Quantum Dot Microlenses T2 - European Conference on Lasers and Electro-Optics - European Quantum Electronics Conference Y1 - 2015 U6 - https://doi.org/10.1364/IPRSN.2015.IS4A.6 SP - EA_8_5 ER - TY - THES A1 - Schäfer, Patrick T1 - Scalable Time Series Similarity Search for Data Analytics Y1 - 2015 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=42117 ER - TY - GEN A1 - Fujisawa, Katsuki A1 - Shinano, Yuji A1 - Waki, Hayato T1 - Optimization in the Real World T2 - Mathematics for Industry (MFI) Y1 - 2015 SN - 978-4-431-55419-6 U6 - https://doi.org/10.1007/978-4-431-55420-2 VL - 13 PB - Springer Tokyo Heidelberg New York Dordrecht London ER - TY - CHAP A1 - Barth, Carlo A1 - Jäger, Klaus A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Design of Photonic Crystals with Near-Surface Field Enhancement T2 - Light, Energy and the Environement 2015 Y1 - 2015 U6 - https://doi.org/10.1364/PV.2015.JTu5A.9 SP - JTu5A.9 ER - TY - CHAP A1 - Jäger, Klaus A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Sinusoidal Nanotextures for Coupling Light into c-Si Thin-Film Solar Cells T2 - Light, Energy and the Environement 2015 Y1 - 2015 U6 - https://doi.org/10.1364/PV.2015.PTu4B.3 SP - PTu4B.3 ER - TY - JOUR A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Siebert, Heike T1 - Complementing ODE-based System Analysis Using Boolean Networks Derived from an Euler-like Transformation JF - PLOS ONE Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0140954 ER - TY - GEN A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Stötzel, Claudia A1 - Röblitz, Susanna T1 - A systems biology approach to bovine fertility and metabolism: Development of a glucose insulin model. N2 - To counteract the antagonistic relationship between milk yield and fertility in dairy cow, a deeper understanding of the underlying biological mechanisms is required. For this purpose, we study physiological networks related to reproduction and metabolism in dairy cows. We interactively develop dynamic, mechanistic models by fitting the models to experimental data and mechanistic knowledge. We have already developed models for potassium balance and hormonal regulation of fertility in the dairy cow, which will briefly be reviewed here. The main focus of this article is a glucose-insulin model currently developed by us. This model links the bovine hormonal cycle and the potassium balance to glucose and thus to energy metabolism. The models can be applied in scientific research, education, experimental planning, drug development and production on farms. T3 - ZIB-Report - 15-51 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56453 SN - 1438-0064 ER - TY - GEN A1 - Ahmadi, Sepideh A1 - Gritzbach, Sascha F. A1 - Lund-Nguyen, Kathryn A1 - McCullough-Amal, Devita T1 - Rolling Stock Rotation Optimization in Days of Strike: An Automated Approach for Creating an Alternative Timetable N2 - The operation of a railway network as large as Deutsche Bahn's Intercity Express (ICE) hinges on a number of factors, such as the availability of personnel and the assignment of physical vehicles to a timetable schedule, a problem known as the rolling stock rotation problem (RSRP). In this paper, we consider the problem of creating an alternative timetable in the case that there is a long-term disruption, such as a strike, and the effects that this alternative timetable has on the resulting vehicle rotation plan. We define a priority measure via the Analytic Hierarchy Process (AHP) to determine the importance of each trip in the timetable and therefore which trips to cancel or retain. We then compare our results with those of a limited timetable manually designed by Deutsche Bahn (DB). We find that while our timetable results in a more expensive rotation plan, its flexibility lends itself to a number of simple improvements. Furthermore, our priority measure has the potential to be integrated into the rolling stock rotation optimization process, in particular, the Rotation Optimizer for Railways (ROTOR) software, via the cost function. Ultimately, our method provides the foundation for an automated way of creating a new timetable quickly, and potentially in conjunction with a new rotation plan, in the case of a limited scenario. T3 - ZIB-Report - 15-52 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56425 SN - 1438-0064 ER - TY - JOUR A1 - Schütte, Christof A1 - Sarich, Marco T1 - A Critical Appraisal of Markov State Models JF - The European Physical Journal Special Topics N2 - Markov State Modelling as a concept for a coarse grained description of the essential kinetics of a molecular system in equilibrium has gained a lot of atten- tion recently. The last 10 years have seen an ever increasing publication activity on how to construct Markov State Models (MSMs) for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecu- lar sensors to molecular aggregation. Simultaneously the accompanying theory behind MSM building and approximation quality has been developed well be- yond the concepts and ideas used in practical applications. This article reviews the main theoretical results, provides links to crucial new developments, outlines the full power of MSM building today, and discusses the essential limitations still to overcome. Y1 - 2015 U6 - https://doi.org/10.1140/epjst/e2015-02421-0 VL - 224 IS - 12 SP - 2445 EP - 2462 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael T1 - Solving Open MIP Instances with ParaSCIP on Supercomputers using up to 80,000 Cores N2 - This paper describes how we solved 12 previously unsolved mixed-integer program- ming (MIP) instances from the MIPLIB benchmark sets. To achieve these results we used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper we describe the basic parallelization mechanism of ParaSCIP, improvements of the dynamic load balancing and novel techniques to exploit the power of parallelization for MIP solving. We give a detailed overview of computing times and statistics for solving open MIPLIB instances. T3 - ZIB-Report - 15-53 KW - Mixed Integer Programming KW - Parallel processing KW - Node merging KW - Racing ParaSCIP KW - Ubiquity Generator Framework KW - MIPLIB Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56404 SN - 1438-0064 ER - TY - CHAP A1 - Noack, Matthias A1 - Wende, Florian A1 - Oertel, Klaus-Dieter ED - Reinders, James ED - Jeffers, Jim T1 - OpenCL: There and Back Again T2 - High Performance Parallelism Pearls Y1 - 2015 SN - 978-0-12-803819-2 VL - 2 SP - 355 EP - 378 PB - Morgan Kaufman, Elsevier ER - TY - CHAP A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Reduced basis methods for optimization of nano-photonic devices T2 - Proc. Int. Conf. Numerical Simulation of Optoelectronic Devices (NUSOD) Y1 - 2015 U6 - https://doi.org/10.1109/NUSOD.2015.7292871 SP - 159 ER - TY - GEN A1 - Lamas-Rodríguez, Julián A1 - Ehlke, Moritz A1 - Hoffmann, René A1 - Zachow, Stefan T1 - GPU-accelerated denoising of large tomographic data sets with low SNR BT - Application for non-invasive analysis of paleontological data N2 - Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time. T3 - ZIB-Report - 15-14 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56339 SN - 1438-0064 ER - TY - CHAP A1 - Boeth, Heide A1 - Duda, Georg A1 - Hinzmann, Daniel A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Witaschek, Tom A1 - Buttgereit, Frank T1 - Objektive Quantifizierung der Morgensteifigkeit als Parameter für rheumatoide Arthritis im Metacarpophalangealgelenk T2 - 9. Jahrestagung der Deutschen Gesellschaft für Biomechanik (DGfB), Bonn Y1 - 2015 ER - TY - JOUR A1 - Kryven, Ivan A1 - Röblitz, Susanna A1 - Schütte, Christof T1 - Solution of the chemical master equation by radial basis functions approximation with interface tracking JF - BMC Systems Biology N2 - Background. The chemical master equation is the fundamental equation of stochastic chemical kinetics. This differential-difference equation describes temporal evolution of the probability density function for states of a chemical system. A state of the system, usually encoded as a vector, represents the number of entities or copy numbers of interacting species, which are changing according to a list of possible reactions. It is often the case, especially when the state vector is high-dimensional, that the number of possible states the system may occupy is too large to be handled computationally. One way to get around this problem is to consider only those states that are associated with probabilities that are greater than a certain threshold level. Results. We introduce an algorithm that significantly reduces computational resources and is especially powerful when dealing with multi-modal distributions. The algorithm is built according to two key principles. Firstly, when performing time integration, the algorithm keeps track of the subset of states with significant probabilities (essential support). Secondly, the probability distribution that solves the equation is parametrised with a small number of coefficients using collocation on Gaussian radial basis functions. The system of basis functions is chosen in such a way that the solution is approximated only on the essential support instead of the whole state space. Discussion. In order to demonstrate the effectiveness of the method, we consider four application examples: a) the self-regulating gene model, b) the 2-dimensional bistable toggle switch, c) a generalisation of the bistable switch to a 3-dimensional tristable problem, and d) a 3-dimensional cell differentiation model that, depending on parameter values, may operate in bistable or tristable modes. In all multidimensional examples the manifold containing the system states with significant probabilities undergoes drastic transformations over time. This fact makes the examples especially challenging for numerical methods. Conclusions. The proposed method is a new numerical approach permitting to approximately solve a wide range of problems that have been hard to tackle until now. A full representation of multi-dimensional distributions is recovered. The method is especially attractive when dealing with models that yield solutions of a complex structure, for instance, featuring multi-stability. Electronic version: http://www.biomedcentral.com/1752-0509/9/67 Y1 - 2015 U6 - https://doi.org/10.1186/s12918-015-0210-y VL - 9 IS - 67 SP - 1 EP - 12 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schulz, Christof A1 - Seidl, Stephan A1 - Weider, Steffen T1 - Integration of Duty Scheduling and Rostering to Increase Driver Satisfaction N2 - Integrated treatment of hitherto individual steps in the planning process of public transit companies discloses opportunities to reduce costs and to improve the quality of service. The arising integrated planning problems are complex and their solution requires the development of novel mathematical methods. This article proposes a mathematical optimization approach to integrate duty scheduling and rostering in public transit, which allows to significantly increase driver satisfaction at almost zero cost. This is important in order to to increase the attractiveness of the driver profession. The integration is based on coupling the subproblems by duty templates, which, compared to a coupling by duties, drastically reduces the problem complexity. T3 - ZIB-Report - 15-50 KW - Benders decomposition KW - driver satisfaction KW - duty templates KW - duty scheduling KW - rostering Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56299 SN - 1438-0064 ER - TY - GEN A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Siebert, Heike T1 - Complementing ODE-based System Analysis Using Boolean Networks Derived from an Euler-like Transformation N2 - In this paper, we present a systematic transition scheme for a large class of ordinary differential equations (ODEs) into Boolean networks. Our transition scheme can be applied to any system of ODEs whose right hand sides can be written as sums and products of monotone functions. It performs an Euler-like step which uses the signs of the right hand sides to obtain the Boolean update functions for every variable of the corresponding discrete model. The discrete model can, on one hand, be considered as another representation of the biological system or, alternatively, it can be used to further the analysis of the original ODE model. Since the generic transformation method does not guarantee any property conservation, a subsequent validation step is required. Depending on the purpose of the model this step can be based on experimental data or ODE simulations and characteristics. Analysis of the resulting Boolean model, both on its own and in comparison with the ODE model, then allows to investigate system properties not accessible in a purely continuous setting. The method is exemplarily applied to a previously published model of the bovine estrous cycle, which leads to new insights regarding the regulation among the components, and also indicates strongly that the system is tailored to generate stable oscillations. T3 - ZIB-Report - 15-46 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56164 SN - 1438-0064 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Neue Planungsinstrumente nutzen: Das Verkehrsangebot verbessern und Kosten sparen JF - Verkehr und Technik N2 - Wir illustrieren anhand des Liniennetzes der Stadt Potsdam das Potenzial mathematischer Methoden der Angebotsplanung. Wir zeigen, dass das "bestmögliche" Verkehrsangebot stark von planerischen Vorgaben beeinflusst wird, mit denen man die Erreichung unterschiedlicher und teilweise gegenläufiger Ziele steuern kann. Die Komplexität des Systems führt zum Auftreten von Rückkoppelungseffekten, die man nicht mit Hilfe von Daumenregeln beherrschen kann. Vielmehr ist der Einsatz moderner Planungsverfahren in einer interdisziplinären Zusammenarbeit von politischen Entscheidungsträgern, Verkehrsingenieuren und Mathematikern notwendig, um die aktuellen Herausforderungen in der Verkehrsplanung zu meistern. Der Artikel dokumentiert einen Beitrag zum 7. ÖPNV Innovationskongress des Ministeriums für Verkehr und Infrastruktur des Landes Baden-Württemberg, der vom 9.-11. März 2015 in Freiburg stattfand. Y1 - 2015 VL - 68 IS - 7 SP - 239 EP - 243 ER - TY - JOUR A1 - Wolff, Christian A1 - Gutsche, Philipp A1 - Steel, Michael J. A1 - Eggleton, Benjamin J. A1 - Poulton, Christopher G. T1 - Power limits and a figure of merit for stimulated Brillouin scattering in the presence of third and fifth order loss JF - Opt. Express N2 - We derive a set of design guidelines and a figure of merit to aid the engineering process of on-chip waveguides for strong Stimulated Brillouin Scattering (SBS). To this end, we examine the impact of several types of loss on the total amplification of the Stokes wave that can be achieved via SBS. We account for linear loss and nonlinear loss of third order (two-photon absorption, 2PA) and fifth order, most notably 2PA-induced free carrier absorption (FCA). From this, we derive an upper bound for the output power of continuous-wave Brillouin-lasers and show that the optimal operating conditions and maximal realisable Stokes amplification of any given waveguide structure are determined by a dimensionless parameter ℱ involving the SBS-gain and all loss parameters. We provide simple expressions for optimal pump power, waveguide length and realisable amplification and demonstrate their utility in two example systems. Notably, we find that 2PA-induced FCA is a serious limitation to SBS in silicon and germanium for wavelengths shorter than 2200nm and 3600nm, respectively. In contrast, three-photon absorption is of no practical significance. Y1 - 2015 U6 - https://doi.org/10.1364/OE.23.026628 VL - 23 IS - 20 SP - 26628 EP - 26638 ER - TY - GEN A1 - Leitner, Markus A1 - Ljubic, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - Two algorithms for solving 3-objective k-ArchConFL and IPs in general N2 - We present two algorithms to solve a 3-objective optimization problem arising in telecommunications access network planning, the k-Architecture Connected Facility Location Problem. The methods can also be used to solve any 3-objective integer linear programming model and can be extended to the multiobjective case. We give some exemplary computations using small and medium-sized instances for our problem. T3 - ZIB-Report - 15-48 KW - multiobjective optimization KW - integer programming KW - telecommunications Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56259 SN - 1438-0064 ER - TY - GEN A1 - Goltz-Fellgiebel, Julia Alexandra T1 - Mobile Applikationen für Bibliotheken im deutschsprachigen Raum N2 - Wir leben in einem digitalen Informationszeitalter, unsere Welt ist geprägt von Bits und Bytes. Unser Alltag wird dabei zunehmend von mobilen technischen Hilfsmitteln bestimmt, das Smartphone ist aus dem alltäglichen und auch dem beruflichen Leben kaum mehr wegzudenken. Für jeden Bedarf gibt es mittlerweile kleine mobile Applikationen (Apps), die das Leben erleichtern sollen. Der digitale Wandel beeinflusst auch die Arbeit und die Ausrichtung von Bibliotheken und anderen Kultureinrichtungen. Neben ihren traditionellen Aufgaben stehen sie vor der Herausforderung, ihre qualitativ hochwertig aufbereiteten Daten und Informationen den Nutzerinnen und Nutzern über webbasierte, also von überall zugängliche, für mobile Geräte aufbereitete, intuitiv anwendbare und attraktive Dienste anzubieten. Im Zuge der strategischen Allianz, die seit Dezember 2007 zwischen dem Kooperativem Bibliotheksverbund Berlin-Brandenburg (KOBV) und dem Bibliotheksverbund Bayern (BVB) besteht, werden gemeinsame Entwicklungsprojekte durchgeführt. In diesem Rahmen entstand bereits die erste Version der Studie „Mobile Applikationen für Bibliotheken im deutsch-sprachigen Raum“ (ZIB-Report 14-06; http://nbn-resolving.de/urn:nbn:de:0297-zib-46931). Das Papier bot einen Überblick zu den mobilen Angeboten der deutsch-sprachigen Bibliothekslandschaft und arbeitete Mehrwerte, die über die Recherche im lokalen Bibliothekskatalog hinausführt, für Wissensinstitutionen aus. In der hier vorliegenden zweiten Version werden zusätzlich rechtliche Rahmenbedingungen und entwicklungsbezogene Herausforderungen, denen Bibliotheken sich im Umgang mit mobilen Applikationen stellen müssen, beleuchtet. Fakten zur Nutzung mobiler Dienste und die Liste der bibliothekarischen mobilen Angebote wurden aktualisiert, anhand neuer Technologien denkbare zukünftige Mehrwerte für bibliothekarische Applikationen wurden spezifiziert. T3 - ZIB-Report - 15-49 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56241 SN - 1438-0064 ET - akt. u. erw. 2. Version ER - TY - CHAP A1 - Burger, Sven A1 - Gutsche, Philipp A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Wohlfeil, Benjamin A1 - Zschiedrich, Lin T1 - Hp-finite-elements for simulating electromagnetic fields in optical devices with rough textures T2 - Proc. SPIE Y1 - 2015 U6 - https://doi.org/10.1117/12.2190119 VL - 9630 SP - 96300S ER - TY - CHAP A1 - Draegert, Andreas A1 - Eisenblätter, Andreas A1 - Gamrath, Inken A1 - Werner, Axel ED - Fujisawa, Katsuki ED - Shinano, Yuji ED - Waki, Hayato T1 - Optimal battery control for smart grid nodes T2 - Optimization in the Real World - Towards Solving Real-World Optimization Problems N2 - Energy storages can be of great value when added to power grids. They introduce the possibility to store and release energy whenever this is favorable. This is particularly relevant, for example, if power supply is volatile (as is the case with renewable energy) and the network is small (so that there are few other nodes that might balance fluctuations in consumption or production). We present models and methods from mathematical optimization for computing an optimized storage schedule for this purpose. We look at alternative optimization objectives, such as smallest possible peak load, low energy costs, or the close approximation of a prescribed load curve. The optimization needs to respect general operational and economic constraints as well as limitations in the use of storage, which are imposed by the chosen storage technology. We therefore introduce alternative approaches for modeling the non-linear properties of energy storages and study their impact on the efficiency of the optimization process. Finally, we present a computational study with batteries as storage devices. We use this to highlight the trade-off between solution quality and computational tractability. A version of the model for the purpose of leveling peaks and instabilities has been implemented into a control system for an office-building smart grid scenario. Y1 - 2015 U6 - https://doi.org/10.1007/978-4-431-55420-2_6 VL - 13 SP - 97 EP - 113 PB - Springer ER - TY - GEN A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - 3D Assessment of Osteosynthesis based on 2D Radiographs N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient-specific surface of the distal femur based on postoperative 2D radiographs. In a first step, the implant geometry is used as a calibration object to relate the implant and the individual X-ray images spatially in a virtual X-ray setup. Second, the patient-specific femoral shape and pose are reconstructed by fitting a deformable statistical shape and intensity model (SSIM) to the X-rays. The relative positioning between femur and implant is then assessed in terms of the displacement between the reconstructed 3D shape of the femur and the plate. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing and, ultimately, to derive load recommendations after surgery. T3 - ZIB-Report - 15-47 KW - 3d-reconstruction from 2d X-rays KW - statistical shape and intensity models KW - osteosynthesis follow-up Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56217 SN - 1438-0064 ER - TY - CHAP A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - 3D Assessment of Osteosynthesis based on 2D Radiographs T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient-specific surface of the distal femur based on postoperative 2D radiographs. In a first step, the implant geometry is used as a calibration object to relate the implant and the individual X-ray images spatially in a virtual X-ray setup. Second, the patient- specific femoral shape and pose are reconstructed by fitting a deformable statistical shape and intensity model (SSIM) to the X-rays. The relative positioning between femur and implant is then assessed in terms of the displacement between the reconstructed 3D shape of the femur and the plate. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing and, ultimately, to derive load recommendations after surgery. KW - 3d-reconstruction from 2d X-rays KW - osteosynthesis follow-up KW - statistical shape and intensity models Y1 - 2015 SP - 317 EP - 321 ER - TY - GEN A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf T1 - A Hall Condition for Normal Hypergraphs N2 - Conforti, Cornuéjols, Kapoor, and Vusković gave a Hall-type condition for the non-existence of a perfect matching in a balanced hypergraph. We generalize this result to the class of normal hypergraphs. T3 - ZIB-Report - 15-45 KW - Matchings in hypergraphs KW - Normal hypergraphs KW - Hall condition Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56175 SN - 1438-0064 ER - TY - JOUR A1 - McPeak, Kevin A1 - van Engers, Christian D. A1 - Bianchi, Sarah A1 - Rossinelli, Aurelio A1 - Poulikakos, Lisa A1 - Bernard, Laetitia A1 - Herrmann, Sven A1 - Kim, David K. A1 - Burger, Sven A1 - Blome, Mark A1 - Jayanti, Sriharsha V. A1 - Norris, David T1 - Ultraviolet Plasmonic Chirality from Colloidal Aluminum Nanoparticles Exhibiting Charge-Selective Protein Detection JF - Adv. Mater. Y1 - 2015 U6 - https://doi.org/10.1002/adma.201503493 VL - 27 SP - 6244 ER - TY - GEN A1 - Poulikakos, Lisa A1 - Gutsche, Philipp A1 - McPeak, Kevin A1 - Burger, Sven A1 - Niegemann, Jens A1 - Hafner, Christian A1 - Norris, David T1 - A Far-Field Interpretation of the Optical Chirality T2 - Frontiers in Nanophotonics (Congressi Stefano Franscini) N2 - A chiral structure is not super-imposable with its mirror image. Most commonly found in organic molecules, chirality can also occur in other systems, such as electromagnetic fields, where circularly polarized light is the most widespread example. Chiral electromagnetic fields can be a useful tool for biosensing applications. In particular, it has been shown that chiral plasmonic nanostructures have the ability to produce strongly enhanced chiral near-fields. Recently, our group has developed chiral plasmonic nanopyramids, which have the ability to focus chiral near-fields at their tip. This could enable chiral sensing at the single-molecule level. Chiral near-fields can be characterized in terms of the “optical chirality density”. This time-even and parity-odd pseudoscalar was first derived by Lipkin and was found to follow a conservation law analogous to the energy conservation of electromagnetic fields. More recently, Tang and Cohen identified the physical meaning of the “optical chirality density” as the degree of asymmetry in the excitation rate of a chiral molecule. However, how this near-field interpretation of the optical chirality could translate into the far-field is not well understood. Here, we formulate a far-field interpretation by investigating the conservation law for optical chirality in matter, and performing time-averaging in analogy to Poynting’s Theorem. In parallel to extinction energy, we define the “global chirality” as the sum of chirality dissipation within a material and the chirality flux leaving the system. With finite-element simulations, we place a dipole source at locations of enhanced local chirality and investigate the global chirality and ellipticity of emitted light in the far-field. Interestingly, we find that lossy materials with a complex dielectric function have the ability to generate global chirality when excited by achiral light. In particular, chiral plasmonic nanostructures are found to act as effective global chirality generators. The global interpretation of optical chirality provides a useful tool for biosensing applications with chiral plasmonic nanostructures, where the detection is routinely performed in the far-field. Y1 - 2015 ER - TY - CHAP A1 - Poulikakos, Lisa A1 - Gutsche, Philipp A1 - McPeak, Kevin A1 - Burger, Sven A1 - Niegemann, Jens A1 - Hafner, Christian A1 - Norris, David T1 - A Far-Field Interpretation of Optical Chirality in Analogy to Poynting’s Theorem T2 - META '15 Proceedings N2 - The optical chirality density is a valuable tool in locally characterizing chiral electromagnetic near-fields. However, how this quantity could translate into the far-field is not well understood. Here, we formulate a far-field interpretation of optical chirality by investigating its conservation law in isotropic media in analogy to Poynting’s Theorem. We define the global chirality and find that lossy materials, in particular plasmonic nanostructures, can act as chirality generators. This can enable chiral sensing applications at the single molecule level. Y1 - 2015 SP - 1215 EP - 1216 ER - TY - GEN A1 - Gutsche, Philipp A1 - Wolff, Christian A1 - Mirnaziry, Sayyed R. A1 - Poulton, Christopher G. T1 - Coupled-Mode Equations for Stimulated Brillouin Scattering T2 - CUDOS 14th Annual Workshop 2015 Handbook N2 - Stimulated Brillouin Scattering (SBS) is a third-order nonlinear optical effect which originates from the interplay of acoustics and optics. Recently, SBS has been harnessed in nano-photonic waveguides for applications such as narrow-linewidth lasers and Brillouin dynamic gratings [1]. Since the timescales of both phenomena differ significantly, coupled-mode equations derived from a slowly varying envelope approximation are well suited for numerical investigations of SBS [2]. We use the Relaxation Method (RM) [3] to study the optical power transfer and spatially resolved power distributions in long waveguides in the steady state limit. Y1 - 2015 ER - TY - GEN A1 - Gutsche, Philipp A1 - Judd, Thomas A1 - Schmidt, Frank T1 - A convergence study of different Rigorous Coupled Wave Analysis (RCWA) approaches to time-harmonic electromagnetic scattering problems with applications to nanooptical structures T2 - Verhandlungen der Deutschen Physikalischen Gesellschaft (DPG-Frühjahrstagung Berlin 2014) N2 - Reliable numerical simulations of nano-optical structures are the key for design and pre-fabrication processes in diverse disciplines such as lithography in semiconductor industries, spectroscopy of biological molecules, optimization of quantum dot cavities for single-photon sources, and computation of atomic forces like the Casimir Effect. For these purposes a variety of different methods, e.g. FDTD, FEM and RCWA, are in use. On the one hand, FDTD and FEM are investigated intensively - both in mathematics and numerical experiments - and their approximations and convergence properties are well known. On the other hand, there is a lack of these insights in RCWA. In spite of this, RCWA is commonly used to simulate a wide range of systems. We review historical and modern contributions to convergence improvements with respect to RCWA from the early sugesstions to modern developments. We study the convergence rates of the open-source software S4 and analyze the algorithmic properties in detail. Furthermore, we compare RCWA and FEM simulations for different classes of problems including 1D-binary gratings and 2D-periodic photonic crystals. Y1 - 2014 ER - TY - THES A1 - Gutsche, Philipp T1 - Convergence Study of the Fourier Modal Method for Nano-optical Scattering Problems in Comparison with the Finite Element Method N2 - Nano-optical scattering problems play an important role in our modern, technologically driven society. Computers, smartphones and all kinds of electronic devices are manufactured by the semiconductor industry which relies on production using photomasks as well as optical process control. The digital world, e.g. the world wide web, is based on optical interconnects and so-called quantum computers based on optics are supposed to be next generation computers. Moreover, global economic progress demands new and sustainable energy resources and one option is to make use of the power stored in optical radiation from the sun. Additionally, understanding fundamental physics such as the optical properties of asymmetric, or chiral, structures could promote future innovations in engineering. In order to understand and manipulate these kinds of processes, physics provides a well established model: the so-called Maxwell’s equations. Stated by James Clerk Maxwell in 1862, this description of the interaction of light and matter still provides a profound basis for the analysis of electromagnetic phenomena. However, real world problems cannot be calculated using simple mathematics. Rather, computer simulations are needed to obtain solutions of the physical model. Finding suitable methods to solve these problems opens up a wide variety of possibilities. On the one hand, there are methods which require long computing times. On the other hand, some algorithms depend on high memory usage. That is why the field of numerics deals with the question which method is optimally suited for specific problems. The aim of this work is to investigate the applicability of the so-called Fourier Modal Method (FMM) to nano-optical scattering problems in general. Since simple analytical solutions are non-existent for most recent physical problems, we use the Finite Element Method (FEM) to double-check performance of the FMM. Mathematics provide reliable procedures to control the errors of numerics using the FEM. Yet up to now it has not been possible to rigorously classify the quality of the Fourier Modal Method’s results. It is not fully understood whether the process of investing more and more computing resources yields more accurate results. So, we have to ask ourselves: does the numerical method invariably converge? In spite of this uncertainty when using the FMM, it is a well established method dating back to the 1980s. This numerical method has recently been used to optimize performance of solar cells [19] as well as to improve the optical properties of so-called single-photon sources [41] which are essential for quantum cryptography. The latter is a promising candidate to increase digital security and revolutionise cryptography techniques. Furthermore, with the help of the Fourier Modal Method an important issue in optics has been partly resolved: angular filtering of light was made possible by using a mirror which becomes transparent at a certain viewing angle [77]. In addition, an improved numerical technique to design so-called Photonic Crystal waveguides based on the FMM was developed recently [15]. Photonic Crystals are used in the fields of optical bio-sensing and for the construction of novel semiconductor devices. Moreover, approaches to link the FMM and the FEM try to combine advantages of both methods to obtain fast and accurate results [81]. These ideas are closely linked to the well-known concept of Domain Decomposition within the FEM [88]. Here, one possibility to couple domains is to use the scattering matrix formalism as it is done in the FMM. In the scope of this convergence study, we state Maxwell’s equations, particularly for periodic geometries. We describe two physical phenomena of nano-optics, namely chirality and opto-electrical coupling, and define the errors of our simulations. Afterwards, the two investigated methods are analysed with respect to their general properties and a way to unify modelling physics when using both algorithms is presented. With the help of various numerical experiments, we explore convergence characteristics of the FMM and draw conclusions about the ability of this approach to provide accurate results and, consequently, its potential for research on technological innovations. KW - Nano-optics KW - Fourier Modal Method (FMM) KW - Rigorous Coupled Wave Analysis (RCWA) KW - Finite Element Method (FEM) Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56084 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Swarat, Elmar A1 - Weider, Steffen T1 - Duty Rostering in Public Transport - Facing Preferences, Fairness, and Fatigue N2 - Duty rostering problems occur in different application contexts and come in different flavors. They give rise to very large scale integer programs which ypically have lots of solutions and extremely fractional LP relaxations. In such a situation, heuristics can be a viable algorithmic choice. We propose an mprovement method of the Lin-Kernighan type for the solution of duty rostering problems. We illustrate its versatility and solution quality on three different applications in public transit, vehicle routing, and airline rostering with a focus on the management of preferences, fairness, and fatigue, respectively. T3 - ZIB-Report - 15-44 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56070 SN - 1438-0064 ER - TY - GEN A1 - Fischer, Frank A1 - Schlechte, Thomas T1 - Comparing two dual relaxations of large scale train timetabling problems N2 - Railway transportation and in particular train timetabling is one of the basic and source application areas of combinatorial optimization and integer programming. We will discuss two well established modeling techniques for the train timetabling problem. In this paper we focus on one major ingredient - the bounding by dual relaxations. We compare two classical dual relaxations of large scale time expanded train timetabling problems - the Lagrangean Dual and Lagrangean Decomposition. We discuss the convergence behavior and show limitations of the Lagrangean Decomposition approach for a configuration based model. We introduce a third dualization approach to overcome those limitations. Finally, we present promising preliminary computational experiments that show that our new approach indeed has superior convergence properties. T3 - ZIB-Report - 15-43 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56068 SN - 1438-0064 ER - TY - BOOK A1 - Deuflhard, Peter A1 - Röblitz, Susanna T1 - A guide to numerical modelling in systems biology Y1 - 2015 SN - 978-3-319-20058-3 U6 - https://doi.org/10.1007/978-3-319-20059-0 VL - 12 PB - Springer ER - TY - JOUR A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Meyer, A1 - Mückter, T1 - Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix JF - KA Korrespondenz Abwasser, Abfall Y1 - 2015 VL - 3/15 SP - 264 EP - 267 ER - TY - JOUR A1 - Koschek, A1 - Durmaz, Vedat A1 - Krylova, A1 - Wieczorek, A1 - Gupta, Pooja A1 - Richter, A1 - Bujotzek, Alexander A1 - Fischer, A1 - Haag, Rainer A1 - Freund, A1 - Weber, Marcus A1 - Rademann, T1 - Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands JF - Beilstein J. Org. Chem. Y1 - 2015 VL - 11 SP - 837 EP - 847 ER - TY - JOUR A1 - Abendroth, Frank A1 - Solleder, Marthe A1 - Welker, Pia A1 - Licha, Kai A1 - Weber, Marcus A1 - Seitz, Oliver A1 - Mangoldt, Dorothea T1 - High affinity flourescence labelled ligands for the estrogen receptor JF - Eur. J. Org. Chem. Y1 - 2015 VL - 2015 IS - 10 SP - 2157 EP - 2166 ER - TY - JOUR A1 - Wolff, Christian A1 - Gutsche, Philipp A1 - Steel, Michael J. A1 - Eggleton, Benjamin J. A1 - Poulton, Christopher G. T1 - Impact of nonlinear loss on stimulated Brillouin scattering JF - J. Opt. Soc. Am. B N2 - We study the impact of two-photon absorption (2PA) and fifth-order nonlinear loss such as 2PA-induced free-carrier absorption in semiconductors on the performance of stimulated Brillouin scattering devices. We formulate the equations of motion including effective loss coefficients, whose explicit expressions are provided for numerical evaluation in any waveguide geometry. We find that 2PA results in a monotonic, algebraic relationship between amplification, waveguide length, and pump power, whereas fifth-order losses lead to a nonmonotonic relationship. We define a figure of merit for materials and waveguide designs in the presence of fifth-order losses. From this, we determine the optimal waveguide length for the case of 2PA alone and upper bounds for the total Stokes amplification for the case of 2PA as well as fifth-order losses. The analysis is performed analytically using a small-signal approximation and is compared to numerical solutions of the full nonlinear modal equations. Y1 - 2015 U6 - https://doi.org/10.1364/JOSAB.32.001968 VL - 32 IS - 9 SP - 1968 EP - 1978 ER - TY - CHAP A1 - Taentzer, Gabriele A1 - Golas, Ulrike ED - Parisi-Presicce, F. ED - Westfechtel, B. T1 - Towards Local Confluence Analysis for Amalgamated Graph Transformation T2 - Graph Transformations. Proceedings of ICGT 2015 N2 - Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-21145-9_5 VL - 9151 SP - 69 EP - 86 PB - Springer ER - TY - CHAP A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Stötzel, Claudia A1 - Röblitz, Susanna T1 - A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model T2 - 15th International Symposium on Mathematical and Computational Biology, Rorkee, India Y1 - 2015 ER - TY - CHAP A1 - Ehrig, Rainald A1 - Dierkes, Thomas A1 - Schäfer, Stefan A1 - Röblitz, Susanna A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Alimguzhin, Vadim A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian A1 - Leeners, Brigitte T1 - An integrative approach for model driven computation of treatments in reproductive medicine T2 - BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India Y1 - 2016 ER - TY - CHAP A1 - Hajizadeh, Maryam A1 - Schütz, Pascal A1 - List, Renate A1 - Boeth, Heide A1 - Ehrig, Rainald A1 - Postolka, Barbara A1 - Freeman, Michael A. R. A1 - Taylor, William R. T1 - Interpretation of tibio-femoral kinematics critically depends upon the kinematic analysis approach T2 - ISB 2015, 25th congress of the International Society of Biomechanics, Glasgow Y1 - 2015 ER - TY - CHAP A1 - Agcos, Emil A1 - Bodermann, Bernd A1 - Burger, Sven A1 - Dai, Gaoliang A1 - Endres, Johannes A1 - Hansen, Poul-Erik A1 - Nielson, Lars A1 - Madsen, Morten A1 - Heidenreich, Sebastian A1 - Krumrey, Michael A1 - Loechel, Bernd A1 - Probst, Jürgen A1 - Scholze, Frank A1 - Soltwisch, Victor A1 - Wurm, Matthias T1 - Scatterometry reference standards to improve tool matching and traceability in lithographical nanomanufacturing T2 - Proc. SPIE Y1 - 2015 U6 - https://doi.org/10.1117/12.2190409 VL - 9556 SP - 955610 ER - TY - GEN A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Influence of pH and sequence in peptide aggregation via molecular simulation N2 - We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse- grained model can account for these details. T3 - ZIB-Report - 15-42 KW - coarse graining KW - peptide aggregation dynamics KW - Monte Carlo Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55805 SN - 1438-0064 ER - TY - GEN A1 - Gelß, Patrick A1 - Matera, Sebastian A1 - Schütte, Christof T1 - Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model N2 - In multiscale models of heterogeneous catalysis, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. This usually is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO_2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased stiffness. T3 - ZIB-Report - 15-41 KW - heterogeneous catalysis KW - master equation KW - kinetic Monte Carlo KW - tensor decompositions KW - tensor train format KW - alternating linear scheme Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55743 SN - 1438-0064 ER - TY - GEN A1 - Djurdjevac Conrad, Natasa A1 - Weber, Marcus A1 - Schütte, Christof T1 - Finding dominant structures of nonreversible Markov processes N2 - Finding metastable sets as dominant structures of Markov processes has been shown to be especially useful in modeling interesting slow dynamics of various real world complex processes. Furthermore, coarse graining of such processes based on their dominant structures leads to better understanding and dimension reduction of observed systems. However, in many cases, e.g. for nonreversible Markov processes, dominant structures are often not formed by metastable sets but by important cycles or mixture of both. This paper aims at understanding and identifying these different types of dominant structures for reversible as well as nonreversible ergodic Markov processes. Our algorithmic approach generalizes spectral based methods for reversible process by using Schur decomposition techniques which can tackle also nonreversible cases. We illustrate the mathematical construction of our new approach by numerical experiments. T3 - ZIB-Report - 15-40 KW - nonreversible Markov processes KW - metastable sets KW - cycle decomposition KW - Schur decomposition Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55739 SN - 1438-0064 ER - TY - CHAP A1 - Schenker, Sebastian A1 - Steingrímsson, Jón Garðar A1 - Borndörfer, Ralf A1 - Seliger, Günther T1 - Modelling of Bicycle Manufacturing via Multi-criteria Mixed Integer Programming T2 - Procedia CIRP Y1 - 2015 U6 - https://doi.org/10.1016/j.procir.2014.07.068 VL - 26 SP - 276 EP - 280 ER - TY - CHAP A1 - Sprösser, Gunther A1 - Schenker, Sebastian A1 - Pittner, Andreas A1 - Borndörfer, Ralf A1 - Rethmeier, Michael A1 - Chang, Ya-Ju A1 - Finkbeiner, Matthias T1 - Sustainable Welding Process Selection based on Weight Space Partitions T2 - Procedia CIRP Y1 - 2016 U6 - https://doi.org/10.1016/j.procir.2016.01.077 VL - 40 SP - 127 EP - 132 ER - TY - CHAP A1 - Gausemeier, Pia A1 - Seliger, Günther A1 - Schenker, Sebastian A1 - Borndörfer, Ralf T1 - Nachhaltige Technologiepfade für unterschiedliche Entwicklungsniveaus mithilfe mehrkriterieller Entscheidungsfindung T2 - Vorausschau und Technologieplanung Y1 - 2014 SN - 978-3-942647-53-3 VL - 334 SP - 65 EP - 94 ER - TY - CHAP A1 - Buchert, Tom A1 - Neugebauer, Sabrina A1 - Schenker, Sebastian A1 - Lindow, Kai A1 - Stark, Rainer T1 - Multi-criteria Decision Making as a Tool for Sustainable Product Development - Benefits and Obstacles T2 - Procedia CIRP Y1 - 2015 U6 - https://doi.org/10.1016/j.procir.2014.07.110 VL - 26 SP - 70 EP - 75 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Metric inequalities for routings on direct connections with application to line planning JF - Discrete Optimization N2 - We consider multi-commodity flow problems in which capacities are installed on paths. In this setting, it is often important to distinguish between flows on direct connection routes, using single paths, and flows that include path switching. We derive a feasibility condition for path capacities supporting such direct connection flows similar to the well-known feasibility condition for arc capacities in ordinary multi-commodity flows. The condition can be expressed in terms of a class of metric inequalities for routings on direct connections. We illustrate the concept on the example of the line planning problem in public transport and present an application to large-scale real-world problems. Y1 - 2015 VL - 18 SP - 56 EP - 73 ER - TY - CHAP A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - Animating articulated characters using wiggly splines T2 - ACM SIGGRAPH / Eurographics Symposium on Computer Animation N2 - We propose a new framework for spacetime optimization that can generate artistic motion with a long planning horizon for complex virtual characters. The scheme can be used for generating general types of motion and neither requires motion capture data nor an initial motion that satisfies the constraints. Our modeling of the spacetime optimization combines linearized dynamics and a novel warping scheme for articulated characters. We show that the optimal motions can be described using a combination of vibration modes, wiggly splines, and our warping scheme. This enables us to restrict the optimization to low-dimensional spaces of explicitly parametrized motions. Thereby the computation of an optimal motion is reduced to a low-dimensional non-linear least squares problem, which can be solved with standard solvers. We show examples of motions created by specifying only a few constraints for positions and velocities. Y1 - 2015 U6 - https://doi.org/10.1145/2786784.2786799 SP - 101 EP - 109 ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Schulz, Christian A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - Real-time Nonlinear Shape Interpolation JF - ACM Transactions on Graphics N2 - We introduce a scheme for real-time nonlinear interpolation of a set of shapes. The scheme exploits the structure of the shape interpolation problem, in particular, the fact that the set of all possible interpolated shapes is a low-dimensional object in a high-dimensional shape space. The interpolated shapes are defined as the minimizers of a nonlinear objective functional on the shape space. Our approach is to construct a reduced optimization problem that approximates its unreduced counterpart and can be solved in milliseconds. To achieve this, we restrict the optimization to a low-dimensional subspace that is specifically designed for the shape interpolation problem. The construction of the subspace is based on two components: a formula for the calculation of derivatives of the interpolated shapes and a Krylov-type sequence that combines the derivatives and the Hessian of the objective functional. To make the computational cost for solving the reduced optimization problem independent of the resolution of the example shapes, we combine the dimensional reduction with schemes for the efficient approximation of the reduced nonlinear objective functional and its gradient. In our experiments, we obtain rates of 20-100 interpolated shapes per second even for the largest examples which have 500k vertices per example shape. Y1 - 2015 U6 - https://doi.org/10.1145/2729972 VL - 34 IS - 3 SP - 34:1 EP - 34:10 ER - TY - CHAP A1 - Gotzes, Uwe A1 - Heinecke, Nina A1 - Hiller, Benjamin A1 - Rövekamp, Jessica A1 - Koch, Thorsten T1 - Regulatory rules for gas markets in Germany and other European countries T2 - Evaluating gas network capacities Y1 - 2015 SN - 978-1-611973-68-6 SP - 45 EP - 64 PB - Society for Industrial and Applied Mathematics ER - TY - CHAP A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Witzig, Jakob T1 - Reoptimization in branch-and-bound algorithms with an application to elevator control T2 - Proceedings of the 12th International Symposium on Experimental Algorithms Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38527-8_33 VL - 7933 SP - 378 EP - 389 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Hayn, Christine A1 - Heitsch, Holger A1 - Henrion, René A1 - Leövey, Hernan A1 - Möller, Andris A1 - Römisch, Werner T1 - Methods for verifying booked capacities T2 - Evaluating gas network capacities Y1 - 2015 SP - 291 EP - 315 PB - Society for Industrial and Applied Mathematics ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for Maxwell's equations with resonance phenomena T2 - Proc. SPIE N2 - Rigorous optical simulations of 3-dimensional nano-photonic structures are an important tool in the analysis and optimization of scattering properties of nano-photonic devices or parameter reconstruction. To construct geometrically accurate models of complex structured nano-photonic devices the finite element method (FEM) is ideally suited due to its flexibility in the geometrical modeling and superior convergence properties. Reduced order models such as the reduced basis method (RBM) allow to construct self-adaptive, error-controlled, very low dimensional approximations for input-output relationships which can be evaluated orders of magnitude faster than the full model. This is advantageous in applications requiring the solution of Maxwell's equations for multiple parameters or a single parameter but in real time. We present a reduced basis method for 3D Maxwell's equations based on the finite element method which allows variations of geometric as well as material and frequency parameters. We demonstrate accuracy and efficiency of the method for a light scattering problem exhibiting a resonance in the electric field. T3 - ZIB-Report - 15-37 KW - reduced basis method KW - finite element method KW - maxwell equation KW - photonic crystal KW - nano-photonics Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55687 SN - 1438-0064 VL - 9630 SP - 96300R ER - TY - CHAP A1 - Thoma, Alexander A1 - Schnauber, Peter A1 - Gschrey, Manuel A1 - Schmidt, Ronny A1 - Wohlfeil, Benjamin A1 - Seifried, Marc A1 - Schulze, Jan-Hindrick A1 - Burger, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Rodt, Sven A1 - Heindel, Tobias A1 - Reitzenstein, Stephan T1 - Indistinguishable Photons from Deterministically Fabricated Quantum Dot Microlenses T2 - Advanced Photonics Y1 - 2015 U6 - https://doi.org/10.1364/IPRSN.2015.IS4A.6 SP - IS4A.6 ER - TY - JOUR A1 - Gschrey, Manuel A1 - Thoma, Alexander A1 - Schnauber, Peter A1 - Seifried, Marc A1 - Schmidt, Ronny A1 - Wohlfeil, Benjamin A1 - Krüger, Luzy A1 - Schulze, Jan-Hindrick A1 - Heindel, Tobias A1 - Burger, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Highly indistinguishable photons from deterministic quantum-dot microlenses utilizing three-dimensional in situ electron-beam lithography JF - Nature Communications Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8662 VL - 6 SP - 7662 ER - TY - JOUR A1 - Matsuyama, Kei A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Freiwald, André T1 - Two new species of erect Bryozoa (Gymnolaemata: Cheilostomata) and the application of non-destructive imaging methods for quantitative taxonomy JF - Zootaxa N2 - Two new species of cheilostome Bryozoa are described from continental-slope habitats off Mauritania, including canyon and coldwater-coral (mound) habitats. Internal structures of both species were visualised and quantified using micro-computed tomographic (micro-CT) methods. Cellaria bafouri n. sp. is characterised by the arrangement of zooids in alternating longitudinal rows, a smooth cryptocyst, and the presence of an ooecial plate with denticles. Smittina imragueni n. sp. exhibits many similarities with Smittina cervicornis (Pallas, 1766), but differs especially in the shape and orientation of the suboral avicularium. Observations on Smittina imragueni and material labelled as Smittina cervicornis suggest that the latter represents a species group, members of which have not yet been discriminated, possibly because of high intracolony variation and marked astogenetic changes in surface morphology. Both new species are known only from the habitats where they were collected, probably reflecting the paucity of bryozoan sampling from this geographic area and depth range. Both species are able to tolerate low oxygen concentration, which is assumed to be compensated by the high nutrient supply off Mauritania. The application of micro-CT for the semiautomatic quantification of zooidal skeletal characters was successfully tested. We were able to automatically distinguish individual zooidal cavities and acquire corresponding morphological datasets. Comparing the obtained results with conventional SEM measurements allowed ascertaining the reliability of this new method. The employment of micro-CT allows the observation and quantification of previously un- seen characters that can be used in describing and differentiating species that were previously indistinguishable. Further- more, this method might help elucidate processes of colony growth and the function of individual zooids during this process. Y1 - 2015 U6 - https://doi.org/10.11646/zootaxa.4020.1.3 VL - 4020 IS - 1 SP - 81 EP - 100 ER - TY - CHAP A1 - Gamrath, Gerald A1 - Hiller, Benjamin A1 - Witzig, Jakob T1 - Reoptimization Techniques in MIP Solvers N2 - Recently, there have been many successful applications of optimization algorithms that solve a sequence of quite similar mixed-integer programs (MIPs) as subproblems. Traditionally, each problem in the sequence is solved from scratch. In this paper we consider reoptimization techniques that try to benefit from information obtained by solving previous problems of the sequence. We focus on the case that subsequent MIPs differ only in the objective function or that the feasible region is reduced. We propose extensions of the very complex branch-and-bound algorithms employed by general MIP solvers based on the idea to ``warmstart'' using the final search frontier of the preceding solver run. We extend the academic MIP solver SCIP by these techniques to obtain a reoptimizing branch-and-bound solver and report computational results which show the effectiveness of the approach. Y1 - 2015 SN - 978-3-319-20086-6 U6 - https://doi.org/10.1007/978-3-319-20086-6_14 VL - 9125 SP - 181 EP - 192 PB - Springer ET - Experimental Algorithms, Lecture Notes in Computer Science ER - TY - GEN A1 - Pfeuffer, Frank A1 - Werner, Axel T1 - Adaptive telecommunication network operation with a limited number of reconfigurations N2 - Rising traffic in telecommunication networks lead to rising energy costs for the network operators. Meanwhile, increased flexibility of the networking hardware may help to realize load-adaptive operation of the networks to cut operation costs. To meet network operators’ concerns over stability, we propose to switch network configurations only a limited number of times per day. We present a method for the integrated computation of optimal switching times and network configurations that alternatingly solves mixed-integer programs and constrained shortest cycle problems in a certain graph. Similarly to the Branch & Bound Algorithm, it uses lower and upper bounds on the optimum value and allows for pivoting strategies to guide the computation and avoid the solution of irrelevant subproblems. The algorithm can act as a framework to be adapted and applied to suitable problems of different origin. T3 - ZIB-Report - 15-36 KW - Telecommunication KW - Network Design KW - Dynamic Traffic KW - Branch and Bound Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55547 SN - 1438-0064 ER - TY - JOUR A1 - Maher, Stephen J. A1 - Murray, John M. T1 - The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences JF - European Journal of Operational Research N2 - This paper presents a novel application of operations research techniques to the analysis of HIV Env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying the key features of Env involves two steps: first, calculating the covariance of amino acid combinations and positions to form a network of related and compensatory mutations; and second, developing an integer program to identify the smallest connected subgraph of the constructed covariance network that exhibits a set covering property. The integer program developed for this analysis, labelled the unrooted set covering connected subgraph problem (USCCSP), integrates a set covering problem and connectivity evaluation, the latter formulated as a network flow problem. The resulting integer program is very large and complex, requiring the use of Benders' decomposition to develop an efficient solution approach. The results will demonstrate the necessity of applying acceleration techniques to the Benders' decomposition solution approach and the effectiveness of these techniques and heuristic approaches for solving the USCCSP. Y1 - 2016 U6 - https://doi.org/doi:10.1016/j.ejor.2015.07.011 VL - 248 IS - 2 SP - 668 EP - 680 ER - TY - GEN A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Winkler, Michael T1 - Structure-based primal heuristics for mixed integer programming N2 - Primal heuristics play an important role in the solving of mixed integer programs (MIPs). They help to reach optimality faster and provide good feasible solutions early in the solving process. In this paper, we present two new primal heuristics which take into account global structures available within MIP solvers to construct feasible solutions at the beginning of the solving process. These heuristics follow a large neighborhood search (LNS) approach and use global structures to define a neighborhood that is with high probability significantly easier to process while (hopefully) still containing good feasible solutions. The definition of the neighborhood is done by iteratively fixing variables and propagating these fixings. Thereby, fixings are determined based on the predicted impact they have on the subsequent domain propagation. The neighborhood is solved as a sub-MIP and solutions are transferred back to the original problem. Our computational experiments on standard MIP test sets show that the proposed heuristics find solutions for about every third instance and therewith help to improve the average solving time. T3 - ZIB-Report - 15-26 KW - mixed-integer programming, large neighborhood search, primal heuristics, domain propagation Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55518 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - G-PCCA: Spectral Clustering for Non-reversible Markov Chains N2 - Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We extend this spectral clustering method also to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension, non-reversible Markov chains can be analyzed. Furthermore, the chains need not have a positive stationary distribution. And additionally to metastabilities, dominant cycles and sinks can be identified, too. T3 - ZIB-Report - 15-35 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55505 ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa A1 - Schütte, Christof T1 - Reactive flows and unproductive cycles for random walks on complex networks JF - The European Physical Journal Special Topics, vol. 224, iss. 12 (2015) pp. 2369-2387 Y1 - 2015 U6 - https://doi.org/10.1140/epjst/e2015-02417-8 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Nardin, Antonella T1 - Towards the fast and robust optimal design of Wireless Body Area Networks JF - Applied Soft Computing N2 - Wireless body area networks are wireless sensor networks whose adoption has recently emerged and spread in important healthcare applications, such as the remote monitoring of health conditions of patients. A major issue associated with the deployment of such networks is represented by energy consumption: in general, the batteries of the sensors cannot be easily replaced and recharged, so containing the usage of energy by a rational design of the network and of the routing is crucial. Another issue is represented by traffic uncertainty: body sensors may produce data at a variable rate that is not exactly known in advance, for example because the generation of data is event-driven. Neglecting traffic uncertainty may lead to wrong design and routing decisions, which may compromise the functionality of the network and have very bad effects on the health of the patients. In order to address these issues, in this work we propose the first robust optimization model for jointly optimizing the topology and the routing in body area networks under traffic uncertainty. Since the problem may result challenging even for a state-of-the-art optimization solver, we propose an original optimization algorithm that exploits suitable linear relaxations to guide a randomized fixing of the variables, supported by an exact large variable neighborhood search. Experiments on realistic instances indicate that our algorithm performs better than a state-of-the-art solver, fast producing solutions associated with improved optimality gaps. Y1 - 2015 U6 - https://doi.org/10.1016/j.asoc.2015.04.037 VL - 37 SP - 971 EP - 982 PB - Elsevier ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Nardin, Antonella T1 - Towards the fast and robust optimal design of Wireless Body Area Networks N2 - Wireless body area networks are wireless sensor networks whose adoption has recently emerged and spread in important healthcare applications, such as the remote monitoring of health conditions of patients. A major issue associated with the deployment of such networks is represented by energy consumption: in general, the batteries of the sensors cannot be easily replaced and recharged, so containing the usage of energy by a rational design of the network and of the routing is crucial. Another issue is represented by traffic uncertainty: body sensors may produce data at a variable rate that is not exactly known in advance, for example because the generation of data is event-driven. Neglecting traffic uncertainty may lead to wrong design and routing decisions, which may compromise the functionality of the network and have very bad effects on the health of the patients. In order to address these issues, in this work we propose the first robust optimization model for jointly optimizing the topology and the routing in body area networks under traffic uncertainty. Since the problem may result challenging even for a state-of-the-art optimization solver, we propose an original optimization algorithm that exploits suitable linear relaxations to guide a randomized fixing of the variables, supported by an exact large variable neighborhood search. Experiments on realistic instances indicate that our algorithm performs better than a state-of-the-art solver, fast producing solutions associated with improved optimality gaps. T3 - ZIB-Report - 15-34 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55475 SN - 1438-0064 ER - TY - GEN A1 - Wilson, David A1 - Bücher, Pia A1 - Grewe, Carl Martin A1 - Anglin, Carolyn A1 - Zachow, Stefan A1 - Michael, Dunbar T1 - Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Point Cloud Data T2 - 15th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery (CAOS) Y1 - 2015 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Neue Planungsinstrumente nutzen: Das Verkehrsangebot verbessern und Kosten sparen N2 - Wir illustrieren anhand des Liniennetzes der Stadt Potsdam das Potenzial mathematischer Methoden der Angebotsplanung. Wir zeigen, dass das "bestmögliche" Verkehrsangebot stark von planerischen Vorgaben beeinflusst wird, mit denen man die Erreichung unterschiedlicher und teilweise gegenläufiger Ziele steuern kann. Die Komplexität des Systems führt zum Auftreten von Rückkoppelungseffekten, die man nicht mit Hilfe von Daumenregeln beherrschen kann. Vielmehr ist der Einsatz moderner Planungsverfahren in einer interdisziplinären Zusammenarbeit von politischen Entscheidungsträgern, Verkehrsingenieuren und Mathematikern notwendig, um die aktuellen Herausforderungen in der Verkehrsplanung zu meistern. Der Artikel dokumentiert einen Beitrag zum 7. ÖPNV Innovationskongress des Ministeriums für Verkehr und Infrastruktur des Landes Baden-Württemberg, der vom 9.-11. März 2015 in Freiburg stattfand. T3 - ZIB-Report - 15-33 KW - Linienplan KW - Optimierung Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55439 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Schwartz, Stephan T1 - An Extended Network Interdiction Problem for Optimal Toll Control N2 - We study an extension of the shortest path network interdiction problem and present a novel real-world application in this area. We consider the problem of determining optimal locations for toll control stations on the arcs of a transportation network. We handle the fact that drivers can avoid control stations on parallel secondary roads. The problem is formulated as a mixed integer program and solved using Benders decomposition. We present experimental results for the application of our models to German motorways. T3 - ZIB-Report - 15-32 KW - network interdiction Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55405 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Timetabling and Passenger Routing in Public Transport T2 - Appeard in: Proceedings of Conference on Advanced Systems in Public Transport 2015 (CASPT2015) N2 - The task of timetabling is to schedule the trips in a public transport system by determining periodic arrival and departure times at every station. The goal is to provide a service that is both attractive for passengers and can be operated economically. To date, timetable optimization is generally done with respect to fixed passenger routes, i.e., it is assumed that passengers do not respond to changes in the timetable. This is unrealistic and ignores potentially valuable degrees of freedom. We investigate in this paper periodic timetabling models with integrated passenger routing. We propose several models that differ in the allowed passenger paths and the objectives. We compare these models theoretically and report on computations on real-world instances for the city of Wuppertal. T3 - ZIB-Report - 15-31 KW - Passenger routing KW - Periodic timetabling KW - Public transport Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55305 SN - 1438-0064 ER - TY - CHAP A1 - Andersson, Stefan A1 - Sachs, Stephen A1 - Tuma, Christian A1 - Schütt, Thorsten T1 - DataWarp: First Experiences T2 - Cray User Group Y1 - 2015 ER - TY - CHAP A1 - Wende, Florian A1 - Noack, Matthias A1 - Schütt, Thorsten A1 - Sachs, Stephen A1 - Steinke, Thomas T1 - Application Performance on a Cray XC30 Evaluation System with Xeon Phi Coprocessors at HLRN-III T2 - Cray User Group Y1 - 2015 ER - TY - GEN A1 - Gleixner, Ambros A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Iterative Refinement for Linear Programming N2 - We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the objective function, right-hand side, and variable bounds. Exact computation is used to compute and store the exact representation of the transformed problems, while numeric computation is used for solving LPs. At all steps of the algorithm the LP bases encountered in the transformed problems correspond directly to LP bases in the original problem description. We show that this algorithm is effective in practice for computing extended precision solutions and that it leads to a direct improvement of the best known methods for solving LPs exactly over the rational numbers. Our implementation is publically available as an extension of the academic LP solver SoPlex. T3 - ZIB-Report - 15-15 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55118 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2014 T3 - Jahresbericht - 2014 KW - Jahresbericht Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55050 SN - 0934-5892 VL - 2014 ER - TY - JOUR A1 - Humpola, Jesco A1 - Fügenschuh, Armin T1 - Convex reformulations for solving a nonlinear network design problem JF - Computational Optimization and Applications N2 - We consider a nonlinear nonconvex network design problem that arises, for example, in natural gas or water transmission networks. Given is such a network with active and passive components, that is, valves, compressors, control valves (active) and pipelines (passive), and a desired amount of flow at certain specified entry and exit nodes in the network. The active elements are associated with costs when used. Besides flow conservation constraints in the nodes, the flow must fulfill nonlinear nonconvex pressure loss constraints on the arcs subject to potential values (i.e., pressure levels) in both end nodes of each arc. The problem is to compute a cost minimal setting of the active components and numerical values for the flow and node potentials. We examine different (convex) relaxations for a subproblem of the design problem and benefit from them within a branch-and-bound approach. We compare different approaches based on nonlinear optimization numerically on a set of test instances. Y1 - 2015 U6 - https://doi.org/10.1007/s10589-015-9756-2 VL - 62 IS - 3 SP - 717 EP - 759 PB - Springer US ER - TY - GEN A1 - Schäfer, Patrick T1 - Bag-Of-SFA-Symbols in Vector Space (BOSS VS) N2 - Time series classification mimics the human understanding of similarity. When it comes to larger datasets, state of the art classifiers reach their limits in terms of unreasonable training or testing times. One representative example is the 1-nearest-neighbor DTW classifier (1-NN DTW) that is commonly used as the benchmark to compare to and has several shortcomings: it has a quadratic time and it degenerates in the presence of noise. To reduce the computational complexity lower bounding techniques or recently a nearest centroid classifier have been introduced. Still, execution times to classify moderately sized datasets on a single core are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space (BOSS VS) classifier that is robust and accurate due to invariance to noise, phase shifts, offsets, amplitudes and occlusions. We show that it is as accurate while being multiple orders of magnitude faster than state of the art classifiers. Using the BOSS VS allows for mining massive time series datasets and real-time analytics. T3 - ZIB-Report - 15-30 KW - Time Series KW - Classification KW - Data Mining Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54984 SN - 1438-0064 ER - TY - CHAP A1 - Hayn, Christine A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Schewe, Lars A1 - Schweiger, Jonas A1 - Spreckelsen, Klaus T1 - Perspectives T2 - Evaluating Gas Network Capacities N2 - After we discussed approaches to validate nominations and to verify bookings, we consider possible future research paths. This includes determining technical capacities and planning of network extensions. Y1 - 2015 SN - 9781611973686 VL - SIAM-MOS series on Optimization ER - TY - GEN A1 - Taentzer, Gabriele A1 - Golas, Ulrike T1 - Local Confluence Analysis for Amalgamated Graph Transformation: Long Version N2 - Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence. T3 - ZIB-Report - 15-29 KW - amalgamated graph transformation KW - parallel independence KW - critical pair analysis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54943 SN - 1438-0064 ER - TY - CHAP A1 - Greenhalgh, Chris A1 - Benford, Steve A1 - Drozd, Adam A1 - Flintham, Martin A1 - Hampshire, Alastair A1 - Oppermann, Leif A1 - Smith, Keir A1 - Tycowicz, Christoph von T1 - EQUIP2: A Platform for Mobile Phone-based Game Development T2 - Concepts and Technologies for Pervasive Games - A Reader for Pervasive Gaming Research Y1 - 2007 SN - 978-3-8322-6223-5 VL - 1 SP - 153 EP - 178 PB - Shaker Verlag ER - TY - CHAP A1 - Oppermann, Leif A1 - Jacobs, R. A1 - Watkins, M. A1 - Shackford, R. A1 - Tycowicz, Christoph von A1 - Wright, M. A1 - Capra, M. A1 - Greenhalgh, Chris A1 - Benford, Steve T1 - Love City: A Text-Driven, Location-Based Mobile Phone Game Played Between 3 Cities T2 - Pervasive Gaming Applications - A Reader for Pervasive Gaming Research Y1 - 2007 SN - 978-3-8322-6224-2 VL - 2 SP - 285 EP - 312 PB - Shaker Verlag ER - TY - CHAP A1 - Polthier, Konrad A1 - Bobenko, Alexander A1 - Hildebrandt, Klaus A1 - Kornhuber, Ralf A1 - Tycowicz, Christoph von A1 - Yserentant, Harry A1 - Ziegler, Günter M. T1 - Geometry processing T2 - MATHEON - Mathematics for Key Technologies Y1 - 2014 SN - 978-3-03719-137-8 U6 - https://doi.org/10.4171/137 VL - 1 SP - 341 EP - 355 PB - EMS Publishing House ER - TY - THES A1 - Tycowicz, Christoph von T1 - Concepts and Algorithms for the Deformation, Analysis, and Compression of Digital Shapes N2 - This thesis concerns model reduction techniques for the efficient numerical treatment of physical systems governing the deformation behavior of geometrically complex shapes. We present new strategies for the construction of simplified, low-dimensional models that capture the main features of the original complex system and are suitable for use in interactive computer graphics applications. To demonstrate the effectiveness of the new techniques we propose frameworks for real-time simulation and interactive deformation-based modeling of elastic solids and shells and compare them to alternative approaches. In addition, we investigate differential operators that are derived from the physical models and hence can serve as alternatives to the Laplace-Beltrami operator for applications in modal shape analysis. Furthermore, this thesis addresses the compression of digital shapes. In particular, we present a lossless compression scheme that is adapted to the special characteristics of adaptively refined, hierarchical meshes. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000096721-7 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000096721 ER - TY - CHAP A1 - Greenhalgh, Chris A1 - Benford, Steve A1 - Drozd, Adam A1 - Flintham, Martin A1 - Hampshire, Alastair A1 - Oppermann, Leif A1 - Smith, Keir A1 - Tycowicz, Christoph von T1 - Addressing Mobile Phone Diversity in Ubicomp Experience Development T2 - UbiComp 2007: Ubiquitous Computing, 9th International Conference N2 - Mobile phones are a widely-available class of device with supporting communications infrastructure which can be appropriated and exploited to support ubicomp experiences. However mobile phones vary hugely in their capabilities. We explore how a single dimension of phone application type embodies the critical trade-off between capability and availability, i.e. between what can be done and the fraction of potential participants’ phones that can do this. We describe four different mobile phone ubicomp experiences that illustrate different points along this continuum (SMS, WAP/Web, and J2ME, Python and native applications) and the common software platform/toolkit, EQUIP2, that has been co-developed to support them. From this we propose four development strategies for addressing mobile phone diversity: prioritise support for server development (including web integration), migrate functionality between server(s) and handset(s), support flexible communication options, and use a loosely coupled (data-driven and component-based) software approach. Y1 - 2007 U6 - https://doi.org/10.1007/978-3-540-74853-3_26 VL - 4717 SP - 447 EP - 464 ER - TY - CHAP A1 - Tycowicz, Christoph von A1 - Loviscach, Jörn T1 - Measuring and Enhancing the Legibility of GPU-rendered Text T2 - Eurographics 2008 Short Papers N2 - The limited spatial resolution of standard computer displays impedes the legibility of text. To improve the rendering, we have developed a number of strategies that employ GPU-based shader programs and appropriate preprocessing steps. We devised and implemented a set of methods that may be used alone or in combination ranging from simple measures such as gamma-correct MIPmapping to complex ones such as RGB subpixel rendering combined with supersampling. We have researched into their performance in terms of both legibility and speed. We difinded a psychovisual test that quantifies legibility quickly enough to compare a selection of promising techniques. The results allow to choose the optimum blend of rendering methods for a given set of requirements. Y1 - 2008 SP - 45 EP - 48 ER - TY - CHAP A1 - Kälberer, Felix A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Lossless Compression of Adaptive Multiresolution Meshes T2 - XXII Brazilian Symposium on Computer Graphics and Image Processing N2 - We present a novel coder for lossless compression of adaptive multiresolution meshes that exploits their special hierarchical structure. The heart of our method is a new progressive connectivity coder that can be combined with leading geometry encoding techniques. The compressor uses the parent/child relationships inherent to the hierarchical mesh. We use the rules that accord to the refinement scheme and store bits only where it leaves freedom of choice, leading to compact codes that are free of redundancy. To illustrate our scheme we chose the widespread red-green refinement, but the underlying concepts can be directly transferred to other adaptive refinement schemes as well. The compression ratio of our method exceeds that of state-of-the-art coders by a factor of 2 to 3 on most of our benchmark models. Y1 - 2009 U6 - https://doi.org/10.1109/SIBGRAPI.2009.53 SP - 80 EP - 87 ER - TY - GEN A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad ED - Mourrain, Bernard ED - Schaefer, Scott ED - Xu, Guoliang T1 - Eigenmodes of Surface Energies for Shape Analysis T2 - Advances in Geometric Modeling and Processing (Proceedings of Geometric Modeling and Processing 2010) N2 - In this work, we study the spectra and eigenmodes of the Hessian of various discrete surface energies and discuss applications to shape analysis. In particular, we consider a physical model that describes the vibration modes and frequencies of a surface through the eigenfunctions and eigenvalues of the Hessian of a deformation energy, and we derive a closed form representation for the Hessian (at the rest state of the energy) for a general class of deformation energies. Furthermore, we design a quadratic energy, such that the eigenmodes of the Hessian of this energy are sensitive to the extrinsic curvature of the surface. Based on these spectra and eigenmodes, we derive two shape signatures. One that measures the similarity of points on a surface, and another that can be used to identify features of the surface. In addition, we discuss a spectral quadrangulation scheme for surfaces. Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-13411-1_20 VL - 6130 SP - 296 EP - 314 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Kälberer, Felix A1 - Polthier, Konrad T1 - Context-based Coding of Adaptive Multiresolution Meshes JF - Computer Graphics Forum N2 - Multiresolution meshes provide an efficient and structured representation of geometric objects. To increase the mesh resolution only at vital parts of the object, adaptive refinement is widely used. We propose a lossless compression scheme for these adaptive structures that exploits the parent-child relationships inherent to the mesh hierarchy. We use the rules that correspond to the adaptive refinement scheme and store bits only where some freedom of choice is left, leading to compact codes that are free of redundancy. Moreover, we extend the coder to sequences of meshes with varying refinement. The connectivity compression ratio of our method exceeds that of state-of-the-art coders by a factor of 2 to 7. For efficient compression of vertex positions we adapt popular wavelet-based coding schemes to the adaptive triangular and quadrangular cases to demonstrate the compatibility with our method. Akin to state-of-the-art coders, we use a zerotree to encode the resulting coefficients. Using improved context modeling we enhanced the zerotree compression, cutting the overall geometry data rate by 7% below those of the successful Progressive Geometry Compression. More importantly, by exploiting the existing refinement structure we achieve compression factors that are 4 times greater than those of coders which can handle irregular meshes. Y1 - 2011 U6 - https://doi.org/10.1111/j.1467-8659.2011.01972.x VL - 30 IS - 8 SP - 2231 EP - 2245 ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Modal Shape Analysis beyond Laplacian JF - Computer Aided Geometric Design N2 - In recent years, substantial progress in shape analysis has been achieved through methods that use the spectra and eigenfunctions of discrete Laplace operators. In this work, we study spectra and eigenfunctions of discrete differential operators that can serve as an alternative to the discrete Laplacians for applications in shape analysis. We construct such operators as the Hessians of surface energies, which operate on a function space on the surface, or of deformation energies, which operate on a shape space. In particular, we design a quadratic energy such that, on the one hand, its Hessian equals the Laplace operator if the surface is a part of the Euclidean plane, and, on the other hand, the Hessian eigenfunctions are sensitive to the extrinsic curvature (e.g. sharp bends) on curved surfaces. Furthermore, we consider eigenvibrations induced by deformation energies, and we derive a closed form representation for the Hessian (at the rest state of the energy) for a general class of deformation energies. Based on these spectra and eigenmodes, we derive two shape signatures. One that measures the similarity of points on a surface, and another that can be used to identify features of surfaces. Y1 - 2012 U6 - https://doi.org/10.1016/j.cagd.2012.01.001 VL - 29 IS - 5 SP - 204 EP - 2018 ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Interactive surface modeling using modal analysis JF - ACM Transactions on Graphics N2 - We propose a framework for deformation-based surface modeling that is interactive, robust and intuitive to use. The deformations are described by a non-linear optimization problem that models static states of elastic shapes under external forces which implement the user input. Interactive response is achieved by a combination of model reduction, a robust energy approximation, and an efficient quasi-Newton solver. Motivated by the observation that a typical modeling session requires only a fraction of the full shape space of the underlying model, we use second and third derivatives of a deformation energy to construct a low-dimensional shape space that forms the feasible set for the optimization. Based on mesh coarsening, we propose an energy approximation scheme with adjustable approximation quality. The quasi-Newton solver guarantees superlinear convergence without the need of costly Hessian evaluations during modeling. We demonstrate the effectiveness of the approach on different examples including the test suite introduced in [Botsch and Sorkine 2008]. Y1 - 2011 U6 - https://doi.org/10.1145/2019627.2019638 VL - 30 IS - 5 SP - 119:1 EP - 119:11 ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Interactive spacetime control of deformable objects JF - ACM Transactions on Graphics N2 - Creating motions of objects or characters that are physically plausible and follow an animator’s intent is a key task in computer animation. The spacetime constraints paradigm is a valuable approach to this problem, but it suffers from high computational costs. Based on spacetime constraints, we propose a technique that controls the motion of deformable objects and offers an interactive response. This is achieved by a model reduction of the underlying variational problem, which combines dimension reduction, multipoint linearization, and decoupling of ODEs. After a preprocess, the cost for creating or editing a motion is reduced to solving a number of one-dimensional spacetime problems, whose solutions are the wiggly splines introduced by Kass and Anderson [2008]. We achieve interactive response using a new fast and robust numerical scheme for solving a set of one-dimensional problems based on an explicit representation of the wiggly splines. Y1 - 2012 U6 - https://doi.org/10.1145/2185520.2185567 VL - 31 IS - 4 SP - 71:1 EP - 71:8 PB - ACM ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Schulz, Christian A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - An Efficient Construction of Reduced Deformable Objects JF - ACM Transactions on Graphics N2 - Many efficient computational methods for physical simulation are based on model reduction. We propose new model reduction techniques for the approximation of reduced forces and for the construction of reduced shape spaces of deformable objects that accelerate the construction of a reduced dynamical system, increase the accuracy of the approximation, and simplify the implementation of model reduction. Based on the techniques, we introduce schemes for real-time simulation of deformable objects and interactive deformation-based editing of triangle or tet meshes. We demonstrate the effectiveness of the new techniques in different experiments with elastic solids and shells and compare them to alternative approaches. Y1 - 2013 U6 - https://doi.org/10.1145/2508363.2508392 VL - 32 IS - 6 SP - 213:1 EP - 213:10 PB - ACM ER - TY - CHAP A1 - Krämer, Martin A1 - Herrmann, Karl-Heinz A1 - Boeth, Heide A1 - Tycowicz, Christoph von A1 - König, Christian A1 - Zachow, Stefan A1 - Ehrig, Rainald A1 - Hege, Hans-Christian A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - Measuring 3D knee dynamics using center out radial ultra-short echo time trajectories with a low cost experimental setup T2 - ISMRM (International Society for Magnetic Resonance in Medicine), 23rd Annual Meeting 2015, Toronto, Canada Y1 - 2015 ER - TY - JOUR A1 - Quitzsch, Nicole T1 - Vorbei die Zeiten von Gebrauchsanweisungen für Bibliotheksportale : Nutzerbeteiligung und Co-Design am Beispiel des neuen KOBV-Portals T1 - Gone are the times of operating instructions for library portals : User participation and co-design, exemplified by the new KOBV Portal JF - Bibliotheksdienst N2 - Bibliotheken stehen heute mehr denn je vor der Frage, wie sie ihre Dienste attraktiv gestalten können. Da liegt es nahe, Nutzerinnen und Nutzer aktiv in den Designprozess einzubinden. Die Neuentwicklung des KOBV-Portals (http://portal.kobv.de), einer regionalen Suche über die Bestände der Bibliotheken in Berlin und Brandenburg, geht konsequent den Weg des Co-Designs. Nutzerinnen und Nutzer werden als Entwicklungspartner verstanden. Als Projektpartner wurde das Institut für Bibliotheks- und Informationswissenschaft (IBI) der Humboldt-Universität zu Berlin gewonnen. N2 - More than ever, libraries today are faced with the question of how to make their services more attractive. Thus, it only seems logical to actively integrate users into the design process. The re-implementation of the KOBV Portal (http://portal.kobv.de), a regional search in the holdings of libraries in Berlin and Brandenburg, consistently follows the path of co-design. Users are regarded as development partners. The Berlin School of Library and Information Science acts as a project partner. Y1 - 2014 U6 - https://doi.org/10.1515/bd-2014-0097 VL - 48 IS - 10 SP - 795 EP - 806 ER - TY - CHAP A1 - Hendel, Gregor T1 - Enhancing MIP Branching Decisions by Using the Sample Variance of Pseudo Costs T2 - Integration of AI and OR Techniques in Constraint Programming N2 - The selection of a good branching variable is crucial for small search trees in Mixed Integer Programming. Most modern solvers employ a strategy guided by history information, mainly the variable pseudo-costs, which are used to estimate the objective gain. At the beginning of the search, such information is usually collected via an expensive look-ahead strategy called strong branching until variables are considered reliable. The reliability notion is thereby mostly based on fixed-number thresholds, which may lead to ineffective branching decisions on problems with highly varying objective gains. We suggest two new notions of reliability motivated by mathematical statistics that take into account the sample variance of the past observations on each variable individually. The first method prioritizes additional strong branching look-aheads on variables whose pseudo-costs show a large variance by measuring the relative error of a pseudo-cost confidence interval. The second method performs a specialized version of a two-sample Student’s t -test for filtering branching candidates with a high probability to be better than the best history candidate. Both methods were implemented in the MIP-solver SCIP and computational results on standard MIP test sets are presented. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-18008-3_14 VL - 9075 SP - 199 EP - 214 ER - TY - GEN A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack - A solver for STP and variants with parallelization extensions N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem specific. In contrast, this paper introduces a general purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This is achieved by transforming various problem variants into a general form and solving them using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. T3 - ZIB-Report - 15-27 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54648 SN - 1438-0064 N1 - A revised version is provided here: http://nbn-resolving.de/urn:nbn:de:0297-zib-60170. ER - TY - GEN A1 - Hendel, Gregor T1 - Enhancing MIP branching decisions by using the sample variance of pseudo-costs N2 - The selection of a good branching variable is crucial for small search trees in Mixed Integer Programming. Most modern solvers employ a strategy guided by history information, mainly the variable pseudo-costs, which are used to estimate the objective gain. At the beginning of the search, such information is usually collected via an expensive look-ahead strategy called strong-branching until variables are considered reliable. The reliability notion is thereby mostly based on fixed-number thresholds, which may lead to ineffective branching decisions on problems with highly varying objective gains. We suggest two new notions of reliability motivated by mathematical statistics that take into account the sample variance of the past observations on each variable individually. The first method prioritizes additional strong-branching look-aheads on variables whose pseudo-costs show a large variance by measuring the relative error of a pseudo-cost confidence interval. The second method performs a two-sample Student-t test for filtering branching candidates with a high probability to be better than the best history candidate. Both methods were implemented in the MIP-solver SCIP and computational results on standard MIP test sets are presented. T3 - ZIB-Report - 15-28 KW - mixed-integer programming KW - reliability branching Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54591 SN - 1438-0064 ER - TY - GEN A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume A1 - Oliveira, Nuno M.C. T1 - A robust minimax Semidefinite Programming formulation for optimal design of experiments for model parametrization N2 - Model-based optimal design of experiments (M-bODE) is a crucial step in model parametrization since it encloses a framework that maximizes the amount of information extracted from a battery of lab experiments. We address the design of M-bODE for dynamic models considering a continuous representation of the design. We use Semidefinite Programming (SDP) to derive robust minmax formulations for nonlinear models, and extend the formulations to other criteria. The approaches are demonstrated for a CSTR where a two-step reaction occurs. T3 - ZIB-Report - 15-03 KW - Optimal design of experiments KW - Semidefinite Programming KW - Robust minmax designs Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54626 SN - 1438-0064 ER - TY - GEN A1 - Willenbockel, Christian Tobias A1 - Schütte, Christof T1 - A Variational Bayesian Algorithm for Clustering of Large and Complex Networks N2 - We propose the Blockloading algorithm for the clustering of large and complex graphs with tens of thousands of vertices according to a Stochastic Block Model (SBM). Blockloading is based on generalized Variational Bayesian EM (VBEM) schemes and works for weighted and unweighted graphs. Existing Variational (Bayesian) EM methods have to consider each possible number of clusters sepa- rately to determine the optimal number of clusters and are prone to converge to local optima making multiple restarts necessary. These factors impose a severe restriction on the size and complexity of graphs these methods can handle. In con- trast, the Blockloading algorithm restricts restarts to subnetworks in a way that provides error correction of an existing cluster assignment. The number of clusters need not be specified in advance because Blockloading will return it as a result. We show that Blockloading outperforms all other variational methods regarding reliability of the results and computational efficiency. T3 - ZIB-Report - 15-25 KW - Clustering KW - Variational Bayes EM KW - Model Selection, KW - Stochastic Block Model KW - Networks KW - unsupervised classification Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54588 SN - 1438-0064 ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Parameter Identification in a Tuberculosis Model for Cameroon JF - PLOS ONE N2 - A deterministic model of tuberculosis in Cameroon is designed and analyzed with respect to its transmission dynamics. The model includes lack of access to treatment and weak diagnosis capacity as well as both frequency- and density-dependent transmissions. It is shown that the model is mathematically well-posed and epidemiologically reasonable. Solutions are non-negative and bounded whenever the initial values are non-negative. A sensitivity analysis of model parameters is performed and the most sensitive ones are identified by means of a state-of-the-art Gauss-Newton method. In particular, parameters representing the proportion of individuals having access to medical facilities are seen to have a large impact on the dynamics of the disease. The model predicts that a gradual increase of these parameters could significantly reduce the disease burden on the population within the next 15 years. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0120607 ER - TY - GEN A1 - Weitzmann, John H. A1 - Klimpel, Paul ED - digiS - Servicestelle Digitalisierung Berlin, T1 - Rechtliche Rahmenbedingungen für Digitalisierungsprojekte von Gedächtnisinstitutionen N2 - Kulturerbe- und Gedächtnisinstitutionen sammeln, bewahren, dokumentieren und vermitteln Zeugnisse und Objekte des kulturellen Erbes. Die Digitalisierung eröffnet für alle diese Handlungsfelder neue Möglichkeiten, aber gleichzeitig auch neue Herausforderungen. Diese berühren sowohl organisatorische und technische als auch rechtliche Aspekte. Gerade letztere sind oft mit schwer kalkulierbaren Risiken für die Kultureinrichtungen behaftet. Die vorliegende Handreichung, die von iRights im Auftrag der Servicestelle Digitalisierung des Landes Berlin (digiS) erstellt wurde, soll eine Einführung für die Mitarbeiter der Kulturinstitutionen in die Themen Urheber- und Leistungsschutzrechte sein. Sie soll für rechtliche Risiken sensibilisieren und Handlungsspielräume aufzeigen. Die ursprüngliche Version 1.0 wurde im Nachgang des Workshops der Autoren am ZIB noch einmal überarbeitet. Neu hinzugekommen sind zwei Abschnitte zu den Themen Archivkopie und elektronischer Leseplatz. Y1 - 2014 U6 - https://doi.org/10.12752/2.0.002.1 ER - TY - GEN A1 - Müller, Anja A1 - Bartholmei, Stephan A1 - Fischer, Barbara A1 - Hahn, Helene T1 - Der GLAM-Hackathon "Coding da Vinci" N2 - Coding da Vinci, der erste deutsche Kultur-Hackathon, wurde gemeinsam von der Open Knowledge Foundation Deutschland, der Servicestelle Digitalisierung Berlin, Wikimedia Deutschland und der Deutschen Digitalen Bibliothek veranstaltet. Zwischen Ende April und Anfang Juli haben 150 Teilnehmer (Coder, Webdesigner, Kulturinteressierte u.a.) an Webseiten, mobilen Apps,Spielen, Hardwareprojekten und anderen Anwendungen offener Daten gearbeitet. Die Daten wurden von 16 Kultur-Einrichtungen bereitgestellt. Im Verlauf des Hackathons wurden daraus 17 funktionsfähige Prototypen entwickelt, öffentlich präsentiert und fünf davon auch prämiert.Doch was genau ist ein Hackathon? Wie kommen Kulturinstitutionen und Hacker zusammen? Wie gelangt eine Kulturinstitution zu offenen Daten? Welche Herausforderungen und Chancen bietet ein Hackathon für den Kulturbereich? Welche neue Qualität erwächst aus einem partizipativen Zugang zum digitalen Kulturerbe und der Möglichkeit mit Daten zu arbeiten? Was bleibt zu tun,um die Ergebnisse nachhaltig zu sichern? Diese Fragen sollen anhand der Ergebnisse von CdV diskutiert werden. Unter dem Motto „lessons learned“ wagen wir den Ausblick auf Coding da Vinci 2015. T3 - ZIB-Report - 15-23 KW - Hackathon KW - open data KW - GLAM KW - Kulturinstitutionen Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54566 SN - 1438-0064 ER - TY - JOUR A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - Animating Deformable Objects Using Sparse Spacetime Constraints JF - ACM Transactions on Graphics N2 - We propose a scheme for animating deformable objects based on spacetime optimization. The main feature is that it robustly and quickly (within a few seconds) generates interesting motion from a sparse set of spacetime constraints. Providing only partial (as opposed to full) keyframes for positions and velocities is sufficient. The computed motion satisfies the constraints and the remaining degrees of freedom are determined by physical principles using elasticity and the spacetime constraints paradigm. Our modeling of the spacetime optimization problem combines dimensional reduction, modal coordinates, wiggly splines, and rotation strain warping. Controlling the warped motion requires the derivative of the warp map. We derive a representation of the derivative that can be efficiently and robustly evaluated. Our solver is based on a theorem that characterizes the solutions of the optimization problem and allows us to restrict the optimization to very low-dimensional search spaces. This treatment of the optimization problem avoids a time discretization and the resulting method can robustly deal with sparse input and wiggly motion. Y1 - 2014 U6 - https://doi.org/10.1145/2601097.2601156 VL - 33 IS - 4 SP - 109:1 EP - 109:10 ER - TY - THES A1 - Berthold, Timo T1 - Heuristic algorithms in global MINLP solvers N2 - In the literature for mixed integer programming, heuristic algorithms (particularly primal heuristics) are often considered as stand-alone procedures; in that context, heuristics are treated as an alternative to solving a problem to proven optimality. This conceals the fact that heuristic algorithms are a fundamental component of state-of-the-art global solvers for mixed integer linear programming (MIP) and mixed integer nonlinear programming (MINLP). In the present thesis, we focus on this latter aspect; we study heuristic algorithms that are tightly integrated within global MINLP solvers and analyze their impact on the overall solution process. Our contributions comprise generalizations of primal heuristics for MIP towards MINLP as well as novel ideas for MINLP primal heuristics and for heuristic algorithms to take branching decisions and to collect global information in MIP. These are: - Shift-and-Propagate, a novel propagation heuristic for MIP that does not require the solution to an LP relaxation, - a generic way to generalize large neighborhood search (LNS) heuristics from MIP to MINLP, - an Objective Feasibility Pump heuristic for nonconvex MINLP that uses second-order information and a dynamic selection of rounding procedures, - RENS, an LNS start heuristic for MINLP that optimizes over the set of feasible roundings of an LP solution, - Undercover, an LNS start heuristic for MINLP that solves a largest sub-MIP of a given MINLP, - Rapid Learning, a heuristic algorithm to generate globally valid conflict constraints for MIPs, - Cloud Branching, a heuristic algorithm that exploits dual degeneracy to reduce the number of candidates for branching variable selection. Additionally, we propose a new performance measure, the primal integral, that captures the benefits of primal heuristics better than traditional methods. In our computational study, we compare the performance of the MIP and MINLP solver SCIP with and without primal heuristics on six test sets with altogether 983 instances from academic and industrial sources, including our project partners ForNe, SAP, and Siemens. We observe that heuristics improve the solver performance regarding all measures that we used - by different orders of magnitude. We further see that the harder a problem is to solve to global optimality, the more important the deployment of primal heuristics becomes. The algorithms presented in this thesis are available in source code as part of the solver SCIP, of which the author has been a main developer for the last years. Methods described in this thesis have also been re-implemented within several commercial and noncommercial MIP and MINLP software packages, including Bonmin, CBC, Cplex, Gams, Sulum, and Xpress. KW - mixed integer nonlinear programming KW - primal heuristic KW - mixed integer programming KW - branching rule KW - large neighborhood search KW - solver software Y1 - 2014 UR - http://www.zib.de/berthold/Berthold2014.pdf SN - 978-3-8439-1931-9 PB - Dr. Hut Verlag ER - TY - CHAP A1 - Baumann, Wolfgang A1 - Laubender, Guido A1 - Läuter, Matthias A1 - Reinefeld, Alexander A1 - Schimmel, Christian A1 - Steinke, Thomas A1 - Tuma, Christian A1 - Wollny, Stefan ED - Vetter, Jeffrey S. T1 - HLRN-III at Zuse Institute Berlin T2 - Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two Y1 - 2015 UR - http://www.crcpress.com/product/isbn/9781498700627 SN - 9781498700627 SP - 81 EP - 114 PB - Chapman and Hall/CRC ER - TY - THES A1 - Knötel, David T1 - Segmentation of ray and shark tesserae N2 - Rays and sharks are cartilaginous fishes. Most of the cartilaginous skeleton is covered with calcified tiles to improve the stability of the skeleton. These tiles are called tesserae and enclose areas of uncalcified cartilage. Because of the special properties of the tesserae, biologists are interested to understand shape and structure of tessellated cartilage. This thesis presents a segmentation pipeline for the separation of tesserae on the cartilaginous skeleton of rays and sharks. The segmentation pipeline consists of an automatic initial segmentation step followed by manual error corrections by the user. The initial segmentation is based on the contour tree data structure that tracks the evolution of level sets in a dataset during iso-value changes. The presented segmentation concepts are not limited to the segmentation of tesserae but also viable for similar kinds of tiled structures. The input datasets are given as micro-CT scans. The contribution of this thesis is the development of a segmentation pipeline. The pipeline uses a newly developed fast version of the contour-tree-based segmentation algorithm that, after a preprocessing step, does not need to iterate over all voxels in the dataset. Visualizations and computations are done with the software system ZIBAmira. Used algorithms are either implemented as new ZIBAmira modules or they extend already existing ZIBAmira modules. KW - segmentation, contour tree, watershed, distance map Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54429 ER - TY - THES A1 - Hendel, Gregor T1 - Empirical Analysis of Solving Phases in Mixed Integer Programming N2 - Modern solving software for mixed-integer programming (MIP) incorporates numerous algorithmic components whose behavior is controlled by user parameter choices, and whose usefulness dramatically varies depending on the progress of the solving process. In this thesis, our aim is to construct a phase-based solver that dynamically reacts on phase transitions with an appropriate change of its component behavior. Therefore, we decompose the branch-and-bound solving process into three distinct phases: The first phase objective is to find a feasible solution. During the second phase, a sequence of incumbent solutions gets constructed until the incumbent is eventually optimal. Proving optimality is the central objective of the remaining third phase. Based on the MIP-solver SCIP we construct a phase-based solver to make use of the phase concept in two steps: First, we identify promising components for every solving phase individually and show that their combination is beneficial on a test bed of practical MIP instances. We then present and evaluate three heuristic criteria to make use of the phase-based solver in practice, where it is infeasible to distinguish between the last two phases before the termination of the solving process. KW - mixed-integer programming KW - branch-and-cut Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54270 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio T1 - Revisiting wireless network jamming by SIR-based considerations and Multiband Robust Optimization JF - Optimization Letters N2 - We revisit the mathematical models for wireless network jamming introduced by Commander et al. (2007,2008): we first point out the strong connections with classical wireless network design and then we propose a new model based on the explicit use of signal-to-interference quantities. Moreover, to address the uncertain nature of the jamming problem and tackle the peculiar right-hand-side uncertainty of the corresponding model, we propose an original robust cutting-plane algorithm drawing inspiration from multiband robust optimization. Finally, we assess the performance of the proposed cutting plane algorithm by experiments on realistic network instances. Y1 - 2014 U6 - https://doi.org/10.1007/s11590-014-0839-2 VL - 9 SP - 1495 EP - 1510 PB - Springer ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Di Lullo, Michela A1 - Felici, Giovanni A1 - Lacalandra, Fabrizio T1 - A Unified View on Tight Formulations for the Unit Commitment Problem with Optimal Transmission Switching T2 - Gaspard Monge Program for Optimization - Conference on Optimization & Practices in Industry : PGMO-COPI '14 N2 - The classical Unit Commitment Problem (UC) consists in determining the production of a set of thermal and hydro power generation units over a given time horizon, in order to meet a forecast energy demand and minimize a cost function. In the last years, in connection with the UC, increasingly attention has been given to active switching, namely the possibility of changing the topology of the transmission network by tripping some of the lines. Active switching has been indeed recognized as an important way to improve capacity and reliability of the network. Modifying the network topology is also very useful in modern electricity systems, where the penetration of on-programmable renewable energy sources is high and tends to be very concentrated in some zones of the network. As a consequence, the interest for automatic and optimized switching procedures is currently spreading. In this paper, we address the UC when complemented by active switching, thus leading to so-called Unit Commitment with Optimal Transmission Switching (UCOTS). We formulate the UCOTS as a mixed integer linear program, where we unify tight formulations recently proposed in literature for relevant subfamilies of constraints of the problem. Concerning the cost function, in our formulation we approximate the quadratic thermal cost objective function by a piecewise linear function based on perspective cuts and we propose a new simple and effective way to perturb it, with the aim of breaking symmetries induced by optimal transmission switching decision variables. Our original solution approach also exploits specialized branching priorities. Computational experiments on realistic UCOTS instances highlight that our new framework is able to find optimal and near-optimal solutions in reasonable amount of time by direct use of a state-of-the-art commercial MIP solver. Y1 - 2014 ER - TY - GEN A1 - Witzig, Jakob A1 - Gamrath, Gerald A1 - Hiller, Benjamin T1 - Reoptimization Techniques in MIP Solvers N2 - Recently, there have been many successful applications of optimization algorithms that solve a sequence of quite similar mixed-integer programs (MIPs) as subproblems. Traditionally, each problem in the sequence is solved from scratch. In this paper we consider reoptimization techniques that try to benefit from information obtained by solving previous problems of the sequence. We focus on the case that subsequent MIPs differ only in the objective function or that the feasible region is reduced. We propose extensions of the very complex branch-and-bound algorithms employed by general MIP solvers based on the idea to ``warmstart'' using the final search frontier of the preceding solver run. We extend the academic MIP solver SCIP by these techniques to obtain a reoptimizing branch-and-bound solver and report computational results which show the effectiveness of the approach. T3 - ZIB-Report - 15-24 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54375 SN - 1438-0064 ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Bowong, Samuel A1 - Kurths, Jürgen T1 - Parameter Estimation of a Tuberculosis Model in a Patchy Environment: Case of Cameroon JF - BIOMAT - Proceedings of the 12th International Symposium on Mathematical and Computational Biology, Toronto, 2013 Y1 - 2014 U6 - https://doi.org/10.1142/9789814602228_0021 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials N2 - Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time. T3 - ZIB-Report - 15-20 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54353 SN - 1438-0064 ER - TY - GEN A1 - Gul, Raheem A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Mathematical modeling and sensitivity analysis of arterial anastomosis in arm arteries N2 - Cardiovascular diseases are one of the major problems in medicine today and the number of patients increases worldwide. To find the most efficient treatment, prior knowledge about function and dysfunction of the cardiovas- cular system is required and methods need to be developed that identify the disease in an early stage. Mathematical modeling is a powerful tool for prediction and investigation of cardiovascular diseases. It has been shown that the Windkessel model, being based on an analogy between electrical circuits and fluid flow, is a simple but effective method to model the human cardiovascular system. In this paper, we have applied parametric local sensitivity analysis (LSA) to a linear elastic model of the arm arteries, to find and rank sensitive param- eters that may be helpful in clinical diagnosis. A computational model for end-to-side anastomosis (superior ulnar collateral anastomosis with posterior ulnar recurrent, SUC-PUR) is carried out to study the effects of some clinically relevant haemodynamic parameters like blood flow resistance and terminal re- sistance on pressure and flow at different locations of the arm artery. In this context, we also discuss the spatio-temporal dependency of local sensitivities. The sensitivities with respect to cardiovascular parameters reveal the flow resistance and diameter of the vessels as most sensitive parameters. These parameters play a key role in diagnosis of severe stenosis and aneurysms. In contrast, wall thickness and elastic modulus are found to be less sensitive. T3 - ZIB-Report - 15-22 KW - computational cardiovascular model KW - cardiovascular parameters KW - sensitivity analysis KW - anastomosis KW - Windkessel model Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54339 SN - 1438-0064 ER - TY - JOUR A1 - Mücklich, Frank A1 - Webel, Johannes A1 - Aboulfadl, Hisham A1 - Lindow, Norbert A1 - Hege, Hans-Christian T1 - Correlative Tomography – Extraction of Reliable Information with Adequate Resolution from mm Scale Down to Sub-nm Scale JF - Microsc. Microanal. Y1 - 2014 U6 - https://doi.org/10.1017/S1431927614005911 VL - 20 IS - Suppl 3 SP - 838 EP - 839 ER - TY - JOUR A1 - Karbstein, Marika T1 - Ohne Umsteigen ans Ziel JF - OR News N2 - Die Anforderungen an das Liniennetz eines Verkehrsunternehmens sind vielfältig: kurze Fahrzeiten, viele Direktverbindungen und geringe Kosten. Mathematische Optimierungsmethoden können die Planung von Liniennetzen unterstützen und beste Kompromisse bzgl. aller Anforderungen berechnen. Y1 - 2014 VL - 52 SP - 12 EP - 14 ER - TY - JOUR A1 - Cournia, Zoe A1 - Allen, Toby W. A1 - Andricioaei, Ioan A1 - Antonny, Bruno A1 - Baum, Daniel A1 - Brannigan, Grace A1 - Buchete, Nicolae-Viorel A1 - Deckman, Jason T. A1 - Delemotte, Lucie A1 - del Val, Coral A1 - Friedman, Ran A1 - Gkeka, Paraskevi A1 - Hege, Hans-Christian A1 - Hénin, Jérôme A1 - Kasimova, Marina A. A1 - Kolocouris, Antonios A1 - Klein, Michael L. A1 - Khalid, Syma A1 - Lemieux, Joanne A1 - Lindow, Norbert A1 - Roy, Mahua A1 - Selent, Jana A1 - Tarek, Mounir A1 - Tofoleanu, Florentina A1 - Vanni, Stefano A1 - Urban, Sinisa A1 - Wales, David J. A1 - Smith, Jeremy C. A1 - Bondar, Ana-Nicoleta T1 - Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory JF - Journal of Membrane Biology Y1 - 2015 U6 - https://doi.org/10.1007/s00232-015-9802-0 VL - 248 IS - 4 SP - 611 EP - 640 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - De Pol-Holz, Ricardo A1 - López Correa, Matthias A1 - Forster, Nina A1 - Flögel, Sascha A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Aggradation and carbonate accumulation of Holocene Norwegian cold-water coral reefs JF - Sedimentology Y1 - 2015 U6 - https://doi.org/10.1111/sed.12206 VL - 62 IS - 7 SP - 1873 EP - 1898 PB - Wiley ER - TY - JOUR A1 - Weber, Marcus A1 - Zoschke, Christian A1 - Sedighi, Amir A1 - Fleige, Emanuel A1 - Haag, Rainer A1 - Schäfer-Korting, Monika T1 - Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters JF - J Nanomed Nanotechnol Y1 - 2014 U6 - https://doi.org/10.4172/2157-7439.1000234 VL - 5 IS - 5 SP - 234 ER - TY - GEN A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - Assessing the Relative Positioning of an Osteosynthesis Plate to the Patient-Specific Femoral Shape from Plain 2D Radiographs N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient­specific surface of the distal femur based on 2D X­ray images. Our goal is to study from clinical data, how the plate­to­bone distance affects bone healing. The patient­specific 3D shape of the femur is, however, seldom recorded for cases of femoral osteosynthesis since this typically requires Computed Tomography (CT), which comes at high cost and radiation dose. Our method instead utilizes two postoperative X­ray images to derive the femoral shape and thus can be applied on radiographs that are taken in clinical routine for follow­up. First, the implant geometry is used as a calibration object to relate the implant and the individual X­ray images spatially in a virtual X­ray setup. In a second step, the patient­specific femoral shape and pose are reconstructed in the virtual setup by fitting a deformable statistical shape and intensity model (SSIM) to the images. The relative positioning between femur and implant is then assessed in terms of displacement between the reconstructed 3D shape of the femur and the plate. A preliminary evaluation based on 4 cadaver datasets shows that the method derives the plate­to­bone distance with a mean absolute error of less than 1mm and a maximum error of 4.7 mm compared to ground truth from CT. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing. T3 - ZIB-Report - 15-21 KW - 3d-­reconstruction from 2d X­rays KW - statistical shape and intensity models KW - fracture fixation of the distal femur KW - pose estimation Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54268 SN - 1438-0064 ER - TY - CHAP A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - Assessing the relative positioning of an osteosynthesis plate to the patient-specific femoral shape from plain 2D radiographs T2 - Proceedings of the 15th Annual Meeting of CAOS-International (CAOS) N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient­specific surface of the distal femur based on 2D X­ray images. Our goal is to study from clinical data, how the plate­to­bone distance affects bone healing. The patient­specific 3D shape of the femur is, however, seldom recorded for cases of femoral osteosynthesis since this typically requires Computed Tomography (CT), which comes at high cost and radiation dose. Our method instead utilizes two postoperative X­ray images to derive the femoral shape and thus can be applied on radiographs that are taken in clinical routine for follow­up. First, the implant geometry is used as a calibration object to relate the implant and the individual X­ray images spatially in a virtual X­ray setup. In a second step, the patient­specific femoral shape and pose are reconstructed in the virtual setup by fitting a deformable statistical shape and intensity model (SSIM) to the images. The relative positioning between femur and implant is then assessed in terms of displacement between the reconstructed 3D shape of the femur and the plate. A preliminary evaluation based on 4 cadaver datasets shows that the method derives the plate­to­bone distance with a mean absolute error of less than 1mm and a maximum error of 4.7 mm compared to ground truth from CT. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing. KW - 3d-­reconstruction from 2d X­rays KW - statistical shape and intensity models KW - fracture fixation of the distal femur KW - pose estimation Y1 - 2015 ER - TY - GEN A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa A1 - Schütte, Christof T1 - Reactive flows and unproductive cycles for random walks on complex networks N2 - We present a comprehensive theory for analysis and understanding of transition events between an initial set A and a target set B for general ergodic finite-state space Markov chains or jump processes, including random walks on networks as they occur, e.g., in Markov State Modelling in molecular dynamics. The theory allows us to decompose the probability flow generated by transition events between the sets A and B into the productive part that directly flows from A to B through reaction pathways and the unproductive part that runs in loops and is supported on cycles of the underlying network. It applies to random walks on directed networks and nonreversible Markov processes and can be seen as an extension of Transition Path Theory. Information on reaction pathways and unproductive cycles results from the stochastic cycle decomposition of the underlying network which also allows to compute their corresponding weight, thus characterizing completely which structure is used how often in transition events. The new theory is illustrated by an application to a Markov State Model resulting from weakly damped Langevin dynamics where the unproductive cycles are associated with periodic orbits of the underlying Hamiltonian dynamics. T3 - ZIB-Report - 15-19 KW - Complex networks KW - molecular transition networks KW - transition path theory KW - cycle decomposition KW - reactive trajectories KW - Markow State Methods Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54239 SN - 1438-0064 ER - TY - GEN A1 - Schütte, Christof A1 - Sarich, Marco T1 - A Critical Appraisal of Markov State Models N2 - Markov State Modelling as a concept for a coarse grained description of the essential kinetics of a molecular system in equilibrium has gained a lot of atten- tion recently. The last 10 years have seen an ever increasing publication activity on how to construct Markov State Models (MSMs) for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecu- lar sensors to molecular aggregation. Simultaneously the accompanying theory behind MSM building and approximation quality has been developed well be- yond the concepts and ideas used in practical applications. This article reviews the main theoretical results, provides links to crucial new developments, outlines the full power of MSM building today, and discusses the essential limitations still to overcome. T3 - ZIB-Report - 15-18 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54218 SN - 1438-0064 ER - TY - THES A1 - Schwartz, Stephan T1 - Bilevel Programming to Optimize the Use of Traffic Control Gantries for Toll Enforcement Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54180 ER - TY - GEN A1 - Wende, Florian T1 - SIMD Enabled Functions on Intel Xeon CPU and Intel Xeon Phi Coprocessor N2 - To achieve high floating point compute performance, modern processors draw on short vector SIMD units, as found e.g. in Intel CPUs (SSE, AVX1, AVX2 as well as AVX-512 on the roadmap) and the Intel Xeon Phi coprocessor, to operate an increasingly larger number of operands simultaneously. Making use of SIMD vector operations therefore is essential to get close to the processor’s floating point peak performance. Two approaches are typically used by programmers to utilize the vector units: compiler driven vectorization via directives and code annotations, and manual vectorization by means of SIMD intrinsic operations or assembly. In this paper, we investigate the capabilities of the current Intel compiler (version 15 and later) to generate vector code for non-trivial coding patterns within loops. Beside the more or less uniform data-parallel standard loops or loop nests, which are typical candidates for SIMDfication, the occurrence of e.g. (conditional) function calls including branching, and early returns from functions may pose difficulties regarding the effective use of vector operations. Recent improvements of the compiler's capabilities involve the generation of SIMD-enabled functions. We will study the effectiveness of the vector code generated by the compiler by comparing it against hand-coded intrinsics versions of different kinds of functions that are invoked within innermost loops. T3 - ZIB-Report - 15-17 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54163 SN - 1438-0064 ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Herrmann, Sven A1 - Schmidt, Frank T1 - hp-finite element method for simulating light scattering from complex 3D structures T2 - Proc. SPIE Y1 - 2015 U6 - https://doi.org/10.1117/12.2085795 VL - 9424 SP - 94240Z ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials JF - Computer Graphics Forum N2 - The current characterization methods of the Bulk Heterojunction (BHJ) - the main material of the new Organic Photovoltaic solar cells - are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual charac- terization and exploration of local structure-performance correlations. We propose a new formula that correlates the structural features to the performance bottlenecks. Since research into BHJ materials is highly multidisci- plinary, we enable a visual feedback strategy that allows the scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characteri- zations. We furthermore show that our approach could reduce the previous work-flow time from days to minutes. Y1 - 2015 U6 - https://doi.org/10.1111/cgf.12652 VL - 34 IS - 3 SP - 401 EP - 410 PB - Wiley ER - TY - CHAP A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Steinle, Gunther A1 - Ledentsov, Jr., Nikolay A1 - Choquette, Kent D. A1 - Burger, Sven A1 - Schmidt, Frank T1 - Engineering of optical modes in vertical-cavity microresonators by aperture placement: applications to single-mode and near-field lasers T2 - Proc. SPIE Y1 - 2015 U6 - https://doi.org/10.1117/12.2077012 VL - 9381 SP - 93810V ER - TY - THES A1 - Witzig, Jakob T1 - Reoptimization Techniques in MIP Solvers N2 - Many optimization problems can be modeled as Mixed Integer Programs (MIPs). In general, MIPs cannot be solved efficiently, since solving MIPs is NP-hard, see, e.g., Schrijver, 2003. Common methods for solving NP-hard problems are branch-and-bound and column generation. In the case of column generation, the original problem becomes decomposed or re-formulated into one ore more smaller subproblems, which are easier to solve. Each of these subproblems is solved separately and recurrently, which can be interpreted as solving a sequence of optimization problems. In this thesis, we consider a sequence of MIPs which only differ in the respective objective functions. Furthermore, we assume each of these MIPs get solved with a branch-and-bound algorithm. This thesis aims to figure out whether the solving process of a given sequence of MIPs can be accelerated by reoptimization. As reoptimization we understand starting the solving process of a MIP of this sequence at a given frontier of a search tree corresponding to another MIP of this sequence. At the beginning we introduce an LP-based branch-and-bound algorithm. This algorithm is inspired by the reoptimizing algorithm of Hiller, Klug, and the author of this thesis, 2013. Since most of the state-of-the-art MIP solvers come to decisions based on dual information, which leads to the loss of feasible solutions after changing the objective function, we present a technique to guarantee optimality despite using these information. A decision is based on a dual information if this decision is valid for at least one feasible solution, whereas a decision is based on a primal information if this decision is valid for all feasible solutions. Afterwards, we consider representing the search frontier of the tree by a set of nodes of a given size. We call this the Tree Compression Problem. Moreover, we present a criterion characterizing the similarity of two objective functions. To evaluate our approach of reoptimization we extend the well-known and well-maintained MIP solver SCIP to an LP-based branch-and-bound framework, introduce two heuristics for solving the Tree Compression Problem, and a primal heuristic which is especially fitted to column generation. Finally, we present computational experiments on several problem classes, e.g., the Vertex Coloring and k-Constrained Shortest Path. Our experiments show, that a straightforward reoptimization, i.e., without additional heuristics, provides no benefit in general. However, in combination with the techniques and methods presented in this thesis, we can accelerate the solving of a given sequence up to the factor 14. For this purpose it is essential to take the differences of the objective functions into account and to restart the reoptimization, i.e., solve the subproblem from scratch, if the objective functions are not similar enough. Finally, we discuss the possibility to parallelize the solving process of the search frontier at the beginning of each solving process. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54067 ER - TY - GEN A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An affine covariant composite step method for optimization with PDEs as equality constraints N2 - We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery. T3 - ZIB-Report - 15-09 KW - composite step methods KW - cubic regularization KW - affine covariant KW - optimization with PDEs Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53954 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald A1 - Melchiori, Anna A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Salvagnin, Domenico T1 - Branching on multi-aggregated variables N2 - In mixed-integer programming, the branching rule is a key component to a fast convergence of the branch-and-bound algorithm. The most common strategy is to branch on simple disjunctions that split the domain of a single integer variable into two disjoint intervals. Multi-aggregation is a presolving step that replaces variables by an affine linear sum of other variables, thereby reducing the problem size. While this simplification typically improves the performance of MIP solvers, it also restricts the degree of freedom in variable-based branching rules. We present a novel branching scheme that tries to overcome the above drawback by considering general disjunctions defined by multi-aggregated variables in addition to the standard disjunctions based on single variables. This natural idea results in a hybrid between variable- and constraint-based branching rules. Our implementation within the constraint integer programming framework SCIP incorporates this into a full strong branching rule and reduces the number of branch-and-bound nodes on a general test set of publicly available benchmark instances. For a specific class of problems, we show that the solving time decreases significantly. T3 - ZIB-Report - 15-10 KW - mixed-integer programming, branch-and-bound, branching rule, strong branching Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53829 SN - 1438-0064 ER - TY - CHAP A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Shchukin, Vitaly A1 - Steinle, Gunther A1 - Ledentsov, Jr., Nikolay A1 - Turkiewicz, Jarek P. A1 - Wu, Bo A1 - Shaofeng, Qiu A1 - Ma, Yanan A1 - Zhiyong, Feng A1 - Burger, Sven A1 - Schmidt, Frank A1 - Caspar, Christoph A1 - Freund, Ronald A1 - Choquette, Kent D. T1 - High-speed modulation, wavelength, and mode control in vertical-cavity surface-emitting lasers T2 - Proc. SPIE Y1 - 2015 U6 - https://doi.org/10.1117/12.2082951 VL - 9381 SP - 93810F ER - TY - GEN A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf A1 - Knoben, Loes A1 - Kretz, David A1 - Uetz, Marc T1 - The S-Bahn Challenge in Berlin N2 - The S-Bahn Challenge in Berlin is a challenge in which one has to travel the entire S-Bahn network of Berlin in the shortest possible time. We explain how the problem can be modeled and solved mathematically. Furthermore, we report on our record attempt on January 10, 2015. T3 - ZIB-Report - 15-13 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53792 UR - https://gor.uni-paderborn.de/index.php?id=362 SN - 1438-0064 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Fusseis, Florian A1 - Hoffmann, René T1 - A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells JF - Paleobiology N2 - The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell. Y1 - 2015 U6 - https://doi.org/10.1017/pab.2014.17 VL - 41 IS - 2 SP - 313 EP - 329 PB - Cambridge University Press CY - Cambridge ER - TY - JOUR A1 - Humpola, Jesco A1 - Fügenschuh, Armin A1 - Koch, Thorsten T1 - Valid inequalities for the topology optimization problem in gas network design JF - OR Spectrum N2 - One quarter of Europe's energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euro per km extending the European pipeline network is already a multi-billion Euro business. Therefore, automatic planning tools that support the decision process are desired. Unfortunately, current mathematical methods are not capable of solving the arising network design problems due to their size and complexity. In this article, we will show how to apply optimization methods that can converge to a proven global optimal solution. By introducing a new class of valid inequalities that improve the relaxation of our mixed-integer nonlinear programming model, we are able to speed up the necessary computations substantially. Y1 - 2016 U6 - https://doi.org/https://doi.org/10.1007/s00291-015-0390-2 VL - 38 IS - 3 SP - 597 EP - 631 PB - Springer CY - Berlin Heidelberg ER - TY - GEN A1 - Uslu, Svenja A1 - Werner, Axel T1 - A Two-Phase Method for the Biobjective k-Architecture Connected Facility Location Problem and Hypervolume Computation N2 - We apply customized versions of the ε-constraint Method and the Two-Phase Method to a problem originating in access network planning. We introduce various notions of quality measures for approximated/partial sets of nondominated points, utilizing the concept of hypervolume for biobjective problems. We report on computations to assess the performance of the two methods in terms of these measures. T3 - ZIB-Report - 15-08 KW - Biobjective Optimization KW - Connected Facility Location KW - Hypervolume Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53753 SN - 1438-0064 ER - TY - GEN A1 - Coniglio, Stefano A1 - Grimm, Boris A1 - Koster, Arie M.C.A. A1 - Tieves, Martin A1 - Werner, Axel T1 - Optimal offline virtual network embedding with rent-at-bulk aspects N2 - Network virtualization techniques allow for the coexistence of many virtual networks (VNs) jointly sharing the resources of an underlying substrate network. The Virtual Network Embedding problem (VNE) arises when looking for the most profitable set of VNs to embed onto the substrate. In this paper, we address the offline version of the problem. We propose a Mixed-Integer Linear Programming formulation to solve it to optimality which accounts for acceptance and rejection of virtual network requests, allowing for both splittable and unsplittable (single path) routing schemes. Our formulation also considers a Rent-at-Bulk (RaB) model for the rental of substrate capacities where economies of scale apply. To better emphasize the importance of RaB, we also compare our method to a baseline one which only takes RaB into account a posteriori, once a solution to VNE, oblivious to RaB, has been found. Computational experiments show the viability of our approach, stressing the relevance of addressing RaB directly with an exact formulation. Y1 - 2015 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Klug, Torsten A1 - Lamorgese, Leonardo A1 - Mannino, Carlo A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Recent Success Stories on Optimization of Railway Systems N2 - Planning and operating railway transportation systems is an extremely hard task due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. Because of that, however, mathematical models and optimization techniques can result in large gains for both railway cus- tomers and operators, e.g., in terms of cost reductions or service quality improvements. In the last years a large and growing group of researchers in the OR community have devoted their attention to this domain devel- oping mathematical models and optimization approaches to tackle many of the relevant problems in the railway planning process. However, there is still a gap to bridge between theory and practice, with a few notable exceptions. In this paper we address three success stories, namely, long-term freight train routing (part I), mid-term rolling stock rotation planning (part II), and real-time train dispatching (part III). In each case, we describe real-life, successful implementations. We will dis- cuss the individual problem setting, survey the optimization literature, and focus on particular aspects addressed by the mathematical models. We demonstrate on concrete applications how mathematical optimization can support railway planning and operations. This gives proof that math- ematical optimization can support the planning of rolling stock resources. Thus, mathematical models and optimization can lead to a greater effi- ciency of railway operations and will serve as a powerful and innovative tool to meet recent challenges of the railway industry. T3 - ZIB-Report - 14-47 KW - railway planning KW - railway operations KW - capacity optimization Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53726 SN - 1438-0064 ER - TY - JOUR A1 - Maher, Stephen J. T1 - A novel passenger recovery approach for the integrated airline recovery problem JF - Computers & Operations Research N2 - Schedule disruptions require airlines to intervene through the process of recovery; this involves modifications to the planned schedule, aircraft routings, crew pairings and passenger itineraries. Passenger recovery is generally considered as the final stage in this process, and hence passengers experience unnecessarily large impacts resulting from flight delays and cancellations. Most recovery approaches considering passengers involve a separately defined module within the problem formulation. However, this approach may be overly complex for recovery in many aviation and general transportation applications. This paper presents a unique description of the cancellation variables that models passenger recovery by prescribing the alternative travel arrangements for passengers in the event of flight cancellations. The results will demonstrate that this simple, but effective, passenger recovery approach significantly reduces the operational costs of the airline and increases passenger flow through the network. The integrated airline recovery problem with passenger reallocation is solved using column-and-row generation to achieve high quality solutions in short runtimes. An analysis of the column-and-row generation solution approach is performed, identifying a number of enhancement techniques to further improve the solution runtimes. Y1 - 2015 U6 - https://doi.org/10.1016/j.cor.2014.11.005 VL - 57 SP - 123 EP - 137 ER - TY - GEN A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. T3 - ZIB-Report - 15-11 KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53707 SN - 1438-0064 ER - TY - CHAP A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement Of Pelvic Parameters From AP Radiographs Using Articulated 3D Models T2 - Computer Assisted Radiology and Surgery (CARS) N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Buwaya, Julia A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - Network spot-checking games: Theory and application to toll enforcing in transportation networks JF - Networks N2 - We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. In an SC game, the pure strategies of network users correspond to paths in a graph, and the pure strategies of the inspectors are subset of arcs to be controlled. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium (SSE) is more relevant for this problem and we give a mixed integer programming (MIP) formulation for this problem. We show that the computation of such an equilibrium is NP-hard. More generally, we prove that it is NP-hard to compute a SSE in a polymatrix game, even if the game is pairwise zero-sum. Then, we give some bounds on the price of spite, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we report computational experiments on instances constructed from real data, for an application to the enforcement of a truck toll in Germany. These numerical results show the efficiency of the proposed methods, as well as the quality of the bounds derived in this article. Y1 - 2015 U6 - https://doi.org/10.1002/net.21596 VL - 65 SP - 312 EP - 328 PB - Wiley Periodicals, Inc. ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Harman, Radoslav ED - Steland, Ansgar ED - Rafajłowicz, Ewaryst ED - Szajowski, Krzysztof T1 - Optimal Designs for Steady-state Kalman filters T2 - Stochastic Models, Statistics and Their Applications N2 - We consider a stationary discrete-time linear process that can be observed by a finite number of sensors. The experimental design for the observations consists of an allocation of available resources to these sensors. We formalize the problem of selecting a design that maximizes the information matrix of the steady-state of the Kalman filter, with respect to a standard optimality criterion, such as $D-$ or $A-$optimality. This problem generalizes the optimal experimental design problem for a linear regression model with a finite design space and uncorrelated errors. Finally, we show that under natural assumptions, a steady-state optimal design can be computed by semidefinite programming. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-13881-7_17 VL - 122 SP - 149 EP - 157 PB - Springer ER - TY - CHAP A1 - Harman, Radoslav A1 - Sagnol, Guillaume ED - Steland, Ansgar ED - Rafajłowicz, Ewaryst ED - Szajowski, Krzysztof T1 - Computing D-optimal experimental designs for estimating treatment contrasts under the presence of a nuisance time trend T2 - Stochastic Models, Statistics and Their Applications N2 - We prove a mathematical programming characterisation of approximate partial D-optimality under general linear constraints. We use this characterisation with a branch-and-bound method to compute a list of all exact D-optimal designs for estimating a pair of treatment contrasts in the presence of a nuisance time trend up to the size of 24 consecutive trials. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-13881-7_10 VL - 122 SP - 83 EP - 91 PB - Springer ER - TY - GEN A1 - Harman, Radoslav A1 - Sagnol, Guillaume T1 - Computing D-optimal experimental designs for estimating treatment contrasts under the presence of a nuisance time trend N2 - We prove a mathematical programming characterisation of approximate partial D-optimality under general linear constraints. We use this characterisation with a branch-and-bound method to compute a list of all exact D-optimal designs for estimating a pair of treatment contrasts in the presence of a nuisance time trend up to the size of 24 consecutive trials. T3 - ZIB-Report - 15-02 KW - optimal design of experiments KW - nuisance trend KW - branch and bound Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53640 SN - 1438-0064 ER - TY - THES A1 - Götschel, Sebastian T1 - Adaptive Lossy Trajectory Compression for Optimal Control of Parabolic PDEs N2 - Optimal control problems governed by nonlinear, time-dependent PDEs on three-dimensional spatial domains are an important tool in many fields, ranging from engineering applications to medicine. For the solution of such optimization problems, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results that are accurate enough, in many cases very fine discretizations in time and space are necessary, leading to a significant amount of data to be stored and transmitted to mass storage. This thesis deals with the development and analysis of methods for lossy compression of such finite element solutions. The algorithms are based on a change of basis to reduce correlations in the data, combined with quantization. This is achieved by transforming the finite element coefficient vector from the nodal to the hierarchical basis, followed by rounding the coefficients to a prescribed precision. Due to the inexact reconstruction, and thus inexact data for the adjoint equation, the error induced in the reduced gradient, and reduced Hessian, has to be controlled, to not impede convergence of the optimization. Accuracy requirements of different optimization methods are analyzed, and computable error estimates for the influence of lossy trajectory storage are derived. These tools are used to adaptively control the accuracy of the compressed data. The efficiency of the algorithms is demonstrated on several numerical examples, ranging from a simple linear, scalar equation to a semi-linear system of reaction-diffusion equations. In all examples considerable reductions in storage space and bandwidth requirements are achieved, without significantly influencing the convergence behavior of the optimization methods. Finally, to go beyond pointwise error control, the hierarchical basis transform can be replaced by more sophisticated wavelet transforms. Numerical experiments indicate that choosing suitable norms for error control allows higher compression factors. KW - optimal control KW - semi-linear parabolic PDEs KW - adjoint gradient computation KW - trajectory storage KW - lossy compression Y1 - 2015 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000098552 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Junosza-Szaniawski, Konstanty A1 - Klug, Torsten A1 - Kwasiborski, Slawomir A1 - Schlechte, Thomas T1 - Fastest, average and quantile schedule N2 - We consider problems concerning the scheduling of a set of trains on a single track. For every pair of trains there is a minimum headway, which every train must wait before it enters the track after another train. The speed of each train is also given. Hence for every schedule - a sequence of trains - we may compute the time that is at least needed for all trains to travel along the track in the given order. We give the solution to three problems: the fastest schedule, the average schedule, and the problem of quantile schedules. The last problem is a question about the smallest upper bound on the time of a given fraction of all possible schedules. We show how these problems are related to the travelling salesman problem. We prove NP-completeness of the fastest schedule problem, NP-hardness of quantile of schedules problem, and polynomiality of the average schedule problem. We also describe some algorithms for all three problems. In the solution of the quantile problem we give an algorithm, based on a reverse search method, generating with polynomial delay all Eulerian multigraphs with the given degree sequence and a bound on the number of such multigraphs. A better bound is left as an open question. T3 - ZIB-Report - 14-49 KW - eulerian multigraphs KW - scheduling Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53592 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Reinefeld, Alexander T1 - The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing N2 - With the growing number of hardware components and the increasing software complexity in the upcoming exascale computers, system failures will become the norm rather than an exception for long-running applications. Fault-tolerance can be achieved by the creation of checkpoints during the execution of a parallel program. Checkpoint/Restart (C/R) mechanisms allow for both task migration (even if there were no hardware faults) and restarting of tasks after the occurrence of hardware faults. Affected tasks are then migrated to other nodes which may result in unfortunate process placement and/or oversubscription of compute resources. In this paper we analyze the impact of unfortunate process placement and oversubscription of compute resources on the performance and scalability of two typical HPC application workloads, CP2K and MOM5. Results are given for a Cray XC30/40 with Aries dragonfly topology. Our results indicate that unfortunate process placement has only little negative impact while oversubscription substantially degrades the performance. The latter might be only (partially) beneficial when placing multiple applications with different computational characteristics on the same node. T3 - ZIB-Report - 15-05 KW - Fault-tolerance KW - Process placement KW - Oversubscription Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53560 SN - 1438-0064 ER - TY - GEN A1 - Draegert, Andreas A1 - Eisenblätter, Andreas A1 - Gamrath, Inken A1 - Werner, Axel T1 - Optimal Battery Controlling for Smart Grid Nodes N2 - Energy storages can be of great value when added to power grids. They introduce the possibility to store and release energy whenever this is favorable. This is particularly relevant, for example, if power supply is volatile (as is the case with renewable energy) and the network is small (so that there are few other nodes that might balance fluctuations in consumption or production). We present models and methods from mathematical optimization for computing an optimized storage schedule for this purpose. We look at alternative optimization objectives, such as smallest possible peak load, low energy costs, or the close approximation of a prescribed load curve. The optimization needs to respect general operational and economic constraints as well as limitations in the use of storage, which are imposed by the chosen storage technology. We therefore introduce alternative approaches for modeling the non-linear properties of energy storages and study their impact on the efficiency of the optimization process. Finally, we present a computational study with batteries as storage devices. We use this to highlight the trade-off between solution quality and computational tractability. A version of the model for the purpose of leveling peaks and instabilities has been implemented into a control system for an office-building smart grid scenario. T3 - ZIB-Report - 15-06 KW - energy optimization, non-linear optimization, smart grid Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53550 SN - 1438-0064 ER - TY - JOUR A1 - Petrik, Peter A1 - Kumar, Nitish A1 - Fried, Miklos A1 - Fodor, Bálint A1 - Juhász, György A1 - Pereira, Silvania A1 - Burger, Sven A1 - Urbach, H. Paul T1 - Fourier ellipsometry – an ellipsometric approach to Fourier scatterometry JF - J. Eur. Opt. Soc.-Rapid Y1 - 2015 U6 - https://doi.org/10.2971/jeos.2015.15002 VL - 10 SP - 15002 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Metric Inequalities for Routings on Direct Connections with Application in Line Planning N2 - We consider multi-commodity flow problems in which capacities are installed on paths. In this setting, it is often important to distinguish between flows on direct connection routes, using single paths, and flows that include path switching. We derive a feasibility condition for path capacities supporting such direct connection flows similar to the feasibility condition for arc capacities in ordinary multi-commodity flows. The concept allows to solve large-scale real-world line planning problems in public transport including a novel passenger routing model that favors direct connections over connections with transfers. T3 - ZIB-Report - 15-07 KW - combinatorial optimization KW - integer programming KW - line planning KW - transfers KW - direct connection KW - metric inequalities Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53507 SN - 1438-0064 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Lehmann, Thomas A1 - Lenz, Ralf A1 - Morsi, Antonio A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Willert, Bernhard T1 - Computational results for validation of nominations T2 - Evaluating Gas Network Capacities N2 - The different approaches to solve the validation of nomination problem presented in the previous chapters are evaluated computationally in this chapter. Each approach is analyzed individually, as well as the complete solvers for these problems. We demonstrate that the presented approaches can successfully solve large-scale real-world instances. Y1 - 2015 SN - 9781611973686 VL - SIAM-MOS series on Optimization ER - TY - GEN A1 - Humpola, Jesco T1 - Sufficient Pruning Conditions for MINLP in Gas Network Design N2 - One quarter of Europe’s energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euros per kilometer the extension of the European pipeline network is already a multi billion Euro business. Therefore, automatic planning tools that support the decision process are desired. We model the topology extension problem in gas networks by a mixed-integer nonlinear program (MINLP). This gives rise to a so-called active transmission problem, a continuous nonlinear non-convex feasibility problem which emerges from the MINLP model by fixing all integral variables. In this article we offer novel sufficient conditions for proving the infeasibility of this active transmission problem. These conditions can be expressed in the form of a mixed-integer program (MILP), i.e., the infeasibility of a non-convex NLP can be certified by solving an MILP. These results provide an efficient bounding procedure in a branch-and-bound algorithm. Our computational results demonstrate a substantial speed-up for the necessary computations. T3 - ZIB-Report - 15-04 KW - Network Design KW - Mixed-Integer Nonlinear Programming KW - Infeasibility Detection Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53489 ER - TY - GEN A1 - Brett, Charles A1 - Hoberg, Rebecca A1 - Pacheco, Meritxell A1 - Smith, Kyle A1 - Borndörfer, Ralf A1 - Euler, Ricardo A1 - Gamrath, Gerwin A1 - Grimm, Boris A1 - Heismann, Olga A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Tesch, Alexander T1 - G-RIPS 2014 RailLab - Towards robust rolling stock rotations N2 - The Graduate-Level Research in Industrial Projects (G-RIPS) Program provides an opportunity for high-achieving graduate-level students to work in teams on a real-world research project proposed by a sponsor from industry or the public sector. Each G-RIPS team consists of four international students (two from the US and two from European universities), an academic mentor, and an industrial sponsor. This is the report of the Rail-Lab project on the definition and integration of robustness aspects into optimizing rolling stock schedules. In general, there is a trade-off for complex systems between robustness and efficiency. The ambitious goal was to explore this trade-off by implementing numerical simulations and developing analytic models. In rolling stock planning a very large set of industrial railway requirements, such as vehicle composition, maintenance constraints, infrastructure capacity, and regularity aspects, have to be considered in an integrated model. General hypergraphs provide the modeling power to tackle those requirements. Furthermore, integer programming approaches are able to produce high quality solutions for the deterministic problem. When stochastic time delays are considered, the mathematical programming problem is much more complex and presents additional challenges. Thus, we started with a basic variant of the deterministic case, i.e., we are only considering hypergraphs representing vehicle composition and regularity. We transfered solution approaches for robust optimization from the airline industry to the setting of railways and attained a reasonable measure of robustness. Finally, we present and discuss different methods to optimize this robustness measure. T3 - ZIB-Report - 14-34 KW - robust optimization, rolling stock planning Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53475 SN - 1438-0064 N1 - ZIB-Report 14-34 ER - TY - CHAP A1 - Humpola, Jesco A1 - Fügenschuh, Armin A1 - Hiller, Benjamin A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Lenz, Ralf A1 - Schwarz, Robert A1 - Schweiger, Jonas T1 - The Specialized MINLP Approach T2 - Evaluating Gas Network Capacities N2 - We propose an approach to solve the validation of nominations problem using mixed-integer nonlinear programming (MINLP) methods. Our approach handles both the discrete settings and the nonlinear aspects of gas physics. Our main contribution is an innovative coupling of mixed-integer (linear) programming (MILP) methods with nonlinear programming (NLP) that exploits the special structure of a suitable approximation of gas physics, resulting in a global optimization method for this type of problem. Y1 - 2015 SN - 9781611973686 VL - SIAM-MOS series on Optimization ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Pulaj, Jonad T1 - A Fast Hybrid Primal Heuristic for Multiband Robust Capacitated Network Design with Multiple Time Periods N2 - We investigate the Robust Multiperiod Network Design Problem, a generalization of the Capacitated Network Design Problem (CNDP) that, besides establishing flow routing and network capacity installation as in a canonical CNDP, also considers a planning horizon made up of multiple time periods and protection against fluctuations in traffic volumes. As a remedy against traffic volume uncertainty, we propose a Robust Optimization model based on Multiband Robustness (Büsing and D'Andreagiovanni, 2012), a refinement of classical Gamma-Robustness by Bertsimas and Sim (2004) that uses a system of multiple deviation bands. Since the resulting optimization problem may prove very challenging even for instances of moderate size solved by a state-of-the-art optimization solver, we propose a hybrid primal heuristic that combines a randomized fixing strategy inspired by ant colony optimization and an exact large neighbourhood search. Computational experiments on a set of realistic instances from the SNDlib (2010) show that our original heuristic can run fast and produce solutions of extremely high quality associated with low optimality gaps. T3 - ZIB-Report - 14-40 KW - Capacitated Network Design KW - Multiperiod Design KW - Multiband Robust Optimization KW - Traffic Uncertainty KW - Metaheuristic KW - Ant Colony Optimization KW - Exact Large Neighborhood Search Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52862 SN - 1438-0064 ER - TY - GEN A1 - Hoerth, Rebecca M. A1 - Baum, Daniel A1 - Knötel, David A1 - Prohaska, Steffen A1 - Willie, Bettina M. A1 - Duda, Georg A1 - Hege, Hans-Christian A1 - Fratzl, Peter A1 - Wagermaier, Wolfgang T1 - Registering 2D and 3D Imaging Data of Bone during Healing N2 - Purpose/Aims of the Study: Bone’s hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue’s calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes. T3 - ZIB-Report - 15-01 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53426 SN - 1438-0064 ER - TY - BOOK ED - Ciccotti, Giovanni ED - Ferrario, Mauro ED - Schütte, Christof T1 - Molecular Dynamics Simulation T3 - Entropy (special issue) Y1 - 2014 PB - Multidisciplinary Digital Publishing Institute (MDPI) ER - TY - GEN A1 - Bertelmann, Roland A1 - Gebauer, Petra A1 - Hasler, Tim A1 - Kirchner, Ingo A1 - Peters-Kottig, Wolfgang A1 - Razum, Matthias A1 - Recker, Astrid A1 - Ulbricht, Damian A1 - van Gasselt, Stephan T1 - Einstieg ins Forschungsdatenmanagement in den Geowissenschaften N2 - Nur wenn eine Kultur der Nachnutzung und des freien Teilens von Wissen entsteht, werden Wissenschaftler auch die eigenen Forschungsdaten für die Langzeitverfügbarkeit aufbereiten und freigeben. Zu diesem Zweck ist diese Handreichung als Einstieg in das Thema Forschungsdatenmanagement entstanden. Y1 - 2014 U6 - https://doi.org/10.2312/lis.14.01 ER - TY - BOOK A1 - Koch, Thorsten A1 - Hiller, Benjamin A1 - Pfetsch, Marc A1 - Schewe, Lars T1 - Evaluating Gas Network Capacities Y1 - 2015 SN - 978-1-611973-68-6 PB - SIAM ER - TY - JOUR A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Computing the nearest reversible Markov chain JF - Numerical Linear Algebra with Applications N2 - Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem. KW - Reversible Markov Chain KW - Convex Optimization KW - MSM Y1 - 2015 U6 - https://doi.org/10.1002/nla.1967 VL - 22 IS - 3 SP - 483 EP - 499 ER - TY - GEN A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Computing the nearest reversible Markov chain N2 - Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem. T3 - ZIB-Report - 14-48 KW - Reversible Markov Chain KW - Convex Optimization KW - MSM Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53292 SN - 1438-0064 ER - TY - THES A1 - Humpola, Jesco T1 - Gas Network Optimization by MINLP N2 - One quarter of Europe's energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euros per kilometer the extension of the European pipeline network is already a multi billion Euro business. The challenging question is how to expand and operate the network in order to facilitate the transportation of specified gas quantities at minimum cost. This task can be formulated as a mathematical optimization problem that reflects to real-world instances of enormous size and complexity. The aim of this thesis is the development of novel theory and optimization algorithms which make it possible to solve these problems. Gas network topology optimization problems can be modeled as nonlinear mixed-integer programs (MINLPs). Such an MINLP gives rise to a so-called active transmission problem (ATP), a continuous nonlinear non-convex feasibility problem which emerges from the MINLP model by fixing all integral variables. The key to solving the ATP as well as the overall gas network topology optimization problem and the main contribution of this thesis is a novel domain relaxation of the variable bounds and constraints in combination with a penalization in the objective function. In case the domain relaxation does not yield a primal feasible solution for the ATP we offer novel sufficient conditions for proving the infeasibility of the ATP. These conditions can be expressed in the form of an MILP, i.e., the infeasibility of a non-convex NLP can be certified by solving an MILP. These results provide an efficient bounding procedure in a branch-and-bound algorithm. If the gas network consists only of pipes and valves, the ATP turns into a passive transmission problem (PTP). Although its constraints are non-convex, its domain relaxation can be proven to be convex. Consequently, the feasibility of the PTP can be checked directly in an efficient way. Another advantage of the passive case is that the solution of the domain relaxation gives rise to a cutting plane for the overall topology optimization problem that expresses the infeasibility of the PTP. This cut is obtained by a Benders argument from the Lagrange function of the domain relaxation augmented by a specially tailored pc-regularization. These cuts provide tight lower bounds for the passive gas network topology optimization problem. The domain relaxation does not only provide certificates of infeasibility and cutting planes, it can also be used to construct feasible primal solutions. We make use of parametric sensitivity analysis in order to identify binary variables to be switched based on dual information. This approach allows for the first time to compute directly MINLP solutions for large-scale gas network topology optimization problems. All the research in this thesis has been realized within the collaborative research project "Forschungskooperation Netzoptimierung (ForNe)". The developed software is in use by the cooperation partner Open Grid Europe GmbH. Parts of this thesis have been published in book chapters, journal articles and technical reports. An overview of the topics and solution approaches within the research project is given by Martin et al. (2011) and Fügenschuh et al. (2013). Gas network operation approaches and solution methods are described in detail by Pfetsch et al. (2014) and with a special focus on topology optimization in Fügenschuh et al. (2011). The primal heuristic presented in this thesis is published by Humpola et al. (2014b). The method for pruning nodes of the branch-and-bound tree for an approximation of the original problem is described in Fügenschuh and Humpola (2013) and Humpola et al. (2014a). The Benders like inequality is introduced by Humpola and Fügenschuh (2013). N2 - Ein Viertel des europäischen Energiebedarfs wird durch Gas gedeckt, das durch ein europaweites Pipelinesystem verteilt wird. Aufgrund von Ausbaukosten von 1 Mio. Euro pro Kilometer ist der Netzausbau ein Milliardenunterfangen. Die größte Herausforderung besteht darin zu entscheiden, wie das Netzwerk kostengünstig ausgebaut und genutzt werden kann, um notwendige Gasmengen zu transportieren. Diese Aufgabe kann mit Hilfe eines mathematischen Optimierungsproblems formuliert werden, wobei anwendungsnahe Instanzen eine enorme Größe und Komplexität aufweisen. Ziel der vorliegenden Arbeit ist die Entwicklung neuer mathematischer Theorien und damit einhergehender Optimierungsalgorithmen, die es ermöglichen, derartige Probleme zu lösen. Die Optimierung der Topologie eines Gasnetzwerks kann mit Hilfe eines nichtlinearen gemischt-ganzzahligen Programms (MINLP) modelliert werden. Durch Fixierung aller ganzzahligen Variablen ergibt sich ein kontinuierliches Zulässigkeitsproblem, das als aktives Transmissionsproblem (ATP) bezeichnet wird. Die zentrale Methode um dieses ATP zu lösen, ist eine neuartige Relaxierung, welche Variablenschranken und einige Nebenbedingungen relaxiert und in der Zielfunktion bestraft. Diese Relaxierung bildet den Kern der in dieser Arbeit vorgestellten Theorie und ermöglicht so die effiziente Lösung der Topologieoptimierung eines Gasnetzwerkes. Für den Fall, dass die Relaxierung keine Primallösung für das ATP liefert, ist es uns gelungen, hinreichende Bedingungen für die Unzulässigkeit des ATP zu formulieren, die durch ein MILP dargestellt werden. Kurz gefasst kann die Unzulässigkeit eines nicht-konvexen NLP durch Lösung eines MILP bewiesen werden. Beide Methoden liefern effiziente Schranken in einem branch-and-bound Lösungsverfahren. Besteht ein Gasnetzwerk nur aus Rohren und Schiebern, dann wird das ATP als passives Transmissionsproblem (PTP) bezeichnet. Obwohl die Nebenbedingungen des PTP nicht konvex sind, konnten wir zeigen, dass seine Relaxierung konvex ist. Daher kann die Unzulässigkeit des PTP direkt auf effiziente Weise geprüft werden. Außerdem können mit Hilfe der Relaxierung in diesem speziellen Fall Schnittebenen für das Topologieoptimierungsproblem aufgestellt werden. Diese repräsentieren die Unzulässigkeit des PTP und folgen aus der Lagrange Funktion der Relaxierung zusammen mit einer speziellen Erweiterung, der sogenannten pc-Regularisierung. Abgesehen von den genannten Klassifizierungen kann die Relaxierung auch genutzt werden, um primale Lösungen zu konstruieren. Hier nutzen wir die parametrische Sensitivitätsanalyse, um mit Hilfe dualer Informationen Binärvariablen des ATP zu identifizieren, deren Werte angepasst werden müssen. Dieser Ansatz erlaubt es zum ersten Mal, direkt MINLP Lösungen für das Topologieoptimierungsproblem realer Gasnetzwerke zu berechnen. Die Resultate dieser Arbeit wurden im Rahmen des Forschungsprojekts "Forschungskooperation Netzoptimierung (ForNe)" erarbeitet. Die entwickelte Software wird vom Kooperationspartner Open Grid Europe GmbH aktiv genutzt. Teile dieser Arbeit sind in Buchkapiteln, Journalen und technischen Berichten publiziert. Eine Übersicht über die Themen und Lösungsansätze im ForNe-Projekt veröffentlichten Martin u. a. (2011) und Fügenschuh u. a. (2013). Für Lösungsmethoden für die operative Nutzung von Gasnetzwerken verweisen wir auf Pfetsch u. a. (2014). Ansätze für eine Topologieoptimierung wurden von Fügenschuh u. a. (2011) beschrieben. Die in dieser Arbeit präsentierte primale Heuristik ist publiziert von Humpola u. a. (2014b). Die genannte Methode, um Knoten innerhalb des branch-and-bound Baums abzuschneiden, wurde für eine Approximation des Topologieproblems von Fügenschuh und Humpola (2013) und Humpola u. a. (2014a) beschrieben. Ein Bericht über die Ungleichungen nach Benders ist in Humpola und Fügenschuh (2013) nachzulesen. T2 - Gas Netzwerk Optimierung mittels MINLP Y1 - 2014 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/5904 ER - TY - CHAP A1 - Wiesendanger, Samuel A1 - Bischoff, Thomas A1 - Jovanov, Vladislav A1 - Knipp, Dietmar A1 - Burger, Sven A1 - Lederer, Falk A1 - Rockstuhl, Carsten T1 - Numerical investigations on the effects of film growth modes on light trapping in silicon thin film solar cells T2 - Light, Energy and the Environment Y1 - 2014 U6 - https://doi.org/10.1364/PV.2014.PF4C.4 SP - PF4C.4 PB - OSA ER - TY - JOUR A1 - Schmid, Martina A1 - Manley, Phillip T1 - Nano- and microlenses as concepts for enhanced performance of solar cells JF - J. Photon. Energy Y1 - 2014 U6 - https://doi.org/10.1117/1.JPE.5.057003 VL - 5 SP - 057003 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Ortmann, Karl Michael T1 - On the efficient utilisation of duration JF - Insurance: Mathematics and Economics N2 - In this article we present a new approach to estimate the change of the present value of a given cashflow pattern caused by an interest rate shift. Our approximation is based on analysing the evolution of the present value function through a linear differential equation. The outcome is far more accurate than the standard approach achieved by a Taylor expansion. Furthermore, we derive an approximation formula of second order that produces nearly accurate results. In particular, we prove that our method is superior to any known alternative approximation formula based on duration. In order to demonstrate the power of this improved approximation we apply it to coupon bonds, level annuities, and level perpetuities. We finally generalise the approach to a non-flat term structure. As for applications in insurance, we estimate the change of the discounted value of future liabilities due to a proportional shift in the set of capital accumulation factors. These findings are of particular importance to capital adequacy calculations with respect to interest rate stress scenarios that are part of regulatory solvency requirements. Y1 - 2015 U6 - https://doi.org/10.1016/j.insmatheco.2014.11.002 VL - 60 SP - 29 EP - 37 ER - TY - CHAP A1 - Wohlfeil, Benjamin A1 - Stamatiadis, Christos A1 - Jäger, Matthias A1 - Zimmermann, Lars A1 - Burger, Sven A1 - Petermann, Klaus T1 - Integrated optical fiber grating coupler on SOI for the excitation of several higher order fiber modes T2 - Optical Communication (ECOC), 2014 European Conference on Y1 - 2014 U6 - https://doi.org/10.1109/ECOC.2014.6963980 SP - 1 EP - 3 ER - TY - GEN A1 - Wilson, David A1 - Bücher, Pia A1 - Grewe, Carl Martin A1 - Mocanu, Valentin A1 - Anglin, Carolyn A1 - Zachow, Stefan A1 - Dunbar, Michael T1 - Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Data T2 - Orthopedic Research Society Annual Meeting Y1 - 2015 CY - Las Vegas, Nevada ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Dittbrenner, Bastian A1 - Langenhan, Andreas A1 - Seidl, Stephan A1 - Weider, Steffen T1 - Integrierte Dienst- und Dienstreihenfolgeplanung zur Erhöhung der Fahrerzufriedenheit JF - Straßenverkehrstechnik Y1 - 2014 IS - 9 SP - 583 EP - 591 ER - TY - CHAP A1 - Menzel, Christoph A1 - Hebestreit, Erik A1 - Mühlig, Stefan A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Lederer, Falk A1 - Pertsch, Thomas ED - Zouhdi, Said ED - Al-Naimiy, Hamid T1 - Towards homogeneous magnetic metamaterials - a comprehensive multipole analysis T2 - Proc. META'13 Y1 - 2013 SN - 978-2-9545460-0-1 SP - 502 EP - 503 ER - TY - JOUR A1 - Schäfer, Patrick T1 - Experiencing the Shotgun Distance for Time Series Analysis JF - Transactions on Machine Learning and Data Mining Y1 - 2014 SN - 1864-9734 VL - 7 IS - 1 SP - 3 EP - 25 ER - TY - JOUR A1 - Hoerth, Rebecca M. A1 - Baum, Daniel A1 - Knötel, David A1 - Prohaska, Steffen A1 - Willie, Bettina M. A1 - Duda, Georg A1 - Hege, Hans-Christian A1 - Fratzl, Peter A1 - Wagermaier, Wolfgang T1 - Registering 2D and 3D Imaging Data of Bone during Healing JF - Connective Tissue Research Y1 - 2015 U6 - https://doi.org/10.3109/03008207.2015.1005210 VL - 56 IS - 2 SP - 133 EP - 143 PB - Taylor & Francis ER - TY - GEN A1 - Wang, Han A1 - Schütte, Christof T1 - Building Markov State Models for Periodically Driven Non-Equilibrium Systems N2 - Recent years have seen an increased interest in non-equilibrium molecular dynamics (NEMD) simulations, especially for molecular systems with periodic forcing by external fields, e.g., in the context of studying effects of electromagnetic radiation on the human body tissue. Lately, an NEMD methods with local thermostating has been proposed that allows for studying non-equilibrium processes in a statistically reliable and thermodynamically consistent way. In this article, we demonstrate how to construct Markov State Models (MSMs) for such NEMD simulations. MSM building has been well-established for systems in equilibrium where MSMs with just a few (macro-)states allow for accurate reproduction of the essential kinetics of the molecular system under consideration. Non-equilibrium MSMs have been lacking so far. The article presents how to construct such MSMs and illustrates their validity and usefulness for the case of conformation dynamics of alanine dipeptide in an external electric field. T3 - ZIB-Report - 14-46 KW - Non-equilibrium KW - Markov states model KW - Alanine dipeptide KW - Electric field KW - Floquet theory Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53167 SN - 1438-0064 N1 - To appear in: Journal of Chemical Theory and Computation ER - TY - JOUR A1 - Kossick, Regine A1 - Schulte (Fotos), Philip A1 - Kuiper (Fotos), Jens-Hendrik T1 - Die Bibliothek des Konrad-Zuse-Zentrums für Informationstechnik "Überall ist Mathematik drin" JF - One Person Libraries Berlin. 10 Jahre Arbeitskreis OPL Berlin/Brandenburg Y1 - 2010 SP - 18 EP - 23 ER - TY - GEN A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Udvary, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Generation of dense statistical connectomes from sparse morphological data N2 - Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and sub-cellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results. T3 - ZIB-Report - 14-43 KW - 3D neural network KW - Dense connectome KW - Reconstruction Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53075 SN - 1438-0064 ER - TY - THES A1 - Dovica, Ivan T1 - Robust tail assignment N2 - The first part of this thesis is devoted to the general problem of stochastic shortest path problem. It is about searching for the shortest path in a graph in which arc lengths are uncertain and specified by continuous random variables. This problem is at the core of various applications, especially in robust transportation planning where paths correspond to aircraft, train, or bus rotations, crew duties or rosters, etc. We propose a novel solution method based on a discretisation of random variables which is applicable to any class of continuous random variables. We also give bounds on the approximation error of the discretised path lengths compared to the continuous path lengths. In addition, we provide theoretical results for the computational complexity of this method. In the second part we apply this method to a real world airline transportation problem: the so-called tail assignment problem. The goal of the tail assignment problem is to construct aircraft rotations, routes consisting of flight segments, for a set of individual aircraft in order to cover a set of flight segments (legs) while considering operational constraints of each individual aircraft as well as short- to long-term individual maintenance requirements. We state a stochastic programming formulation of this problem and we show how to solve it efficiently by using our method within a column generation framework. We show the gain of our stochastic approach in comparison to standard KPI in terms of less propagated delay and thus less operational costs without growth of computational complexity. A key point of our complex approach to robust optimisation problem is the fit of the underlying stochastic model with reality. We propose a delay propagation model that is realistic, not overfitted, and can therefore be used for forecasting purposes. We benchmark our results using extensive simulation. We show a significant decrease of arrival delays and thus monetary savings on average as well as in the majority of our disruption scenarios. We confirm these benefits in even more life-like benchmarks as simulation where recovery actions are taken and in scenarios which use historical delays directly instead of the stochastic model. KW - Flugzeug-Umlaufplanung KW - Spaltenerzeugung KW - Verspätungspropagation KW - column generation KW - delay propagation KW - stochastic shortest path problem KW - tail assignment Y1 - 2014 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/5664 ER - TY - CHAP A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin A1 - Gottwald, Robert Lion A1 - Grösser, Stefan T1 - Modern Nonlinear Optimization Techniques for an Optimal Control of System Dynamics Models T2 - Proceedings of the 32nd International Conference of the System Dynamics Society N2 - We study System Dynamics models with several free parameters that can be altered by the user. We assume that the user's goal is to achieve a certain dynamic behavior of the model by varying these parameters. In order to find best possible combination of parameter settings, several automatic parameter tuning methods are described in the literature and readily available within existing System Dynamic software packages. We give a survey on the available techniques in the market and describe their theoretical background. Some of these methods are already six decades old, and meanwhile newer and more powerful optimization methods have emerged in the mathematical literature. One major obstacle for their direct use are tabled data in System Dynamics models, which are usually interpreted as piecewise linear functions. However, modern optimization methods usually require smooth functions which are twice continuously differentiable. We overcome this problem by a smooth spline interpolation of the tabled data. We use a test set of three complex System Dynamic models from the literature, describe their individual transition into optimization problems, and demonstrate the applicability of modern optimization algorithms to these System Dynamics Optimization problems. Y1 - 2014 ER - TY - CHAP A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin T1 - A Global Approach to the Optimal Control of System Dynamics Models T2 - Proceedings of the 31st International Conference of the System Dynamics Society N2 - The System Dynamics (SD) methodology is a framework for modeling and simulating the dynamic behavior of socioeconomic systems. Characteristic for the description of such systems is the occurrence of feedback loops together with stocks and flows. The mathematical equations that describe the system are usually ordinary differential equations and nonlinear algebraic constraints. Seemingly simple systems can show a nonintuitive, unpredictable behavior over time. Controlling a dynamical system means to specify potential interventions from outside that should keep the system on the desired track, and to define an evaluation schema to compare different controls among each other, so that a ``best'' control can be defined in a meaningful way. The central question is how to compute such globally optimal control for a given SD model, that allows the transition of the system into a desired state with minimum effort. We propose a mixed-integer nonlinear programming (MINLP) reformulation of the System Dynamics Optimization (SDO) problem. MINLP problems can be solved by linear programming based branch-and-bound approach. We demonstrate that standard MINLP solvers are not able to solve SDO problem. To overcome this obstacle, we introduce a special-tailored bound propagation method. Numerical results for these test cases are presented. Y1 - 2013 ER - TY - CHAP A1 - Gschrey, Manuel A1 - Seifried, Marc A1 - Krüger, Luzy A1 - Schmidt, Ronny A1 - Schulze, Jan-Hindrick A1 - Heindel, Tobias A1 - Burger, Sven A1 - Rodt, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Reitzenstein, Stephan T1 - Advanced Quantum Light Sources: Modelling and Realization by Deterministic Nanofabrication Technologies T2 - Integrated Photonics Research, Silicon and Nanophotonics Y1 - 2014 U6 - https://doi.org/10.1364/IPRSN.2014.IW1A.3 VL - IPRSN SP - IW1A.3 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Pulaj, Jonad T1 - A fast hybrid primal heuristic for multiband robust capacitated network design with multiple time periods JF - Applied Soft Computing N2 - We investigate the Robust Multiperiod Network Design Problem, a generalization of the Capacitated Network Design Problem (CNDP) that, besides establishing flow routing and network capacity installation as in a canonical CNDP, also considers a planning horizon made up of multiple time periods and protection against fluctuations in traffic volumes. As a remedy against traffic volume uncertainty, we propose a Robust Optimization model based on Multiband Robustness (Büsing and D'Andreagiovanni, 2012), a refinement of classical Gamma-Robustness by Bertsimas and Sim (2004) that uses a system of multiple deviation bands. Since the resulting optimization problem may prove very challenging even for instances of moderate size solved by a state-of-the-art optimization solver, we propose a hybrid primal heuristic that combines a randomized fixing strategy inspired by ant colony optimization and an exact large neighbourhood search. Computational experiments on a set of realistic instances from the SNDlib (2010) show that our original heuristic can run fast and produce solutions of extremely high quality associated with low optimality gaps. Y1 - 2014 U6 - https://doi.org/10.1016/j.asoc.2014.10.016 VL - 26 SP - 497 EP - 507 ER - TY - GEN A1 - Karbstein, Marika T1 - Integrated Line Planning and Passenger Routing: Connectivity and Transfers N2 - The integrated line planning and passenger routing problem is an important planning problem in service design of public transport. A major challenge is the treatment of transfers. A main property of a line system is its connectivity. In this paper we show that analysing the connecvitiy aspect of a line plan gives a new idea to handle the transfer aspect of the line planning problem. T3 - ZIB-Report - 14-42 KW - line planning, transfers,Steiner connectivity problem Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52986 SN - 1438-0064 ER - TY - GEN A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms N2 - Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts’ opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort. T3 - ZIB-Report - 14-41 KW - electron tomography KW - microtubules KW - serial sectioning KW - image analysis KW - geometry reconstruction KW - image and geometry alignment KW - point correspondence Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52958 SN - 1438-0064 ER - TY - CHAP A1 - Hege, Hans-Christian T1 - Visual analysis of molecular dynamics data using geometric and topological methods T2 - Forum "Math for Industry" 2014 Y1 - 2014 VL - 57 SP - 45 EP - 46 PB - Institute of Mathematics for Industry, Kyushu University CY - Fukuoka, Japan ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - A Coarse-To-Fine Approach to the Railway Rolling Stock Rotation Problem T2 - 14th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems N2 - We propose a new coarse-to-fine approach to solve certain linear programs by column generation. The problems that we address contain layers corresponding to different levels of detail, i.e., coarse layers as well as fine layers. These layers are utilized to design efficient pricing rules. In a nutshell, the method shifts the pricing of a fine linear program to a coarse counterpart. In this way, major decisions are taken in the coarse layer, while minor details are tackled within the fine layer. We elucidate our methodology by an application to a complex railway rolling stock rotation problem. We provide comprehensive computational results that demonstrate the benefit of this new technique for the solution of large scale problems. Y1 - 2014 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2014.79 VL - 42 SP - 79 EP - 91 ER - TY - THES A1 - Sniegula, Erik T1 - Histogram-based Visualization and Analysis of Vector Fields using Stream Line Projection Plots N2 - Field lines in vector fields, e.g. stream lines, path lines, streak lines or time lines, play an important role in the analysis of vector fields. They improve the classification of flow features and its characteristics in particular. Because of the variety of structural information in field lines the effective processing, analysis and visualization play an important role. More effective techniques may contribute to an improved understanding of struc- tural phenomena in a wide range of applications of vector field visualization, such as gaseous flow (e.g. development of cars and aircrafts), design of machines (e.g. turbines), chemistry (e.g. simulation of molecules) and fluid flow in technical or medical applications (e.g. bloodvessel and ocean simulations). This master thesis focuses on the histogram-based visualization and analysis of vec- tor fields using field line projection plots, stream lines in particular. The goal of this work is to develop a hand full of selection criteria to answer specific applica- tion relevant questions about the characteristics and structures of their vector fields. Therefore we present a powerful analysis tool for vector fields or more precisely for their field lines. KW - Vector Field Visualization, Trajectory Visualization Y1 - 2014 ER - TY - JOUR A1 - Betker, Andreas A1 - Gamrath, Inken A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Lehmann, Heiko A1 - Pfeuffer, Frank A1 - Simon, Felix A1 - Werner, Axel T1 - Comprehensive Topology and Traffic Model of a Nationwide Telecommunication Network JF - Journal of Optical Communications and Networking N2 - As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered. Y1 - 2014 U6 - https://doi.org/10.1364/JOCN.6.001038 VL - 6 IS - 11 SP - 1038 EP - 1047 ER - TY - CHAP A1 - Reuther, Markus T1 - Local Search for the Resource Constrained Assignment Problem T2 - 14th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems N2 - The resource constrained assignment problem (RCAP) is to find a minimal cost cycle partition in a directed graph such that a resource constraint is fulfilled. The RCAP has its roots in an application that deals with the covering of a railway timetable by rolling stock vehicles. Here, the resource constraint corresponds to maintenance constraints for rail vehicles. Moreover, the RCAP generalizes several variants of vehicle routing problems. We contribute a local search algorithm for this problem that is derived from an exact algorithm which is similar to the Hungarian method for the standard assignment problem. Our algorithm can be summarized as a k-OPT heuristic, exchanging k arcs of an alternating cycle of the incumbent solution in each improvement step. The alternating cycles are found by dual arguments from linear programming. We present computational results for instances from our railway application at Deutsche Bahn Fernverkehr AG as well as for instances of the vehicle routing problem from the literature. Y1 - 2014 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2014.62 VL - 42 SP - 62 EP - 78 ER - TY - GEN T1 - Annual Report 2013 T3 - Jahresbericht - 2013 KW - Jahresbericht Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52848 SN - 0934-5892 VL - 2013 ER - TY - JOUR A1 - Schöneich, Marc A1 - Stommel, Markus A1 - Kratz, Andrea A1 - Zobel, Valentin A1 - Scheuermann, Gerik A1 - Hotz, Ingrid A1 - Burgeth, Bernhard T1 - Optimization strategy for the design of ribbed plastic components JF - International Journal of Plastics Technology Y1 - 2014 IS - 10 SP - 160 EP - 175 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Harman, Radoslav T1 - Optimal Designs for Steady-state Kalman filters N2 - We consider a stationary discrete-time linear process that can be observed by a finite number of sensors. The experimental design for the observations consists of an allocation of available resources to these sensors. We formalize the problem of selecting a design that maximizes the information matrix of the steady-state of the Kalman filter, with respect to a standard optimality criterion, such as $D-$ or $A-$optimality. This problem generalizes the optimal experimental design problem for a linear regression model with a finite design space and uncorrelated errors. Finally, we show that under natural assumptions, a steady-state optimal design can be computed by semidefinite programming. T3 - ZIB-Report - 14-39 KW - Optimal Design KW - Kalman Filter KW - Semidefinite programming Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52808 SN - 1438-0064 ER - TY - CHAP A1 - Kratz, Andrea A1 - Schöneich, Marc A1 - Zobel, Valentin A1 - Burgeth, Bernhard A1 - Scheuermann, Gerik A1 - Hotz, Ingrid A1 - Stommel, Markus T1 - Tensor Visualization Driven Mechanical Component Design T2 - Proc. IEEE Pacific Visualization Symposium 2014 Y1 - 2014 U6 - https://doi.org/10.1109/PacificVis.2014.51 SP - 145 EP - 152 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Mehrgardt, Julika A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - The Cycle Embedding Problem N2 - Given two hypergraphs, representing a fine and a coarse "layer", and a cycle cover of the nodes of the coarse layer, the cycle embedding problem (CEP) asks for an embedding of the coarse cycles into the fine layer. The CEP is NP-hard for general hypergraphs, but it can be solved in polynomial time for graphs. We propose an integer rogramming formulation for the CEP that provides a complete escription of the CEP polytope for the graphical case. The CEP comes up in railway vehicle rotation scheduling. We present computational results for problem instances of DB Fernverkehr AG that justify a sequential coarse-first-fine-second planning approach. T3 - ZIB-Report - 14-37 KW - cycle embedding problem KW - railway vehicle rotation scheduling KW - sequential coarse-first-fine-second planning approach Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52788 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - The Price of Spite in Spot-checking games N2 - We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium is more relevant for this problem, but we show that this is NP-hard. However, we give some bounds on the \emph{price of spite}, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we demonstrate the quality of these bounds for a real-world application, namely the enforcement of a truck toll on German motorways. T3 - ZIB-Report - 14-38 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52775 SN - 1438-0064 ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Swarat, Elmar ED - Lavi, Ron T1 - The Price of Spite in Spot-checking games T2 - 7th International Symposium on Algorithmic Game Theory (SAGT'2014) N2 - We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium is more relevant for this problem, but we show that this is NP-hard. However, we give some bounds on the \emph{price of spite}, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we demonstrate the quality of these bounds for a real-world application, namely the enforcement of a truck toll on German motorways. Y1 - 2014 SN - 978-3-662-44802-1 U6 - https://doi.org/10.1007/978-3-662-44803-8 N1 - Brief Announcement included in Back Matter p. 293 following VL - 8768 SP - 293 PB - Springer ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung T1 - Fair ticket pricing in public transport as a constrained cost allocation game JF - Annals of Operations Research N2 - Ticket pricing in public transport usually takes a welfare maximization point of view. Such an approach, however, does not consider fairness in the sense that users of a shared infrastructure should pay for the costs that they generate. We propose an ansatz to determine fair ticket prices that combines concepts from cooperative game theory and linear and integer programming. The ticket pricing problem is considered to be a constrained cost allocation game, which is a generalization of cost allocation games that allows to deal with constraints on output prices and on the formation of coalitions. An application to pricing railway tickets for the intercity network of the Netherlands is presented. The results demonstrate that the fairness of prices can be improved substantially in this way. A preliminary version of this paper appeared in the Proceedings of HPSC 2009 (Borndörfer and Hoang 2012). This journal article introduces better model and algorithms. Y1 - 2014 U6 - https://doi.org/10.1007/s10479-014-1698-z VL - 226 SP - 51 EP - 68 ER - TY - CHAP A1 - Kruber, Nico A1 - Schintke, Florian A1 - Berlin, Michael T1 - A Relational Database Schema on the Transactional Key-Value Store Scalaris T2 - Proceedings of 2nd Workshop on Scalable Cloud Data Management Y1 - 2014 U6 - https://doi.org/10.1109/BigData.2014.7004441 ER - TY - JOUR A1 - Froyland, Gary A1 - Maher, Stephen J. A1 - Wu, Cheng-Lung T1 - The recoverable robust tail assignment problem JF - Transportation Science N2 - Schedule disruptions are commonplace in the airline industry with many flight-delaying events occurring each day. Recently there has been a focus on introducing robustness into airline planning stages to reduce the effect of these disruptions. We propose a recoverable robustness technique as an alternative to robust optimisation to reduce the effect of disruptions and the cost of recovery. We formulate the recoverable robust tail assignment problem (RRTAP) as a stochastic program, solved using column generation in the master and subproblems of the Benders' decomposition. We implement a two-phase algorithm for the Benders' decomposition and identify pareto-optimal cuts. The RRTAP includes costs due to flight delays, cancellation, and passenger rerouting, and the recovery stage includes cancellation, delay, and swapping options. To highlight the benefits of simultaneously solving planning and recovery problems in the RRTAP we compare our tail assignment solution against current approaches from the literature. Using airline data we demonstrate that by developing a better tail assignment plan via the RRTAP framework, one can reduce recovery costs in the event of a disruption. Y1 - 2014 U6 - https://doi.org/10.1287/trsc.2013.0463 VL - 48 IS - 3 SP - 351 EP - 372 ER - TY - CHAP A1 - Matuschke, Jannik A1 - Bley, Andreas A1 - Müller, Benjamin ED - Bodlaender, Hans L. ED - Italiano, Giuseppe F. T1 - Approximation Algorithms for Facility Location with Capacitated and Length-Bounded Tree Connections N2 - We consider a generalization of the uncapacitated facility location problem that occurs in planning of optical access networks in telecommunications. Clients are connected to open facilities via depth-bounded trees. The total demand of clients served by a tree must not exceed a given tree capacity. We investigate a framework for combining facility location algorithms with a tree-based clustering approach and derive approximation algorithms for several variants of the problem, using techniques for approximating shallow-light Steiner trees via layer graphs, simultaneous approximation of shortest paths and minimum spanning trees, and greedy coverings. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-40450-4_60 VL - Algorithms -- ESA 2013 SP - 707 EP - 718 PB - Springer ER - TY - GEN A1 - Betker, Andreas A1 - Gamrath, Inken A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Lehmann, Heiko A1 - Pfeuffer, Frank A1 - Simon, Felix A1 - Werner, Axel T1 - Comprehensive Topology and Traffic Model of a Nation-wide Telecommunication Network N2 - As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies, but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load-adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered. T3 - ZIB-Report - 14-36 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52670 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - A Coarse-To-Fine Approach to the Railway Rolling Stock Rotation Problem N2 - We propose a new coarse-to-fine approach to solve certain linear programs by column generation. The problems that we address contain layers corresponding to different levels of detail, i.e., coarse layers as well as fine layers. These layers are utilized to design efficient pricing rules. In a nutshell, the method shifts the pricing of a fine linear program to a coarse counterpart. In this way, major decisions are taken in the coarse layer, while minor details are tackled within the fine layer. We elucidate our methodology by an application to a complex railway rolling stock rotation problem. We provide comprehensive computational results that demonstrate the benefit of this new technique for the solution of large scale problems. T3 - ZIB-Report - 14-26 KW - column generation KW - coarse-to-fine approach KW - multi-layer approach KW - rolling stock rotation problem Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51009 SN - 1438-0064 ER - TY - JOUR A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms JF - PLoS ONE Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0113222 SP - e113222 ER - TY - JOUR A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Steinle, Gunther A1 - Ledentsov, Jr., Nikolay A1 - Burger, Sven A1 - Schmidt, Frank T1 - Single-Mode Vertical Cavity Surface Emitting Laser via Oxide-Aperture-Engineering of Leakage of High Order Transverse Modes JF - IEEE J. Quant. Electron. Y1 - 2014 U6 - https://doi.org/10.1109/JQE.2014.2364544 VL - 50 IS - 12 SP - 990 EP - 995 ER - TY - THES A1 - von Hafe Pérez Ferreira da Silva, Maria Isabel T1 - Computational Left-Ventricle Reconstruction from MRI Data for Patient-specific Cardiac Simulations Y1 - 2014 ER - TY - THES A1 - Hildebrandt, Thomas T1 - Das Konzept der Rhinorespiratorischen Homöostase – ein neuer theoretischer Ansatz für die Diskussion physiologischer und physikalischer Zusammenhänge bei der Nasenatmung Y1 - 2011 UR - http://www.freidok.uni-freiburg.de/volltexte/8177/pdf/Hildebrandt_Dissertation.pdf ER - TY - THES A1 - Kubiack, Kim T1 - Erstellung eines statistischen Formmodells des Mittelgesichts zur Planung individueller Templates für die navigationsgestützte Rekonstruktion des Mittelgesichtsschädels Y1 - 2013 ER - TY - JOUR A1 - Humpola, Jesco A1 - Lehmann, Thomas A1 - Fügenschuh, Armin T1 - A primal heuristic for optimizing the topology of gas networks based on dual information JF - EURO Journal on Computational Optimization N2 - We present a novel heuristic to identify feasible solutions of a mixed-integer nonlinear programming problem arising in natural gas transportation: the selection of new pipelines to enhance the network's capacity to a desired level in a cost-efficient way. We solve this problem in a linear programming based branch-and-cut approach, where we deal with the nonlinearities by linear outer approximation and spatial branching. At certain nodes of the branching tree, we compute a KKT point of a nonlinear relaxation. Based on the information from the KKT point we alter some of the binary variables in a locally promising way exploiting our problem-specific structure. On a test set of real-world instances, we are able to increase the chance of identifying feasible solutions by some order of magnitude compared to standard MINLP heuristics that are already built in the general-purpose MINLP solver SCIP. Y1 - 2015 U6 - https://doi.org/10.1007/s13675-014-0029-0 VL - 3 IS - 1 SP - 53 EP - 78 ER - TY - THES A1 - Zöckler, Maja T1 - Modellgebundene Cranioplastie - Operationstechnik zur Umformung frühkindlicher Schädeldeformitäten unter Verwendung dreidimensionaler Standardformmodelle aus MRT-basierten Rekonstruktionen nicht deformierter Kinder Y1 - 2006 ER - TY - THES A1 - Kulagina, Svetlana T1 - Distributed Multi-Stage Time Series Similarity Search Y1 - 2014 ER - TY - THES A1 - Fajerski, Jan T1 - Map Reduce on Distributed Hash Tables Y1 - 2014 ER - TY - GEN A1 - Sarich, Marco A1 - Schütte, Christof ED - Bowman, Gregory R. ED - Pande, Vijay S. ED - Noé, Frank T1 - Markov Model Theory T2 - An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation N2 - This section reviews the relation between the continuous dynamics of a molecular system in thermal equilibrium and the kinetics given by a Markov State Model (MSM). We will introduce the dynamical propagator, an error-less, alternative description of the continuous dynamics, and show how MSMs result from its discretization. This allows for an precise understanding of the approximation quality of MSMs in comparison to the continuous dynamics. The results on the approximation quality are key for the design of good MSMs. While this section is important for understanding the theory of discretization and related systematic errors, practitioners wishing only to learn how to construct MSMs may skip directly to the discussion of Markov model estimation. Y1 - 2014 U6 - https://doi.org/10.1007/978-94-007-7606-7 VL - 797 SP - 23 EP - 44 PB - Springer ER - TY - GEN A1 - Deuflhard, Peter A1 - Weber, Marcus ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Mathematics without pain T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 U6 - https://doi.org/10.4171/137 VL - 1 SP - 26 EP - 28 PB - European Mathematical Society ER - TY - GEN A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack - A massively parallel STP solver N2 - In this article we describe the impact from embedding a 15 year old model for solving the Steiner tree problem in graphs in a state-of-the-art MIP-Framework, making the result run in a massively parallel environment and extending the model to solve as many variants as possible. We end up with a high-perfomance solver that is capable of solving previously unsolved instances and, in contrast to its predecessor, is freely available for academic research. T3 - ZIB-Report - 14-35 KW - Steiner Tree Problem KW - Mixed-Integer Programming KW - Branch-and-Cut KW - DIMACS Challenge Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52293 SN - 1438-0064 ER - TY - GEN ED - Linsen, Lars ED - Hagen, Hans ED - Hamann, Bernd ED - Hege, Hans-Christian T1 - Visualization in Medicine and Life Sciences II Y1 - 2012 SN - 978-3-642-21607-7 U6 - https://doi.org/10.1007/978-3-642-21608-4 PB - Springer CY - Berlin ER - TY - THES A1 - Kuhn, Alexander T1 - Lagrangian Methods for Visualization and Analysis of Time-dependent Vector Fields N2 - Time-dependent vector fields are of high relevance to describe a wide range of physical phenomena based on particle motion, including stall effects in technical engineering, blood flow anomalies, and atmospheric mass trans- port. The efficient analysis and fundamental understanding of intrinsic field properties can lead to significant improvements when interacting with such phenomena based on the available field data. So called Lagrangian methods are a particularly established technique for this purpose. They are based on the evaluation of time-dependent particle trajectories. This work will present an overview of the state of the art in time-dependent vector field analysis and visualization, with special focus on topology-oriented and Lagrangian methods. The first core aspect of this work is the introduction of a novel concept for a more objective and qualitative benchmark of existing Lagrangian approaches. Based on this benchmark, this work contributes and evaluates a set of novel concepts, that offer new perspectives towards established approaches with respect to computational handling, quality and efficiency. The second core aspect is the empirical application and validation of Lagrangian methods with respect to practically relevant analysis scenarios. Each application case includes an introduction into the underlying problem statement and an efficient solution using Lagrangian methods. The validation focuses on the comparison with existing flow analysis concepts and aspects of the quantitative evaluation in each case. Together, both topics of this work contribute towards a more consistent formalization, but also to the improved applicability of Lagrangian methods. KW - Flow Visualization, Time-dependent Vector Fields Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:gbv:ma9:1-4177 UR - http://edoc2.bibliothek.uni-halle.de/hs/id/31067 ER - TY - CHAP A1 - Bonneau, Georges-Pierre A1 - Hege, Hans-Christian A1 - Johnson, Chris R. A1 - Oliveira, Manuel M. A1 - Potter, Kristin A1 - Rheingans, Penny A1 - Schultz, Thomas T1 - Overview and State-of-the-Art of Uncertainty Visualization T2 - Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization N2 - The goal of visualization is to effectively and accurately communicate data. Visualization research has often overlooked the errors and uncertainty which accompany the scientific process and describe key characteristics used to fully understand the data. The lack of these representations can be attributed, in part, to the inherent difficulty in defining, characterizing, and controlling this uncertainty, and in part, to the difficulty in including additional visual metaphors in a well designed, potent display. However, the exclusion of this information cripples the use of visualization as a decision making tool due to the fact that the display is no longer a true representation of the data. This systematic omission of uncertainty commands fundamental research within the visualization community to address, integrate, and expect uncertainty information. In this chapter, we outline sources and models of uncertainty, give an overview of the state-of-the-art, provide general guidelines, outline small exemplary applications, and finally, discuss open problems in uncertainty visualization. Y1 - 2014 SN - 978-1-4471-6496-8 U6 - https://doi.org/10.1007/978-1-4471-6497-5_1 SP - 3 EP - 27 PB - Springer ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 JF - Communications in Mathematical Sciences N2 - Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodeficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs. Y1 - 2014 U6 - https://doi.org/10.4310/CMS.2014.v12.n5.a4 VL - 12 IS - 5 SP - 859 EP - 877 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - von Kleist, Max T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation N2 - In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and nontrivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes. Y1 - 2014 U6 - https://doi.org/10.1021/ct400993e VL - 10 IS - 4 SP - 1376 EP - 1386 ER - TY - CHAP A1 - Pfister, Hanspeter A1 - Kaynig, Verena A1 - Botha, Charl P. A1 - Bruckner, Stefan A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Roerdink, Jos B.T.M. ED - Hansen, Charles D. ED - Chen, Min ED - Johnson, Christopher R. ED - Kaufman, Arie E. ED - Hagen, Hans T1 - Visualization in Connectomics T2 - Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization N2 - Connectomics is a branch of neuroscience that attempts to create a connectome, i.e., a complete map of the neuronal system and all connections between neuronal structures. This representation can be used to understand how functional brain states emerge from their underlying anatomical structures and how dysfunction and neuronal diseases arise. We review the current state-of-the-art of visualization and image processing techniques in the field of connectomics and describe a number of challenges. After a brief summary of the biological background and an overview of relevant imaging modalities, we review current techniques to extract connectivity information from image data at macro-, meso- and microscales. We also discuss data integration and neural network modeling, as well as the visualization, analysis and comparison of brain networks. Y1 - 2014 SN - 978-1-4471-6496-8 U6 - https://doi.org/10.1007/978-1-4471-6497-5_21 SP - 221 EP - 245 PB - Springer ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1 JF - International Journal of Biomathematics and Biostatistics N2 - We present the theory of “Markov decision processes (MDP) with rare state observation” and apply it to optimal treatment scheduling and diagnostic testing to mitigate HIV-1 drug resistance development in resource-poor countries. The developed theory assumes that the state of the process is hidden and can only be determined by making an examination. Each examination produces costs which enter into the considered cost functional so that the resulting optimization problem includes finding optimal examination times. This is a realistic ansatz: In many real world applications, like HIV-1 treatment scheduling, the information about the disease evolution involves substantial costs, such that examination and control are intimately connected. However, a perfect compliance with the optimal strategy can rarely be achieved. This may be particularly true for HIV-1 resistance testing in resource-constrained countries. In the present work, we therefore analyze the sensitivity of the costs with respect to deviations from the optimal examination times both analytically and for the considered application. We discover continuity in the cost-functional with respect to the examination times. For the HIV-application, moreover, sensitivity towards small deviations from the optimal examination rule depends on the disease state. Furthermore, we compare the optimal rare-control strategy to (i) constant control strategies (one action for the remaining time) and to (ii) the permanent control of the original, fully observed MDP. This comparison is done in terms of expected costs and in terms of life-prolongation. The proposed rare-control strategy offers a clear benefit over a constant control, stressing the usefulness of medical testing and informed decision making. This indicates that lower-priced medical tests could improve HIV treatment in resource-constrained settings and warrants further investigation. Y1 - 2013 VL - 2 IS - 1 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - A pH-dependent coarse-grained model for peptides JF - Soft Matter N2 - We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer their main physical features to the coarse-grained resolution according to the principle of “consistency across the scales”. The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use such a parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different responses to pH variations, showing a highly satisfactory performance of the model. Y1 - 2013 U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - CHAP A1 - Heller, Markus O. A1 - Wurl, Alexander A1 - Perka, Carsten A1 - Hege, Hans-Christian T1 - In vivo gluteus medius volume and shape variations across gender and disease status BT - Proceedings of ESB2012 - 18th Congress of the European Society of Biomechanics, Lisbon, Portugal, 1–4 July 2012 T2 - Journal of Biomechanics Y1 - 2012 U6 - https://doi.org/10.1016/S0021-9290(12)70359-7 VL - 45, Suppl. 1 SP - S358 ER - TY - JOUR A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - Advected Tangent Curves: A General Scheme for Characteristic Curves of Flow Fields JF - Computer Graphics Forum N2 - We present the first general scheme to describe all four types of characteristic curves of flow fields – stream, path, streak, and time lines – as tangent curves of a derived vector field. Thus, all these lines can be obtained by a simple integration of an autonomous ODE system. Our approach draws on the principal ideas of the recently introduced tangent curve description of streak lines. We provide the first description of time lines as tangent curves of a derived vector field, which could previously only be constructed in a geometric manner. Furthermore, our scheme gives rise to new types of curves. In particular, we introduce advected stream lines as a parameter-free variant of the time line metaphor. With our novel mathematical description of characteristic curves, a large number of feature extraction and analysis tools becomes available for all types of characteristic curves, which were previously only available for stream and path lines. We will highlight some of these possible applications including the computation of time line curvature fields and the extraction of cores of swirling advected stream lines. Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03063.x VL - 31 IS - 2pt4 SP - 825 EP - 834 ER - TY - JOUR A1 - Sips, Mike A1 - Kothur, Patrick A1 - Unger, Andrea A1 - Hege, Hans-Christian A1 - Dransch, Doris T1 - A Visual Analytics Approach to Multiscale Exploration of Environmental Time Series JF - IEEE Transactions on Visualization and Computer Graphics N2 - We present a Visual Analytics approach that addresses the detection of interesting patterns in numerical time series, specifically from environmental sciences. Crucial for the detection of interesting temporal patterns are the time scale and the starting points one is looking at. Our approach makes no assumption about time scale and starting position of temporal patterns and consists of three main steps: an algorithm to compute statistical values for all possible time scales and starting positions of intervals, visual identification of potentially interesting patterns in a matrix visualization, and interactive exploration of detected patterns. We demonstrate the utility of this approach in two scientific scenarios and explain how it allowed scientists to gain new insight into the dynamics of environmental systems. Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2012.191 VL - 18 IS - 12 SP - 2899 EP - 2907 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Schaller, Jens A1 - Kertzscher, Ulrich A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas T1 - Reproducibility of Image-Based Analysis of Cerebral Aneurysm Geometry and Hemodynamics: An In-Vitro Study of Magnetic Resonance Imaging, Computed Tomography, and Three-Dimensional Rotational Angiography JF - Journal of Neurological Surgery, Part A: Central European Neurosurgery Y1 - 2013 U6 - https://doi.org/10.1055/s-0033-1342937 VL - 74 IS - 5 SP - 294 EP - 302 ER - TY - THES A1 - Stoppel, Sergej T1 - Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering KW - Volume Rendering Y1 - 2013 ER - TY - THES A1 - Bressler, David T1 - Pattern Analysis for Flow Visualization KW - Flow Visualization Y1 - 2012 ER - TY - THES A1 - Zoufahl, Andre T1 - Explorative Analysis of Vortex Structures in 2D Flows KW - Flow Visualization Y1 - 2012 ER - TY - CHAP A1 - Stoppel, Sergej A1 - Hege, Hans-Christian A1 - Wiebel, Alexander T1 - Visibility-driven depth determination of surface patches in direct volume rendering T2 - EuroVis - Short Papers 2014 N2 - This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a visible and typically rather smooth surface. In the last step the selected surface is displayed. We provide examples for results using artificially generated and real-world data sets. Y1 - 2014 U6 - https://doi.org/10.2312/eurovisshort.20141164 SP - 97 EP - 101 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Spuler, Andreas A1 - Schaller, Jens A1 - Wiegmann, Nils A1 - Berthe, Andre A1 - Hege, Hans-Christian A1 - Affeld, Klaus A1 - Kertzscher, Ulrich T1 - In vitro study of hemodynamic treatment improvement: Hunterian ligation of a fenestrated basilar artery aneurysm after coiling JF - The International Journal of Artificial Organs N2 - Hunterian ligation affecting hemodynamics in vessels was proposed to avoid rebleeding in a case of a fenestrated basilar artery aneurysm after incomplete coil occlusion. We studied the hemodynamics in vitro to predict the hemodynamic changes near the aneurysm remnant caused by Hunterian ligation. A transparent model was fabricated based on three-dimensional rotational angiography imaging. Arteries were segmented and reconstructed. Pulsatile flow in the artery segments near the partially occluded (coiled) aneurysm was investigated by means of particle image velocimetry. The hemodynamic situation was investigated before and after Hunterian ligation of either the left or the right vertebral artery (LVA/RVA). Since post-ligation flow rate in the basilar artery was unknown, reduced and retained flow rates were simulated for both ligation options. Flow in the RVA and in the corresponding fenestra vessel is characterized by a vortex at the vertebrobasilar junction, whereas the LVA exhibits undisturbed laminar flow. Both options (RVA or LVA ligation) cause a significant flow reduction near the aneurysm remnant with a retained flow rate. The impact of RVA ligation is, however, significantly higher. This in vitro case study shows that flow reduction near the aneurysm remnant can be achieved by Hunterian ligation and that this effect depends largely on the selection of the ligated vessel. Thus the ability of the proposed in vitro pipe-line to improve hemodynamic impact of the proposed therapy was successfully proved. Y1 - 2014 U6 - https://doi.org/10.5301/ijao.5000314 VL - 37 IS - 4 SP - 325 EP - 335 ER - TY - CHAP A1 - Soltwisch, Victor A1 - Wernecke, Jan A1 - Haase, Anton A1 - Probst, Jürgen A1 - Schoengen, Max A1 - Scholze, Frank A1 - Pomplun, Jan A1 - Burger, Sven T1 - Determination of line profile on nanostructured surfaces using EUV and x-ray scattering T2 - Proc. SPIE Y1 - 2014 U6 - https://doi.org/10.1117/12.2066165 VL - 9235 SP - 92351D ER - TY - CHAP A1 - Weiser, Martin A1 - Scacchi, Simone T1 - Spectral Deferred Correction methods for adaptive electro-mechanical coupling in cardiac simulation T2 - G. Russo et al.(eds.) Progress in Industrial Mathematics at ECMI 2014 N2 - We investigate spectral deferred correction (SDC) methods for time stepping and their interplay with spatio-temporal adaptivity, applied to the solution of the cardiac electro-mechanical coupling model. This model consists of the Monodomain equations, a reaction-diffusion system modeling the cardiac bioelectrical activity, coupled with a quasi-static mechanical model describing the contraction and relaxation of the cardiac muscle. The numerical approximation of the cardiac electro-mechanical coupling is a challenging multiphysics problem, because it exhibits very different spatial and temporal scales. Therefore, spatio-temporal adaptivity is a promising approach to reduce the computational complexity. SDC methods are simple iterative methods for solving collocation systems. We exploit their flexibility for combining them in various ways with spatio-temporal adaptivity. The accuracy and computational complexity of the resulting methods are studied on some numerical examples. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-23413-7_42 SP - 321 EP - 328 PB - Springer ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Banisch, Ralf A1 - Schütte, Christof T1 - Modularity of Directed Networks: Cycle Decomposition Approach JF - Journal of Computational Dynamics 2 (2015) pp. 1-24 N2 - The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarsegrained description of complex systems, often revealing functional subunits of these systems. A variety of module detection algorithms have been proposed, mostly oriented towards finding hard partitionings of undirected networks. Despite the increasing number of fuzzy clustering methods for directed networks, many of these approaches tend to neglect important directional information. In this paper, we present a novel random walk based approach for finding fuzzy partitions of directed, weighted networks, where edge directions play a crucial role in defining how well nodes in a module are interconnected. We will show that cycle decomposition of a random walk process connects the notion of network modules and information transport in a network, leading to a new, symmetric measure of node communication. Finally, we will use this measure to introduce a communication graph, for which we will show that although being undirected it inherits all necessary information about modular structures from the original network. Y1 - 2015 U6 - https://doi.org/10.3934/jcd.2015.2.1 ER - TY - JOUR A1 - Boeth, Heide A1 - Duda, Georg A1 - Hinzmann, Daniel A1 - Hermann, Sandra A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Witaschek, Tom A1 - Buttgereit, Frank T1 - A Novel Approach to Quantify Morning Stiffness in Patients with Rheumatoid Arthritis JF - Annual European Congress of Rheumatology, EULAR 2015, Rome Y1 - 2015 ER - TY - JOUR A1 - Hochfeld, Mascha A1 - Lamecker, Hans A1 - Thomale, Ulrich W. A1 - Schulz, Matthias A1 - Zachow, Stefan A1 - Haberl, Hannes T1 - Frame-based cranial reconstruction JF - Journal of Neurosurgery: Pediatrics N2 - The authors report on the first experiences with the prototype of a surgical tool for cranial remodeling. The device enables the surgeon to transfer statistical information, represented in a model, into the disfigured bone. The model is derived from a currently evolving databank of normal head shapes. Ultimately, the databank will provide a set of standard models covering the statistical range of normal head shapes, thus providing the required template for any standard remodeling procedure as well as customized models for intended overcorrection. To date, this technique has been used in the surgical treatment of 14 infants (age range 6-12 months) with craniosynostosis. In all 14 cases, the designated esthetic result, embodied by the selected model, has been achieved, without morbidity or mortality. Frame-based reconstruction provides the required tools to precisely realize the surgical reproduction of the model shape. It enables the establishment of a self-referring system, feeding back postoperative growth patterns, recorded by 3D follow-up, into the model design. Y1 - 2014 U6 - https://doi.org/10.3171/2013.11.PEDS1369 VL - 13 IS - 3 SP - 319 EP - 323 ER - TY - THES A1 - Kirschner, Bruno T1 - Interaktives Planungstool zur 3D Rekonstruktion von Knochenresektion Y1 - 2013 ER - TY - THES A1 - Amiranashvili, Tamaz T1 - Fitting Smooth Strips to Rough Surfaces Y1 - 2014 ER - TY - THES A1 - Haack, Fiete T1 - Representative Spectral Clustering for Large Data Sets applied to Gene Expression Data Y1 - 2009 ER - TY - THES A1 - Lie, Han Cheng T1 - A Meshless Method for Conformational Analysis Y1 - 2012 ER - TY - THES A1 - Josten, Jan-Martin T1 - Östrogenitäts-Approximation mittels physikochemischem Oberflächenvergleich Y1 - 2012 ER - TY - THES A1 - Jeschke, Björn-Marcel T1 - Spezielle Eigenschaften von Simulated Annealing Y1 - 2012 ER - TY - THES A1 - Riesland, Mark Daniel T1 - Anwendbarkeit von Thermostaten in der moleküldynamischen Simulation Y1 - 2012 ER - TY - THES A1 - Pommer, Daniel T1 - Konditionsverbesserung von Markov-Modellen Y1 - 2013 ER - TY - THES A1 - Toudic, Remi T1 - Confjump: A method for biomolecular sampling Y1 - 2013 ER - TY - THES A1 - Schmiedel, Jessica T1 - Singulärwertzerlegung mit Zufallsalgorithmen Y1 - 2013 ER - TY - THES A1 - Solleder, Marthe T1 - Bewertung von Transformationsprodukten im Wasserkreislauf durch Computersimulationen Y1 - 2014 ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the Minimal Rebinding Effect Included in a Given Kinetics JF - Multiscale Model. Simul. N2 - The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory. Y1 - 2014 U6 - https://doi.org/10.1137/13091124X VL - 12 IS - 1 SP - 318 EP - 334 ER - TY - JOUR A1 - Andrae, Karsten A1 - Merkel, Stefan A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Köppen, Robert A1 - Weber, Marcus A1 - Koch, Matthias T1 - Investigation of the Ergopeptide Epimerization Process JF - Computation N2 - Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that “folding” the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations. Y1 - 2014 U6 - https://doi.org/10.3390/computation2030102 VL - 2 IS - 3 SP - 102 EP - 111 ER - TY - JOUR A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Udvary, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Generation of dense statistical connectomes from sparse morphological data JF - Frontiers in Neuroanatomy Y1 - 2014 U6 - https://doi.org/10.3389/fnana.2014.00129 VL - 8 IS - 129 ER - TY - CHAP A1 - Skibina, Julia A1 - Bock, Martin A1 - Fischer, Dorit A1 - Grunwald, Rüdiger A1 - Steinmeyer, Günter A1 - Wedell, Reiner A1 - Bretschneider, Mario A1 - Burger, Sven A1 - Beloglazov, Valentin T1 - 10-fs fiber based pulse delivery T2 - Conference on Lasers, Applications, and Technologies (LAT) Y1 - 2013 SP - LWF5 ER - TY - JOUR A1 - Zhang, Wei A1 - Wang, Han A1 - Hartmann, Carsten A1 - Weber, Marcus A1 - Schütte, Christof T1 - Applications of the cross-entropy method to importance sampling and optimal control of diffusions JF - Siam Journal on Scientific Computing Y1 - 2014 U6 - https://doi.org/10.1137/14096493X VL - 36 IS - 6 SP - A2654 EP - A2672 ER - TY - GEN A1 - Werner, Axel A1 - Aurzada, Frank A1 - Bley, Andreas A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Guillemard, Mijail A1 - Kutyniok, Gitta A1 - Philipp, Friedrich A1 - Raack, Christian A1 - Scheutzow, Michael ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Mathematics for telecommunications T2 - MATHEON - Mathematics for Key Technologies Y1 - 2014 U6 - https://doi.org/10.4171/137 VL - 1 SP - 75 EP - 89 PB - European Mathematical Society ET - EMS Series in Industrial and Applied Mathematics ER - TY - GEN A1 - Stein, Christoph A1 - Weber, Marcus A1 - Scharkoi, Olga A1 - Deuflhard, Peter T1 - Method and system for identifying compounds that bind and preferably activate a target opioid receptor in a pH-dependent manner T2 - European Patent Application, Bulletin 2013/28 Y1 - 2013 ER - TY - THES A1 - Hoppmann, Heide T1 - A Configuration Model for the Line Planning Problem N2 - In this thesis we present a novel extended formulation for the line planning problem that is based on what we call "configurations" of lines and frequencies. Configurations are combinatorial building blocks of primal solutions; they rule out the "capacity numerics" and make the problem purely combinatorial. The concept of configurations can also be adapted to other capacitated network design problems. The configuration model is strong in the sense that it implies several facet-defining inequalities for the standard model: set cover, symmetric band, multicover, and MIR inequalities. These theoretical findings can be confirmed in computations, however, the enormous number of configurations can blow up the formulation for large instances. We propose a mixed model that enriches the standard model by a judiciously chosen subset of configurations that provide a good compromise between model strength and size. Computational results for large-scale line planning problems are presented. N2 - Das Linienplanungsproblem ist ein wichtiges Teilproblem der Angebotsplanung im öffentlichen Nahverkehr. Dabei werden Routen und Betriebsfrequenzen von Linien in einem gegebenen Infrastrukturnetzwerk gesucht, sodass ein gegebener Beförderungsbedarf gedeckt wird und die Kosten minimal sind. Praktische Ansätze zum Lösen dieser Probleme beruhen auf ganzzahliger Programmierung. Ein Schwachpunkt klassischer Modelle ist, dass schon kleine Änderungen der Eingabeparameter eine Vergrößerung oder Verkleinerung der Menge der zulässigen fraktionalen Lösungen bewirken können, auch wenn die Menge der ganzzahligen Lösungen unverändert bleibt. Wir betrachten in dieser Arbeit einen neuen kombinatorischen Ansatz, welcher die Möglichkeiten den Bedarf auf einer Verbindung im Netzwerk mit Frequenzen zu überdecken mit Hilfe von diskreten "Konfigurationen" beschreibt und dieses Problem eliminiert. Um die Vorteile dieses Konfigurationsmodells aufzuzeigen, vergleichen wir es mit einem klassischen Ansatz, den wir Standardmodell nennen. Wir zeigen, dass das Konfigurationsmodell mehrere facettendefinierende Ungleichungen des Standardmodells impliziert: Setcover-, symmetrische Band-, Multicover- und MIR-Ungleichungen. Diese theoretischen Ergebnisse können wir mit Rechenergebnissen bestätigen. Um die Anzahl dieser Variablen auch für große Instanzen zu beschränken, schlagen wir ein weiteres Modell vor, welches nur eine Teilmenge der Konfigurationsvariablen enthält. Dieses stellt sich als ein sehr guter Kompromiss zwischen der Größe und der Stärke des Modells heraus. Da das Linienplanungsproblem eine Spezialisierung des Netzwerkdesignproblems ist, können unsere Methoden auch auf andere Problemklassen übertragen werden. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51610 ER - TY - GEN A1 - Stein, Christoph A1 - Weber, Marcus A1 - Zöllner, Christian A1 - Scharkoi, Olga T1 - Fentanyl derivatives as pH-dependent opioid receptor agonists T2 - European Patent Application, Bulletin 2013/08 Y1 - 2013 ER - TY - CHAP A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Sinisi, Stefano A1 - Tronci, Enrico A1 - Davi, Francesco A1 - Dierkes, Thomas A1 - Ehrig, Rainald A1 - Röblitz, Susanna A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian T1 - Patient-Specific Models from Inter-Patient Biological Models and Clinical Records T2 - Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014) Y1 - 2014 SP - 207 EP - 214 ER - TY - GEN A1 - Stötzel, Claudia A1 - Apri, Mochamad A1 - Röblitz, Susanna T1 - A reduced ODE model of the bovine estrous cycle N2 - This work deals with the reduction of a previously developed ODE model for the bovine estrous cycle. After applying a method for exploring the parameter space by Apri et al. (2012), we perform structure-based reduction steps and several system specific adaptations. Overall, the original model consisting of 15 ODEs and 60 parameters is reduced to a model of 10 odes and 38 parameters. The reduced model qualitatively reproduces the state trajectories of the original model. T3 - ZIB-Report - 14-33 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51594 SN - 1438-0064 ER - TY - JOUR A1 - Stötzel, Claudia A1 - Ehrig, Rainald A1 - Boer, H. Marike T. A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis JF - BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, Bedlewo, Poland N2 - Cows typically have different numbers of follicular waves during their hormonal cycle. Understanding the underlying regulations leads to insights into the reasons for declined fertility, a phenomenon that has been observed during the last decades. We present a systematic approach based on Fourier analysis to examine how parameter changes in a model of the bovine estrous cycle lead to different wave patterns. Even without any biological considerations, this allows to detect the responsible model parameters that control the type of periodicity of the solution, thus supporting experimental planning of animal scientists. Y1 - 2014 ER - TY - THES A1 - Stötzel, Claudia T1 - Numerical and Discrete Modeling of Reproductive Endocrinological Networks N2 - This thesis deals with the mathematical modeling of endocrinological networks that are underlying the female hormone cycle. These networks consist of a variety of biological mechanisms in different parts of the organism. Their interaction leads to periodic changes of various substances that are necessary for reproduction. In every cycle, hormones are secreted from the hypothalamic-pituitary-gonadal axis into the bloodstream, where they distribute and influence several functions in the body. Their most important task in reproduction is to regulate processes in the ovaries, where follicles and corpus luteum develop. These produce steroids that are released into the blood and from therein regulate the processes in the hypothalamic-pituitary-gonadal axis. The hormonal cycle is thus a result of a large feedback loop, whose self-regulation is a complex interplay of multiple components. For the modeling of these processes, a high abstraction level is required, which can be realized by various modeling approaches. In this work, some of these approaches are implemented. The first step in all approaches is the representation of the most important mechanisms in a flowchart. In the next step, this can be implemented as a system of ordinary differential equations using Hill functions, as a piecewise defined affine differential equation model, or directly as a purely regulatory model. Using this approach, a differential equation model for the hormonal cycle of cows is developed. This is compared with a more advanced model of the menstrual cycle in humans. Both models are validated by comparing simulations with measured values, and by studying external influences such as drug administration. For the example of the bovine estrous cycle, continuous analysis methods are used to investigate stability, follicular wave patterns, and robustness with respect to parameter perturbations. Furthermore, the model is substantially reduced while preserving the main simulation results. To take a look at alternative modeling approaches, corresponding discrete models are derived, exemplified for the bovine model. For a piecewise affine version of the model, parameter constraints for the continuous model are calculated. Stability is analyzed globally for a purely discrete model. In addition, core discrete models are derived, which retain the dynamic properties of the original model. Y1 - 2014 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface JF - IEEE Transactions on Visualization and Computer Graphics N2 - The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes – including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules. Y1 - 2014 U6 - https://doi.org/10.1109/TVCG.2014.2346404 VL - 20 IS - 12 SP - 2486 EP - 2495 ER - TY - JOUR A1 - Högqvist, Mikael A1 - Reinefeld, Alexander T1 - RECODE: Reconfigurable, Consistent and Decentralized Data Services JF - IEEE International Conference on Peer-to-Peer Computing (P2P’13) Y1 - 2013 U6 - https://doi.org/10.1109/P2P.2013.6688705 SP - 1 EP - 10 PB - IEEE ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schütt, Thorsten A1 - Döbbelin, Robert T1 - Analyzing the performance of SMP memory allocators with iterative MapReduce applications JF - Parallel Computing Y1 - 2013 U6 - https://doi.org/10.1016/j.parco.2013.09.007 VL - 39 IS - 12 SP - 879 EP - 889 PB - Elsevier ER - TY - GEN A1 - Benkrid, Khaled A1 - El-Araby, Esam A1 - Huang, Miaoqing A1 - Sano, Kentaro A1 - Steinke, Thomas T1 - High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing T2 - International Journal of Reconfigurable Computing Y1 - 2012 U6 - https://doi.org/10.1155/2012/104963 VL - 2012 SP - 1 EP - 2 ER - TY - GEN ED - McIntosh-Smith, Simon ED - Gillan, Charles ED - Sanna, Nico ED - Scott, Stan ED - Steinke, Thomas T1 - Special issue of the Journal of Parallel and Distributed Computing (JDPC) on novel architectures for high-performance computing T2 - Journal of Parallel and Distributed Computing Y1 - 2013 U6 - https://doi.org/10.1016/j.jpdc.2013.08.013 SN - 0743-7315 VL - 73 IS - 11 SP - 1415 EP - 1416 ER - TY - JOUR A1 - Schäfer, Patrick T1 - The BOSS is concerned with time series classification in the presence of noise JF - Data Mining and Knowledge Discovery Y1 - 2014 U6 - https://doi.org/10.1007/s10618-014-0377-7 VL - 29 IS - 6 SP - 1505 EP - 1530 PB - Springer ER - TY - JOUR A1 - Maher, Stephen J. T1 - Solving the integrated airline recovery problem using column-and-row generation JF - Transportation Science N2 - Airline recovery presents very large and difficult problems requiring high quality solutions within very short time limits. To improve computational performance, the complete airline recovery problem is generally formulated as a series of sequential stages. While the sequential approach greatly simplifies the complete recovery problem, there is no guarantee of global optimality or solution quality. To address this, there has been increasing interest in the development of efficient solution techniques to solve an integrated recovery problem. In this paper, an integrated airline recovery problem is proposed by integrating the schedule, crew and aircraft recovery stages. To achieve short runtimes and high quality solutions, this problem is solved using column-and-row generation. Column-and-row generation achieves an improvement in solution runtimes by reducing the problem size and thereby achieving a faster execution of each LP solve. Further, the results demonstrate that a good upper bound achieved early in the solution process, indicating an improved solution quality with the early termination of the algorithm. This paper also details the integration of the row generation procedure with branch-and-price, which is used to achieve integral optimal solutions. The benefits of applying column-and-row generation to solve the integrated recovery problem are demonstrated with a comparison to a standard column generation technique. Y1 - 2015 U6 - https://doi.org/10.1287/trsc.2014.0552 VL - 50 IS - 1 SP - 216 EP - 239 ER - TY - JOUR A1 - Maher, Stephen J. A1 - Desaulniers, Guy A1 - Soumis, Francois T1 - Recoverable robust single day aircraft maintenance routing problem JF - Computers & Operations Research N2 - Aircraft maintenance planning is of critical importance to the safe and efficient operations of an airline. It is common to solve the aircraft routing and maintenance planning problems many months in advance, with the solution spanning multiple days. An unfortunate consequence of this approach is the possible infeasibility of the maintenance plan due to frequent perturbations occurring in operations. There is an emerging concept that focuses on the generation of aircraft routes for a single day to ensure maintenance coverage that night, alleviating the effects of schedule perturbations from preceding days. In this paper, we present a novel approach to ensure that a sufficient number of aircraft routes are provided each day so maintenance critical aircraft receive maintenance that night. By penalising the under supply of routes terminating at maintenance stations from each overnight airport, we construct a single day routing to provide the best possible maintenance plan. This single day aircraft maintenance routing problem (SDAMRP) is further protected from disruptions by applying the recoverable robustness framework. To efficiently solve the recoverable robust SDAMRP acceleration techniques, such as identifying Pareto-optimal cuts and a trust region approach, have been applied. The SDAMRP is evaluated against a set of flight schedules and the results demonstrate a significantly improved aircraft maintenance plan. Further, the results demonstrate the magnitude of recoverability improvement that is achieved by employing recoverable robustness to the SDAMRP. Y1 - 2014 U6 - https://doi.org/10.1016/j.cor.2014.03.007 VL - 51 SP - 130 EP - 145 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Reinefeld, Alexander ED - Reinders, James ED - Jeffers, Jim T1 - Concurrent Kernel Offloading T2 - High Performance Parallelism Pearls Y1 - 2014 UR - http://store.elsevier.com/High-Performance-Parallelism-Pearls/James-Reinders/isbn-9780128021187/ SN - 978-0128021187 N1 - Target publication date: Nov, 2014 PB - Morgan Kaufman, Elsevier ER - TY - JOUR A1 - Agarwal, Animesh A1 - Wang, Han A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Chemical potential of liquids and mixtures via Adaptive Resolution Simulation JF - The Journal of Chemical Physics Y1 - 2014 U6 - https://doi.org/10.1063/1.4886807 VL - 141 SP - 034102 ER - TY - GEN A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Pfetsch, Marc ED - Jünger, Michael ED - Reinelt, Gerhard T1 - Progress in Academic Computational Integer Programming T2 - Facets of Combinatorial Optimization Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38189-8_19 SP - 483 EP - 506 PB - Springer ER - TY - JOUR A1 - Schütte, Christof A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Markov State Models and Molecular Alchemy JF - Molecular Physics N2 - In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed. KW - MSM KW - Reweighting KW - Girsanov Y1 - 2015 U6 - https://doi.org/10.1080/00268976.2014.944597 VL - 113 IS - 1 SP - 69 EP - 78 ER - TY - JOUR A1 - Tuma, Christian A1 - Laino, Teodoro A1 - Martin, Elyette A1 - Stolz, Steffen A1 - Curioni, Alessandro T1 - Modeling the Impact of Solid Surfaces in Thermal Degradation Processes JF - ChemPhysChem Y1 - 2013 U6 - https://doi.org/10.1002/cphc.201200921 VL - 14 SP - 88 EP - 91 ER - TY - JOUR A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Vorschrift oder Thunfisch? – Zur Langzeitverfügbarkeit von Forschungsdaten JF - LIBREAS - Library Ideas Y1 - 2013 IS - 23 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Mehrgardt, Julika A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Waas, Kerstin T1 - Re-Optimization of Rolling Stock Rotations N2 - The Rolling Stock Rotation Problem is to schedule rail vehicles in order to cover timetabled trips by a cost optimal set of vehicle rotations. The problem integrates several facets of railway optimization, such as vehicle composition, maintenance constraints, and regularity aspects. In industrial applications existing vehicle rotations often have to be re-optimized to deal with timetable changes or construction sites. We present an integrated modeling and algorithmic approach to this task as well as computational results for industrial problem instances of DB Fernverkehr AG. Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-07001-8_8 SP - 49 EP - 55 PB - Springer International Publishing ET - Operations Research Proceedings 2013 ER - TY - THES A1 - Ruthenberg, Gunnar T1 - Hybrid Transactions for Intel’s Transactional Synchronization Extensions Y1 - 2014 N1 - Es handelt sich um eine Diplomarbeit ER - TY - CHAP A1 - Blanco, Marco A1 - Schlechte, Thomas T1 - Analysis of Micro–Macro Transformations of Railway Networks T2 - Operations Research Proceedings 2013 N2 - A common technique in the solution of large or complex optimization problems is the use of micro–macro transformations. In this paper, we carry out a theoretical analysis of such transformations for the track allocation problem in railway networks. We prove that the cumulative rounding technique of Schlechte et al. satisfies two of three natural optimality criteria and that this performance cannot be improved. We also show that under extreme circumstances, this technique can perform inconveniently by underestimating the global optimal value. Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-07001-8_6 SP - 37 EP - 42 ER - TY - CHAP A1 - Noack, Matthias A1 - Wende, Florian A1 - Steinke, Thomas A1 - Cordes, Frank T1 - A Unified Programming Model for Intra- and Inter-Node Offloading on Xeon Phi Clusters T2 - SC '14: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis. SC14, November 16-21, 2014, New Orleans, Louisiana, USA N2 - Standard offload programming models for the Xeon Phi, e.g. Intel LEO and OpenMP 4.0, are restricted to a single compute node and hence a limited number of coprocessors. Scaling applications across a Xeon Phi cluster/supercomputer thus requires hybrid programming approaches, usually MPI+X. In this work, we present a framework based on heterogeneous active messages (HAM-Offload) that provides the means to offload work to local and remote (co)processors using a unified offload API. Since HAM-Offload provides similar primitives as current local offload frameworks, existing applications can be easily ported to overcome the single-node limitation while keeping the convenient offload programming model. We demonstrate the effectiveness of the framework by using it to enable a real-world application from the field of molecular dynamics to use multiple local and remote Xeon Phis. The evaluation shows good scaling behavior. Compared with LEO, performance is equal for large offloads and significantly better for small offloads. Y1 - 2014 UR - http://dl.acm.org/citation.cfm?id=2683616 U6 - https://doi.org/10.1109/SC.2014.22 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU T2 - Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013 Y1 - 2013 U6 - https://doi.org/http://dx.doi.org/10.1145/2503210.2503254 ER - TY - CHAP A1 - Wende, Florian A1 - Laubender, Guido A1 - Steinke, Thomas T1 - Integration of Intel Xeon Phi Servers into the HLRN-III Complex: Experiences, Performance and Lessons Learned T2 - CUG2014 Proceedings Y1 - 2014 ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - Concurrent Kernel Execution on Xeon Phi within Parallel Heterogeneous Workloads T2 - Euro-Par 2014: Parallel Processing. 20th International Conference, Porto, Portugal, August 25-29, 2014, Proceedings Y1 - 2014 UR - http://www.springer.com/computer/swe/book/978-3-319-09872-2 U6 - https://doi.org/10.1007/978-3-319-09873-9_66 VL - 8632 SP - 788 EP - 799 ER - TY - GEN A1 - Costa, Marta A1 - Ostrovsky, Aaron D. A1 - Manton, James D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases T2 - bioRxiv preprint Y1 - 2015 U6 - https://doi.org/10.1101/006346 ER - TY - GEN A1 - Redemann, Stefanie A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Hyman, Anthony A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Müller-Reichert, Thomas T1 - The Segmentation of Microtubules in Electron Tomograms Using Amira T2 - Mitosis: Methods and Protocols Y1 - 2014 U6 - https://doi.org/10.1007/978-1-4939-0329-0_12 SP - 261 EP - 278 PB - Springer ER - TY - JOUR A1 - Todt, Ingo A1 - Lamecker, Hans A1 - Ramm, Heiko A1 - Ernst, Arneborg T1 - A computed tomographic data-based vibrant bonebridge visualization tool JF - Cochlear Implants International N2 - Information about the temporal bone size and variations of anatomical structures are crucial for a safe positioning of the Vibrant Bonebridge B-FMT. A radiological based preoperative planning of the surgical procedure decreases the surgical time and minimizes the risk of complications. We developed a software tool, which allows a catch up of foreign DICOM data based CT temporal bone scans. The individual CT scan is transmitted into a 3D reconstructed pattern of the temporal bone. In this 3D reconstruction the individually favored position of the B- FMT should be found. The software allows a determination of a safe B-FMT position by identifying the individual relation of middle fossa, jugular bulb and external auditory canal. Skull thickness and screw length are contained parameters for the surgical planning. An easy to handle software tool allows a radiologically data based safe and fast surgical positioning of the B-FMT. Y1 - 2014 U6 - https://doi.org/10.1179/1467010014Z.000000000155 VL - 15 IS - S1 SP - 72 EP - 74 ER - TY - JOUR A1 - Todt, Ingo A1 - Lamecker, Hans A1 - Ramm, Heiko A1 - Frenzel, Henning A1 - Wollenberg, Barbara A1 - Beleites, Thomas A1 - Zahnert, Thomas A1 - Thomas, Jan Peter A1 - Dazert, Stefan A1 - Ernst, Arneborg T1 - Entwicklung eines CT-Daten-basierten Vibrant-Bonebridge-Viewers JF - HNO N2 - Die Positionierung des B-FMT der Vibrant Bonebridge kann aufgrund der anatomischen Verhältnisse des Mastoids und der Größe des Aktuators ohne eine vorherige Beurteilung der individuellen Computertomographie (CT) des Felsenbeins problematisch sein. Die Entwicklung eines einfach zu bedienenden Viewers, welcher eine Positionierung des B-FMT im Felsenbeinmodell ermöglicht und hier auf individuelle potenzielle anatomische Konflikte hinweist sowie Lösungsmöglichkeiten anbietet, kann ein hilfreiches Werkzeug zur präoperativen Positionierung sein. Ziel der Arbeit war die Definition von Anforderungen und die Anfertigung eines Prototyps eines Vibrant-Bonebridge-Viewers. Auf der Basis einer ZIBAmira-Software-Version und der Inklusion eines B-FMT-Modells unter Erstellung eines Felsenbeinmodells, welches die intuitive Beurteilung von Konflikten ermöglicht, erfolgte die Erstellung des Prototyps eines Vibrant-Bonebridge-Viewers.Ergebnisse. Die Segmentierungszeit der individuellen DICOM-Daten („digital imaging and communications in medicine“) beträgt etwa 5 min. Eine Positionierung im individuellen 3-D-Felsenbeinmodell ermöglicht die quantitative und qualitative Beurteilung von Konflikten (Sinus sigmoideus, mittlere Schädelgrube) und das Aufsuchen einer bevorzugten Position. Das Anheben des B-FMT mittels virtueller Unterlegscheiben kann simuliert werden. Der erstellte Vibrant-Bonebridge-Viewer ermöglicht verlässlich eine Simulation der B-FMT-Positionierung. Die klinische Anwendbarkeit muss evaluiert werden. Y1 - 2014 U6 - https://doi.org/10.1007/s00106-014-2851-3 VL - 62 SP - 439 EP - 442 PB - Springer ER - TY - JOUR A1 - Campoli, Gianni A1 - Baka, Nora A1 - Kaptein, Bart A1 - Valstar, Edward A1 - Zachow, Stefan A1 - Weinans, Harrie A1 - Zadpoor, Amir Abbas T1 - Relationship between the shape and density distribution of the femur and its natural frequencies of vibration JF - Journal of Biomechanics N2 - It has been recently suggested that mechanical loads applied at frequencies close to the natural frequencies of bone could enhance bone apposition due to the resonance phenomenon. Other applications of bone modal analysis are also suggested. For the above-mentioned applications, it is important to understand how patient-specific bone shape and density distribution influence the natural frequencies of bones. We used finite element models to study the effects of bone shape and density distribution on the natural frequencies of the femur in free boundary conditions. A statistical shape and appearance model that describes shape and density distribution independently was created, based on a training set of 27 femora. The natural frequencies were then calculated for different shape modes varied around the mean shape while keeping the mean density distribution, for different appearance modes around the mean density distribution while keeping the mean bone shape, and for the 27 training femora. Single shape or appearance modes could cause up to 15% variations in the natural frequencies with certain modes having the greatest impact. For the actual femora, shape and density distribution changed the natural frequencies by up to 38%. First appearance mode that describes the general cortical bone thickness and trabecular bone density had one of the strongest impacts. The first appearance mode could therefore provide a sensitive measure of general bone health and disease progression. Since shape and density could cause large variations in the calculated natural frequencies, patient-specific FE models are needed for accurate estimation of bone natural frequencies. Y1 - 2014 U6 - https://doi.org/10.1016/j.jbiomech.2014.08.008 VL - 47 SP - 3334 EP - 3343 PB - Elsevier ER - TY - BOOK A1 - Lavrinenko, Andrei A1 - Laegsgaard, Jesper A1 - Gregersen, Niels A1 - Schmidt, Frank A1 - Soendergaard, Thomas ED - Wyant, James C. T1 - Numerical Methods in Photonics Y1 - 2014 SN - 9781466563889 PB - CRC Press ER - TY - GEN A1 - Sarich, Marco A1 - Schütte, Christof T1 - Utilizing hitting times for finding metastable sets in non-reversible Markov chains N2 - Techniques for finding metastable or almost invariant sets have been investigated, e.g., for deterministic dynamical systems in set-oriented numerics, for stochastic processes in molecular dynamics, and for random walks on complex networks. Most prominent algorithms are based on spectral apporaches and identify metastable sets via the doimant eigenvalues of the transfer operator associated with the dynamical system under consideration. These algorithms require the dominant eigenvalues to be real-valued. However, for many types of dynamics, e.g. for non-reversible Markov chains, this condition is not met. In this paper we utilize the hitting time apporach to metastable sets and demonstrate how the wellknown statements about optimal metastable decompositions of reversible chains can be reformulated for non-reversible chains if one switches from a spectral approach to an exit time approach. The performance of the resulting algorithm is illustrated by numerical experiments on random walks on complex networks. T3 - ZIB-Report - 14-32 KW - metastability KW - hitting times KW - non-reversible Markov chain KW - directed networks KW - random walk Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51209 SN - 1438-0064 ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface N2 - The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes – including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules. T3 - ZIB-Report - 14-27 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51194 SN - 1438-0064 ER - TY - GEN A1 - Djurdjevac Conrad, Natasa A1 - Banisch, Ralf A1 - Schütte, Christof T1 - Modularity of Directed Networks: Cycle Decomposition Approach N2 - The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarsegrained description of complex systems, often revealing functional subunits of these systems. A variety of module detection algorithms have been proposed, mostly oriented towards finding hard partitionings of undirected networks. Despite the increasing number of fuzzy clustering methods for directed networks, many of these approaches tend to neglect important directional information. In this paper, we present a novel random walk based approach for finding fuzzy partitions of directed, weighted networks, where edge directions play a crucial role in defining how well nodes in a module are interconnected. We will show that cycle decomposition of a random walk process connects the notion of network modules and information transport in a network, leading to a new, symmetric measure of node communication. Finally, we will use this measure to introduce a communication graph, for which we will show that although being undirected it inherits all necessary information about modular structures from the original network. T3 - ZIB-Report - 14-31 KW - directed networks, modules, cycle decomposition, measure of node communication Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51166 SN - 1438-0064 ER - TY - JOUR A1 - Kaschke, Johannes A1 - Blome, Mark A1 - Burger, Sven A1 - Wegener, Martin T1 - Tapered N-helical metamaterials with three-fold rotational symmetry as improved circular polarizers JF - Opt. Expr. Y1 - 2014 U6 - https://doi.org/10.1364/OE.22.019936 VL - 22 IS - 17 SP - 19936 EP - 19946 ER - TY - THES A1 - Michels, Maximilian T1 - Request-Based Load Balancing in Distributed Hash Tables Y1 - 2014 ER - TY - CHAP A1 - Scholze, Frank A1 - Bodermann, Bernd A1 - Burger, Sven A1 - Endres, Johannes A1 - Haase, Anton A1 - Krumrey, Michael A1 - Laubis, Christian A1 - Soltwisch, Victor A1 - Ullrich, Albrecht A1 - Wernecke, Jan T1 - Determination of line profiles on photomasks using DUV, EUV and X-ray scattering T2 - Proc. SPIE Y1 - 2014 U6 - https://doi.org/10.1117/12.2065941 VL - 9231 SP - 92310M ER - TY - JOUR A1 - Becker, Christiane A1 - Wyss, Philippe A1 - Eisenhauer, David A1 - Probst, Jürgen A1 - Preidel, Veit A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - 5 x 5 cm2 silicon photonic crystal slabs on glass and plastic foil exhibiting broadband absorption and high-intensity near-fields JF - Sci. Rep. Y1 - 2014 U6 - https://doi.org/10.1038/srep05886 VL - 4 SP - 5886 ER - TY - GEN A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf T1 - An Approximation Result for Matchings in Partitioned Hypergraphs N2 - We investigate the matching and perfect matching polytopes of hypergraphs having a special structure, which we call partitioned hypergraphs. We show that the integrality gap of the standard LP-relaxation is at most $2\sqrt{d}$ for partitioned hypergraphs with parts of size $\leq d$. Furthermore, we show that this bound cannot be improved to $\mathcal{O}(d^{0.5-\epsilon})$. T3 - ZIB-Report - 14-30 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51083 ER - TY - GEN A1 - Schweiger, Jonas T1 - Gas network extension planning for multiple demand scenarios N2 - Today's gas markets demand more flexibility from the network operators which in turn have to invest into their network infrastructure. As these investments are very cost-intensive and long-living, network extensions should not only focus on one bottleneck scenario, but should increase the flexibility to fulfill different demand scenarios. We formulate a model for the network extension problem for multiple demand scenarios and propose a scenario decomposition. We solve MINLP single-scenario sub-problems and obtain valid bounds even without solving them to optimality. Heuristics prove capable of improving the initial solutions substantially. Results of computational experiments are presented. T3 - ZIB-Report - 14-29 KW - Gas Network Planning KW - Scenario Decomposition Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51030 SN - 1438-0064 ER - TY - CHAP A1 - Heismann, Olga A1 - Borndörfer, Ralf T1 - A Generalization of Odd Set Inequalities for the Set Packing Problem T2 - Operations Research Proceedings 2013 N2 - The set packing problem, sometimes also called the stable set problem, is a well-known NP-hard problem in combinatorial optimization with a wide range of applications and an interesting polyhedral structure, that has been the subject of intensive study. We contribute to this field by showing how, employing cliques, odd set inequalities for the matching problem can be generalized to valid inequalities for the set packing polytope with a clear combinatorial meaning. Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-07001-8_26 SP - 193 EP - 199 ER - TY - GEN A1 - Heismann, Olga A1 - Borndörfer, Ralf T1 - A Generalization of Odd Set Inequalities for the Set Packing Problem N2 - The set packing problem, sometimes also called the stable set problem, is a well-known NP-hard problem in combinatorial optimization with a wide range of applications and an interesting polyhedral structure, that has been the subject of intensive study. We contribute to this field by showing how, employing cliques, odd set inequalities for the matching problem can be generalized to valid inequalities for the set packing polytope with a clear combinatorial meaning. T3 - ZIB-Report - 14-28 KW - set packing KW - matching KW - hypergraph KW - inequality KW - facet Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51010 SN - 1438-0064 ER - TY - GEN A1 - Agarwal, Animesh A1 - Wang, Han A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Chemical potential of liquids and mixtures via Adaptive Resolution Simulation N2 - We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonicallike version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $μ^{ex}$, of various liquids and mixtures. We compare our results with those obtained from full atomistic simulations using the technique of thermodynamic integration and show a satisfactory agreement. In GC-AdResS the procedure to calculate $μ^{ex}$ corresponds to the process of standard initial equilibration of the system; this implies that, independently of the specific aim of the study, $μ^{ex}$, for each molecular species, is automatically calculated every time a GC-AdResS simulation is performed. T3 - ZIB-Report - 14-25 KW - Coarse graining KW - adaptive resolution KW - molecular dynamics KW - chemical potential Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50972 SN - 1438-0064 ER - TY - THES A1 - Heismann, Olga T1 - The Hypergraph Assignment Problem N2 - This thesis deals with the hypergraph assignment problem (HAP), a set partitioning problem in a special type of hypergraph. The HAP generalizes the assignment problem from bipartite graphs to what we call bipartite hypergraphs, and is motivated by applications in railway vehicle rotation planning. The main contributions of this thesis concern complexity, polyhedral results, analyses of random instances, and primal methods for the HAP. We prove that the HAP is NP-hard and APX-hard even for small hyperedge sizes and hypergraphs with a special partitioned structure. We also study the complexity of the set packing and covering relaxations of the HAP, and present for certain cases polynomial exact or approximation algorithms. A complete linear description is known for the assignment problem. We therefore also study the HAP polytope. There, we have a huge number of facet-defining inequalities already for a very small problem size. We describe a method for dividing the inequalities into equivalence classes without resorting to a normal form. Within each class, facets are related by certain symmetries and it is sufficient to list one representative of each class to give a complete picture of the structural properties of the polytope. We propose the algorithm "HUHFA" for the classification that is applicable not only to the HAP but combinatorial optimization problems involving symmetries in general. In the largest possible HAP instance for which we could calculate the complete linear description, we have 14049 facets, which can be divided into 30 symmetry classes. We can combinatorially interpret 16 of these classes. This is possible by employing cliques to generalize the odd set inequalities for the matching problem. The resulting inequalities are valid for the polytope associated with the set packing problem in arbitrary hypergraphs and have a clear combinatorial meaning. An analysis of random instances provides a better insight into the structure of hyperassignments. Previous work has extensively analyzed random instances for the assignment problem theoretically and practically. As a generalization of these results for the HAP, we prove bounds on the expected value of a minimum cost hyperassignment that uses half of the maximum possible number of hyperedges that are not edges. In a certain complete partitioned hypergraph G2,2n with i. i. d. exponential random variables with mean 1 as hyperedge costs it lies between 0.3718 and 1.8310 if the vertex number tends to infinity. Finally, we develop an exact combinatorial solution algorithm for the HAP that combines three methods: A very large-scale neighborhood search, the composite columns method for the set partitioning problem, and the network simplex algorithm. N2 - Diese Arbeit beschäftigt sich mit dem Hypergraph Assignment Problem (Abkürzung "HAP", dt.: Zuordnungsproblem auf Hypergraphen), einem Mengenzerlegungsproblem auf einem speziellen Typ von Hypergraphen. Das HAP verallgemeinert das Zuordnungsproblem von bipartiten Graphen auf eine Struktur, die wir bipartite Hypergraphen nennen, und ist durch eine Anwendung in der Umlaufplanung im Schienenverkehr motiviert. Die Hauptresultate betreffen die Komplexität, polyedrische Ergebnisse, die Analyse von Zufallsinstanzen sowie primale Methoden für das HAP. Wir beweisen, dass das HAP NP-schwer und APX-schwer ist, sogar wenn wir uns auf kleine Hyperkantengrößen und Hypergraphen mit einer speziellen, partitionierten Struktur beschränken. Darüber hinaus untersuchen wir die Komplexität der Mengenpackungs- sowie Mengenüberdeckungsrelaxierung und geben für bestimmte Fälle Approximations- und exakte Algorithmen mit einer polynomiellen Laufzeit an. Für das Polytop des Zuordnungsproblems ist eine vollständige lineare Beschreibung bekannt. Wir untersuchen daher auch das HAP-Polytop. Dafür ist die Anzahl der Facettenungleichungen schon für sehr kleine Problemgrößen sehr groß. Wir beschreiben eine Methode zur Aufteilung der Ungleichungen in Äquivalenzklassen, die ohne die Verwendung von Normalformen auskommt. Die Facetten in jeder Klasse können durch Symmetrien ineinander überführt werden. Es genügt, einen Repräsentanten aus jeder Klasse anzugeben, um ein vollständiges Bild der Polytopstruktur zu erhalten. Wir beschreiben den Algorithmus "HUHFA", der diese Klassifikation nicht nur für das HAP, sondern für beliebige kombinatorische Optimierungsprobleme, die Symmetrien enthalten, durchführt. Die größtmögliche HAP-Instanz, für die wir die vollständige lineare Beschreibung berechnen konnten, hat 14049 Facetten, die in 30 Symmetrieklassen aufgeteilt werden können. Wir können 16 dieser Klassen kombinatorisch interpretieren. Dafür verallgemeinern wir Odd-Set-Ungleichungen für das Matchingproblem unter Verwendung von Cliquen. Die Ungleichungen, die wir erhalten, sind gültig für Mengenpackungsprobleme in beliebigen Hypergraphen und haben eine klare kombinatorische Bedeutung. Die Analyse von Zufallsinstanzen erlaubt einen besseren Einblick in die Struktur von Hyperzuordnungen. Eine solche ausführliche Analyse wurde in der Literatur theoretisch und praktisch bereits für das Zuordnungsproblem durchgeführt. Als eine Verallgemeinerung dieser Ergebnisse für das HAP beweisen wir Schranken für den Erwartungswert einer Hyperzuordnung mit minimalen Kosten, die genau die Hälfte der maximal möglichen Anzahl an Hyperkanten, die keine Kanten sind, benutzt. In einem sog. vollständigen partitionierten Hypergraphen G2,2n mit Hyperkantenkosten, die durch unabhängig identisch exponentiell verteilte Zufallsvariablen mit Erwartungswert 1 bestimmt sind, liegt dieser Wert zwischen 0.3718 und 1.8310, wenn die Knotenanzahl gegen unendlich strebt. Schließlich entwickeln wir eine exakte kombinatorische Lösungsmethode für das HAP, die drei Ansätze kombiniert: Eine Nachbarschaftssuche mit Nachbarschaften exponentieller Größe, die Composite-Columns-Methode für das Mengenzerlegungsproblem sowie den Netzwerksimplexalgorithmus. KW - assignment KW - bipartite KW - hyperassignment KW - hypergraph KW - set partitioning Y1 - 2014 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/5321 ER - TY - GEN A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ebell, Gino A1 - Ehrig, Karsten A1 - Heyn, Andreas A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben N2 - Kurzfassung. Durch die Alkalität des Betons wird Betonstahl dauerhaft vor Korrosion geschützt. Infolge von Chlorideintrag kann dieser Schutz nicht länger aufrechterhalten werden und führt zu Lochkorrosion. Die zerstörungsfreie Prüfung von Stahlbetonproben mit 3D-CT bietet die Möglichkeit, eine Probe mehrfach gezielt vorzuschädigen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung des Schädigungsgrades müssen die bei dieser Untersuchung anfallenden großen Bilddaten mit Bildverarbeitungsmethoden ausgewertet werden. Ein wesentlicher Schritt dabei ist die Segmentierung der Bilddaten, bei der zwischen Korrosionsprodukt (Rost), Betonstahl (BSt), Beton, Rissen, Poren und Umgebung unterschieden werden muss. Diese Segmentierung bildet die Grundlage für statistische Untersuchungen des Schädigungsfortschritts. Hierbei sind die Änderung der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Veränderung über die Zeit sowie ihrer räumlichen Verteilung in der Probe von Interesse. Aufgrund der Größe der CT-Bilddaten ist eine manuelle Segmentierung nicht durchführbar, so dass automatische Verfahren unabdingbar sind. Dabei ist insbesondere die Segmentierung der Korrosionsprodukte in den Bilddaten ein schwieriges Problem. Allein aufgrund der Grauwerte ist eine Zuordnung nahezu unmöglich, denn die Grauwerte von Beton und Korrosionsprodukt unterscheiden sich kaum. Eine formbasierte Suche ist nicht offensichtlich, da die Korrosionsprodukte in Beton diffuse Formen haben. Allerdings lässt sich Vorwissen über die Ausbreitung der Korrosionsprodukte nutzen. Sie bilden sich in räumlicher Nähe des BSt (in Bereichen vorheriger Volumenabnahme des BSt), entlang von Rissen sowie in Porenräumen, die direkt am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der Korrosionsprodukterkennung zunächst eine BSt-Volumen-, Riss- und Porenerkennung durchgeführt. Dieser in der Arbeit näher beschriebene Schritt erlaubt es, halbautomatisch Startpunkte (Seed Points) für die Korrosionsprodukterkennung zu finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte Algorithmen auf ihre Eignung untersucht werden. T3 - ZIB-Report - 14-24 KW - Beton KW - Korrosionserkennung KW - Bildverarbeitung KW - Computertomografie KW - concrete KW - corrosiondetection KW - image processing KW - computed tomography Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50912 SN - 1438-0064 ER - TY - JOUR A1 - Cook, William A1 - Koch, Thorsten A1 - Steffy, Daniel A1 - Wolter, Kati T1 - A hybrid branch-and-bound approach for exact rational mixed-integer programming JF - Mathematical Programming Computation N2 - We present an exact rational solver for mixed-integer linear programming that avoids the numerical inaccuracies inherent in the floating-point computations used by existing software. This allows the solver to be used for establishing theoretical results and in applications where correct solutions are critical due to legal and financial consequences. Our solver is a hybrid symbolic/numeric implementation of LP-based branch-and-bound, using numerically-safe methods for all binding computations in the search tree. Computing provably accurate solutions by dynamically choosing the fastest of several safe dual bounding methods depending on the structure of the instance, our exact solver is only moderately slower than an inexact floating-point branch-and-bound solver. The software is incorporated into the SCIP optimization framework, using the exact LP solver QSopt_ex and the GMP arithmetic library. Computational results are presented for a suite of test instances taken from the MIPLIB and Mittelmann libraries and for a new collection of numerically difficult instances. Y1 - 2013 U6 - https://doi.org/10.1007/s12532-013-0055-6 VL - 5 IS - 3 SP - 305 EP - 344 ER - TY - CHAP A1 - Kleineweber, Christoph A1 - Reinefeld, Alexander A1 - Schütt, Thorsten T1 - QoS-aware Storage Virtualization for Cloud File Systems T2 - Proceedings of the 1st ACM International Workshop on Programmable File Systems Y1 - 2014 U6 - https://doi.org/10.1145/2603941.2603944 SP - 19 EP - 26 ER - TY - JOUR A1 - Gabriel, Karsten A1 - Braatz, Benjamin A1 - Ehrig, Hartmut A1 - Golas, Ulrike T1 - Finitary M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000321 VL - 24 IS - 4 SP - 1 EP - 40 ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 1: Parallelism, Concurreny and Amalgamation JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000357 VL - 24 IS - 4 SP - 1 EP - 48 ER - TY - JOUR A1 - Hermann, Frank A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Orejas, Fernando T1 - Formal Analysis of Model Transformations Based on Triple Graph Grammars JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000370 VL - 24 IS - 4 SP - 1 EP - 57 ER - TY - JOUR A1 - Golas, Ulrike A1 - Habel, A. A1 - Ehrig, Hartmut T1 - Multi-Amalgamation of Rules with Application Conditions in M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000345 VL - 24 IS - 4 SP - 1 EP - 68 ER - TY - THES A1 - Fischer, Jens V. T1 - A Gossiping Framework for Scalaris Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50685 ER - TY - GEN A1 - Arnold, Thomas A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Henrion, René A1 - Grötschel, Martin A1 - Koch, Thorsten A1 - Tischendorf, Caren A1 - Römisch, Werner ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - A Jack of all Trades? Solving stochastic mixed-integer nonlinear constraint programs T2 - MATHEON - Mathematics for Key Technologies N2 - Natural gas is one of the most important energy sources in Germany and Europe. In recent years, political regulations have led to a strict separation of gas trading and gas transport, thereby assigning a central role in energy politics to the transportation and distribution of gas. These newly imposed political requirements influenced the technical processes of gas transport in such a way that the complex task of planning and operating gas networks has become even more intricate. Mathematically, the combination of discrete decisions on the configuration of a gas transport network, the nonlinear equations describing the physics of gas, and the uncertainty in demand and supply yield large-scale and highly complex stochastic mixed-integer nonlinear optimization problems. The Matheon project "Optimization of Gas Transport" takes the key role of making available the necessary core technology to solve the mathematical optimization problems which model the topology planning and the operation of gas networks. An important aspect of the academic impact is the free availability of our framework. As a result of several years of research and development, it is now possible to download a complete state-of-the-art framework for mixed-integer linear and nonlinear programming in source code at http://scip.zib.de Y1 - 2014 U6 - https://doi.org/10.4171/137 VL - 1 SP - 135 EP - 146 PB - European Mathematical Society ER - TY - CHAP A1 - Manley, Phillip A1 - Schmidt, Frank A1 - Schmid, Martina T1 - Light extraction from plasmonic particles with dielectric shells and overcoatings T2 - Renewable Energy and the Environment Y1 - 2013 U6 - https://doi.org/10.1364/PV.2013.PW3B.7 SP - PW3B.7 PB - Optical Society of America ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Weiser, Martin A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Optimal control for a tuberculosis model with undetected cases in Cameroon JF - Communications in Nonlinear Science and Numerical Simulation N2 - This paper considers the optimal control of tuberculosis through education, diagnosis campaign and chemoprophylaxis of latently infected. A mathematical model which includes important components such as undiagnosed infectious, diagnosed infectious, latently infected and lost-sight infectious is formulated. The model combines a frequency dependent and a density dependent force of infection for TB transmission. Through optimal control theory and numerical simulations, a cost-effective balance of two different intervention methods is obtained. Seeking to minimize the amount of money the government spends when tuberculosis remain endemic in the Cameroonian population, Pontryagin's maximum principle is used to characterize the optimal control. The optimality system is derived and solved numerically using the forward-backward sweep method (FBSM). Results provide a framework for designing cost-effective strategies for diseases with multiple intervention methods. It comes out that combining chemoprophylaxis and education, the burden of TB can be reduced by 80 % in 10 years. Y1 - 2015 U6 - https://doi.org/10.1016/j.cnsns.2014.06.037 VL - 20 IS - 3 SP - 986 EP - 1003 ER - TY - GEN A1 - Deuflhard, Peter A1 - Kornhuber, Ralf A1 - Sander, Oliver A1 - Schiela, Anton A1 - Weiser, Martin ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Mathematics cures virtual patients T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 7 EP - 25 PB - European Mathematical Society ER - TY - GEN A1 - Weiser, Martin A1 - Scacchi, Simone T1 - Spectral Deferred Correction methods for adaptive electro-mechanical coupling in cardiac simulation N2 - We investigate spectral deferred correction (SDC) methods for time stepping and their interplay with spatio-temporal adaptivity, applied to the solution of the cardiac electro-mechanical coupling model. This model consists of the Monodomain equations, a reaction-diffusion system modeling the cardiac bioelectrical activity, coupled with a quasi-static mechanical model describing the contraction and relaxation of the cardiac muscle. The numerical approximation of the cardiac electro-mechanical coupling is a challenging multiphysics problem, because it exhibits very different spatial and temporal scales. Therefore, spatio-temporal adaptivity is a promising approach to reduce the computational complexity. SDC methods are simple iterative methods for solving collocation systems. We exploit their flexibility for combining them in various ways with spatio-temporal adaptivity. The accuracy and computational complexity of the resulting methods are studied on some numerical examples. T3 - ZIB-Report - 14-22 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50695 SN - 1438-0064 ER - TY - CHAP A1 - Schlosser, Michael A1 - Werner, Axel A1 - Schlenk, Ralph A1 - Jungel, Tobias A1 - Lange, Christoph T1 - Demonstrating energy-efficiency improvements in load-adaptive dynamic multilayer optical networks T2 - Tagungsband Photonische Netze N2 - The discussion about sustainability and climate change as well as the energy cost perspective of network operators gives increasing attention to the energy efficiency of telecommunication networks. A promising way to improve the energy efficiency of such networks is the load-adaptive operation in which the network capacity is adjusted to the actual timevarying traffic transport needs. In this paper the concept of load-adaptive operation in the core network is explained, with the respective underlying optical network and the associated mathematical optimization. Within the DESI project a demonstrator has been realized with a commercially available WDM/OTN system. As results, concrete proven power and energy savings and the projected savings for a nationwide multilayer core network are reported. Y1 - 2014 VL - 248 SP - 42 EP - 46 PB - VDE-Verlag ER - TY - CHAP A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - An Automated Approach for Estimating the Memory Footprint of Non-linear Data Objects T2 - Euro-Par 2013: Parallel Processing Workshops Y1 - 2014 U6 - https://doi.org/10.1007/978-3-642-54420-0_25 VL - 8374 SP - 249 EP - 258 ER - TY - GEN A1 - Noack, Matthias T1 - HAM - Heterogenous Active Messages for Efficient Offloading on the Intel Xeon Phi N2 - The applicability of accelerators is limited by the attainable speed-up for the offloaded computations and by the offloading overheads. While GPU programming models like CUDA and OpenCL only allow to optimise the application code and its speed-up, the available low-level APIs for the Intel Xeon Phi provide opportunity to address the overheads, too. This work presents an Heterogeneous Active Message (HAM) layer that minimises software overheads for offloading on Intel’s Xeon Phi. It provides the basis for an offload API with similar semantics as the Intel Language Extensions for Offload (LEO). In contrast to LEO, HAM works within the C++ language and needs no additional compiler support. We evaluated HAM on top of SCIF and MPI as communication backends. While the SCIF backend offers the best performance, the MPI backend allows for inter-node offloads which are not possible with other offload solutions. Benchmark results show that the cost for offloading a function call can be decreased by a factor up to 18 compared with LEO. T3 - ZIB-Report - 14-23 KW - Intel Xeon Phi KW - MIC KW - Active message KW - Offloading KW - SCIF KW - MPI KW - LEO KW - HAM Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50610 SN - 1438-0064 ER - TY - JOUR A1 - Potamitis, Ilyas A1 - Schäfer, Patrick T1 - On Classifying Insects from their Wing-Beat: New Results JF - Ecology and acoustics: emergent properties from community to landscape, Paris, France Y1 - 2014 ER - TY - JOUR A1 - Krüger, Jens A1 - Grunzke, Richard A1 - Gesing, Sandra A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - de la Garza, Luis A1 - Kohlbacher, Oliver A1 - Kruse, Martin A1 - Nagel, Wolfgang A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schärfe, Charlotta A1 - Steinke, Thomas A1 - Schlemmer, Tobias A1 - Warzecha, Klaus Dieter A1 - Zink, Andreas A1 - Herres-Pawlis, Sonja T1 - The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1021/ct500159h VL - 10 IS - 6 SP - 2232 EP - 2245 ER - TY - CHAP A1 - Schäfer, Patrick T1 - Towards Time Series Classification without Human Preprocessing T2 - MLDM 2014 Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-08979-9_18 VL - 8556 SP - 228 EP - 242 ER - TY - JOUR A1 - Wiesendanger, Samuel A1 - Bischoff, Thomas A1 - Jovanov, Vladislav A1 - Knipp, Dietmar A1 - Burger, Sven A1 - Lederer, Falk A1 - Rockstuhl, Carsten T1 - Effects of film growth modes on light trapping in silicon thin film solar cells JF - Appl. Phys. Lett. Y1 - 2014 U6 - https://doi.org/10.1063/1.4882997 VL - 104 IS - 23 SP - 231103 ER - TY - CHAP A1 - Gschrey, Manuel A1 - Seifried, Marc A1 - Krüger, Luzy A1 - Schmidt, Ronny A1 - Schulze, Jan-Hindrick A1 - Heindel, Tobias A1 - Burger, Sven A1 - Rodt, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Reitzenstein, Stephan T1 - Boosting the photon-extraction efficiency of nanophotonic structures by deterministic microlenses T2 - CLEO: 2014 Y1 - 2014 U6 - https://doi.org/10.1364/CLEO_QELS.2014.FF2K.2 SP - FF2K.2 PB - Optical Society of America ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Lockau, Daniel A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Optical modelling of incoherent substrate light-trapping in silicon thin film multi-junction solar cells with finite elements and domain decomposition N2 - In many experimentally realized applications, e.g. photonic crystals, solar cells and light-emitting diodes, nano-photonic systems are coupled to a thick substrate layer, which in certain cases has to be included as a part of the optical system. The finite element method (FEM) yields rigorous, high accuracy solutions of full 3D vectorial Maxwell's equations [1] and allows for great flexibility and accuracy in the geometrical modelling. Time-harmonic FEM solvers have been combined with Fourier methods in domain decomposition algorithms to compute coherent solutions of these coupled system. [2,3] The basic idea of a domain decomposition approach lies in a decomposition of the domain into smaller subdomains, separate calculations of the solutions and coupling of these solutions on adjacent subdomains. In experiments light sources are often not perfectly monochromatic and hence a comparision to simulation results might only be justified if the simulation results, which include interference patterns in the substrate, are spectrally averaged. In this contribution we present a scattering matrix domain decomposition algorithm for Maxwell's equations based on FEM. We study its convergence and advantages in the context of optical simulations of silicon thin film multi-junction solar cells. This allows for substrate light-trapping to be included in optical simulations and leads to a more realistic estimation of light path enhancement factors in thin-film devices near the band edge. T3 - ZIB-Report - 14-21 KW - finite element method KW - rigorous optical modeling KW - domain decomposition KW - multi-junction solar cells KW - thin-film silicon solar cells KW - incoherent layers KW - incoherent light-trapping Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50410 SN - 1438-0064 ER - TY - GEN A1 - Hammerschmidt, Martin A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Adaptive sampling strategies for efficient parameter scans in nano-photonic device simulations N2 - Rigorous optical simulations are an important tool in optimizing scattering properties of nano-photonic devices and are used, for example, in solar cell optimization. The finite element method (FEM) yields rigorous, time-harmonic, high accuracy solutions of the full 3D vectorial Maxwell's equations [1] and furthermore allows for great flexibility and accuracy in the geometrical modeling of these often complex shaped 3D nano-structures. A major drawback of frequency domain methods is the limitation of single frequency evaluations. For example the accurate computation of the short circuit current density of an amorphous silicon / micro-crystalline multi-junction thin film solar cell may require the solution of Maxwell's equations for over a hundred different wavelengths if an equidistant sampling strategy is employed. Also in optical metrology, wavelength scans are frequently used to reconstruct unknown geometrical and material properties of optical systems numerically from measured scatterometric data. In our contribution we present several adaptive numerical integration and sampling routines and study their efficiency in the context of the determination of generation rate profiles of solar cells. We show that these strategies lead to a reduction in the computational effort without loss of accuracy. We discuss the employment of tangential information in a Hermite interpolation scheme to achieve similar accuracy on coarser grids. We explore the usability of these strategies for scatterometry and solar cell simulations. T3 - ZIB-Report - 14-20 KW - finite element method KW - optical simulations KW - adaptive sampling KW - optical metrology KW - parameter scans KW - solar cells Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50395 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Cordes, Frank T1 - Multi-threaded Kernel Offloading to GPGPU Using Hyper-Q on Kepler Architecture N2 - Small-scale computations usually cannot fully utilize the compute capabilities of modern GPGPUs. With the Fermi GPU architecture Nvidia introduced the concurrent kernel execution feature allowing up to 16 GPU kernels to execute simultaneously on a shared GPU device for a better utilization of the respective resources. Insufficient scheduling capabilities in this respect, however, can significantly reduce the theoretical concurrency level. With the Kepler GPU architecture Nvidia addresses this issue by introducing the Hyper-Q feature with 32 hardware managed work queues for concurrent kernel execution. We investigate the Hyper-Q feature within heterogeneous workloads with multiple concurrent host threads or processes offloading computations to the GPU each. By means of a synthetic benchmark kernel and a hybrid parallel CPU-GPU real-world application, we evaluate the performance obtained with Hyper-Q on GPU and compare it against a kernel reordering mechanism introduced by the authors for the Fermi architecture. T3 - ZIB-Report - 14-19 KW - GPGPU KW - Hyper-Q KW - Concurrent Kernel Execution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50362 SN - 1438-0064 ER - TY - JOUR A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank T1 - Transparent boundary conditions based on the pole condition for time-dependent, two-dimensional problems JF - Numerical Methods for Partial Differential Equations Y1 - 2013 U6 - https://doi.org/10.1002/num.21759 VL - 29 IS - 4 SP - 1367 EP - 1390 ER - TY - GEN A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleo-ontological cephalopod research N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. T3 - ZIB-Report - 14-18 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50300 SN - 1438-0064 ER - TY - JOUR A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Ebell, Gino A1 - Meinel, Dietmar A1 - Heyn, Andreas T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben JF - DGZfP-Jahrestagung 2014 Konferenzband Y1 - 2014 ER - TY - GEN A1 - Grötschel, Martin A1 - Borndörfer, Ralf T1 - Mathematik im Verkehr N2 - Nach einem kurzen Abriss über die Bedeutung des Verkehrssektors als eine wichtige Schlüsseltechnologie im gesamten Verlauf der Menschheitsgeschichte skizzieren wir die Rolle der Mathematik für Verkehr und Transport. Wir spekulieren dann über zukünftige Entwicklungen, insbesondere im Bereich des öffentlichen Personenverkehrs, und begründen, dass die in diesem Bereich anstehenden Herausforderungen nur mit dem Einsatz mathematischer Methoden angemessen bewältigt werden können. Die demographischen Prozesse, die in verschiedenen Teilen der Welt unterschiedlich verlaufen, wie z.B. Überalterung in Europa oder dynamische Trends zu Megastädten in Entwicklungsländern, sich ändernde Lebens- und Produktionsverhältnisse, stark wachsender Bedarf nach Mobilität und enormes Anwachsen der Komplexität der Verkehrsplanung und -durchführung, machen einen verstärkten Zugriff auf mathematische Modellierung, Simulation und Optimierung notwendig. Diese Entwicklung stellt sowohl große Herausforderungen an die Mathematik, wo vielfach noch keine geeigneten Methoden vorhanden sind, als auch an die Praktiker im Bereich von Verkehr und Transport, die sich mit neuen Planungs- und Steuerungstechnologien befassen und diese effizient einsetzen müssen. Hier wird intensive Kooperation zwischen vielen beteiligten Akteuren gefragt sein. T3 - ZIB-Report - 14-03 KW - Optimierung KW - öffentlicher Verkehr Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50287 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Dittbrenner, Bastian A1 - Langenhan, Andreas A1 - Seidl, Stephan A1 - Weider, Steffen T1 - Integrierte Dienst- und Dienstreihenfolgeplanung zur Erhöhung der Fahrerzufriedenheit N2 - Wir stellen einen mathematischen Optimierungsansatz zur integrierten Dienst- und Dienstreihenfolgeplanung im öffentlichen Nahverkehr vor, mit dem sich bei konstanten Personalkosten die Fahrerzufriedenheit deutlich steigern lässt. T3 - ZIB-Report - 14-02 KW - duty scheduling KW - duty rostering KW - integrated scheduling KW - Benders' decomposition Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50270 SN - 1438-0064 ER - TY - GEN A1 - Stoppel, Sergej A1 - Hege, Hans-Christian A1 - Wiebel, Alexander T1 - Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering N2 - This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a very visible but relatively smooth surface. In the last step the selected surface is displayed. We provide examples for the results in real-world dataset as well as in artificially generated datasets. T3 - ZIB-Report - 14-11 KW - Interaction Techniques KW - Volume Rendering KW - Picking KW - Surfaces Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50266 SN - 1438-0064 ER - TY - BOOK ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - MATHEON - Mathematics for Key Technologies Y1 - 2014 SN - 978-3-03719-137-8 U6 - https://doi.org/10.4171/137 VL - 1 PB - European Mathematical Society ER - TY - CHAP A1 - Lockau, Daniel A1 - Hammerschmidt, Martin A1 - Haschke, Jan A1 - Blome, Mark A1 - Ruske, Florian A1 - Schmidt, Frank A1 - Rech, Bernd T1 - A comparison of scattering and non-scattering anti-reflection designs for back contacted polycrystalline thin film silicon solar cells in superstrate configuration T2 - Proc. SPIE Y1 - 2014 U6 - https://doi.org/10.1117/12.2052362 VL - 9140 SP - 914006 ER - TY - GEN A1 - Bockmayr, Alexander A1 - Siebert, Heike A1 - Röblitz, Susanna A1 - Schütte, Christof A1 - Deuflhard, Peter ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutela, Martin ED - Sprekels, Jürgen T1 - Advanced mathematical modeling in systems biology T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 29 EP - 44 PB - European Mathematical Society ER - TY - GEN A1 - Vega, Iliusi A1 - Schütte, Christof A1 - Conrad, Tim T1 - SAIMeR: Self-adapted method for the identification of metastable states in real-world time series N2 - In the framework of time series analysis with recurrence networks, we introduce SAIMeR, a heuristic self-adapted method that determines the elusive recurrence threshold and identifies metastable states in complex time series. To identify metastable states as well as the transitions between them, we use graph theory concepts and a fuzzy partitioning clustering algorithm. We illustrate SAIMeR by applying it to three real-world time series and show that it is able to identify metastable states in real-world data with noise and missing data points. Finally, we suggest a way to choose the embedding parameters used to construct the state space in which this method is performed, based on the analysis of how the values of these parameters affect two recurrence quantitative measurements: recurrence rate and entropy. T3 - ZIB-Report - 14-16 KW - time series analysis KW - application in statistical physics KW - recurrence quantification analysis KW - threshold KW - metastability KW - non-linear dynamics Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50130 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Laubender, Guido A1 - Steinke, Thomas T1 - Integration of Intel Xeon Phi Servers into the HLRN-III Complex: Experiences, Performance and Lessons Learned N2 - The third generation of the North German Supercomputing Alliance (HLRN) compute and storage facilities comprises a Cray XC30 architecture with exclusively Intel Ivy Bridge compute nodes. In the second phase, scheduled for November 2014, the HLRN-III configuration will undergo a substantial upgrade together with the option of integrating accelerator nodes into the system. To support the decision-making process, a four-node Intel Xeon Phi cluster is integrated into the present HLRN-III infrastructure at ZIB. This integration includes user/project management, file system access and job management via the HLRN-III batch system. For selected workloads, in-depth analysis, migration and optimization work on Xeon Phi is in progress. We will report our experiences and lessons learned within the Xeon Phi installation and integration process. For selected examples, initial results of the application evaluation on the Xeon Phi cluster platform will be discussed. T3 - ZIB-Report - 14-15 KW - Performance and usage measurement KW - System management KW - System integration KW - Xeon Phi cluster Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49990 UR - https://cug.org/proceedings/cug2014_proceedings/includes/files/pap194-file2.pdf SN - 1438-0064 ER - TY - GEN A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Tabelow, Karsten A1 - Polzehl, Jörg ED - Deuflhard, Peter ED - et al., T1 - Image Processing T2 - MATHEON - Mathematics for Key Technologies Y1 - 2014 U6 - https://doi.org/10.4171/137 SP - 359 EP - 376 PB - European Mathematical Society ER - TY - GEN A1 - Polthier, Konrad A1 - Sullivan, John A1 - Ziegler, Günter M. A1 - Hege, Hans-Christian ED - Deuflhard, Peter ED - et al., T1 - Visualization T2 - MATHEON - Mathematics for Key Technologies Y1 - 2014 SN - 978-3-03719-137-8 U6 - https://doi.org/10.4171/137 SP - 335 EP - 339 PB - European Mathematical Society ER - TY - GEN A1 - Arnold, Thomas A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Henrion, René A1 - Grötschel, Martin A1 - Koch, Thorsten A1 - Tischendorf, Caren A1 - Römisch, Werner T1 - A Jack of all Trades? Solving stochastic mixed-integer nonlinear constraint programs N2 - Natural gas is one of the most important energy sources in Germany and Europe. In recent years, political regulations have led to a strict separation of gas trading and gas transport, thereby assigning a central role in energy politics to the transportation and distribution of gas. These newly imposed political requirements influenced the technical processes of gas transport in such a way that the complex task of planning and operating gas networks has become even more intricate. Mathematically, the combination of discrete decisions on the configuration of a gas transport network, the nonlinear equations describing the physics of gas, and the uncertainty in demand and supply yield large-scale and highly complex stochastic mixed-integer nonlinear optimization problems. The Matheon project "Optimization of Gas Transport" takes the key role of making available the necessary core technology to solve the mathematical optimization problems which model the topology planning and the operation of gas networks. An important aspect of the academic impact is the free availability of our framework. As a result of several years of research and development, it is now possible to download a complete state-of-the-art framework for mixed-integer linear and nonlinear programming in source code at http://scip.zib.de T3 - ZIB-Report - 14-14 KW - gas transport optimization KW - mixed integer nonlinear programming Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49947 SN - 1438-0064 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Blome, Therese A1 - Greiner, Horst T1 - Simulation of advanced OLED light extraction structures with novel FEM methods T2 - Organic Photonics VI Y1 - 2014 U6 - https://doi.org/10.1117/12.2054146 VL - 9137 SP - 91370O ER - TY - GEN A1 - Schütte, Christof A1 - Conrad, Tim ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Showcase 3: Information-based medicine T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 66 EP - 67 PB - European Mathematical Society ER - TY - GEN A1 - Amiranashvili, Shalva A1 - Bandelow, Uwe A1 - Blome, Mark A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schmidt, Kersten A1 - Zschiedrich, Lin ED - Deuflhard, Peter ED - et al., T1 - Nanophotonics and nonlinear fiber optics T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 U6 - https://doi.org/10.4171/137 VL - 1 SP - 257 EP - 275 PB - European Mathematical Society ER - TY - GEN A1 - Lockau, Daniel A1 - Hammerschmidt, Martin A1 - Blome, Mark A1 - Schmidt, Frank ED - Deuflhard, Peter ED - et al., T1 - Optics of thin film solar cells T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 U6 - https://doi.org/10.4171/137 VL - 1 SP - 278 EP - 279 PB - European Mathematical Society ER - TY - GEN A1 - Deuflhard, Peter A1 - Schütte, Christof ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Life Sciences T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 1 EP - 5 PB - European Mathematical Society ER - TY - GEN A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Noé, Frank A1 - Weber, Marcus ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Design of functional molecules T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 49 EP - 65 PB - European Mathematical Society ER - TY - GEN A1 - Banisch, Ralf A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Module Detection in Directed Real-World Networks N2 - We investigate the problem of finding modules (or clusters, communities) in directed networks. Until now, most articles on this topic have been oriented towards finding complete network partitions despite the fact that this often is unwanted. We present a novel random walk based approach for non-complete partitions of the directed network into modules in which some nodes do not belong to only one of the modules but to several or to none at all. The new random walk process is reversible even for directed networks but inherits all necessary information about directions and structure of the original network. We demonstrate the performance of the new method in application to a real-world earthquake network. T3 - ZIB-Report - 14-13 KW - Module identification and classification KW - cycle decomposition KW - communication KW - directed networks Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49849 SN - 1438-0064 ER - TY - GEN A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Akbari Shandiz, Mohsen A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Robust Measurement of Natural Acetabular Orientation from AP Radiographs using Articulated 3D Shape and Intensity Models T3 - ZIB-Report - 14-12 KW - articulated shape and intensity models KW - 3D reconstruction KW - acetabular orientation KW - image registration Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49824 SN - 1438-0064 ER - TY - JOUR A1 - McPeak, Kevin A1 - van Engers, Christian D. A1 - Blome, Mark A1 - Park, Jong Hyuk A1 - Burger, Sven A1 - Gosalvez, Miguel A. A1 - Faridi, Ava A1 - Ries, Yasmina A1 - Sahu, Ayaskanta A1 - Norris, David T1 - Complex Chiral Colloids and Surfaces via High-Index Off-Cut Silicon JF - Nano Lett. Y1 - 2014 U6 - https://doi.org/10.1021/nl501032j VL - 14 IS - 5 SP - 2934 EP - 2940 ER - TY - GEN A1 - Zhang, Wei A1 - Wang, Han A1 - Hartmann, Carsten A1 - Weber, Marcus A1 - Schütte, Christof T1 - Applications of the cross-entropy method to importance sampling and optimal control of diffusions N2 - We study the cross-entropy method for diffusions. One of the results is a versatile cross-entropy algorithm that can be used to design efficient importance sampling strategies for rare events or to solve optimal control problems. The approach is based on the minimization of a suitable cross-entropy functional, with a parametric family of exponentially tilted probability distributions. We illustrate the new algorithm with several numerical examples and discuss algorithmic issues and possible extensions of the method. T3 - ZIB-Report - 14-10 KW - important sampling KW - optimal control KW - cross-entropy method KW - rare events KW - change of measure Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49720 SN - 1438-0064 ER - TY - THES A1 - Yousef, Kaveh T1 - Stress responses in Escherichia coli and HIV as model systems of adaptation to the environment Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000096054 ER - TY - THES A1 - Aiche, Stephan T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000095370 ER - TY - THES A1 - Winkelmann, Stefanie T1 - Markov Decision Processes with Information Costs Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094689 ER - TY - THES A1 - Gupta, Pooja T1 - Integrating high-density marker information into the genetic evaluation of the honey bee Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000093870 ER - TY - THES A1 - Bujotzek, Alexander T1 - Molecular Simulation of Multivalent Ligand-Receptor Systems Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094981 ER - TY - JOUR A1 - Menzel, Christoph A1 - Hebestreit, Erik A1 - Mühlig, Stefan A1 - Rockstuhl, Carsten A1 - Burger, Sven A1 - Lederer, Falk A1 - Pertsch, Thomas T1 - The spectral shift between near- and far-field resonances of optical nano-antennas JF - Opt. Expr. Y1 - 2014 U6 - https://doi.org/10.1364/OE.22.009971 VL - 22 IS - 8 SP - 9971 EP - 9982 ER - TY - JOUR A1 - Menzel, Christoph A1 - Hebestreit, Erik A1 - Alaee, Rasoul A1 - Albooyeh, Mohammad A1 - Mühlig, Stefan A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Simovski, Constantin A1 - Tretyakov, Sergei A1 - Lederer, Falk A1 - Pertsch, Thomas T1 - Extreme Coupling: a route towards local magnetic metamaterials JF - Phys. Rev. B Y1 - 2014 U6 - https://doi.org/10.1103/PhysRevB.89.155125 VL - 89 SP - 155125 ER - TY - THES A1 - Winter, Bianca T1 - Mathematische Optimierungsverfahren für die Konferenzplanung Y1 - 2011 ER - TY - THES A1 - Roos, Stephanie T1 - Analysis of Routing on Sparse Small-World Topologies Y1 - 2011 ER - TY - THES A1 - Tesch, Alexander T1 - Optimization of Large-Scale Conference Schedules N2 - Scientific conferences play an important role in almost all areas of today’s science and research. They offer a wide platform for international researchers and developers for communication and scientific exchange of current problems, experiences and knowledge in nearly all fields of research. Such conferences usually consist of talks about different topics that are given by authorized speakers. The planning process of a conference includes the creation of a scientific program schedule, that means a local and temporal allocation of all available talks. As the number of talks can grow into thousands for large-scale conferences, the conference scheduling becomes a complex challenge. Furthermore there exist a great bandwidth on various and individual requirements on the allocation of the talks. In this thesis we discuss the major problems that occur during the development of a conference schedule and provide a framework how proper conference schedules can be generated computationally. For that, we use Mixed-Integer-Programming techniques to find sched- ules that respect the difficult range of additional constraints. The basis of this thesis was the development of an optimized conference schedule of the International Symposium on Mathematical Programming 2012 (ISMP 2012) in Berlin, Germany. The ISMP is one of the largest conferences in the field of applied mathematics and mathematical optimization and constitutes a great attraction for in- ternational mathematicians and researchers. We will present our results based on the problem instance that we used for the ISMP 2012. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49506 ER - TY - THES A1 - Laaser, A. T1 - Gröbnerbasen und das Resource-Constrained-Shortest-Path Problem Y1 - 2013 ER - TY - THES A1 - Radke, A. T1 - Das Travelling Salesman Problem als Modell für Kapazitätsanalysen im Schienenverkehr Y1 - 2013 ER - TY - THES A1 - Jung, S. T1 - Optimierung der Bahnplanung für eine Pick-and-Place-Maschine Y1 - 2012 ER - TY - THES A1 - Koch, Thorsten T1 - Progress in computational integer programming Y1 - 2013 ER - TY - JOUR A1 - Shinano, Yuji A1 - Inui, Nobuo A1 - Fukagawa, Youzou A1 - Takakura, Noburu T1 - Optimizing Movement Sequences for Step-and-Scan Lithography Equipment JF - Journal of Advanced Mechanical Design, Systems, and Manufacturing N2 - The purpose of this work is to improve the throughput of step-and-scan lithography equipment to shorten the production time of a wafer. For this purpose, we propose a method for solving the MSOP (Movement Sequence Optimization Problem), which is the problem of computing the fastest schedule for visiting all shots on a wafer. It is well-known that the MSOP on step-and-repeat lithography equipment can be modeled as a traveling salesman problem. In contrast to step-and-repeat lithography equipment, a schedule for step-and-scan lithography equipment must also indicate the scanning direction of each shot, in addition to the sequence of the shots. For this reason, the traveling salesman problem formulation for step-and-repeat lithography equipment cannot be applied to solve the MSOP on step-and-scan lithography equipment directly. We overcame this difficulty by introducing auxiliary vertices to model the scanning directions in the traveling salesman problem formulation. By this method, we were able to compute exact optimal sequences considering the scanning directions of shots for several MSOP instances. Our numerical experiments demonstrated that our proposed method was capable of computing exact optimal solutions for real-world MSOP instances having up to 232 shots on a wafer. These optimal solutions gave a 0.25% to 4.66% improvement in productivity over solutions computed by previously known methods. Y1 - 2013 U6 - https://doi.org/10.1299/jamdsm.7.608 VL - 7 IS - 4 SP - 608 EP - 618 ER - TY - GEN A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - Optimization of energy supply systems by MILP branch and bound method in consideration of hierarchical relationship between design and operation N2 - To attain the highest performance of energy supply systems, it is necessary to rationally determine types, capacities, and numbers of equipment in consideration of their operational strategies corresponding to seasonal and hourly variations in energy demands. In the combinatorial optimization method based on the mixed-integer linear programming (MILP), integer variables are used to express the selection, numbers, and on/off status of operation of equipment, and the number of these variables increases with those of equipment and periods for variations in energy demands, and affects the computation efficiency significantly. In this paper, a MILP method utilizing the hierarchical relationship between design and operation variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized independently at each period by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified. T3 - ZIB-Report - 14-09 KW - Energy supply systems KW - Optimal design KW - Optimal operation KW - Mixed-integer linear programming KW - Branch and bound method KW - Hierarchical approach Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49413 SN - 1438-0064 ER - TY - THES A1 - Fügenschuh, Armin T1 - Computational aspects of time in scheduling and dynamic flow problems Y1 - 2011 ER - TY - THES A1 - Cardonha, Carlos T1 - Applied Methods for the Vehicle Positioning Problem N2 - This dissertation is dedicated to the Vehicle Positioning Problem (VPP), a classical combinatorial optimization problem in public transport in which vehicles should be assigned to parking positions in a depot in such a way that shunting moves are minimized. We investigate several models and solution methods to solve the VPP and the VPPp, a multi-periodic extension of the problem which was not previously studied. In the first part of the thesis, the basic version of the problem is introduced and several formulations, theoretical properties, and concepts are investigated. In particular, we propose a mixed integer quadratic constrained formulation of the VPP whose QP relaxation produces the first known nontrivial lower bound on the number of shunting moves. The second part of our work describes two advanced solution methods. In the first approach, a set partitioning formulation is solved by a branch-and-price framework. We present efficient algorithms for the pricing problem and in order to improve the performance of the framework, we introduce heuristics and discuss strategies to reduce symmetry. The second approach consists of an iterative technique in which we try to optimize an ILP by solving some of its projections, which are smaller and therefore easier to compute. Both techniques are able to produce satisfactory solutions for large-scale instances of the VPPp. In the third part, advanced aspects of the problem are investigated. We propose and analyze several solution methods for the VPP+ and for the VPPp+, which are extended and more challenging versions of the VPP and of the VPPp, respectively. Finally, the role of uncertainty in the problem is discussed. In particular, we introduce a new criteria to evaluate the robustness of assignment plans, a formulation based on this concept, and a new online algorithm for the VPP. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-34211 ER - TY - THES A1 - Erdogan, Cemil T1 - Computing Prices for Track Allocations Y1 - 2009 ER - TY - THES A1 - Paetsch, Nils T1 - Multiobjective Duty Scheduling Y1 - 2009 ER - TY - THES A1 - Schumann, Christian T1 - Multikriterielle Umlaufplanung im ÖPNV Y1 - 2009 ER - TY - THES A1 - Erol, Berkan T1 - Models For The Train Timetabling Problem Y1 - 2009 ER - TY - THES A1 - Trillhaase, Anja T1 - Hierarchische Telekommunikationsnetze: ein Überblick zu Methoden der gemeinsamen Planung von Zugangs- und Kernnetzen Y1 - 2009 ER - TY - THES A1 - Klähne, Roman T1 - Models for Survivable Multi-layer Network Reconfiguration Y1 - 2009 ER - TY - THES A1 - Spiegelberg, Ingo T1 - Cardinality Constrained Polymatroids and LP Decoding Y1 - 2009 ER - TY - THES A1 - Warszawski, Maciej T1 - Lagrange-Relaxierungen der Multi-Fluss-Formulierung für das Distance-Constrained-Vehicle-Routing-Problem und das Travelling-Salesman-Problem Y1 - 2010 ER - TY - THES A1 - Dammer, René T1 - Integrierte und robuste Planung von Flugzeugen und Personal im Luftverkehr Y1 - 2010 ER - TY - THES A1 - Meirich, Robert T1 - Polyedrische Untersuchungen eines Linienplanungsproblems Y1 - 2010 ER - TY - THES A1 - Schulz, Christof T1 - Eine parallele Variante des Netzwerksimplexalgorithmus Y1 - 2010 ER - TY - THES A1 - Hansknecht, Christoph T1 - Valid Cuts for Mixed-Integer Programming Y1 - 2011 ER - TY - THES A1 - Hennig, Kai T1 - Sensor networks: Localizing nodes from noisy data Y1 - 2011 ER - TY - THES A1 - Simon, Felix T1 - Postoptimierung bei der Planung von FTTx-Netzen Y1 - 2011 ER - TY - THES A1 - Opel, Katharina T1 - Experimente in der multikriteriellen linearen Optimierung Y1 - 2011 ER - TY - THES A1 - Traverso, Laura T1 - Autobahn Toll: Heuristic Control Methods Y1 - 2012 ER - TY - THES A1 - Uwazie, Daniel T1 - Approaches to Makespan Y1 - 2012 ER - TY - THES A1 - Grimm, Boris T1 - Train Dispatching by Disjunctive Programming Y1 - 2012 ER - TY - THES A1 - Barckmann, Jana T1 - Optimizing cable and duct installations in FTTx networks Y1 - 2012 ER - TY - THES A1 - Rockstroh, Tina T1 - Die Primal-Dual-Methode: Überblick und Anwendung auf Netzwerk- und Approximationsalgorithmen Y1 - 2012 ER - TY - THES A1 - Bolik, Tsima T1 - Netzwerk-Design von Schleimpilzen im Performance-Vergleich mit Methoden der kombinatorischen Optimierung Y1 - 2013 ER - TY - THES A1 - Walther, Tom T1 - A SCIP Constraint Handler for Piecewise Linear Functions N2 - In this thesis, we study different modelling approaches for piecewise linear functions, in particular with respect to their occurrence in mathematical optimization problems. Reviewing the quality of the classical MIP models from the literature, we will see that all but the disaggregated convex combination method yield both sharp and locally ideal formulations. In the main part, we will present an alternative approach for modelling constraints involving piecewise linear functions, based on ideas of constraint programming and using a convex hull relaxation. For the purpose of developing a branch-and-bound procedure specifically adapted to our constraint formulation within SCIP, all required components such as propagation, branching and separation will be discussed. In particular, we will focus on adapting well-known MIP strategies for the selection of branching variables to our type of piecewise linear constraints. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49112 ER - TY - THES A1 - Pins, Sonja T1 - Optimizing the energy consumption in optical networks by flexible bit rates and lightpath reconfiguration Y1 - 2013 ER - TY - CHAP A1 - Tyminski, Jacek A1 - Pomplun, Jan A1 - Renwick, Stephen P. T1 - Impact of topographic mask models on scanner matching solutions T2 - Proc. SPIE: Optical Microlithography XXVII Y1 - 2014 U6 - https://doi.org/10.1117/12.2045919 VL - 9052 SP - 905218 ER - TY - THES A1 - Rehfeldt, Daniel T1 - Zweistufige Zielfunktionen in gemischt-ganzzahligen Programmen Y1 - 2013 ER - TY - JOUR A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Heller, Markus O. A1 - Yntema, Caroline A1 - Jung, Tobias A1 - Doyscher, Ralf A1 - Ehrig, Rainald A1 - Zhong, Yanlin A1 - Taylor, William R. T1 - Towards understanding knee joint laxity: Errors in non-invasive assessment of joint rotation can be corrected JF - Medical Engineering and Physics Y1 - 2014 U6 - https://doi.org/doi.org/10.1016/j.medengphy.2014.03.017 VL - 36 IS - 7 SP - 889 EP - 895 ER - TY - CHAP A1 - Manley, Phillip A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schmid, Martina ED - Sakabe, Shuji ED - Lienau, Christoph ED - Grunwald, Rüdiger T1 - Design Principles for Plasmonic Nanoparticle Devices T2 - Progress in Nonlinear Nano-Optics Y1 - 2015 UR - http://www.springer.com/978-3-319-12216-8 U6 - https://doi.org/10.1007/978-3-319-12217-5_13 VL - XXI SP - 223 EP - 247 PB - Springer ET - Nano-Optics and Nanophotonics ER - TY - THES A1 - Seidl, Stephan T1 - Ein Benders-Dekompositionsverfahren zur Lösung integrierter Dienst- und Dienstreihenfolgeprobleme Y1 - 2014 ER - TY - THES A1 - Richter, Stephanie T1 - Mathematische Behandlung von Dienstreihenfolgeregeln in der Wochenschemaoptimierung Y1 - 2013 ER - TY - THES A1 - Mehrgardt, Julika T1 - Kreiseinbettungen von Hypergraphen und ihre Anwendung in der Umlaufoptimierung Y1 - 2013 ER - TY - THES A1 - Przybylowicz, Steffen T1 - Diskrete Ereignis-Basierte Simulation von Autobahn-Mautkontrollen Y1 - 2013 ER - TY - THES A1 - Brückner, Michael T1 - Polyedrische Approximation von Punktwolke und ihre Anwendung in der ICE-Abstellungsplanung Y1 - 2012 ER - TY - THES A1 - Dod, Markus T1 - Darstellungsoptimierung von Fahrzeugumläufen Y1 - 2010 ER - TY - THES A1 - Hoang, Nam-Dung T1 - Algorithmic Cost Allocation Games: Theory and Applications Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-28185 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Held, Harald A1 - Huang, Wei A1 - Vigerske, Stefan T1 - Towards globally optimal operation of water supply networks JF - Numerical Algebra, Control and Optimization N2 - This paper is concerned with optimal operation of pressurized water supply networks at a fixed point in time. We use a mixed-integer nonlinear programming (MINLP) model incorporating both the nonlinear physical laws and the discrete decisions such as switching pumps on and off. We demonstrate that for instances from our industry partner, these stationary models can be solved to ε-global optimality within small running times using problem-specific presolving and state-of-the-art MINLP algorithms. In our modeling, we emphasize the importance of distinguishing between what we call real and imaginary flow, i.e., taking into account that the law of Darcy-Weisbach correlates pressure difference and flow along a pipe if and only if water is available at the high pressure end of a pipe. Our modeling solution extends to the dynamic operative planning problem. Y1 - 2012 U6 - https://doi.org/10.3934/naco.2012.2.695 VL - 2 IS - 4 SP - 695 EP - 711 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - Delle Site, Luigi T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 10 IS - 4 SP - 1376 EP - 1386 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study JF - Molecular Physics Y1 - 2013 U6 - https://doi.org/10.1080/00268976.2013.827254 VL - 111 IS - 22-23 SP - 3363 EP - 3371 ER - TY - JOUR A1 - Nikitin, B. A. A1 - Wulkow, Michael A1 - Schütte, Christof T1 - Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique JF - Macromolecular Theory and Simulation Y1 - 2013 U6 - https://doi.org/10.1002/mats.201300125 VL - 22 IS - 9 SP - 475 EP - 489 ER - TY - THES A1 - Borgers, Philipp T1 - Erweiterung eines verteilten Key-Value-Stores (Riak) um einen räumlichen Index Y1 - 2012 ER - TY - THES A1 - Reinbacher, Uwe T1 - Implementierung und Evaluierung eines FPGA-basierten statischen Paketfilters Y1 - 2013 ER - TY - THES A1 - Merkulow, Igor T1 - Parameter selection and evaluation for programming of heterogeneous architectures Y1 - 2013 ER - TY - THES A1 - Borchert, Sebastian T1 - Generische Templates zur Kommunikation in heterogenen Manycore-Systemen Y1 - 2011 ER - TY - THES A1 - Beick, Matthias T1 - On-Line Processing of Streams and Time Series – An Evaluation Y1 - 2010 ER - TY - THES A1 - Langner, Felix T1 - Überlastungsschutz mit Anfragepriorisierung für das Internetdateisystem XtreemFS Y1 - 2012 ER - TY - THES A1 - Münnich, Bert T1 - Kürzeste-Wege-Suche mit Grafikkarten Y1 - 2011 ER - TY - THES A1 - Hoffmann, Marie T1 - Ein agglomeratives, gossipbasiertes Clustering-Verfahren für verteilte Systeme implementiert in Scalaris Y1 - 2009 ER - TY - THES A1 - Lorenz, Christian T1 - Leistungsverbesserung der Datenübertragung bei der Replikation von nicht veränderlichen Dateien in einem verteilten Dateisystem Y1 - 2009 ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Linear response theory and optimal control for a molecular system under nonequilibrium conditions JF - Molecular Physics Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1297/ U6 - https://doi.org/10.1080/00268976.2013.844370 VL - 111 SP - 3555 EP - 3564 ER - TY - JOUR A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010258 VL - 16 IS - 1 SP - 258 EP - 286 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010350 VL - 16 IS - 1 SP - 350 EP - 376 ER - TY - JOUR A1 - Paulus, Florian A1 - Weiss, Maximilian A1 - Steinhilber, Dirk A1 - Nikitin, Anatoly A1 - Schütte, Christof A1 - Haag, Rainer T1 - Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights JF - Macromolecules Y1 - 2013 U6 - https://doi.org/10.1021/ma401712w VL - 46 IS - 21 SP - 8458 EP - 8466 ER - TY - BOOK A1 - Schütte, Christof A1 - Sarich, Marco T1 - Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches Y1 - 2013 N1 - Courant Lecture Notes No. 32, American Mathematical Society PB - American Mathematical Society ER - TY - THES A1 - Karbstein, Marika T1 - Line Planning and Connectivity N2 - This thesis introduces the Steiner connectivity problem. It is a generalization of the well known Steiner tree problem. Given a graph G = (V, E) and a subset T ⊆ V of the nodes, the Steiner tree problem consists in finding a cost minimal set of edges connecting all nodes in T . The Steiner connectivity problem chooses, instead of edges, from a given set of paths a subset to connect all nodes in T . We show in the first part of this thesis that main results about complexity, approximation, integer programming formulations, and polyhedra can be generalized from the Steiner tree problem to the Steiner connectivity problem. An example for a straightforward generalization are the Steiner partition inequalities, a fundamental class of facet defining inequalities for the Steiner tree problem. They can be defined for the Steiner connectivity problem in an analogous way as for the Steiner tree problem. An example for a generalization that needs more effort is the definition of a directed cut formulation and the proof that this dominates the canonical undirected cut formulation enriched by all Steiner partition inequalities. For the Steiner connectivity problem this directed cut formulation leads to extended formulations, a concept that is not necessary for the Steiner tree problem. There are also major differences between both problems. For instance, the case T = V for the Steiner connectivity problem is equivalent to a set covering problem and, hence, not a polynomial solvable case as in the Steiner tree problem. The Steiner connectivity problem is not only an interesting generalization of the Steiner tree problem but also the underlying connectivity problem in line planning with inte- grated passenger routing. The integrated line planning and passenger routing problem is an important planning problem in service design of public transport and the topic of the second part. Given is the infrastructure network of a public transport system where the edges correspond to streets and tracks and the nodes correspond to stations/stops of lines. The task is to find paths in the infrastructure network for lines and passengers such that the capacities of the lines suffice to transport all passengers. Existing models in the literature that integrate a passenger routing in line planning either treat transfers in a rudimentary way and, hence, neglect an important aspect for the choice of the pas- senger routes, or they treat transfers in a too comprehensive way and cannot be solved for large scale real world problems. We propose a new model that focuses on direct connections. The attractiveness of transfer free connections is increased by introducing a transfer penalty for each non-direct connection. In this way, a passenger routing is computed that favors direct connections. For the computation of this model we also implemented algorithms influenced by the results for the Steiner connectivity problem. We can compute with our model good solutions that minimize a weighted sum of line operating costs and passengers travel times. These solutions improve the solutions of an existing approach, that does not consider direct connections, by up to 17%. In contrast to a comprehensive approach, that considers every transfer and for which we could not even solve the root LP within 10 hours for large instances, the solutions of the new model, computed in the same time, are close to optimality (<1%) or even optimal for real world instances. In a project with the Verkehr in Potsdam GmbH to compute the line plan for 2010 we showed that our approach is applicable in practice and can be used to solve real world problems. Y1 - 2013 UR - www.zib.de/karbstein/scplpp.pdf SN - 978-3-8439-1062-0 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Pfetsch, Marc T1 - Models for Fare Planning in Public Transport JF - Discrete Applied Mathematics Y1 - 2012 U6 - https://doi.org/10.1016/j.dam.2012.02.027 VL - 160 IS - 18 SP - 2591 EP - 2605 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Jäger, Ulrich T1 - Planning Problems in Public Transit JF - Production Factor Mathematics Y1 - 2010 SN - 978-3-642-11247-8 U6 - https://doi.org/10.1007/978-3-642-11248-5 SP - 95 EP - 122 PB - acatech and Springer CY - Berlin Heidelberg ER - TY - JOUR A1 - Grötschel, Martin T1 - Vertrauen in die/in der Wissenschaft: Einführung JF - DEBATTE Y1 - 2013 SN - 978-3-939818-41-0 IS - Heft 12, Zweiter Teil SP - 63 EP - 69 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - JOUR A1 - Grötschel, Martin T1 - Vertrauen in die/in der Wissenschaft: Einführung in das Thema JF - DEBATTE Y1 - 2013 SN - 978-3-939818-41-0 IS - Heft 12, Erster Teil SP - 9 EP - 16 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - JOUR A1 - Grötschel, Martin A1 - Stephan, Rüdiger T1 - Characterization of Facets of the Hop Constrained Chain Polytope via Dynamic Programming JF - Discrete Applied Mathematics Y1 - 2014 U6 - https://doi.org/10.1016/j.dam.2013.08.015 VL - 162 SP - 229 EP - 246 ER - TY - JOUR A1 - Gamrath, Gerald T1 - Improving strong branching by domain propagation JF - EURO Journal on Computational Optimization N2 - One of the essential components of a branch-and-bound based mixed-integer linear programming (MIP) solver is the branching rule. Strong branching is a method used by many state-of-the-art branching rules to select the variable to branch on. It precomputes the dual bounds of potential child nodes by solving auxiliary linear programs (LPs) and thereby helps to take good branching decisions that lead to a small search tree. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Domain propagation is a technique MIP solvers usually apply at every node of the branch-and-bound tree to tighten the local domains of variables. Computational experiments on standard MIP instances indicate that our improved strong branching method significantly improves the quality of the predictions and causes almost no additional effort. For a full strong branching rule, we are able to obtain substantial reductions of the branch-and-bound tree size as well as the solving time. Moreover, the state-of-the-art hybrid branching rule can be improved this way as well. This paper extends previous work by the author published in the proceedings of the CPAIOR 2013. Y1 - 2014 U6 - https://doi.org/10.1007/s13675-014-0021-8 VL - 2 IS - 3 SP - 99 EP - 122 PB - Springer CY - Berlin Heidelberg ER - TY - CHAP A1 - Schlechte, Thomas T1 - Railway Track Allocation BT - Selected Papers of the International Annual Conference of the German Operations Research Society (GOR), Leibniz University of Hannover, Germany, September 5-7, 2012 T2 - Operations Research Proceedings Y1 - 2012 U6 - https://doi.org/10.1007/978-3-319-00795-314 SP - 15 EP - 20 ER - TY - CHAP A1 - Berthold, Timo A1 - Gleixner, Ambros ED - Bonami, Pierre ED - Liberti, Leo ED - Miller, Andrew J. ED - Sartenaer, Annick T1 - Undercover – a primal heuristic for MINLP based on sub-MIPs generated by set covering T2 - Proceedings of the European Workshop on Mixed Integer Nonlinear Programming, April 12-16, 2010, Marseilles, France N2 - We present Undercover, a primal heuristic for mixed-integer nonlinear programming (MINLP). The heuristic constructs a mixed-integer linear subproblem (sub-MIP) of a given MINLP by fixing a subset of the variables. We solve a set covering problem to identify a minimal set of variables which need to be fixed in order to linearise each constraint. Subsequently, these variables are fixed to approximate values, e.g. obtained from a linear outer approximation. The resulting sub-MIP is solved by a mixed-integer linear programming solver. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. Although general in nature, the heuristic seems most promising for mixed-integer quadratically constrained programmes (MIQCPs). We present computational results on a general test set of MIQCPs selected from the MINLPLib. Y1 - 2010 SP - 103 EP - 112 ER - TY - CHAP A1 - Gleixner, Ambros A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Improving the Accuracy of Linear Programming Solvers with Iterative Refinement T2 - ISSAC '12. Proceedings of the 37th International Symposium on Symbolic and Algebraic Computation Y1 - 2012 U6 - https://doi.org/10.1145/2442829.2442858 SP - 187 EP - 194 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Pfetsch, Marc T1 - The Steiner connectivity problem JF - Mathematical Programming A Y1 - 2013 U6 - https://doi.org/10.1007/s10107-012-0564-5 VL - 142 IS - 1 SP - 133 EP - 167 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Schweiger, Jonas T1 - Multistage Stochastic Programming in Strategic Telecommunication Network Planning JF - Computational Management Science N2 - Mobile communication is nowadays taken for granted. Having started primarily as a service for speech communication, data service and mobile Internet access are now driving the evolution of network infrastructure. Operators are facing the challenge to match the demand by continuously expanding and upgrading the network infrastructure. However, the evolution of the customer's demand is uncertain. We introduce a novel (long-term) network planning approach based on multistage stochastic programming, where demand evolution is considered as a stochastic process and the network is extended as to maximize the expected profit. The approach proves capable of designing large-scale realistic UMTS networks with a time-horizon of several years. Our mathematical optimization model, the solution approach, and computational results are presented in this paper. Y1 - 2012 U6 - https://doi.org/10.1007/s10287-012-0143-5 VL - 9 IS - 3 SP - 303 EP - 321 PB - Springer ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Szabo, Jacint T1 - Gas Network Topology Optimization for Upcoming Market Requirements T2 - International Conference on the European Energy Market (EEM) N2 - Gas distribution networks are complex structures that consist of passive pipes, and active, controllable elements such as valves and compressors. Controlling such network means to find a suitable setting for all active components such that a nominated amount of gas can be transmitted from entries to exits through the network, without violating physical or operational constraints. The control of a large-scale gas network is a challenging task from a practical point of view. In most companies the actual controlling process is supported by means of computer software that is able to simulate the flow of the gas. However, the active settings have to be set manually within such simulation software. The solution quality thus depends on the experience of a human planner. When the gas network is insufficient for the transport then topology extensions come into play. Here a set of new pipes or active elements is determined such that the extended network admits a feasible control again. The question again is how to select these extensions and where to place them such that the total extension costs are minimal. Industrial practice is again to use the same simulation software, determine extensions by experience, add them to the virtual network, and then try to find a feasible control of the active elements. The validity of this approach now depends even more on the human planner. Another weakness of this manual simulation-based approach is that it cannot establish infeasibility of a certain gas nomination, unless all settings of the active elements are tried. Moreover, it is impossible to find a cost-optimal network extension in this way. In order to overcome these shortcomings of the manual planning approach we present a new approach, rigorously based on mathematical optimization. Hereto we describe a model for finding feasible controls and then extend this model such that topology extensions can additionally and simultaneously be covered. Numerical results for real-world instances are presented and discussed. Y1 - 2011 U6 - https://doi.org/10.1109/EEM.2011.5953035 SP - 346 EP - 351 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - An Exact Reoptimization Algorithm for the Scheduling of Elevator Groups JF - Flexible Services and Manufacturing Journal Y1 - 2013 U6 - https://doi.org/10.1007/s10696-013-9175-6 SP - 1 EP - 24 ER - TY - CHAP A1 - Heinz, Stefan A1 - Schulz, Jens T1 - Explanations for the Cumulative Constraint: An Experimental Study T2 - Experimental Algorithms Y1 - 2011 VL - 6630 SP - 400 EP - 409 ER - TY - CHAP A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Schulz, Jens T1 - An approximative Criterion for the Potential of Energetic Reasoning T2 - Theory and Practice of Algorithms in (Computer) Systems Y1 - 2011 VL - 6595 SP - 229 EP - 239 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Vierhaus, Ingmar T1 - System Dynamic Optimization in the Sustainability Assessment of a World-Model T2 - 11th Global Conference on Sustainable Manufacturing : Proceedings N2 - The System Dynamics (SD) methodology is a framework for modeling and simulating the dynamic behavior of socioeconomic systems. Characteristic for the description of such systems is the occurrence of feedback loops together with stocks and flows. The mathematical equations that describe the system are usually nonlinear. Therefore seemingly simple systems can show a nonintuitive, nonpredictable behavior over time. Controlling a dynamical system means to define a desired final state in which the system should be, and to specify potential interventions from outside that should keep the system on the right track. The central question is how to compute such globally optimal control for a given SD model. We propose a branch-and-bound approach that is based on a bound propagation method, primal heuristics, and spatial branching. We apply our new SD-control method to a small System Dynamics model, that describes the evolution of a social-economic system over time. We examine the problem of steering this system on a sustainable consumption path. Y1 - 2013 SP - 530 EP - 535 PB - Universitätsverlag der TU Berlin CY - Berlin ER - TY - CHAP A1 - Heinz, Stefan A1 - Beck, J. Christopher T1 - Reconsidering Mixed Integer Programming and MIP-based Hybrids for Scheduling T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems (CPAIOR 2012) Y1 - 2012 VL - 7298 SP - 211 EP - 227 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - van Veldhuizen, Roel A1 - Vierhaus, Ingmar T1 - Production Planning for Non-Cooperating Companies with Nonlinear Optimization T2 - 11th Global Conference on Sustainable Manufacturing : Proceedings N2 - We consider a production planning problem where two competing companies are selling their items on a common market. Moreover, the raw material used in the production is a limited non-renewable resource. The revenue per item sold depends on the total amount of items produced by both players. If they collaborate they could apply a production strategy that leads to the highest combined revenue. Usually the formation of such syndicates is prohibited by law; hence we assume that one company does not know how much the other company will produce. We formulate the problem for company A to find an optimal production plan without information on the strategy of company B as a nonlinear mathematical optimization problem. In its naive formulation the model is too large, making its solution practically impossible. After a reformulation we find a much smaller model, which we solve by spatial branch-and-cut methods and linear programming. We discuss the practical implications of our solutions. Y1 - 2013 SP - 536 EP - 541 PB - Universitätsverlag der TU Berlin CY - Berlin ER - TY - CHAP A1 - Brose, Achim A1 - Fügenschuh, Armin A1 - Gausemeier, Pia A1 - Vierhaus, Ingmar A1 - Seliger, Günther T1 - A System Dynamic Enhancement for the Scenario Technique T2 - Proc. 11th Global Conference on Sustainable Manufacturing N2 - The Scenario Technique is a strategic planning method that aims to describe and analyze potential developments of a considered system in the future. Its application consists of several steps, from an initial problem analysis over an influence analysis to projections of key factors and a definition of the scenarios to a final interpretation of the results. The technique itself combines qualitative and quantitative methods and is an enhancement of the standard Scenario Technique. We use the numerical values gathered during the influence analysis, and embed them in a System Dynamics framework. This yields a mathematically rigorous way to achieve predictions of the system‘s future behavior from an initial impulse and the feedback structure of the factors. The outcome of our new method is a further way of projecting the present into the future, which enables the user of the Scenario Technique to obtain a validation of the results achieved by the standard method. Y1 - 2013 SP - 561 EP - 566 PB - Universitätsverlag der TU Berlin CY - Berlin ER - TY - CHAP A1 - Scheumann, René A1 - Vierhaus, Ingmar A1 - Chang, Ya-Ju A1 - Fügenschuh, Armin A1 - Finkbeiner, Matthias T1 - Identification of trade-offs for sustainable manufacturing of a Bamboo Bike by System Dynamics T2 - Proceedings of the 27. Conference on Environmental Informatics - Informatics for Environmental Protection, Sustainable Development and Risk Management N2 - We develop a generic System Dynamic model to simulate the production, machines, employees, waste, and capital flows of a manufacturing company. In a second step, this model is specialised by defining suit-able input data to represent a bicycle manufacturing company in a developing country. We monitor a set of sustainability indicators to understand the social, environmental and economic impact of the company, and to estimate managerial decisions to be taken in order to improve on these criteria. We show that the social and environmental situation can be improved over time without sacrificing the economic success of the company's business. Y1 - 2013 SP - 523 EP - 531 ER - TY - CHAP A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - SCIP Optimization Suite を利用した 混合整数(線形/非線形) 計画問題の解法 T2 - Proceedings of the 24th RAMP symposium. The Operations Society of Japan, RAMP: Research Association of Mathematical Programming N2 - この論文ではソフトウェア・パッケージSCIP Optimization Suite を紹介し,その3つの構成要素:モデリン グ言語Zimpl, 線形計画(LP: linear programming) ソルバSoPlex, そして,制約整数計画(CIP: constraint integer programming) に対するソフトウェア・フレームワークSCIP, について述べる.本論文では,この3つの 構成要素を利用して,どのようにして挑戦的な混合整数線形計画問題(MIP: mixed integer linear optimization problems) や混合整数非線形計画問題(MINLP: mixed integer nonlinear optimization problems) をモデル化 し解くのかを説明する.SCIP は,現在,最も高速なMIP,MINLP ソルバの1つである.いくつかの例により, Zimpl, SCIP, SoPlex の利用方法を示すとともに,利用可能なインタフェースの概要を示す.最後に,将来の開 発計画の概要について述べる. N2 - This paper introduces the SCIP Optimization Suite and discusses the capabilities of its three components: the modeling language Zimpl, the linear programming solver SoPlex, and the constraint integer programming framework SCIP. We explain how in concert these can be used to model and solve challenging mixed integer linear and nonlinear optimization problems. SCIP is currently one of the fastest non-commercial MIP and MINLP solvers. We demonstrate the usage of Zimpl, SCIP, and SoPlex by selected examples, we give an overview over available interfaces, and outline plans for future development. Y1 - 2012 SP - 165 EP - 192 ER - TY - CHAP A1 - Berthold, Timo A1 - Gleixner, Ambros ED - Bonifaci, Vincenzo ED - Demetrescu, Camil ED - Marchetti-Spaccamela, Alberto T1 - Undercover Branching T2 - Experimental Algorithms, 12th International Symposium, SEA 2013, Rome, Italy, June 5-7, 2013, Proceedings N2 - In this paper, we present a new branching strategy for nonconvex MINLP that aims at driving the created subproblems towards linearity. It exploits the structure of a minimum cover of an MINLP, a smallest set of variables that, when fixed, render the remaining system linear: whenever possible, branching candidates in the cover are preferred. Unlike most branching strategies for MINLP, Undercover branching is not an extension of an existing MIP branching rule. It explicitly regards the nonlinearity of the problem while branching on integer variables with a fractional relaxation solution. Undercover branching can be naturally combined with any variable-based branching rule. We present computational results on a test set of general MINLPs from MINLPLib, using the new strategy in combination with reliability branching and pseudocost branching. The computational cost of Undercover branching itself proves negligible. While it turns out that it can influence the variable selection only on a smaller set of instances, for those that are affected, significant improvements in performance are achieved. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38527-8_20 VL - 7933 SP - 212 EP - 223 ER - TY - CHAP A1 - Gleixner, Ambros A1 - Weltge, Stefan T1 - Learning and Propagating Lagrangian Variable Bounds for Mixed-Integer Nonlinear Programming T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 10th International Conference, CPAIOR 2013, Yorktown Heights, NY, USA, May 18-22, 2013 N2 - Optimization-based bound tightening (OBBT) is a domain reduction technique commonly used in nonconvex mixed-integer nonlinear programming that solves a sequence of auxiliary linear programs. Each variable is minimized and maximized to obtain the tightest bounds valid for a global linear relaxation. This paper shows how the dual solutions of the auxiliary linear programs can be used to learn what we call Lagrangian variable bound constraints. These are linear inequalities that explain OBBT's domain reductions in terms of the bounds on other variables and the objective value of the incumbent solution. Within a spatial branch-and-bound algorithm, they can be learnt a priori (during OBBT at the root node) and propagated within the search tree at very low computational cost. Experiments with an implementation inside the MINLP solver SCIP show that this reduces the number of branch-and-bound nodes and speeds up solution times. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38171-3_26 VL - 7874 SP - 355 EP - 361 ER - TY - JOUR A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Vigerske, Stefan T1 - Analyzing the computational impact of MIQCP solver components JF - Numerical Algebra, Control and Optimization N2 - We provide a computational study of the performance of a state-of-the-art solver for nonconvex mixed-integer quadratically constrained programs (MIQCPs). Since successful general-purpose solvers for large problem classes necessarily comprise a variety of algorithmic techniques, we focus especially on the impact of the individual solver components. The solver SCIP used for the experiments implements a branch-and-cut algorithm based on a linear relaxation to solve MIQCPs to global optimality. Our analysis is based on a set of 86 publicly available test instances. Y1 - 2012 U6 - https://doi.org/10.3934/naco.2012.2.739 VL - 2 IS - 4 SP - 739 EP - 748 ER - TY - GEN A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin A1 - Gottwald, Robert Lion A1 - Grösser, Stefan N. T1 - Modern Nonlinear Optimization Techniques for an Optimal Control of System Dynamics Models N2 - We study System Dynamics models with several free parameters that can be altered by the user. We assume that the user's goal is to achieve a certain dynamic behavior of the model by varying these parameters. In order to the find best possible combination of parameter settings, several automatic parameter tuning methods are described in the literature and readily available within existing System Dynamic software packages. We give a survey on the available techniques in the market and describe their theoretical background. Some of these methods are already six decades old, and meanwhile newer and more powerful optimization methods have emerged in the mathematical literature. One major obstacle for their direct use are tabled data in System Dynamics models, which are usually interpreted as piecewise linear functions. However, modern optimization methods usually require smooth functions which are twice continuously differentiable. We overcome this problem by a smooth spline interpolation of the tabled data. We use a test set of three complex System Dynamic models from the literature, describe their individual transition into optimization problems, and demonstrate the applicability of modern optimization algorithms to these System Dynamics Optimization problems. T3 - ZIB-Report - 14-08 KW - System Dynamics KW - Optimal Control KW - Nonlinear Optimization KW - Spline Interpolation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-48159 SN - 1438-0064 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Mannino, Carlo T1 - An Optimization Model for WiMAX Network Planning and Optimization T2 - WiMAX Network Planning and Optimization Y1 - 2009 SN - 978-1-4200-6662-3 SP - 369 EP - 386 PB - Auerbach Publications ER - TY - CHAP A1 - D'Andreagiovanni, Fabio T1 - A Hybrid Exact-ACO Algorithm for the Joint Scheduling, Power and Cluster Assignment in Cooperative Wireless Networks T2 - BIONETICS 2012 Y1 - 2012 ER - TY - CHAP A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Raymond, Annie T1 - Robust optimization under multiband uncertainty T2 - CTW 2013 Y1 - 2013 SP - 35 EP - 38 ER - TY - BOOK A1 - D'Andreagiovanni, Fabio ED - Carlucci Aiello, Luigia T1 - New perspectives on Wireless Network Design - Strong, stable and robust 0-1 models by Power Discretization Y1 - 2012 PB - Sapienza Editrice ER - TY - CHAP A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Raymond, Annie T1 - 0-1 Multiband Robust Optimization T2 - Operations Research Proceedings 2013 Y1 - 2013 ER - TY - CHAP A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio T1 - A New Theoretical Framework for Robust Optimization Under Multi-Band Uncertainty T2 - Operations Research Proceedings 2012 Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-00795-3_17 SP - 115 EP - 121 ER - TY - CHAP A1 - Bley, Andreas A1 - D'Andreagiovanni, Fabio A1 - Karch, Daniel T1 - WDM Fiber Replacement Scheduling T2 - Proceedings of INOC 2013 Y1 - 2013 U6 - https://doi.org/10.1016/j.endm.2013.05.092 VL - 41 SP - 189 EP - 196 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Pulaj, Jonad T1 - A hybrid primal heuristic for Robust Multiperiod Network Design T2 - EvoApplications 2014 Y1 - 2014 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Raymond, Annie T1 - Multiband Robust Optimization and its Adoption in Harvest Scheduling T2 - Proc. of FORMATH 2013 Y1 - 2014 ER - TY - CHAP A1 - Bley, Andreas A1 - D'Andreagiovanni, Fabio A1 - Karch, Daniel T1 - Scheduling technology migration in WDM Networks T2 - Photonic Networks, 14. 2013 ITG Symposium. Proceedings Y1 - 2013 SP - 1 EP - 5 ER - TY - GEN A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio T1 - Robust Optimization under Multiband Uncertainty T2 - 2013 Mixed Integer Programming Workshop - MIP 2013 Y1 - 2013 ER - TY - CHAP A1 - Zakrzewska, Anna A1 - D'Andreagiovanni, Fabio A1 - Ruepp, Sarah A1 - Berger, Michael S. T1 - Biobjective Optimization of Radio Access Technology Selection and Resource Allocation in Heterogeneous Wireless Networks T2 - Proceedings of the 11th International Symposium on Modeling & Optimization in Mobile, Ad Hoc & Wireless Networks (WiOpt 2013) - RAWNET/WNC3’13 Y1 - 2013 SP - 652 EP - 658 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Vehicle Rotation Planning for Intercity Railways JF - Proceedings of Conference on Advanced Systems for Public Transport 2012 (CASPT12) N2 - This paper provides a generic formulation for rolling stock planning problems in the context of intercity passenger traffic. The main contributions are a graph theoretical model and a Mixed-Integer-Programming formulation that integrate all main requirements of the considered Vehicle-Rotation-Planning problem (VRPP). We show that it is possible to solve this model for real-world instances provided by our industrial partner DB Fernverkehr AG using modern algorithms and computers. Y1 - 2012 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Rapid Branching JF - Public Transport N2 - We propose rapid branching (RB) as a general branch-and-bound heuristic for solving large scale optimization problems in traffic and transport. The key idea is to combine a special branching rule and a greedy node selection strategy in order to produce solutions of controlled quality rapidly and efficiently. We report on three successful applications of the method for integrated vehicle and crew scheduling, railway track allocation, and railway vehicle rotation planning. Y1 - 2013 VL - 5 IS - 1 SP - 3 EP - 23 PB - Springer Berlin Heidelberg ER - TY - CHAP A1 - Scheumann, René A1 - Fügenschuh, Armin A1 - Schenker, Sebastian A1 - Vierhaus, Ingmar A1 - Borndörfer, Ralf A1 - Finkbeiner, Matthias ED - Seliger, Günther T1 - Global Manufacturing: How to Use Mathematical Optimisation Methods to Transform to Sustainable Value Creation BT - (GCSM 2012) T2 - Proceedings of the 10th Global Conference on Sustainable Manufacturing Y1 - 2012 SN - 978-605-63463-1-6 SP - 538 EP - 545 ER - TY - JOUR A1 - Powell, Gary A1 - Weiser, Martin T1 - Views, A new form of container adaptors JF - C/C++ Users Journal N2 - The C++ standard template library has many useful containers for data. The standard library includes two adpators, queue, and stack. The authors have extended this model along the lines of relational database semantics. Sometimes the analogy is striking, and we will point it out occasionally. An adaptor allows the standard algorithms to be used on a subset or modification of the data without having to copy the data elements into a new container. The authors provide many useful adaptors which can be used together to produce interesting views of data in a container. Y1 - 2000 VL - 18 IS - 4 SP - 40 EP - 51 ER - TY - CHAP A1 - Hendel, Gregor A1 - Berthold, Timo A1 - Achterberg, Tobias T1 - Rounding and Propagation Heuristics for Mixed Integer Programming T2 - Operations Research Proceedings 2011 N2 - Primal heuristics are an important component of state-of-the-art codes for mixed integer programming. In this paper, we focus on primal heuristics that only employ computationally inexpensive procedures such as rounding and logical deductions (propagation). We give an overview of eight different approaches. To assess the impact of these primal heuristics on the ability to find feasible solutions, in particular early during search, we introduce a new performance measure, the primal integral. Computational experiments evaluate this and other measures on MIPLIB~2010 benchmark instances. Y1 - 2011 SP - 71 EP - 76 ER - TY - JOUR A1 - Bauschert, Thomas A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Koster, Arie M.C.A. A1 - Kutschka, Manuel A1 - Steglich, Uwe T1 - Network planning under demand uncertainty with robust optimization JF - IEEE Communications Magazine Y1 - 2014 U6 - https://doi.org/10.1109/MCOM.2014.6736760 VL - 52 IS - 2 SP - 178 EP - 185 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio T1 - On Improving the Capacity of Solving Large-scale Wireless Network Design Problems by Genetic Algorithms T2 - Applications of Evolutionary Computation - EvoApplications 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-20520-0_2 VL - 6625 SP - 11 EP - 20 ER - TY - CHAP A1 - D'Andreagiovanni, Fabio A1 - Mannino, Carlo A1 - Sassano, Antonio T1 - Negative Cycle Separation in Wireless Network Design T2 - Network Optimization - INOC 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-21527-8_7 VL - 6701 SP - 51 EP - 56 ER - TY - JOUR A1 - Dely, Peter A1 - D'Andreagiovanni, Fabio A1 - Kassler, Andreas T1 - Fair Optimization of Mesh-Connected WLAN Hotspots JF - Wireless Communications and Mobile Computing Y1 - 2013 U6 - https://doi.org/10.1002/wcm.2393 VL - 15 IS - 5 SP - 924 EP - 946 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio T1 - Pure 0-1 programming approaches to wireless network design JF - 4OR Y1 - 2012 U6 - https://doi.org/10.1007/s10288-011-0162-z VL - 10 IS - 2 SP - 211 EP - 212 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Mannino, Carlo A1 - Sassano, Antonio T1 - GUB Covers and Power-Indexed Formulations for Wireless Network Design JF - Management Science Y1 - 2013 U6 - https://doi.org/10.1287/mnsc.1120.1571 VL - 59 IS - 1 SP - 142 EP - 156 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - A Case Study on Optimizing Toll Enforcements on Motorways T2 - 3rd Student Conference on Operational Research N2 - In this paper we present the problem of computing optimal tours of toll inspectors on German motorways. This problem is a special type of vehicle routing problem and builds up an integrated model, consisting of a tour planning and a duty rostering part. The tours should guarantee a network-wide control whose intensity is proportional to given spatial and time dependent traffic distributions. We model this using a space-time network and formulate the associated optimization problem by an integer program (IP). Since sequential approaches fail, we integrated the assignment of crews to the tours in our model. In this process all duties of a crew member must fit in a feasible roster. It is modeled as a Multi-Commodity Flow Problem in a directed acyclic graph, where specific paths correspond to feasible rosters for one month. We present computational results in a case-study on a German subnetwork which documents the practicability of our approach. Y1 - 2012 U6 - https://doi.org/10.4230/OASIcs.SCOR.2012.1 VL - 22 SP - 1 EP - 10 ER - TY - GEN A1 - Goltz-Fellgiebel, Julia Alexandra T1 - Mobile Applikationen für Bibliotheken im deutschsprachigen Raum N2 - Wir leben im digitalen Informationszeitalter, unsere Welt ist geprägt von Bits und Bytes. Unser Alltag wird zunehmend von technischen Hilfsmitteln bestimmt, das Handy ist zu unserem täglichen Begleiter geworden. Für jeden Bedarf gibt es mittlerweile eine kleine mobile Applikation (App), die uns das Leben erleichtern soll. Der Wandel von analog zu digital beeinflusst auch das Arbeitsumfeld von Bibliotheken und anderen Informationseinrichtungen. Im Zuge der strategischen Allianz, die seit Dezember 2007 zwischen Kooperativem Bibliotheksverbund Berlin-Brandenburg (KOBV) und Bayerischem Bibliotheksverbund (BVB) besteht, werden gemeinsame Entwicklungsprojekte durchgeführt. Die vorliegende Arbeit ist im Rahmen dieser strategischen Allianz entstanden, sie soll einen Überblick zu mobilen Angeboten der deutschsprachigen Bibliothekslandschaft bieten und damit zusammenhängende Mehrwerte für die Institutionen herausarbeiten. T3 - ZIB-Report - 14-06 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-46931 SN - 1438-0064 ER - TY - JOUR A1 - Szott, Sascha T1 - Vom Prototypen zum nachhaltigen Hosting-Service: die Resource Discovery Lösung ALBERT JF - Bibliotheksdienst Y1 - 2012 UR - http://digital.zlb.de/viewer/image/019591853_2012/683/ VL - 46 IS - 8/9 SP - 683 EP - 686 ER - TY - JOUR A1 - Bertelmann, Roland A1 - Szott, Sascha A1 - Höhnow, Tobias T1 - Discovery jenseits von “all you can eat” und “one size fits all” JF - Bibliothek Forschung und Praxis Y1 - 2012 U6 - https://doi.org/10.1515/bfp-2012-0050 VL - 36 IS - 3 SP - 369 EP - 376 ER - TY - JOUR A1 - Thiede, Doreen T1 - Bericht zum 78. World Library and Information Congress (WLIC) Y1 - 2012 UR - http://www.bi-international.de/download/berichte/224_bericht_wlic2012.pdf ER - TY - JOUR A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Thiede, Doreen T1 - Conference Report on the 20th BOBCATSSS Symposium JF - IFLA SET Bulletin Y1 - 2012 UR - http://www.ifla.org/files/set/Bulletin/_SET_Bulletin2012-July%202012%20Vol.13n2.pdf VL - 13 IS - 2 SP - 18 EP - 19 ER - TY - JOUR A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groh, Melanie A1 - Kinstler, Till A1 - Kropf, Katrin A1 - Weiser, Evelyn T1 - Cycling for Libraries 2012 - The Baltic States JF - BuB Y1 - 2012 UR - http://www.b-u-b.de/pdfarchiv/Heft-BuB_10_2012.pdf IS - 10 SP - 670 ER - TY - JOUR A1 - Herschel, Melanie A1 - Naumann, Felix A1 - Szott, Sascha A1 - Taubert, Maik T1 - Scalable Iterative Graph Duplicate Detection JF - IEEE Transactions on Knowledge and Data Engineering N2 - Duplicate detection determines different representations of real-world objects in a database. Recent research has considered the use of relationships among object representations to improve duplicate detection. In the general case where relationships form a graph, research has mainly focused on duplicate detection quality/effectiveness. Scalability has been neglected so far, even though it is crucial for large real-world duplicate detection tasks. We scale-up duplicate detection in graph data (ddg) to large amounts of data and pairwise comparisons, using the support of a relational database management system. To this end, we first present a framework that generalizes the ddg process. We then present algorithms to scale ddg in space (amount of data processed with bounded main memory) and in time. Finally, we extend our framework to allow batched and parallel ddg, thus further improving efficiency. Experiments on data of up to two orders of magnitude larger than data considered so far in ddg show that our methods achieve the goal of scaling ddg to large volumes of data. Y1 - 2012 U6 - https://doi.org/10.1109/TKDE.2011.99 VL - 24 IS - 11 SP - 2094 EP - 2108 ER - TY - JOUR A1 - Bleiholder, Jens A1 - Szott, Sascha A1 - Herschel, M. A1 - Naumann, Felix T1 - Complement union for data integration JF - Data Engineering Workshops (ICDEW), 2010 IEEE 26th International Conference on N2 - A data integration process consists of mapping source data into a target representation (schema mapping), identifying multiple representations of the same real-word object (duplicate detection), and finally combining these representations into a single consistent representation (data fusion). Clearly, as multiple representations of an object are generally not exactly equal, during data fusion, we have to take special care in handling data conflicts. This paper focuses on the definition and implementation of complement union, an operator that defines a new semantics for data fusion. Y1 - 2010 U6 - https://doi.org/10.1109/ICDEW.2010.5452760 SP - 183 EP - 186 ER - TY - JOUR A1 - Bleiholder, Jens A1 - Szott, Sascha A1 - Herschel, Melanie A1 - Kaufer, Frank A1 - Naumann, Felix T1 - Subsumption and Complementation As Data Fusion Operators JF - Proceedings of the 13th International Conference on Extending Database Technology N2 - The goal of data fusion is to combine several representations of one real world object into a single, consistent representation, e.g., in data integration. A very popular operator to perform data fusion is the minimum union operator. It is defined as the outer union and the subsequent removal of subsumed tuples. Minimum union is used in other applications as well, for instance in database query optimization to rewrite outer join queries, in the semantic web community in implementing Sparql's optional operator, etc. Despite its wide applicability, there are only few efficient implementations, and until now, minimum union is not a relational database primitive. This paper fills this gap as we present implementations of subsumption that serve as a building block for minimum union. Furthermore, we consider this operator as database primitive and show how to perform optimization of query plans in presence of subsumption and minimum union through rule-based plan transformations. Experiments on both artificial and real world data show that our algorithms outperform existing algorithms used for subsumption in terms of runtime and they scale to large volumes of data. In the context of data integration, we observe that performing data fusion calls for more than subsumption and minimum union. Therefore, another contribution of this paper is the definition of the complementation and complement union operators. Intuitively, these allow to merge tuples that have complementing values and thus eliminate unnecessary null-values. Y1 - 2010 U6 - https://doi.org/10.1145/1739041.1739103 SP - 513 EP - 524 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - An IP Approach to Toll Enforcement Optimization on German Motorways T2 - Operations Research Proceedings 2011 N2 - This paper proposes the first model for toll enforcement optimization on German motorways. The enforcement is done by mobile control teams and our goal is to produce a schedule achieving network-wide control, proportional to spatial and time-dependent traffic distributions. Our model consists of two parts. The first plans control tours using a vehicle routing approach with profits and some side constraints. The second plans feasible rosters for the control teams. Both problems can be modeled as Multi-Commodity Flow Problems. Adding additional coupling constraints produces a large-scale integrated integer programming formulation. We show that this model can be solved to optimality for real world instances associated with a control area in East Germany. Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-29210-1_51 SP - 317 EP - 322 ER - TY - GEN A1 - Nadobny, Johanna A1 - Weihrauch, Mirko A1 - Weiser, Martin A1 - Gellermann, Johanna A1 - Wlodarczyk, Waldemar A1 - Budach, Volker A1 - Wust, Peter T1 - Advances in the Planning and Control of the MR-guided Regional Hyperthermia Applications T2 - Proc. Int. Conf. Electromagnetics in Advanced Applications, ICEAA 2007, Torino, Italy Y1 - 2007 SP - 1010 EP - 1013 ER - TY - JOUR A1 - Schlechte, Thomas T1 - Railway Track Allocation - Simulation and Optimization JF - Proceedings of 4th International Seminar on Railway Operations Modelling and Analysis (IAROR) N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway infrastructure provider. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market. This leads to an increase of slot requests and then it is natural that conflicts occur among them. Furthermore, railway infrastructure networks consist of very expensive assets, even more they are rigid due to the long-term upgrade process. In order to make best use of these valuable infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithmic methodology can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and a general framework to support the integration of simulation and optimization for railway capacity allocation. Y1 - 2011 VL - 4 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Railway Track Allocation -- Simulation, Aggregation, and Optimization JF - Proc. 1st International Workshop on High-speed and Intercity Railways (IWHIR 2011) N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway company. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market in Europe. This leads to more potential conflicts between trains caused by an increasing demand of train paths. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. In order to make best use of the infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithms can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and an associated concept for track allocation, that consists of three important parts, simulation, aggregation, and optimization. Furthermore, we present results of our general framework for real world data. Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-27963-8 VL - 2 IS - 148 SP - 53 EP - 70 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - A Hypergraph Model for Railway Vehicle Rotation Planning JF - 11th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems N2 - We propose a model for the integrated optimization of vehicle rotations and vehicle compositions in long distance railway passenger transport. The main contribution of the paper is a hypergraph model that is able to handle the challenging technical requirements as well as very general stipulations with respect to the ``regularity'' of a schedule. The hypergraph model directly generalizes network flow models, replacing arcs with hyperarcs. Although NP-hard in general, the model is computationally well-behaved in practice. High quality solutions can be produced in reasonable time using high performance Integer Programming techniques, in particular, column generation and rapid branching. We show that, in this way, large-scale real world instances of our cooperation partner DB Fernverkehr can be solved. Y1 - 2011 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2011.146 VL - OpenAccess Series in Informatics (OASIcs) IS - 20 SP - 146 EP - 155 ER - TY - JOUR A1 - Harrod, Steven A1 - Schlechte, Thomas T1 - A Direct Comparison of Physical Block Occupancy Versus Timed Block Occupancy in Train Timetabling Formulations JF - Transportation Research Part E: Logistics and Transportation Review N2 - Two fundamental mathematical formulations for railway timetabling are compared on a common set of sample problems, representing both multiple track high density services in Europe and single track bidirectional operations in North America. One formulation, ACP, enforces against conflicts by constraining time intervals between trains, while the other formulation, RCHF, monitors physical occupation of controlled track segments. The results demonstrate that both ACP and RCHF return comparable solutions in the aggregate, with some significant differences in select instances, and a pattern of significant differences in performance and constraint enforcement overall. Y1 - 2013 U6 - https://doi.org/10.1016/j.tre.2013.04.003 VL - 54 SP - 50 EP - 66 ER - TY - CHAP A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Pfetsch, Marc A1 - Vigerske, Stefan T1 - Large Neighborhood Search beyond MIP T2 - Proceedings of the 9th Metaheuristics International Conference (MIC 2011) N2 - Large neighborhood search (LNS) heuristics are an important component of modern branch-and-cut algorithms for solving mixed-integer linear programs (MIPs). Most of these LNS heuristics use the LP relaxation as the basis for their search, which is a reasonable choice in case of MIPs. However, for more general problem classes, the LP relaxation alone may not contain enough information about the original problem to find feasible solutions with these heuristics, e.g., if the problem is nonlinear or not all constraints are present in the current relaxation. In this paper, we discuss a generic way to extend LNS heuristics that have been developed for MIP to constraint integer programming (CIP), which is a generalization of MIP in the direction of constraint programming (CP). We present computational results of LNS heuristics for three problem classes: mixed-integer quadratically constrained programs, nonlinear pseudo-Boolean optimization instances, and resource-constrained project scheduling problems. Therefore, we have implemented extended versions of the following LNS heuristics in the constraint integer programming framework SCIP: Local Branching, RINS, RENS, Crossover, and DINS. Our results indicate that a generic generalization of LNS heuristics to CIP considerably improves the success rate of these heuristics. Y1 - 2011 SN - 978-88-900984-3-7 SP - 51 EP - 60 ER - TY - JOUR A1 - Berthold, Timo T1 - Measuring the impact of primal heuristics JF - Operations Research Letters N2 - In modern MIP solvers, primal heuristics play a major role in finding and improving feasible solutions early in the solution process. However, classical performance measures such as time to optimality or number of branch-and-bound nodes reflect the impact of primal heuristics on the overall solving process badly. This article discusses the question of how to evaluate the effect of primal heuristics. Therefore, we introduce a new performance measure, the "primal integral" which depends on the quality of solutions found during the solving process as well as on the points in time when they are found. Our computational results reveal that heuristics improve the performance of MIP solvers in terms of the primal bound by around 80%. Further, we compare five state-of-the-art MIP solvers w.r.t. the newly proposed measure. Y1 - 2013 U6 - https://doi.org/10.1016/j.orl.2013.08.007 VL - 41 IS - 6 SP - 611 EP - 614 ER - TY - GEN A1 - Berthold, Timo A1 - Salvagnin, Domenico ED - Gomes, Carla ED - Sellmann, Meinolf T1 - Cloud branching T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems N2 - Branch-and-bound methods for mixed-integer programming (MIP) are traditionally based on solving a linear programming (LP) relaxation and branching on a variable which takes a fractional value in the (single) computed relaxation optimum. In this paper we study branching strategies for mixed-integer programs that exploit the knowledge of multiple alternative optimal solutions (a cloud) of the current LP relaxation. These strategies naturally extend state-of-the-art methods like strong branching, pseudocost branching, and their hybrids. We show that by exploiting dual degeneracy, and thus multiple alternative optimal solutions, it is possible to enhance traditional methods. We present preliminary computational results, applying the newly proposed strategy to full strong branching, which is known to be the MIP branching rule leading to the fewest number of search nodes. It turns out that cloud branching can reduce the mean running time by up to 30% on standard test sets. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38171-3_3 VL - 7874 SP - 28 EP - 43 PB - Springer ER - TY - CHAP A1 - Bley, Andreas T1 - On the Hardness of Finding Small Shortest Path Routing Conflicts T2 - Proceedings of 4th International Network Optimization Conference (INOC2009) N2 - Nowadays most data networks use shortest path protocols such as OSPF or IS-IS to route traffic. Given administrative routing lengths for the links of a network, all data packets are sent along shortest paths with respect to these lengths from their source to their destination. One of the most fundamental problems in planning shortest path networks is to decide whether a given set of routing paths forms a valid routing and, if this is not the case, to find a small subset of the given paths that cannot be shortest paths simultaneously for any routing lengths. In this paper we show that it is NP-hard to approximate the size of the smallest shortest path conflict by a factor less than 7/6. Y1 - 2009 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Insensitive bounds for the moments of the sojourn times in M/GI systems under state-dependent processor sharing JF - Advances in Applied Probability N2 - We consider a system with Poisson arrivals and i.i.d. service times and where the requests are served according to the state-dependent (Cohen's generalized) processor sharing discipline, where each request in the system receives a service capacity which depends on the actual number of requests in the system. For this system we derive asymptotically tight upper bounds for the moments of the conditional sojourn time of a request with given required service time. The bounds generalize corresponding results, recently given for the single-server processor sharing system by Cheung et al. and for the state-dependent processor sharing system with exponential service times by the authors. Analogous results hold for the waiting times. Y1 - 2010 U6 - https://doi.org/10.1239/aap/1269611152 VL - 42 IS - 1 SP - 246 EP - 267 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Vigerske, Stefan ED - Lee, Jon ED - Leyffer, Sven T1 - Extending a CIP framework to solve MIQCPs T2 - Mixed Integer Nonlinear Programming N2 - This paper discusses how to build a solver for mixed integer quadratically constrained programs (MIQCPs) by extending a framework for constraint integer programming (CIP). The advantage of this approach is that we can utilize the full power of advanced MIP and CP technologies. In particular, this addresses the linear relaxation and the discrete components of the problem. For relaxation, we use an outer approximation generated by linearization of convex constraints and linear underestimation of nonconvex constraints. Further, we give an overview of the reformulation, separation, and propagation techniques that are used to handle the quadratic constraints efficiently. We implemented these methods in the branch-cut-and-price framework SCIP. Computational experiments indicates the potential of the approach. Y1 - 2012 SN - 978-1-4614-1927-3 VL - 154 SP - 427 EP - 444 PB - Springer ER - TY - CHAP A1 - Bley, Andreas A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Vigerske, Stefan T1 - Comparing MIQCP Solvers to a Specialised Algorithm for Mine Production Scheduling T2 - Modeling, Simulation and Optimization of Complex Processes. Proceedings of the Fourth International Conference on High Performance Scientific Computing, March 2-6, 2009, Hanoi, Vietnam N2 - In this paper we investigate the performance of several out-of-the box solvers for mixed-integer quadratically constrained programmes (MIQCPs) on an open pit mine production scheduling problem with mixing constraints. We compare the solvers BARON, Couenne, SBB, and SCIP to a problem-specific algorithm on two different MIQCP formulations. The computational results presented show that general-purpose solvers with no particular knowledge of problem structure are able to nearly match the performance of a hand-crafted algorithm. Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-25707-0_3 SP - 25 EP - 39 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Cardonha, Carlos T1 - A Binary Quadratic Programming Approach to the Vehicle Positioning Problem T2 - Modeling, Simulation and Optimization of Complex Processes -- Proceedings of the Fourth International Conference on High Performance Scientific Computing, March 2-6, 2009 N2 - The Vehicle Positioning Problem (VPP) consists of the assignment of vehicles (buses, trams or trains) of a public transport or railway company to parking positions in a depot and to timetabled trips. Such companies have many different types of vehicles, and each trip can be performed only by vehicles of some of these types. These assignments are non-trivial due to the topology of depots. The parking positions are organized in tracks, which work as one- or two-sided stacks or queues. If a required type of vehicle is not available in the front of any track, shunting movements must be performed in order to change vehicles' positions, which is undesirable and should be avoided. In this text we present integer linear and non-linear programming formulations for some versions of the problem and compare them from a theoretical and a computational point of view. Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-25707-0 SP - 41 EP - 52 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Neumann, Marika T1 - Linienoptimierung - reif für die Praxis? T2 - Heureka '11 : Optimierung in Verkehr und Transport N2 - Wir stellen in dieser Arbeit ein mathematisches Optimierungsmodell zur Bestimmung eines optimalen Linienplans vor, das sowohl die Fahrzeiten und die Anzahl der Umstiege berücksichtigt als auch die Kosten des Liniennetzes. Dieses Modell deckt wichtige praktische Anforderungen ab, die in einem gemeinsamen Projekt mit den Verkehrsbetrieben in Potsdam (ViP) formuliert wurden. In diesem Projekt wurde der Linienplan 2010 für Potsdam entwickelt. Unsere Berechnungen zeigen, dass die mathematische Optimierung in nichts einer "Handplanung" des Liniennetzes nachsteht. Im Gegenteil, mit Hilfe des Optimierungsprogramms ist es möglich, durch Veränderung der Parameter mehrere verschiedene Szenarien zu berechnen, miteinander zu vergleichen und Aussagen über minimale Kosten und Fahrzeiten zu machen. Y1 - 2011 ER - TY - JOUR A1 - Schlechte, Thomas A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Swarat, Elmar T1 - Micro–macro transformation of railway networks JF - Journal of Rail Transport Planning & Management N2 - In this paper a bottom-up approach of automatic simplification of a railway network is presented. Starting from a very detailed, microscopic level, as it is used in railway simulation, the network is transformed by an algorithm to a less detailed level (macroscopic network), that is sufficient for long-term planning and optimization. In addition running and headway times are rounded to a pre-chosen time discretization by a special cumulative method, which we will present and analyse in this paper. After the transformation we fill the network with given train requests to compute an optimal slot allocation. Then the optimized schedule is re-transformed into the microscopic level and can be simulated without any conflicts occuring between the slots. The algorithm is used to transform the network of the very dense Simplon corridor between Swiss and Italy. With our aggregation it is possible for the first time to generate a profit maximal and conflict free timetable for the corridor across a day by a simultaneously optimization run. Y1 - 2011 U6 - https://doi.org/10.1016/j.jrtpm.2011.09.001 VL - 1 IS - 1 SP - 38 EP - 48 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Workload and busy period for M/GI/1 with a general impatience mechanism JF - Queueing Systems N2 - The paper deals with the workload and busy period for the M/GI/1 system under FCFS discipline, where the customers may become impatient during their waiting for service with generally distributed maximal waiting times and also during their service with generally distributed maximal service times depending on the time waited for service. This general impatience mechanism, originally introduced by Kovalenko (1961) and considered by Daley (1965), too, covers the special cases of impatience on waiting times as well as impatience on sojourn times, for which Boxma et al. (2010), (2011) gave new results and outlined special cases recently. Our unified approach bases on the vector process of workload and busy time. Explicit representations for the LSTs of workload and busy period are given in case of phase-type distributed impatience. Y1 - 2013 U6 - https://doi.org/10.1007/s11134-013-9373-7 VL - 75 IS - 2-4 SP - 189 EP - 209 ER - TY - JOUR A1 - Brandt, Manfred A1 - Brandt, Andreas T1 - Additive functionals with application to sojourn times in infinite-server and processor sharing systems JF - Queueing Systems N2 - We deal with an infinite-server system where the service speed is governed by a stationary and ergodic process with countably many states. Applying a random time transformation such that the service speed becomes one, the sojourn time of a class of virtual requests with given required service time is equal in distribution to an additive functional defined via a stationary version of the time-changed process. Thus bounds for the expectation of functions of additive functionals yield bounds for the expectation of functions of virtual sojourn times, in particular bounds for fractional moments and the distribution function. Interpreting the $GI(n)/GI(n)/\infty$ system or equivalently the $GI(n)/GI$ system under state-dependent processor sharing as an infinite-server system with random states given by the number $n$ of requests in the system provides results for sojourn times of virtual requests. In case of $M(n)/GI(n)/\infty$, the sojourn times of arriving and added requests are equal in distribution to sojourn times of virtual requests in modified systems, which yields many results for the sojourn times of arriving and added requests. In case of integer moments, the bounds generalize earlier results for $M/GI(n)/\infty$. In particular, the mean sojourn times of arriving and added requests in $M(n)/GI(n)/\infty$ are proportional to the required service time, generalizing Cohen's famous result for $M/GI(n)/\infty$. Y1 - 2012 U6 - https://doi.org/10.1007/s11134-012-9282-1 VL - 70 IS - 4 SP - 369 EP - 409 ER - TY - JOUR A1 - Poss, Michael A1 - Raack, Christian T1 - Affine recourse for the robust network design problem: Between static and dynamic routing JF - Networks - Special Issue: INOC 2011 Conference, June 13–16, 2011, Hamburg, Germany N2 - Affinely-Adjustable Robust Counterparts provide tractable alternatives to (two-stage) robust programs with arbitrary recourse. We apply them to robust network design with polyhedral demand uncertainty, introducing the affine routing principle. We compare the affine routing to the well-studied static and dynamic routing schemes for robust network design. All three schemes are embedded into the general framework of two-stage network design with recourse. It is shown that affine routing can be seen as a generalization of the widely used static routing still being tractable and providing cheaper solutions. We investigate properties on the demand polytope under which affine routings reduce to static routings and also develop conditions on the uncertainty set leading to dynamic routings being affine. We show however that affine routings suffer from the drawback that (even totally) dominated demand vectors are not necessarily supported by affine solutions. Uncertainty sets have to be designed accordingly. Finally, we present computational results on networks from SNDlib. We conclude that for these instances the optimal solutions based on affine routings tend to be as cheap as optimal network designs for dynamic routings. In this respect the affine routing principle can be used to approximate the cost for two-stage solutions with free recourse which are hard to compute. Y1 - 2013 U6 - https://doi.org/10.1002/net.21482 VL - 61 IS - 2 SP - 180 EP - 198 ER - TY - JOUR A1 - Berthold, Timo A1 - Gleixner, Ambros T1 - Undercover: a primal MINLP heuristic exploring a largest sub-MIP JF - Mathematical Programming N2 - We present Undercover, a primal heuristic for nonconvex mixed-integer nonlinear programming (MINLP) that explores a mixed-integer linear subproblem (sub-MIP) of a given MINLP. We solve a vertex covering problem to identify a minimal set of variables that need to be fixed in order to linearize each constraint, a so-called cover. Subsequently, these variables are fixed to values obtained from a reference point, e.g., an optimal solution of a linear relaxation. We apply domain propagation and conflict analysis to try to avoid infeasibilities and learn from them, respectively. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. We present computational results on a test set of mixed-integer quadratically constrained programs (MIQCPs) and general MINLPs from MINLPLib. It turns out that the majority of these instances allow for small covers. Although general in nature, the heuristic appears most promising for MIQCPs, and complements nicely with existing root node heuristics in different state-of-the-art solvers. Y1 - 2014 U6 - https://doi.org/10.1007/s10107-013-0635-2 VL - 144 IS - 1-2 SP - 315 EP - 346 ER - TY - JOUR A1 - Hoang, Nam-Dung A1 - Koch, Thorsten T1 - Steiner tree packing revisited JF - Mathematical Methods of Operations Research N2 - The Steiner tree packing problem (STPP) in graphs is a long studied problem in combinatorial optimization. In contrast to many other problems, where there have been tremendous advances in practical problem solving, STPP remains very difficult. Most heuristics schemes are ineffective and even finding feasible solutions is already NP-hard. What makes this problem special is that in order to reach the overall optimal solution non-optimal solutions to the underlying NP-hard Steiner tree problems must be used. Any non-global approach to the STPP is likely to fail. Integer programming is currently the best approach for computing optimal solutions. In this paper we review some “classical” STPP instances which model the underlying real world application only in a reduced form. Through improved modelling, including some new cutting planes, and by emplyoing recent advances in solver technology we are for the first time able to solve those instances in the original 3D grid graphs to optimimality. Y1 - 2012 U6 - https://doi.org/10.1007/s00186-012-0391-8 VL - 76 IS - 1 SP - 95 EP - 123 ER - TY - CHAP A1 - Menne, Ulrich A1 - Raack, Christian A1 - Wessäly, Roland A1 - Kharitonov, Daniel T1 - Optimal Degree of Optical Circuit Switching in IP-over-WDM Networks T2 - Optical Network Design and Modeling (ONDM), 2012 16th International Conference on N2 - In this paper, we study the influence of technology, traffic properties and price trends on optimized design of a reference IP-over-WDM network with rich underlying fiber topology. In each network node, we investigate the optimal degree of traffic switching in an optical (lambda) domain versus an electrical (packet) domain, also known as measure of \emph{node transparency}. This measure is studied in connection to changes in traffic volume, demand affinity, optical circuit speeds and equipment cost. By applying variable design constraints, we assess the relative roles of the two distinct equipment groups, IP routers and optical cross-connects, with respect to resulting changes in cost-sensitive network architectures. Y1 - 2012 U6 - https://doi.org/10.1109/ONDM.2012.6210206 SP - 1 EP - 6 ER - TY - GEN A1 - Wust, Peter A1 - Weihrauch, Mirko A1 - Weiser, Martin A1 - Gellermann, Johanna A1 - Eisenhardt, Steffen A1 - Chobrok, Thorsten A1 - Budach, Volker ED - Dössel, O. ED - Schlegel, W. ED - Magjarevic, R. T1 - Optimization of clinical radiofrequency hyperthermia by use of MR-thermography in a hybrid system T2 - World Congress on Medical Physics and Biomedical Engineering, September 2009, Munich, Germany Y1 - 2010 SP - 174 EP - 175 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin T1 - Einblicke in die diskrete Mathematik JF - Der Mathematikunterricht N2 - „Diskrete Mathematik, was ist das?“, ist eine typische Frage von Lehrern mit traditioneller Mathematikausbildung, denn dort kam und kommt diskrete Mathematik kaum vor. Die etwas Aufgeschlosseneren fragen: „Wenn (schon wieder) etwas Neues unterrichtet werden soll, was soll denn dann im Lehrplan gestrichen werden?“ Auf die zweite Frage wird hier nicht eingegangen. Das Ziel dieses Aufsatzes ist es, in diskrete Mathematik einzuführen, Interesse an diesem Fachgebiet zu wecken und dazu anzuregen, dieses auch im Schulunterricht (ein wenig) zu berücksichtigen. Die Schüler und Schülerinnen werden dafür dankbar sein – eine Erfahrung, die in vielen Unterrichtsreihen gemacht wurde. Y1 - 2012 VL - 58 IS - 2 SP - 4 EP - 17 ER - TY - JOUR A1 - Wilhelms, Mathias A1 - Seemann, Gunnar A1 - Weiser, Martin A1 - Dössel, Olaf T1 - Benchmarking Solvers of the Monodomain Equation in Cardiac Electrophysiological Modeling JF - Biomed. Engineer. Y1 - 2010 U6 - https://doi.org/10.1515/BMT.2010.712 VL - 55 SP - 99 EP - 102 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Deuflhard, Peter ED - Wilson, E. ED - Fitt, A. ED - Ockendon, H. ED - Norbury, J. T1 - On Efficiency and Accuracy in Cardioelectric Simulation T2 - Progress in Industrial Mathematics at ECMI 2008 N2 - Reasons for the failure of adaptive methods to deliver improved efficiency when integrating monodomain models for myocardiac excitation are discussed. Two closely related techniques for reducing the computational complexity of linearly implicit integrators, deliberate sparsing and splitting, are investigated with respect to their impact on computing time and accuracy. Y1 - 2010 SP - 371 EP - 376 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - Neumann, Gerald T1 - 10 Jahre TELOTA JF - Jahrbuch 2011 / Berlin-Brandenburgische Akademie der Wissenschaften N2 - Das TELOTA-Projekt - zunächst nur für zwei Jahre gestartet - feierte am 15. Juni 2011 sein 10-jähriges Bestehen im Rahmen eines Workshops mit einem abschließenden Festvortrag von Richard Stallmann zum Thema „Copyright versus community in the age of computer networks“. Diese Veranstaltung zeigte, wie aktuell die TELOTA-Themen weiterhin sind und dass diese eine große Resonanz in der allgemeinen Öffentlichkeit finden. Die TELOTA-Aktivitäten haben sich als wichtiger Bestandteil der IT-Infrastruktur der BBAW erwiesen, gehen aber weit über reinen Service hinaus. Sie beeinflussen die Forschung selbst und führen zu neuen interessanten wissenschaftlichen Fragestellungen. Der Rückblick auf die ersten zehn Jahre der TELOTA-Initiative in diesem Artikel soll einen kleinen Eindruck von dem geben, was bisher geleistet wurde. Y1 - 2012 SN - 978-3-05-005641-8 SP - 202 EP - 215 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Gollmer, Ralf A1 - Hayn, Christine A1 - Henrion, René A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Mirkov, Radoslava A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Willert, Bernhard T1 - Mathematical optimization for challenging network planning problems in unbundled liberalized gas markets JF - Energy Systems N2 - The recently imposed new gas market liberalization rules in Germany lead to a change of business of gas network operators. While previously network operator and gas vendor were united, they were forced to split up into independent companies. The network has to be open to any other gas trader at the same conditions, and free network capacities have to be identified and publicly offered in a non-discriminatory way. We discuss how these changing paradigms lead to new and challenging mathematical optimization problems. This includes the validation of nominations, that asks for the decision if the network’s capacity is sufficient to transport a specific amount of flow, the verification of booked capacities and the detection of available freely allocable capacities, and the topological extension of the network with new pipelines or compressors in order to increase its capacity. In order to solve each of these problems and to provide meaningful results for the practice, a mixture of different mathematical aspects have to be addressed, such as combinatorics, stochasticity, uncertainty, and nonlinearity. Currently, no numerical solver is available that can deal with such blended problems out-of-the-box. The main goal of our research is to develop such a solver, that moreover is able to solve instances of realistic size. In this article, we describe the main ingredients of our prototypical software implementations. Y1 - 2013 U6 - https://doi.org/10.1007/s12667-013-0099-8 VL - 5 IS - 3 SP - 449 EP - 473 PB - Springer Berlin Heidelberg CY - Berlin ER - TY - GEN A1 - Weiser, Martin T1 - Delayed Residual Compensation for Bidomain Equations T2 - AIP Conference Proceedings N2 - The biodomain model of cardioelectric excitation consists of a reaction‐diffusion equation, an elliptic algebraic constraint, and a set of pointwise ODEs. Fast reaction enforces small time steps, such that for common mesh sizes the reaction‐diffusion equation is easily solved implicitly due to a dominating mass matrix. In contrast, the elliptic constraint does not benefit from small time steps and requires a comparably expensive solution. We propose a delayed residual compensation that improves the solution of the elliptic constraint and thus alleviates the need for long iteration times. Y1 - 2010 U6 - https://doi.org/10.1063/1.3498495 VL - 1281 SP - 419 EP - 422 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Friedow, Isabel A1 - Karbstein, Marika T1 - Optimierung des Linienplans 2010 in Potsdam JF - Der Nahverkehr Y1 - 2012 VL - 30 IS - 4 SP - 34 EP - 39 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Karbstein, Marika A1 - Koch, Thorsten A1 - Martin, Alexander ED - Jünger, Michael ED - Reinelt, Gerhard T1 - How many Steiner terminals can you connect in 20 years? T2 - Facets of Combinatorial Optimization; Festschrift for Martin Grötschel Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38189-8_10 SP - 215 EP - 244 PB - Springer ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Karbstein, Marika ED - Delling, Daniel ED - Liberti, Leo T1 - A Direct Connection Approach to Integrated Line Planning and Passenger Routing T2 - ATMOS 2012 - 12th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems Y1 - 2012 U6 - https://doi.org/http://dx.doi.org/10.4230/OASIcs.ATMOS.2012.47 VL - 25 SP - 47 EP - 57 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika ED - Frigioni, Daniele ED - Stiller, Sebastian T1 - A Configuration Model for the Line Planning Problem T2 - ATMOS 2013 - 13th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems Y1 - 2013 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2013.68 VL - 33 SP - 68 EP - 79 PB - Schloss Dagstuhl--Leibniz-Zentrum für Informatik ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - State Trajectory Compression in Optimal Control JF - PAMM N2 - In optimal control problems with nonlinear time-dependent 3D PDEs, the computation of the reduced gradient by adjoint methods requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. Since the state enters into the adjoint equation, the storage of a 4D discretization is necessary. We propose a lossy compression algorithm using a cheap predictor for the state data, with additional entropy coding of prediction errors. Analytical and numerical results indicate that compression factors around 30 can be obtained without exceeding the FE discretization error. Y1 - 2010 U6 - https://doi.org/10.1002/pamm.201010282 VL - 10 IS - 1 SP - 579 EP - 580 ER - TY - JOUR A1 - Heinz, Stefan A1 - Schlechte, Thomas A1 - Stephan, Rüdiger A1 - Winkler, Michael T1 - Solving steel mill slab design problems JF - Constraints N2 - The steel mill slab design problem from the CSPLIB is a combinatorial optimization problem motivated by an application of the steel industry. It has been widely studied in the constraint programming community. Several methods were proposed to solve this problem. A steel mill slab library was created which contains 380 instances. A closely related binpacking problem called the multiple knapsack problem with color constraints, originated from the same industrial problem, was discussed in the integer programming community. In particular, a simple integer program for this problem has been given by Forrest et al. (INFORMS J Comput 18:129–134, 2006). The aim of this paper is to bring these different studies together. Moreover, we adapt the model of Forrest et al. (INFORMS J Comput 18:129–134, 2006) for the steel mill slab design problem. Using this model and a state-of-the-art integer program solver all instances of the steel mill slab library can be solved efficiently to optimality. We improved, thereby, the solution values of 76 instances compared to previous results (Schaus et al., Constraints 16:125–147, 2010). Finally, we consider a recently introduced variant of the steel mill slab design problem, where within all solutions which minimize the leftover one is interested in a solution which requires a minimum number of slabs. For that variant we introduce two approaches and solve all instances of the steel mill slab library with this slightly changed objective function to optimality. Y1 - 2012 U6 - https://doi.org/10.1007/s10601-011-9113-8 VL - 17 IS - 1 SP - 39 EP - 50 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Omont, Bertrand A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - A Stackelberg game to optimize the distribution of controls in transportation networks T2 - Proceedings of the 3rd International Conference on Game Theory for Networks (GAMENETS 2012) N2 - We propose a game theoretic model for the spatial distribution of inspectors on a transportation network. The problem is to spread out the controls so as to enforce the payment of a transit toll. We formulate a linear program to find the control distribution which maximizes the expected toll revenue, and a mixed integer program for the problem of minimizing the number of evaders. Furthermore, we show that the problem of finding an optimal mixed strategy for a coalition of $N$ inspectors can be solved efficiently by a column generation procedure. Finally, we give experimental results from an application to the truck toll on German motorways. Y1 - 2012 U6 - https://doi.org/http://dx.doi.org/10.1007/978-3-642-35582-0_17 VL - 105 SP - 224 EP - 235 ER - TY - JOUR A1 - Pfetsch, Marc A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Geißler, Nina A1 - Gollmer, Ralf A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Vigerske, Stefan A1 - Willert, Bernhard T1 - Validation of Nominations in Gas Network Optimization: Models, Methods, and Solutions JF - Optimization Methods and Software N2 - In this article we investigate methods to solve a fundamental task in gas transportation, namely the validation of nomination problem: Given a gas transmission network consisting of passive pipelines and active, controllable elements and given an amount of gas at every entry and exit point of the network, find operational settings for all active elements such that there exists a network state meeting all physical, technical, and legal constraints. We describe a two-stage approach to solve the resulting complex and numerically difficult feasibility problem. The first phase consists of four distinct algorithms applying linear, and methods for complementarity constraints to compute possible settings for the discrete decisions. The second phase employs a precise continuous programming model of the gas network. Using this setup, we are able to compute high quality solutions to real-world industrial instances that are significantly larger than networks that have appeared in the mathematical programming literature before. Y1 - 2014 U6 - https://doi.org/10.1080/10556788.2014.888426 PB - Taylor & Francis ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Buwaya, Julia A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - Optimizing Toll Enforcement in Transportation Networks: a Game-Theoretic Approach T2 - Proceedings of INOC'2013 N2 - We present a game-theoretic approach to optimize the strategies of toll enforcement on a motorway network. In contrast to previous approaches, we consider a network with an arbitrary topology, and we handle the fact that users may choose their Origin-Destination path; in particular they may take a detour to avoid sections with a high control rate. We show that a Nash equilibrium can be computed with an LP (although the game is not zero-sum), and we give a MIP for the computation of a Stackelberg equilibrium. Experimental results based on an application to the enforcement of a truck toll on German motorways are presented. Y1 - 2013 U6 - https://doi.org/http://dx.doi.org//10.1016/j.endm.2013.05.100 VL - 41 SP - 253 EP - 260 ER - TY - CHAP A1 - Hildenbrandt, Achim A1 - Reinelt, Gerhard A1 - Heismann, Olga T1 - Integer Programming Models for the Target Visitation Problem T2 - Proceedings of the 16th International Multiconference INFORMATION SOCIETY - IS 2013 N2 - The target visitation problem (TVP) is concerned with finding a route to visit a set of targets starting from and returning to some base. In addition to the distance traveled a tour is evaluated by taking also preferences into account which address the sequence in which the targets are visited. The problem thus is a combination of two well-known combinato- rial optimization problems: the traveling salesman and the linear ordering problem. In this paper we present several possible IP-Models for this problem and compared them to their usability for branch-and-cut approaches. Y1 - 2013 SP - 569 EP - 572 ER - TY - CHAP A1 - Sagnol, Guillaume T1 - Network-related problems in optimal experimental design and second order cone programming T2 - Proceedings of PROBASTAT'2011, Tatra Mountains Mathematical Publications N2 - In the past few years several applications of optimal experimental designs have emerged to optimize the measurements in communication networks. The optimal design problems arising from this kind of applications share three interesting properties: (i) measurements are only available at a small number of locations of the network; (ii) each monitor can simultaneously measure several quantities, which can be modeled by ``multiresponse experiments"; (iii) the observation matrices depend on the topology of the network. In this paper, we give an overview of these experimental design problems and recall recent results for the computation of optimal designs by Second Order Cone Programming (SOCP). New results for the network-monitoring of a discrete time process are presented. In particular, we show that the optimal design problem for the monitoring of an AR1 process can be reduced to the standard form and we give experimental results. Y1 - 2012 U6 - https://doi.org/10.2478/v10127-012-0016-x VL - 51 SP - 161 EP - 171 ER - TY - JOUR A1 - Sagnol, Guillaume T1 - Approximation of a maximum-submodular-coverage problem involving spectral functions, with application to experimental designs JF - Discrete Applied Mathematics N2 - We study a family of combinatorial optimization problems defined by a parameter $p\in[0,1]$, which involves spectral functions applied to positive semidefinite matrices, and has some application in the theory of optimal experimental design. This family of problems tends to a generalization of the classical maximum coverage problem as $p$ goes to $0$, and to a trivial instance of the knapsack problem as $p$ goes to $1$. In this article, we establish a matrix inequality which shows that the objective function is submodular for all $p\in[0,1]$, from which it follows that the greedy approach, which has often been used for this problem, always gives a design within $1-1/e$ of the optimum. We next study the design found by rounding the solution of the continuous relaxed problem, an approach which has been applied by several authors. We prove an inequality which generalizes a classical result from the theory of optimal designs, and allows us to give a rounding procedure with an approximation factor which tends to $1$ as $p$ goes to $1$. Y1 - 2013 U6 - https://doi.org/10.1016/j.dam.2012.07.016 VL - 161 IS - 1-2 SP - 258 EP - 276 ER - TY - JOUR A1 - Sagnol, Guillaume T1 - On the semidefinite representation of real functions applied to symmetric matrices JF - Linear Algebra and its Applications N2 - We present a new semidefinite representation for the trace of a real function f applied to symmetric matrices, when a semidefinite representation of the convex function f is known. Our construction is intuitive, and yields a representation that is more compact than the previously known one. We also show with the help of matrix geometric means and the Riemannian metric of the set of positive definite matrices that for a rational number p in the interval (0,1], the matrix X raised to the exponent p is the largest element of a set represented by linear matrix inequalities. We give numerical results for a problem inspired from the theory of experimental designs, which show that the new semidefinite programming formulation yields a speed-up factor in the order of 10. Y1 - 2013 U6 - https://doi.org/10.1016/j.laa.2013.08.021 VL - 439 IS - 10 SP - 2829 EP - 2843 ER - TY - CHAP A1 - Heismann, Olga A1 - Borndörfer, Ralf T1 - The Random Hypergraph Assignment Problem T2 - Proceedings of the 16th International Multiconference INFORMATION SOCIETY - IS 2013 N2 - The analysis of random instances of a combinatorial optimization problem, especially their optimal values, can provide a better insight into its structure. Such an extensive analysis was theoretically and practically done for the assignment problem ("random assignment problem") and several of its generalizations. For a recent generalization of the assignment problem to bipartite hypergraphs, the hypergraph assignment problem, such results do not exist so far. We consider a random version of the hypergraph assignment problem for the simplest possible complete bipartite hypergraphs. They have only edges and proper hyperedges of size four and follow a special structure, but the hypergraph assignment problem for this type of hypergraphs is, however, already NP-hard. It can be viewed as a combination of two assignment problems. For random hyperedge costs exponentially i.i.d. with mean 1 we show computational results that suggest that the expected value of minimum cost hyperassignments converges to some value around 1.05 with a small standard deviation. The computational results also suggest that the optimal value is most probably attained with half of the maximum possible number of proper hyperedges. The main result of this paper is the proof that the expected value of a minimum cost hyperassignment which uses exactly half the possible maximum number of proper hyperedges if the vertex number tends to infinity lies between 0.3718 and 1.8310 when hyperedge costs are exponentially i.i.d. with mean 1. Y1 - 2013 SP - 599 EP - 602 ER - TY - JOUR A1 - Sagnol, Guillaume T1 - A class of Semidefinite Programs with rank-one solutions JF - Linear Algebra and its Applications N2 - We show that a class of semidefinite programs (SDP) admits a solution that is a positive semidefinite matrix of rank at most $r$, where $r$ is the rank of the matrix involved in the objective function of the SDP. The optimization problems of this class are semidefinite packing problems, which are the SDP analogs to vector packing problems. Of particular interest is the case in which our result guarantees the existence of a solution of rank one: we show that the computation of this solution actually reduces to a Second Order Cone Program (SOCP). We point out an application in statistics, in the optimal design of experiments. Y1 - 2011 U6 - https://doi.org/10.1016/j.laa.2011.03.027 VL - 435 IS - 6 SP - 1446 EP - 1463 ER - TY - JOUR A1 - Langenhan, Andreas A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Schulz, Christof A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Duty Scheduling Templates JF - Proceedings of Conference on Advanced Systems for Public Transport 2012 (CASPT12) N2 - We propose duty templates as a novel concept to produce similar duty schedules for similar days of operation in public transit. Duty templates can conveniently handle various types of similarity requirements, and they can be implemented with ease using standard algorithmic techniques. They have produced good results in practice. Y1 - 2012 ER - TY - CHAP A1 - Heismann, Olga A1 - Borndörfer, Ralf T1 - Minimum Cost Hyperassignments with Applications to ICE/IC Rotation Planning T2 - Operations Research Proceedings 2011 N2 - Vehicle rotation planning is a fundamental problem in rail transport. It decides how the railcars, locomotives, and carriages are operated in order to implement the trips of the timetable. One important planning requirement is operational regularity, i.e., using the rolling stock in the same way on every day of operation. We propose to take regularity into account by modeling the vehicle rotation planning problem as a minimum cost hyperassignment problem (HAP). Hyperassignments are generalizations of assignments from directed graphs to directed hypergraphs. Finding a minimum cost hyperassignment is NP-hard. Most instances arising from regular vehicle rotation planning, however, can be solved well in practice. We show that, in particular, clique inequalities strengthen the canonical LP relaxation substantially. Y1 - 2012 SP - 59 EP - 64 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Buwaya, Julia A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - Network Spot Checking Games: Theory and Application to Toll Enforcing in Transportation Networks N2 - We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. In an SC game, the pure strategies of network users correspond to paths in a graph, and the pure strategies of the inspectors are subset of edges to be controlled. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium is more relevant for this problem, but we show that this is NP-hard. However, we give some bounds on the \emph{price of spite}, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we demonstrate the quality of these bounds for a real-world application, namely the enforcement of a truck toll on German motorways. T3 - ZIB-Report - 14-07 KW - Game Theory KW - Stackelberg Equilibrium KW - Security Games KW - Mixed Integer Programming KW - Price of Anarchy Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-47139 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Maierhofer, Christiane A1 - Richter, Regina ED - Cardone, Gennaro T1 - Data Enhancement for Active Thermography T2 - E-book Proceedings, 11th International Conference on Quantitative Infrared Thermography, Naples N2 - Pulse thermography is a non-destructive testing method based on infrared imaging of transient thermal patterns. Heating the surface of the structure under test for a short period of time generates a non-stationary temperature distribution and thus a thermal contrast between the defect and the sound material. Due to measurement noise, preprocessing of the experimental data is necessary, before reconstruction algorithms can be applied. We propose a decomposition of the measured temperature into Green's function solutions to eliminate noise. Y1 - 2012 ER - TY - JOUR A1 - Blome, Mark A1 - Maurer, HR A1 - Greenhalgh, S. T1 - Geoelectric experimental design — Efficient acquisition and exploitation of complete pole-bipole data sets JF - GEOPHYSICS Y1 - 2011 U6 - https://doi.org/10.1190/1.3511350 VL - 76 IS - 1 SP - F15 EP - F26 ER - TY - CHAP A1 - Blome, Mark A1 - Maurer, H. A1 - Hertrich, M. A1 - Greenhalgh, S. T1 - Experimental design of parallel 3D geoelectric measurements T2 - EAGE Near Surface 2010, Zürich, Switzerland Y1 - 2010 ER - TY - CHAP A1 - Blome, Mark A1 - Maurer, H. T1 - Advances in 3d geoelectric forward solver T2 - 4th International Symposium on Three-Dimensional Electromagnetics, Freiberg Y1 - 2007 ER - TY - JOUR A1 - Plattner, A. A1 - Maurer, H. A1 - Vorloeper, J. A1 - Blome, Mark T1 - 3-D electrical resistivity tomography using adaptive wavelet parameter grids JF - Geophysical Journal International Y1 - 2012 VL - 189 SP - 317 EP - 330 ER - TY - CHAP A1 - Blome, Mark A1 - Maurer, H. T1 - A new boundary-element-based singularity removal approach for geoelectric forward solver T2 - EAGE Near surface, Palermo, Italien Y1 - 2005 ER - TY - JOUR A1 - Reimund, V. A1 - Blome, Mark A1 - Pelkner, M. A1 - Kreutzbruck, M. T1 - Fast defect parameter estimation based on magnetic flux leakage measurements with GMR sensors JF - International Journal of Applied Electromagnetics and Mechanics Y1 - 2011 U6 - https://doi.org/10.3233/JAE-2011-1391 VL - 37 IS - 2-3 SP - 199 EP - 205 ER - TY - CHAP A1 - Pelkner, M. A1 - Blome, Mark A1 - Reimund, V. A1 - Thomas, H.-M. A1 - Kreutzbruck, M. T1 - Flux Leakage Measurements for Defect Characterization Using a High Precision 3-AXIAL Gmr Magnetic Sensor T2 - AIP Conference Proceedings Y1 - 2011 VL - 1335 SP - 380 EP - 387 ER - TY - CHAP A1 - Blome, Mark A1 - Reimund, V. A1 - Kreutzbruck, M. T1 - Fast defect-shape reconstruction based on magnetic flux leakage measurements with GMR sensors T2 - XI-th International Workshop on Optimization and Inverse Problems in Electromagnetism, Sophia, Bulgaria Y1 - 2010 ER - TY - JOUR A1 - Ranneberg, Maximilian A1 - Weiser, Martin A1 - Weihrauch, Mirko A1 - Budach, Volker A1 - Gellermann, Johanna A1 - Wust, Peter T1 - Regularized Antenna Profile Adaptation in Online Hyperthermia Treatment JF - Medical Physics Y1 - 2010 U6 - https://doi.org/10.1118/1.3488896 VL - 37 SP - 5382 EP - 5394 ER - TY - JOUR A1 - Weiser, Martin A1 - Röllig, Mathias A1 - Arndt, Ralf A1 - Erdmann, Bodo T1 - Development and test of a numerical model for pulse thermography in civil engineering JF - Heat and Mass Transfer N2 - Pulse thermography of concrete structures is used in civil engineering for detecting voids, honeycombing and delamination. The physical situation is readily modeled by Fourier's law. Despite the simplicity of the PDE structure, quantitatively realistic numerical 3D simulation faces two major obstacles. First, the short heating pulse induces a thin boundary layer at the heated surface which encapsulates all information and therefore has to be resolved faithfully. Even with adaptive mesh refinement techniques, obtaining useful accuracies requires an unsatisfactorily fine discretization. Second, bulk material parameters and boundary conditions are barely known exactly. We address both issues by a semi-analytic reformulation of the heat transport problem and by parameter identification. Numerical results are compared with measurements of test specimens. Y1 - 2010 VL - 46 IS - 11-12 SP - 1419 EP - 1428 ER - TY - JOUR A1 - Blome, Mark A1 - Maurer, H R A1 - Schmidt, K. T1 - Advances in three-dimensional geoelectric forward solver techniques JF - Geophysical Journal International Y1 - 2009 U6 - https://doi.org/10.1111/j.1365-246X.2008.04006.x VL - 176 IS - 3 SP - 740 EP - 752 ER - TY - GEN A1 - Schiela, Anton A1 - Weiser, Martin ED - Diehl, M. ED - Glineur, F. ED - Jarlebring, E. ED - Michiels, W. T1 - Barrier methods for a control problem from hyperthermia treatment planning T2 - Recent Advances in Optimization and its Applications in Engineering (Proceedings of 14th Belgian-French-German Conference on Optimization 2009) N2 - We consider an optimal control problem from hyperthermia treatment planning and its barrier regularization. We derive basic results, which lay the groundwork for the computation of optimal solutions via an interior point path-following method. Further, we report on a numerical implementation of such a method and its performance at an example problem. Y1 - 2010 SP - 419 EP - 428 PB - Springer ER - TY - GEN A1 - Günther, Andreas A1 - Lamecker, Hans A1 - Weiser, Martin ED - Pennec, X. ED - Joshi, S. ED - Nielsen, M. T1 - Direct LDDMM of Discrete Currents with Adaptive Finite Elements T2 - Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability N2 - We consider Large Deformation Diffeomorphic Metric Mapping of general $m$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete $m$-current attributes. Y1 - 2011 SP - 1 EP - 14 ER - TY - JOUR A1 - Weiser, Martin A1 - Götschel, Sebastian T1 - State Trajectory Compression for Optimal Control with Parabolic PDEs JF - SIAM J. Sci. Comput. N2 - In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and quasi-Newton methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy coding maintaining an error bound is sufficient. Y1 - 2012 U6 - https://doi.org/10.1137/11082172X VL - 34 IS - 1 SP - A161 EP - A184 ER - TY - JOUR A1 - Weiser, Martin T1 - Faster SDC convergence on non-equidistant grids by DIRK sweeps JF - BIT Numerical Mathematics N2 - Spectral deferred correction methods for solving stiff ODEs are known to converge rapidly towards the collocation limit solution on equidistant grids, but show a much less favourable contraction on non-equidistant grids such as Radau-IIa points. We interprete SDC methods as fixed point iterations for the collocation system and propose new DIRK-type sweeps for stiff problems based on purely linear algebraic considerations. Good convergence is recovered also on non-equidistant grids. The properties of different variants are explored on a couple of numerical examples. Y1 - 2015 U6 - https://doi.org/10.1007/s10543-014-0540-y VL - 55 IS - 4 SP - 1219 EP - 1241 ER - TY - GEN A1 - Schütte, Christof A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Markov State Models and Molecular Alchemy N2 - In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic ex- periments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multi- valent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular proper- ties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective en- ergy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed. T3 - ZIB-Report - 14-05 KW - Girsanov Theorem KW - Stochastic Differential Equation KW - Importance Sampling Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-46718 SN - 1438-0064 ER - TY - BOOK A1 - Dieter, H. H. A1 - Götz, K. A1 - Kümmerer, K. A1 - Rechenberg, B. A1 - Keil, F. ED - Dieter, H.H. ED - Götz, K. ED - Kümmerer, K. ED - Rechenberg, B. ED - Keil, F. T1 - Handlungsmöglichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren Rückständen in das Roh- und Trinkwasser. Y1 - 2010 PB - Umweltbundesamt ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Schiela, Anton ED - Dedner, A. ED - Flemisch, B. ED - Klöfkorn, R. T1 - Solving Optimal Control Problems with the Kaskade 7 Finite Element Toolbox T2 - Advances in DUNE N2 - This paper presents concepts and implementation of the finite element toolbox Kaskade 7, a flexible C++ code for solving elliptic and parabolic PDE systems. Issues such as problem formulation, assembly and adaptivity are discussed at the example of optimal control problems. Trajectory compression for parabolic optimization problems is considered as a case study. Y1 - 2012 SP - 101 EP - 112 PB - Springer ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Local Refinements in Classical Molecular Dynamics Simulations JF - J. Phys. Conf. Ser. Y1 - 2014 VL - 490 SP - 012016 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Schiela, Anton A1 - Weiser, Martin T1 - Mathematical Cancer Therapy Planning in Deep Regional Hyperthermia JF - Acta Numerica N2 - This paper surveys the required mathematics for a typical challenging problem from computational medicine, the cancer therapy planning in deep regional hyperthermia. In the course of many years of close cooperation with clinics, the medical problem gave rise to quite a number of subtle mathematical problems, part of which had been unsolved when the common project started. Efficiency of numerical algorithms, i.e. computational speed and monitored reliability, play a decisive role for the medical treatment. Off-the-shelf software had turned out to be not sufficient to meet the requirements of medicine. Rather, new mathematical theory as well as new numerical algorithms had to be developed. In order to make our algorithms useful in the clinical environment, new visualization software, a virtual lab, including 3D geometry processing of individual virtual patients had to be designed and implemented. Moreover, before the problems could be attacked by numerical algorithms, careful mathematical modelling had to be done. Finally, parameter identification and constrained optimization for the PDEs had to be newly analyzed and realized over the individual patient's geometry. Our new techniques had an impact on the specificity of the individual patients' treatment and on the construction of an improved hyperthermia applicator. Y1 - 2012 VL - 21 SP - 307 EP - 378 ER - TY - JOUR A1 - Weiser, Martin T1 - On goal-oriented adaptivity for elliptic optimal control problems JF - Opt. Meth. Softw. N2 - The paper proposes goal-oriented error estimation and mesh refinement for optimal control problems with elliptic PDE constraints using the value of the reduced cost functional as quantity of interest. Error representation, hierarchical error estimators, and greedy-style error indicators are derived and compared to their counterparts when using the all-at-once cost functional as quantity of interest. Finally, the efficiency of the error estimator and generated meshes are demonstrated on numerical examples. Y1 - 2013 VL - 28 IS - 13 SP - 969 EP - 992 ER - TY - JOUR A1 - Bujotzek, Alexander A1 - Schütt, Ole A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling JF - Journal of Mathematical Chemistry Y1 - 2014 U6 - https://doi.org/10.1007/s10910-013-0265-1 VL - 52 IS - 3 SP - 781 EP - 804 ER - TY - JOUR A1 - Günther, Andreas A1 - Lamecker, Hans A1 - Weiser, Martin T1 - Flexible Shape Matching with Finite Element Based LDDMM JF - International Journal of Computer Vision N2 - We consider Large Deformation Diffeomorphic Metric Mapping of general $m$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete $m$-current attributes. Y1 - 2013 U6 - https://doi.org/10.1007/s11263-012-0599-3 VL - 105 IS - 2 SP - 128 EP - 143 ER - TY - JOUR A1 - Shan, Min A1 - Bujotzek, Alexander A1 - Abendroth, Frank A1 - Seitz, Oliver A1 - Weber, Marcus A1 - Haag, Rainer T1 - Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding JF - ChemBioChem, 12(17) Y1 - 2011 U6 - https://doi.org/10.1002/cbic.201100529 SP - 2587 EP - 2598 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, O. A1 - Weber, Marcus T1 - Soft Versus Hard Metastable Conformations in Molecular Simulations JF - Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.) Y1 - 2011 SP - 899 EP - 909 ER - TY - JOUR A1 - Weber, Marcus T1 - Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization JF - XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series Y1 - 2013 SP - 147 EP - 157 ER - TY - JOUR A1 - Shan, Min A1 - Carlson, Kathryn E. A1 - Bujotzek, Alexander A1 - Wellner, Anja A1 - Gust, Ronald A1 - Weber, Marcus A1 - Katzenellenbogen, John A. A1 - Haag, Rainer T1 - Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor JF - ACS Chem. Biol. Y1 - 2013 VL - 8 IS - 4 SP - 707 EP - 715 ER - TY - JOUR A1 - Tyagi, Rahul A1 - Malhotra, Shashwat A1 - Thünemann, Andreas F. A1 - Sedighi, Amir A1 - Weber, Marcus A1 - Schäfer, Andreas A1 - Haag, Rainer T1 - Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles JF - J. Phys. Chem. C Y1 - 2013 VL - 117 IS - 23 SP - 12307 EP - 12317 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Schmidt, Sebastian A1 - Sabri, Peggy A1 - Piechotta, Christian A1 - Weber, Marcus T1 - A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens JF - Journal of Chemical Information and Modeling Y1 - 2013 VL - 53 IS - 10 SP - 2681 EP - 2688 ER - TY - JOUR A1 - Scharkoi, Olga A1 - Esslinger, Susanne A1 - Becker, Roland A1 - Weber, Marcus A1 - Nehls, Irene T1 - Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane JF - Molecular Simulation Y1 - 2014 U6 - https://doi.org/10.1080/08927022.2014.898845 ER - TY - JOUR A1 - Scharkoi, O. A1 - Esslinger, Susanne A1 - Becker, Roland A1 - Weber, Marcus A1 - Nehls, Irene T1 - Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites JF - Organohalogen Compounds Y1 - 2011 VL - 73 SP - 730 EP - 733 ER - TY - JOUR A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An optimal control problem in polyconvex hyperelasticity JF - SIAM J. Control Opt. N2 - We consider a shape implant design problem that arises in the context of facial surgery. We introduce a reformulation as an optimal control problem, where the control acts as a boundary force. The state is modelled as a minimizer of a polyconvex hyperelastic energy functional. We show existence of optimal solutions and derive - on a formal level - first order optimality conditions. Finally, preliminary numerical results are presented. Y1 - 2014 U6 - https://doi.org/10.1137/120876629 VL - 52 IS - 3 SP - 1403 EP - 1422 ER - TY - JOUR A1 - Andrae, Karsten A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Scharkoi, Olga A1 - Weber, Marcus T1 - Medizin aus dem Computer JF - Der Anaesthesist Y1 - 2013 U6 - https://doi.org/10.1007/s00101-013-2202-x VL - 62 IS - 7 SP - 561 EP - 557 PB - Springer ER - TY - THES A1 - Nielsen, Adam T1 - Von Femtosekunden zu Minuten Y1 - 2012 UR - http://www.zib.de/nielsen/Masterarbeit.pdf ER - TY - JOUR A1 - Haack, Fiete A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Weber, Marcus A1 - Schmidt, Burkhard T1 - Adaptive spectral clustering with application to tripeptide conformation analysis JF - The Journal of Chemical Physics Y1 - 2013 U6 - https://doi.org/10.1063/1.4830409 VL - 139 SP - 110 EP - 194 ER - TY - THES A1 - Lockau, Daniel T1 - Optical modeling of thin film silicon solar cells with random and periodic light management textures Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-38759 ER - TY - THES A1 - Kettner, Benjamin T1 - Detection of spurious modes in resonance mode computations Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000038256-7 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000038256 ER - TY - THES A1 - Pomplun, Jan T1 - Reduced basis method for electromagnetic scattering problems Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000017571-3 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000017571 ER - TY - JOUR A1 - Tsarev, Sergey A1 - Wolf, Thomas T1 - Hyperdeterminants as integrable discrete systems JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2009 U6 - https://doi.org//10.1088/1751-8113/42/45/454023 VL - 42 ER - TY - JOUR A1 - Neun, Winfried A1 - Sturm, Thomas A1 - Vigerske, Stefan T1 - Supporting Global Numerical Optimization of Rational Functions by Generic Symbolic Convexity Tests JF - Computer Algebra in Scientific Computing Y1 - 2010 SN - 978-3-642-15273-3 VL - LNCS 6244 SP - 205 EP - 219 ER - TY - JOUR A1 - Wolf, Thomas T1 - Positions in the Game of Go as Complex Systems JF - Proceedings of 2009 IEEE Toronto International Conference (TIC-STH 2009) - Science and Technology for Humanity Y1 - 2009 SN - 978-1-4244-3878-5 ER - TY - JOUR A1 - Hussin, V. A1 - Kiselev, A. V. A1 - Krutov, A.O. A1 - Wolf, Thomas T1 - N=2 Supersymmetric a=4 - Korteweg-de Vries hierarchy derived via Gardner's deformation of Kaup-Bousinesq equation JF - Journal of Mathematical Physics Y1 - 2010 U6 - https://doi.org/10.1063/1.3447731 VL - 51 ER - TY - JOUR A1 - Wolf, Thomas T1 - A Dynamical Systems Approach for Static Evaluation in Go JF - Computational Intelligence and AI in Games, IEEE Transactions on N2 - In the paper, arguments are given as to why the concept of static evaluation has the potential to be a useful extension to Monte Carlo tree search. A new concept of modeling static evaluation through a dynamical system is introduced and strengths and weaknesses are discussed. The general suitability of this approach is demonstrated. Y1 - 2011 U6 - https://doi.org/10.1109/TCIAIG.2011.2141669 VL - 3 IS - 2 SP - 129 EP - 141 ER - TY - JOUR A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Symmetry analysis and exact solutions of semilinear heat flow in multi-dimensions JF - Journal of Mathematical Analysis and Applications Y1 - 2011 U6 - https://doi.org/10.1016/j.jmaa.2011.01.073 VL - 379 IS - 2 SP - 748 EP - 763 ER - TY - JOUR A1 - Wolf, Thomas A1 - Efimovskaya, Olga T1 - On Integrability of the Kontsevich Non-Abelian ODE System JF - Letters in Mathematical Physics Y1 - 2012 U6 - https://doi.org/10.1007/s11005-011-0527-4 VL - 100 IS - 2 SP - 161 EP - 170 ER - TY - JOUR A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Exact Solutions of Nonlinear Partial Differential Equations by the Method of Group Foliation Reduction JF - SIGMA 7 N2 - A novel symmetry method for finding exact solutions to nonlinear PDEs is illustrated by applying it to a semilinear reaction-diffusion equation in multi-dimensions. The method uses a separation ansatz to solve an equivalent first-order group foliation system whose independent and dependent variables respectively consist of the invariants and differential invariants of a given one-dimensional group of point symmetries for the reaction-diffusion equation. With this group-foliation reduction method, solutions of the reaction-diffusion equation are obtained in an explicit form, including group-invariant similarity solutions and travelling-wave solutions, as well as dynamically interesting solutions that are not invariant under any of the point symmetries admitted by this equation. Y1 - 2011 U6 - https://doi.org/10.3842/SIGMA.2011.066 ER - TY - JOUR A1 - Anco, Stephen A1 - Mohiuddin, Mohammad A1 - Wolf, Thomas T1 - Traveling waves and conservation laws for complex mKdV-type equations Y1 - 2012 U6 - https://doi.org/10.1016/j.amc.2012.06.061 VL - 219 IS - 2 SP - 679 EP - 698 ER - TY - JOUR A1 - Euler, Marianna A1 - Euler, Norbert A1 - Wolf, Thomas T1 - The Two-Component Camassa-Holm Equations CH(2,1) and CH(2,2): First-Order Integrating Factors and Conservation Laws JF - Journal of Nonlinear Mathematical Physics N2 - Recently, Holm and Ivanov, proposed and studied a class of multi-component generalizations of the Camassa–Holm equations [D. D. Holm and R. I. Ivanov, Multi-component generalizations of the CH equation: geometrical aspects, peakons and numerical examples, J. Phys A: Math. Theor. 43 (2010) 492001 (20pp)]. We consider two of those systems, denoted by Holm and Ivanov by CH(2,1) and CH(2,2), and report a class of integrating factors and its corresponding conservation laws for these two systems. In particular, we obtain the complete set of first-order integrating factors for the systems in Cauchy–Kovalevskaya form and evaluate the corresponding sets of conservation laws for CH(2,1) and CH(2,2). Y1 - 2013 U6 - https://doi.org/10.1142/S1402925112400025 VL - 19 IS - 1 SP - 13 EP - 22 ER - TY - JOUR A1 - Wolf, Thomas A1 - Schrüfer, Eberhard A1 - Webster, Kenneth T1 - Solving large linear algebraic systems in the context of integrable non-abelian Laurent ODEs JF - Programming and Computer Software Y1 - 2012 U6 - https://doi.org/10.1134/S0361768812020065 SN - 0361-7688 VL - 38 IS - 2 SP - 73 EP - 83 ER - TY - JOUR A1 - Anco, Stephen A1 - MacNaughton, Steven A. A1 - Wolf, Thomas T1 - Conservation laws and symmetries of quasilinear radial wave equations in multi-dimensions JF - Journal of Mathematical Physics Y1 - 2012 U6 - https://doi.org/10.1063/1.4711814 VL - 53 IS - 5 ER - TY - JOUR A1 - Odesskii, Alexander A1 - Wolf, Thomas T1 - Compatible quadratic Poisson brackets related to a family of elliptic curves JF - Journal of Geometry and Physics Y1 - 2013 SN - 0393-0440 VL - 63 IS - 0 SP - 107 EP - 117 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Maierhofer, Christiane A1 - Richter, Regina A1 - Röllig, Mathias T1 - Fast Defect Shape Reconstruction Based on the Travel Time in Pulse Thermography JF - Nondestructive Testing of Materials and Structures Y1 - 2013 VL - 6 SP - 83 EP - 89 ER - TY - THES A1 - Meisel, Kristin T1 - Mathematische Modellierung der Knochenremodellierung Y1 - 2012 ER - TY - THES A1 - Berg, Mascha T1 - Laufzeitoptimierung der Robusten Perron Cluster Analyse (PCCA+) Y1 - 2012 ER - TY - THES A1 - Knöchel, Jane T1 - Mathematische Modellierung metabolischer Einflussfaktoren auf den Milchkuhzyklus N2 - In den letzten Jahren ist die reproduktive Leistung von Milchkühen parallel zur steigenden Milchleistung drastisch gesunken. Um die zu Grunde liegenden biologischen Mechanismen besser zu verstehen, wurde in dieser Arbeit eine Modellerweiterung des vorhandenen Modells von Stötzel et al. (2011) um metabolische Einflussfaktoren angestrebt. Hierfür wurde zuerst aus veröffentlichten, experimentell gewonnen Erkenntnissen herausgearbeitet, wie die metabolischen Faktoren auf das periodische Zyklusverfahren der Milchkuh Einfluss nehmen. Daraus wurde ersichtlich, dass Glukose, Insulin und IGF-I die wichtigsten metabolischen Faktoren sind, aber lediglich IGF-I als dynamische Größe in das Modell eingeht. Zur Validierung des erweiterten Modells, wurden im Rahmen dieser Arbeit Szenarien aus der Literatur entwickelt, welche eine negative Energiebilanz oder den Effekt von Diätrestriktionen auf den Milchkuhzyklus simulieren sollten. Ferner wurden Messdaten für IGF, E2 und P4 von Kawashima et al. (2007) und Cerri et al. (2011) bereit gestellt. Das erweiterte Modell umfasst lediglich 8 Parameter mehr als das Ursprungsmodell, wobei gezeigt werden konnte, dass weder die Bedingung für die Lösbarkeit noch die Stabilität in den Anfangswerten eingebüßt wurde. Die Modellkurven konnten mittels des NLSCON erfolgreich an die bereitgestellten Messdaten für IGF, E2 und P4 angepasst werden. Anhand der Ergebnisse aus den Szenarien ließ sich zeigen, dass es teilweise gelingt über die metabolischen Einflussfaktoren eine negative Energiebilanz für unterernährte Kühe darzustellen. Die Rückführung in das periodische Zyklusverhalten verlief jedoch im Vergleich zu in vivo Beobachtungen zu schnell ab. Eine mögliche Erklärung hierfür ist ein zu geringer Einfluss von IGF-I auf das Modell. Darüber hinaus kam es trotz (stark) reduzierter LH-Konzentration zur Ovulation. Auf diesen Erkenntnissen aufbauend könnte in Zukunft die Follikelmodellierung modifiziert oder die Hillfunktion, die die Ovulation darstellt, überarbeitet werden. N2 - During the last few years there has been a drastic decline in the fertility of dairy cows. Therefore the goal of this work is to identify the underlying mechanisms for this problem by extending the model from Stötzel et al. (2011) to include the influence of metabolic factors. For this purpose the influence of the metabolic factors was determined based on published, experimentally obtained findings. The important metabolic factors were glucose, insulin and IGF-I, but only IGF-I was shown to be dynamic over the course of a cycle and therefore implemented into the model. To validate the chosen model extension we developed scenarios from the literature in order to simulate the impact of negative energy balance as well as the effect of diet restrictions on the bovine oestrous cycle. Furthermore we got measurement data from Kawashima et al. (2007) and Cerri et al. (2011) for IGF, E2 and P4. The new model has just 8 parameters more, while maintaining the same solvability and stability in the initial values. It was possible to fit the model with the use of NLSCON to the measurement data for IGF, E2 and P4. In addition the scenarios allowed us to show that the model is able to simulate a negative energy balance in parts. Merely the return into the cyclic behaviour was faster than observed in vivo. One possible explanation would be, that the influence of IGF-I on the model is not strong enough. The model showed a deficit while simulating the scenarios since a marked reduction of the LH concentration still led to ovulation. Thus future research could be done in this direction, where it would probably be necessary to modify the follicle function or the hill function responsible for ovulation. KW - Systembiologie Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-46170 N1 - Diplomarbeit ER - TY - THES A1 - Brüggemann, Jo Andrea T1 - Numerical Modelling of the human menstrual cycle applied to ovulation prediction N2 - In this Master Thesis, the modelling process and the required biological background to adequately describe the hormonal dynamics of the human menstrual cycle are presented. The aim of this Master thesis project is to establish a mathematical routine that enables prediction of potentially fertile time windows. A system of four parameter dependent ordinary differential equations coupled with two algebraic equations is built, accounting for the main kinetic drivers of the human menstrual cycle { basal body temperature, estradiol, progesterone, luteinizing and follicle stimulating hormone. The key parameters are identifed using a nonlinear least squares approach to match the model to individual data. Aiming to solve the optimality problem arising, the Newton and Gauss-Newton method are examined and their local convergence theory is outlined. By the nature of the application, a globalised Gauss-Newton method seems more convenient. An adaptive trust region approach to determine the step lengths is chosen, which together with an linearly-implicit Euler extrapolation for the given differential algebraic equation system makes parameter estimation possible. The simulation results are discussed particularly in view of limitations and problems arising through the modelling approach. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-46168 ER - TY - JOUR A1 - Röblitz, Susanna A1 - Weber, Marcus T1 - Fuzzy Spectral Clustering by PCCA+ JF - Classification and Clustering: Models, Software and Applications Y1 - 2009 UR - http://www.wias-berlin.de/publications/wias-publ/run.jsp?template=abstract&type=Report&year=2009&number=26 IS - WIAS Report No. 26 SP - 73 EP - 79 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Nagaiah, Chamakuri A1 - Kunisch, Karl A1 - Weiser, Martin T1 - Lossy Compression in Optimal Control of Cardiac Defibrillation JF - J. Sci. Comput. N2 - This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples. Y1 - 2014 U6 - https://doi.org/10.1007/s10915-013-9785-x VL - 60 IS - 1 SP - 35 EP - 59 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Röblitz, Susanna A1 - Stötzel, Claudia T1 - Mathematical Systems Biology at Zuse Institute Berlin (ZIB) JF - BioTOPics - Journal of Biotechnology in Berlin-Brandenburg Y1 - 2010 VL - 39 ER - TY - CHAP A1 - Götschel, Sebastian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad A1 - Weiser, Martin ED - Carraro, T. ED - Geiger, M. ED - Koerkel, S. ED - Rannacher, R. T1 - Reducing Memory Requirements in Scientific Computing and Optimal Control T2 - Multiple Shooting and Time Domain Decomposition Methods Y1 - 2015 SP - 263 EP - 287 PB - Springer ER - TY - JOUR A1 - Lügger, Joachim T1 - Zum Nutzen des Web 2.0 für „Die kleine Kollaboration“ in den Wissenschaften JF - ABI Technik -- Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen N2 - Gemeinsame Web-Auftritte zu organisieren, die sich über mehrere Institutionen und Fachgebiete erstrecken, ist eine anspruchsvolle und faszinierende Aufgabe, die auf verschiedene Weise gelingen, aber auch scheitern kann. Wer sich daran versucht, tut gut daran, sich über bestimmte Prinzipien und technische Mittel zu informieren, die das fortgeschrittene Web ihm heute bietet. Das Internet, das World Wide Web und das moderne Web 2.0 sind in einer fast zwanzig Jahre dauernden Kollaboration einer globalen Gemeinschaft von Entwicklern und Anwendern entstanden. Es enthält heute eine Fülle sofort einsetzbarer Komponenten, von der „Benutzerdefinierten Google-Suche Beta“ mit Google‘s PageRanking auf ausgewählten Web-Seiten bis hin zum automatisierten Web-Server mit Content-Management für das „Mitmach-Web“. Der Artikel stellt nur eine kleine Auswahl solcher Lösungen vor und macht den Versuch, einige Prinzipien des Web 2.0 so herauszuarbeiten, dass die notwendige Kommunikation zwischen Managern, Technikern, Redakteuren und Organisatoren in der kleinen Kollaboration unterstützt wird. „Kleine Kollaboration“ bedeutet hier, dass es nicht um die globale Vernetzung von technischen Großgeräten der e-Science gehen soll, auch nicht um die Super-Suchmaschine in Europa, sondern um die Unterstützung der Zusammenarbeit und Kommunikation von Wissenschaftlern und Museumsfachleuten mit Ihren Nutzern. Y1 - 2009 SN - 2191-4664 VL - 29 IS - 1 SP - 1 EP - 11 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Veränderungen der Publikations- und Kommunikationswelt: Open Access, Google, etc. JF - Gegenworte: Hefte für den Disput über Wissen N2 - Beim Schreiben dieses Artikels, der auf Veränderungen der Kommunikations- und Publikationstechniken und ihre Bedeutung hinweist, ist uns mehr als je zuvor bewusst geworden, wie beschränkt das Medium Papier ist. Es gibt z. B. keine Hyperlinks, durch die man unmittelbar das Erwähnte erleben oder überprüfen kann. Ein schneller Wechsel vom Wort zum Bild, zum Ton oder Video ist nicht möglich. Wer will schon lange URLs abtippen und Medienbrüche erleiden? Wir haben uns daher entschlossen, eine textidentische Version dieses Artikels mit allen URLs – sie liegt Ihnen hier vor – elektronisch anzubieten und in der für die "Gegenworte" (BBAW) gekürzten Fassung nur durch [URL] anzudeuten, dass der Leser an dieser Stelle einfach in der elektronischen Version einen Klick ins Internet machen sollte. Und damit sind wir bereits mitten im Thema. Y1 - 2009 VL - 21 IS - 21 SP - 69 EP - 72 ER - TY - CHAP A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Heller, Markus O. T1 - An imageless method to quantify the Mechanical Femoral-Tibial Angle (MFTA) using functionally defined joint centers and axes. T2 - 6th Annual meeting of the German Society for Biomechanics (DGfB) Y1 - 2009 ER - TY - CHAP A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Heller, Markus O. T1 - Frontal plane lower limb alignment using functionally determined joint centers and axes T2 - International Conference on Computational Bioengineering Y1 - 2009 ER - TY - GEN A1 - Kuberek, Monika ED - Föhl, Patrick S. ED - Neisener, Iken T1 - Strategien für die Zukunft der regionalen Informationsinfrastruktur - der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) T2 - Regionale Kooperationen im Kulturbereich. Theoretische Grundlagen und Praxisbeispiele N2 - Eines der Hauptanliegen bei der Initiierung des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) war die Schaffung einer modernen, leistungsfähigen Informationsinfrastruktur unter Einbeziehung möglichst aller Bibliotheken der in ihrer Dichte und Vielfalt in Deutschland einmaligen Bibliothekslandschaft. Sie wurde beim Aufbau des KOBV durch die Wahl des Verbundmodelles mit seinen offenen, integrativen Strukturen befördert. Die Ziele und Strategien des KOBV leiten sich aus dem Grundauftrag der Bibliotheken her, ihre NutzerInnen optimal mit Medien und Informationen zu versorgen. Mit dem KOBV haben die Bibliotheken eine gemeinsame Plattform und ein regionales Netzwerk geschaffen, mit deren Hilfe sie die Informationsinfrastruktur in Berlin und Brandenburg zusammen aufgebaut und grundlegend verbessert haben. Nach rund elf Jahren ist der KOBV in eine neue Phase eingetreten, indem er – unter Wahrung seiner institutionellen Eigenständigkeit – eine Strategische Allianz mit dem Bibliotheksverbund Bayern (BVB) eingegangen ist und die bislang auf die Region bezogene Kooperation der Bibliotheken überregional ausgeweitet hat. Wenn auch die Universalbibliotheken des KOBV in dieser Zusammenarbeit einen Kurswechsel zur zentralen Katalogisierung vollziehen, bedeutet dies für den KOBV insgesamt keinen Paradigmenwechsel: Er bleibt ein dezentraler Verbund und wird sein flexibles technisches Mischkonzept von verteilter und zentraler Datenhaltung fortführen. Dieses lässt den Bibliotheken die Freiheit zu entscheiden, ob sie zentral oder dezentral katalogisieren möchten. Die KOBV-Zentrale, die im KOBV keine Aufgaben in der Katalogisierung wahrnimmt, wird wie bislang allen Mitgliedsbibliotheken die ASP-Dienste und weiteren Angebote gleichermaßen zur Verfügung stellen und die Dienstleistungen für NutzerInnen und Bibliotheken weiter ausbauen. Mit dem vorhandenen Know How, der eingesetzten modernen Technologie und der strategischen Entscheidung, Ressourcen und Kompetenzen mit dem BVB zu bündeln und durch verbundübergreifende arbeitsteilige Verfahren Synergien zu gewinnen, ist der KOBV gut aufgestellt, um die Herausforderungen der kommenden Jahre anzugehen und das Leistungsspektrum der KOBV-Bibliotheken durch die Entwicklung neuer Dienste auszuweiten. Y1 - 2009 SN - ISBN 978-3-8376-1050-5 SP - 251 EP - 259 ER - TY - CHAP A1 - Gottwald, Susanne A1 - Tolksdorf, Robert T1 - Planning Teams with Semantic Web Technologies T2 - INFORMATIK 2009 - Im Focus das Leben N2 - When planning teams for projects with specific goals, employees of a company have to group together so well, that all necessary knowledge for conquering the project’s challenges are met within the member’s skills. A tool that facilitates semantic web technologies can support the team recruiter, who is responsible for chosing the members of the team, in terms of finding the most efficient combinations of the company’s employees based on their expertises. Y1 - 2009 SN - ISBN 978-3-88579-248-2 SN - ISSN 1617-5468 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - E - Learning and the Working Mathematician T2 - Grundfragen Multimedialen Lehrens und Lernens - Tagungsband GML 2009 N2 - Eigentlich war der erste Autor nur zu einem Grußwort zur Tagung „GML 2009 - Grundfragen Multimedialen Lehrens und Lernens“ eingeladen. Aber wie es bei der Vorbereitung zu solchen „Auftritten“ manchmal so kommt, wurde daraus ein E-Learning-bezogener Vortrag, der – basierend auf Erfahrungen im Fach Mathematik – einen kritischen Blick auf die E-Learning-Szene in Deutschland wirft und diese mit entsprechenden Aktivitäten weltweit vergleicht. Dies ist die in seinen mathematischen Teilen gekürzte, in den E-Learning-Anteilen ein wenig erweiterte schriftliche Fassung des Vortrags. Y1 - 2009 SN - ISBN 978 - 3 - 7983 - 2143 - 4 SP - 8 EP - 27 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy Compression for PDE-constrained Optimization: Adaptive Error Control JF - Comput. Optim. Appl. N2 - For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the ad-joint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances. Y1 - 2015 VL - 62 IS - 1 SP - 131 EP - 155 PB - Springer ER - TY - THES A1 - Lehmann, Felix T1 - Inexaktheit in Newton-Lagrange-Verfahren für Optimierungsprobleme mit Elliptischen PDGL-Nebenbedingungen N2 - Bei der numerischen Lösung von Optimalsteuerungsproblemen mit elliptischen partiellen Differentialgleichungen als Nebenbedingung treten unvermeidlich Diskretisierungs- und Iterationsfehler auf. Man ist aus Aufwandsgründen daran interessiert die dabei entstehenden Fehler nicht sehr klein wählen zu müssen. In der Folge werden die linearisierten Nebenbedingungen in einem Composite-Step-Verfahren nicht exakt erfüllt. In dieser Arbeit wird der Einfluss dieser Ungenauigkeit auf das Konvergenzverhalten von Newton-Lagrange-Verfahren untersucht. Dabei sollen mehrere einschlägige lokale Konvergenzresultate diskutiert werden. Anschließend wird ein konkretes Composite-Step-Verfahren formuliert, in dem die Genauigkeit der inneren Iterationsverfahren adaptiv gesteuert werden kann. Am Ende der Arbeit wird an zwei Musterproblemen die hohe Übereinstimmung der analytischen Voraussagen und der tatsächlichen Performanz der dargestellten Methoden demonstriert. KW - PDE KW - adaptive Newton KW - inexact Newton-Lagrange Y1 - 2013 UR - urn:nbn:de:0297-zib-41972 ER - TY - CHAP A1 - Wenzel, Hans A1 - Crump, Paul A1 - Ekhteraei, Hossein A1 - Schultz, Christoph M. A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Erbert, Götz T1 - Theoretical and experimental analysis of the lateral modes of high-power broad-area lasers T2 - Numerical Simulation of Optoelectronic Devices Y1 - 2011 U6 - https://doi.org/10.1109/NUSOD.2011.6041183 SP - 143 EP - 144 ER - TY - JOUR A1 - Müller, Anja A1 - Rusch, Beate A1 - Amrhein, Kilian A1 - Klindt, Marco T1 - Unfertige Dialoge – Das Berliner Förderprogramm Digitalisierung JF - Bibliotheksdienst N2 - Das Förderprogramm Digitalisierung des Landes Berlin fördert Digitalisierungsprojekte in Berliner Kulturerbeeinrichtungen und hat parallel dazu die Servicestelle Digitalisierung (digiS) als zentrale Beratungs- und Koordinierungsstelle eingerichtet. Ziel ist dabei, eine technische und organisatorische Infrastruktur für die Projekte sowie zur Sicherung der Langzeitverfügbarkeit digitalen Kulturguts vorzuhalten. Der Artikel beschreibt das Förderprogramm, das Aufgabenspektrum von digiS und die Herausforderungen, die sich für Kulturerbeinstitutionen ergeben, wenn sie sich auf den offenen Dialog mit ihren Nutzern einlassen und ihre Objekte digital langzeitverfügbar halten wollen. Y1 - 2013 U6 - https://doi.org/10.1515/bd-2013-0104 VL - 47 IS - 12 SP - 931 EP - 942 ER - TY - CHAP A1 - Skibina, Julia A1 - Iliew, Rumen A1 - Bethge, Jens A1 - Bock, Martin A1 - Fischer, Dorit A1 - Beloglazov, Valentin A1 - Wedell, Reiner A1 - Burger, Sven A1 - Steinmeyer, Günter T1 - A chirped photonic crystal fiber for ultrashort laser pulse delivery T2 - CLEO Europe - EQEC Y1 - 2009 U6 - https://doi.org/10.1109/CLEOE-EQEC.2009.5196579 ER - TY - CHAP A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schmidt, Frank A1 - Burger, Sven T1 - Finite Element Simulation of Radiation Losses in Photonic Crystal Fibers T2 - Nanophotonic Materials: Photonic Crystals, Plasmonics, and Metamaterials Y1 - 2008 U6 - https://doi.org/10.1002/9783527621880.ch17 SP - 313 EP - 331 PB - Wiley-VCH ER - TY - CHAP A1 - Zschiedrich, Lin A1 - März, Reinhard A1 - Burger, Sven A1 - Schmidt, Frank T1 - Efficient 3D Finite Element Simulation of Fiber-Chip Coupling T2 - Integrated Photonics Research and Applications/Nanophotonics Y1 - 2006 U6 - https://doi.org/10.1364/IPRA.2006.ITuF1 SP - ITuF1 ER - TY - JOUR A1 - Albrecht, Rita A1 - Ceynowa, Klaus A1 - Degkwitz, Andreas A1 - Kende, Jiri A1 - Koch, Thorsten A1 - Messmer, Gabriele A1 - Risch, Uwe A1 - Rusch, Beate A1 - Scheuerl, Robert A1 - Voß, Michael T1 - Cloudbasierte Infrastruktur für Bibliotheksdaten – auf dem Weg zu einer Neuordnung der deutschen Verbundlandschaft JF - Bibliothek Forschung und Praxis N2 - Im Oktober 2012 hatte die Deutsche Forschungsgemeinschaft (DFG) ein Förderprogramm zur Neuausrichtung überregionaler Informationsservices ausgeschrieben, um eine umfassende Reorganisation bestehender Infrastrukturen anzustoßen, die mit den Empfehlungen des Wissenschaftsrates zur Zukunft der bibliothekarischen Verbundsysteme in Deutschland gefordert wurde. Im Themenfeld „Bibliotheksdateninfrastruktur und Lokale Systeme“ der DFG-Ausschreibung wurde das vom Hessischen Bibliotheksinformationssystem (HeBIS), vom Bibliotheksverbund Bayern (BVB) und vom Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) beantragte Vorhaben „Cloudbasierte Infrastruktur für Bibliotheksdaten“ (CIB) bewilligt. Das Projekt zielt auf die Überführung bibliothekarischer Workflows und Dienste in cloudbasierte Arbeitsumgebungen und die sukzessive Ablösung traditioneller Verbund- und Lokalsysteme durch internationale Systemplattformen. Zu den Arbeitspaketen des Vorhabens gehört u. a. die Einbindung von Norm- und Fremddatenangeboten und von weiteren Services in diese Plattformen. Y1 - 2013 U6 - https://doi.org/10.1515/bfp-2013-0044 VL - 37 IS - 3 SP - 279 EP - 287 ER - TY - THES A1 - Lubkoll, Lars T1 - Optimal Control in Implant Shape Design KW - optimal control Y1 - 2011 ER - TY - CHAP A1 - Wohlfeil, Benjamin A1 - Burger, Sven A1 - Stamatiadis, Christos A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Zimmermann, Lars A1 - Petermann, Klaus T1 - Numerical Simulation of Grating Couplers for Mode Multiplexed Systems T2 - Proc. SPIE Y1 - 2014 U6 - https://doi.org/10.1117/12.2044461 VL - 8988 SP - 89880K ER - TY - JOUR A1 - Röblitz, Susanna A1 - Weber, Marcus T1 - Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification JF - Advances in Data Analysis and Classification Y1 - 2013 U6 - https://doi.org/10.1007/s11634-013-0134-6 VL - 7 IS - 2 SP - 147 EP - 179 ER - TY - CHAP A1 - Streicher, Doreen A1 - Paetsch, Olaf A1 - Seiler, Robert A1 - Prohaska, Steffen A1 - Krause, Martin A1 - Boller, Christian T1 - 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira T2 - Proc. DGZfP-Jahrestagung 2011 Y1 - 2011 ER - TY - THES A1 - Rosanwo, Olufemi T1 - Interactive Multi-Object Segmentation with Max-Tree Filtering Y1 - 2009 ER - TY - CHAP A1 - Ritter, Zully A1 - Prohaska, Steffen A1 - Brand, R. A1 - Friedmann, A. A1 - Hege, Hans-Christian A1 - Goebbels, Jürgen A1 - Felsenberg, Dieter T1 - Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study T2 - Proc. ISB 2011 Y1 - 2011 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimal Toll Enforcement - an Integration of Vehicle Routing and Duty Rostering N2 - We present the problem of planning mobile tours of inspectors on German motorways to enforce the payment of the toll for heavy good trucks. This is a special type of vehicle routing problem with the objective to conduct as good inspections as possible on the complete network. In addition, the crews of the tours have to be scheduled. Thus, we developed a personalized crew rostering model. The planning of daily tours and the rostering are combined in a novel integrated approach and formulated as a complex and large scale Integer Program. The paper focuses first on different requirements for the rostering and how they can be modeled in detail. The second focus is on a bicriterion analysis of the planning problem to find the balance between the control quality and the roster acceptance. On the one hand the tour planning is a profit maximization problem and on the other hand the rostering should be made in a employee friendly way. Finally, computational results on real-world instances show the practicability of our method. T3 - ZIB-Report - 13-79 KW - vehicle routing KW - crew rostering KW - integer programming KW - bicriteria optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-45107 SN - 1438-0064 ER - TY - THES A1 - Jalda, Dworzak T1 - Reconstruction of the Human Rib Cage from 2D Projection Images using a Statistical Shape Model Y1 - 2009 ER - TY - THES A1 - Renard, Maximilien T1 - Improvement of Image Segmentation Based on Statistical Shape and Intensity Models Y1 - 2011 ER - TY - THES A1 - Bindernagel, Matthias T1 - Articulated Statistical Shape Models Y1 - 2013 ER - TY - THES A1 - Krabi, Marianne T1 - Implementierung einer Methode zur automatischen Erkennung von Nervenzellkörpern in 3D Mikroskopbildern Y1 - 2011 ER - TY - THES A1 - Kainmüller, Dagmar T1 - Deformable Meshes for Accurate Automatic Segmentation of Medical Image Data Y1 - 2013 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Metric Inequalities for Routings on Direct Connections N2 - We consider multi-commodity flow problems in which capacities are installed on paths. In this setting, it is often important to distinguish between flows on direct connection routes, using single paths, and flows that include path switching. We show that the concept of metric inequalities to characterize capacities that support a multi-commodity flow can be generalized to deal with direct connections. T3 - ZIB-Report - 14-04 KW - metric inequalities KW - direct connection KW - multi-commodity flow problem Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-44219 SN - 1438-0064 ER - TY - GEN A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Raymond, Annie T1 - 0-1 Multiband Robust Optimization N2 - We provide an overview of new theoretical results that we obtained while further investigating multiband robust optimization, a new model for robust optimization that we recently proposed to tackle uncertainty in mixed-integer linear programming. This new model extends and refines the classical Gamma-robustness model of Bertsimas and Sim and is particularly useful in the common case of arbitrary asymmetric distributions of the uncertainty. Here, we focus on uncertain 0-1 programs and we analyze their robust counterparts when the uncertainty is represented through a multiband set. Our investigations were inspired by the needs of our industrial partners in the research project ROBUKOM. T3 - ZIB-Report - 13-77 KW - Combinatorial Optimization, Robust Optimization, Multiband Robustness, Network Design Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-44093 SN - 1438-0064 ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Pulaj, Jonad T1 - A hybrid primal heuristic for Robust Multiperiod Network Design N2 - We investigate the Robust Multiperiod Network Design Problem, a generalization of the classical Capacitated Network Design Problem that additionally considers multiple design periods and provides solutions protected against traffic uncertainty. Given the intrinsic difficulty of the problem, which proves challenging even for state-of-the art commercial solvers, we propose a hybrid primal heuristic based on the combination of ant colony optimization and an exact large neighborhood search. Computational experiments on a set of realistic instances from the SNDlib show that our heuristic can find solutions of extremely good quality with low optimality gap. T3 - ZIB-Report - 13-78 KW - Multiperiod Network Design, Traffic Uncertainty, Robust Optimization, Multiband Robustness, Hybrid Heuristics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-44081 SN - 1438-0064 ER - TY - JOUR A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Gerden, S. R. A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleontological cephalopod research JF - Biogeosciences N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. Y1 - 2014 U6 - https://doi.org/10.5194/bg-11-2721-2014 N1 - To access the corresponding discussion paper go to www.biogeosciences-discuss.net/10/18803/2013/ - Biogeosciences Discuss., 10, 18803-18851, 2013 VL - 11 IS - 10 SP - 2721 EP - 2739 ER - TY - JOUR A1 - Lamas-Rodríguez, Julián A1 - Heras, Dora Blanco A1 - Argüello, Francisco A1 - Kainmüller, Dagmar A1 - Zachow, Stefan A1 - Bóo, Montserrat T1 - GPU-accelerated level-set segmentation JF - Journal of Real-Time Image Processing Y1 - 2013 UR - http://dx.doi.org/10.1007/s11554-013-0378-6 U6 - https://doi.org/10.1007/s11554-013-0378-6 SN - 1861-8200 SP - 1 EP - 15 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - CHAP A1 - Ramm, Heiko A1 - Victoria Morillo, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans ED - Freysinger, Wolfgang T1 - Visual Support for Positioning Hearing Implants T2 - Proceedings of the 12th annual meeting of the CURAC society Y1 - 2013 SP - 116 EP - 120 ER - TY - JOUR A1 - Oeltze, Steffen A1 - Lehmann, Dirk J. A1 - Kuhn, Alexander A1 - Janiga, Gábor A1 - Theisel, Holger A1 - Preim, Bernhard T1 - Blood Flow Clustering and Applications in Virtual Stenting of Intracranial Aneurysms JF - IEEE Transactions on Visualization and Computer Graphics, 2014 Y1 - 2013 U6 - https://doi.org/10.1109/TVCG.2013.2297914 SN - 0934-5892 VL - 20 IS - 5 SP - 686 EP - 701 ER - TY - JOUR A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Rössl, Christian A1 - Hadwiger, Markus A1 - Theisel, Holger T1 - Time Line Cell Tracking for the Approximation of Lagrangian Coherent Structures with Subgrid Accuracy JF - Computer Graphics Forum Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43990 SN - 0934-5892 VL - 33 SP - 222 EP - 234 PB - Wiley Blackwell ER - TY - GEN A1 - Vincens, Eric A1 - Witt, Karl Josef A1 - Homberg, Ulrike T1 - Approaches to Determine the Constriction Size Distribution for Understanding Filtration Phenomena in Granular Materials N2 - Granular filters in hydraulically loaded earth structures constitute the ultimate barrier for the blockage of small particles moving through the structure regularly or along concentrated leaks. If filters are inefficient to block small particles several types of internal erosion may be initiated. A corresponding phenomenon appears during suffusion in a wide graded hydraulically loaded fill, when fine particles, embedded in the pore structure of a soil skeleton, are washed out. The cumulative constriction size distribution (CSD) is physically the key property that qualifies the soils retention capability as like a spatial acting sieve. Constrictions are defined as the narrowest sections of channels between larger volumes (pores) within the pore network of granular material and they are the main obstacles for a small particle to overcome when flowing along pathways. At least three different approaches are available to determine and compute the CSD, i.e. experimental, numerical and analytical methods. The purpose of this review is to present and discuss these methods pointing out their limits, advantages and significance related to internal erosion phenomena. T3 - ZIB-Report - 14-01 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43960 SN - 1438-0064 ER - TY - JOUR A1 - Vincens, Eric A1 - Witt, Karl Josef A1 - Homberg, Ulrike T1 - Approaches to Determine the Constriction Size Distribution for Understanding Filtration Phenomena in Granular Materials JF - Acta Geotechnica Y1 - 2015 U6 - https://doi.org/10.1007/s11440-014-0308-1 VL - 10 IS - 3 SP - 291 EP - 303 PB - Springer ER - TY - CHAP A1 - Meinel, Dietmar A1 - Ehrig, Karsten A1 - Lhostis, Valrie A1 - Muzeau, Benoist A1 - Paetsch, Olaf T1 - Examination of Damage Processes in Concrete with CT T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2014 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2012 SP - 321 EP - 330 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Breßler, David A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben T2 - Tagungsband der DGZfP Jahrestagung 2013 Y1 - 2013 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie T2 - Tagungsband der DACH Jahrestagung 2012 Y1 - 2012 ER - TY - JOUR A1 - Reininghaus, Jan A1 - Kasten, Jens A1 - Weinkauf, Tino A1 - Hotz, Ingrid T1 - Efficient Computation of Combinatorial Feature Flow Fields JF - Transactions on Visualization and Computer Graphics Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2011.269 VL - 18 IS - 9 SP - 1563 EP - 1573 ER - TY - GEN A1 - Reininghaus, Jan A1 - Hotz, Ingrid ED - Peikert, Ronald ED - Carr, Hamish ED - Hauser, Helwig T1 - Computational Discrete Morse Theory for Divergence-Free 2D Vector Fields T2 - Topological Methods in Data Analysis and Visualization. Theory, Algorithms, and Applications. (TopoInVis 2011) Y1 - 2012 SP - 3 EP - 14 PB - Springer ER - TY - CHAP A1 - Kasten, Jens A1 - Hotz, Ingrid A1 - Noack, Bernd A1 - Hege, Hans-Christian T1 - Vortex Merge Graphs in Two-dimensional Unsteady Flow Fields T2 - EuroVis – Short Papers Y1 - 2012 UR - http://diglib.eg.org/EG/DL/PE/EuroVisShort/EuroVisShort2012/001-005.pdf U6 - https://doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/001-005 SP - 1 EP - 5 PB - Eurographics Association CY - Vienna, Austria ER - TY - JOUR A1 - Günther, David A1 - Reininghaus, Jan A1 - Wagner, Hubert A1 - Hotz, Ingrid T1 - Efficient Computation of 3D Morse-Smale Complexes and Persistent Homology using Discrete Morse Theory JF - The Visual Computer Y1 - 2012 U6 - https://doi.org/10.1007/s00371-012-0726-8 VL - 28 IS - 10 SP - 959 EP - 969 ER - TY - CHAP A1 - Kasten, Jens A1 - Zoufahl, Andre A1 - Hege, Hans-Christian A1 - Hotz, Ingrid T1 - Analysis of Vortex Merge Graphs T2 - VMV 2012: Vision, Modeling and Visualization Y1 - 2012 U6 - https://doi.org/10.2312/PE/VMV/VMV12/111-118 SP - 111 EP - 118 PB - Eurographics Association ER - TY - GEN A1 - Reininghaus, Jan A1 - Günther, David A1 - Hotz, Ingrid A1 - Weinkauf, Tino A1 - Seidel, Hans Peter T1 - Combinatorial Gradient Fields for 2D Images with Empirically Convergent Separatrices Y1 - 2012 UR - http://arxiv.org/abs/1208.6523 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Lockau, Daniel A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Optical modelling of incoherent substrate light-trapping in silicon thin film multi-junction solar cells with finite elements and domain decomposition T2 - Proc. SPIE: Physics and Simulation of Optoelectronic Devices XXII Y1 - 2014 U6 - https://doi.org/10.1117/12.2036346 VL - 8980 SP - 898007 PB - SPIE ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Adaptive sampling strategies for effcient parameter scans in nano-photonic device simulations T2 - Proc. SPIE Y1 - 2014 U6 - https://doi.org/10.1117/12.2036363 VL - 8980 SP - 89801O PB - SPIE ER - TY - JOUR A1 - Kirner, Simon A1 - Hammerschmidt, Martin A1 - Schwanke, Christoph A1 - Lockau, Daniel A1 - Calnan, Sonya A1 - Frijnts, Tim A1 - Neubert, Sebastian A1 - Schöpke, Andreas A1 - Schmidt, Frank A1 - Zollondz, Jens-Hendrik A1 - Heidelberg, Andreas A1 - Stannowski, Bernd A1 - Rech, Bernd A1 - Schlatmann, Rutger T1 - Implications of TCO Topography on Intermediate Reflector Design for a-Si/μc-Si Tandem Solar Cells — Experiments and Rigorous Optical Simulations JF - IEEE Journal of Photovoltaics Y1 - 2014 U6 - https://doi.org/10.1109/JPHOTOV.2013.2279204 VL - 4 IS - 1 SP - 10 EP - 15 ER - TY - JOUR A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Ruske, Florian A1 - Hammerschmidt, Martin A1 - Becker, Christiane A1 - Schmidt, Frank A1 - Rech, Bernd T1 - Advanced microhole arrays for light trapping in thin film silicon solar cells JF - Solar Energy Materials and Solar Cells Y1 - 2014 U6 - https://doi.org/10.1016/j.solmat.2013.11.024 VL - 125 SP - 298 EP - 304 ER - TY - JOUR A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Back, Franziska A1 - Rudigier-Voigt, Eveline A1 - Löchel, Bernd A1 - Erko, Alexei A1 - Schmidt, Frank A1 - Schnegg, Alexander A1 - Lips, Klaus A1 - Becker, Christiane A1 - Rech, Bernd T1 - Correlation between structural and opto-electronic characteristics of crystalline Si microhole arrays for photonic light management JF - Journal of Applied Physics Y1 - 2013 U6 - https://doi.org/10.1063/1.4829008 VL - 114 IS - 17 SP - 173513 PB - AIP Publishing ER - TY - JOUR A1 - Becker, Christiane A1 - Amkreutz, Daniel A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Haschke, Jan A1 - Jogschies, Lisa A1 - Klimm, Carola A1 - Merkel, Janis J. A1 - Plocica, Paul A1 - Steffens, Simon A1 - Rech, Bernd T1 - Polycrystalline silicon thin-film solar cells: Status and perspectives JF - Solar Energy Materials and Solar Cells Y1 - 2013 U6 - https://doi.org/10.1016/j.solmat.2013.05.043 VL - 119 SP - 112 EP - 123 ER - TY - JOUR A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Back, Franziska A1 - Rudigier-Voigt, Eveline A1 - Rech, Bernd A1 - Becker, Christiane T1 - Analysis of absorption enhancement in tailor-made periodic polycrystalline silicon microarrays JF - physica status solidi (RRL)-Rapid Research Letters Y1 - 2013 U6 - https://doi.org/10.1002/pssr.201308098 VL - 7 IS - 12 SP - 1045 EP - 1049 PB - WILEY-VCH Verlag ER - TY - JOUR A1 - Schmid, Martina A1 - Andrae, Patrick A1 - Manley, Phillip T1 - Plasmonic and photonic scattering and near fields of nanoparticles JF - Nanoscale Research Letters Y1 - 2014 U6 - https://doi.org/10.1186/1556-276X-9-50 VL - 9 SP - 50 ER - TY - THES A1 - Raack, Christian T1 - Capacitated Network Design - Multi-Commodity Flow Formulations, Cutting Planes, and Demand Uncertainty N2 - In this thesis, we develop methods in mathematical optimization to dimension networks at minimal cost. Given hardware and cost models, the challenge is to provide network topologies and efficient capacity plans that meet the demand for network traffic (data, passengers, freight). We incorporate crucial aspects of practical interest such as the discrete structure of available capacities as well as the uncertainty of demand forecasts. The considered planning problems typically arise in the strategic design of telecommunication or public transport networks and also in logistics. One of the essential aspects studied in this work is the use of cutting planes to enhance solution approaches based on multi-commodity flow formulations. Providing theoretical and computational evidence for the efficacy of inequalities based on network cuts, we extend existing theory and algorithmic work in different directions. First, we prove that special-purpose techniques, originally designed to solve capacitated network design problems, can be successfully integrated into general-purpose mixed integer programming (MIP) solvers. Our approach relies on an automatic detection of network structure within the constraint matrix of general mixed in teger programs. More precisely, we identify multi-commodity (MCF) network sub-matrices and resolve the isomorphisms of the commodity blocks as well as the original graph structure. In the subsequent separation framework, we guide the constraint aggregation of available cutting plane procedures (e. g. based on mixed integer rounding) to produce strong cutting planes that reflect the structure of the constructed network. The new MCF-separator integrates network design specific methodology into general optimization tools which is of particular importance for practitioners that tend to use MIP solvers as black boxes. Extensive computational tests show that our network detection procedure operates accurately and reliably. Moreover, due to the generated cutting planes, we achieve an average speed-up of a factor of two for pure network design problems with general MIP solvers. Many of these instances can only be solved to optimality in reasonable time if the new MCF-separator is active. In 9 % of the instances of general MIP test sets we find consistent embedded networks and generate violated inequalities. In this case the computation time decreases by 18 % on average with almost no degradation for unaffected instances. Second, we generalize concepts, models, and cutting planes from deterministic network design to robust network design, incorporating the uncertainty of traffic demands. We enhance and compare strategies that are able to handle a polyhedral set of different traffic scenarios. In particular, we consider two correlated solution methods, based on separating extreme demand scenarios and dualizing the linear description of the demand polytope, respectively. We consider robust network design as two-stage robust optimization with recourse. First stage capacity decisions are fixed for all scenarios while the second stage flow depends on the realized demands. In order to reroute the traffic as a function of the demand dynamics, we consider three alternative recourse actions, namely, static, affine, and dynamic routing. We analyze properties of the new affine routing and show that it combines advantages of the well-known static and dynamic models. Using the concept of robust cut-set polyhedra and the corresponding lifting theorems, we develop several classes of facet-defining inequalities based on network cuts that can be used to further accelerate solution strategies for robust network design. Among them are the well-known (flow) cut-set inequalities, which we generalize to general demand polytopes, but also new classes of potential cutting planes, so-called envelope inequalities. The practical importance of the developed cutting planes is revealed by a series of computational tests. Similar to the results for the MCF-separator we achieve speed-ups of two and more using the generalized classes of strong inequalities. To evaluate the robustness of solutions that are computed with our framework we use real-life measurements of traffic dynamics from different existing telecommunication networks, among them data from the German and the European research network. Our results indicate that traffic peaks do not necessarily occur all simultaneously with respect to different source-destination pairs, which is of practical importance for the design of uncertainty sets. It is, in particular, not necessary to dimension networks for a scenario that assumes all source-destination traffic is at its peak simultaneously. With our solutions we save up to 20 % of the corresponding solution cost compared to this artificial scenario and achieve comparable levels of robustness. KW - combinatorial optimization KW - cutting planes KW - integer programming KW - network design KW - robustness Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-36167 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/3407 ER - TY - JOUR A1 - Krause, Dorian A1 - Fackeldey, Konstantin A1 - Krause, Rolf ED - Griebel, Michael T1 - A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements JF - Singular Phenomena and Scaling in Mathematical Models Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-00786-1_14 SP - 327 EP - 346 PB - Springer International Publishing ER - TY - JOUR A1 - Leitner, Markus A1 - Ljubić, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - On the Two-Architecture Connected Facility Location Problem JF - Electronic Notes in Discrete Mathematics Y1 - 2013 U6 - https://doi.org//10.1016/j.endm.2013.05.113 VL - 41 SP - 359 EP - 366 CY - Costa Adeje ER - TY - JOUR A1 - Betker, Andreas A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Pfeuffer, Frank A1 - Raack, Christian A1 - Werner, Axel ED - Helber, Stefan ED - Breitner, Michael ED - Rösch, Daniel ED - Schön, Cornelia ED - Graf von der Schulenburg, Johann-Matthias ED - Sibbertsen, Philipp ED - Steinbach, Marc ED - Weber, Stefan ED - Wolter, Anja T1 - Energy efficiency in extensive IP-over-WDM networks with protection JF - Operations Research Proceedings 2012 Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-00795-3_14 SP - 93 EP - 99 PB - Springer ER - TY - JOUR A1 - Raack, Christian A1 - Raymond, Annie A1 - Schlechte, Thomas A1 - Werner, Axel T1 - Standings in sports competitions using integer programming JF - Journal of Quantitative Analysis in Sports Y1 - 2013 U6 - https://doi.org/10.1515/jqas-2013-0111 VL - 10 IS - 2 SP - 131 EP - 137 PB - De Gruyter ER - TY - JOUR A1 - Grötschel, Martin A1 - Raack, Christian A1 - Werner, Axel T1 - Towards optimizing the deployment of optical access networks JF - EURO Journal on Computational Optimization Y1 - 2013 U6 - https://doi.org/10.1007/s13675-013-0016-x VL - 2 SP - 17 EP - 53 PB - Springer ER - TY - GEN A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio T1 - Robust Optimization under Multi-band Uncertainty - Part I: Theory N2 - The classical single-band uncertainty model introduced by Bertsimas and Sim has represented a breakthrough in the development of tractable robust counterparts of Linear Programs. However, adopting a single deviation band may be too limitative in practice: in many real-world problems, observed deviations indeed present asymmetric distributions over asymmetric ranges, so that getting a higher modeling resolution by partitioning the band into multiple sub-bands is advisable. The critical aim of our work is to close the knowledge gap on the adoption of multi-band uncertainty in Robust Optimization: a general definition and intensive theoretical study of a multi-band model are actually still missing. Our new developments have been also strongly inspired and encouraged by our industrial partners, interested in getting a better modeling of arbitrary shaped distributions, built on historical data about the uncertainty affecting the considered real-world problems. T3 - ZIB-Report - 13-10 KW - Robust Optimization, Multiband Uncertainty, Compact Robust Counterpart, Cutting Planes, Probabilistic Bound Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43469 SN - 1438-0064 N1 - Submitted for publication in 2012. Preprint also available in Optimization Online (13-01-3748) and arXiv (1301.2734) ER - TY - JOUR A1 - Hoch, Hannelore A1 - Wessel, Andreas A1 - Asche, Manfred A1 - Baum, Daniel A1 - Beckmann, Felix A1 - Bräunig, Peter A1 - Ehrig, Karsten A1 - Mühlethaler, Roland A1 - Riesemeier, Heinrich A1 - Staude, Andreas A1 - Stelbrink, Björn A1 - Wachmann, Ekkehard A1 - Weintraub, Phyllis A1 - Wipfler, Benjamin A1 - Wolff, Carsten A1 - Zilch, Mathias T1 - Non-Sexual Abdominal Appendages in Adult Insects Challenge a 300 Million Year Old Bauplan JF - Current Biology Y1 - 2014 U6 - https://doi.org/10.1016/j.cub.2013.11.040 VL - 24 IS - 1 SP - R16 EP - R17 ER - TY - JOUR A1 - Burger, Sven A1 - Cataliotti, F. S. A1 - Fort, C. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo T1 - Quasi 2D Bose-Einstein condensation in an optical lattice JF - EPL Y1 - 2002 U6 - https://doi.org/10.1209/epl/i2002-00532-1 VL - 57 IS - 1 SP - 1 EP - 6 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Hellweg, D. A1 - Arlt, J. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus ED - Aspect, Alain ED - Dalibard, J. T1 - Coherent manipulation and guiding of Bose-Einstein condensates by optical dipole potentials JF - Dossier Optique et interférometrie atomiques Y1 - 2001 VL - 2 SP - 671 PB - C. R. Acad. Sci. Paris - Series IV ER - TY - JOUR A1 - Ahufinger, Verònica A1 - Corbalán, R. A1 - Cataliotti, F. S. A1 - Burger, Sven A1 - Minardi, F. A1 - Fort, C. T1 - Electromagnetically induced transparency in a Bose-Einstein condensate JF - Opt. Comm. Y1 - 2002 U6 - https://doi.org/10.1016/S0030-4018(02)01826-6 VL - 211 SP - 159 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Hellweg, D. A1 - Kottke, M. A1 - Dettmer, S. A1 - Rinkleff, T. A1 - Cacciapuoti, L. A1 - Arlt, J. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang T1 - Spectroscopy of Dark Soliton States in Bose-Einstein Condensates JF - J. Opt. B: Quantum Semiclass. Opt. Y1 - 2003 U6 - https://doi.org/10.1088/1464-4266/5/2/369 VL - 5 SP - S124 ER - TY - GEN A1 - Franck, Hildegard A1 - Lohrum, Stefan A1 - Polojannis, Jannis T1 - Automatisierte Fernleihe im KOBV - Handbuch für Bibliotheken - 4. Auflage N2 - Im Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) wird für die automatisierte Fernleihe der Zentrale-Fernleihserver (ZFL-Server) der Firma Sisis eingesetzt. Die Software ist in der KOBVZentrale installiert. Der ZFL-Server dient im KOBV sowohl für die Bestellung von Monographien als auch für die Bestellung von Aufsatzkopien aus Zeitschriften. Prinzipiell gibt es zwei Verfahren, mit denen sich Bibliotheken an der automatisierten Fernleihe beteiligen können: das E-Mail-Verfahren und das SLNP-Verfahren. Auf beide wird im Handbuch eingegangen. Die automatisierte Fernleihe wurde im KOBV eingeführt, um die Fernleihe für die Benutzer zu beschleunigen, das Verfahren für die Bibliotheksmitarbeiter zu vereinfachen und den Arbeitsaufwand zu reduzieren. Sie basiert darauf, dass eine Bestellung anhand eines gefundenen Treffers ausgelöst wird – d.h. die bibliographischen Daten sind bereits verifiziert und in einem Katalog nachgewiesen. Anschließend werden die Bestellungen über den ZFL-Server automatisch ausgeführt und verwaltet – sowohl in der regionalen KOBV-Fernleihe als auch in der verbundübergreifenden Fernleihe mit den deutschen Bibliotheksverbünden. Der ZFL-Server besteht aus verschiedenen technischen Komponenten. Eine dieser Komponenten ist das Bibliothekskonto, eine Internetanwendung, in der die Bestellverwaltung des ZFL-Servers für die Bibliotheksbediensteten transparent abläuft. Dazu hat jede Bibliothek im Bibliothekskonto eine eigene, Passwort-geschützte Dienstoberfläche. Im Laufe der Jahre 2012-2013 hat die KOBV-Zentrale das Bibliothekskonto grundlegend überarbeitet; die neue Version wurde im September 2013 freigegeben. Neben der Überarbeitung des Interfaces– so wird den Bibliotheken auf der Startseite nun eine Übersicht ihrer laufenden Bestellungen angezeigt und dient als direkter Einstieg in die Bearbeitung – wurde das Bibliothekskonto um folgende Funktionen erweitert: Umstellung des Zeichensatzes auf UTF8, Möglichkeit zur elektronische Lieferung von Aufsatzkopien zwischen Bibliotheken (EDL-Lieferung). Das Handbuch, das die Vorgänge der Bestellverwaltung im Bibliothekskonto beschreibt, wurde in der nun vorliegenden 4. Auflage um die Beschreibung der neuen Funktionen ergänzt. T3 - ZIB-Report - 13-35 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43409 SN - 1438-0064 ER - TY - GEN A1 - D'Andreagiovanni, Fabio A1 - Raymond, Annie T1 - Multiband Robust Optimization and its Adoption in Harvest Scheduling N2 - A central assumption in classical optimization is that all the input data of a problem are exact. However, in many real-world problems, the input data are subject to uncertainty. In such situations, neglecting uncertainty may lead to nominally optimal solutions that are actually suboptimal or even infeasible. Robust optimization offers a remedy for optimization under uncertainty by considering only the subset of solutions protected against the data deviations. In this paper, we provide an overview of the main theoretical results of multiband robustness, a new robust optimization model that extends and refines the classical theory introduced by Bertsimas and Sim. After introducing some new results for the special case of pure binary programs, we focus on the harvest scheduling problem and show how multiband robustness can be adopted to tackle the uncertainty affecting the volume of produced timber and grant a reduction in the price of robustness. T3 - ZIB-Report - 13-76 KW - Data Uncertainty KW - Robust Optimization KW - Multiband Robustness KW - Harvest Scheduling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43380 SN - 1438-0064 ER - TY - JOUR A1 - Gertzen, Thomas L. A1 - Grötschel, Martin ED - Grötschel, Martin T1 - Flinders Petrie, the Travelling Salesman Problem, and the Beginning of Mathematical Modeling in Archaeology JF - Optimization Stories Y1 - 2012 UR - http://www.mathematik.uni-bielefeld.de/documenta/vol-ismp/35_gertzen-thomas-groetschel-martin.pdf VL - Extra Vol.: Optim. Stories SP - 199 EP - 210 PB - Documenta Mathematica CY - Bielefeld ER - TY - JOUR A1 - Gamrath, Gerald A1 - Lübbecke, Marco ED - Festa, P. T1 - Experiments with a Generic Dantzig-Wolfe Decomposition for Integer Programs JF - Experimental Algorithms Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-13193-6_21 VL - 6049 SP - 239 EP - 252 PB - Springer-Verlag CY - Berlin ER - TY - JOUR A1 - Gamrath, Gerald ED - Gomes, Carla ED - Sellmann, Meinolf T1 - Improving strong branching by propagation JF - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems N2 - Strong branching is an important component of most variable selection rules in branch-and-bound based mixed-integer linear programming solvers. It predicts the dual bounds of potential child nodes by solving auxiliary LPs and thereby helps to keep the branch-and-bound tree small. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Computational experiments on standard MIP instances indicate that this is beneficial in three aspects: It helps to reduce the average number of LP iterations per strong branching call, the number of branch-and-bound nodes, and the overall solving time. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38171-3_25 VL - 7874 SP - 347 EP - 354 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Grötschel, Martin A1 - Yuan, Ya-xiang ED - Grötschel, Martin T1 - Euler, Mei-Ko Kwan, Königsberg, and a Chinese Postman JF - Documenta Mathematica - Optimization Stories Y1 - 2012 UR - http://www.mathematik.uni-bielefeld.de/documenta/vol-ismp/16_groetschel-martin-yuan-ya-xiang.pdf VL - Extra Vol.: Optim. Stories SP - 43 EP - 50 PB - Documenta Mathematica CY - Bielefeld ER - TY - BOOK ED - Grötschel, Martin T1 - Optimization Stories T3 - Documenta Mathematica - Journal der Deutschen Mathematiker-Vereinigung Y1 - 2012 SN - 978-3-936609-58-5 VL - Extra Volume ISMP (2012) ER - TY - BOOK ED - Biermann, Katja ED - Grötschel, Martin ED - Lutz-Westphal, Brigitte T1 - Besser als Mathe - Moderne angewandte Mathematik aus dem Matheon zum Mitmachen Y1 - 2013 SN - 978-3-658-01003-4 U6 - https://doi.org/10.1007/978-3-658-01004-1 PB - Springer Spektrum CY - Wiesbaden ET - 2., aktualisierte Auflage ER - TY - GEN A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Kock, Christiaan P.J. A1 - Oberlaender, Marcel ED - Cuntz, Hermann ED - Remme, Michiel W.H. ED - Torben-Nielsen, Benjamin T1 - Reverse Engineering the 3D Structure and Sensory-Evoked Signal Flow of Rat Vibrissal Cortex T2 - The Computing Dendrite Y1 - 2014 U6 - https://doi.org/10.1007/978-1-4614-8094-5_8 VL - 11 SP - 127 EP - 145 PB - Springer CY - New York ER - TY - JOUR A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology JF - NeuroInformatics Y1 - 2014 U6 - https://doi.org/10.1007/s12021-013-9213-2 VL - 12 IS - 2 SP - 325 EP - 339 PB - Springer US ER - TY - GEN A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - On a Generalized Transfer Operator N2 - We introduce a generalized operator for arbitrary stochastic processes by using a pre-kernel, which is a generalization of the Markov kernel. For deterministic processes, such an operator is already known as the Frobenius-Perron operator, which is defined for a large class of measures. For Markov processes, there exists transfer operators being only well defined for stationary measures in $L^2$. Our novel generalized transfer operator is well defined for arbitrary stochastic processes, in particular also for deterministic ones. We can show that this operator is acting on $L^1$. For stationary measures, this operator is also an endomorphism of $L^2$ and, therefore, allows for a mathematical analysis in Hilbert spaces. T3 - ZIB-Report - 13-74 KW - Transfer Operator KW - Pre Kernel KW - Perron Frobenius Generalization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43162 SN - 1438-0064 ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology N2 - Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator. T3 - ZIB-Report - 13-75 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43157 SN - 1438-0064 ER - TY - GEN A1 - Moualeu-Ngangue, Dany Pascal A1 - Weiser, Martin A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Optimal control for a tuberculosis model with undetected cases in Cameroon N2 - This paper considers the optimal control of tuberculosis through education, diagnosis campaign and chemoprophylaxis of latently infected. A mathematical model which includes important components such as undiagnosed infectious, diagnosed infectious, latently infected and lost-sight infectious is formulated. The model combines a frequency dependent and a density dependent force of infection for TB transmission. Through optimal control theory and numerical simulations, a cost-effective balance of two different intervention methods is obtained. Seeking to minimize the amount of money the government spends when tuberculosis remain endemic in the Cameroonian population, Pontryagin's maximum principle is used to characterize the optimal control. The optimality system is derived and solved numerically using the forward-backward sweep method (FBSM). Results provide a framework for designing cost-effective strategies for diseases with multiple intervention methods. It comes out that combining chemoprophylaxis and education, the burden of TB can be reduced by 80 % in 10 years T3 - ZIB-Report - 13-73 KW - Tuberculosis KW - Optimal control KW - Nonlinear dynamical systems Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43142 SN - 1438-0064 ER - TY - THES A1 - Kairies, Lukas T1 - Leistungsanalyse von XtreemFS als Ersatz für HDFS in Hadoop N2 - In dieser Arbeit wird die Leistungsfähigkeit des MapReduce-Framework Hadoop mit XtreemFS als verteiltes und POSIX-konformes Dateisystem bestimmt. Damit wird XtreemFS das für die Nutzung mit Hadoop entwickelte Dateisystem HDFS ersetzen. HDFS und XtreemFS werden verglichen und XtreemFS für Nutzung unter Hadoop konfiguriert. Zudem werden Optimierungen an der Hadoop-Schnittstelle von XtreemFS vorgenommen. Die Leistung von Hadoop mit XtreemFS wird mittels synthetischer Benchmarks und realer Hadoop Anwendungen gemessen und mit der Leistung von Hadoop mit HDFS verglichen. KW - XtreemFS KW - HDFS KW - Hadoop KW - Benchmark Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43130 ER - TY - GEN A1 - Humpola, Jesco A1 - Fügenschuh, Armin A1 - Lehmann, Thomas T1 - A Primal Heuristic for MINLP based on Dual Information N2 - We present a novel heuristic algorithm to identify feasible solutions of a mixed-integer nonlinear programming problem arising in natural gas transportation: the selection of new pipelines to enhance the network's capacity to a desired level in a cost-efficient way. We solve this problem in a linear programming based branch-and-cut approach, where we deal with the nonlinearities by linear outer approximation and spatial branching. At certain nodes of the branching tree, we compute a KKT point for a nonlinear relaxation. Based on the information from the KKT point we alter some of the integer variables in a locally promising way. We describe this heuristic for general MINLPs and then show how to tailor the heuristic to exploit our problem-specific structure. On a test set of real-world instances, we are able to increase the chance of identifying feasible solutions by some order of magnitude compared to standard MINLP heuristics that are already built in the general-purpose MINLP solver SCIP. T3 - ZIB-Report - 13-49 KW - Mixed-Integer Nonlinear Programming KW - Relaxations KW - Heuristics KW - Duality KW - Nonlinear Network Design Applications Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43110 SN - 1438-0064 ER - TY - THES A1 - Dillmann, Johannes T1 - Konsistentes Hinzufügen und Entfernen von Replikaten in XtreemFS N2 - In replizierten Systemen muss es möglich sein ausgefallene Server zu ersetzen und Replikate dynamisch hinzuzufügen oder zu entfernen. Veränderungen an der Menge der eingesetzten Replikate können zu inkonsistenten Daten führen. In dieser Arbeit wird ein Algorithmus für das konsistente Hinzufügen und Entfernen von Replikaten für das verteilte Dateisystem XtreemFS vorgestellt. Der Algorithmus nutzt einen fehlertoleranten Service, der die Replikatliste speichert sowie Veränderungen koordiniert und diese aus globaler Sicht atomar ausführt. KW - replication KW - dynamic reconfiguration KW - distributed storage systems Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43109 ER - TY - GEN A1 - Moualeu-Ngangue, Dany Pascal A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Parameter Identification for a Tuberculosis Model in Cameroon N2 - A deterministic model of tuberculosis in sub-Saharan Africa in general and Cameroon in particular including lack of access to the treatment and weak diagnose capacity is designed and analyzed with respect to its transmission dynamics. The model includes both frequency- and density-dependent transmissions. It is shown that the model is mathematically well-posed and epidemiologically reasonable. Solutions are non-negative and bounded whenever the initial values are non-negative. A sensitivity analysis of model parameters is performed and most sensitive parameters of the model are identified using a state-of-the-art Gauss-Newton Method. In particular, parameters representing the proportion of individuals having access to medical facilities have a large impact on the dynamics of the disease. It has been shown that an increase of these parameter values over the time can significantly reduce the disease burden in the population within the next 15 years. T3 - ZIB-Report - 13-72 KW - Tuberculosis, parameter identification, sensitivity analysis, Gauss-Newton method, Nonlinear dynamical systems. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43087 SN - 1438-0064 ER - TY - GEN A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Rössl, Christian A1 - Hadwiger, Markus A1 - Theisel, Holger T1 - Time Line Cell Tracking for the Approximation of Lagrangian Coherent Structures with Subgrid Accuracy N2 - Lagrangian Coherent Structures (LCS) have become a widespread and powerful method to describe dynamic motion patterns in time-dependent flow fields. The standard way to extract LCS is to compute height ridges in the Finite Time Lyapunov Exponent (FTLE) field. In this work, we present an alternative method to approximate Lagrangian features for 2D unsteady flow fields that achieves subgrid accuracy without additional particle sampling. We obtain this by a geometric reconstruction of the flow map using additional material constraints for the available samples. In comparison to the standard method, this allows for a more accurate global approximation of LCS on sparse grids and for long integration intervals. The proposed algorithm works directly on a set of given particle trajectories and without additional flow map derivatives. We demonstrate its application for a set of computational fluid dynamic examples, as well as trajectories acquired by Lagrangian methods, and discuss its benefits and limitations. T3 - ZIB-Report - 13-71 KW - time-dependent vector fields KW - flow field visualization KW - Lagrangian Coherent Structures (LCS) KW - finite-time Lyapunov exponents (FTLE) KW - time lines Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43050 SN - 1438-0064 ER - TY - THES A1 - Moualeu-Ngangue, Dany Pascal T1 - A Mathematical Tuberculosis Model in Cameroon N2 - This thesis firstly presents a nonlinear extended deterministic model for the transmission dynamics of tuberculosis, based on realistic assumptions and data collected from the WHO. This model enables a comprehensive qualitative analysis of various aspects in the outbreak and control of tuberculosis in Sub-Saharan Africa countries and successfully reproduces the epidemiology of tuberculosis in Cameroon for the past (from 1994-2010). Some particular properties of the model and its solution have been presented using the comparison theorem applied to the theory of differential equations. The existence and the stability of a disease free equilibrium has been discussed using the Perron-Frobenius theorem and Metzler stable matrices. Furthermore, we computed the basic reproduction number, i.e. the number of cases that one case generates on average over the course of its infectious period. Rigorous qualitative analysis of the model reveals that, in contrast to the model without reinfections, the full model with reinfection exhibits the phenomenon of backward bifurcation, where a stable disease-free equilibrium coexists with a stable endemic equilibrium when a certain threshold quantity, known as the basic reproduction ratio (R0), is less than unity. The global stability of the disease-free equilibrium has been discussed using the concepts of Lyapunov stability and bifurcation theory. With the help of a sensitivity analysis using data of Cameroon, we identified the relevant parameters which play a key role for the transmission and the control of the disease. This was possible applying sophisticated numerical methods (POEM) developed at ZIB. Using advanced approaches for optimal control considering the costs for chemoprophylaxis, treatment and educational campaigns should provide a framework for designing realistic cost effective strategies with different intervention methods. The forward-backward sweep method has been used to solve the numerical optimal control problem. The numerical result of the optimal control problem reveals that combined effort in education and chemoprophylaxis may lead to a reduction of 80\% in the number of infected people in 10 years. The mathematical and numerical approaches developed in this thesis could be similarly applied in many other Sub-Saharan countries where TB is a public health problem. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000095327-7 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000095327 ER - TY - GEN A1 - Klindt, Marco A1 - Amrhein, Kilian A1 - Müller, Anja A1 - Peters-Kottig, Wolfgang T1 - Dealing with all the data – Participating in workflows to transform digital data about cultural heritage objects within a digital long-term preservation infrastructure N2 - Cultural heritage institutions are on the verge of making their artefacts available in digital form. During this transition they are faced with conceptual and technical challenges that have only little overlap with their traditional domains but provide them with a lot of opportunities. We aim at empowering them to deal with some of these challenges by designing workflows attached to the data flow within a digital long-term preservation system. The preservation framework processes data by utilising micro-services. These are tailored to accommodate data transformations that can help institutions making their data available if they choose to participate in the interconnected digital world T3 - ZIB-Report - 13-69 KW - data management KW - data workflows KW - digital preservation KW - cultural heritage Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43020 SN - 1438-0064 ER - TY - GEN A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Vorschrift oder Thunfisch? – Zur Langzeitverfügbarkeit von Forschungsdaten N2 - „Ich mache ihm ein Angebot, das er nicht ablehnen kann.” Diese Aussage aus einem gänzlich anderen Kontext lässt sich recht treffend übertragen als Wunsch von Dienstleistern und Zweck von Dienstleistungen für Datenproduzenten im Forschungsdatenmanagement. Zwar wirkt Druck zur Datenübergabe nicht förderlich, die Eröffnung einer Option aber sehr wohl. Im vorliegenden Artikel geht es um das Verständnis der Nachhaltigkeit von Forschung und ihren Daten anhand der Erkenntnisse und Erfahrungen aus der ersten Phase des DFG-Projekts EWIG. [Fn 01] Eine Auswahl von Fallstricken beim Forschungsdatenmanagement wird anhand der Erkenntnisse aus Expertengesprächen und eigenen Erfahrungen beim Aufbau von LZA-Workflows vorgestellt. Erste Konzepte in EWIG zur Datenübertragung aus unterschiedlich strukturierten Datenquellen in die „Langfristige Domäne” werden beschrieben. N2 - "I'm gonna make him an offer he can't refuse". This quote from a completely different context can be aptly rendered as a statement of service providers as well as the purpose of services for data producers in the field of research data management. Although pressure is not the leverage of choice if you want researchers to deposit their research data in some kind of repository, offering an option does the trick quite well. In this article we present some of the concepts for sustainability of research and its data from the first phase the of the project EWIG, funded by the Deutsche Forschungsgemeinschaft. A selection of pitfalls in research data management is presented based on the findings from expert interviews and our own experiences in the construction of LTP workflows. First concepts in EWIG to transfer data from differently structured data sources into the "Permanent Domain" are described. T3 - ZIB-Report - 13-70 KW - Langzeitverfügbarkeit KW - Forschungsdatenmanagement Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43010 UR - http://libreas.eu/ausgabe23/08hasler/ SN - 1438-0064 ER - TY - GEN A1 - Müller, Anja A1 - Rusch, Beate A1 - Amrhein, Kilian A1 - Klindt, Marco T1 - Unfertige Dialoge – Das Berliner Förderprogramm Digitalisierung N2 - Das Förderprogramm Digitalisierung des Landes Berlin fördert Digitalisierungsprojekte in Berliner Kulturerbeeinrichtungen und hat parallel dazu die Servicestelle Digitalisierung (digiS) als zentrale Beratungs- und Koordinierungsstelle eingerichtet. Ziel ist dabei, eine technische und organisatorische Infrastruktur für die Projekte sowie zur Sicherung der Langzeitverfügbarkeit digitalen Kulturguts vorzuhalten. Der Artikel beschreibt das Förderprogramm, das Aufgabenspektrum von digiS und die Herausforderungen, die sich für Kulturerbeinstitutionen ergeben, wenn sie sich auf den offenen Dialog mit ihren Nutzern einlassen und ihre Objekte digital langzeitverfügbar halten wollen. N2 - The city state of Berlin supports digitisation projects in its cultural heritage institutions and has established the Service Center for Digitisation (digiS) as a central supporting and coordinational unit. As a goal, a technical and organisational infrastructure for the projects as well as matters for the digital preservation of cultural heritage objects shall be provided. The article describes the support program, the range of tasks of digiS and the challenges that arise for cultural heritage institutions, if they want to open up and digitally preserve their objects for a long time. T3 - ZIB-Report - 13-68 KW - Kulturgut KW - Digitalisierung KW - Langzeitverfügbarkeit Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42991 SN - 1438-0064 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Grösser, Stefan N. A1 - Vierhaus, Ingmar T1 - A Global Approach to the Control of an Industry Structure System Dynamics Model N2 - We consider a system dynamics model that describes the effect of human activity on natural resources. The central stocks are the accumulated profit, the industry structures, and the water resources. The model can be controlled through two time-dependent parameters. The goal in this paper is to find a parameter setting that leads to a maximization of a performance index, which reflects both environmental and economic aspects. Thus, the goal is to identify the most sustainable stock of industry structures within the model's constraints and assumptions. In order to find a proven global optimal parameter set, we formulate the System Dynamics Optimization model as a mixed-integer nonlinear problem that is accessible for numerical solvers. Due to the dynamic structure of the model, certain steps of the solution process must be handled with greater care, compared to standard non-dynamic problems. We describe our approach of solving the industry structure model and present computational results. In addition, we discuss the limitations of the approach and next steps. T3 - ZIB-Report - 13-67 KW - System Dynamics; Mixed-Integer Nonlinear Optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42932 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael T1 - Solving hard MIPLIB2003 problems with ParaSCIP on Supercomputers: An update N2 - Contemporary supercomputers can easily provide years of CPU time per wall-clock hour. One challenge of today's software development is how to harness this wast computing power in order to solve really hard mixed integer programming instances. In 2010, two out of six open MIPLIB2003 instances could be solved by ParaSCIP in more than ten consecutive runs, restarting from checkpointing files. The contribution of this paper is threefold: For the first time, we present computational results of single runs for those two instances. Secondly, we provide new improved upper and lower bounds for all of the remaining four open MIPLIB2003 instances. Finally, we explain which new developments led to these results and discuss the current progress of ParaSCIP. Experiments were conducted on HLRNII, on HLRN III, and on the Titan supercomputer, using up to 35,200 cores. T3 - ZIB-Report - 13-66 KW - Mixed Integer Programming KW - MIPLIB2003 KW - ParaSCIP KW - Ubiquity Generator Framework KW - Supercomputer Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42888 SN - 1438-0064 ER - TY - THES A1 - Müller, Magnus T1 - Flexible Routing Tables in a Distributed Key-Value Store N2 - We present our implementation of Flexible Routing Tables (FRT) in the distributed key-value store Scalaris. Classic routing table generators like Chord structure routing tables by considering node identifiers only. Secondary requirements such as latency properties are considered after the general structure, eliminating potential performance gains. FRT aims to allow multiple requirements when creating routing tables. The concept is based on lazy routing table entries learning and filtering entries when a routing table is full. Entries are filtered such that the resulting table is best among all other possible tables where one node was filtered. FRT uses a total order to define which of the possible routing tables is best. We implemented two instances of FRT, namely FRT-Chord and grouped FRT-Chord (GFRT-Chord). We compare our implementation with the existing implementation of Chord in Scalaris and evaluate the advantages and disadvantages of more flexible routing schemes. KW - FRT KW - FRT-Chord KW - GFRT-Chord KW - Routing KW - DHT KW - Scalaris Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42742 ER - TY - GEN A1 - Blanco, Marco A1 - Schlechte, Thomas T1 - Analysis of Micro-Macro Transformations of Railway Networks N2 - A common technique in the solution of large or complex optimization problems is the use of micro-macro transformations. In this paper, we carry out a theoretical analysis of such transformations for the track allocation problem in railway networks. We prove that the cumulative rounding technique of Schlechte et al. satisfies two of three natural optimality criteria and that this performance cannot be improved. We also show that under extreme circumstances, this technique can perform inconvieniently by underestimating the global optimal value. T3 - ZIB-Report - 13-65 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42710 ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Finite-element based electromagnetic field simulations: Benchmark results for isolated structures T2 - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2026213 VL - 8880 SP - 88801Z ER - TY - GEN A1 - Götschel, Sebastian A1 - von Tycowicz, Christoph A1 - Polthier, Konrad A1 - Weiser, Martin T1 - Reducing Memory Requirements in Scientific Computing and Optimal Control N2 - In high accuracy numerical simulations and optimal control of time-dependent processes, often both many time steps and fine spatial discretizations are needed. Adjoint gradient computation, or post-processing of simulation results, requires the storage of the solution trajectories over the whole time, if necessary together with the adaptively refined spatial grids. In this paper we discuss various techniques to reduce the memory requirements, focusing first on the storage of the solution data, which typically are double precision floating point values. We highlight advantages and disadvantages of the different approaches. Moreover, we present an algorithm for the efficient storage of adaptively refined, hierarchic grids, and the integration with the compressed storage of solution data. T3 - ZIB-Report - 13-64 KW - optimal control KW - trajectory storage KW - mesh compression KW - compression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42695 SN - 1438-0064 ER - TY - GEN A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio T1 - A new theoretical framework for Robust Optimization under multi-band uncertainty N2 - We provide an overview of our main results about studying Linear Programming Problems whose coefficient matrix is subject to uncertainty and the uncertainty is modeled through a multi-band set. Such an uncertainty set generalizes the classical one proposed by Bertsimas and Sim and is particularly suitable in the common case of arbitrary non-symmetric distributions of the parameters. Our investigations were inspired by practical needs of our industrial partner in ongoing projects with focus on the design of robust telecommunications networks. T3 - ZIB-Report - 13-61 KW - Robust Optimization, Uncertainty Set, Multiband Robustness, Network Design Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42644 UR - http://www.springer.com/business+%26+management/operations+research/book/978-3-319-00794-6 SN - 1438-0064 ER - TY - GEN A1 - Bley, Andreas A1 - D'Andreagiovanni, Fabio A1 - Karch, Daniel T1 - Scheduling technology migration in WDM Networks N2 - The rapid technological evolution of telecommunication networks demands service providers to regularly update their technology, with the aim of remaining competitive in the marketplace. However, upgrading the technology in a network is not a trivial task. New hardware components need to be installed in the network and during the installation network connectivity may be temporarily compromised. The Wavelength Division Multiplexing (WDM) technology, whose upgrade is considered in here, shares fiber links among several optical connections and tearing down a single link may disrupt several optical connections at once. When the upgrades involve large parts of a network, typically not all links can be upgraded in parallel, which may lead to an unavoidable longer disruption of some connections. A bad scheduling of the overall endeavor, however, can dramatically increase the disconnection time of parts of the networks, causing extended service disruption. In this contribution, we study the problem of finding a schedule of the fiber link upgrades that minimizes the total service disruption time. To the best of our knowledge, this problem has not yet been formalized and investigated. The aim of our work is to close this gap by presenting a mathematical optimization model for the problem and an innovative solution algorithm that tackles the intrinsic difficulties of the problem. Computational experience on realistic instances completes our study. Our original investigations have been driven by real needs of DFN, operator of the German National Research and Education Network and our partner in the BMBF research project ROBUKOM (http://www.robukom.de/). T3 - ZIB-Report - 13-62 KW - Scheduling, Extended Formulations, Network Migration, WDM Networks Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42654 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6507677&isnumber=6507670 SN - 1438-0064 ER - TY - GEN A1 - Zakrzewska, Anna A1 - D'Andreagiovanni, Fabio A1 - Ruepp, Sarah A1 - Berger, Michael S. T1 - Biobjective Optimization of Radio Access Technology Selection and Resource Allocation in Heterogeneous Wireless Networks N2 - We propose a novel optimization model for resource assignment in heterogeneous wireless network. The model adopts two objective functions maximizing the number of served users and the minimum granted utility at once. A distinctive feature of our new model is to consider two consecutive time slots, in order to include handover as an additional decision dimension. Furthermore, the solution algorithm that we propose refines a heuristic solution approach recently proposed in literature, by considering a real joint optimization of the considered resources. The simulation study shows that the new model leads to a significant reduction in handover frequency, when compared to a traditional scheme based on maximum SNR. T3 - ZIB-Report - 13-63 KW - Heterogeneous Wireless Networks, Biobjective Optimization, Mixed Integer Linear Programming, Simulation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42675 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6576416&isnumber=6576384 SN - 1438-0064 ER - TY - CHAP A1 - Becker, Christiane A1 - Xavier, Jolly A1 - Preidel, Veit A1 - Wyss, Philippe A1 - Sontheimer, Tobias A1 - Rech, Bernd A1 - Probst, Jürgen A1 - Hülsen, Christoph A1 - Löchel, Bernd A1 - Erko, Alexei A1 - Burger, Sven A1 - Schmidt, Frank A1 - Back, Franziska A1 - Rudigier-Voigt, Eveline T1 - Nanophotonic light trapping in polycrystalline silicon thin-film solar cells using periodically nanoimprint-structured glass substrates T2 - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2023871 VL - 8824 SP - 88240D ER - TY - CHAP A1 - Carr, L. A1 - Brand, J. A1 - Burger, Sven A1 - Öhberg, P. A1 - Sanpera, Anna T1 - Dark soliton creation and interactions in Bose-Einstein condensates T2 - APS Meeting Abstracts Y1 - 2001 SP - 40045 ER - TY - GEN A1 - Shinano, Yuji A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - FiberSCIP - A shared memory parallelization of SCIP N2 - Recently, parallel computing environments have become significantly popular. In order to obtain the benefit of using parallel computing environments, we have to deploy our programs for these effectively. This paper focuses on a parallelization of SCIP (Solving Constraint Integer Programs), which is a MIP solver and constraint integer programming framework available in source code. There is a parallel extension of SCIP named ParaSCIP, which parallelizes SCIP on massively parallel distributed memory computing environments. This paper describes FiberSCIP, which is yet another parallel extension of SCIP to utilize multi-threaded parallel computation on shared memory computing environments, and has the following contributions: First, the basic concept of having two parallel extensions and the relationship between them and the parallelization framework provided by UG (Ubiquity Generator) is presented, including an implementation of deterministic parallelization. Second, the difficulties to achieve a good performance that utilizes all resources on an actual computing environment and the difficulties of performance evaluation of the parallel solvers are discussed. Third, a way to evaluate the performance of new algorithms and parameter settings of the parallel extensions is presented. Finally, current performance of FiberSCIP for solving mixed-integer linear programs (MIPs) and mixed-integer non-linear programs (MINLPs) in parallel is demonstrated. T3 - ZIB-Report - 13-55 KW - parallel KW - branch-and-bound KW - deterministic parallelism KW - constraint integer programming KW - mixed integer programming KW - mixed integer nonlinear programming KW - SCIP KW - MIP KW - MINLP Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42595 SN - 1438-0064 ER - TY - GEN A1 - Bujotzek, Alexander A1 - Schütt, Ole A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Efficient Conformational Analysis by Partition-of-Unity Coupling T2 - Math Chem N2 - Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent. T3 - ZIB-Report - 13-58 KW - Markov State Models KW - Meshfree KW - Molecular Simulation KW - Partition of Unity Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42570 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Mehrgardt, Julika A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Waas, Kerstin T1 - Re-optimization of Rolling Stock Rotations N2 - The Rolling Stock Rotation Problem is to schedule rail vehicles in order to cover timetabled trips by a cost optimal set of vehicle rotations. The problem integrates several facets of railway optimization, i.e., vehicle composition, maintenance constraints, and regularity aspects. In industrial applications existing schedules often have to be re-optimized to integrate timetable changes or construction sites. We present an integrated modeling and algorithmic approach for this task as well as computational results for industrial problem instances of DB Fernverkehr AG. T3 - ZIB-Report - 13-60 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42569 SN - 1438-0064 ER - TY - GEN A1 - Bauschert, Thomas A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Koster, Arie M.C.A. A1 - Kutschka, Manuel A1 - Steglich, Uwe T1 - Network Planning under Demand Uncertainty with Robust Optimization N2 - The planning of a communication network is inevitably depending on the quality of both the planning tool and the demand forecast used. In this article, we show exemplarily how the emerging area of Robust Optimization can advance the network planning by a more accurate mathematical description of the demand uncertainty. After a general introduction of the concept and its application to a basic network design problem, we present two applications: multi-layer and mixed-line-rate network design. We conclude with a discussion of extensions of the robustness concept to increase the accuracy of handling uncertainties. T3 - ZIB-Report - 13-59 KW - Network Design, Demand Uncertainty, Robust Optimization, Telecommunications Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42557 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Miltenberger, Matthias A1 - Weninger, Dieter T1 - Progress in Presolving for Mixed Integer Programming N2 - Presolving attempts to eliminate redundant information from the problem formulation and simultaneously tries to strengthen the formulation. It can be very effective and is often essential for solving instances. Especially for mixed integer programming problems, fast and effective presolving algorithms are very important. In this paper, we report on three new presolving techniques. The first method searches for singleton continuous columns and tries to fix the corresponding variables. Then we present a presolving technique which exploits a partial order of the variables to induce fixings. Finally, we show an approach based on connected components in graphs. Our computational results confirm the profitable use of the algorithms in practice. T3 - ZIB-Report - 13-48 KW - mixed-integer programming KW - presolving KW - preprocessing Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42530 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald T1 - Improving strong branching by domain propagation N2 - One of the essential components of a branch-and-bound based mixed-integer linear programming (MIP) solver is the branching rule. Strong branching is a method used by many state-of-the-art branching rules to select the variable to branch on. It precomputes the dual bounds of potential child nodes by solving auxiliary linear programs (LPs) and thereby helps to take good branching decisions that lead to a small search tree. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Domain propagation is a technique usually used at every node of the branch-and-bound tree to tighten the local domains of variables. Computational experiments on standard MIP instances indicate that our improved strong branching method significantly improves the quality of the predictions and causes almost no additional effort. For a full strong branching rule, we are able to obtain substantial reductions of the branch-and-bound tree size as well as the solving time. Moreover, also the state-of-the-art hybrid branching rule can be improved this way. This paper extends previous work by the author published in the proceedings of the CPAIOR 2013. T3 - ZIB-Report - 13-47 KW - mixed-integer programming KW - branch-and-bound KW - branching rule KW - variable selection KW - strong branching KW - domain propagation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42546 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung A1 - Karbstein, Marika A1 - Koch, Thorsten A1 - Martin, Alexander T1 - How Many Steiner Terminals Can You Connect in 20 Years? N2 - Steiner trees are constructed to connect a set of terminal nodes in a graph. This basic version of the Steiner tree problem is idealized, but it can effectively guide the search for successful approaches to many relevant variants, from both a theoretical and a computational point of view. This article illustrates the theoretical and algorithmic progress on Steiner tree type problems on two examples, the Steiner connectivity and the Steiner tree packing problem. T3 - ZIB-Report - 13-57 KW - Steiner tree KW - Steiner connectivity KW - Steiner tree packing Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42524 SN - 1438-0064 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials N2 - An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation. T3 - ZIB-Report - 13-56 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42510 SN - 1438-0064 ER - TY - GEN A1 - Ramm, Heiko A1 - Morillo Victoria, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Visual Support for Positioning Hearing Implants N2 - We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit. T3 - ZIB-Report - 13-53 KW - bone anchored hearing implant KW - surgery planning KW - segmentation KW - visualization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42495 SN - 1438-0064 ER - TY - THES A1 - Beckenbach, Isabel T1 - Special cases of the hypergraph assignment problem N2 - In this thesis we investigate the hyperassignment problem with a special focus on connections to the theory of hypergraphs, in particular balanced and normal hyper- graphs, as well as its relation to the Stable Set Problem. The main point is the investigation of the matching and perfect matching polytope for partitioned hypergraphs. Therefore, valid inequalities, facets, and the dimension of some polytopes are given. Furthermore, we show that the trivial LP-relaxation of the Hyperassignment Problem obtained by relaxing x_i ∈ {0, 1} by 0 ≤ x_i ≤ 1 has an arbitrarily large integrality gap, even after adding all clique inequalities. Whereas the integrality gap of the trivial LP-relaxation of the maximum weight matching problem for partitioned hypergraphs with maximum part size M is at most 2M − 1. Additionally, computational results for small partitioned hypergraphs of part size two are presented. Using symmetry it was possible to calculate all minimal fractional vertices of the fractional perfect matching polytope of partitioned hypergraphs with part size two having at most twelve vertices. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42480 ER - TY - GEN A1 - Wiebel, Alexander A1 - Müller, Cornelius A1 - Garth, Christoph A1 - Knösche, Thomas ED - Westin, Carl-Frederic ED - Burgeth, Bernhard ED - Vilanova, Anna T1 - A System for Combined Visualization of EEG and Diffusion Tensor Imaging Tractography Data T2 - Visualization and Processing of Tensors and Higher-Order Descriptors for Multi-field Data Y1 - 2014 SP - 325 EP - 337 PB - Springer ER - TY - THES A1 - Kratz, Andrea T1 - Three-Dimensional Second-Order Tensor Fields: Exploratory Visualization and Anisotropic Sampling N2 - Tensors provide a powerful mathematical language to describe physical phenomena. Consequently, they have a long tradition in physics and appear in various application areas, either as intermediate product or as output of simulations or measurements. The potential of tensors to describe complex anisotropic behavior, however, concurrently complicates their interpretation. The central research question of this thesis is how three-dimensional tensor fields of second order are visualized effectively so that, as a long term goal, their interpretation becomes easier. The focus of this thesis lies on the class of indefinite tensors. The methods that are proposed in this thesis fall into two main categories: (1.) the interactive exploration of the three-dimensional tensor data, and (2.) the geometric reduction of the data to two-dimensional planes or triangulated surfaces. In both cases, possible visualization approaches are presented. For interactive exploration of the data, we propose to combine diagram views with three-dimensional hybrid visualizations. We show that this facilitates familiarizing with the data and leads to exciting analytic queries. If a geometric data reduction is possible, we focus on glyph- and texture-based methods. In this context, the thesis is concerned with methods to improve their quality. Therefore, we propose two algorithms for the efficient creation of anisotropic sample distributions. Moreover, we present a novel visualization method that works on planar slices as well as on triangulated surfaces. The basic idea of this method is to use anisotropic sample distributions for the efficient computation of anisotropic Voronoi cells, which then are used as base elements for texture mapping. Hence, the usage of textures to encode the tensor’s various degrees of freedom becomes possible. We evaluate our methods for the interactive exploration on stress tensor fields from structure simulations. To show the ffectiveness of novel visualization methods, various datasets are presented. KW - visualization KW - tensors of second order KW - exploratory visualization KW - anisotropic sampling of tensor fields Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094629 ER - TY - THES A1 - Maier, Robert T1 - Massiv-parallele Suche und effiziente Heuristiken N2 - Pattern Datenbanken (PDBs) werden in der heuristischen Suche eingesetzt, um irrelevante Pfade in der Suche auszuschließen. Da die Leistung einer PDB mit ihrer Größe steigt und für die effektive heuristische Suche in großen Zustandsräumen große PDBs nötig sind, ist ein paralleler Ansatz notwendig, um sehr große PDBs zu erzeugen. Diese Arbeit erweitert einen, auf MapReduce basierenden, Algorithmus von Reinefeld und Schütt (2009) zur massiv-parallelen Breitensuche so, dass damit sehr große PDBs erzeugt werden können. So entsteht die erste vollständige 8+8+8 PDB für das 24er-Puzzle. Reinefeld und Schütt implementieren ebenfalls das heuristische Suchverfahren BFIDA* für MapReduce. In dieser Arbeit wird dieser Implementation ein Speedup von 857 bei 2039 Kernen nachgewiesen. Weiterhin führt diese Arbeit ein Schema ein, mit dem PDBs bei der Suche direkt von der Festplatte gelesen werden können. Des Weiteren wird der Nutzen von großen PDBs in einer Gruppe von PDBs untersucht, deren Heuristikwerte maximiert werden. Dazu wird analysiert, wie sich Gruppen von PDBs mit unterschiedlicher Größe verhalten und welche Faktoren bei solchen Konstellationen zum Erfolg der Gruppe beitragen. Es wird gezeigt, dass der Einsatz von großen PDBs effizient ist, wenn der zur Verfügung stehende Hauptspeicher ausreicht, eine Gruppe zusammen mit einigen kleineren PDBs zu bilden. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42448 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - A Primal-Dual Approximation Algorithm for the Steiner Connectivity Problem N2 - We extend the primal-dual approximation technique of Goemans and Williamson to the Steiner connectivity problem, a kind of Steiner tree problem in hypergraphs. This yields a (k+1)-approximation algorithm for the case that k is the minimum of the maximal number of nodes in a hyperedge minus 1 and the maximal number of terminal nodes in a hyperedge. These results require the proof of a degree property for terminal nodes in hypergraphs which generalizes the well-known graph property that the average degree of terminal nodes in Steiner trees is at most 2. T3 - ZIB-Report - 13-54 KW - Primal-Dual Approximation KW - Steiner Connectivity Problem KW - Degree Property KW - Hypergraph Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42430 SN - 1438-0064 ER - TY - GEN A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics N2 - Rare but important transition events between long lived states are a key feature of many molecular systems. In many cases the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible even on the most powerful computers because of the immensely long simulation timescales needed. Recently a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls. T3 - ZIB-Report - 13-52 KW - rare events KW - Markov state models KW - long timescales KW - optimal control Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42420 SN - 1438-0064 ER - TY - GEN A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics N2 - A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski's equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods. T3 - ZIB-Report - 13-51 KW - rare events KW - moleculare dynamics KW - optimal pathways KW - stochastic control KW - dynamic programming KW - change of measure KW - cumulant generating function Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42410 SN - 1438-0064 ER - TY - JOUR A1 - Grunzke, Richard A1 - Breuers, Sebastian A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kruse, Martin A1 - Blunk, Dirk A1 - de la Garza, Luis A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schärfe, Charlotta A1 - Schlemmer, Tobias A1 - Steinke, Thomas A1 - Schuller, Bernd A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Nagel, Wolfgang A1 - Atkinson, Malcolm A1 - Krüger, Jens T1 - Standards-based metadata management for molecular simulations JF - Concurrency and Computation: Practice and Experience Y1 - 2013 U6 - https://doi.org/10.1002/cpe.3116 ER - TY - THES A1 - Berlin, Michael T1 - Popularitätsbasierte Anpassung des Replikationsfaktors in verteilten Dateisystemen T1 - Popularity-based Adjustment of the Replication Factor in Distributed File Systems N2 - Verteilte Dateisysteme erlauben es zusätzliche Replikate von Dateien anzulegen, um Client-Zugriffe auf mehrere Server zu verteilen. Bei einer einheitlichen Festlegung des Replikationsfaktors für alle Dateien wird der beschränkte verfügbare Speicherplatz jedoch nicht effizient genutzt, da es nur einen geringen Anteil von Dateien gibt, die häufig angefragt werden, während die restlichen Dateien unnötig Speicherplatz belegen. Der erste Teil dieser Arbeit beschreibt daher ein Verfahren den Replikationsfaktor einer Datei in Abhängigkeit ihrer Popularität festzulegen. Im Kontext des verteilten Dateisystems XtreemFS wurde dazu ein zentraler Dienst für die dynamische Replikation implementiert und mit einem Trace simuliert. Die Auswertung zeigt, dass die popularitätsbasierte Anpassung ein geeignetes Verfahren ist den Replikationsfaktor dynamisch festzulegen, da bei einer wöchentlichen Ermittlung der Popularität weniger als durchschnittlich 3,1% zusätzliche Replikate angelegt wurden. Da der Dienst selbst nicht mit einer beliebigen Anzahl von Dateien skaliert, muss er in mehrere Partitionen unterteilt und dezentral ausgeführt werden. Darum entwickelt der zweite Teil der Arbeit eine dezentrale Variante des Dienstes und zeigt, dass der Replikationsfaktor identisch zum zentralen Fall festgelegt werden kann. Nur im Fall eines Netzwerkausfalls oder nicht synchronisierter lokaler Uhren tritt eine Abweichung der Replikationsfaktoren auf, deren Ausmaß in der Simulation untersucht wurde. N2 - Distributed file systems allow the creation of additional file replicas in order to spread requests across several servers. However, setting a uniform number of replicas for every file would not utilize the available storage space in an efficient manner. As there are only few popular files, the majority of files would unnecessarily use up the limited space. Therefore the first part of this thesis presents a method to adjust the replication factor depending on the popularity of the files. This method was implemented as a central service for dynamic replication in the context of the distributed file system XtreemFS. The service was then simulated using a trace. A weekly observation of the popularity resulted in an average creation rate of 3.1% compared to all replicas. This shows that popularity-based adjustment is a feasible way to set the replication factor dynamically. As the service itself does not scale with the number of observed files, it needs to be partitioned and executed in a distributed manner. Therefore the second part of this thesis develops a distributed version of the service and shows that it determines replication factors equal to the result of the central version. However, the replication factor may vary if there is a network outage or a drift of the local clocks. The degree of variation was analyzed in simulations. Y1 - 2011 N1 - Thesis for the German Diplom degree (comparable to a Master degree) in Computer Science. ER - TY - THES A1 - Hoffmann, Marie T1 - Approximate Algorithms for Distributed Systems N2 - Peer-to-peer (P2P) systems form a special class of distributed systems. Typically, nodes in a P2P system are flat and share the same responsabilities. In this thesis we focus on three problems that occur in P2P systems: the storage of data replicates, quantile computation on distributed data streams, and churn rate estimation. Data replication is one of the oldest techniques to maintain stored data in a P2P system and to reply to read requests. Applications, which use data replication are distributed databases. They are part of an abstract overlay network and do not see the underlying network topology. The question is how to place a set of data replicates in a distributed system such that response times and failure probabilities become minimal without a priori knowledge of the topology of the underlying hardware nodes? We show how to utilize an agglomerative clustering procedure to reach this goal. State-of-the-art algorithms for aggregation of distributed data or data streams require at some point synchronization, or merge data aggregates hierarchically, which does not accompany the basic principle of P2P systems. We test whether randomized communication and merging of data aggregates are able to produce the same results. These data aggregates serve for quantile queries. Constituting and maintaining a P2P overlay network requires frequent message passing. It is a goal to minimize the number of maintenance messages since they consume bandwidth which might be missing for other applications. The lower bound of the frequency for mainte- nance messages is highly dependent on the churn rate of peers. We show how to estimate the mean lifetime of peers and to reduce the frequency for maintenance messages without destabilizing the infrastructure of the constituting overlay. KW - peer-to-peer, machine learning, approximate, clustering, quantile, linear regression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42370 ER - TY - GEN A1 - Krause, Dorian A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements N2 - It is the ultimate goal of concurrent multiscale methods to provide computational tools that allow to simulation physical processes with the accuracy of micro-scale and the computational speed of macro-scale models. As a matter of fact, the efficient and scalable implementation of concurrent multiscale methods on clusters and supercomputers is a complicated endeavor. In this article we present the parallel multiscale simulation tool MACI which has been designed for efficient coupling between molecular dynamics and finite element codes. We propose a specification for a thin yet versatile interface for the coupling of molecular dynamics and finite element codes in a modular fashion. Further we discuss the parallelization strategy pursued in MACI, in particular, focusing on the parallel assembly of transfer operators and their efficient execution. T3 - ZIB-Report - 13-50 KW - Parallel KW - Atomistic to Continuum KW - Multiscale KW - MACI KW - Meshfree Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42354 SN - 1438-0064 ER - TY - THES A1 - Buwaya, Julia T1 - Optimizing control in a transportation network when users may choose their OD-path N2 - This thesis represents a game-theoretic investigation of the allocation of inspectors in a transportation network, comparing Nash and Stackelberg equilibrium strategies to a strategy in which inspections are conducted proportionally to the traffic volume. It contains specifications for the integration of space and time dependencies and extensive experimental tests for the application on the transportation network of German motorways using real data. Main results are that - although the formulated spot-checking game is not zero-sum - we are able to compute a Nash equilibrium using linear programming and secondly, that experimental results yield that a Nash equilibrium strategy represents a good trade-off for the Stackelberg equilibrium strategy between efficiency of controls and computation time. KW - Optimization KW - Transportation Network KW - Game Theory KW - Stackelberg Equilibrium KW - Mixed Integer Programming KW - Security Game KW - Linear Programming KW - Nash Equilibrium Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42330 ER - TY - THES A1 - Lange, Maik T1 - Effiziente Reparatur von Repliken in Distributed Hash Tables N2 - Eine distributed hash Table (DHT) stellt eine über multiple Rechner strukturiert verteilte Tabelle von Schlüssel-Wert-Paaren dar. Ein verteiltes System unterliegt zumeist einer Teilnehmerdynamik in Form von ausfallenden oder beitretenden Knoten, wodurch Daten verloren gehen können. Zur Sicherstellung der Verfügbarkeit aller Schlüssel-Wert-Paare ist Redundanz notwendig. Die Einführung einer Redundanzschicht erhöht die Verfügbarkeit der Daten erheblich auf Kosten einer verringerten Leistungsfähigkeit. Der Fokus dieser Arbeit liegt im Erhalt der Redundanz, was die Regeneration verlorener Kopien sowie eine Aktualisierung veralteter Kopien umfasst. Die Regeneration verlorener Kopien ist notwendig um die Verfügbarkeit langfristig zu sichern. Die Aktualisierung ist optional und verbessert die Leselatenz in geografisch weit verteilten Systemen. Die vorgestellte Lösung besteht aus drei Komponenten. Der Set Reconciliation Dienst ermöglicht den effizienten Vergleich zweier Knoten zur Identifikation verlorener und veralteter Kopien. Der Aktualisierungsdienst synchronisiert die verglichenen Knoten durch die Übertragung der Differenzen. Die dritte Komponente ist ein Anti-Entropie Protokoll, dass die Auswahl eines jeden Knotens als Synchronisationspartner sicherstellt. Das Ziel dieser Arbeit liegt in dem Vergleich dreier Set Reconciliation Algorithmen, deren Eignung und Leistungsfähigkeit für die Erkennung verlorener und veralteter Kopien evaluiert werden soll. Ausgewählt wurden der Bloom Filter, der Merkle-Tree sowie deren Kombination der Approximate Reconciliation Tree. Die Evaluation zeigte, dass der Merkle-Tree die höchste Genauigkeit besitzt und spätestens nach einer initiierten Synchronisation eines jeden Knotens zur vollständigen Synchronität in der DHT führt. Der Bloom Filter besitzt bei der Erkennung verlorener Repliken nur die halbe Genauigkeit gegenüber veralteten Repliken, wodurch die Konvergenzgeschwindigkeit dementsprechend geringer ist gegenüber dem Merkle-Tree. Dafür sind die Übertragungskosten des Bloom Filter um bis zu 80% geringer als beim Merkle-Tree und weisen kaum nennenswerte Spitzen auf. Die Übertragungskosten des Merkle-Tree sind abhängig von der Anzahl der Differenzen, sodass bei einer Differenz von Null nur eine Signatur mit weniger als einem kByte übertragen werden muss. Ist die Differenz größer, steigen die Kosten je nach Bucket-Größe an. Der Approximate Reconciliation Tree ist ein als Bloom Filter codierter Merkle-Tree, der je nach Parameterkonstellation die Eigenschaften einer der beiden Strukturen aufweist. Die Bloom Filter ähnlichen Konfigurationen bieten keinen Vorteil, wohingegen die Merkle-Tree ähnlichen nur zwei Mitteilungsrunden benötigen bei einer leichten Genauigkeitsverringerung gegenüber dem Merkle-Tree. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42275 ER - TY - THES A1 - Keidel, Stefan T1 - Snapshots in Scalaris N2 - Eines der größten Hindernisse beim praktischen Einsatz von Scalaris, einer skalierbaren Implementierung einer verteilten Hashtabelle mit Unterstützung für Transaktionen, ist das Fehlen eines Verfahrens zur Aufnahme eines konsistenten Zustandes des gesamten Systems. Wir stellen in dieser Arbeit ein einfaches Protokoll vor, dass diese Aufgabe erfüllt und sich, auf Grund der von uns gewählten Herangehensweise, leicht implementieren lässt. Als Ausgangspunkt dafür wählen wir aus einer Reihe von „klassischen“ Snapshot-Algorithmen ein 1993 von Mattern entworfenes Verfahren, welches auf dem Algorithmus von Lai und Yang basiert, aus. Diese Entscheidung basiert auf einer gründlichen Analyse der Protokolle unter Berücksichtigung der Architektur der existierenden Software. Im nächsten Arbeitsschritt benutzen wir unser vollständiges Wissen über die Interna des Transaktionssystems von Scalaris und vereinfachen damit das Verfahren hinsichtlich Benutzbarkeit und Implementierungskomplexität, ohne die Anforderungen an den aufgenommenen Zustand aufzuweichen. Statt einer losen Anhäufung lokaler Zustände der einzelnen Teilnehmerknoten können wir am Ende eine große Schlüssel-Wert-Tabelle als Ergebnis erzeugen, die konsistent ist, sich leicht weiterverarbeiten lässt und die einem Zustand entspricht, in dem sich das System einmal befunden haben könnte. Nachdem wir das Verfahren dann in Software umgesetzt haben, werten wir die Ergebnisse hinsichtlich des Einflusses auf die Performanz des Gesamtsystems aus und diskutieren mögliche Weiterentwicklungen. KW - scalaris KW - dht KW - algorithm Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42282 ER - TY - THES A1 - Hupfeld, Felix T1 - Causal weak-consistency replication – a systems approach Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?nbn:de:kobv:11-100100235 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=29970 ER - TY - GEN A1 - Heismann, Olga A1 - Hildenbrandt, Achim A1 - Silvestri, Francesco A1 - Reinelt, Gerhard A1 - Borndörfer, Ralf T1 - HUHFA: A Framework for Facet Classification N2 - Usually complete linear descriptions of polytopes consist of an enormous number of facet-defining inequalities already for very small problem sizes. In this paper, we describe a method for dividing the inequalities into equivalence classes without resorting to a normal form. Within each class, facets are related by certain symmetries and it is sufficient to list one representative of each class to give a complete picture of the structural properties of a polytope. We propose an algorithm for the classification and illustrate its efficiency on a broad range of combinatorial optimization problems including the Traveling Salesman and the Linear Ordering Problem. T3 - ZIB-Report - 13-45 KW - facet classification KW - symmetry KW - polyhedral structure Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42230 SN - 1438-0064 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects N2 - Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces. T3 - ZIB-Report - 13-46 KW - memory footprint KW - non-linear objects KW - static analysis KW - dynamic analysis Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42224 SN - 1438-0064 ER - TY - THES A1 - Witzig, Jakob T1 - Effiziente Reoptimierung in Branch&Bound-Verfahren für die Steuerung von Aufzügen N2 - Heutzutage ist eine Vielzahl der mehrstöckigen Gebäude mit Personenaufzugsgruppen ausgestattet. Uns wohl bekannt sind die sogenannten konventionellen Systeme. Bei diesen Systemen betätigt jeder ankommende Passagier eine der beiden Richtungstasten und teilt dem dahinterstehenden Steuerungsalgorithmus seine gewünschte Startetage und Fahrtrichtung mit. Betreten wird der zuerst auf der Startetage ankommende Aufzug mit gleicher Fahrtrichtung und ausreichend Kapazität. Die entsprechende Zieletage wird dem System erst nach dem Betreten der Fahrgastkabine mitgeteilt. Neben diesen konventionellen Systemen gibt es Aufzugsgruppen mit Zielrufsteuerung. Die Besonderheit eines zielrufgesteuerten Systems ist, dass ein ankommender Passagier bereits auf der Startetage seine gewünschte Zieletage angibt und eine Rückmeldung vom System erhält, welchen Aufzug er nutzen soll. Diese Zuweisung durch das System hat das Ziel, die Warte- und Reisezeiten der Passagiere zu minimieren. Ein wesentlicher Faktor bei der Berechnung warte- und reisezeitminimaler Fahrpläne ist das momentane Verkehrsmuster. Eine Einteilung der Verkehrsszenarien lässt sich am besten bei Bürogebäuden vornehmen. So ist es typisch für die Morgenstunden, dass jeder Passagier auf einer Zugangsebene seine Fahrt beginnt und alle Passagiere die gleiche Fahrtrichtung haben. Unter einer Zugangsebene ist z. B. der Haupteingang oder ein Parkdeck zu verstehen. Ein weiterer wesentlicher Punkt bei Zielrufsystemen ist die Art der Zuweisung der Passagiere durch das System. Zum einen gibt es unmittelbar zuweisende (UZ-) Systeme. In einem UZ-System wird nach jeder Ankunft eines Passagiers eine Momentaufnahme des momentanen Verkehrs erstellt und es findet eine Neuplanung und Zuweisung statt. Eine solche Momentaufnahme werden wir im späteren Verkauf als Schnappschussproblem bezeichnen. Jeder Passagier bekommt im Anschluss an die Lösung des Schnappschussproblems eine Mitteilung vom System, z. B. über ein Display, welchen Aufzug er benutzen soll. Zum anderen gibt es verzögert zuweisende (VZ-) Systeme. In diesen Systemen wird die Erstellung und Lösung eines Schnappschussproblems bis kurz vor Ankunft eines Aufzuges auf einer Etage verzögert. In einem VZ-System teilt das System allen wartenden Passagieren die geplanten Zieletagen des ankommenden Aufzugs mit. Jeder Passagier, der einen Ruf getätigt hat und zu einer dieser Zieletagen fahren will, kann jetzt diesen Aufzug betreten. Durch die Verzögerung muss im Vergleich zu einem UZ-System eine weitaus größere Menge von Passagieren zugewiesen werden. Dadurch kann der Lösungsprozess bedeutend aufwändiger werden. Vorteil eines VZ-Systems ist hingegen der größere Freiheitsgrad bei der Optimierung, da aufgrund der späten Zuweisung die weitere Verkehrsentwicklung mit einbezogen werden kann. VZ-Systeme sind aufgrund des größeren Freiheitsgrades interessant für die Praxis ist, wir uns demzufolge in dieser Arbeit mit einer effizienteren Lösung dieser Art von Schnappschussproblemen befassen. Es genügt dabei den Lösungsprozess eines Schnappschussproblems zu betrachten. Das Ziel ist eine Reduzierung der benötigten Rechenzeit. Unter Reoptimierung verstehen wir die Konstruktion zulässiger Spalten in den jeweiligen Iterationsrunden der Spaltengenerierung innerhalb eines Schnappschussproblems. Als eine Iterationsrunde bezeichnet wir einer Menge zulässiger Touren mit negativen reduzierten Kosten. Eine effiziente Reoptimierung zeichnet sich durch die Wiederverwendung und Aufbereitung von Informationen aus vorangegangenen Iterationsrunden desselben Schnappschussproblems aus. Zu den wichtigen Informationen gehört der konstruierte Suchbaum der vorherigen Iterationsrunde mit seinen ausgeloteten (abgeschnittenen) Blättern sowie konstruierten Touren bzw. Spalten, welche in der Iterationsrunde ihrer Konstruktion nicht zur Lösung des Teilproblems der Spaltengenerierung beitrugen. Eine solche Wiederverwendung und Aufbereitung von Informationen nennen wir Warmstart. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42210 ER - TY - GEN A1 - Lie, Han Cheng A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - A square root approximation of transition rates for a Markov State Model N2 - Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge. T3 - ZIB-Report - 13-43 KW - Markov State Models KW - Markov chains KW - meshfree methods KW - metastability KW - Voronoi KW - linear programming Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42195 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU N2 - Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated. T3 - ZIB-Report - 13-44 KW - Swendsen-Wang Multi-Cluster Algorithm KW - Ising Model KW - Xeon Phi KW - GPGPU KW - Connected Component Labeling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42187 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo T1 - Primal MINLP Heuristics in a nutshell N2 - Primal heuristics are an important component of state-of-the-art codes for mixed integer nonlinear programming (MINLP). In this article we give a compact overview of primal heuristics for MINLP that have been suggested in the literature of recent years. We sketch the fundamental concepts of different classes of heuristics and discuss specific implementations. A brief computational experiment shows that primal heuristics play a key role in achieving feasibility and finding good primal bounds within a global MINLP solver. T3 - ZIB-Report - 13-42 KW - Primal Heuristic KW - MINLP KW - Mixed Integer Nonlinear Programming KW - Feasibility Pump KW - Large Neighborhood Search Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42170 SN - 1438-0064 ER - TY - THES A1 - Wende, Florian T1 - Dynamic Load Balancing on Massively Parallel Computer Architectures N2 - This thesis reports on using dynamic load balancing methods on massively parallel computers in the context of multithreaded computations. In particular we investigate the applicability of a randomized work stealing algorithm to ray tracing and breadth-first search as representatives of real-world applications with dynamic work creation. For our considerations we made use of current massively parallel hardware accelerators: Nvidia Tesla M2090, and Intel Xeon Phi. For both of the two we demonstrate the suitability of the work stealing scheme for the said real-world applications. Also the necessity of dynamic load balancing for irregular computations on such hardware is illustrated. N2 - Vorliegende Bachelorarbeit befasst sich mit Methoden der dynamischen Lastbalancierung auf massiv parallelen Computern im Rahmen von mehrprozess gestützten Ausführungen von Programmen. Im einzelnen wird die Eignung eines randomisierten Work-Stealing Algorithmus für die Ausführung realer Anwendungen mit dynamischer Arbeitserzeugung, wie Ray-Tracing und Breitensuche, untersucht. Für die entsprechenden Betrachtungen wer den aktuelle massiv parallele Hardwarebeschleuniger vom Typ Nvidia Tesla M2090 und Intel Xeon Phi verwendet. Für beide Beschleunigertypen konnte die Tauglichkeit des Work-Stealing Schemas für die genannten Anwendungen gezeigt werden. Ebenfalls wird die Notwendigkeit der Verwendung dynamischer Lastausgleichsmethoden für irreguläre Berechnungen auf der genannten Hardware verdeutlicht. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42166 ER - TY - THES A1 - Wende, Florian T1 - Simulation of Spin Models on Nvidia Graphics Cards using CUDA N2 - This thesis reports on simulating spin models on Nvidia graphics cards using the CUDA programming model; a particular approach for making GPGPU (General Purpose Computation on Graphics Processing Units) available for a wide range of software developers not necessarily acquainted with (massively) parallel programming. By comparing program execution times for simulations of the Ising model and the Ising spin glass by means of the Metropolis algorithm on Nvidia Tesla C1060 graphics cards and an Intel Core i7-920 quad-core x86 CPU (we used OpenMP to make our simulations run on all 4 execution units of the CPU), we noticed that the Tesla C1060 performed about a factor 5-10 faster than the Core i7-920, depending on the particular model and the accuracy of the calculations (32-bit or 64-bit). We also investigated the reliability of GPGPU computations, especially with respect to the occurrence of soft-errors as suggested in [23]. We noticed faulty program outputs during long-time simulations of the Ising model on ''large'' lattices. We were able to link these problems to overheating of the corresponding graphics cards. Doing Monte Carlo simulations on parallel computer architectures, as was the case in this thesis, suggests to also generate random numbers in a parallel manner. We present implementations of the random number generators Ranlux and Mersenne Twister. In addition, we give an alternative and very efficient approach for producing parallel random numbers on Nvidia graphics cards. We successfully tested all random number generators used in this thesis for their quality by comparing Monte Carlo estimates against exact calculations. N2 - Vorliegende Diplomarbeit befasst sich mit der Simulation von Spin-Modellen auf Nvidia Grafikkarten. Hierbei wird das Programmiermodell CUDA verwendet, welches einer breiten Masse von Softwareentwicklern den Zugang zu GPGPU (General Purpose Computation on Graphics Processing Units) gestattet ohne dass diese notwendigerweise mit (massiv) paralleler Programmierung vertraut sein müssen. Im Rahmen von Vergleichen der Programmlaufzeiten für Simulationen des Ising- Modells sowie des Ising-Spin-Glases auf Nvidia Tesla C1060 Grafikkarten und einer Intel Core i7-920 x86 Quad-Core-CPU war zu vermerken, dass, abhängig vom konkreten Modell und der Rechengenauigkeit (32-bit oder 64-bit), die Tesla C1060 zwischen 5-10 mal schneller arbeitete als die Core i7-920 Quad-Core-CPU. Wir haben uns ebenfalls mit der Zuverlässigkeit von GPGPU-Rechnungen befasst, gerade in Hinblick auf das Auftreten von Soft-Errors, wie es in [23] angedeutet wird. Wir beobachteten falsche Programmausgaben bei langen Simulationen des Ising-Modells auf ,,großen'''' Gittern. Es gelang uns die auftretenden Probleme mit Überhitzung der entsprechenden Grafikkarten in Verbindung zu bringen. Für die Durchführung von Monte-Carlo-Simulationen auf Parallelrechnerarchitekturen, wie es in vorliegender Arbeit der Fall ist, liegt es nahe auch Zufallszahlen parallel zu erzeugen. Wir präsentieren Implementierungen der Zufallszahlengeneratoren Ranlux und Mersenne Twister. Zusätzlich stellen wir eine alternative und sehr effiziente Möglichkeit vor parallele Zufallszahlen auf Nvidia Grafikkarten zu erzeugen. Alle verwendeten Zufallszahlengeneratoren wurden erfolgreich auf ihre Qualität getestet indem Monte-Carlo-Schätzer exakten Rechnungen gegenübergestellt wurden. Y1 - 2010 UR - http://edoc.hu-berlin.de/master/wende-florian-2010-10-20/PDF/wende.pdf ER - TY - JOUR A1 - Burger, Sven A1 - Bongs, Kai A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang ED - Martellucci, Sergio ED - Chester, Arthur N. ED - Aspect, Alain ED - Inguscio, Massimo T1 - Atom Optics With Bose-Einstein Condensates JF - Bose-Einstein Condensates and Atom Lasers Y1 - 2002 U6 - https://doi.org/10.1007/0-306-47103-5_7 SP - 97 EP - 115 PB - Springer US ER - TY - CHAP A1 - Skibina, Julia A1 - Iliew, Rumen A1 - Bethge, Jens A1 - Bock, Martin A1 - Fischer, Dorit A1 - Beloglazov, Valentin A1 - Wedell, Reiner A1 - Burger, Sven A1 - Steinmeyer, Günter T1 - A chirped photonic crystal fiber for high-fidelity guiding of sub-100 fs pluses T2 - CLEO/QELS Y1 - 2009 U6 - https://doi.org/10.1364/CLEO.2009.CMHH1 SP - CMHH1 ER - TY - CHAP A1 - Burger, Sven A1 - Bongs, Kai A1 - Dettmer, S. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus A1 - Sanpera, Anna A1 - Shlyapnikov, Gora A1 - Lewenstein, Maciej T1 - Dark solitons in Bose-Einstein condensates T2 - Quantum Electronics and Laser Science Conference (QELS 2000) Y1 - 2000 SP - 214 EP - 215 ER - TY - CHAP A1 - Bongs, Kai A1 - Burger, Sven A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang T1 - Atom optics with Bose-Einstein condensates T2 - Quantum Electronics and Laser Science Conference (QELS 2000) Y1 - 2000 SP - 98 ER - TY - CHAP A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus A1 - Sanpera, Anna A1 - Shlyapnikov, Gora A1 - Lewenstein, Maciej T1 - Soliton dynamics in Bose-Einstein condensates T2 - Quantum Electronics Conference Y1 - 2000 U6 - https://doi.org/10.1109/IQEC.2000.907800 SP - 1 ER - TY - CHAP A1 - Pomplun, Jan A1 - Burger, Sven A1 - Rozova, Maria A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Finite element simulation of optical modes in VCSELs T2 - Numerical Simulation of Optoelectronic Devices (NUSOD), 11th International Conference on Y1 - 2011 U6 - https://doi.org/10.1109/NUSOD.2011.6041170 SP - 119 EP - 120 ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle T2 - Workshop on Computer Games Y1 - 2013 ER - TY - GEN A1 - Pyszkalski, Wolfgang T1 - Übersicht über die Datenhaltung im ZIB und die Möglichkeiten einer Nutzung durch Projekte N2 - Dieser Bericht beschreibt in allgemein verständlicher Form die Struktur der Datenhaltung im Zuse‐Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer stärker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten über im Grunde unbegrenzte Zeit. T3 - ZIB-Report - 13-16 KW - Langfristige Datenhaltung KW - Speichersysteme KW - Magnetband KW - Vertrauenswürdigkeit des Langzeitspeichers KW - Sicherstellung der Lesbarkeit des Bandmaterials Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42060 SN - 1438-0064 ER - TY - CHAP A1 - Hlawitschka, Mario A1 - Hotz, Ingrid A1 - Kratz, Andrea A1 - Marai, G. Elisabeta A1 - Moreno, Rodrigo A1 - Scheuermann, Gerik A1 - Stommel, Markus A1 - Wiebel, Alexander A1 - Zhang, Eugene ED - Westin, Carl-Frederic ED - Burgeth, Bernhard ED - Vilanova, Anna T1 - Top Challenges in the Visualization of Engineering Tensor Fields T2 - Visualization and Processing of Tensors and Higher-Order Descriptors for Multi-Field Data Y1 - 2014 SP - 3 EP - 15 PB - Springer ER - TY - GEN A1 - Meisel, Kristin A1 - Röblitz, Susanna T1 - Mathematische Modellierung der Knochenremodellierung N2 - Knochenremodellierung beinhaltet den Auf- und Abbau der Knochenmasse durch die verschiedenen Knochenzellen und findet fast überall, auch am Skelett Erwachsener, statt. Für die Erneuerung der Knochensubstanz sind die Osteoblasten zuständig. Sie ersetzen exakt die Menge der Knochenmasse, welche zuvor durch Osteoklasten abgebaut wurde. Störungen dieses, durch viele Faktoren beeinflussten Prozesses führen zu pathologischen Veränderungen, beispielsweise zu Osteoporose oder Arthritis. Auf der Grundlage analysierter publizierter Modelle wurde ein Modell entwickelt, welches den Einfluss einiger dieser Faktoren realistisch abbildet. Auf diese Weise kann die Wirkung von basalem PTH, des RANKL-OPG-Systems ( RANKL: Receptor activator of nuclear factor kappa-B ligand, OPG: Osteoprotegerin) und des Estradiols auf den Knochenstoffwechsel am vorgestellten System untersucht werden. Außerdem wurde durch Estradiolmangel hervorgerufene Osteoporose und der kurative Effekt von synthetischen Medikamenten wie Estradiol oder intermittierend verabreichtem PTH modelliert. Mit der Parameterschätzung anhand des Gauß-Newton-Verfahrens wird des Weiteren eine Methode vorgestellt, die es ermöglicht, mathematische Modelle bestmöglich durch Variation der Parameterwerte an experimentelle Daten anzupassen. Das am Zuse-Institut Berlin entwickelte Softwarepaket POEM wendet diesen Algorithmus an und wird ebenfalls erläutert. T3 - ZIB-Report - 13-41 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42010 SN - 1438-0064 ER - TY - GEN A1 - Lehmann, Felix T1 - Inexaktheit in Newton-Lagrange-Verfahren für Optimierungsprobleme mit Elliptischen PDGL-Nebenbedingungen N2 - Bei der numerischen Lösung von Optimalsteuerungsproblemen mit elliptischen partiellen Differentialgleichungen als Nebenbedingung treten unvermeidlich Diskretisierungs- und Iterationsfehler auf. Man ist aus Aufwandsgründen daran interessiert die dabei entstehenden Fehler nicht sehr klein wählen zu müssen. In der Folge werden die linearisierten Nebenbedingungen in einem Composite-Step-Verfahren nicht exakt erfüllt. In dieser Arbeit wird der Einfluss dieser Ungenauigkeit auf das Konvergenzverhalten von Newton-Lagrange-Verfahren untersucht. Dabei sollen mehrere einschlägige lokale Konvergenzresultate diskutiert werden. Anschließend wird ein konkretes Composite-Step-Verfahren formuliert, in dem die Genauigkeit der inneren Iterationsverfahren adaptiv gesteuert werden kann. Am Ende der Arbeit wird an zwei Musterproblemen die hohe Übereinstimmung der analytischen Voraussagen und der tatsächlichen Performanz der dargestellten Methoden demonstriert. T3 - ZIB-Report - 13-37 KW - optimal control KW - PDE KW - inexact Newton Lagrange KW - adaptive Newton Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41972 SN - 1438-0064 ER - TY - GEN A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 N2 - Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodefficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs. T3 - ZIB-Report - 13-34 KW - information costs KW - hidden state KW - bellmann equation KW - optimal therapeutic policies KW - diagnostic frequency KW - resource-poor KW - resource-rich Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41955 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume A1 - Harman, Radoslav T1 - Computing exact D-optimal designs by mixed integer second order cone programming N2 - Let the design of an experiment be represented by an $s$-dimensional vector $\vec{w}$ of weights with non-negative components. Let the quality of $\vec{w}$ for the estimation of the parameters of the statistical model be measured by the criterion of $D$-optimality defined as the $m$-th root of the determinant of the information matrix $M(\vec{w})=\sum_{i=1}^s w_iA_iA_i^T$, where $A_i$, $i=1,...,s$, are known matrices with $m$ rows. In the paper, we show that the criterion of $D$-optimality is second-order cone representable. As a result, the method of second order cone programming can be used to compute an approximate $D$-optimal design with any system of linear constraints on the vector of weights. More importantly, the proposed characterization allows us to compute an \emph{exact} $D$-optimal design, which is possible thanks to high-quality branch-and-cut solvers specialized to solve mixed integer second order cone problems. We prove that some other widely used criteria are also second order cone representable, for instance the criteria of $A$-, and $G$-optimality, as well as the criteria of $D_K$- and $A_K$-optimality, which are extensions of $D$-, and $A$-optimality used in the case when only a specific system of linear combinations of parameters is of interest. We present several numerical examples demonstrating the efficiency and universality of the proposed method. We show that in many cases the mixed integer second order cone programming approach allows us to find a provably optimal exact design, while the standard heuristics systematically miss the optimum. T3 - ZIB-Report - 13-39 KW - Optimal Design of Experiments KW - D-optimality KW - SOCP Representability KW - Exact Designs Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41932 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - A Configuration Model for the Line Planning Problem N2 - We propose a novel extended formulation for the line planning problem in public transport. It is based on a new concept of frequency configurations that account for all possible options to provide a required transportation capacity on an infrastructure edge. We show that this model yields a strong LP relaxation. It implies, in particular, general classes of facet defining inequalities for the standard model. T3 - ZIB-Report - 13-40 KW - combinatorial optimization KW - polyhedral combinatorics KW - line planning Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41903 SN - 1438-0064 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes N2 - We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements. T3 - ZIB-Report - 13-38 KW - digitally reconstructed radiographs KW - volume rendering KW - mesh deformation KW - statistical shape and intensity models KW - image registration KW - GPU acceleration Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41896 SN - 1438-0064 ER - TY - BOOK A1 - Hege, Hans-Christian A1 - (Eds.), Konrad T1 - Visualization and Mathematics - Experiments, Simulations and Environments Y1 - 1997 SN - ISBN 3-540-61269-6 PB - Springer-Verlag, Berlin/Heidelberg ER - TY - BOOK A1 - Hege, Hans-Christian A1 - Polthier, Konrad T1 - VideoMath - Festival at ICM 98 T3 - Springer VideoMath Y1 - 1998 SN - 978-3-540-21385-7 ER - TY - BOOK A1 - Hege, Hans-Christian A1 - (Eds.), Konrad T1 - Mathematical Visualization - Algorithms, Applications, and Numerics Y1 - 1998 SN - ISBN 3-540-63991-8 PB - Springer CY - Heidelberg ER - TY - BOOK ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Visualization and Mathematics III Y1 - 2003 SN - 3-540-01295-8 PB - Springer ER - TY - BOOK ED - Hege, Hans-Christian ED - Machiraju, Raghu T1 - Volume Graphics 2007 Y1 - 2007 SN - 978-1-56881-367-7 PB - AK Peters ER - TY - GEN ED - Polthier, Konrad ED - Aigner, Martin ED - M. Apostol, Tom ED - Emmer, Michele ED - Hege, Hans-Christian ED - Weinberg, Ulrich T1 - MathFilm Festival 2008 Y1 - 2008 ER - TY - BOOK ED - Hege, Hans-Christian ED - Laidlaw, David ED - Pajarola, Renato ED - Staadt, Oliver T1 - Volume and Point-Based Graphics 2008 Y1 - 2008 SN - 978-3-905674-12-5 PB - Eurographics Association ER - TY - BOOK ED - Scheuermann, Gerik ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Topology-based Methods in Visualization II T3 - Mathematics and Visualization Y1 - 2009 SN - 978-3-540-88605-1 PB - Springer ER - TY - BOOK ED - Hege, Hans-Christian ED - Hotz, Ingrid ED - Munzner, Tamara T1 - EuroVis 2009 Y1 - 2009 PB - Blackwell Publishing ER - TY - GEN ED - Hege, Hans-Christian ED - Machiraju, Raghu ED - Laidlaw, David T1 - Volume Graphics and Point-Based Graphics Y1 - 2010 N1 - Collection of selected and extended papers of international IEEE/EG Symposia Volume Graphics and Point-Based Graphics 2008, Special Section in IEEE Trans. Vis. Comput. Graph., 16:4, pp. 529-608, 2010 ER - TY - BOOK ED - Hege, Hans-Christian T1 - VideoMath T3 - Video Series Y1 - 2010 PB - Springer-Verlag ER - TY - BOOK ED - Hege, Hans-Christian T1 - Visualization and Mathematics T3 - Book Series Y1 - 2010 PB - Springer-Verlag ER - TY - THES A1 - Höllerer, Tobias T1 - Volume Rendering auf irregulären Gittern - Theorie und Implementierung Y1 - 1995 ER - TY - THES A1 - Battke, Henrik T1 - Entwicklung textur-basierter Verfahren zur Vektorfeldvisualisierung Y1 - 1996 ER - TY - THES A1 - Anders, Thomas T1 - Effiziente Algorihmen zur Isoflächengenerierung aus Volumendaten Y1 - 1996 ER - TY - THES A1 - Brenner, Thomas T1 - Volume Rendering - Ein Projektionsansatz für den Cray T3D Y1 - 1996 ER - TY - THES A1 - Wunderling, Roland T1 - Paralleler und objektorientierter Simplex-Algorithmus Y1 - 1996 ER - TY - THES A1 - Ganß, Michael T1 - LR-Zerlegung dünnbesetzter Matrizen für Parallelrechner mit verteiltem Speicher Y1 - 1997 ER - TY - THES A1 - Zöckler, Malte T1 - Molekulardynamische Simulation des Wachstums zirkumstellarer Silikatstaubteilchen Y1 - 1997 ER - TY - THES A1 - Schirmacher, Hartmut T1 - Extracting Graphs from Three Dimensional Neuron Data Sets Y1 - 1998 ER - TY - THES A1 - Schmidt-Ehrenberg, Johannes T1 - Visualisierung chemischer Ratennetzwerke Y1 - 1998 ER - TY - THES A1 - Decker, Ingmar T1 - Dokumentensuche über Bilder - Konzeption und Aufbau eines Image Retrieval Service für die Electronic Visualization Library Y1 - 1998 ER - TY - THES A1 - Runge, Daniel T1 - Algorithms and Methods for the Visualization of Molecular Surfaces and Interfaces Y1 - 1999 ER - TY - THES A1 - Lange, Thomas T1 - Regionenbasierte Segmentierungsverfahren für dreidimensionale biomedizinische Bilddaten Y1 - 1999 ER - TY - THES A1 - Westerhoff, Natascha T1 - Geometrische Methoden zur 3D-Segmentierung Y1 - 1999 ER - TY - THES A1 - Zachow, Stefan T1 - Design and Implementation of a planning system for episthetic surgery T2 - Entwurf und Implementierung eines chirurgischen Planungssystems für Einsatz in der Epithetik Y1 - 1999 ER - TY - THES A1 - Coconu, Liviu T1 - Semi-automatic Segmentation of Bronchoscopic Images Y1 - 2001 ER - TY - THES A1 - Zaharescu, Valentin-Florian T1 - Semi-automatic Volume Slices Alignment for 3D Reconstruction and Analysis Y1 - 2001 ER - TY - THES A1 - Sander, Oliver T1 - Constructing Boundary and Interface Parametrizations for Finite Element Solvers Y1 - 2001 ER - TY - THES A1 - Trepczynski, Adam T1 - Schnittmodellierung auf triangulierten Polygonoberflächen Y1 - 2002 ER - TY - THES A1 - (née Zöckler), Malte T1 - Efficient Visualization and Reconstruction of 3D Geometric from Neuro-Biological Confocal Microscope Scans Y1 - 2003 ER - TY - THES A1 - Adolfson, Jon A1 - Helgesson, Johan T1 - Generation of Smooth Non-Manifold Surfaces from Segmented Image Data Y1 - 2004 ER - TY - THES A1 - Benger, Werner T1 - Visualization of General Relativistic Tensor Fields via a Fiber Bundle Data Model Y1 - 2004 N1 - ISBN 3-86541-108-8 ER - TY - THES A1 - Baumeister, Timm T1 - Modellierung der freien Solvatisierungsenthalpie und Anwendung als Scoringfunktion Y1 - 2004 ER - TY - THES A1 - Schudoma, Christian T1 - Application of a Combined Sequence and Structure Alignment for RNA 3D Modeling Y1 - 2004 ER - TY - THES A1 - Wenckebach, Thomas T1 - Volumetrische Registrierung zur medizinischen Bildanalyse Y1 - 2004 ER - TY - GEN A1 - Wenckebach, Thomas T1 - Das Korrespondenzproblem für Statistische 3D-Formmodelle in biomedizinischen Anwendungen Y1 - 2004 ER - TY - THES A1 - Zachow, Stefan T1 - Computer assisted osteotomy planning in cranio-maxillofacial surgery under consideration of facial soft tissue changes T2 - Computergestützte Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung Y1 - 2005 UR - www.dr.hut-verlag.de/titelMedizininformatik.html ER - TY - THES A1 - Clasen, Malte T1 - Beleuchtung von Landschaften in interaktiver Darstellung Y1 - 2005 ER - TY - THES A1 - Schudoma, Christian T1 - A Fragment Based Approach to RNA Threading Y1 - 2006 ER - TY - THES A1 - Beckmann, Philipp T1 - Consistent Cell-Decomposition of Homeomorphic Simplicial Surfaces Y1 - 2006 ER - TY - THES A1 - Zilske, Michael T1 - Adaptive remeshing of non-manifold triangulations T2 - Adaptives Remeshing von nicht-mannigfaltigen Dreicksnetzen Y1 - 2007 ER - TY - THES A1 - Papazov, Chavdar T1 - Morphing zwischen triangulierten Nicht-Mannigfaltigkeiten unter Berücksichtigung topologischer Änderungen Y1 - 2007 ER - TY - THES A1 - Schmidt-Ehrenberg, Johannes T1 - Analysis and Visualization of Molecular Conformations Y1 - 2008 ER - TY - THES A1 - Weinkauf, Tino T1 - Extraction of Topological Structures in 2D and 3D Vector Fields Y1 - 2008 ER - TY - THES A1 - Weber, Britta T1 - Merkmalskurven auf triangulierten Oberflächen Y1 - 2008 ER - TY - THES A1 - Wade, Moritz T1 - Automatic Textbook-Like Layout of Biological Networks Y1 - 2008 ER - TY - THES A1 - Singer, Jochen T1 - Entwicklung einer Anpassungsstrategie zur Autosegmentierung des Gehirns der Honigbiene Apis mellifera mittels eines statistischen Formmodells Y1 - 2008 ER - TY - THES A1 - Lienhard, Matthias T1 - Aufbau und Analyse eines statistischen Formmodells des Gehirns der Honigbiene Apis Mellifera Y1 - 2008 ER - TY - THES A1 - Sahner, Jan T1 - Extraction of Vortex Structures in 3D Flow Fields Y1 - 2009 ER - TY - THES A1 - Gensel, Maria T1 - Visualisierungsmethoden zur Verdeutlichung der räumlichen Beziehungen zwischen linien- und flächenartigen Strukturen am Beispiel neurobiologischer Daten Y1 - 2009 ER - TY - THES A1 - van den Bruck, Nils T1 - Techniken zur Artefaktreduktion für GPU-basiertes Ray Casting Y1 - 2009 ER - TY - THES A1 - Winkler, Charlotte T1 - Graph-Cut Segmentation for 3D Single-Plane Illumination Microscopy Images Y1 - 2009 ER - TY - THES A1 - Löwen, Christian T1 - Parallele Berechnung kombinatorischer Vektorfelder mit CUDA Y1 - 2009 ER - TY - THES A1 - Nietfeld, Jan T1 - Oberflächenrekonstruktion aus nicht-parallelen Konturdaten Y1 - 2010 ER - TY - THES A1 - Zobel, Valentin T1 - Spectral Analysis of the Hodge Laplacian on Discrete Manifolds Y1 - 2010 ER - TY - THES A1 - Lindow, Norbert T1 - Dynamische Moleküloberflächen T1 - Dynamic Molecular Surfaces Y1 - 2010 ER - TY - THES A1 - Wittmers, Antonia T1 - Ein Werkzeug zur Erzeugung konsistenter Netze auf triangulierten Oberflächen Y1 - 2011 ER - TY - THES A1 - Schuberth, Sebastian T1 - High-Performance Tomographic Reconstruction using OpenCL Y1 - 2011 ER - TY - THES A1 - Seidel, Paul T1 - Interaktive Visualisierung und Filterung großer Volumendaten mittels Volumenrendering Y1 - 2011 ER - TY - THES A1 - Retzlaff, Michelle T1 - Brushing and Linking Methods by the Example of Tensor Visualization Y1 - 2011 ER - TY - THES A1 - Reininghaus, Jan T1 - Computational discrete Morse theory Y1 - 2012 ER - TY - THES A1 - Kettlitz, Nino T1 - Anisotropes Sampling in der Tensorfeldvisualisierung Y1 - 2011 ER - TY - THES A1 - Kasten, Jens T1 - Lagrangian feature extraction in two-dimensional unsteady flows Y1 - 2012 ER - TY - THES A1 - Kahnt, Max T1 - Generation of constrained high-quality multi-material tetrahedral meshes Y1 - 2012 ER - TY - THES A1 - Ehlke, Moritz T1 - Simulating X-ray images from deformable shape and intensity models on the GPU Y1 - 2012 ER - TY - THES A1 - Surma, Alexander T1 - Automatisierte Registrierung von 2D-Daten in 3-dimensionalen Volumen mit Hilfe von ZIBAmira T1 - Automated Registration of 2D Data in 3-dimensional Volumina using ZIBAmira Y1 - 2012 ER - TY - THES A1 - Ruben, Karl T1 - Kugelpackungen in arbiträr geformten Volumina T1 - Sphere Packings in Arbitrarily Bounded Volumes Y1 - 2012 ER - TY - THES A1 - Orgiu, Sara T1 - Automatic liver segmentation in contrast enhanced CT data using 3D free-form deformation based on optimal graph searching Y1 - 2012 ER - TY - THES A1 - Malinowski, Jana T1 - Ein kontinuierliches Optimierungsverfahren für die Segmentierung medizinischer Bilddaten mit Hilfe von Formmodellen Y1 - 2012 ER - TY - THES A1 - Nguyen, The Duy T1 - Automatic segmentation for dental operation planning Y1 - 2012 ER - TY - THES A1 - Preis, Philipp T1 - Sichtbarkeitsorientiertes Picking in Direct Volume Renderings mit Beleuchtungsmodellen Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/preis_MA.pdf ER - TY - THES A1 - Tenbusch, Tobias T1 - Rendering von Partikeleffekten in einem Deferred Renderer Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/Tenbusch-MA_2012.pdf ER - TY - THES A1 - Lange, Martin T1 - Shadow Volumes für dynamische Dreiecksnetze auf CPU und GPU Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/Lange-MA_2012.pdf ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Stüben, Hinnerk T1 - Vectorization and Parallelization of Irregular Problems via Graph Coloring T2 - Proc. of the ACM Int. Conf. on Supercomputing Y1 - 1991 U6 - https://doi.org/10.1145/109025.109042 SP - 47 EP - 56 CY - Cologne ER - TY - JOUR A1 - Akemi, K. A1 - Forcrand, Ph. de A1 - Fujisaki, M. A1 - Hashimoto, T. A1 - Hege, Hans-Christian A1 - Hioki, S. A1 - Makino, J. A1 - Miyamura, O. A1 - Nakamura, A. A1 - Okuda, M. A1 - Stamatescu, I. O. A1 - Tago, Yoshio A1 - Takaishi, T. T1 - QCD on the Highly Parallel Computer AP 1000 JF - Nucl. Phys. B Proc. Suppl. 26 Y1 - 1992 U6 - https://doi.org/10.1016/0920-5632(92)90358-Y SP - 644 EP - 646 ER - TY - JOUR A1 - Akemi, K. A1 - Forcrand, Ph. de A1 - Fujisaki, M. A1 - Hashimoto, T. A1 - Hege, Hans-Christian A1 - Hioki, S. A1 - Makino, J. A1 - Miyamura, O. A1 - Nakamura, A. A1 - Okuda, M. A1 - Stamatescu, I. O. A1 - Tago, Yoshio A1 - Takaishi, T. T1 - SU(3) Renormalization Group Study on Parallel Computer AP 1000 JF - Nucl. Phys. B Proc. Suppl. 26 Y1 - 1992 U6 - https://doi.org/10.1016/0920-5632(92)90293-2 SP - 420 EP - 422 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Hadron Spectroscopy on a 32^3 * 48 Lattice JF - Nucl. Phys. B Proc. Suppl. 26 Y1 - 1992 U6 - https://doi.org/10.1016/0920-5632(92)90257-S SP - 293 EP - 295 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Knecht, Renate T1 - Conference Report: Parallel Computing 91 JF - Parallel Computing Y1 - 1992 VL - 18 IS - 4 SP - 473 EP - 476 ER - TY - GEN A1 - Wunderling, Roland A1 - Hege, Hans-Christian T1 - AGIL - the Adaptable Graphical Interface Layer, Programmierer-Handbuch Y1 - 1992 SP - 34pp. PB - Interner Report, Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB), Germany ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Monte Carlo Renormalization Study at Large beta in the Confinement Region JF - Nuclear Phys. B. Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90263-6 VL - 30 SP - 517 EP - 520 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Study of Spatial Size Effects in Quenched Wilson Hadron Spectroscopy at beta = 6.3 JF - Nucl. Phys. B Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90230-4 VL - 30 SP - 373 EP - 376 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Autocorrelation in Updating Pure SU(3) Lattice Gauge Theory by the Use of Overrelaxed Algorithms JF - Nucl. Phys. B Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90202-H VL - 30 SP - 253 EP - 256 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - QCD on the Massively Parallel Computer AP 1000 JF - Int. J. Mod. Phys. Y1 - 1993 U6 - https://doi.org/10.1142/S0129183193000975 VL - 4 IS - 6 SP - 1233 EP - 1253 ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Scaling study of pure SU(3) theory - the QCD-TARO collaboration JF - Nucl. Phys. B Proc. Suppl. Y1 - 1994 U6 - https://doi.org/10.1016/0920-5632(94)90358-1 VL - 34 SP - 246 EP - 252 ER - TY - CHAP A1 - Wunderling, Roland A1 - Grammel, Martin A1 - Hege, Hans-Christian T1 - Parallele LU-Zerlegung großer, unsymmetrischer, dünn besetzter Matrizen bei hohen Kommunikationslatenzen T2 - GI/ITG-Workshop, Sept.1994, Mitteilungen der Fachgruppe PARS der Gesellschaft für Informatik (GI) Y1 - 1994 VL - 13 SP - 191 EP - 200 CY - Potsdam ER - TY - CHAP A1 - Grammel, Martin A1 - Back, Godmar A1 - Wunderling, Roland A1 - Hege, Hans-Christian T1 - Ein paralleles C++/C-Programmiermodell für ein objektorientiertes B&C-Framework T2 - GI/ITG-Workshop, Sept.1994, Mitteilungen der Fachgruppe PARS der Gesellschaft für Informatik (GI) Y1 - 1994 VL - 13 SP - 50 EP - 59 CY - Potsdam ER - TY - CHAP A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Scientific Computing in der Theoretischen Physik - Collected Abstracts T2 - Tagung organisiert von der DMV-Fachgruppe Scientific Computing in Kooperation mit dem GAMM Fachausschuss Scientific Computing Y1 - 1994 CY - Berlin ER - TY - JOUR A1 - Akemi, K. A1 - deForcrand, Ph. A1 - Fujisaki, M. A1 - Hashimoto, T. A1 - Hege, Hans-Christian A1 - Hioki, S. A1 - Miyamura, O. A1 - Nakamura, A. A1 - Okuda, M. A1 - Stamatescu, I. O. A1 - Tago, Yoshio A1 - Takaishi, T. T1 - Quantum Chromodynamics Simulations on a Non-Dedicated Highly Parallel Computer JF - Comp. Phys. Comm Y1 - 1995 U6 - https://doi.org/10.1016/0010-4655(95)00082-Q VL - 90 SP - 201 EP - 214 ER - TY - JOUR A1 - Limbach, Daniel T1 - Parallel MPEG-Encoder for Real-Time Online Encoding JF - SuParCup95 Adward Contribution 2nd Student Price, Supercomputer Seminar Y1 - 1995 CY - Mannheim ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Stüben, Hinnerk T1 - Daten "sehen" - Wissenschaftliche Visualisierung im RTB Berlin JF - DFN Mitteilungen Y1 - 1995 VL - 38 SP - 10 EP - 12target ER - TY - CHAP A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Höllerer, Tobias T1 - Visualization and 3D-Interaction for Hyperthermia Treatment Planning T2 - Proc. CAR 95 Computer Assisted Radiology, 9th International Symposium and Exhibition Y1 - 1995 SP - 1216 EP - 1222 CY - Berlin ER - TY - CHAP A1 - Gellermann, Johanna A1 - Wust, Peter A1 - Stalling, Detlev A1 - Felix, Roland T1 - Optimisation Strategies in Hyperthermia Planning Compared with those Used in Radiotherapy Planning T2 - Proc. CAR 95 Computer Assisted Radiology Y1 - 1995 SP - 1083 EP - 1087 CY - Berlin ER - TY - CHAP A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Design and Implementation of a Hyperthermia Planning System T2 - Tagungsband zum 4. Freiburger Workshop Digitale Bildverarbeitung in der Medizin Y1 - 1995 CY - Freiburg/Breisgau ER - TY - JOUR A1 - Seebaß, Martin A1 - Wust, Peter A1 - Gellermann, Johanna A1 - Stalling, Detlev A1 - Nadobny, Jacek A1 - Felix, Roland T1 - Dreidimensionale Simulation der nicht-invasiven Radiowellen-Hyperthermie JF - Minimal Invasive Medizin Y1 - 1995 VL - 6 IS - 1 SP - 29 EP - 35 ER - TY - CHAP A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast and Resolution-Independent Line Integral Convolution T2 - Proceedings of SIGGRAPH ’95 Y1 - 1995 U6 - https://doi.org/10.1145/218380.218448 SP - 249 EP - 256 PB - Computer Graphics Annual Conference Series, ACM SIGGRAPH CY - Los Angeles, California ER - TY - JOUR A1 - Höllerer, Tobias A1 - Tönnies, Klaus A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - Der Einfluß der Datenapproximation bei Volume Rendering durch ein Emissions/Absorptions-Modell JF - Visualisierung - Dynamik und Komplexität Y1 - 1995 PB - CEVIS Universität Bremen und Fachgruppe 4.2.1 der Gesellschaft für Informatik CY - Bremen, Germany ER - TY - CHAP A1 - Höllerer, Tobias A1 - Tönnies, Klaus A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - Volume Rendering on Irregular Grids (Abstract) T2 - Int. Workshop on Mathematics and Visualization Y1 - 1995 CY - Berlin, Germany ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Problems and Solutions: Product of Chebyshev Polynomials JF - Orthogonal Polynomials and Special Functions Y1 - 1996 VL - 6 (2) SP - 12 ER - TY - JOUR A1 - Wust, Peter A1 - Seebaß, Martin A1 - Nadobny, Jacek A1 - Deuflhard, Peter A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Simulation Studies Promote Technological Development of Radiofrequency Phased Array Hyperthermia JF - Int. Journal of Hyperthermia Y1 - 1996 VL - 12 SP - 477 EP - 494 ER - TY - CHAP A1 - Stalling, Detlev A1 - Seebaß, Martin A1 - Hege, Hans-Christian A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland T1 - HyperPlan - an Integrated System for Treatment Planning in Regional Hyperthermia T2 - Proceedings of the 17th Congress on Hyperthermic Oncology Y1 - 1996 VL - 2 SP - 552 EP - 554 CY - Rome, Italy ER - TY - CHAP A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Intelligent Scissors for Medical Image Segmentation T2 - Tagungsband zum 4. Freiburger Workshop Digitale Bildverarbeitung in der Medizin Y1 - 1996 SP - 32 EP - 36 CY - Freiburg ER - TY - CHAP A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter T1 - Three-Dimensional Finite Elements Mesh Generation for Numerical Simulations of Hyperthermia Treatments T2 - Proceedings of the 17th Congress on Hyperthermic Oncology Y1 - 1996 VL - 2 SP - 547 EP - 548 CY - Rome, Italy ER - TY - CHAP A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Wlodarczyk, Waldemar A1 - Seebaß, Martin A1 - Deuflhard, Peter A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Simulation Studies for Combination of Hyperthermia and Magnetic Resonance Systems T2 - Proceedings of the 17th Congress on Hyperthermic Oncology Y1 - 1996 VL - 2 SP - 549 EP - 551 CY - Rome, Italy ER - TY - JOUR A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Seebaß, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Volume Surface Integral Equation Method for Solving Maxwell’s Equations in Electrically Inhomogeneous Media Using Tetrahedral Grids JF - IEEE Transactions Microwave Theory Techn. Y1 - 1996 U6 - https://doi.org/10.1109/22.491022 VL - 44 IS - 4 SP - 543 EP - 554 ER - TY - CHAP A1 - Beck, Rudolf A1 - Hege, Hans-Christian A1 - Seebaß, Martin A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Adaptive Finite Element Codes for Numerical Calculations in Hyperthermia Treatment Planning T2 - Proceedings of the 17th Congress on Hyperthermic Oncology Y1 - 1996 VL - 2 SP - 515 EP - 517 CY - Rome, Italy ER - TY - CHAP A1 - Korzen, Manfred A1 - Schriever, Robert A1 - Ziener, Kai-Uwe A1 - Paetsch, Olaf A1 - Zumbusch, Gerd ED - Ziebs, J. al. T1 - Real-Time 3-D Visualization of Surface Temperature Fields Measured by Thermocouples on Steel Strutures in Fire Engineering T2 - Proc. Int. Symposium Local Strain and Temperature Measurements in Non-Uniform Fields at Elevated Temperatures Y1 - 1996 SP - 253 EP - 262 PB - Woodhead CY - England ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Höllerer, Tobias A1 - Stalling, Detlev T1 - Volume Rendering: Mathematical Models and Algorithmic Aspects JF - Partielle Differentialgleichungen, Numerik und Anwendungen, Konferenzen des Forschungszentrum Jülich GmbH Y1 - 1996 SP - 227 EP - 255 PB - W. Nagel ER - TY - CHAP A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebaß, Martin A1 - Stalling, Detlev ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Numerical Algorithms and Visualization in Medical Treatment Planning T2 - Visualization and Mathematics 1997 Y1 - 1996 SP - 303 EP - 328 PB - Springer, Heidelberg ER - TY - CHAP A1 - Zöckler, Malte A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Interactive Visualization of 3D-Vector Fields Using Illuminated Streamlines T2 - Proc. IEEE Visualization 1996 Y1 - 1996 U6 - https://doi.org/10.1109/VISUAL.1996.567777 SP - 107 EP - 113 CY - San Fransisco ER - TY - CHAP A1 - Battke, Henrik A1 - Stalling, Detlev A1 - Hege, Hans-Christian ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Fast Line Integral Convolution for Arbitrary Surfaces in 3D T2 - Visualization and Mathematics 1997 Y1 - 1996 SP - 181 EP - 195 PB - Springer, Heidelberg ER - TY - CHAP A1 - Zöckler, Malte A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Parallel Line Integral Convolution T2 - Proc. First Eurographics Workshop on Parallel Graphics and Visualization Y1 - 1996 U6 - https://doi.org/10.1016/S0167-8191(97)00039-2 SP - 111 EP - 128 CY - Bristol, U.K. ER - TY - GEN A1 - Paetsch, Olaf A1 - Stalling, Detlev A1 - Korzen, Manfred T1 - Online-Visualisierung von Brandversuchen an Bauteilen Y1 - 1997 PB - Konrad-Zuse-Zentrum für Informationstechnik, Berlin (ZIB) / Bundesanstalt für Materialfoschung und -prüfung (BAM) Berlin ER - TY - CHAP A1 - Wust, Peter A1 - Nadobny, Jacek A1 - Gellermann, Johanna A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Patient Models and Algorithms for Hyperthermia Planning T2 - Proceedings of the 16th Annual Meeting of the European Society for Hyperthermic Oncology ESHO-97 Y1 - 1997 ER - TY - CHAP A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Quantitative Comparison Between VSIE and the FDTD Method Using Electrically Equivalent Patient and Antenna Models T2 - Proceedings of 16th Annual Meeting of the European Society for Hyperthermic Oncology ESHO-97 Y1 - 1997 SP - 145 CY - Berlin, Germany ER - TY - CHAP A1 - Deuflhard, Peter A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Beck, Rudolf A1 - Hege, Hans-Christian ED - Sydow, Achim T1 - Hyperthermia Treatment Planning in Clinical Therapy T2 - Computational Physics, Chemistry and Biology (Proceedings of the 15th IMACS World Congress 1997 on Scientific Computation 3, Modelling and Applied Mathematics) Y1 - 1997 SP - 9 EP - 17 PB - Wissenschaft und Technik Verlag ER - TY - CHAP A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Hege, Hans-Christian A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter T1 - Surface Mesh Generation for Numerical Simulations of Hyperthermia Treatments T2 - Proceedings of the 16th Annual Meeting of the European Society for Hyperthermic Oncology (ESHO-97) Y1 - 1997 SP - 146 ER - TY - CHAP A1 - Wegner, Susan A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Oswald, H. A1 - Fleck, E. ED - Arnolds, B. ED - Müller, H. ED - Saupe, D. ED - Tolxdorff, Thomas T1 - Die 3D-Wasserscheidentransformation auf Graphenebene - eine Anwendung für die Hyperthermieplannung T2 - Digitale Bildverarbeitung in der Medizin, Tagungsband zum 5. Freiburger Workshop Y1 - 1997 SP - 31 EP - 36 CY - Freiburg ER - TY - JOUR A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Hege, Hans-Christian T1 - Fast Display of Illuminated Field Lines JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 1997 U6 - https://doi.org/10.1109/2945.597795 VL - 3 IS - 2 SP - 118 EP - 128 ER - TY - CHAP A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - LIC on Surfaces T2 - Texture Synthesis with Line Integral Convolution, Siggraph 97, 24. Int. Conf. Computer Graphics and Interactive Techniques Y1 - 1997 SP - 51 EP - 64 CY - Los Angeles ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - LIC: Acceleration, Animation, Zoom T2 - Texture Synthesis with Line Integral Convolution, Siggraph 97, 24. Int. Conf. Computer Graphics and Interactive Techniques Y1 - 1997 SP - 17 EP - 49 CY - Los Angeles ER - TY - JOUR A1 - Decker, Ingmar A1 - Müller, Peter A1 - Limbach, Daniel T1 - VisInfo-Fachinformationsdienst Visualisierung JF - DFN-Mitteilungen Y1 - 1998 VL - Heft 46 SP - 6 EP - 7 ER - TY - JOUR A1 - Wust, Peter A1 - Gellermann, Johanna A1 - Beier, Jürgen A1 - Wegner, Susan A1 - Tilly, Wolfgang A1 - Tröger, Jens A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Evaluation of Segmentation Algorithms for Generation of Patient Models in Radiofrequency Hyperthermia JF - Phys. Med. Biol. Y1 - 1998 U6 - https://doi.org/10.1088/0031-9155/43/11/009 VL - 43 (11) SP - 3295 EP - 3307 ER - TY - CHAP A1 - Wlodarczyk, Waldemar A1 - Nadobny, Jacek A1 - Fähling, Horst A1 - Wust, Peter A1 - Mönich, Gerhard T1 - Antennenkonzepte und Realisierungsbeispiele für die HF-Hyperthermie T2 - ITG-Fachbericht 149 Antennen Y1 - 1998 SP - 335 EP - 338 PB - VDE Verlag ER - TY - CHAP A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Fähling, Horst A1 - Stalling, Detlev A1 - Seebaß, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Numerical and Experimental Evaluation of E-Field and Absorbed Power in the Pelvic Region Using a Bone-Equivalent Phantom T2 - Proc. PIERS Progress in Electromagnetic Research Symposium Y1 - 1998 SP - 264 CY - Nantes ER - TY - JOUR A1 - Nadobny, Jacek A1 - Sullivan, Dennis A1 - Wust, Peter A1 - Seebaß, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A High-Resolution Interpolation at Arbitary Interfaces for the FDTD Method JF - IEEE Trans. Microwave Theory Tech. Y1 - 1998 U6 - https://doi.org/10.1109/22.734576 VL - 46 IS - 11 SP - 1759 EP - 1766 ER - TY - CHAP A1 - Nadobny, Jacek A1 - Wlodarczyk, Waldemar A1 - Wust, Peter A1 - Fähling, Horst A1 - Mönich, Gerhard A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Design and Optimization of Short Antennas for Phased-Array Hyperthermia Applicator T2 - Proc. PIERS Progress in Electromagnetic Research Symposium Y1 - 1998 SP - 839 CY - Nantes ER - TY - CHAP A1 - Wlodarczyk, Waldemar A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Whole Body Hyperthermia Applicator Inside MR Systems: Simulation of Influence of RF Shield of MR Scanner on the Performance of Hyperthermia Applicator T2 - Proc. ISMRM Inter. Soc Magn. Reson. Med. 6th Scientific Meeting Y1 - 1998 SP - 651 CY - Sidney ER - TY - CHAP A1 - Wlodarczyk, Waldemar A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Fähling, Horst A1 - Salah, Adel A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Numerical Studies for Electromagnetic Compatibility of Phased Array Hyperthermia Applicator and Magnetic Resonance Tomography T2 - Proc. PIERS Progress in Electromagnetic Research Symposium Y1 - 1998 SP - 840 CY - Nantes ER - TY - JOUR A1 - Kühn, Wolfgang A1 - Kühn, Zuzana T1 - Cutting High Dimensional Cakes JF - American Mathematical Monthly Y1 - 1998 VL - 105 IS - 2 SP - 168 EP - 169 ER - TY - JOUR A1 - Kühn, Wolfgang T1 - Rigorously Computed Orbits of Dynamical Systems without the Wrapping Effect JF - Computing Y1 - 1998 U6 - https://doi.org/10.1007/BF02684450 VL - 61 IS - 1 SP - 47 EP - 67 ER - TY - CHAP A1 - Schirmacher, Hartmut A1 - Zöckler, Malte A1 - Stalling, Detlev A1 - Hege, Hans-Christian ED - Girod, Bernd ED - Niemann, Heinrich ED - Seidel, Hans T1 - Boundary Surface Shrinking - a Continuous Approach to 3D Center Line Extraction T2 - Proc. of IMDSP’98, held in Alpbach Y1 - 1998 SP - 25 EP - 28 CY - Austria ER - TY - GEN A1 - Best, Christoph T1 - A Simple C++ Library for Manipulating Scientific Data Sets as Structured Data Y1 - 1998 PB - ZIB Technical Report TR 98-06 ER - TY - CHAP A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter T1 - New Features of HyperPlan, a Hyperthermia Planning System T2 - Proc. Hyperthermia in Clincal Oncology Y1 - 1998 SP - 16 CY - Venice ER - TY - CHAP A1 - Deuflhard, Peter A1 - Seebaß, Martin ED - Lai, Choi-Hong ED - Bjorstad, Petter ED - Cross, Mark ED - Widlund, Olof T1 - Adaptive Multilevel FEM as Decisive Tools in the Clinical Cancer Therapy Hyerthermia T2 - Proc. Eleventh International Conference on Domain Decomposition Methods in Sciences and Engineering Y1 - 1998 SP - 410 EP - 421 CY - Greenwich, UK ER - TY - CHAP A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Hege, Hans-Christian T1 - Segmentation of 3D Medical Images with Subvoxel Accuracy T2 - Proc. CARS ’98 Computer Assisted Radiology and Surgery Y1 - 1998 SP - 137 EP - 142 CY - Tokyo ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Stalling, Detlev ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Fast LIC with Piecewise Polynomial Filter Kernels T2 - Mathematical Visualization - Algorithms and Applications Y1 - 1998 SP - 295 EP - 314 PB - Springer-Verlag Berlin ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - Identification of Molecular Conformations via Statistical Analysis of Simulation Data JF - Comp. Chem. Y1 - 1999 VL - 20 SP - 1760 EP - 1774 ER - TY - CHAP A1 - Benger, Werner A1 - Foster, Ian A1 - Novotny, Jason A1 - Seidel, Edward A1 - Shalf, John A1 - Smith, Warren A1 - Walker, Paul T1 - Numerical Relativity in a Distributed Environment T2 - Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing Y1 - 1999 ER - TY - CHAP A1 - Stalling, Detlev A1 - Seebaß, Martin A1 - Zachow, Stefan T1 - Mehrschichtige Oberflächenmodelle zur computergestützten Planung in der Chirurgie T2 - Bildverarbeitung für die Medizin 1999 - Algorithmen, Anwendungen Y1 - 1999 SP - 203 EP - 207 PB - Springer-Verlag, Berlin ER - TY - CHAP A1 - Hein, Andreas A1 - Lueth, Tim A1 - Zachow, Stefan A1 - Stien, Malte T1 - A 2D Planning Sytem for Robot-Assisted Interventions T2 - Computer Assisted Radiology and Surgery Y1 - 1999 SP - 1049 PB - Elsevier Science B.V. ER - TY - CHAP A1 - Zachow, Stefan A1 - Lueth, Tim A1 - Stalling, Detlev A1 - Hein, Andreas A1 - Klein, Martin A1 - Menneking, Horst T1 - Optimized Arrangement of Osseointegrated Implants: A Surgical Planning System for the Fixation of Facial Protheses T2 - Computer Assisted Radiology and Surgery (CARS’99) Y1 - 1999 SP - 942 EP - 946 PB - Elsevier Science B.V. ER - TY - BOOK A1 - Stalling, Detlev T1 - Fast Texture-Based Algorithms for Vector Field Visualization Y1 - 1999 SN - 3-8265-4835-3 PB - Shaker ER - TY - CHAP A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - Heisenberg, Martin T1 - A Deformable 3D Model of the Fly Brain T2 - Proc. Int. Conf. Neurobiology of Drosophila Y1 - 1999 PB - Cold Spring Harbor CY - New York, USA ER - TY - CHAP A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - Heisenberg, Martin T1 - A Quantitative 3D Model of the Flybrain: Shape and Arrangement of Neuropils T2 - Proc. First Vogt-Brodmann Symposium: Perspectives of Architectonic Brain Mapping Y1 - 1999 CY - Düsseldorf /Jülich ER - TY - CHAP A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - Heisenberg, Martin ED - Schnitzler, H. T1 - Towards a Quantative 3D Model of the Fly Brain T2 - Proc. 27th Göttingen Neurobiology Report Y1 - 1999 SP - 742 PB - G. Thieme Verlag CY - Stuttgart, Germany ER - TY - JOUR A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - Heisenberg, Martin T1 - A Quantitative Three-Dimensional Model of the Drosophila Optic Lobes JF - Current Biology Y1 - 1999 VL - 9 IS - 2 SP - 93 EP - 96 ER - TY - CHAP A1 - Brandt, Robert A1 - Malun, Dagmar A1 - Steege, A. A1 - Zöckler, Malte A1 - Menzel, Randolf T1 - Three Dimensional Reconstruction of Honey Bee Mushroom Bodies T2 - Annual Meeting of the Society for Neuroscience, Abstr. 25 Y1 - 1999 SP - 861 ER - TY - JOUR A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Seebaß, Martin T1 - Impact of Nonlinear Heat Tansfer on Temperature Control in Regional Hypertermia JF - IEEE Trans. Biomed. Engrg. Y1 - 1999 U6 - https://doi.org/10.1109/10.784145 VL - 46 SP - 1129 EP - 1138 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Jacek A1 - Seebaß, Martin A1 - Stalling, Detlev A1 - Gellermann, Johanna A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Influence of Patient Models and Numerical Methods on Predicted Power Deposition Patterns JF - Int. Journal Hyperthermia Y1 - 1999 VL - 15 IS - 6 SP - 519 EP - 540 ER - TY - CHAP A1 - Wlodarczyk, Waldemar A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Mönich, Gerhard A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Systematic Design of Antennas for a Cylindrical 3D Phased Array Hyperthermia Applicator T2 - Proc. 1999 IEEE Antennas and Propagation Society International Symposium Y1 - 1999 U6 - https://doi.org/10.1109/APS.1999.789482 SP - 1004 EP - 1007 CY - Orlando, FL ER - TY - BOOK A1 - Merzky, André T1 - Fernsteuerung und Fernüberwachung von verteilten Anwendungen Y1 - 1999 PB - RRZN, Universität Hannover ER - TY - CHAP A1 - Nadobny, Jacek A1 - Wlodarczyk, Waldemar A1 - Wust, Peter A1 - Mönich, Gerhard A1 - Deuflhard, Peter A1 - Felix, Roland T1 - 3D Phased Array Applicator for Hyperthermia Treatment in Pelvis T2 - Proc. XXVIth General Assembly of International Union of Radio Science (URSI) Y1 - 1999 SP - 648 CY - Toronto Ontario Canada ER - TY - CHAP A1 - Gotthardt, Jörg A1 - Blömer, Carola A1 - Stalling, Detlev T1 - Visualization of Groundwater Flow Using Line Integral Convolution T2 - Proc. ModelCARE 99 Y1 - 1999 CY - ETH Zürich ER - TY - JOUR A1 - Allen, Gabrielle A1 - Goodale, Tom A1 - Lanfermann, Gerd A1 - Seidel, Edward A1 - Benger, Werner A1 - Hege, Hans-Christian A1 - Merzky, André A1 - Masso, Joan A1 - Shalf, John T1 - Solving Einstein’s Equations on Supercomputers JF - IEEE Computer Y1 - 1999 U6 - https://doi.org/10.1109/2.809251 SP - 52 EP - 59 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Benger, Werner A1 - Merzky, André A1 - Kasper, Friedbert A1 - Radke, Thomas A1 - Seidel, Edward T1 - Schwarze Löcher in Sicht - Immersive Überwachung und Steuerung von Remote-Simulationen JF - DFN-Mitteilungen Y1 - 2000 VL - 52 IS - 2 SP - 4 EP - 6 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebaß, Martin T1 - Progress Towards a Combined MRI/Hyperthermia System T2 - Proceedings Second International Congress HIGH CARE 2000 Y1 - 2000 CY - Bochum ER - TY - CHAP A1 - Benger, Werner A1 - Hege, Hans-Christian A1 - Heusler, Stefan T1 - Visions of Numerical Relativity T2 - Proceedings of the 3d International Conference on the Interaction of Art and Fluid Mechanics (SCART2000) Y1 - 2000 SP - 239 EP - 246 PB - Kluwer Academic Publishers CY - ETH Zürich Zwitzerland ER - TY - JOUR A1 - Zöckler, Malte A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast and Intuitive Generation of Geometric Shape Transitions JF - The Visual Computer Y1 - 2000 U6 - https://doi.org/10.1007/PL00013396 VL - 16(5) SP - 241 EP - 253 ER - TY - JOUR A1 - Wust, Peter A1 - Beck, Rudolf A1 - Berger, Jörn A1 - Fähling, Horst A1 - Seebaß, Martin A1 - Wlodarczyk, Waldemar A1 - Hoffmann, Werner A1 - Nadobny, Jacek T1 - Electric Field Distributions in a Phased-Array Applicator with 12 Channels - Measurements and Numerical Simulations JF - Medical Physics Y1 - 2000 VL - 27 SP - 2565 EP - 2579 ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Finite-Element Simulation of Soft Tissue Deformation T2 - Computer Assisted Radiology and Surgey (CARS) Y1 - 2000 SP - 23 EP - 28 PB - Elsevier Science B.V. ER - TY - CHAP A1 - Zeilhofer, Hans-Florian A1 - Sader, Robert A1 - Apostolescu, Victor A1 - Hoffmann, Karl-Heinz A1 - Göbel, Martin A1 - Hege, Hans-Christian T1 - Die Bedeutung breitbandiger und leistungsfähiger Kommunikationsinfrastrukturen für die kraniomaxillofaziale Chirurgie - Möglichkeiten der netzbasierten Bildverarbeitung T2 - Bildverarbeitung für die Medizin 2000 (Abstract) Y1 - 2000 CY - München ER - TY - CHAP A1 - Benger, Werner A1 - Hege, Hans-Christian A1 - Merzky, André A1 - Radke, Thomas A1 - Seidel, Edward T1 - Efficient Distributed File I/O for Visualization in Grid Environments T2 - Simulation and Visualization on the Grid Y1 - 2000 VL - 13 SP - 1 EP - 6 PB - Springer Verlag ER - TY - JOUR A1 - Seebaß, Martin A1 - Beck, Rudolf A1 - Gellermann, Johanna A1 - Nadobny, Jacek A1 - Wust, Peter T1 - Electromagnetic Phased Arrays for Regional Hyperthermia - Optimal Frequency and Antenna Arrangement JF - Int. J. Hyperthermia Y1 - 2000 VL - 17(4) SP - 321 EP - 326 ER - TY - JOUR A1 - Gellermann, Johanna A1 - Wust, Peter A1 - Stalling, Detlev A1 - Seebaß, Martin A1 - Nadobny, Jacek A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Clinical evaluation and verification of the hyperthermia treatment planning system HyperPlan JF - Int. J. Radiat. Oncol. Biol. Phys. Y1 - 2000 U6 - https://doi.org/10.1016/S0360-3016(00)00425-9 VL - 47(4) SP - 1145 EP - 1156 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Seebaß, Martin T1 - A New Nonlinear Elliptic Multilevel FEM Applied to Regional Hyperthermia JF - Comput. Visual. Sci. Y1 - 2000 U6 - https://doi.org/10.1007/PL00013546 VL - 3 SP - 1 EP - 6 ER - TY - GEN A1 - Hege, Hans-Christian T1 - Virtuelle Experimente Sieben Hügel - Bilder und Zeichen des 21. Jahrhunderts Y1 - 2000 ER - TY - CHAP A1 - Giehl, Michael A1 - Gowin, Wolfgang A1 - Engelke, Klaus A1 - Karolczak, Marek A1 - Hege, Hans-Christian A1 - Schmidt-Ehrenberg, Johannes A1 - Felsenberg, Dieter T1 - Micro-CT zur Darstellung kontrastgebender Strukturen im Weichteilgewebe T2 - 81. Deutscher Röntgenkongress Y1 - 2000 CY - Wiesbaden ER - TY - CHAP A1 - Allen, Gabrielle A1 - Benger, Werner A1 - Goodale, Tom A1 - Hege, Hans-Christian A1 - Lanfermann, Gerd A1 - Merzky, André A1 - Radke, Thomas A1 - Seidel, Edward A1 - Shalf, John T1 - The Cactus Code: A Problem Solving Environment for the Grid T2 - High Performance Distributed Computing (HPDC-2000) Y1 - 2000 U6 - https://doi.org/10.1109/HPDC.2000.868657 SP - 253 EP - 260 ER - TY - CHAP A1 - Fiorio, Christophe A1 - Gustedt, Jens A1 - Lange, Thomas T1 - Union-find volume segmentation T2 - In 7th International Workshop on Combinatorial Image Analysis (IWCIA’00) Y1 - 2000 SP - 181 EP - 197 CY - Caen, France ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - FE-based heuristic approach for the estimation of person-specific facial mimics T2 - Proceedings of Euro-Par 2001: 5-th International Symposium on Computer Methods Y1 - 2001 CY - Rome, Italy ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Mun, Seong T1 - Validation of a Linear Elastic Model for Soft Tissue Simulation in Craniofacial Surgery T2 - Proc. SPIE Medical Imaging 2001 Y1 - 2001 U6 - https://doi.org/10.1117/12.428061 VL - 4319 SP - 27 EP - 35 CY - San Diego, USA ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Validierung eines linear elastischen Modells für die Weichgewebesimulation in der Mund-Kiefer-Gesichtschirurgie T2 - Bildverarbeitung für die Medizin (BVM) Y1 - 2001 SP - 57 EP - 61 CY - Lübeck, Germany ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Virtual Fibers: A Robust Approach for Muscle Simulation T2 - IX Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON) Y1 - 2001 SP - 961 EP - 964 CY - Pula, Croatia ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - A Biomechanical Model for Soft Tissue Simulation in Craniofacial Surgery T2 - Medical Imaging and Augmented Reality (MIAR) Y1 - 2001 U6 - https://doi.org/10.1109/MIAR.2001.930276 SP - 137 EP - 141 CY - Hong Kong, China ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Zeilhofer, Hans-Florian A1 - Sader, Robert T1 - 3D Osteotomieplanung in der MKG-Chirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung T2 - Rechner- und sensorgestützte Chirurgie, GI Proc. zur SFB 414 Tagung Y1 - 2001 SP - 217 EP - 226 CY - Heidelberg ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Zeilhofer, Hans-Florian A1 - Sader, Robert T1 - Improved 3D Osteotomy Planning in Cranio-Maxillofacial Surgery T2 - Proc. Medical Image Computing and Computer-Assisted Intervention (MICCAI 2001) Y1 - 2001 U6 - https://doi.org/10.1007/3-540-45468-3_57 SP - 473 EP - 481 CY - Utrecht, The Netherlands ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Towards a Realistic Simulation of Individual Facial Mimics T2 - Vision Modeling and Visualization 2001 (VMV) Y1 - 2001 SP - 129 EP - 134 CY - Stuttgart, Germany ER - TY - CHAP A1 - Stockinger, Heinz A1 - F. Rana, Omer A1 - Moore, Reagan A1 - Merzky, André ED - Hertzberger, Louis ED - G. Hoekstra, Alfons ED - Williams, Roy T1 - Data Management for Grid Environments T2 - Proceedings of HPCN Europe 2001 - 9th International Conference on High-Performance Computing and Networking Y1 - 2001 U6 - https://doi.org/10.1007/3-540-48228-8 VL - 2110 SP - 151 EP - 160 PB - Springer Verlag, Berlin Heidelberg 2001 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Polthier, Konrad A1 - Rumpf, Martin T1 - MathInsight 2002 Y1 - 2001 ER - TY - CHAP A1 - Allen, Gabrielle A1 - Benger, Werner A1 - Dramlitsch, Thomas A1 - Goodale, Tom A1 - Hege, Hans-Christian A1 - Lanfermann, Gerd A1 - Merzky, André A1 - Radke, Thomas A1 - Seidel, Edward ED - Sakellariou, Rizos ED - Keane, Jon ED - Gurd, John ED - Freeman, Len T1 - Cactus Grid Computing: Review of Current Devlopment T2 - Proceedings of Euro-Par 2001: 7th International Euro-Par Conference on Parallel Processing Y1 - 2001 U6 - https://doi.org/10.1007/3-540-44681-8_115 VL - 2150 SP - 817 EP - 824 PB - Springer Verlag, Berlin Heidelberg 2001 ER - TY - JOUR A1 - Allen, Gabrielle A1 - Benger, Werner A1 - Dramlitsch, Thomas A1 - Goodale, Tom A1 - Hege, Hans-Christian A1 - Lanfermann, Gerd A1 - Merzky, André A1 - Radtke, Thomas A1 - Seidel, Edward A1 - Shalf, John T1 - Cactus Tools for Grid Applications JF - Cluster Computing Y1 - 2001 U6 - https://doi.org/10.1023/A:1011491422534 VL - 4 IS - 3 SP - 179 EP - 188 ER - TY - JOUR A1 - Schmidt-Ehrenberg, Johannes A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Visually stunning - Molecular conformations JF - The Biochemist Y1 - 2001 VL - 23 IS - 5 SP - 22 EP - 26 ER - TY - JOUR A1 - Best, Christoph A1 - Hege, Hans-Christian T1 - Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories JF - IEEE Computing in Science & Engineering Y1 - 2002 U6 - https://doi.org/10.1109/5992.998642 VL - 4(3) SP - 68 EP - 75 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger ED - Skala, Václav T1 - Curvature Measures of 3D Vector Fields and their Applications T2 - Journal of WSCG Y1 - 2002 UR - http://www.zib.de/weinkauf/ U6 - https://doi.org/10.1109/TPAMI.2006.36 VL - 10 SP - 507 EP - 514 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger ED - Skala, Václav T1 - Vector Field Metrics Based on Distance Measures of First Order Critical Points T2 - Journal of WSCG, Short Communication Papers Y1 - 2002 VL - 10 SP - 121 EP - 128 ER - TY - JOUR A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Trepczynski, Adam A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - 3D Osteotomy Planning in Cranio-Maxillofacial Surgery: Experiences and Results of Surgery Planning and Volumetric Finite-Element Soft Tissue Prediction in Three Clinical Cases JF - Computer Assisted Radiology and Surgery (CARS) Y1 - 2002 SP - 983 EP - 987 PB - Springer Verlag ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Towards Patient Specific, Anatomy Based Simulation of Facial Mimics for Surgical Nerve Rehabilitation T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2002 SP - 3 EP - 6 PB - Springer Verlag ER - TY - CHAP A1 - Allen, Gabrielle A1 - Angulo, Dave A1 - Goodale, Tom A1 - Kielmann, Thilo A1 - Merzky, André A1 - Nabrzysk, Jarek A1 - Pukacki, Juliusz A1 - Russel, Michael A1 - Radke, Thomas A1 - Seidel, Edward A1 - Shalf, John A1 - Taylor, Ian T1 - GridLab – Enabling Applications on the Grid: A Progress Report T2 - Lecture Notes in Computer Science (LNCS) Y1 - 2002 N1 - 3rd Int. Workshop on Grid Computing, Supercomputing 2002 VL - 2536 SP - 39 EP - 45 ER - TY - CHAP A1 - Olbrich, Stephan A1 - Weinkauf, Tino A1 - Merzky, André A1 - Knipp, Harald A1 - Hege, Hans-Christian A1 - Pralle, Helmut ED - Knop, J. von T1 - Lösungsansätze zur Visualisierung im High Performance Computing und Networking Kontext T2 - Zukunft der Netze - Die Verletzbarkeit meistern. Y1 - 2002 SP - 269 EP - 279 CY - Düsseldorf, Germany ER - TY - JOUR A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Texture-based volume rendering of adaptive mesh refinement data JF - The Visual Computer Y1 - 2002 VL - 18 IS - 8 SP - 491 EP - 492 ER - TY - CHAP A1 - Böhm, Thilo T1 - Web Service Based Data Management for Grid Applications T2 - Euroweb 2002 - The Web and the GRID Y1 - 2002 SP - 126 EP - 135 CY - Oxford, UK ER - TY - CHAP A1 - Lamecker, Hans A1 - Lange, Thomas A1 - Seebaß, Martin T1 - A Statistical Shape Model for the Liver T2 - MICCAI 2002 Y1 - 2002 U6 - https://doi.org/10.1007/3-540-45787-9_53 SP - 422 EP - 427 PB - Springer ER - TY - JOUR A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Felsenberg, Dieter T1 - Femoral Neck Fractures: Reasons for the Most Common Location of Fractures JF - Acta Orthop. Scand. (Suppl. 304) Y1 - 2002 VL - 73 SP - 26 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Kurths, Jürgen A1 - Gowin, Wolfgang T1 - Bone Modeling and Structural Measures of Complexity JF - Journal of Gravitational Physiology Y1 - 2002 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 9 SP - 175 EP - 176 ER - TY - GEN A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Felsenberg, Dieter A1 - Kurths, Jürgen A1 - Zaikin, Alexei A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Regional Structural Skeletal Discordance Assessed by Measures of Complexity Y1 - 2002 ER - TY - JOUR A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Visual Analysis of Trabecular Bone Structure JF - Journal of Gravitational Physiology Y1 - 2002 VL - 9 (1) SP - 171 EP - 172 ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Schirmacher, Hartmut A1 - Westerhoff, Malte A1 - Lamecker, Hans A1 - Prohaska, Steffen A1 - Zachow, Stefan T1 - From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models T2 - Proceedings of the Japan Korea Computer Graphics Conference 2002 Y1 - 2002 PB - Kanazawa University CY - Kanazawa City, Ishikawa, Japan ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Mun, Seong T1 - Shape-based Modeling Approach for the Estimation of Individual Facial Mimics in Craniofacial Surgery Planning T2 - Proc. SPIE Medical Imaging 2002: Visualization, Image-Guided Procedures, and Display Y1 - 2002 VL - 4681 SP - 242 EP - 248 CY - San Diego, USA target ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - K. Mun, Seong T1 - Adaptive Nonlinear Elastic FEM for Realistic Prediction of Soft Tissue in Craniofacial Surgery Simulations T2 - Proc. SPIE Medical Imaging 2002 Y1 - 2002 U6 - https://doi.org/10.1117/12.466906 VL - 4681 SP - 1 EP - 8 CY - San Diego, USA ER - TY - JOUR A1 - Busch, Hubert A1 - Merzky, André T1 - Supercomputer: Auf zwei Standorte verteiltes Rechnersystem wird im Wissenschaftsnetz zum virtuellen Supercomputer JF - DFN-Mitteilungen, Heft 59 Y1 - 2002 SP - 8 EP - 10 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Merzky, André T1 - GriKSL - Immersive Überwachung und Steuerung von Simulationen auf entfernten Supercomputern JF - DFN-Mitteilungen, Heft 59 Y1 - 2002 SP - 5 EP - 7 ER - TY - CHAP A1 - Coconu, Liviu A1 - Hege, Hans-Christian ED - Gibson, Simon ED - Debevec, Paul T1 - Hardware-Accelerated Point-Based Rendering of Complex Scenes T2 - Proceedings of the 13th Eurographics Workshop on Rendering Techniques Y1 - 2002 SP - 43 EP - 52 CY - Pisa, Italy ER - TY - CHAP A1 - Cosnard, Michel A1 - Merzky, André ED - Monien, Burkhard ED - Feldmann, Rainer T1 - Meta- and Grid-Computing T2 - Lectures Notes in Computer Science Y1 - 2002 U6 - https://doi.org/10.1007/3-540-45706-2_121 VL - 2400 SP - 861 EP - 862 PB - Springer ER - TY - JOUR A1 - Allen, Gabrielle A1 - Merzky, André A1 - Nabrzysk, Jarek A1 - Seidel, Edward T1 - GridLab - A Grid Application Toolkit and Testbed JF - Future Generation Computer Systems Y1 - 2002 VL - 18(8) SP - 1143 EP - 1153 ER - TY - CHAP A1 - Schmidt-Ehrenberg, Johannes A1 - Baum, Daniel A1 - Hege, Hans-Christian ED - J. Moorhead, Robert ED - Gross, Markus ED - I. Joy, Kenneth T1 - Visualizing Dynamic Molecular Conformations T2 - Proceedings of IEEE Visualization 2002 Y1 - 2002 U6 - https://doi.org/10.1109/VISUAL.2002.1183780 SP - 235 EP - 242 PB - IEEE Computer Society Press CY - Boston MA, USA ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - J. Moorhead, Robert ED - Gross, Markus ED - I. Joy, Kenneth T1 - Fast Visualization of Plane-Like Structures in Voxel Data T2 - Proceedings of IEEE Visualization 2002 Y1 - 2002 U6 - https://doi.org/10.1109/VISUAL.2002.1183753 SP - 29 EP - 36 PB - IEEE Computer Society Press CY - Boston MA, USA ER - TY - CHAP A1 - Kähler, Ralf A1 - Cox, Donna A1 - Patterson, Robert A1 - Levy, Stuart A1 - Hege, Hans-Christian A1 - Abel, Tom ED - J. Moorhead, Robert ED - Gross, Markus ED - I. Joy, Kenneth T1 - Rendering The First Star in The Universe - A Case Study T2 - Proceedings of IEEE Visualization 2002 Y1 - 2002 U6 - https://doi.org/10.1109/VISUAL.2002.1183824 SP - 537 EP - 540 PB - IEEE Computer Society Press CY - Boston MA, USA ER - TY - CHAP A1 - Hierl, Thomas A1 - Wollny, Gert A1 - Zachow, Stefan A1 - Klöppel, Rainer T1 - Visualisierung von Knochen und Weichteilveränderungen in der Distraktionsosteogenese des Mittelgesichtes T2 - Proc. 10. Jahrestagung der Deutschen Gesellschaft für Schädelbasischirurgie Y1 - 2002 SP - 111 EP - 116 CY - Heidelberg ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Kähler, Ralf A1 - Seidel, Edward A1 - Radke, Thomas T1 - GriKSL zeigt Live-Demos auf der iGrid2002 JF - DFN-Mitteilungen, Heft 60 Y1 - 2002 SP - 21 EP - 22 ER - TY - JOUR A1 - Zeilhofer, Hans-Florian A1 - Hege, Hans-Christian T1 - Operieren im Medizin-Grid JF - DFN-Mitteilungen, Heft 60 Y1 - 2002 SP - 19 EP - 20 ER - TY - CHAP A1 - Westerhoff, Malte A1 - Maye, Alexander A1 - Brandt, Robert A1 - Menzel, Randolf T1 - 3D Geometry Reconstruction in Neuroanatomy T2 - International Neuroscience Summit Abstract Book Y1 - 2002 SP - 49 CY - Berlin, Germany ER - TY - CHAP A1 - Lange, Thomas A1 - Lamecker, Hans A1 - Eulenstein, Sebastian T1 - Automatische Segmentierung von Lebergewebe für die präoperative Planung von Resektionen T2 - 1. Jahrestagung der Deutschen Gesellschaft für Computer- Roboterassistierte Chirugie CURAC Y1 - 2002 ER - TY - JOUR A1 - Zöckler, Malte A1 - Stalling, Detlev T1 - Using confocal microscopy and advanced 3-d visualization to investigate the Drosophila brain JF - Scientific Computing & Instrumentation Y1 - 2002 ER - TY - JOUR A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - T. Mader, Michael A1 - Grübel, Cornelia A1 - Heisenberg, Martin T1 - The Drosophila Standard Brain JF - Current Biology Y1 - 2002 U6 - https://doi.org/10.1016/S0960-9822(02)00656-5 VL - 12 IS - 3 SP - 227 EP - 231 ER - TY - JOUR A1 - V. Dörffel, W. A1 - Sugano, Yoshimi A1 - Stalling, Detlev A1 - Coconu, Liviu T1 - Lasergestützte endoskopische Vermessung der großen Atemwege JF - Pneumonologie Y1 - 2003 U6 - https://doi.org/10.1055/s-2003-42220 VL - 57(3) SP - 503 EP - 509 ER - TY - CHAP A1 - Lamecker, Hans A1 - Lange, Thomas A1 - Seebaß, Martin A1 - Eulenstein, Sebastian A1 - Westerhoff, Malte A1 - Hege, Hans-Christian T1 - Automatic Segmentation of the Liver for Preoperative Planning of Resections T2 - Proc. MMVR 2003 Y1 - 2003 SP - 171 EP - 173 PB - IOS press CY - Newport Beach, CA ER - TY - CHAP A1 - Thomsen, Jesper A1 - Koller, Bruno A1 - Laib, Andreas A1 - Prohaska, Steffen A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Comparison between Static Histomorphometric Measures Conducted by Traditionally 2D Histomorphometry and 3D μ-CT in Human Tibial Biopsies T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Kurths, Jürgen A1 - Gowin, Wolfgang T1 - 2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures. T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Belle, Stefan A1 - Felsenberg, Dieter T1 - Architectural Reasons for the Femoral Neck Fracture Location T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - JOUR A1 - Kähler, Ralf A1 - Simon, Mark A1 - Hege, Hans-Christian T1 - Interactive Volume Rendering of Large Data Sets Using Adaptive Mesh Refinement Hierarchies JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2003 U6 - https://doi.org/10.1109/TVCG.2003.1207442 VL - 9 IS - 3 SP - 341 EP - 351 ER - TY - CHAP A1 - Lange, Thomas A1 - Lamecker, Hans A1 - Seebaß, Martin T1 - Ein Softwarepaket für die modellbasierte Segmentierung anatomischer Strukturen T2 - Proc. BVM 2003 Y1 - 2003 SP - 111 EP - 116 CY - Erlangen ER - TY - CHAP A1 - Lamecker, Hans A1 - Lange, Thomas A1 - Seebaß, Martin T1 - Erzeugung statistischer 3D-Formmodelle zur Segmentierung medizinischer Bilddaten T2 - Proc. BVM 2003 Y1 - 2003 SP - 398 EP - 403 PB - Springer CY - Erlangen ER - TY - CHAP A1 - Saparin, Peter A1 - Gowin, Wolfgang A1 - Zaikin, Alexei A1 - Prohaska, Steffen T1 - Quantification of changes in human bone structure at different skeletal locations using measures of complexity T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Interactive Visualization to Support Quantification of Bone Biopsies T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Hege, Hans-Christian T1 - Creation and Visualization of Anatomical Models with Amira T2 - Proc. of 3D Modelling 2003 Y1 - 2003 SP - 7pp. CY - Paris ER - TY - CHAP A1 - Saparin, Peter A1 - Gowin, Wolfgang A1 - Zaikin, Alexei A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Kurths, Jürgen T1 - Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity T2 - 14th IAA Humans in Space Symposium Y1 - 2003 CY - Banff, Alberta, Canada ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - A Virtual Laboratory for Assessment of Bone Biopsies T2 - 14th IAA Humans in Space Symposium Y1 - 2003 SP - 7 CY - Banff, Alberta, Canada ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Draw & Cut: Intuitive 3D Osteotomy Planning on Polygonal Bone Models T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2003 U6 - https://doi.org/10.1016/S0531-5131(03)00272-3 SP - 362 EP - 369 CY - London, UK ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - On constitutive modeling of soft tissue for the long-term prediction of cranio-maxillofacial surgery outcome T2 - International Congress Series, CARS2003, Computer Assisted Radiology and Surgery, Proceedings of the 17th International Congress and Exhibition Y1 - 2003 U6 - https://doi.org/10.1016/S0531-5131(03)00500-4 VL - 1256 SP - 343 EP - 348 ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Galloway, Robert T1 - Realistic prediction of individual facial emotion expressions for craniofacial surgery simulations T2 - Proc. SPIE medical Imaging 2003 Y1 - 2003 U6 - https://doi.org/10.1117/12.479584 VL - 5029 SP - 520 EP - 527 CY - San Diego, CA, USA ER - TY - CHAP A1 - Kadooka, Yoshimasa A1 - Onishi, Naoki A1 - Choi, Jang-Woon A1 - Lee, Young-Ho A1 - Hege, Hans-Christian A1 - Tago, Yoshio ED - Kim, Kyung T1 - A Study on the PIV Virtual Laboratory by Web Grid Technology T2 - CD ROM Proc. PIV'03 - 5th Int. Symp. on Particle Image Velocimetry Y1 - 2003 PB - The Korean Society of Visualization CY - Busan, Korea ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Hutanu, Andrei A1 - Kähler, Ralf A1 - Merzky, André A1 - Radke, Thomas A1 - Seidel, Edward A1 - Ullmer, Brygg T1 - Progressive Retrieval and Hierarchical Visualization of Large Remote Data T2 - Proceedings of the 2003 Workshop on Adaptive Grid Middleware Y1 - 2003 SP - 60 EP - 72 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Schlegel, Michael A1 - Dillmann, Andreas ED - Ajaev, V. ED - Willis, D. T1 - Coherent structures in a transitional flow around a backward-facing step T2 - Physics of Fluids Y1 - 2003 VL - 15 SP - S3 ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Saddle Connectors - An Approach to Visualizing the Topological Skeleton of Complex 3D Vector Fields T2 - Proc. IEEE Visualization 2003 Y1 - 2003 U6 - https://doi.org/10.1109/VISUAL.2003.1250376 SP - 225 EP - 232 CY - Seattle ER - TY - CHAP A1 - Ullmer, Brygg A1 - Hutanu, Andrei A1 - Benger, Werner A1 - Hege, Hans-Christian ED - Staadt, Oliver T1 - Emerging Tangible Interfaces for Facilitating Collaborative Immersive Visualizations T2 - Proc. of NSF Lake Tahoe Workshop on Collaborative Virtual Reality and Visualization (extended abstract) Y1 - 2003 ER - TY - CHAP A1 - Seebaß, Martin A1 - Lamecker, Hans A1 - Lange, Thomas A1 - Gellermann, Johanna A1 - Wust, Peter T1 - A Statistical Shape Model of the Pelvic Bone for Segmentation T2 - European Society for Hyperthermic Oncology Annual Meeting Proceedings Y1 - 2003 SP - 91 EP - 92 ER - TY - CHAP A1 - Petz, Christoph A1 - Stalling, Detlev A1 - Goubergrits, Leonid A1 - Affeld, Klaus A1 - Spuler, Andreas ED - Tolxdorff, Thomas T1 - Validierung von Strömungssimulationen in kardiovaskulären Anwendungen T2 - Bildverabeitung für die Medizin 2004 Y1 - 2004 SP - 356 EP - 360 ER - TY - CHAP A1 - Zachow, Stefan A1 - Erdmann, Bodo A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Advances in 3D osteotomy planning with 3D soft tissue prediction T2 - Proc. 2nd International Symposium on Computer Aided Surgery around the Head, Abstract Y1 - 2004 SP - 31 CY - Bern ER - TY - CHAP A1 - Benger, Werner A1 - Hege, Hans-Christian T1 - Tensor splats T2 - Visualization and Data Analysis 2004, Proc. of SPIE Y1 - 2004 U6 - https://doi.org/10.1117/12.549300 VL - 5295 SP - 151 EP - 162 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Boundary switch connectors for topological visualization of complex 3D vector fields T2 - Proc. Joint Eurographics - IEEE TCVG Symposium on Visualization (VisSym ’04) Y1 - 2004 SP - 183 EP - 192 CY - Konstanz, Germany ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological construction and visualization of higher order 3D vector fields T2 - Computer Graphics Forum Y1 - 2004 U6 - https://doi.org/10.1109/VISUAL.2005.1532842 VL - 23(3) SP - 469 EP - 478 CY - Grenoble, France ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Stream line and path line oriented topology for 2D time-dependent vector fields T2 - Proc. IEEE Visualization 2004 Y1 - 2004 U6 - https://doi.org/10.1109/VIS.2004.99 SP - 321 EP - 328 CY - Austin, U.S.A. ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Polthier, Konrad T1 - Anisotropic filtering of non-linear surface features JF - Computer Graphics Forum Y1 - 2004 VL - 23(3) SP - 391 EP - 400 CY - Grenoble, France ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Distributed visualization and analysis of fluid dynamics data T2 - Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration Y1 - 2004 SP - 145 EP - 150 CY - Sendai, Japan ER - TY - JOUR A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Anatomy- and physics-based facial animation for craniofacial surgery simulations JF - Med Biol Eng Comput. Y1 - 2004 U6 - https://doi.org/10.1007/BF02344627 VL - 42(2) SP - 167 EP - 170 ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Aktuelle Anwendungen der Wissenschaftlichen Visualisierung (Current Applications of Scientific Visualization) JF - it - Information Technology Y1 - 2004 U6 - https://doi.org/10.1524/itit.46.3.142.34213 VL - 46(3) SP - 142 EP - 147 ER - TY - CHAP A1 - Lamecker, Hans A1 - Seebaß, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Fitzpatrick, J. ED - Sonka, Milan T1 - A 3D statistical shape model of the pelvic bone for segmentation T2 - Proceedings of SPIE - Volume 5370 Medical Imaging 2004 Y1 - 2004 U6 - https://doi.org/10.1117/12.534145 SP - 1341 EP - 1351 ER - TY - CHAP A1 - Lange, Thomas A1 - Tunn, Per-Ulf A1 - Lamecker, Hans A1 - Scheinemann, Peter A1 - Eulenstein, Sebastian A1 - Schlag, Peter-Michael ED - Tolxdorff, Thomas T1 - Computerunterstützte Prothesenkonstruktion mittels statistischem Formmodell bei Beckenresektion T2 - Proceedings BVM, Informatik aktuell Y1 - 2004 SP - 30 EP - 34 PB - Springer ER - TY - CHAP A1 - Eulenstein, Sebastian A1 - Lange, Thomas A1 - Hünerbein, Michael A1 - Schlag, Peter A1 - Lamecker, Hans T1 - Ultrasound based navigation system incorporating preoperative planning for liver surgery T2 - Proceedings CARS Y1 - 2004 U6 - https://doi.org/10.1016/j.ics.2004.03.121 target VL - 1268 SP - 758 EP - 763 PB - Elsevier ER - TY - CHAP A1 - Seebaß, Martin A1 - Lamecker, Hans A1 - Gellermann, Johanna A1 - Wust, Peter T1 - The impact of segmentation accuracy on treatment planning for regional hyperthermia T2 - Proceedings of the 9th International Congress on Hyperthermic Oncology Y1 - 2004 ER - TY - CHAP A1 - Lange, Thomas A1 - Eulenstein, Sebastian A1 - Hünerbein, Michael A1 - Lamecker, Hans A1 - Schlag, Peter-Michael ED - Barrilot, Christian T1 - Augmenting intraoperative 3D ultrasound with preoperative models for navigation in liver surgery T2 - Proceedings MICCAI Y1 - 2004 SP - 543 EP - 541 PB - Springer ER - TY - CHAP A1 - Lange, Thomas A1 - Wenckebach, Thomas A1 - Seebaß, Martin A1 - Lamecker, Hans A1 - Hünerbein, Michael T1 - Registration of different phases of contrast-enhanced MR data for liver surgery T2 - 3. Jahrestagung der Deutschen Gesellschaft für Computer-Roboterassistierte Chirurgie CURAC Y1 - 2004 ER - TY - CHAP A1 - Zachow, Stefan A1 - Hierl, Thomas A1 - Erdmann, Bodo T1 - Über die Genauigkeit einer 3D Weichgewebeprädiktion in der MKG-Cirurgie T2 - Workshop ’Bildverarbeitung für die Medizin’ (BVM) Y1 - 2004 SP - 75 EP - 79 CY - Berlin, Germany ER - TY - CHAP A1 - Zachow, Stefan A1 - Hierl, Thomas A1 - Erdmann, Bodo T1 - On the Predictability of tissue changes after osteotomy planning in maxillofacial surgery T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2004 U6 - https://doi.org/10.1016/j.ics.2004.03.043 SP - 648 EP - 653 CY - Chicago, USA ER - TY - JOUR A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Benz, Michaela A1 - Maier, Tobias A1 - Veit, Klaus A1 - Kramer, Manuel A1 - Benz, St. A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Lell, Michael T1 - Fusion of computed tomography data and optical 3D images of the dentition for streak artefact correction in the simulation of orthognathic surgery JF - Journal of Dento-Maxillofacial Radiology Y1 - 2004 U6 - https://doi.org/10.1259/dmfr/27071199 VL - 33 SP - 226 EP - 232 ER - TY - JOUR A1 - Haberl, Hannes A1 - Hell, Bertold A1 - Zöckler, Maja A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Sarrafzadeh, Asita A1 - Riecke, B. A1 - Langsch, Wolfgang A1 - Deuflhard, Peter A1 - Bier, Jürgen A1 - Brock, Mario T1 - Technical aspects and results of surgery for craniosynostosis JF - Zentralblatt für Neurochirurgie Y1 - 2004 VL - 65 IS - 2 SP - 65 EP - 74 ER - TY - JOUR A1 - Hierl, Thomas A1 - Zachow, Stefan A1 - Wollny, Gert A1 - Berti, Guntram A1 - Schmidt, Jens-Georg A1 - Fingberg, Jochen T1 - Concepts of computer-based simulation in orthognathic surgery JF - Journal of Cranio-Maxillofacial Surgery 32 Suppl. 1 Y1 - 2004 SP - 81 EP - 82 ER - TY - JOUR A1 - Hierl, Thomas A1 - Zachow, Stefan A1 - Wollny, Gert A1 - Berti, Guntram A1 - Schmidt, Jens-Georg A1 - Fingberg, Jochen T1 - Computer-based simulation in distraction osteogenesis JF - Proc. of 3rd Int. Oxford Distraction Symposium of the Craniofacial Skeleton Y1 - 2004 SP - 33 EP - 34 ER - TY - CHAP A1 - Zachow, Stefan A1 - Hierl, Thomas A1 - Erdmann, Bodo T1 - A quantitative evaluation of 3D soft tissue prediction in maxillofacial surgery planning T2 - Proc. 3. Jahrestagung der Deutschen Gesellschaft für Computer- und Roboter-assistierte Chirurgie e.V. Y1 - 2004 CY - München ER - TY - CHAP A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Computergestützte Operationsplanung in der Gesichtschirurgie T2 - Proc. VDE Kongress 2004 - Innovationen für Menschen, Band 2, Fachtagungsberichte DGBMT - GMM - GMA Y1 - 2004 SP - 53 EP - 58 ER - TY - CHAP A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte A1 - Cassot, Francis A1 - Mazel, Christophe A1 - Asselot, Didier A1 - Marc-Vergnes, Jean-Pierre T1 - Squelettisation par blocs pour des grands volumes de données 3D T2 - Reconnaissance des Formes et Intelligence Artificielle (RFIA 2004) Y1 - 2004 CY - Toulouse, France ER - TY - CHAP A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte A1 - Cassot, Francis A1 - Mazel, Christophe A1 - Asselot, Didier A1 - Marc-Vergnes, Jean-Pierre T1 - Skeletonization by blocks for large 3D datasets: Application to brain microcirculation T2 - IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'04) Y1 - 2004 U6 - https://doi.org/10.1109/ISBI.2004.1398481 SP - 89 EP - 92 CY - Arlington, Virginia ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hutanu, Andrei A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Interactive exploration of large remote micro-CT scans T2 - Proc. IEEE Visualization 2004 Y1 - 2004 U6 - https://doi.org/10.1109/VIS.2004.51 SP - 345 EP - 352 CY - Austin, Texas ER - TY - JOUR A1 - Prohaska, Steffen A1 - Dreher, Matthew A1 - Dewhirst, Mark A1 - Chilkoti, Ashutosh A1 - Pries, Axel T1 - 3-D reconstruction of tumor vascular networks JF - J. Vas. Res. Y1 - 2004 VL - 41 SP - 463 ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Grid-independent detection of closed stream lines in 2D vector fields T2 - Proc. Vision, Modeling and Visualization 2004 Y1 - 2004 SP - 421 EP - 428 CY - Stanford, U.S.A. ER - TY - CHAP A1 - Majewski, Mirek A1 - Polthier, Konrad T1 - Using MuPAD and JavaView to visualize mathematics on the Internet T2 - Proc. of the 9th Asian Technology Conference in Mathematics Y1 - 2004 SP - 465 EP - 474 ER - TY - JOUR A1 - Alonso, Sergio A1 - Kähler, Ralf A1 - S. Mikhailov, Alexander A1 - Sagués, Francisco T1 - Expanding scroll rings and negative tension turbulence in a model of excitable media JF - Phys. Rev. E Y1 - 2004 U6 - https://doi.org/10.1103/PhysRevE.70.056201 VL - 70 IS - 5 SP - 056201 PB - American Physical Society ER - TY - CHAP A1 - Lange, Thomas A1 - Wenckebach, Thomas A1 - Lamecker, Hans A1 - Seebaß, Martin A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Schlag, Peter-Michael T1 - Registration of different phases of contrast-enhanced CT/MRI data for computer-assisted liver surgery planning T2 - Int. J. Medical Robotics and Computer Assisted Surgery Y1 - 2005 U6 - https://doi.org/10.1002/rcs.23 VL - 1 (3) SP - 6 EP - 20 PB - Wiley ER - TY - CHAP A1 - Lange, Thomas A1 - Wenckebach, Thomas A1 - Lamecke, Hans A1 - Seebaß, Martin A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Schlag, Peter-Michael ED - Lemke, Heinz T1 - Registration of portal and hepatic venous phase of MR/CT data for computer-assisted liver surgery planning T2 - Proc. Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/10.1016/j.ics.2005.03.332 SP - 768 EP - 772 PB - Elsevier ER - TY - JOUR A1 - Saparin, Peter A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Zaikin, Alexei A1 - Kurths, Jürgen A1 - Hege, Hans-Christian A1 - Gowin, Wolfgang T1 - Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity JF - Acta Astronautica Y1 - 2005 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 56 IS - 9-12 SP - 820 EP - 830 ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Maxillofacial surgery planning with 3D soft tissue prediction - modeling, planning, simulation JF - 2. Int. Conf. on Advanced Digital Technology in Head and Neck Reconstruction, Abstract 33 Y1 - 2005 SP - 64 CY - Banff, Alberta, CA ER - TY - JOUR A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological methods for 2D time-dependent vector fields based on stream lines and path lines JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2005 U6 - https://doi.org/10.1109/TVCG.2005.68 VL - 11 IS - 4 ER - TY - JOUR A1 - Westermark, Anders A1 - Zachow, Stefan A1 - Eppley, Barry T1 - 3D osteotomy planning in maxillofacial surgery, including 3D soft tissue prediction JF - Journal of Craniofacial Surgery Y1 - 2005 VL - 16(1) SP - 100 EP - 104 ER - TY - CHAP A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Hannes A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Statistical shape modeling for craniosynostosis planning T2 - 2nd International Conference Advanced Digital Technology in Head and Neck Reconstruction 2005, Abstract Volume Y1 - 2005 SP - 64 CY - Banff, Alberta ER - TY - GEN A1 - Stalling, Detlev A1 - Westerhoff, Malte A1 - Hege, Hans-Christian ED - Hansen, Charles ED - Johnson, Christopher T1 - Amira: A highly interactive system for visual data analysis T2 - The Visualization Handbook Y1 - 2005 U6 - https://doi.org/10.1016/B978-012387582-2/50040-X SP - 749 EP - 767 PB - Elsevier ER - TY - CHAP A1 - Wenckebach, Thomas A1 - Lamecker, Hans A1 - Hege, Hans-Christian ED - Christensen, Gary ED - Sonka, Milan T1 - Capturing anatomical shape variability using B-spline registration T2 - Information Processing in Medical Imaging: 19th International Conference (IPMI 2005) Y1 - 2005 U6 - https://doi.org/10.1007/b137723 VL - 3565/2005 SP - 578 EP - 590 PB - Springer-Verlag GmbH CY - Glenwood Springs, CO, USA ER - TY - JOUR A1 - Brandt, Robert A1 - Rohlfing, Torsten A1 - Rybak, Jürgen A1 - Krofczik, Sabine A1 - Maye, Alexander A1 - Westerhoff, Malte A1 - Hege, Hans-Christian A1 - Menzel, Randolf T1 - A three-dimensional average-shape atlas of the honeybee brain and its applications JF - Journal of Comparative Neurology Y1 - 2005 VL - 492(1) SP - 1 EP - 19 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Fast cross-sectional display of large data sets T2 - IAPR Conference on Machine Vision Applications Y1 - 2005 SP - 336 EP - 339 CY - Tsukuba, Japan ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Towards distributed visualization and analysis of large flow data JF - JSME International Journal, Series B Y1 - 2005 VL - 48 (2) SP - 241 EP - 246 ER - TY - CHAP A1 - Hildebrandt, Klaus A1 - Polthier, Konrad A1 - Wardetzky, Max T1 - Smooth feature lines on surface meshes T2 - Third Eurographics Symposium on Geometry Processing Y1 - 2005 SP - 85 EP - 90 ER - TY - JOUR A1 - Kälberer, Felix A1 - Polthier, Konrad A1 - Reitebuch, Ulrich A1 - Wardetzky, Max T1 - Free Lence - Coding with free valences JF - Computer Graphics Forum Y1 - 2005 U6 - https://doi.org/10.1111/j.1467-8659.2005.00872.x VL - 24 IS - Issue 3 SP - 469 EP - 478 ER - TY - CHAP A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Häusler, Gerd T1 - Fusion von optischen 3D- und CT-Daten des Gebisses zur Metallartefaktkorrektur vor computerassistierter Planung MKG-chirurgischer Eingriffe T2 - Symposium der Arbeitsgemeinschaf für Kieferchirurgie Y1 - 2005 CY - Bad Homburg v.d.H ER - TY - CHAP A1 - Nkenke, Emeka A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Zachow, Stefan T1 - Streak artifact correction of CT data by optical 3D imaging in the simulation of orthognathic surgery T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/doi:10.1016/j.ics.2005.03.278 CY - Berlin Germany ER - TY - CHAP A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Reconstruction of mandibular dysplasia using a statistical 3D shape model T2 - Proc. Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/10.1016/j.ics.2005.03.339 SP - 1238 EP - 1243 CY - Berlin, Germany ER - TY - JOUR A1 - Werner, Armin A1 - Deussen, Oliver A1 - Döllner, Jürgen A1 - Hege, Hans-Christian A1 - Paar, Philip A1 - Rekittke, Jörg ED - Buhmann, Erich ED - Paar, Philip ED - Bishop, Ian ED - Lange, Eckart T1 - Lenné 3D walking through landscape plan JF - Trends in Real-Time Landscape Visualization and Participation Y1 - 2005 SP - 48 EP - 59 PB - Wichmann Verlag ER - TY - JOUR A1 - Lange, Carsten A1 - Polthier, Konrad T1 - Anisotropic fairing of point sets JF - Special Issue of CAGD 2005 Y1 - 2005 U6 - https://doi.org/10.1016/j.cagd.2005.06.010 ER - TY - CHAP A1 - Clasen, Malte A1 - Hege, Hans-Christian ED - Buhmann, Erich ED - Paar, Philip ED - Bishop, Ian ED - Lange, Eckart T1 - Realistic illumination of vegetation in real-time environments T2 - Trends in Real-Time Landscape Visualization and Participation Y1 - 2005 SP - 107 EP - 114 PB - Wichmann Verlag ER - TY - CHAP A1 - Coconu, Liviu A1 - Colditz, Carsten A1 - Hege, Hans-Christian A1 - Deussen, Oliver ED - Buhmann, Erich ED - Paar, Philip ED - Bishop, Ian ED - Lange, Eckart T1 - Seamless integration of stylized renditions in computer-generated landscape visualization T2 - Trends in Real-Time Landscape Visualization and Participation Y1 - 2005 SP - 88 EP - 96 PB - Wichmann Verlag CY - Heidelberg ER - TY - CHAP A1 - Colditz, Carsten A1 - Coconu, Liviu A1 - Deussen, Oliver A1 - Hege, Hans-Christian ED - Buhmann, Erich ED - Paar, Philip ED - Bishop, Ian ED - Lange, Eckart T1 - Real-time rendering of complex photorealistic landscapes using hybrid level-of-detail approaches T2 - Trends in Real-Time Landscape Visualization and Participation Y1 - 2005 SP - 97 EP - 106 PB - Wichmann Verlag ER - TY - CHAP A1 - Theisel, Holger A1 - Sahner, Jan A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Extraction of parallel vector surfaces in 3D time-dependent fields and application to vortex core line tracking T2 - Proc. IEEE Visualization 2005 Y1 - 2005 SP - 559 EP - 566 CY - Minneapolis, USA ER - TY - CHAP A1 - Sahner, Jan A1 - Weinkauf, Tino A1 - Hege, Hans-Christian ED - Brodlie, K. ED - Duke, D. ED - Joy, K. T1 - Galilean invariant extraction and iconic representation of vortex core lines T2 - Proc. Eurographics / IEEE VGTC Symposium on Visualization (EuroVis ’05) Y1 - 2005 U6 - https://doi.org/10.2312/VisSym/EuroVis05/151-160 SP - 151 EP - 160 CY - Leeds, UK ER - TY - CHAP A1 - Wardetzky, Max ED - I. Bobenko, Alexander ED - Sullivan, John ED - Ziegler, Günter T1 - Convergence of the Cotan formula - an overview T2 - Discrete Differential Geometry Y1 - 2008 U6 - https://doi.org/10.1007/978-3-7643-8621-4 SP - 275 EP - 286 PB - Birkhäuser Basel ER - TY - CHAP A1 - Polthier, Konrad ED - Hass, J. ED - Hoffman, D. ED - Jaffe, A. ED - Rosenberg, H. ED - Schoen, R. ED - Wol, M. T1 - Computational aspects of discrete minimal surfaces T2 - Global Theory of Minimal Surfaces, Proc. of the Clay Mathematics Institute Summer School, CMI/AMS Y1 - 2005 ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Remote data access for interactive visualization T2 - 13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies Y1 - 2005 SP - 17 EP - 22 ER - TY - JOUR A1 - Thomsen, Jesper A1 - Laib, Andreas A1 - Koller, Bruno A1 - Prohaska, Steffen A1 - Mosekilde, L. A1 - Gowin, Wolfgang T1 - Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies JF - Journal of Microscopy Y1 - 2005 VL - 218 SP - 171 EP - 179 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Shi, Kuangyu A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological simplification of 3D vector fields and extracting higher order critical points T2 - Proc. IEEE Visualization 2005 Y1 - 2005 SP - 631 EP - 638 CY - Minneapolis, USA ER - TY - CHAP A1 - Kähler, Ralf A1 - Prohaska, Steffen A1 - Hutanu, Andrei A1 - Hege, Hans-Christian T1 - Visualization of time-dependent remote adaptive mesh refinement data T2 - Proc. IEEE Visualization 2005 Y1 - 2005 U6 - https://doi.org/10.1109/VISUAL.2005.1532793 SP - 175 EP - 182 CY - Minneapolis, USA ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Haberl, Hannes A1 - Stiller, Michael T1 - Medical applications for statistical shape models JF - Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik Y1 - 2005 VL - 17 (258) SP - 61 ER - TY - CHAP A1 - Schmidt-Ehrenberg, Johannes A1 - Hege, Hans-Christian T1 - Visual analysis of molecular conformations by means of a dynamic density mixture model T2 - Computational Life Sciences: First International Symposium, CompLife 2005 Y1 - 2005 VL - 3695 SP - 229 EP - 240 PB - Springer CY - Konstanz, Germany ER - TY - CHAP A1 - Baum, Daniel T1 - Multiple semi-flexible 3D superposition of drug-sized molecules T2 - Computational Life Sciences: First International Symposium, CompLife 2005 Y1 - 2005 U6 - https://doi.org/10.1007/11560500_18 VL - 3695 SP - 198 EP - 207 PB - Springer CY - Konstanz, Germany ER - TY - CHAP A1 - Deussen, Oliver A1 - Colditz, Carsten A1 - Coconu, Liviu A1 - Hege, Hans-Christian ED - Bishop, Ian ED - Lange, Eckart T1 - Efficient modelling and rendering of landscapes T2 - Visualization in Landscape and Environmental Planning Y1 - 2005 SP - 56 EP - 61 PB - Spon Press CY - London ER - TY - CHAP A1 - Hildebrandt, Klaus A1 - Polthier, Konrad A1 - Preuß, Eike T1 - Evolution of 3D curves under strict spatial constraints T2 - IEEE Proceedings on Ninth International Conference on Computer Aided Design and Computer Graphics (CAD/CG 2005) Y1 - 2005 U6 - https://doi.org/10.1109/CAD-CG.2005.38 SP - 40 EP - 45 ER - TY - CHAP A1 - AO-99-030, ESA-MAP-Team ED - Wilson, A. T1 - Assessment of bone structure and its changes in microgravity T2 - SP-1290: Microgravity Applications Programme: Successful Teaming of Science and Industry Y1 - 2005 SP - 282 EP - 305 PB - European Space Agency ER - TY - CHAP A1 - Röhricht, W. A1 - Clasen, Malte T1 - Multum, non multi - Hierarchische Bit Trees bei der Pflanzenverteilung mit oik T2 - Simulation in Umwelt- und Geowissenschaften. Workshop Dresden 2005 Y1 - 2005 PB - Shaker CY - Aachen ER - TY - GEN A1 - Hege, Hans-Christian T1 - Hintergrundinformationen zum Artikel ‘Neue Bilder für die Medizin?’ Y1 - 2005 PB - DFG-Research Center Matheon, Report, 19 pages ER - TY - JOUR A1 - Ziegler, Günter M. A1 - Hege, Hans-Christian A1 - Duda, Georg T1 - Neue Bilder für die Medizin? JF - DFN-Mitteilungen Y1 - 2005 VL - 13(3) SP - 163 EP - 167 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Kurths, Jürgen A1 - Prohaska, Steffen A1 - Gowin, Wolfgang T1 - Modeling resorption in 2D-CT and 3D μ-CT bone images JF - Int. J. of Bif. and Chaos Y1 - 2005 VL - 15(9) SP - 2995 EP - 3009 ER - TY - GEN A1 - Petz, Christoph A1 - Weinkauf, Tino A1 - Streckwall, Heinrich A1 - Salvatore, Franceso A1 - Noack, Bernd R. A1 - Hege, Hans-Christian T1 - Vortex Structures at a Rotating Ship Propeller Y1 - 2006 PB - Presented at the 24th Annual Gallery of Fluid Motion exhibit, held at the 59th Annual Meeting of the American Physical Society, Division of Fluid Dynamics, Tampa Bay ER - TY - JOUR A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte T1 - Blockwise processing applied to brain micro-vascular network study JF - IEEE Transactions on Medical Imaging Y1 - 2006 U6 - https://doi.org/10.1109/TMI.2006.880670 VL - 25 IS - 10 SP - 1319 EP - 1328 ER - TY - JOUR A1 - Cassot, Francis A1 - Lauwers, Frederic A1 - Fouard, Céline A1 - Prohaska, Steffen A1 - Lauwer-Cances, Valerie T1 - A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex JF - Microcirculation Y1 - 2006 VL - 13 SP - 15 EP - 32 ER - TY - JOUR A1 - Maye, Alexander A1 - Wenckebach, Thomas A1 - Hege, Hans-Christian T1 - Visualization, reconstruction, and integration of neuronal structures in digital brain atlases JF - Int. Journal of Neuroscience Y1 - 2006 VL - 116(4) SP - 431 EP - 459 ER - TY - JOUR A1 - Benger, Werner A1 - Bartsch, Hauke A1 - Hege, Hans-Christian A1 - Kitzler, Hagen A1 - Shumilina, Anna A1 - Werner, Annett T1 - Visualizing neuronal structures in the human brain via Diffusion Tensor MRI JF - Int. Journal of Neuroscience Y1 - 2006 VL - 116(4) SP - 461 EP - 514 ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Weber, Rainer A1 - Heppt, Werner T1 - CFD simulation of nasal airflow: Towards treatment planning for functional rhinosurgery JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 165 EP - 167 PB - Springer ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Is the course of the mandibular nerve deducible from the shape of the mandible? JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 415 EP - 417 PB - Springer ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Computer assisted planning in cranio-maxillofacial surgery JF - Journal of Computing and Information Technology Y1 - 2006 VL - 14(1) SP - 53 EP - 64 ER - TY - JOUR A1 - Benger, Werner A1 - Hege, Hans-Christian T1 - Strategies for direct visualization of second-rank tensor fields JF - Visualization and Processing of Tensor Fields Y1 - 2006 U6 - https://doi.org/10.1007/3-540-31272-2_11 SP - 191 EP - 214 PB - Springer Verlag ER - TY - CHAP A1 - Benger, Werner A1 - Hege, Hans-Christian T1 - Analysing curved spacetimes with tensor splats T2 - Proceedings of the Tenth Marcel Grossmann Meeting in Theoretical and Experimental General Relativity, Gravitation and Relativistic Field Theories Y1 - 2006 U6 - https://doi.org/10.1142/9789812704030_0164 VL - 3 SP - 1619 EP - 1624 PB - World Scientific CY - Singapore ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Zöckler, Maja T1 - Surgical treatment of craniosynostosis based on a statistical 3D-shape model JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 U6 - https://doi.org/10.1007/s11548-006-0024-x VL - 1(1) SP - 253 EP - 254 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Wittmers, Antonia A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Automatic segmentation of mandibles in low-dose CT-data JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 VL - 1(1) SP - 393 EP - 395 ER - TY - CHAP A1 - Coconu, Liviu A1 - Deussen, Oliver A1 - Hege, Hans-Christian T1 - Real-time pen-and-ink illustration of landscapes T2 - NPAR '06: Proceedings of the 3rd International Symposium on Non-photorealistic Animation and Rendering Y1 - 2006 U6 - https://doi.org/10.1145/1124728.1124734 SP - 27 EP - 35 PB - ACM press CY - New York, NY, USA ER - TY - JOUR A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological structures in two-parameter-dependent 2D vector fields JF - Computer Graphics Forum Y1 - 2006 U6 - https://doi.org/10.1111/j.1467-8659.2006.00980.x VL - 25 (3) SP - 607 EP - 616 ER - TY - CHAP A1 - Shi, Kuangyu A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hauser, Helwig A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Path line oriented topology for periodic 2D time-dependent vector fields T2 - Proc. Eurographics / IEEE VGTC Symposium on Visualization Y1 - 2006 SP - 139 EP - 146 CY - Lisbon, Portugal ER - TY - CHAP A1 - Lamecker, Hans A1 - Wenckebach, Thomas A1 - Hege, Hans-Christian A1 - N. Duda, Georg A1 - Heller, Markus T1 - Atlas-basierte 3D-Rekonstruktion des Beckens aus 2D-Projektionsbildern T2 - Bildverarbeitung für die Medizin 2006: Algorithmen - Systeme - Anwendungen Y1 - 2006 U6 - https://doi.org/10.1007/3-540-32137-3_6 SP - 26 EP - 30 PB - Springer Berlin Heidelberg ER - TY - CHAP A1 - Clasen, Malte A1 - Hege, Hans-Christian T1 - Terrain rendering using spherical clipmaps T2 - EuroVis 2006 - Eurographics / IEEE VGTC Symposium on Visualization Y1 - 2006 SP - 91 EP - 98 ER - TY - CHAP A1 - Lamecker, Hans A1 - Wenckebach, Thomas A1 - Hege, Hans-Christian T1 - Atlas-based 3D-shape reconstruction from x-ray images T2 - Proc. Int. Conf. of Pattern Recognition (ICPR2006) Y1 - 2006 U6 - https://doi.org/10.1109/ICPR.2006.279 VL - Volume I SP - 371 EP - 374 PB - IEEE Computer Society ER - TY - CHAP A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - A Point-matching based algorithm for 3D surface alignment of drug-sized molecules T2 - Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006 Y1 - 2006 U6 - https://doi.org/10.1007/11875741_18 VL - 4216 SP - 183 EP - 193 PB - Springer ER - TY - GEN A1 - Horenko, Illia A1 - Schmidt-Ehrenberg, Johannes A1 - Schütte, Christof T1 - Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models T2 - Computational Life Sciences II Y1 - 2006 VL - 4216 SP - 98 EP - 115 PB - Springer ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Timmel, Tobias A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Characterization of an artificial valve flow using the numerical dye washout visualization technique JF - Artificial Organs Y1 - 2006 VL - 30(8) SP - 642 EP - 650 ER - TY - CHAP A1 - Prohaska, Steffen T1 - Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen T2 - Kartographische Schriften Y1 - 2006 VL - 10 SP - 103 EP - 110 ER - TY - CHAP A1 - Kähler, Ralf A1 - Wise, John A1 - Abel, Tom A1 - Hege, Hans-Christian T1 - A framework for interactive, high-quality volume rendering of cosmological simulations T2 - Proc. Int. Workshop on Volume Graphics (VG06) Y1 - 2006 SP - 103 EP - 110 PB - Eurographics / IEEE VGTC 2006 CY - Boston ER - TY - JOUR A1 - Hutanu, Andrei A1 - Allen, Gabrielle A1 - Beck, Stephen A1 - Holub, Petr A1 - Kaiser, Hartmut A1 - Kulshrestha, Archit A1 - Liska, Milos A1 - MacLaren, Jon A1 - Matyska, Ludek A1 - Paruchuri, Ravi A1 - Prohaska, Steffen A1 - Seidel, Edward A1 - Ullmer, Brygg A1 - Venkataraman, Shalini T1 - Distributed and collaborative visualization of large data sets using high-speed networks JF - Future Generation Comp. Syst Y1 - 2006 U6 - https://doi.org/10.1016/j.future.2006.03.026 VL - 22(8) SP - 1004 EP - 1010 ER - TY - CHAP A1 - Seim, Heiko A1 - Dornheim, Jana A1 - Preim, Uta T1 - Ein 2-Fronten-Feder-Masse-Modell zur Segmentierung von Lymphknoten in CT-Daten des Halses T2 - Bildverarbeitung für die Medizin Y1 - 2006 U6 - https://doi.org/10.1007/3-540-32137-3_22 SP - 106 EP - 110 PB - Springer-Verlag ER - TY - CHAP A1 - Dornheim, Lars A1 - Dornheim, Jana A1 - Seim, Heiko A1 - Tönnies, Klaus T1 - Aktive Sensoren: Kontextbasierte Filterung von Merkmalen zur modellbasierten Segmentierung T2 - Bildverarbeitung für die Medizin Y1 - 2006 U6 - https://doi.org/10.1007/3-540-32137-3_20 SP - 96 EP - 100 PB - Springer-Verlag ER - TY - GEN A1 - Kamer, Lukas A1 - Noser, Hansrudi A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Wittmers, Antonia A1 - Kaup, Thomas A1 - Schramm, Alexander A1 - Hammer, Beat T1 - Three-dimensional statistical shape analysis - A useful tool for developing a new type of orbital implant? Y1 - 2006 SP - 20 EP - 21 PB - AO Development Institute, New Products Brochure 2/06 ER - TY - CHAP A1 - Duffy, Alex A1 - Harris, Stefan A1 - Marzi, Jochen A1 - Petz, Christoph A1 - Wu, Zichao T1 - VIRTUE: Integrating CFD Ship Design T2 - Proc. of 7th International Conference on Hydrodynamics Y1 - 2006 ER - TY - JOUR A1 - Dornheim, Jana A1 - Seim, Heiko A1 - Preim, Bernhard A1 - Hertel, Ilka A1 - Strauß, Gero T1 - Segmentation of neck lymph nodes in CT datasets with stable 3D mass-spring models JF - Academic Radiology (2) Y1 - 2007 U6 - https://doi.org/10.1016/j.acra.2007.09.001 VL - 14(2) SP - 1389 EP - 1399 ER - TY - JOUR A1 - Gubatz, Sabine A1 - Dercksen, Vincent J. A1 - Brüß, Cornelia A1 - Weschke, Winfriede A1 - Wobus, Ulrich T1 - Analysis of barley (hordeum vulgare) grain development using three-dimensional digital models JF - The Plant Journal Y1 - 2007 U6 - https://doi.org/10.1111/j.1365-313X.2007.03260.x VL - 52 IS - 4 SP - 779 EP - 790 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Sahner, Jan A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - A unified feature extraction architecture T2 - Active Flow Control Y1 - 2007 U6 - https://doi.org/10.1007/978-3-540-71439-2_8 SP - 119 EP - 133 PB - Springer Berlin/Heidelberg ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino T1 - On the Applicability of Topological Methods for Complex Flow Data T2 - Topology-based Methods in Visualization Y1 - 2007 U6 - https://doi.org/10.1007/978-3-540-70823-0_8 SP - 105 EP - 120 PB - Springer ER - TY - CHAP A1 - Günther, Bert A1 - Thiele, Frank A1 - Petz, Ralf A1 - Nitsche, Wolfgang A1 - Sahner, Jan A1 - Weinkauf, Tino A1 - Hege, Hans-Christian T1 - Control of Separation on the Flap of a Three-Element High-Lift Configuration T2 - 45th AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2007 CY - Reno, NV, U.S.A. ER - TY - JOUR A1 - Weinkauf, Tino A1 - Sahner, Jan A1 - Theisel, Holger A1 - Hege, Hans-Christian T1 - Cores of Swirling Particle Motion in Unsteady Flows JF - IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2007) Y1 - 2007 U6 - https://doi.org/10.1109/TVCG.2007.70545 VL - 13 IS - 6 SP - 1759 EP - 1766 ER - TY - CHAP A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Feature Flow Fields in Out-of-Core Settings T2 - Topology-based Methods in Visualization Y1 - 2007 SP - 51 EP - 64 PB - Springer ER - TY - GEN A1 - Sahner, Jan A1 - Weinkauf, Tino A1 - Teuber, Nathalie A1 - Hege, Hans-Christian T1 - Vortex and strain skeletons in Eulerian and Lagrangian frames Y1 - 2007 U6 - https://doi.org/10.1109/TVCG.2007.1053 SP - 980 EP - 990 ER - TY - CHAP A1 - Kuß, Anja A1 - Hege, Hans-Christian A1 - Krofczik, Sabine A1 - Börner, Jana T1 - Pipeline for the creation of surface-based averaged brain atlases T2 - Proceedings of WSCG 2007 - the 15-th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision Y1 - 2007 VL - 15 SP - 17 EP - 24 CY - Plzen, Czech Republic ER - TY - CHAP A1 - Shi, Kuangyu A1 - Theisel, Holger A1 - Hauser, Helwig A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Path Line Attributes - an Information Visualization Approach to Analyzing the Dynamic Behavior of 3D Time-Dependent Flow Fields T2 - Topology-Based Methods in Visualization II Y1 - 2009 U6 - https://doi.org/10.1007/978-3-540-88606-8_6 SP - 75 EP - 88 PB - Springer CY - Berlin ER - TY - GEN A1 - Shi, Kuangyu A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hauser, Helwig A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Extracting separation surfaces of path line oriented topology in periodic 2D time-dependent vector fields Y1 - 2007 SP - 75 EP - 82 ER - TY - CHAP A1 - Lange, Thomas A1 - Lamecker, Hans A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Beller, Sigfried A1 - Schlag, Peter ED - Horsch, A. T1 - A new class of distance measures for registration of tubular models to image data T2 - Proc. Bildverarbeitung für die Medizin (BVM) Y1 - 2007 U6 - https://doi.org/10.1007/978-3-540-71091-2_21 SP - 101 EP - 105 PB - Springer ER - TY - JOUR A1 - Lamecker, Hans A1 - Kamer, Lukas A1 - Wittmers, Antonia A1 - Zachow, Stefan A1 - Kaup, Thomas A1 - Schramm, Alexander A1 - Noser, Hansrudi A1 - Hammer, Beat T1 - A method for the three-dimensional statistical shape analysis of the bony orbit JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 94 EP - 97 ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Heppt, Werner T1 - Understanding nasal airflow via CFD simulation and visualization JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 173 EP - 176 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Heppt, Werner T1 - Innovation in der Funktionell-Ästhetischen Nasenchirurgie: Rhino-CFD JF - Face, Int. Mag. of Orofacial Esthetics Y1 - 2007 SP - 20 EP - 23 PB - Oemus Journale Leipzig ER - TY - JOUR A1 - Gessat, Michael A1 - Zachow, Stefan A1 - Burgert, Oliver A1 - Lemke, Heinz T1 - Geometric Meshes in Medical Applications - Steps towards a specification of Geometric Models in DICOM JF - Int. J. of Computer Assisted Radiology and Surgery (CARS) Y1 - 2007 U6 - https://doi.org/10.1007/s11548-007-0112-6 SP - 440 EP - 442 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lange, Thomas A1 - Lamecker, Hans T1 - Shape constrained automatic segmentation of the liver based on a heuristic intensity model JF - Proc. MICCAI Workshop 3D Segmentation in the Clinic Y1 - 2007 SP - 109 EP - 116 ER - TY - CHAP A1 - Neubert, Kerstin A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Menzel, Randolf A1 - Rybak, Jürgen T1 - Model-based autosegmentation of brain structures in the honeybee using statistical shape models T2 - Proc. 8th Int. Congr. of Neuroethology (ICN) Y1 - 2007 ER - TY - CHAP A1 - Zachow, Stefan A1 - Zilske, Michael A1 - Hege, Hans-Christian T1 - 3D Reconstruction of Individual Anatomy from Medical Image Data: Segmentation and Geometry Processing T2 - 25. ANSYS Conference & CADFEM Users’ Meeting Y1 - 2007 CY - Dresden ER - TY - JOUR A1 - Heppt, Werner A1 - Hildebrandt, Thomas A1 - Steinmann, Alexander A1 - Zachow, Stefan T1 - Aesthetic and Function in Rhinoplasty JF - Springer Journal Y1 - 2007 VL - 264 (Suppl 1), RL 126 SP - 307 ER - TY - JOUR A1 - Lange, Thomas A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Beller, Sigfried A1 - Schlag, Peter A1 - Lamecker, Hans T1 - A Distance Measure for Non-Rigid Registration of Geometrical Models to Intensity Data JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2007 VL - 2, Suppl. 1 SP - 204 EP - 206 PB - Springer ER - TY - CHAP A1 - Clasen, Malte A1 - Hege, Hans-Christian ED - Schulze, Thomas ED - Preim, Bernhard ED - Schumann, Heidrun T1 - Clipmap-based Terrain Data Synthesis T2 - Proc. SimVis 2007 Y1 - 2007 SP - 385 EP - 398 PB - SCS Publishing House e.V. ER - TY - JOUR A1 - Paar, Philip A1 - Clasen, Malte T1 - Earth, Landscape, Biotope, Plant. Interactive visualisation with Biosphere3D JF - Proceedings of CORP - 12th International Conference on Urban Planning and Spatial Development in the Information Society, May 20th - 23rd Y1 - 2007 SP - 207 EP - 214 ER - TY - GEN A1 - Bodden, Eric A1 - Clasen, Malte A1 - Kneis, Joachim T1 - Arithmetic coding revealed - a guided tour from theory to praxis Y1 - 2007 PB - Technical Report SABLE-TR-2007-5, Sable Research Group, School of Computer Science, McGill University ER - TY - CHAP A1 - Kähler, Ralf A1 - Abel, Tom A1 - Hege, Hans-Christian T1 - Simultaneous GPU-Assisted Raycasting of Unstructured Point Sets and Volumetric Grid Data T2 - Proceedings of IEEE/EG International Symposium on Volume Graphics 2007 Y1 - 2007 SP - 49 EP - 56 PB - A K Peters CY - Prague, Czech Republic ER - TY - JOUR A1 - Heller, Markus O. A1 - Matziolis, Georg A1 - König, Christian A1 - Taylor, William R. A1 - Hinterwimmer, S. A1 - Graichen, H. A1 - Hege, Hans-Christian A1 - Bergmann, G. A1 - Perka, Carsten A1 - Duda, G. N. T1 - Muskuloskelettale Biomechanik des Kniegelenks - Grundlagen für die präoperative Planung von Umstellung und Gelenkersatz JF - Der Orthopäde Y1 - 2007 U6 - https://doi.org/10.1007/s00132-007-1115-2 VL - 36 IS - 7 SP - 628 EP - 634 ER - TY - CHAP A1 - Poethke, Jens A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Spuler, Andreas A1 - Petz, Christoph A1 - Hege, Hans-Christian ED - Jos Vander Sloten, Pascal ED - Haueisen, Jens T1 - Impact of imaging modality for analysis of a cerebral aneurysm: Comparison between CT, MRI and 3DRA T2 - Proceedings of the 4th European Conference of the International Federation for Medical and Biological Engineering Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-89208-3 SP - 1889 EP - 1893 PB - Springer-Verlag CY - Antwerp, Belgium ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Brüß, Cornelia A1 - Stalling, Detlev A1 - Gubatz, Sabine A1 - Seiffert, Udo A1 - Hege, Hans-Christian T1 - Towards automatic generation of 3D models of biological objects based on serial sections T2 - Visualization in Medicine and Life Sciences Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-72630-2 SP - 3 EP - 25 PB - Springer-Verlag Berlin Heidelberg ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino T1 - Morphological Representations of Vector Fields T2 - Shape Analysis and Structuring Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-33265-7 PB - Springer ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Stalling, Detlev T1 - Numerical Dye Washout Method as a Tool for Characterizing the Heart Valve Flow JF - ASAIO Journal Y1 - 2008 U6 - https://doi.org/10.1097/MAT.0b013e31815c5e38 VL - 54(1) SP - 50 EP - 57 ER - TY - JOUR A1 - Steinmann, Alexander A1 - Bartsch, Peter A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Breathing Easily: Simulation of airflow in human noses can become a useful rhinosurgery planning tool JF - ANSYS Advantage Y1 - 2008 VL - Vol. II, No. 1 SP - 30 EP - 31 ER - TY - GEN A1 - Lange, Thomas A1 - Lamecker, Hans A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Beller, Sigfried A1 - Schlag, Peter T1 - Validation Metrics for Non-Rigid Registration of Medical Images containing Vessel Trees Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-78640-5_17 SP - 82 EP - 86 PB - Springer ER - TY - CHAP A1 - Dornheim, Jana A1 - Born, Silvia A1 - Zachow, Stefan A1 - Gessat, Michael A1 - Wellein, Daniela A1 - Strauß, Gero A1 - Preim, Bernhard A1 - Bartz, Dirk ED - Hauser, Helwig T1 - Bildanalyse, Visualisierung und Modellerstellung für die Implantatplanung im Mittelohr T2 - Proc. of Simulation and Visualization 2008 Y1 - 2008 SP - 139 EP - 154 ER - TY - CHAP A1 - Neugebauer, Mathias A1 - Janiga, Gabor A1 - Zachow, Stefan A1 - Krischek, Özlem A1 - Preim, Bernhard ED - Hauser, Helwig T1 - Generierung qualitativ hochwertiger Modelle für die Simulation von Blutfluss in zerebralen Aneurysmen T2 - Proc. of Simulation and Visualization 2008 Y1 - 2008 SP - 221 EP - 235 ER - TY - CHAP A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Segmentation of Bony Structures with Ligament Attachment Sites T2 - Bildverarbeitung für die Medizin 2008 Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-78640-5_42 SP - 207 EP - 211 PB - Springer ER - TY - CHAP A1 - Zilske, Michael A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Adaptive Remeshing of Non-Manifold Surfaces T2 - Eurographics 2008 Annex to the Conf. Proc. Y1 - 2008 SP - 207 EP - 211 ER - TY - JOUR A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Computergestützte Planung in der kraniofazialen Chirurgie JF - Face 01/08, Int. Mag. of Orofacial Esthetics Y1 - 2008 SP - 43 EP - 49 PB - Oemus Journale Leipzig ER - TY - CHAP A1 - Weinkauf, Tino A1 - Sahner, Jan A1 - Günther, Bert A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Thiele, Frank T1 - Feature-based Analysis of a Multi-Parameter Flow Simulation T2 - Proc. of 19th Simulation and Visualization Conference (SimVis 2008) Y1 - 2008 SP - 237 EP - 251 CY - Magdeburg, Germany ER - TY - CHAP A1 - Shi, Kuangyu A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Finite-Time Transport Structures of Flow Fields T2 - Proc. IEEE Pacific Visualization 2008 Y1 - 2008 U6 - https://doi.org/10.1109/PACIFICVIS.2008.4475460 SP - 63 EP - 70 CY - Kyoto, Japan ER - TY - JOUR A1 - Sahner, Jan A1 - Weber, Britta A1 - Lamecker, Hans A1 - Prohaska, Steffen T1 - Extraction of feature Lines on surface meshes based on discrete Morse theory JF - Computer Graphics Forum Y1 - 2008 U6 - https://doi.org/10.1111/j.1467-8659.2008.01202.x VL - 27 IS - 3 SP - 735 EP - 742 CY - Eindhoven, Netherlands ER - TY - CHAP A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Hege, Hans-Christian T1 - Near-Wall Flow Visualization in Flattened Surface Neighborhoods T2 - Proc. Simulation and Visualization 2008 Y1 - 2008 UR - http://www.simvis.org/Tagung2008/sv-proceedings.html SP - 93 EP - 105 CY - Magdeburg, Germany ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Schöneberg, Bastian A1 - Wellnhofer, Ernst A1 - Petz, Christoph T1 - CFD analysis in an anatomically realistic coronary artery model based on non-invasive 3D imaging JF - Int. J. Cardiovasc. Imaging Y1 - 2008 U6 - https://doi.org/10.1007/s10554-007-9275-z VL - 24(4) SP - 411 EP - 421 ER - TY - CHAP A1 - Goubergrits, Leonid A1 - Pöthke, Jens A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas A1 - Kertzscher, Ulrich T1 - 3D Bildgebung von zerebralen Aneurysmen T2 - Bildverarbeitung für die Medizin Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-78640-5_31 SP - 153 EP - 157 ER - TY - CHAP A1 - Papazov, Chavdar A1 - Dercksen, Vincent J. A1 - Lamecker, Hans A1 - Hege, Hans-Christian T1 - Visualizing morphogenesis and growth by temporal interpolation of surface-based 3D atlases T2 - Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging Y1 - 2008 U6 - https://doi.org/10.1109/ISBI.2008.4541123 SP - 824 EP - 827 ER - TY - CHAP A1 - von Funck, Wolfram A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian T1 - Smoke Surfaces: An Interactive Flow Visualization Technique Inspired by Real-World Flow Experiments T2 - IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2008) Y1 - 2008 U6 - https://doi.org/10.1109/TVCG.2008.163 VL - 14 IS - 6 SP - 1396 EP - 1403 ER - TY - JOUR A1 - Shi, Kuangyu A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Visualizing Transport Structures of Time-Dependent Flow Fields JF - IEEE Computer Graphics and Applications Y1 - 2008 U6 - https://doi.org/10.1109/MCG.2008.106 SP - 24 EP - 35 ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Meyer, Björn A1 - Rybak, Jürgen A1 - Hege, Hans-Christian T1 - Ontology-Based Visualization of Hierarchical Neuroanatomical Structures T2 - Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008 Y1 - 2008 SP - 177 EP - 184 ER - TY - JOUR A1 - Diederichs, Gerd A1 - Seim, Heiko A1 - Meyer, Henning A1 - Issever, Ahi A1 - M. Link, Thomas A1 - J. Schröder, Ralf A1 - Scheibel, Markus T1 - CT-based patient-specific modeling of glenoid rim defects: A feasibility study JF - AJR Am J Roentgenol Y1 - 2008 U6 - https://doi.org/10.2214/AJR.08.1091 VL - 191 IS - 5 SP - 1406 EP - 1411 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin T2 - acatech diskutiert, Produktionsfaktor Mathematik - Wie Mathematik Technik und Wirtschaft bewegt Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-89435-3 SP - 435 EP - 459 PB - Springer ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Heller, Markus O. A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model T2 - Eurographics Workshop on Visual Computing for Biomedicine (VCBM) Y1 - 2008 SP - 93 EP - 100 CY - Delft, Netherlands ER - TY - CHAP A1 - Dworzak, Jalda A1 - Lamecker, Hans A1 - von Berg, Jens A1 - Klinder, Tobias A1 - Lorenz, Cristian A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Towards model-based 3-D reconstruction of the human rib cage from radiographs T2 - Proc. 7. Jahrestagung der Deutschen Gesellschaft für Computer-Roboterassistierte Chirurgie (CURAC) Y1 - 2008 SP - 193 EP - 196 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Kuss, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Menzel, Randolf A1 - Rybak, Juergen T1 - Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models T2 - Proc. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain Y1 - 2008 U6 - https://doi.org/10.3389/conf.neuro.11.2008.01.064 ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heller, Markus O. A1 - Hege, Hans-Christian T1 - Multi-Object Segmentation with Coupled Deformable Models T2 - Proc. Medical Image Understanding and Analysis Y1 - 2008 SP - 34 EP - 38 ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Coupling Deformable Models for Multi-object Segmentation T2 - Proc. Int. Symp. on Computational Models for Biomedical Simulation (ISBMS) Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-70521-5_8 SP - 69 EP - 78 ER - TY - JOUR A1 - Laramee, Robert S. A1 - Erlebacher, Gordon A1 - Garth, Christoph A1 - Schafhitzel, Tobias A1 - Theisel, Holger A1 - Tricoche, Xavier A1 - Weinkauf, Tino A1 - Weiskopf, Daniel T1 - Applications of Texture-Based Flow Visualization JF - Engineering Applications of Computational Fluid Mechanics Y1 - 2008 UR - http://www.cs.swan.ac.uk/~csbob/research/application/ VL - 2 IS - 3 SP - 264 EP - 274 ER - TY - CHAP A1 - Paar, Philip A1 - Appleton, Katy A1 - Clasen, Malte A1 - Gensel, Maria A1 - Jude, Simon A1 - Lovett, Andrew T1 - Interactive Visual Simulation of Coastal Landscape Change T2 - ISDE Summit Y1 - 2008 ER - TY - GEN A1 - Oberlaender, Marcel A1 - Dercksen, Vincent J. A1 - Broser, Philip J. A1 - Bruno, Randy M. A1 - Sakmann, Bert T1 - NeuroMorph and NeuroCount: Automated tools for fast and objective acquisition of neuronal morphology for quantitative structural analysis T2 - Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics Y1 - 2008 U6 - https://doi.org/10.3389/conf.neuro.11.2008.01.065 ER - TY - CHAP A1 - Semar, Olivier A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Kalbe, Ute A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Slowik, Volker A1 - Witt, Karl Josef T1 - Conditions for Suffosive Erosion Phemomena in Soils – Concept and Approach T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 29 EP - 35 ER - TY - CHAP A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Homberg, Ulrike A1 - Slowik, Volker T1 - Modelling and Analysis of Particle and Pore Structures in Soils T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 53 EP - 60 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Binner, Richard A1 - Prohaska, Steffen A1 - Dercksen, Vincent J. A1 - Kuß, Anja A1 - Kalbe, Ute T1 - Determining Geometric Grain Structure from X-Ray Micro-Tomograms of Gradated Soil T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 37 EP - 52 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Wellnhofer, Ernst A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Coronary Artery WSS Profiling Using a Geometry Reconstruction Based on Biplane Angiography JF - Annals of Biomedical Engineering Y1 - 2009 U6 - https://doi.org/s10439-009-9656-7 VL - 37 IS - 4 SP - 682 EP - 691 PB - Springer ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Weber, Sarah A1 - Petz, Christoph A1 - Spuler, Andreas A1 - Pöthke, Jens A1 - Berthe, André A1 - Hege, Hans-Christian T1 - Wall-PIV as a Near Wall Flow Validation Tool for CFD JF - Journal of Visualization Y1 - 2009 VL - 12 IS - 3 SP - 241 EP - 250 ER - TY - GEN A1 - Oberlaender, Marcel A1 - Bruno, Randy M. A1 - de Kock, Christiaan P. J. A1 - Meyer, Hanno A1 - Dercksen, Vincent J. A1 - Sakmann, Bert T1 - 3D distribution and sub-cellular organization of thalamocortical VPM synapses for individual excitatory neuronal cell types in rat barrel cortex T2 - Conference Abstract No. 173.19/Y35, 39th Annual Meeting of the Society for Neuroscience (SfN) Y1 - 2009 ER - TY - GEN A1 - Oberlaender, Marcel A1 - Dercksen, Vincent J. A1 - Lang, Stefan A1 - Sakmann, Bert T1 - 3D mapping of synaptic connections within “in silico” microcircuits of full compartmental neurons in extended networks on the example of VPM axons projecting into S1 of rats. T2 - Conference Abstract, Neuroinformatics Y1 - 2009 U6 - https://doi.org/10.3389/conf.neuro.11.2009.08.092 ER - TY - JOUR A1 - Oberlaender, Marcel A1 - Dercksen, Vincent J. A1 - Egger, Robert A1 - Gensel, Maria A1 - Sakmann, Bert A1 - Hege, Hans-Christian T1 - Automated three-dimensional detection and counting of neuron somata JF - Journal of Neuroscience Methods Y1 - 2009 U6 - https://doi.org/10.1016/j.jneumeth.2009.03.008 VL - 180 IS - 1 SP - 147 EP - 160 ER - TY - GEN A1 - Reininghaus, Jan A1 - Hotz, Ingrid ED - Pascucci, Valerio ED - Tricoche, Xavier ED - Hagen, Hans ED - Tierny, Julien T1 - Combinatorial 2D Vector Field Topology Extraction and Simplification T2 - Topological Methods in Data Analysis and Visualization Y1 - 2011 SN - 978-3-642-15013-5 U6 - https://doi.org/10.1007/978-3-642-15014-2_9 SP - 103 EP - 114 PB - Springer ER - TY - CHAP A1 - Rybak, Jürgen A1 - Kuß, Anja A1 - Holler, Wolfgang A1 - Brandt, Robert A1 - Hege, Hans-Christian A1 - Menzel, Randolf T1 - The HoneyBee Standard Brain (HSB) - a versatile atlas tool for integrating data and data exchange in the neuroscience community T2 - BMC Neuroscience Y1 - 2009 U6 - https://doi.org/10.1186/1471-2202-10-S1-P1 VL - 10 (Suppl 1):P1 ER - TY - CHAP A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian ED - Eades, Peter ED - Ertl, Thomas ED - Shen, Han-Wei T1 - Dual Streamline Seeding T2 - Proceedings of the IEEE Pacific Visualization Symposium Y1 - 2009 SP - 9 EP - 16 CY - Beijing, China ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Ernst T1 - Computergestützte Planung zur chirurgischen Korrektur von frühkindlichen Schädelfehlbildungen (Craniosynostosen) JF - Face 02/09, Int. Mag. of Orofacial Esthetics, Oemus Journale Leipzig Y1 - 2009 SP - 48 EP - 53 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Heller, Markus O. A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Automatic Extraction of Anatomical Landmarks from Medical Image Data: An Evaluation of Different Methods T2 - Proc. of IEEE Int. Symposium on Biomedical Imaging (ISBI) Y1 - 2009 SP - 538 EP - 541 CY - Boston, MA, USA ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - An Articulated Statistical Shape Model for Accurate Hip Joint Segmentation T2 - EBMC 2009. Int. Conf. of the IEEE Eng. in Med. and Biol. Society (EMBC) Y1 - 2009 SP - 6345 EP - 6351 CY - Minneapolis, USA ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zinser, Max A1 - Zachow, Stefan ED - Yang, Guang-Zhong ED - J. Hawkes, David ED - Rueckert, Daniel ED - Noble, J. Alison ED - J. Taylor, Chris T1 - Automatic Extraction of Mandibular Nerve and Bone from Cone-Beam CT Data T2 - Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2009 SP - 76 EP - 83 CY - London, UK ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Weber, Britta A1 - Günther, David A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Automatic alignment of stacks of filament data T2 - Proc. IEEE International Symposium on Biomedical Imaging Y1 - 2009 SP - 971 EP - 974 PB - IEEE press CY - Boston, USA ER - TY - JOUR A1 - Petz, Christoph A1 - Kasten, Jens A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Hierarchical Vortex Regions in Swirling Flow JF - Computer Graphics Forum Y1 - 2009 VL - 28 IS - 3 SP - 863 EP - 870 ER - TY - JOUR A1 - Barth, Ingo A1 - Hege, Hans-Christian A1 - Ikeda, Hiroshi A1 - Kenfack, Anatole A1 - Koppitz, Michael A1 - Manz, Jörn A1 - Marquardt, Falko A1 - K. Paramonov, Guennaddi T1 - Concerted Quantum Effects of Electronic and Nuclear Fluxes in Molecules JF - Chem. Phys. Lett. Y1 - 2009 U6 - https://doi.org/10.1016/j.cplett.2009.09.011 VL - 481 IS - 1-3 SP - 118 EP - 123 PB - Elsevier ER - TY - JOUR A1 - Bischof, Horst A1 - Rau, Anne-Mareike A1 - Raicu, Daniela S. T1 - Comparison and Evaluation of Methods for Liver Segmentation from CT Datasets JF - IEEE Transactions on Medical Imaging Y1 - 2009 VL - 28(8) SP - 1251 EP - 1265 ER - TY - CHAP A1 - Lamecker, Hans A1 - Mansi, Tomaso A1 - Relan, Jatin A1 - Billet, Florence A1 - Sermesant, Maxime A1 - Ayache, Nicholas A1 - Delingette, Hervé T1 - Adaptive Tetrahedral Meshing for Personalized Cardiac Simulations T2 - Proc. MICCAI Workshop on Cardiovascular Interventional Imaging and Biophysical Modelling (CI2BM) Y1 - 2009 SP - 149 EP - 158 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - A System for Unsupervised Extraction of Orthopaedic Parameters from CT Data T2 - GI Workshop Softwareassistenten - Computerunterstützung für die medizinische Diagnose und Therapieplanung Y1 - 2009 SP - 1328 EP - 1337 CY - Lübeck, Germany ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Multi-object segmentation of head bones JF - MIDAS Journal Y1 - 2009 ER - TY - JOUR A1 - Zachow, Stefan A1 - Muigg, Philipp A1 - Hildebrandt, Thomas A1 - Doleisch, Helmut A1 - Hege, Hans-Christian T1 - Visual Exploration of Nasal Airflow JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2009 U6 - https://doi.org/10.1109/TVCG.2009.198 VL - 15 IS - 8 SP - 1407 EP - 1414 ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Gensel, Maria A1 - Kuß, Anja T1 - Visual Accentuation of Spatial Relationships between Filamentous and Voluminous Surface Structures T2 - Conference Abstract, Eurographics / IEEE Symposium on Visualization Y1 - 2009 ER - TY - CHAP A1 - Kuß, Anja A1 - Hege, Hans-Christian T1 - Knowledge Representation for Digital Atlases T2 - Conference Abstracts: Workshop of the Working Group 'Ontologies in Biomedicine and the Life Science' Y1 - 2009 PB - Max-Planck Institute for Evolutionary Anthropology CY - Leipzig ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Rybak, Jürgen T1 - Using Ontologies for the Visualization of Hierarchical Neuroanatomical Structures T2 - Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics Y1 - 2009 U6 - https://doi.org/10.3389/conf.neuro.11.2009.08.017 ER - TY - CHAP A1 - Kasten, Jens A1 - Petz, Christoph A1 - Hotz, Ingrid A1 - Noack, Bernd R. A1 - Hege, Hans-Christian ED - Magnor, Marcus ED - Rosenhahn, Bodo ED - Theisel, Holger T1 - Localized Finite-time Lyapunov Exponent for Unsteady Flow Analysis T2 - Vision Modeling and Visualization Y1 - 2009 SN - 978-3-9804874-8-1 VL - 1 SP - 265 EP - 274 PB - Universität Magdeburg, Inst. f. Simulation u. Graph. ER - TY - JOUR A1 - Weinkauf, Tino A1 - Günther, David T1 - Separatrix Persistence: Extraction of Salient Edges on Surfaces Using Topological Methods JF - Computer Graphics Forum (Proc. SGP’09) Y1 - 2009 U6 - https://doi.org/10.1111/j.1467-8659.2009.01528.x VL - 28 IS - 5 SP - 1519 EP - 1528 ER - TY - CHAP A1 - Auer, Cornelia A1 - Sreevalsan-Nair, Jaya A1 - Zobel, Valentin A1 - Hotz, Ingrid ED - Hagen, Hans T1 - 2D Tensor Field Segmentation T2 - Scientific Visualization: Interactions, Features, Metaphors Y1 - 2009 U6 - https://doi.org/10.4230/DFU.Vol2.SciViz.2011.17 VL - 2 SP - 17 EP - 35 PB - Schloss Dagstuhl–Leibniz-Zentrum für Informatik ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Multi-object Segmentation with Coupled Deformable Models JF - Annals of the British Machine Vision Association (BMVA) Y1 - 2009 VL - 5 SP - 1 EP - 10 ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Hotz, Ingrid A1 - Munzner, Tamara T1 - Euro Vis 2009 - Eurographics/IEEE-VGTC Symposium on Visualization T2 - Comput. Graphics. Forum Y1 - 2009 N1 - Preface of Proceedings VL - 28 ER - TY - CHAP A1 - Heimann, Tobias A1 - Chung, François A1 - Lamecker, Hans A1 - Delingette, Hervé T1 - Subject-Specific Ligament Models: Towards Real-Time Simulation of the Knee Joint T2 - Proc. Computational Biomechanics for Medicine IV Workshop Y1 - 2009 U6 - https://doi.org/10.1007/978-1-4419-5874-7 SP - 107 EP - 119 PB - Springer New York ER - TY - GEN A1 - Sreevalsan-Nair, Jaya A1 - Auer, Cornelia A1 - Hamann, Bernd A1 - Hotz, Ingrid ED - Pascucci, Valerio ED - Tricoche, Xavier ED - Hagen, Hans ED - Tierny, Julien T1 - Eigenvector-based Interpolation and Segmentation of 2D Tensor Fields T2 - Topological Methods in Data Analysis and Visualization Y1 - 2011 SN - 978-3-642-15013-5 U6 - https://doi.org/10.1007/978-3-642-15014-2_12 SP - 139 EP - 150 PB - Springer ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Laidlaw, David A1 - Machiraju, Raghu T1 - Guest Editor's Introduction: Special Section on Volume Graphics and Point-Based Graphics JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2010 U6 - https://doi.org/10.1109/TVCG.2010.72 VL - 16 IS - 4 SP - 531 EP - 532 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Thamsen, Bente A1 - Berthe, André A1 - Poethke, Jens A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Hoch, Heinrich A1 - Spuler, Andreas T1 - In Vitro Study of Near-Wall Flow in a Cerebral Aneurysm Model with and without Coils JF - American Journal of Neuroradiology Y1 - 2010 U6 - https://doi.org/10.3174/ajnr.A2121 VL - 31:8 SP - 1521 EP - 1528 ER - TY - JOUR A1 - Otto, Mathias A1 - Germer, Tobias A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - Uncertain 2D Vector Field Topology JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01604.x VL - 29 SP - 347 EP - 356 ER - TY - CHAP A1 - Kasten, Jens A1 - Weinkauf, Tino A1 - Petz, Christoph A1 - Hotz, Ingrid A1 - Noack, Bernd R. A1 - Hege, Hans-Christian T1 - Extraction of Coherent Structures from Natural and Actuated Flows T2 - Active Flow Control II Y1 - 2010 SN - 978-3-642-11734-3 U6 - https://doi.org/10.1007/978-3-642-11735-0_24 VL - 108 SP - 373 EP - 387 PB - Springer, Berlin ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - JOUR A1 - Rybak, Jürgen A1 - Kuß, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Lienhard, Matthias A1 - Singer, Jochen A1 - Neubert, Kerstin A1 - Menzel, Randolf T1 - The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System JF - Front. Syst. Neurosci. Y1 - 2010 U6 - https://doi.org/10.3389/fnsys.2010.00030 VL - 4 IS - 30 ER - TY - CHAP A1 - Reininghaus, Jan A1 - Günther, David A1 - Hotz, Ingrid A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory T2 - Mathematical Software - ICMS 2010 Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15582-6_35 VL - 6327 SP - 198 EP - 208 PB - Springer ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Accelerated Visualization of Dynamic Molecular Surfaces JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01693.x VL - 29 SP - 943 EP - 952 ER - TY - JOUR A1 - Lacarelle, Arnaud A1 - P. Moeck, Jonas A1 - Paschereit, Christian A1 - Gelbert, Gregor A1 - King, Rudibert A1 - M. Luchtenburg, Dirk A1 - Noack, Bernd R. A1 - Kasten, Jens A1 - Hege, Hans-Christian T1 - Modeling a Fuel/Air Mixing to Control the Pressure Pulsations and NOx Emissions in a Lean Premixed Combustor JF - Active Flow Control II Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-11735-0_20 VL - 108 SP - 307 EP - 321 PB - Springer, Berlin ER - TY - CHAP A1 - Günther, David A1 - McGuire, Patrick C. A1 - Walter, Sebastian A1 - Weinkauf, Tino A1 - Hege, Hans-Christian T1 - Extraction of Valley Networks in Mars Elevation Maps T2 - Proc. European Planetary Science Congress Y1 - 2010 VL - 5 SP - EPSC2010 EP - 216 ER - TY - JOUR A1 - Dworzak, Jalda A1 - Lamecker, Hans A1 - von Berg, Jens A1 - Klinder, Tobias A1 - Lorenz, Cristian A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - 3D Reconstruction of the Human Rib Cage from 2D Projection Images using a Statistical Shape Model JF - Int. J. Comput. Assist. Radiol. Surg. Y1 - 2010 U6 - https://doi.org/10.1007/s11548-009-0390-2 SN - 1861-6410 VL - 5 IS - 2 SP - 111 EP - 124 PB - Springer ER - TY - JOUR A1 - Kenfack, Anatole A1 - Marquardt, Falko A1 - K. Paramonov, Gennadij A1 - Barth, Ingo A1 - Lasser, Caroline A1 - Paulus, Beate T1 - Initial-state dependence of coupled electronic and nuclear fluxes in molecules JF - Phys. Rev. A Y1 - 2010 U6 - https://doi.org/10.1103/PhysRevA.81.052502 VL - 81 IS - 5 SP - 052502 PB - American Physical Society ER - TY - CHAP A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Identification of Descriptive Parameters of the Soil Pore Structure using Experiments and CT Data T2 - Proceedings of the 5th International Conference on Scour and Erosion (ICSE-5) Y1 - 2010 SP - 397 EP - 407 PB - American Society of Civil Engineers (ASCE) ER - TY - CHAP A1 - Lamecker, Hans A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Automatische 3D Rekonstruktion des Unterkiefers und der Mandibulärnerven auf Basis dentaler Bildgebung T2 - Proc. BMT, Biomed Tech Y1 - 2010 VL - 55 (Suppl. 1) SP - 35 EP - 36 PB - Walter de Gruyter-Verlag ER - TY - CHAP A1 - Zachow, Stefan A1 - Kubiack, Kim A1 - Malinowski, Jana A1 - Lamecker, Hans A1 - Essig, Harald A1 - Gellrich, Nils-Claudius T1 - Modellgestützte chirurgische Rekonstruktion komplexer Mittelgesichtsfrakturen T2 - Proc. BMT, Biomed Tech 2010 Y1 - 2010 VL - 55 (Suppl 1) SP - 107 EP - 108 PB - Walter de Gruyter-Verlag ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan A1 - Hege, Hans-Christian ED - Navab, Tianzi ED - P. W. Pluim, Josien ED - Viergever, Max T1 - Improving Deformable Surface Meshes through Omni-directional Displacements and MRFs T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15705-9_28 VL - 6361 SP - 227 EP - 234 PB - Springer ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - CHAP A1 - Zachow, Stefan A1 - Hahn, Horst A1 - Lange, Thomas ED - Schlag, Peter ED - Eulenstein, Sebastian ED - Lange, Thomas T1 - Computerassistierte Chirugieplanung T2 - Computerassistierte Chirurgie Y1 - 2010 SP - 119 EP - 149 PB - Elsevier ER - TY - JOUR A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Craniofacial Surgery Planning Based on Virtual Patient Models JF - it - Information Technology Y1 - 2010 U6 - https://doi.org/10.1524/itit.2010.0600 VL - 52 IS - 5 SP - 258 EP - 263 PB - Oldenbourg Verlagsgruppe ER - TY - JOUR A1 - Kasten, Jens A1 - Petz, Christoph A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Tadmor, Gilead T1 - Lagrangian Feature Extraction of the Cylinder Wake JF - Physics of Fluids Y1 - 2010 U6 - https://doi.org/10.1063/1.3483220 VL - 22 IS - 9 SP - 091108 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Bindernagel, Matthias A1 - Malinowski, Jana A1 - Zachow, Stefan ED - v. Ginneken, B. T1 - Model-based Auto-Segmentation of Knee Bones and Cartilage in MRI Data T2 - Proc. MICCAI Workshop Medical Image Analysis for the Clinic Y1 - 2010 SP - 215 EP - 223 ER - TY - CHAP A1 - Clasen, Malte A1 - Prohaska, Steffen T1 - Image-Error-Based Level of Detail for Landscape Visualization T2 - Proc. VMV 2010 Y1 - 2010 SP - 267 EP - 274 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - More Mathematics into Medicine! T2 - Production Factor Mathematics Y1 - 2010 UR - http://www.springer.com/mathematics/book/978-3-642-11247-8 SP - 357 EP - 378 PB - Springer ER - TY - JOUR A1 - Lamecker, Hans A1 - Pennec, Xavier T1 - Atlas to Image-with-Tumor Registration based on Demons and Deformation Inpainting JF - Proc. MICCAI Workshop on Computational Imaging Biomarkers for Tumors - From Qualitative to Quantitative (CIBT’2010) Y1 - 2010 CY - Beijing, China ER - TY - GEN A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Oberleithner, Kilian A1 - Hotz, Ingrid A1 - Noack, Bernd A1 - Hege, Hans-Christian T1 - Flow over a Cavity – Evolution of the Vortex Skeleton Y1 - 2010 PB - Visualization at 28th Annual Gallery of Fluid Motion exhibit, held at the 63th Annual Meeting of the American Physical Society, Division of Fluid Dynamics (Long Beach, CA, USA, November 21-23, 2010). ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Wygnanski, Israel T1 - Self Excited Oscillations in Swirling Jets: Stability Analysis and Empirical Mode Construction JF - Bulletin of the American Physical Society Y1 - 2010 UR - http://meetings.aps.org/link/BAPS.2010.DFD.GE.8 N1 - 63rd Annual Meeting of the APS Division of Fluid Dynamics, November 21-23, 2010, Long Beach, CA VL - 55 IS - 16 SP - GE.00008 ER - TY - GEN A1 - Bredtmann, Timm A1 - Marquardt, Falko A1 - Andrae, Dirk A1 - Barth, Ingo A1 - Hege, Hans-Christian A1 - Manz, Jörn A1 - Paulus, Beate T1 - Electronic and Nuclear Fluxes During Pericyclic Reactions: Quantum Simulations for the Cope Rearrangement of Semibullvalene Y1 - 2010 N1 - Abstract and Poster PB - CSTC 2010 - 17th Canadian Symposium on Theoretical Chemistry, July 25-30, 2010, Edmonton, Alberta, Canada ER - TY - GEN A1 - Bredtmann, Timm A1 - Marquardt, Falko A1 - Andrae, Dirk A1 - Barth, Ingo A1 - Hege, Hans-Christian A1 - Hoki, Kunihito A1 - Kenfack, Anatole A1 - Kono, Hirohiko A1 - Manz, Jörn A1 - Paulus, Beate T1 - Electronic and Nuclear Fluxes during Pericyclic Reactions: Quantum Simulations for the Cope Rearrangement of Semibullvalene Y1 - 2010 N1 - Abstract and Poster PB - International Symposium on Theoretical and Computational Chemistry, 28 Feb – 2 March, 2010, Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Manz, Jörn A1 - Marquardt, Falko A1 - Paulus, Beate A1 - Schild, Axel T1 - Electron Flux during Pericyclic Reactions in the Tunneling Limit: Quantum Simulation for Cyclooctatetraene JF - Chem. Phys Y1 - 2010 U6 - https://doi.org/10.1016/j.chemphys.2010.07.033 N1 - Festschrift in Chem. Phys. in honour of Professor Horst Koeppel VL - 376 IS - 1-3 SP - 46 EP - 55 ER - TY - JOUR A1 - Reininghaus, Jan A1 - Löwen, Christian A1 - Hotz, Ingrid T1 - Fast Combinatorial Vector Field Topology JF - IEEE Trans. Computer Graphics and Visualization Y1 - 2011 VL - 17 IS - 10 SP - 1433 EP - 1443 ER - TY - GEN A1 - Kasten, Jens A1 - Hotz, Ingrid A1 - Noack, Bernd A1 - Hege, Hans-Christian ED - Pascucci, Valerio ED - Tricoche, Xavier ED - Hagen, Hans ED - Tierny, Julien T1 - On the Extraction of Long-living Features in Unsteady Fluid Flows T2 - Topological Methods in Data Analysis and Visualization Y1 - 2011 SN - 978-3-642-15013-5 U6 - https://doi.org/10.1007/978-3-642-15014-2_10 SP - 115 EP - 126 PB - Springer CY - Berlin ER - TY - CHAP A1 - Hotz, Ingrid A1 - Sreevalsan-Nair, Jaya A1 - Hamann, Bernd ED - Hagen, Hans T1 - Tensor Field Reconstruction Based on Eigenvector and Eigenvalue Interpolation T2 - Scientific Visualization: Advanced Concepts Y1 - 2010 UR - http://drops.dagstuhl.de/opus/volltexte/2010/2700 SN - 978-3-939897-19-4 U6 - https://doi.org/10.4230/DFU.SciViz.2010.110 VL - 1 SP - 110 EP - 123 PB - Schloss Dagstuhl Leibniz-Zentrum fuer Informatik ER - TY - CHAP A1 - Ehrig, Karsten A1 - Goebbels, Jürgen A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Prohaska, Steffen A1 - Zobel, Valentin T1 - Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography T2 - International Symposium on Digital Industrial Radiology and Computed Tomography Y1 - 2011 ER - TY - JOUR A1 - Torsney-Weir, Thomas A1 - Saad, Ahmed A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weber, Britta A1 - Verbavatz, Jean-Marc T1 - Tuner: Principled Parameter Finding for Image Segmentation Algorithms Using Visual Response Surface Exploration JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2011 VL - 17 IS - 12 SP - 1892 EP - 1901 ER - TY - CHAP A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Prohaska, Steffen T1 - Fast Tracing of Microtubule Centerlines in Electron Tomograms T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen ED - Mücklich, Frank ED - Slussallek, Philipp ED - Schladitz, Katja T1 - Describing and Analyzing the Dual Structures of Porous Media T2 - Proc. 3D-Microstructure Meeting Y1 - 2011 SP - 24 EP - 25 ER - TY - GEN A1 - Kratz, Andrea A1 - Meyer, Björn A1 - Hotz, Ingrid ED - Hagen, Hans T1 - A Visual Approach to Analysis of Stress Tensor Fields T2 - Scientific Visualization: Interactions, Features, Metaphors Y1 - 2011 UR - http://drops.dagstuhl.de/opus/volltexte/2011/3296 U6 - https://doi.org/10.4230/DFU.Vol2.SciViz.2011.188 VL - 2 SP - 188 EP - 211 PB - Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - GEN A1 - Kratz, Andrea A1 - Hadwiger, Markus A1 - Hotz, Ingrid T1 - Improved Visual Exploration and Hybrid Rendering of Stress Tensor Fields via Shape-Space Clustering. Y1 - 2011 PB - Poster presentation at the IEEE VisWeek 2011, Providence ER - TY - CHAP A1 - Kratz, Andrea A1 - Kettlitz, Nino A1 - Hotz, Ingrid T1 - Particle-Based Anisotropic Sampling for Two-Dimensional Tensor Field Visualization T2 - Vision Modeling and Visualization (VMV’11) Y1 - 2011 SP - 145 EP - 152 PB - Eurographics Association target ER - TY - GEN A1 - SK, Saevarsson A1 - GB, Sharma A1 - S, Montgomery A1 - KCT, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - C, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster) Y1 - 2011 SP - 80 ER - TY - CHAP A1 - Kahnt, Max A1 - Galloway, Francis A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Taylor, Mark A1 - Zachow, Stefan T1 - Robust and Intuitive Meshing of Bone-Implant Compounds T2 - CURAC Y1 - 2011 SP - 71 EP - 74 CY - Magdeburg ER - TY - CHAP A1 - Bindernagel, Matthias A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - An Articulated Statistical Shape Model of the Human Knee T2 - Bildverarbeitung für die Medizin 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-19335-4_14 SP - 59 EP - 63 PB - Springer ER - TY - CHAP A1 - von Berg, Jens A1 - Dworzak, Jalda A1 - Klinder, Tobias A1 - Manke, Dirk A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Lorenz, Cristian T1 - Temporal Subtraction of Chest Radiographs Compensating Pose Differences T2 - SPIE Medical Imaging Y1 - 2011 ER - TY - JOUR A1 - Zobel, Valentin A1 - Reininghaus, Jan A1 - Hotz, Ingrid T1 - Generalized Heat Kernel Signature JF - Journal of WSCG, International Conference on Computer Graphics, Visualization and Computer Vision Y1 - 2011 SP - 93 EP - 100target ER - TY - JOUR A1 - Andrae, Dirk A1 - Barth, Ingo A1 - Bredtmann, Timm A1 - Hege, Hans-Christian A1 - Manz, Jörn A1 - Marquardt, Falko A1 - Paulus, Beate T1 - Electronic Quantum Fluxes During Pericyclic Reactions Exemplified for the Cope Rearrangement of Semibullvalene JF - J. Phys. Chem. B Y1 - 2011 U6 - https://doi.org/10.1021/jp110365g VL - 115 IS - 18 SP - 5476 EP - 5483 ER - TY - GEN A1 - Kasten, Jens A1 - Hotz, Ingrid A1 - Hege, Hans-Christian ED - Peikert, Ronald ED - Hauser, Helwig ED - Carr, Hamish ED - Fuchs, Raphael T1 - On the Elusive Concept of Lagrangian Coherent Structures T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23175-9_14 SP - 207 EP - 220 PB - Springer ER - TY - GEN A1 - Günther, David A1 - Reininghaus, Jan A1 - Prohaska, Steffen A1 - Weinkauf, Tino A1 - Hege, Hans-Christian ED - Peikert, Ronny ED - Hauser, Helwig ED - Carr, Hamish T1 - Efficient Computation of a Hierarchy of Discrete 3D Gradient Vector Fields T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23175-9_2 SP - 15 EP - 29 PB - Springer ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - J. Wygnanski, Israel T1 - Three-dimensional Coherent Structures of the Swirling Jet Undergoing Vortex breakdown: Stability Analysis and Empirical Mode Construction JF - J. Fluid Mech. Y1 - 2011 U6 - https://doi.org/10.1017/jfm.2011.141 VL - 679 SP - 383 EP - 414 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Positional Uncertainty of Isocontours: Condition Analysis and Probabilistic Measures JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2010.247 VL - 17 IS - 10 SP - 1393 EP - 1406 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Weber, Britta A1 - Hege, Hans-Christian T1 - Probabilistic Marching Cubes JF - Computer Graphics Forum Y1 - 2011 U6 - https://doi.org/10.1111/j.1467-8659.2011.01942.x VL - 30 IS - 3 SP - 931 EP - 940 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Kasten, Jens A1 - Hotz, Ingrid T1 - Distillation and Visualization of Spatiotemporal Structures in Turbulent Flow Fields JF - J. Phys. Y1 - 2011 U6 - https://doi.org/10.1088/1742-6596/318/6/062009 VL - 318 SP - 062009 ET - 6 ER - TY - CHAP A1 - Goldau, Mathias A1 - Wiebel, Alexander A1 - Gorbach, Nico A1 - Melzer, Corina A1 - Hlawitschka, Mario A1 - Scheuermann, Gerik A1 - Tittgemeyer, Marc T1 - Fiber Stippling: An Illustrative Rendering for Probabilistic Diffusion Tractography Combinatorial Vector Field Topology in 3 Dimensions T2 - 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 U6 - https://doi.org/10.1109/BioVis.2011.6094044 target SP - 23 EP - 30 ER - TY - GEN A1 - Wiebel, Alexander A1 - Hege, Hans-Christian A1 - Ziech, Manon A1 - Caan, Matthan A1 - Stoker, Jaap A1 - Vos, Frans T1 - DCE-MRI-oriented Volume Rendering for Monitoring of Crohn’s Disease. T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - GEN A1 - Wiebel, Alexander A1 - Koch, Stefan A1 - Scheuermann, Gerik ED - Peikert, Ronald ED - Hauser, Helwig ED - Carr, Hamish ED - Fuchs, Raphael T1 - Glyphs for Non-Linear Vector Field Singularities T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2011 SP - 177 EP - 190 PB - Springer CY - Berlin ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Koppitz, Michael A1 - Marquardt, Falko A1 - McDonald, Chris A1 - Mielack, Christopher T1 - Visual Analysis of Quantum Physics Data JF - Quantum Dynamic Imaging Y1 - 2011 U6 - https://doi.org/10.1007/978-1-4419-9491-2_6 SP - 71 EP - 87 PB - Springer ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sakmann, Bert A1 - Hege, Hans-Christian T1 - Light Microscopy-Based Reconstruction and Interactive Structural Analysis of Cortical Neural Networks T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - JOUR A1 - Lang, Stefan A1 - Dercksen, Vincent J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - Simulation of signal flow in 3D reconstructions of an anatomically realistic neural network in rat vibrissal cortex JF - Neural Networks Y1 - 2011 U6 - https://doi.org/doi:10.1016/j.neunet.2011.06.013 VL - 24 IS - 9 SP - 998 EP - 1011 ER - TY - JOUR A1 - Petz, Christoph A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Oliver A1 - Wygnanski, Israel A1 - Noack, Bernd A1 - Hege, Hans-Christian T1 - Global Modes in a Swirling Jet Undergoing Vortex Breakdown JF - Physics of Fluids Y1 - 2011 U6 - https://doi.org/10.1063/1.3640007 VL - 23 SP - 091102 PB - Awarded Visualization; First Prize at 28th Annual Gallery of Fluid Motion exhibit, held at the 63th Annual Meeting of the American Physical Society, Division of Fluid Dynamics (Long Beach, CA, USA, November 21-23, 2010). ER - TY - JOUR A1 - Rigort, Alexander A1 - Günther, David A1 - Hegerl, Reiner A1 - Baum, Daniel A1 - Weber, Britta A1 - Prohaska, Steffen A1 - Medalia, Ohad A1 - Baumeister, Wolfgang A1 - Hege, Hans-Christian T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks JF - Journal of Structural Biology Y1 - 2012 U6 - https://doi.org/10.1016/j.jsb.2011.08.012 VL - 177 SP - 135 EP - 144 ER - TY - JOUR A1 - Kleinfeld, David A1 - Bharioke, Arjun A1 - Blinder, Pablo A1 - Bock, David A1 - Briggman, Kevin A1 - Chklovskii, Dmitri A1 - Denk, Winfried A1 - Helmstaedter, Moritz A1 - Kaufhold, John A1 - Lee, Wei-Chung A1 - Meyer, Hanno A1 - Micheva, Kristina A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Reid, R. A1 - Smith, Stephen A1 - Takemura, Shinya A1 - Tsai, Philbert A1 - Sakmann, Bert T1 - Large-scale automated histology in the pursuit of connectomes JF - Journal of Neuroscience Y1 - 2011 UR - http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf U6 - https://doi.org/10.1523/JNEUROSCI.4077-11.2011 VL - 31 IS - 45 SP - 16125 EP - 16138 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Voronoi-Based Extraction and Visualization of Molecular Paths JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.259 VL - 17 IS - 12 SP - 2025 EP - 2034 ER - TY - CHAP A1 - Auer, Cornelia A1 - Hotz, Ingrid T1 - Complete Tensor Field Topology on 2D Triangulated Manifolds embedded in 3D T2 - Computer Graphics Forum (EuroVis’11) Y1 - 2011 VL - 30 IS - 3 target SP - 831 EP - 840 ER - TY - CHAP A1 - Boyer, Edmond A1 - Bronstein, Alexander A1 - Bronstein, Michael A1 - Bustos, Benjamin A1 - Darom, Tal A1 - Horaud, Radu A1 - Hotz, Ingrid A1 - Keller, Yosi A1 - Keustermans, Johannes A1 - Kovnatsky, Artiom A1 - Litman, Roee A1 - Reininghaus, Jan A1 - Sipiran, Ivan A1 - Smeets, Dirk A1 - Suetens, Paul A1 - Vandermeulen, Dirk A1 - Zaharescu, Andrei A1 - Zobel, Valentin T1 - SHREC 2011: robust feature detection and description benchmark T2 - Proc. Eurographics 2011 Workshop on 3D Object Retrieval (3DOR’11) Y1 - 2011 U6 - https://doi.org/10.2312/3DOR/3DOR11/079-088 target SP - 71 EP - 78 PB - Eurographics Association ER - TY - JOUR A1 - Günther, David A1 - Reininghaus, Jan A1 - Wagner, Hubert A1 - Hotz, Ingrid T1 - Memory-Efficient Computation of Persistent Homology for 3D Images using Discrete Morse Theory JF - Proc. Sibgrapi – Conference on Graphics, Patterns and Images Y1 - 2011 PB - Kluwer Academic Publishers ER - TY - JOUR A1 - Reininghaus, Jan A1 - Kotava, N. A1 - Günther, David A1 - Kasten, Jens A1 - Hagen, Hans A1 - Hotz, Ingrid T1 - A Scale Space Based Persistence Measure for Critical Points in 2D Scalar Fields JF - Visualization and Computer Graphics, IEEE Transactions on Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.159 VL - 17 IS - 12 SP - 2045 EP - 2052 ER - TY - JOUR A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian T1 - Two-Dimensional Time-Dependent Vortex Regions Based on the Acceleration Magnitude JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 VL - 17 IS - 12 SP - 2080 EP - 2087target ER - TY - GEN A1 - Grewe, Carl Martin A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Digital morphometry: The Potential of Statistical Shape Models T2 - Anthropologischer Anzeiger. Journal of Biological and Clinical Anthropology Y1 - 2011 SP - 506 EP - 506 ER - TY - CHAP A1 - Hoffmann, René A1 - Zachow, Stefan T1 - Non-invasive approach to shed new light on the buoyancy business of chambered cephalopods (Mollusca) T2 - Proc. of the Intl. Assoc. for Mathematical Geosciences, Salzburg Y1 - 2011 U6 - https://doi.org/10.5242/iamg.2011.0163 SP - 1 EP - 11 ER - TY - JOUR A1 - Weber, Britta A1 - Greenan, Garrett A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Müller-Reichert, Thomas A1 - Hyman, Anthony A1 - Verbavatz, Jean-Marc T1 - Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos JF - Journal of Structural Biology Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1047847711003509 U6 - https://doi.org/10.1016/j.jsb.2011.12.004 VL - 178 IS - 2 SP - 129 EP - 138 ER - TY - JOUR A1 - Oberlaender, Marcel A1 - de Kock, Christiaan P. J. A1 - Bruno, Randy M. A1 - Ramirez, Alejandro A1 - Meyer, Hanno A1 - Dercksen, Vincent J. A1 - Helmstaedter, Moritz A1 - Sakmann, Bert T1 - Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex JF - Cerebral Cortex Y1 - 2012 U6 - https://doi.org/doi:10.1093/cercor/bhr317 VL - 22 IS - 10 SP - 2375 EP - 2391 ER - TY - CHAP A1 - Auer, Cornelia A1 - Stripf, Claudia A1 - Kratz, Andrea A1 - Hotz, Ingrid T1 - Glyph- and Texture-based Visualization of Segmented Tensor Fields T2 - GRAPP/IVAPP Proc. Int. Conf. on Computer Graphics Theory and Applications and Int. Conf. on Information Visualization Theory and Applications Y1 - 2012 SN - 978-989-8565-02-0 U6 - https://doi.org/10.5220/0003857106700677 SP - 670 EP - 677 PB - SciTePress ER - TY - JOUR A1 - Ho, Karen A1 - Saevarsson, Stefan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Sharma, Gulshan A1 - Rex, Erica A1 - Amiri, Shahram A1 - Wu, Barnabas A1 - Leumann, Andre A1 - Anglin, Carolyn T1 - Computed tomography analysis of knee pose and geometry before and after total knee arthroplasty JF - Journal of biomechanics Y1 - 2012 UR - http://www.ncbi.nlm.nih.gov/pubmed/22796002 U6 - https://doi.org/10.1016/j.jbiomech.2012.06.004 VL - 45 IS - 13 SP - 2215 EP - 21 ER - TY - CHAP A1 - Stefan, Saevarsson A1 - Gulshan, Sharma A1 - Sigrun, Montgomery A1 - Karen, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Hutchison, Carol A1 - Jason, Werle A1 - Carolyn, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - 67th Canadian Orthopaedic Association (COA) Annual Meeting Y1 - 2012 ER - TY - GEN A1 - Sharma, Gulshan A1 - Saevarsson, Stefan A1 - Amiri, Shahram A1 - Montgomery, Sigrun A1 - Ramm, Heiko A1 - Lichti, Derek A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Sequential-Biplane Radiography for Measuring Pre and Post Total Knee Arthroplasty Kinematics T2 - 58th Annual Meeting of the Orthopaedic Research Society (ORS) Y1 - 2012 CY - San Francisco, CA ER - TY - GEN A1 - Sharma, Gulshan A1 - Ho, Karen A1 - Saevarsson, Stefan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Knee Pose and Geometry Pre- and Post-Total Knee Arthroplasty Using Computed Tomography T2 - 58th Annual Meeting of the Orthopaedic Research Society (ORS) Y1 - 2012 CY - San Francisco, CA ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Automatic Extraction and Analysis of Realistic Pore Structures from µCT Data for Pore Space Characterization of Graded Soil T2 - Proceedings of the 6th International Conference on Scour and Erosion (ICSE-6) Y1 - 2012 SP - 345 EP - 352 ER - TY - GEN A1 - Pfister, Hanspeter A1 - Kaynig, Verena A1 - Botha, Charl A1 - Bruckner, Stefan A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Roerdink, Jos T1 - Visualization in Connectomics Y1 - 2012 U6 - https://doi.org/10.1007/978-1-4471-6497-5_21 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Egger, Robert A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Synaptic Connectivity in Anatomically Realistic Neural Networks: Modeling and Visual Analysis T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) Y1 - 2012 U6 - https://doi.org/10.2312/VCBM/VCBM12/017-024 SP - 17 EP - 24 CY - Norrköping, Sweden ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sakmann, Bert A1 - Hege, Hans-Christian ED - Linsen, Lars ED - Hagen, Hans ED - Hamann, Bernd ED - Hege, Hans-Christian T1 - Interactive Visualization – a Key Prerequisite for Reconstruction of Anatomically Realistic Neural Networks T2 - Visualization in Medicine and Life Sciences II Y1 - 2012 UR - http://www.zib.de/visual/publications/sources/src-2012/DercksenVMLS2012web.pdf SP - 27 EP - 44 PB - Springer, Berlin ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Schaller, Jens A1 - Kertzscher, Ulrich A1 - van den Bruck, Nils A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas T1 - Statistical wall shear stress maps of ruptured and unruptured middle cerebral artery aneurysms JF - J. R. Soc. Interface Y1 - 2012 U6 - https://doi.org/10.1098/rsif.2011.0490 VL - 9 IS - 69 SP - 677 EP - 688 ER - TY - JOUR A1 - Petz, Christoph A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Probabilistic Local Features in Uncertain Vector Fields with Spatial Correlation JF - Computer Graphics Forum Y1 - 2012 VL - 31 IS - 3 SP - 1045 EP - 1054 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03128.x target VL - 31 IS - 3 SP - 1325 EP - 1334 ER - TY - CHAP A1 - Vos, Franciscus A1 - Tielbeek, Jeroen A1 - Naziroglu, Robiel A1 - Li, Zhang A1 - Schueffler, Peter A1 - Mahapatra, Dwarikanath A1 - Wiebel, Alexander A1 - Lavini, Christina A1 - Buhmann, Joachim A1 - Hege, Hans-Christian A1 - Stoker, Jaap A1 - van Vliet, Lucas T1 - Computational modeling for assessment of IBD: to be or not to be? T2 - 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) Y1 - 2012 U6 - https://doi.org/10.1109/EMBC.2012.6346837 SP - 3974 EP - 3977 ER - TY - JOUR A1 - Wiebel, Alexander A1 - Vos, Frans A1 - Foerster, David A1 - Hege, Hans-Christian T1 - WYSIWYP: What You See Is What You Pick JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2012.292 VL - 18 IS - 12 SP - 2236 EP - 2244 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Perceptually Linear Parameter Variations JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03054.x target VL - 31 IS - 2 SP - 535 EP - 544 ER - TY - CHAP A1 - Ramm, Heiko A1 - Zachow, Stefan ED - Niederlag, Wolfgang ED - Lemke, Heinz ED - Peitgen, Heinz-Otto ED - Lehrach, Hans T1 - Computergestützte Planung für die individuelle Implantatversorgung T2 - Health Academy Y1 - 2012 VL - 16 SP - 145 EP - 158 ER - TY - CHAP A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Levine, Joshua A. ED - Paulsen, Rasmus R. ED - Zhang, Yongjie T1 - Feature-Preserving, Multi-Material Mesh Generation using Hierarchical Oracles T2 - Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed) Y1 - 2012 VL - 7599 SP - 101 EP - 111 ER - TY - JOUR A1 - Ramm, Heiko A1 - Kahnt, Max A1 - Zachow, Stefan T1 - Patientenspezifische Simulationsmodelle für die funktionelle Analyse von künstlichem Gelenkersatz JF - Computer Aided Medical Engineering (CaMe) Y1 - 2012 VL - 3 IS - 2 SP - 30 EP - 36 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images T2 - Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award) Y1 - 2012 ER - TY - JOUR A1 - Nguyen, The Duy A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Automatic bone and tooth detection for CT-based dental implant planning JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2012 VL - 7, Supplement 1 IS - 1 SP - 293 EP - 294 PB - Springer ER - TY - CHAP A1 - Nguyen, The Duy A1 - Lamecker, Hans A1 - Kainmüller, Dagmar A1 - Zachow, Stefan ED - Ayache, Nicholas ED - Delingette, Hervé ED - Golland, Polina ED - Mori, Kensaku T1 - Automatic Detection and Classification of Teeth in CT Data T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2012 VL - 7510 SP - 609 EP - 616 ER - TY - GEN A1 - Bindernagel, Matthias A1 - Kainmüller, Dagmar A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Analysis of inter-individual anatomical shape variations of joint structures T2 - Proc. Int. Society of Computer Assisted Orthopaedic Surgery (CAOS) Y1 - 2012 IS - 210 ER - TY - CHAP A1 - Pöthkow, Kai A1 - Hege, Hans-Christian ED - Laidlaw, David ED - Vilanova, Anna T1 - Uncertainty Propagation in DT-MRI Anisotropy Isosurface Extraction T2 - New Developments in the Visualization and Processing of Tensor Fields Y1 - 2012 SP - 209 EP - 225 PB - Springer CY - Berlin ER - TY - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization T2 - Proceedings of IEEE Symposium on Biological Data Visualization (biovis’12) Y1 - 2012 U6 - https://doi.org/10.1109/BioVis.2012.6378599 SP - 99 EP - 106 ER - TY - GEN A1 - Deuflhard, Peter A1 - Zachow, Stefan T1 - Mathematische Therapie- und Operationsplanung Y1 - 2012 SP - 89 EP - 90 PB - Berliner Wirtschaftsgespräche e.V. CY - Berlin ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Amiri, Shahram A1 - Montgomery, Sigrun A1 - Ramm, Heiko A1 - Lichti, Derek A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Radiological method for measuring patellofemoral tracking and tibiofemoral kinematics before and after total knee replacement JF - Bone and Joint Research Y1 - 2012 UR - http://www.bjr.boneandjoint.org.uk/content/1/10/263.short U6 - https://doi.org/10.1302/2046-3758.110.2000117 VL - 1 IS - 10 SP - 263 EP - 271 ER - TY - CHAP A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions T2 - EVA 2012 Berlin Y1 - 2012 SP - 150 EP - 155 PB - Gesellschaft zur Förderung angewandter Informatik e.V. CY - Volmerstraße 3, 12489 Berlin ER - TY - CHAP A1 - Klindt, Marco A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian ED - Arnold, David ED - Kaminski, Jaime ED - Niccolucci, Franco ED - Stork, Andre T1 - Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition T2 - VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers Y1 - 2012 UR - http://diglib.eg.org/EG/DL/PE/VAST/VAST12S/025-028.pdf U6 - https://doi.org/10.2312/PE/VAST/VAST12S/025-028 SP - 25 EP - 28 PB - Eurographics Association CY - Brighton, UK ER - TY - JOUR A1 - Zinser, Max A1 - Zachow, Stefan A1 - Sailer, Hermann T1 - Bimaxillary "rotation advancement" procedures in patients with obstructive sleep apnea: A 3-dimensional airway analysis of morphological changes JF - International Journal of Oral & Maxillofacial Surgery Y1 - 2013 U6 - https://doi.org/10.1016/j.ijom.2012.08.002 VL - 42 IS - 5 SP - 569 EP - 578 ER - TY - CHAP A1 - Auer, Cornelia A1 - Kasten, Jens A1 - Kratz, Andrea A1 - Zhang, Eugene A1 - Hotz, Ingrid T1 - Automatic, Tensor-Guided Illustrative Vector Field Visualization T2 - Proc. IEEE Pacific Visualization Symposium 2013 Y1 - 2013 U6 - https://doi.org/10.1109/PacificVis.2013.6596154 SP - 265 EP - 275 CY - Sydney, Australia ER - TY - GEN A1 - Zobel, Valentin A1 - Reininghaus, Jan A1 - Hotz, Ingrid T1 - Visualization of Two-Dimensional Symmetric Tensor Fields Using the Heat Kernel Signature T2 - Topological Methods in Data Analysis and Visualization III Y1 - 2013 SP - 249 EP - 262 CY - Davis, CA, USA ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials BT - Theory, Algorithms, and Applications T2 - Topological Methods in Data Analysis and Visualization III Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-04099-8_15 SP - 235 EP - 248 PB - Springer ER - TY - CHAP A1 - Koch, Stefan A1 - Wiebel, Alexander A1 - Kasten, Jens A1 - Hlawitschka, Mario T1 - Visualizing Linear Neighborhoods in Non-Linear Vector Fields T2 - Proceedings of the IEEE Pacific Visualization Symposium Y1 - 2013 SP - 249 EP - 256 CY - Sydney, Australia ER - TY - JOUR A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Approximate Level-Crossing Probabilities for Interactive Visualization of Uncertain Isocontours JF - International Journal for Uncertainty Quantification Y1 - 2013 U6 - https://doi.org/10.1615/Int.J.UncertaintyQuantification.2012003958 VL - 3 IS - 2 SP - 101 EP - 117 ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Hutchison, Carol A1 - Werle, Jason A1 - Montgomery, Sigrun A1 - Romeo, Carolina A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Kinematic Differences Between Gender Specific And Traditional Knee Implants JF - The Journal of Arthroplasty Y1 - 2013 U6 - https://doi.org/10.1016/j.arth.2013.01.021 VL - 28 IS - 9 SP - 1543 EP - 1550 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Bessler, Stefan A1 - Zachow, Stefan T1 - Evaluation of the Intranasal Flow Field through Computational Fluid Dynamics (CFD) JF - Journal of Facial and Plastic Surgery Y1 - 2013 UR - https://www.thieme-connect.de/DOI/DOI?10.1055/s-0033-1341591 U6 - https://doi.org/10.1055/s-0033-1341591 VL - 29 IS - 2 SP - 93 EP - 98 PB - Thieme ER - TY - GEN A1 - Grewe, Carl Martin A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Hermanussen, Michael T1 - Landmark-based Statistical Shape Analysis T2 - Auxology - Studying Human Growth and Development url Y1 - 2013 UR - http://www.schweizerbart.de/publications/detail/isbn/9783510652785 SP - 199 EP - 201 PB - Schweizerbart Verlag, Stuttgart ER - TY - JOUR A1 - Galloway, Francis A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Worsley, Peter A1 - Zachow, Stefan A1 - Nair, Prasanth A1 - Taylor, Mark T1 - A large scale finite element study of a cementless osseointegrated tibial tray JF - Journal of Biomechanics Y1 - 2013 U6 - https://doi.org//10.1016/j.jbiomech.2013.04.021 VL - 46 IS - 11 SP - 1900 EP - 1906 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Exploring cavity dynamics in biomolecular systems JF - BMC Bioinformatics Y1 - 2013 U6 - https://doi.org/10.1186/1471-2105-14-S19-S5 VL - 14 ET - (Suppl 19):S5 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Nonparametric Models for Uncertainty Visualization JF - Computer Graphics Forum Y1 - 2013 U6 - https://doi.org/10.1111/cgf.12100 target VL - 32 IS - 3 SP - 131 EP - 140 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Kutz, Benjamin A1 - Theisel, Holger T1 - Mass-Dependent Integral Curves in Unsteady Vector Fields JF - Computer Graphics Forum Y1 - 2013 U6 - https://doi.org/10.1111/cgf.12108 VL - 32 SP - 211 EP - 220 ER - TY - CHAP A1 - Kuhn, Alexander A1 - Lindow, Norbert A1 - Günther, Tobias A1 - Wiebel, Alexander A1 - Theisel, Holger A1 - Hege, Hans-Christian T1 - Trajectory Density Projection for Vector Field Visualization T2 - EuroVis 2013, short papers. M. Hlawitschka, Tino Weinkauf (eds.) Y1 - 2013 UR - http://vc.cs.ovgu.de/files/publications/2013/Kuhn_2013_EUROVIS.pdf U6 - https://doi.org/10.2312/PE.EuroVisShort.EuroVisShort2013.031-035 SP - 31 EP - 35 ER - TY - CHAP A1 - Wiebel, Alexander A1 - Preis, Philipp A1 - Vos, Frans A1 - Hege, Hans-Christian ED - Hlawitschka, Mario ED - Weinkauf, Tino T1 - 3D Strokes on Visible Structures in Direct Volume Rendering T2 - EuroVis - Short Papers Y1 - 2013 U6 - https://doi.org/10.2312/PE.EuroVisShort.EuroVisShort2013.091-095 SP - 91 EP - 95 PB - Eurographics Association ER - TY - JOUR A1 - Kratz, Andrea A1 - Auer, Cornelia A1 - Stommel, Markus A1 - Hotz, Ingrid T1 - Visualization and Analysis of Second-Order Tensors: Moving Beyond the Symmetric Positive-Definite Case JF - Computer Graphics Forum - State of the Art Reports Y1 - 2013 U6 - https://doi.org/10.1111/j.1467-8659.2012.03231.x VL - 1 SP - 49 EP - 74 ER - TY - JOUR A1 - Kratz, Andrea A1 - Baum, Daniel A1 - Hotz, Ingrid T1 - Anisotropic Sampling of Planar and Two-Manifold Domains for Texture Generation and Glyph Distribution JF - Transactions on Visualization and Computer Graphics (TVCG) Y1 - 2013 U6 - https://doi.org/10.1109/TVCG.2013.83 VL - 19 SP - 1782 EP - 1794 ER - TY - JOUR A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Fast Generation of Virtual X-ray Images for Reconstruction of 3D Anatomy JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-35928 VL - 19 IS - 12 SP - 2673 EP - 2682 ER - TY - CHAP A1 - Rolia, Jerry A1 - Zhu, Xiaoyun A1 - Arlitt, Martin A1 - Andrzejak, Artur T1 - Statistical Service Assurances for Applications in Utility Grid Environments T2 - 10th International Workshop on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS 2002), 11-16 October 2002, Fort Worth, Texas, USA Y1 - 2002 U6 - https://doi.org/10.1109/MASCOT.2002.1167084 SP - 247 EP - 256 PB - IEEE Computer Society ER - TY - JOUR A1 - Busch, Hubert A1 - Heidl, Sebastian A1 - Staudemeyer, Ralf A1 - Stolle, Manfred T1 - Teleimmersion – Erfahrungen mit der Gigabit-Ethernet-Strecke zwischen Berlin und Hannover JF - DFN-Mitteilungen Y1 - 2002 VL - 58(3) SP - 7 EP - 9 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Stüben, Hinnerk A1 - Schintke, Florian A1 - Din, George T1 - GuiGen: a toolset for creating customized interfaces for Grid user communities JF - Future Generation Comp. Syst. Y1 - 2002 U6 - https://doi.org/10.1016/S0167-739X(02)00086-9 VL - 18 IS - 8 SP - 1075 EP - 1084 ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schintke, Florian ED - Monien, Burkhard ED - Feldmann, Rainer T1 - Concepts and Technologies for a Worldwide Grid Infrastructure T2 - Euro-Par 2002, Parallel Processing, 8th International Euro-Par Conference Paderborn, Germany, August 27-30, 2002, Proceedings Y1 - 2002 U6 - https://doi.org/10.1007/3-540-45706-2_6 VL - 2400 SP - 62 EP - 72 PB - Springer ER - TY - CHAP ED - Bal, H. ED - Löhr, K.-P. ED - Reinefeld, Alexander T1 - 2nd IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2002), 22-24 May 2002, Berlin, Germany Y1 - 2002 SN - 0-7695-1582-7 PB - IEEE Computer Society ER - TY - CHAP A1 - Graupner, Sven A1 - Andrzejak, Artur A1 - Kotov, Vadim ED - Banissi, Ebad ED - Börner, Katy ED - Chen, Chaomei ED - Clapworthy, Gordon ED - Maple, Carsten ED - Lobben, Amy ED - Moore, Christopher ED - Roberts, Jonathan ED - Ursyn, Anna ED - Zhang, Jian-Ping T1 - Visualizing Topology in Self-Organizing Management Overlays T2 - Seventh International Conference on Information Visualization, IV 2003, 16-18 July 2003, London, UK Y1 - 2003 U6 - https://doi.org/10.1109/IV.2003.1217980 SP - 200 EP - 205 PB - IEEE Computer Society ER - TY - CHAP A1 - Wendler, Jan A1 - Bach, Joscha ED - Polani, Daniel ED - Browning, Brett ED - Bonarini, Andrea ED - Yoshida, Kazuo T1 - Recognizing and Predicting Agent Behavior with Case Based Reasoning T2 - RoboCup 2003: Robot Soccer World Cup VII Y1 - 2003 U6 - https://doi.org/10.1007/978-3-540-25940-4_72 VL - 3020 SP - 729 EP - 738 PB - Springer ER - TY - JOUR A1 - Graupner, Sven A1 - Kotov, Vadim A1 - Andrzejak, Artur A1 - Trinks, Holger T1 - Service-Centric Globally Distributed Computing JF - IEEE Internet Computing Y1 - 2003 U6 - https://doi.org/10.1109/MIC.2003.1215658 VL - 7 IS - 4 SP - 36 EP - 43 CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - May, Patrick A1 - Koch, Ina ED - Christophe, C. ED - Lenhof, H.-P. ED - Sagot, M.-F. T1 - PTGL - Protein Topology Graph Library T2 - ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics Y1 - 2003 SP - 193 EP - 194 ER - TY - JOUR A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Modeling Replica Availability in Large Data Grids JF - J. Grid Computing Y1 - 2003 U6 - https://doi.org/10.1023/B:GRID.0000024086.50333.0d VL - 1 IS - 2 SP - 219 EP - 227 ER - TY - CHAP A1 - Andrzejak, Artur ED - Banissi, Ebad ED - Börner, Katy ED - Chen, Chaomei ED - Clapworthy, Gordon ED - Maple, Carsten ED - Lobben, Amy ED - Moore, Christopher ED - Roberts, Jonathan ED - Ursyn, Anna ED - Zhang, Jian-Ping T1 - Memory-Efficient and Fast Enumeration of Global States T2 - Seventh International Conference on Information Visualization, IV 2003, 16-18 July 2003, London, UK Y1 - 2003 U6 - https://doi.org/10.1109/IV.2003.1217978 SP - 189 EP - 193 PB - IEEE Computer Society ER - TY - JOUR A1 - Andrzejak, Artur A1 - Welzl, Emo T1 - In between k-Sets, j-Facets, and i-Faces: (i , j) - Partition JF - Discrete & Computational Geometry Y1 - 2003 U6 - https://doi.org/s00454-002-2778-4 VL - 29 IS - 1 SP - 105 EP - 131 ER - TY - JOUR A1 - Cordes, Frank A1 - Preissner, Robert A1 - Steinke, Thomas T1 - How Does a Protein Work? JF - BioTOPics J. of Biotechnology Berlin-Brandenburg Y1 - 2003 VL - 18 IS - 2 SP - 4 EP - 5 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Grid Computing in Deutschland JF - Spektrum der Wissenschaft Y1 - 2003 SP - 72 EP - 73 PB - Spektrum der Wissenschaft Verlagsgesellschaft, Heidelberg ER - TY - CHAP A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - From Clusters to the Fabric: The Job Management Perspective T2 - 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 1-4 December 2003, Kowloon, Hong Kong, China Y1 - 2003 U6 - https://doi.org/10.1109/CLUSTR.2003.1253351 SP - 468 EP - 473 PB - IEEE Computer Society ER - TY - CHAP A1 - Andrzejak, Artur A1 - Fukuda, Komei ED - Hamza, M. T1 - Debugging Distributed Computations by Reverse Search T2 - The 21st IASTED International Multi-Conference on Applied Informatics (AI 2003), February 10-13, 2003, Innsbruck, Austria Y1 - 2003 SP - 719 EP - 725 PB - IASTED/ACTA Press ER - TY - CHAP A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander ED - Sloot, Peter ED - Abramson, David ED - Bogdanov, Alexander ED - Dongarra, Jack ED - Zomaya, Albert ED - Gorbachev, Yuri T1 - Efficient Synchronization of Replicated Data in Distributed Systems T2 - Computational Science - ICCS 2003, International Conference, Melbourne, Australia and St. Petersburg, Russia, June 2-4, 2003. Proceedings, Part I Y1 - 2003 U6 - https://doi.org/10.1007/3-540-44860-8_28 VL - 2657 SP - 274 EP - 283 PB - Springer ER - TY - CHAP A1 - Rother, Kristian A1 - Trissl, S. A1 - Müller, H. A1 - May, Patrick A1 - Heek, R. A1 - Preissner, Robert A1 - Steinke, Thomas A1 - Koch, Ina A1 - Leser, Ulf A1 - Frömmel, Cornelius ED - Christophe, C. ED - Lenhof, H.-P. ED - Sagot, M.-F. T1 - Columba - A Database of Annotations of Protein Structure T2 - ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics Y1 - 2003 SP - 109 EP - 110 ER - TY - CHAP A1 - Rolia, Jerry A1 - Andrzejak, Artur A1 - Arlitt, Martin ED - Brunner, Marcus ED - Keller, Alexander T1 - Automating Enterprise Application Placement in Resource Utilities T2 - Self-Managing Distributed Systems, 14th IFIP/IEEE International Workshop on Distributed Systems Y1 - 2003 U6 - https://doi.org/10.1007/978-3-540-39671-0_11 VL - 2867 SP - 118 EP - 129 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Graupner, Sven A1 - Andrzejak, Artur A1 - Kotov, Vadim A1 - Trinks, Holger T1 - Adaptive Control Overlay for Service Management T2 - First Workshop on the Design of Self-Managing Systems (AASMS’03) Y1 - 2003 CY - San Francisco ER - TY - JOUR A1 - Rolia, Jerry A1 - Zhu, Xiaoyun A1 - Arlitt, Martin A1 - Andrzejak, Artur T1 - Statistical service assurances for applications in utility Grid environments JF - Performance Evaluation Y1 - 2004 U6 - https://doi.org/10.1016/j.peva.2004.07.015 VL - 58 IS - 2-3 SP - 319 EP - 339 ER - TY - CHAP A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - A Framework for Self-Optimizing Grids Using P2P Components T2 - 14th International Workshop on Database and Expert Systems Applications (DEXA’03), September 1-5, 2003, Prague, Czech Republic Y1 - 2003 U6 - https://doi.org/10.1109/DEXA.2003.1232101 SP - 689 EP - 693 PB - IEEE Computer Society ER - TY - CHAP A1 - May, Patrick A1 - Steinke, Thomas A1 - Meyer, Michael T1 - THESEUS: A Parallel Threading Core T2 - Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow Y1 - 2004 SP - 199 ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Scalable and Self-Optimizing Data Grids T2 - Annual Review of Scalable Computing Y1 - 2004 U6 - https://doi.org/10.1142/9789812794727_0002 VL - 6 IS - chapter 2 SP - 30 EP - 60 PB - World Scientific ER - TY - JOUR A1 - May, Patrick A1 - Barthel, Stefan A1 - Koch, Ina T1 - PTGL - a web-based database application for protein topologies JF - Bioinformatics Y1 - 2004 U6 - https://doi.org/10.1093/bioinformatics/bth367 VL - 20 IS - 17 SP - 3277 EP - 3279 ER - TY - CHAP A1 - Schütt, Thorsten A1 - Merzky, André A1 - Hutanu, Andrei A1 - Schintke, Florian T1 - Remote partial file access using compact pattern descriptions T2 - 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2004), April 19-22, 2004, Chicago, Illinois, USA Y1 - 2004 U6 - https://doi.org/10.1109/CCGrid.2004.1336604 SP - 482 EP - 489 PB - IEEE Computer Society ER - TY - GEN A1 - Campadello, Stefano A1 - De Roure, David A1 - Farshchian, Bahador A1 - Fehse, Meike A1 - Goble, Carole A. A1 - Gui, Yunmiao A1 - Hermenegildo, Manuel V. A1 - Jeffery, Karl A1 - Laforenza, Domenico A1 - Maccallum, Peter A1 - Masso, Jordi A1 - Priol, Thierry A1 - Reinefeld, Alexander A1 - Riguidel, Michel A1 - Snelling, David A1 - Talia, Domenico A1 - Varvarigou, Theodora A. T1 - Next Generation Grids 2 - Requirements and Options for European Grids Research 2005-2010 and Beyond Y1 - 2004 UR - http://www.cordis.lu/ist/grids/pub-report.htm PB - NGG2 Group ER - TY - CHAP A1 - Hupfeld, Felix T1 - Log-Structured Storage for Efficient Weakly-Connected Replication T2 - 24th International Conference on Distributed Computing Systems Workshops (ICDCS 2004 Workshops), 23-24 March 2004, Hachioji, Tokyo, Japan Y1 - 2004 U6 - https://doi.org/10.1109/ICDCSW.2004.1284072 SP - 458 EP - 463 PB - IEEE Computer Society ER - TY - CHAP A1 - Wendler, Jan A1 - Schintke, Florian T1 - Grid-Enabled Computational Fluid Dynamics using FlowGrid T2 - Cracow Grid Workshop ’03 Proceedings Y1 - 2004 SP - 59 EP - 66 PB - Academic Computer Centre CYFRONET AGH CY - ul. Nawojki 11, 30-950 Krakow 61, P.O.Box 386, Poland ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Grid Services: Web Services zur Nutzung verteilter Ressourcen JF - Informatik Spektrum Y1 - 2004 U6 - https://doi.org/10.1007/s00287-004-0379-8 VL - 27 IS - 2 SP - 129 EP - 135 ER - TY - CHAP A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Wendler, Jan T1 - Elastic Grid Reservations with User-Defined Optimization Policies T2 - Proceedings of the 2nd Workshop on Adaptive Grid Middleware (AGridM’04), in conjunction with PACT 2004, Antibes Juan-les-Pins, France Y1 - 2004 ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schintke, Florian ED - von Knop, Jan ED - Haverkamp, Wilhelm ED - Jessen, Eike T1 - Dienste und Standards für das Grid Computing T2 - E-Science and Grid - Ad-hoc-Netze - Medienintegration, 18. DFN-Arbeitstagung über Kommunikationsnetze, Düsseldorf, 2004 Y1 - 2004 UR - http://dl.gi.de/handle/20.500.12116/28585 VL - P-55 SP - 293 EP - 304 PB - GI ER - TY - CHAP A1 - Rother, Kristian A1 - Müller, Heiko A1 - Trißl, Silke A1 - Koch, Ina A1 - Steinke, Thomas A1 - Preissner, Robert A1 - Frömmel, Cornelius A1 - Leser, Ulf ED - Rahm, Erhard T1 - Columba: Multidimensional Data Integration of Protein Annotations T2 - Data Integration in the Life Sciences, First International Workshop, DILS 2004, Leipzig, Germany, March 25-26 Y1 - 2004 U6 - https://doi.org/10.1007/978-3-540-24745-6_11 VL - 2994 SP - 156 EP - 171 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Xiao, Li A1 - Zhang, Xiaodong A1 - Andrzejak, Artur A1 - Chen, Songqing T1 - Building a Large and Efficient Hybrid Peer-to-Peer Internet Caching System JF - IEEE Trans. Knowl. Data Eng. Y1 - 2004 U6 - https://doi.org/10.1109/TKDE.2004.1 VL - 16 IS - 6 SP - 754 EP - 769 ER - TY - JOUR A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Bärring, Olof A1 - Lopez, Maite Barroso A1 - Cancio, German A1 - Chapeland, Sylvain A1 - Chouikh, Karim A1 - Cons, Lionel A1 - Poznanski, Piotr A1 - Defert, Philippe A1 - Iven, Jan A1 - Kleinwort, Thorsten A1 - Panzer-Steindel, Bernd A1 - Polok, Jaroslaw A1 - Rafflin, Catherine A1 - Silverman, Alan A1 - Smith, Tim A1 - van Eldik, Jan A1 - Front, David A1 - Biasotto, Massimo A1 - Aiftimiei, Cristina A1 - Ferro, Enrico A1 - Maron, Gaetano A1 - Chierici, Andrea A1 - dell’Agnello, Luca A1 - Serra, Marco A1 - Michelotto, Michele A1 - Hess, Lord A1 - Lindenstruth, Volker A1 - Pister, Frank A1 - Steinbeck, Timm A1 - Groep, David A1 - Steenbakkers, Martijn A1 - Koeroo, Oscar A1 - de Cerff, Wim A1 - Venekamp, Gerben A1 - Anderson, Paul A1 - Colles, Tim A1 - Holt, Alexander A1 - Scobie, Alastair A1 - George, Michael A1 - Washbrook, Andrew A1 - Leiva, Rafael T1 - Autonomic Management of Large Clusters and Their Integration into the Grid JF - J. Grid Comput. Y1 - 2004 U6 - https://doi.org/10.1007/s10723-004-7647-3 VL - 2 IS - 3 SP - 247 EP - 260 ER - TY - CHAP A1 - Michalsky, E. A1 - Goede, A. A1 - Preissner, Robert A1 - May, Patrick A1 - Steinke, Thomas T1 - A distributed pipeline for structure prediction T2 - CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy Y1 - 2004 SP - 112 EP - 114 ER - TY - CHAP A1 - May, Patrick A1 - Krause, F. A1 - Ehrlich, C. A1 - Maaskola, J. A1 - Steinke, Thomas T1 - ZIB threading pipeline - A webservice-based, distributed structure prediction workflow. T2 - Proceedings of the German Conference on Bioinformatics (GCB) Y1 - 2005 SP - 125 EP - 126 ER - TY - CHAP A1 - Schintke, Florian ED - Cosnard, Michel ED - Getov, Vladimir ED - Laforenza, Domenico ED - Reinefeld, Alexander T1 - The ZIB distributed data management system T2 - Future Generation Grids Y1 - 2005 UR - http://drops.dagstuhl.de/opus/volltexte/2005/26 IS - 04451 SP - 20 PB - Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany CY - Dagstuhl, Germany ER - TY - JOUR A1 - Allen, Gabrielle A1 - Davis, K. A1 - Goodale, Tom A1 - Hutanu, Andrei A1 - Kaiser, Hartmut A1 - Kielmann, Thilo A1 - Merzky, Andre A1 - Nieuwpoort, R. A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Seidel, Edward A1 - Ullmer, Brygg T1 - The Grid Application Toolkit: Toward Generic and Easy Appliction Programming Interfaces for the Grid JF - Procceedings of the IEEE Y1 - 2005 U6 - https://doi.org/10.1109/JPROC.2004.842755 VL - 93 IS - 3 SP - 534 EP - 550 PB - IEEE Computer Society Press ER - TY - CHAP A1 - May, Patrick A1 - Kallies, B. A1 - Steinke, Thomas T1 - THESEUS – a parallel threading core for highthroughput protein structure prediction T2 - Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC) Y1 - 2005 ER - TY - GEN A1 - Roy, P. A1 - Ghodsi, Ali A1 - Haridi, Seif A1 - Stefani, J. B. A1 - Coupaye, T. A1 - Reinefeld, Alexander A1 - Winter, E. A1 - Yap, R. T1 - Self Management of Large-Scale Distributed Systems by Combining Peer-to-Peer Networks and Components Y1 - 2005 UR - http://coregrid.ercim.eu/mambo/images/stories/TechnicalReports/tr-0018.pdf IS - TR-0018 PB - Institute on System Architecture, CoreGRID - Network of Excellence ER - TY - CHAP A1 - Kolbeck, Björn A1 - Schmidt-Gönner, T. A1 - May, Patrick A1 - Knapp, E. T1 - Protein structure alignment based on contact maps and secondary structure. T2 - Proceedings of the German Conference on Bioinformatics (GCB) Y1 - 2005 SP - 122 EP - 123 ER - TY - CHAP A1 - Andrzejak, Artur A1 - Hermann, Ulf A1 - Sahai, Akhil T1 - FEEDBACKFLOW – An Adaptive Workflow Generator for Systems Management T2 - Second International Conference on Autonomic Computing (ICAC 2005), 13-16 June 2005, Seattle, WA, USA Y1 - 2005 U6 - https://doi.org/10.1109/ICAC.2005.30 SP - 335 EP - 336 PB - IEEE Computer Society ER - TY - JOUR A1 - Wendler, Jan A1 - Schintke, Florian T1 - Executing and observing CFD applications on the Grid JF - Future Generation Computer Systems the International Journal of Grid Computing: Theory, Methods and Applications Y1 - 2005 U6 - https://doi.org/10.1016/j.future.2004.09.026 VL - 21 IS - 1 SP - 11 EP - 18 PB - Elsevier Science Publishers ER - TY - JOUR A1 - Trißl, Silke A1 - Rother, Kristian A1 - Müller, Heiko A1 - Steinke, Thomas A1 - Koch, Ina A1 - Preissner, Robert A1 - Frömmel, Cornelius A1 - Leser, Ulf T1 - Columba: an integrated database of proteins, structures, and annotations JF - BMC Bioinformatics Y1 - 2005 U6 - https://doi.org/10.1186/1471-2105-6-81 VL - 6 SP - 81 EP - 92 ER - TY - JOUR A1 - Andrzejak, Artur A1 - Ceyran, Mehmet T1 - Characterizing and Predicting Resource Demand by Periodicity Mining JF - J. Network Syst. Manage., Special Issue on Self-Managing Systems and Networks Y1 - 2005 VL - 13 IS - 2 ER - TY - CHAP A1 - Röblitz, Thomas A1 - Reinefeld, Alexander T1 - Co-reservation with the concept of virtual resources T2 - 5th International Symposium on Cluster Computing and the Grid (CCGrid 2005), 9-12 May, 2005, Cardiff, UK Y1 - 2005 UR - http://doi.ieeecomputersociety.org/10.1109/CCGRID.2005.1558582 SP - 398 EP - 406 PB - IEEE Computer Society ER - TY - CHAP A1 - Talia, Domenico A1 - Trunfio, Paolo A1 - Zeng, Jingdi A1 - Högqvist, Mikael T1 - A Peer-to-Peer Framework for Resource Discovery in Large-Scale Grids T2 - CoreGRID Integration Workshop Y1 - 2006 ER - TY - CHAP A1 - Rolia, Jerry A1 - Cherkasova, Ludmila A1 - Arlitt, Martin A1 - Andrzejak, Artur T1 - A capacity management service for resource pools T2 - Proceedings of the Fifth International Workshop on Software and Performance, WOSP 2005, Palma, Illes Balears, Spain, July 12-14 Y1 - 2005 UR - http://doi.acm.org/10.1145/1071021.1071047 SP - 229 EP - 237 ER - TY - CHAP A1 - May, Patrick A1 - Ehrlich, Hans-Christian A1 - Steinke, Thomas ED - Lehner, Wolfgang ED - Meyer, Norbert ED - Streit, Achim ED - Stewart, Craig T1 - ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services T2 - Euro-Par 2006 Workshops Y1 - 2006 UR - http://dx.doi.org/10.1007/11823285_121 VL - 4375 SP - 1148 EP - 1158 PB - Springer ER - TY - CHAP A1 - Domingues, Patrício A1 - Andrzejak, Artur A1 - Silva, Luís T1 - Using Checkpointing to Enhance Turnaround Time on Institutional Desktop Grids T2 - Second International Conference on e-Science and Grid Technologies (e-Science 2006), 4-6 December 2006, Amsterdam, The Netherlands Y1 - 2006 UR - http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2006.148 SP - 73 PB - IEEE Computer Society ER - TY - JOUR A1 - Hupfeld, Felix A1 - Gordon, M. T1 - Using distributed consistent branching for efficient reconciliation of mobile workspaces JF - International Conference on Collaborative Computing Y1 - 2006 U6 - https://doi.org/10.1109/COLCOM.2006.361837 VL - 0 SP - 8 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Structured Overlay without Consistent Hashing: Empirical Results T2 - Sixth Workshop on Global and Peer-to-Peer Computing (GP2PC’06) at Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006), 16-19 May 2006, Singapore Y1 - 2006 UR - http://doi.ieeecomputersociety.org/10.1109/CCGRID.2006.175 U6 - https://doi.org/10.1109/CCGRID.2006.175 PB - IEEE Computer Society ER - TY - CHAP A1 - Andrzejak, Artur A1 - Graupner, Sven A1 - Plantikow, Stefan T1 - Predicting Resource Demand in Dynamic Utility Computing Environments T2 - 2006 International Conference on Autonomic and Autonomous Systems (ICAS 2006), 16-21 July 2006, Silicon Valley, California, USA Y1 - 2006 U6 - https://doi.org/10.1109/ICAS.2006.44 SP - 6 PB - IEEE Computer Society ER - TY - JOUR A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Resource reservations with fuzzy requests JF - Concurrency and Computation: Practice and Experience Y1 - 2006 UR - http://dx.doi.org/10.1002/cpe.1023 U6 - https://doi.org/10.1002/cpe.1023 VL - 18 IS - 13 SP - 1681 EP - 1703 ER - TY - CHAP A1 - Röblitz, Thomas A1 - Rzadca, Krzysztof ED - Lehner, Wolfgang ED - Meyer, Norbert ED - Streit, Achim ED - Stewart, Craig T1 - On the Placement of Reservations into Job Schedules T2 - Euro-Par 2006 Workshops Y1 - 2006 UR - http://dx.doi.org/10.1007/11823285_21 VL - 4375 SP - 198 EP - 210 PB - Springer ER - TY - CHAP A1 - Andrzejak, Artur A1 - Domingues, Patrício A1 - Silva, Luís ED - Hellerstein, Joseph ED - Stiller, Burkhard T1 - Predicting Machine Availabilities in Desktop Pools T2 - Management of Integrated End-to-End Communications and Services, 10th IEEE/IFIP Network Operations and Management Symposium, NOMS 2006, Vancouver, Canada, April 3-7, 2006. Proceedings Y1 - 2006 U6 - https://doi.org/10.1109/NOMS.2006.1687632 PB - IEEE ER - TY - CHAP A1 - Andrzejak, Artur A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten ED - Getov, Vladimir ED - Laforenza, Domenico ED - Reinefeld, Alexander T1 - On Adaptability in Grid Systems T2 - Future Generation Grids: Proceedings of the Workshop on Future Generation Grids, November 1-5, 2004, Dagstuhl, Germany Y1 - 2006 U6 - https://doi.org/10.1007/978-0-387-29445-2_2 SP - 29 EP - 46 PB - Springer ER - TY - CHAP A1 - Peter, Kathrin A1 - Sobe, Peter T1 - Flexible Definition of Data and Redundancy Layout for Storage Systems T2 - Sixth European Dependable Computing Conference (EDCC-6), Proceedings Supplemental Volume Y1 - 2006 SP - 59 EP - 60 ER - TY - GEN ED - Getov, Vladimir ED - Laforenza, Domenico ED - Reinefeld, Alexander T1 - Future Generation Grids: Proceedings of the Workshop on Future Generation Grids, November 1-5, 2004, Dagstuhl, Germany Y1 - 2006 SN - 978-0-387-27935-0 PB - Springer ER - TY - GEN A1 - Andrzejak, Artur A1 - Silva, Luis T1 - Deterministic Models of Software Aging and Optimal Rejuvenation Schedules Y1 - 2006 UR - http://coregrid.ercim.eu/mambo/images/stories/TechnicalReports/tr-0047.pdf IS - TR-0047 PB - Institute on System Architecture, CoreGRID ER - TY - CHAP A1 - Steinke, Thomas A1 - Reinefeld, Alexander T1 - Experiences with High-Level Programming of FPGAs on Cray XD1 T2 - CUG Proceedings Y1 - 2006 ER - TY - CHAP A1 - Andrzejak, Artur A1 - Plantikow, Stefan T1 - Defining Fuzzy Logic Controllers with Scarce Model Data T2 - First International Workshop on Feedback Control Implementation and Design in Computing Systems and Networks FeBID’06 (colocated with NOMS’06) Y1 - 2006 CY - Vancouver, Canada ER - TY - JOUR A1 - Herrmann, Christoph A1 - Langhammer, Tobias T1 - Combining partial evaluation and staged interpretation in the implementation of domain-specific languages JF - Sci. Comput. Program. Y1 - 2006 U6 - https://doi.org/10.1016/j.scico.2006.02.002 VL - 62 IS - 1 SP - 47 EP - 65 ER - TY - JOUR A1 - Kolbeck, Björn A1 - May, Patrick A1 - Schmidt-Goenner, T. A1 - Steinke, Thomas A1 - Knapp, E. T1 - Connectivity independent protein-structure alignment: a hierarchical approach JF - BMC Bioinformatics Y1 - 2006 VL - 7 SP - 510 ER - TY - GEN A1 - Talia, Domenico A1 - Trunfio, Paolo A1 - Zeng, Jingdi A1 - Högqvist, Mikael T1 - A DHT-based Peer-to-Peer Framework for Resource Discovery in Grids Y1 - 2006 UR - http://coregrid.ercim.eu/mambo/images/stories/TechnicalReports/tr-0048.pdf IS - TR-0048 PB - Institute on System Architecture, CoreGRID - Network of Excellence ER - TY - CHAP A1 - Hupfeld, Felix A1 - Cortes, Toni A1 - Kolbeck, Björn A1 - Stender, Jan A1 - Focht, Erich A1 - Hess, Matthias A1 - Malo, Jesus A1 - Marti, Jonathan A1 - Cesario, Eugenio T1 - XtreemFS: a case for object-based storage in Grid data management T2 - 3rd VLDB Workshop on Data Management in Grids, co-located with VLDB 2007 Y1 - 2007 ER - TY - GEN A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Vorrichtung und Verfahren zum Speichern / Abrufen von Objekten mit mehrdimensional adressierten, elektronischen Daten Y1 - 2007 PB - Europäische Patentanmeldung Nr. 06012030.0 vom 12.06.2006, Patent Nr: 1868114 ER - TY - CHAP A1 - Silva, Luis A1 - Alonso, Javier A1 - Silva, Paulo A1 - Torres, Jordi A1 - Andrzejak, Artur T1 - Using Virtualization to Improve Software Rejuvenation T2 - IEEE International Symposium on Network Computing and Applications (IEEE-NCA) Y1 - 2007 CY - Cambridge, MA, USA ER - TY - GEN A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Vorrichtung und Verfahren zum Abrufen / Speichern von elektronischen Daten in einem System mit mehreren Datenverarbeitungseinheiten Y1 - 2007 PB - Europäisches Patent EP 1 744 257 A1 ER - TY - GEN A1 - Silva, Paulo A1 - Silva, Luis A1 - Andrzejak, Artur T1 - Using Micro-Reboots to Improve Software Rejuvenation in Apache Tomcat Y1 - 2007 UR - http://coregrid.ercim.eu/mambo/images/stories/TechnicalReports/tr-0099.pdf IS - TR-0099 PB - Institute on System Architecture, CoreGRID ER - TY - CHAP A1 - Plantikow, Stefan A1 - Reinefeld, Alexander A1 - Schintke, Florian ED - Clemm, Alexander ED - Granville, Lisandro ED - Stadler, Rolf T1 - Transactions for Distributed Wikis on Structured Overlays T2 - DSOM Y1 - 2007 U6 - https://doi.org/10.1007/978-3-540-75694-1_25 VL - 4785 SP - 256 EP - 267 PB - Springer CY - Silicon Valley, CA, USA ER - TY - CHAP A1 - Högqvist, Mikael A1 - Röblitz, Thomas A1 - Reinefeld, Alexander T1 - Stellaris: An RDF-based Information Service for AstroGrid-D T2 - German e-Science Conference Y1 - 2007 UR - http://edoc.mpg.de/316518 PB - Max Planck Digital Library ER - TY - JOUR A1 - Andrzejak, Artur A1 - Reinefeld, Alexander T1 - Paradigms for Scalable and Dependable Grids JF - Future Generation Computer Systems (FGCS) Y1 - 2007 VL - 23 IS - 7 ER - TY - CHAP A1 - Granzer, Thomas A1 - Breitling, Frank A1 - Braun, Michael A1 - Enke, Harry A1 - Röblitz, Thomas T1 - Providing Remote Access to Robotic Telescopes by Adopting Grid Technology T2 - German e-Science Conference Y1 - 2007 UR - http://edoc.mpg.de/316644 PB - Max Planck Digital Library ER - TY - CHAP A1 - Grimme, Christian A1 - Langhammer, Tobias A1 - Papaspyrou, Alexander A1 - Schintke, Florian T1 - Negotiation-based Choreography of Data-intensive Applications in the C3Grid Project T2 - German E-Science Conference Y1 - 2007 UR - http://edoc.mpg.de/316579 PB - Max Planck Digital Library CY - Baden-Baden ER - TY - CHAP A1 - Stahlberg, Eric A1 - Popig, Daryl A1 - Ryle, Debie A1 - Babst, Michael A1 - Anderson, Mohammed A1 - Steinke, Thomas T1 - Molecular Simulations with Hardware Accelerators T2 - Reconfigurable Systems Summer Institute 2007 (RSSI 2007) Y1 - 2007 CY - National Center for Supercomputing Applications, Urbana/Illinois ER - TY - CHAP A1 - Stahlberg, Eric A1 - Babst, Michael A1 - Popig, Daryl A1 - Steinke, Thomas T1 - Molecular Dynamics with FPGAs: A Portable API Molecular Simulations with Hardware Accelerators: A Portable Interface Definition for FPGA Supported Acceleration T2 - International Supercomputing Conference 2007 (ISC 2007) Y1 - 2007 CY - Dresden ER - TY - CHAP A1 - Kottha, Samatha A1 - Peter, Kathrin A1 - Steinke, Thomas A1 - Bart, Julian A1 - Falkner, Jürgen A1 - Weisbecker, Anette A1 - Viezens, Fred A1 - Mohammed, Yassene A1 - Sax, Ulrich A1 - Hoheisel, Andreas A1 - Ernst, Thilo A1 - Sommerfeld, Dietmar A1 - Krefting, Dagmar A1 - Vossberg, Michael T1 - Medical Image Processing in MediGRID T2 - German E-Science Conference Y1 - 2007 UR - http://edoc.mpg.de/316613 PB - Max Planck Digital Library CY - Baden-Baden ER - TY - CHAP A1 - Alonso, Javier A1 - Silva, Luis A1 - Andrzejak, Artur A1 - Torres, Jordi T1 - High-Available Grid Services through the use of Virtualized Clustering T2 - IEEE-GRID Y1 - 2007 CY - Austin, USA ER - TY - CHAP A1 - Andrzejak, Artur A1 - Moser, Monika A1 - Silva, Luis ED - Clemm, Alexander ED - Granville, Lisandro ED - Stadler, Rolf T1 - Managing Performance of Aging Applications via Synchronized Replica Rejuvenation T2 - 18th IFIP/IEEE Distributed Systems: Operations and Management (DSOM 2007) Y1 - 2007 VL - 4785 PB - Springer CY - Silicon Valley, CA, USA ER - TY - CHAP A1 - Plantikow, Stefan A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Distributed Wikis on Structured Overlays T2 - CoreGrid Workshop on Grid Programming Models, Grid and P2P System Architecture, Grid Systems, Tools and Environments Y1 - 2007 ER - TY - GEN A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Device and method for retrieving / storing electronic data in a system with a plurality of data processing units Y1 - 2007 PB - United States Patent Application Publication No. US 2007/0165619 A1 ER - TY - CHAP A1 - Andrzejak, Artur A1 - Silva, Luis T1 - Deterministic Models of Software Aging and Optimal Rejuvenation Schedules T2 - 10th IFIP/IEEE Symposium on Integrated Management (IM 2007) Y1 - 2007 CY - Munich, Germany ER - TY - JOUR A1 - Meyer, Michael A1 - Steinke, Thomas A1 - Sühnel, Jürgen T1 - Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions JF - Journal of Molecular Modeling Y1 - 2007 UR - http://dx.doi.org/10.1007/s00894-006-0148-5 VL - 13 IS - 2 SP - 335 EP - 345 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Moser, Monika A1 - Haridi, Seif T1 - Atomic Commitment in Transactional DHTs T2 - Proceedings of the CoreGRID Symposium Y1 - 2007 CY - Rennes, France ER - TY - CHAP A1 - Sobe, Peter A1 - Peter, Kathrin T1 - Combining Compression, Encryption and Fault-tolerant Coding for Distributed Storage T2 - 21th International Parallel and Distributed Processing Symposium (IPDPS 2007) Proceedings Y1 - 2007 SP - 1 EP - 8 PB - IEEE ER - TY - CHAP A1 - Enke, Harry A1 - Steinmetz, Matthias A1 - Radke, Thomas A1 - Reiser, Angelika A1 - Röblitz, Thomas A1 - Högqvist, Mikael T1 - AstroGrid-D: Enhancing Astronomic Science with Grid Technology T2 - German e-Science Conference Y1 - 2007 UR - http://edoc.mpg.de/316645 PB - Max Planck Digital Library ER - TY - CHAP A1 - May, Patrick A1 - Klau, Gunnar A1 - Bauer, Markus A1 - Steinke, Thomas ED - Dubitzky, W. T1 - Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs T2 - GCCB Y1 - 2007 VL - 4360 SP - 19 EP - 32 PB - Springer ER - TY - CHAP A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander ED - Kermarrec, Anne-Marie T1 - A Structured Overlay for Multi-dimensional Range Queries T2 - Euro-Par Conference Y1 - 2007 UR - http://dx.doi.org/10.1007/978-3-540-74466-5_54 U6 - https://doi.org/10.1007/978-3-540-74466-5_54 VL - 4641 SP - 503 EP - 513 PB - Springer ER - TY - CHAP A1 - Rodrigues, Nuno A1 - Sousa, Decio A1 - Silva, Luis A1 - Andrzejak, Artur T1 - A Fault-Injector Tool to Evaluate Failure Detectors in Grid-services T2 - CoreGRID Workshop on Grid Programming Model Grid and P2P Systems Architecture Grid Systems Y1 - 2007 CY - Crete, Greece ER - TY - CHAP A1 - Hupfeld, Felix A1 - Kolbeck, Björn A1 - Stender, Jan A1 - Högqvist, Mikael A1 - Cortes, Toni A1 - Martí, Jonathan A1 - Malo, Jesus T1 - FaTLease: Scalable Fault-Tolerant Lease Negotiation with Paxos T2 - ACM/IEEE International Symposium on High Performance Distributed Computing (HPDC) Y1 - 2008 CY - Boston, MA, USA ER - TY - GEN A1 - Cortes, Toni A1 - Franke, Carsten A1 - Jégou, Yvon A1 - Kielmann, Thilo A1 - Laforenza, Domenico A1 - Matthews, Brian A1 - Morin, Christine A1 - Prieto, Luis A1 - Reinefeld, Alexander T1 - XtreemOS: A Vision for a Grid Operating System Y1 - 2008 UR - http://www.xtreemos.eu/ IS - 4 PB - XtreemOS European Integrated Project ER - TY - CHAP A1 - Mejías, B. A1 - Högqvist, Mikael A1 - Roy, P. T1 - Visualizing Transactional Algorithms for DHTs T2 - IEEE P2P Conference Y1 - 2008 CY - Aachen, Germany ER - TY - CHAP A1 - Högqvist, Mikael A1 - Haridi, Seif A1 - Kruber, Nico A1 - Reinefeld, Alexander A1 - Schütt, Thorsten T1 - Using Global Information for Load Balancing in DHTs T2 - Workshop on Decentralized Self Management for Grids, P2P, and User Communities Y1 - 2008 ER - TY - CHAP A1 - Plantikow, Stefan A1 - Reinefeld, Alexander A1 - Schintke, Florian ED - Danelutto, Marco ED - Fragopoulou, Paraskevi ED - Getov, Vladimir T1 - Transactions and Concurrency Control for Peer-to-Peer-Wikis: An Evaluation T2 - Making Grids Work Y1 - 2008 U6 - https://doi.org/10.1007/978-0-387-78448-9_27 SP - 337 EP - 349 ER - TY - CHAP A1 - Stender, Jan A1 - Kolbeck, Björn A1 - Hupfeld, Felix A1 - Cesario, Eugenio A1 - Focht, Erich A1 - Hess, Matthias A1 - Malo, Jesus A1 - Martí, Jonathan T1 - Striping without Sacrifices: Maintaining POSIX Semantics in a Parallel File System T2 - Proceedings of the 1st USENIX Workshop on Large-Scale Computing (LASCO’08) Y1 - 2008 CY - Boston, MA, USA ER - TY - JOUR A1 - Hupfeld, Felix A1 - Cortes, Toni A1 - Kolbeck, Björn A1 - Focht, Erich A1 - Hess, Matthias A1 - Malo, Jesus A1 - Marti, Jonathan A1 - Stender, Jan A1 - Cesario, Eugenio T1 - The XtreemFS architecture - A case for object-based file systems in Grids JF - Concurrency and Computation: Practice and Experience Y1 - 2008 VL - 20 IS - 8 ER - TY - CHAP A1 - Röblitz, Thomas T1 - Specifying and Processing Co-Reservations in the Grid T2 - Proceedings of the 9$^th$ Workshop on Parallel Systems and Algorithms Y1 - 2008 CY - Dresden, Germany ER - TY - CHAP A1 - Krefting, Dagmar A1 - Canisius, Sebastian A1 - Peter, Kathrin A1 - Tolxdorff, Thomas A1 - Penzel, Thomas T1 - Signalanalyse von Polysomnographien unter Verwendung einer Gridinfrastruktur T2 - GMDS 2008 Y1 - 2008 CY - Stuttgart, Germany ER - TY - CHAP A1 - Costa, Paolo A1 - Pierre, Guillaume A1 - Reinefeld, Alexander A1 - Schütt, Thorsten A1 - van Steen, Maarten T1 - Sloppy Management of Structured P2P Services T2 - Proceedings of the 3$^rd$ International Workshop on Hot Topics in Autonomic Computing (HotAC III), co-located with IEEE ICAC’08 Y1 - 2008 CY - Chicago, IL, USA ER - TY - CHAP A1 - Roy, P. A1 - Haridi, Seif A1 - Reinefeld, Alexander A1 - Stefani, J. B. A1 - Yap, R. A1 - Coupaye, T. T1 - Self Management for Large-Scale Distributed Systems T2 - Formal Methods for Components and Objects 2007 (FMCO 2007) Y1 - 2008 PB - Springer LNCS ER - TY - CHAP A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Scalaris: Reliable Transactional P2P Key/Value T2 - ERLANG '08: Proceedings of the 7th ACM SIGPLAN workshop on ERLANG Y1 - 2008 U6 - https://doi.org/10.1145/1411273.1411280 SP - 41 EP - 47 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Range Queries on structured overlay networks JF - Computer Communications Y1 - 2008 U6 - https://doi.org/10.1016/j.comcom.2007.08.027 VL - 31 IS - 2 SP - 280 EP - 291 PB - Elsevier ER - TY - CHAP A1 - Kondo, Derrick A1 - Andrzejak, Artur A1 - Anderson, David T1 - On Correlated Availability in Internet-Distributed Systems T2 - 9th IEEE/ACM International Conference on Grid Computing (Grid 2008) Y1 - 2008 CY - Tsukuba, Japan ER - TY - CHAP A1 - Shafaat, Tallat A1 - Moser, Monika A1 - Ghodsi, Ali A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - On Consistency of Data in Structured Overlay Networks T2 - Coregrid Integration Workshop Y1 - 2008 ER - TY - CHAP A1 - Shafaat, Tallat A1 - Moser, Monika A1 - Ghodsi, Ali A1 - Schütt, Thorsten A1 - Haridi, Seif A1 - Reinefeld, Alexander T1 - Key-Based Consistency and Availability in Structured Overlay Networks T2 - International ICST Conference on Scalable Information Systems Y1 - 2008 ER - TY - CHAP A1 - Röblitz, Thomas T1 - Global Optimization for Scheduling Multiple Co-Reservations in the Grid T2 - Proceedings of the CoreGRID Symposium 2008 Y1 - 2008 CY - Las Palmas de Gran Canaria, Spain ER - TY - GEN A1 - Andrzejak, Artur A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Mastroianni, Carlo A1 - Fragopoulou, Paraskevi A1 - Kondo, Derrick A1 - Malecot, Paul A1 - Cosmin Silaghi, Gheorghe A1 - Moura Silva, Luis A1 - Trunfio, Paolo A1 - Zeinalipour-Yazti, Demetris A1 - Zimeo, Eugenio T1 - Grid Architectural Issues: State-of-the-art and Future Trends Y1 - 2008 UR - http://coregrid.ercim.eu//mambo/images/stories/WhitePapers/whp-0004.pdf IS - WHP-0004 PB - Institute on Architectural Issues: Scalability, Dependability, Adaptability, CoreGRID - Network of Excellence ER - TY - CHAP A1 - Andrzejak, Artur A1 - Kondo, Derrick A1 - Anderson, David T1 - Ensuring Collective Availability in Volatile Resource Pools via Forecasting T2 - 19th IEEE/IFIP Distributed Systems: Operations and Management (DSOM-2008) Y1 - 2008 SP - 149 EP - 161 CY - Samos Island, Greece ER - TY - CHAP A1 - Sobe, Peter A1 - Peter, Kathrin T1 - Flexible Parameterization of XOR based Codes for Distributed Storage T2 - Proceedings of The Seventh IEEE International Symposium on Networking Computing and Applications, NCA 2008, July 10-12, 2008, Cambridge, Massachusetts, USA Y1 - 2008 U6 - https://doi.org/10.1109/NCA.2008.45 SP - 101 EP - 110 PB - IEEE Computer Society ER - TY - CHAP A1 - Plantikow, Stefan A1 - Högqvist, Mikael T1 - Continous Queries over Federated Social Networks T2 - Fourth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2008) Y1 - 2008 CY - Znojmo, Czech Republic ER - TY - CHAP A1 - Schneider, Jörg A1 - Gehr, Julius A1 - Linnert, Barry A1 - Röblitz, Thomas T1 - An Efficient Protocol for Reserving Multiple Grid Resources in Advance T2 - Proceedings of the 3$^rd$ CoreGRID Workshop on Grid Middleware Y1 - 2008 CY - Barcelona, Spain ER - TY - CHAP A1 - Schütt, Thorsten A1 - Moser, Monika A1 - Plantikow, Stefan A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - A Transactional Scalable Distributed Data Store T2 - 1st IEEE International Scalable Computing Challenge, co-located with CCGrid’08 Y1 - 2008 ER - TY - CHAP A1 - Casanovas, Ada A1 - Alonso, Javier A1 - Torres, Jordi A1 - Andrzejak, Artur T1 - Work in Progress: Building a Distributed Generic Stress Tool for Server Performance and Behavior Analysis T2 - ICAS Y1 - 2009 U6 - https://doi.org/10.1109/ICAS.2009.53 SP - 342 EP - 345 PB - IEEE Computer Society ER - TY - CHAP A1 - Talia, Domenico A1 - Trunfio, Paolo A1 - Zeng, Jingdi A1 - Högqvist, Mikael ED - Gorlatch, Sergei ED - Bubak, Marian ED - Priol, Thierry T1 - A Peer-to-Peer Framework for Resource Discovery in Large-Scale Grids T2 - Achievements in European Research on Grid Systems Y1 - 2008 UR - http://dx.doi.org/10.1007/978-0-387-72812-4_10 U6 - https://doi.org//10.1007/978-0-87-72812-4_10 SP - 123 EP - 137 PB - Springer US ER - TY - CHAP A1 - Dickmann, Frank A1 - Kaspar, Mathias A1 - Löhnhardt, Benjamin A1 - Kepper, Nick A1 - Viezens, Fred A1 - Hertel, Frank A1 - Lesnussa, Michael A1 - Mohammed, Yassene A1 - Thiel, Andreas A1 - Steinke, Thomas A1 - Bernarding, Johannes A1 - Krefting, Dagmar A1 - Knoch, Tobias A1 - Sax, Ulrich T1 - Visualization in Health Grid Environments: A Novel Service and Business Approach T2 - GECON Y1 - 2009 U6 - https://doi.org/10.1007/978-3-642-03864-8_12 VL - 5745 SP - 150 EP - 159 PB - Springer ER - TY - CHAP A1 - Högqvist, Mikael A1 - Plantikow, Stefan T1 - Towards Explicit Data Placement in Scalable Key/Value Stores T2 - Architectures and Languages for Self-Managing Distributed Systems (SelfMan@SASO) Y1 - 2009 ER - TY - JOUR A1 - Gentzsch, Wolfgang A1 - Reinefeld, Alexander T1 - Special Section D-Grid JF - Future Generation Comp. Syst. Y1 - 2009 U6 - https://doi.org/10.1016/j.future.2008.09.008 VL - 25 IS - 3 SP - 266 EP - 267 ER - TY - CHAP A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Hennig, C. T1 - Self-Adaptation in Large-Scale Systems: A Study on Structured Overlays Across Multiple Datacenters T2 - Architectures and Languages for Self-Managing Distributed Systems (SelfMan@SASO) Y1 - 2009 U6 - https://doi.org/10.1109/SASOW.2010.65 ER - TY - CHAP A1 - Lützkendorf, Ralf A1 - Viezens, Fred A1 - Hertel, Frank A1 - Krefting, Dagmar A1 - Peter, Kathrin A1 - Bernarding, Johannes T1 - Performanzsteigerung von Diffusion Tensor Image Analyse durch Nutzung gridbasierter Workflows T2 - GMDS Y1 - 2009 U6 - https://doi.org/10.3205/09gmds196 ER - TY - CHAP A1 - Högqvist, Mikael A1 - Kruber, Nico ED - Spyropoulos, Thrasyvoulos ED - Hummel, Karin T1 - Passive/Active Load Balancing with Informed Node Placement in DHTs T2 - IWSOS Y1 - 2009 U6 - https://doi.org/10.1007/978-3-642-10865-5_9 VL - 5918 SP - 101 EP - 112 PB - Springer ER - TY - CHAP A1 - Reinefeld, Alexander ED - Floudas, Christodoulos ED - Pardalos, Panos T1 - Parallel Heuristic Search T2 - Encyclopedia of Optimization Y1 - 2009 U6 - https://doi.org/10.1007/978-0-387-74759-0_500 SP - 2908 EP - 2912 PB - Springer ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schütt, Thorsten T1 - Out-of-Core Parallel Frontier Search with MapReduce T2 - HPCS Y1 - 2009 U6 - https://doi.org/10.1007/978-3-642-12659-8_24 VL - 5976 SP - 323 EP - 336 PB - Springer ER - TY - JOUR A1 - Krefting, Dagmar A1 - Bart, Julian A1 - Beronov, Kamen A1 - Dzhimova, Olga A1 - Falkner, Jürgen A1 - Hartung, Michael A1 - Hoheisel, Andreas A1 - Knoch, Tobias A1 - Lingner, Thomas A1 - Mohammed, Yassene A1 - Peter, Kathrin A1 - Rahm, Erhard A1 - Sax, Ulrich A1 - Sommerfeld, Dietmar A1 - Steinke, Thomas A1 - Tolxdorff, Thomas A1 - Vossberg, Michael A1 - Viezens, Fred A1 - Weisbecker, Anette T1 - MediGRID: Towards A User Friendly Secured Grid Infrastructure JF - Future Generation Computer Systems (FGCS) Y1 - 2009 U6 - https://doi.org/10.1016/j.future.2008.05.005 VL - 25 IS - 3 SP - 281 EP - 289 ER - TY - CHAP A1 - Andrzejak, Artur A1 - Zeinalipour, Demetris A1 - Dikaiakos, Marios T1 - Improving the Dependability of Grids via Short-Term Failure Predictions T2 - CoreGRID Workshop at EuroPAR 2009 Y1 - 2009 CY - Delft, Netherlands ER - TY - GEN A1 - Reinefeld, Alexander ED - Floudas, Christodoulos ED - Pardalos, Panos T1 - Heuristic Search T2 - Encyclopedia of Optimization Y1 - 2009 U6 - https://doi.org//10.1007/978-0-387-74759-0_263 SP - 1506 EP - 1508 PB - Springer ER - TY - CHAP A1 - Andrzejak, Artur T1 - Generic Self-Healing via Rejuvenation: Challenges, Status Quo, and Solutions T2 - Workshop on Architectures and Languages for Self-Managing Distributed Systems (SelfMan@SASO) Y1 - 2009 CY - San Francisco, California, USA ER - TY - CHAP A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Hoffmann, Marie T1 - Gossip-based Topology Inference for Efficient Overlay Mapping on Data Centers T2 - Peer-to-Peer Computing Y1 - 2009 U6 - https://doi.org/10.1109/P2P.2009.5284553 SP - 147 EP - 150 ER - TY - JOUR A1 - Plantikow, Stefan A1 - Peter, Kathrin A1 - Högqvist, Mikael A1 - Grimme, Christian A1 - Papaspyrou, Alexander T1 - Generalizing the Data Management of Three Community Grids JF - Future Generation Computer Systems (FGCS) Y1 - 2009 U6 - https://doi.org/10.1016/j.future.2008.05.001 VL - 25 IS - 3 SP - 281 EP - 289 ER - TY - JOUR A1 - Bauer, Raphael A1 - Rother, Kristian A1 - Moor, Peter A1 - Reinert, Knut A1 - Steinke, Thomas A1 - Bujnicki, Janusz A1 - Preissner, Robert T1 - Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors JF - Algorithms Y1 - 2009 U6 - https://doi.org/10.3390/a2020692 VL - 2 IS - 2 SP - 692 EP - 709 ER - TY - JOUR A1 - Hupfeld, Felix A1 - Kolbeck, Björn A1 - Stender, Jan A1 - Högqvist, Mikael A1 - Cortes, Toni A1 - Martí, Jonathan A1 - Malo, Jesus T1 - FaTLease: scalable fault-tolerant lease negotiation with Paxos JF - Cluster Computing Y1 - 2009 U6 - https://doi.org/10.1007/s10586-009-0074-2 VL - 12 IS - 2 SP - 175 EP - 188 ER - TY - JOUR A1 - Peter, Kathrin T1 - Distributed Erasure Tolerant Storage with Solid State Technology JF - TCPP Ph.D. Forum, Int. Parallel and Distributed Processing Symposium Y1 - 2009 U6 - https://doi.org/10.1109/IPDPS.2009.5160863 SP - 23 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Stender, Jan T1 - Efficient Management of Consistent Backups in a Distributed File System T2 - COMPSAC (1) Y1 - 2009 U6 - https://doi.org/10.1109/COMPSAC.2009.100 SP - 656 EP - 659 PB - IEEE Computer Society ER - TY - CHAP A1 - Hertel, Frank A1 - Krefting, Dagmar A1 - Lützkendorf, Ralf A1 - Viezens, Fred A1 - Thiel, Andreas A1 - Peter, Kathrin A1 - Bernarding, Johannes T1 - Diffusions-Tensor-Imaging als Gridanwendung - Perfomanzsteigerung und standortunabhängiger Zugang zu leistungsfähigen Ressourcen T2 - GI Jahrestagung’09 Y1 - 2009 SP - 1233 EP - 1240 ER - TY - JOUR A1 - Högqvist, Mikael T1 - Architecture and Self-Tuning of a DISC-system JF - TCPP Ph.D. Forum, Int. Parallel and Distributed Processing Symposium Y1 - 2009 U6 - https://doi.org/10.1109/IPDPS.2009.5160863 SP - 16 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Birkenheuer, Georg A1 - Carlson, Arthur A1 - Fölling, Alexander A1 - Högqvist, Mikael A1 - Hoheisel, Andreas A1 - Papaspyrou, Alexander A1 - Rieger, Klaus A1 - Schott, Bernhard A1 - Ziegler, Wolfgang T1 - Connecting Communities on the Meta-Scheduling Level: The DGSI Approach T2 - Proceedings of the Cracow Grid Workshop (CGW) Y1 - 2009 SP - 96 EP - 103 ER - TY - JOUR A1 - Kolbeck, Björn T1 - A Protocol for Efficient and Fault-tolerant File Replication over Wide-Area Networks JF - TCPP Ph.D. Forum, Int. Parallel and Distributed Processing Symposium Y1 - 2009 U6 - https://doi.org/10.1109/IPDPS.2009.5160863 VL - 0 SP - 19 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Haridi, Seif ED - Tselentis, G. ED - Domingue, J. ED - Galis, A. ED - Gavras, A. ED - Hausheer, D. ED - Krco, S. ED - Lotz, V. ED - Zahariadis, T. T1 - A Scalable, Transactional Data Store for Future Internet Services T2 - Towards the Future Internet - A European Research Perspective Y1 - 2009 U6 - https://doi.org/10.3233/978-1-60750-007-0-148 SP - 148 EP - 159 PB - IOS Press ER - TY - CHAP A1 - Reinefeld, Alexander A1 - Schütt, Thorsten A1 - Döbbelin, Robert ED - Hariri, Salim ED - Keahey, Kate T1 - Very large pattern databases for heuristic search T2 - HPDC Y1 - 2010 U6 - https://doi.org/10.1145/1851476.1851592 SP - 803 EP - 809 PB - ACM ER - TY - GEN A1 - Van Roy, P. A1 - Haridi, Seif A1 - Reinefeld, Alexander A1 - Stefani, J. B. T1 - The Clouds of Revolution Y1 - 2010 PB - Public Service Review 19, pp. 449 ER - TY - CHAP A1 - Geibig, Joanna A1 - Bradler, Dirk T1 - Self-organized aggregation in irregular wireless networks T2 - Proceedings of the 3rd IFIP Wireless Days Conference 2010 Y1 - 2010 U6 - https://doi.org/10.1109/WD.2010.5657705 SP - 1 EP - 7 PB - IEEE Computer Society ER - TY - CHAP A1 - Yi, Sangho A1 - Kondo, Derrick A1 - Andrzejak, Artur T1 - Reducing Costs of Spot Instances via Checkpointing in the Amazon Elastic Compute Cloud T2 - Cloud Computing (CLOUD), 2010 IEEE 3rd International Conference on Y1 - 2010 U6 - https://doi.org/10.1109/CLOUD.2010.35 SP - 236 EP - 243 ER - TY - THES A1 - Schütt, Thorsten T1 - Range queries in distributed hash tables Y1 - 2010 UR - http://www.dr.hut-verlag.de/978-3-86853-370-5.html ER - TY - JOUR A1 - Schwiegelshohn, Uwe A1 - Badia, Rosa M. A1 - Bubak, Marian A1 - Danelutto, Marco A1 - Dustdar, Schahram A1 - Gagliardi, Fabrizio A1 - Geiger, Alfred A1 - Hluchy, Ladislav A1 - Kranzlmüller, Dieter A1 - Laure, Erwin A1 - Reinefeld, Alexander A1 - Resch, Michael A1 - Reuter, Andreas A1 - Rienhoff, Otto A1 - Rüter, Thomas A1 - Sloot, Peter A1 - Talia, Domenico A1 - Ullmann, Klaus A1 - Yahyapour, Ramin A1 - von Voigt, Gabriele T1 - Perspectives on Grid Computing JF - Future Generation Computer Systems Y1 - 2010 U6 - https://doi.org/10.1016/j.future.2010.05.010 VL - 26 IS - 8 SP - 1104 EP - 1115 ER - TY - CHAP A1 - Krefting, Dagmar A1 - Lützkendorf, Ralf A1 - Peter, Kathrin A1 - Bernarding, Johannes T1 - Performance Analysis of Diffusion Tensor Imaging in an Academic Production Grid T2 - CCGRID Y1 - 2010 U6 - https://doi.org/10.1109/CCGRID.2010.21 SP - 751 EP - 756 PB - IEEE Computer Socienty ER - TY - JOUR A1 - May, Patrick A1 - Kreuchwig, A. A1 - Steinke, Thomas A1 - Koch, Ina T1 - PTGL: a database for secondary structure-based protein topologies JF - Nucleic Acids Res. Y1 - 2010 VL - 38 SP - D326 EP - 330 ER - TY - CHAP A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Kruber, Nico A1 - Lang, U. A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - Molecular Simulation Grid T2 - 6. German Conference on Chemoinformatics Y1 - 2010 PB - Gesellschaft Deutscher Chemiker (GDCh) ER - TY - GEN A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - d. Santos Vieira, I. A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Kruber, Nico A1 - Krüger, Jens A1 - Lang, U. A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid – A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science T2 - 6. German Conference on Chemoinformatics Y1 - 2010 N1 - Free software session and poster ER - TY - THES A1 - Schintke, Florian T1 - Management verteilter Daten in Grid- und Peer-to-Peer-Systemen Y1 - 2010 UR - http://www.dr.hut-verlag.de/978-3-86853-358-3.html ER - TY - CHAP A1 - Stender, Jan A1 - Högqvist, Mikael A1 - Kolbeck, Björn T1 - Loosely Time-Synchronized Snapshots in Object-Based File Systems T2 - Proceedings of the 29th IEEE International Performance, Computing, and Communications Conference Y1 - 2010 U6 - https://doi.org/10.1109/PCCC.2010.5682311 PB - IEEE Computer Society ER - TY - CHAP A1 - Andrzejak, Artur A1 - Kondo, Derrick A1 - Anderson, David T1 - Exploiting non-dedicated resources for cloud computing T2 - 12th IEEE/IFIP Network Operations & Management Symposium (NOMS 2010) Y1 - 2010 U6 - https://doi.org/10.1109/NOMS.2010.5488488 SP - 341 EP - 348 CY - Osaka, Japan ER - TY - CHAP A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Haridi, Seif A1 - Schütt, Thorsten T1 - Enhanced Paxos Commit for Transactions on DHTs T2 - CCGRID Y1 - 2010 U6 - https://doi.org/10.1109/CCGRID.2010.41 SP - 448 EP - 454 PB - IEEE ER - TY - CHAP A1 - Steinke, Thomas A1 - Peter, Kathrin A1 - Borchert, Sebastian T1 - Efficiency Considerations of Cauchy Reed-Solomon Implementations on Accelerator and Multi-Core Platforms T2 - Symposium on Application Accelerators in High Performance Computing (SAAHPC) Y1 - 2010 UR - http://saahpc.ncsa.illinois.edu/10/papers/paper_12.pdf CY - Knoxville, USA ER - TY - CHAP A1 - Andrzejak, Artur A1 - Kondo, Derrick A1 - Yi, Sangho T1 - Decision Model for Cloud Computing under SLA Constraints T2 - Modeling, Analysis & Simulation of Computer and Telecommunication Systems (MASCOTS), 2010 IEEE International Symposium on Y1 - 2010 U6 - https://doi.org/10.1109/MASCOTS.2010.34 SP - 257 EP - 266 PB - IEEE ER - TY - CHAP A1 - Böse, Joos-Hendrik A1 - Andrzejak, Artur A1 - Högqvist, Mikael T1 - Beyond online aggregation: Parallel and incremental data mining with online Map-Reduce T2 - Proceedings of the 2010 Workshop on Massive Data Analytics on the Cloud Y1 - 2010 U6 - https://doi.org/10.1145/1779599.1779602 SP - 3:1 EP - 3:6 PB - ACM CY - New York, NY, USA ER - TY - JOUR A1 - Schmidt-Goenner, T. A1 - Guerler, A. A1 - Kolbeck, Björn A1 - Knapp, E. T1 - Circular permuted proteins in the universe of protein folds JF - Proteins Y1 - 2010 U6 - https://doi.org/10.1002/prot.22678 VL - 78 SP - 1618 EP - 1630 ER - TY - CHAP A1 - Stender, Jan A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Hupfeld, Felix T1 - BabuDB: Fast and Efficient File System Metadata Storage T2 - Storage Network Architecture and Parallel I/Os, IEEE International Workshop on Y1 - 2010 U6 - https://doi.org/10.1109/SNAPI.2010.14 SP - 51 EP - 58 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Kruber, Nico A1 - Högqvist, Mikael A1 - Schütt, Thorsten T1 - The Benefits of Estimated Global Information in DHT Load Balancing JF - Cluster Computing and the Grid, IEEE International Symposium on Y1 - 2011 U6 - https://doi.org/10.1109/CCGrid.2011.11 VL - 0 SP - 382 EP - 391 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Dickmann, Frank A1 - Falkner, Jürgen A1 - Gunia, Wilfried A1 - Hampe, Jochen A1 - Hausmann, Michael A1 - Herrmann, Alexander A1 - Kepper, Nick A1 - Knoch, Tobias A1 - Lauterbach, Svenja A1 - Lippert, Jörg A1 - Peter, Kathrin A1 - Schmitt, Eberhard A1 - Schwardmann, Ulrich A1 - Solodenko, Juri A1 - Sommerfeld, Dietmar A1 - Steinke, Thomas A1 - Weisbecker, Anette A1 - Sax, Ulrich T1 - Solutions for biomedical grid computing – Case studies from the D-Grid project Services@MediGRID JF - Journal of Computational Science Y1 - 2011 UR - http://www.sciencedirect.com/science/article/pii/S1877750311000603 U6 - https://doi.org/10.1016/j.jocs.2011.06.006 VL - - IS - 0 ER - TY - CHAP A1 - Peter, Kathrin T1 - Reliability Study of Coding Schemes for Wide-Area Distributed Storage Systems T2 - PDP 2011: The 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing Y1 - 2011 U6 - https://doi.org/10.1109/PDP.2011.70 PB - Euromicro ER - TY - CHAP A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Proc. of Grid Workflow Workshop 2011, Cologne, Germany Y1 - 2011 UR - http://CEUR-WS.org/Vol-826/paper02.pdf VL - 826 PB - CEUR Workshop Proceedings ER - TY - CHAP A1 - Plantikow, Stefan A1 - Jorra, Maik ED - Xu, Jianliang ED - Yu, Ge ED - Zhou, Shuigeng ED - Unland, Rainer T1 - Latency-Optimal Walks in Replicated and Partitioned Graphs T2 - Database Systems for Adanced Applications Y1 - 2011 UR - http://dx.doi.org/10.1007/978-3-642-20244-5{\_}3 U6 - https://doi.org/10.1007/978-3-642-20244-5_3 VL - 6637 SP - 14 EP - 27 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Chabarek, F. A1 - Golas, Ulrike ED - Heiß, H.-U. ED - Pepper, P. ED - Schlingloff, H. ED - Schneider, Jörg T1 - Interaktive Vervollständigung der Szenariobasierten Spezifikation eines Parkassistenzsystems T2 - Proceedings of GI-ASE 2011 Y1 - 2011 ER - TY - CHAP A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Balasko, Akos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Herres-Pawlis, Sonja A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver T1 - Granular Security for a Science Gateway in Structural Bioinformatics T2 - Proc. IWSG-Life 2011 Y1 - 2011 ER - TY - JOUR A1 - Golas, Ulrike A1 - Ehrig, Hartmut A1 - Hermann, Frank T1 - Formal Specification of Model Transformations by Triple Graph Grammars with Application Conditions JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/646 VL - 39 SP - 1 EP - 26 ER - TY - JOUR A1 - Golas, Ulrike A1 - Hoffmann, Kathrin A1 - Ehrig, Hartmut A1 - Rein, A. A1 - Padberg, J. T1 - Functorial Analysis of Algebraic Higher-Order Net Systems with Applications to Mobile Ad-Hoc Networks JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/631 VL - 40 SP - 1 EP - 20 ER - TY - JOUR A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Stender, Jan A1 - Hupfeld, Felix T1 - Flease - Lease Coordination Without a Lock Server JF - Parallel and Distributed Processing Symposium, International Y1 - 2011 U6 - https://doi.org/10.1109/IPDPS.2011.94 VL - 0 SP - 978 EP - 988 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Enke, Harry A1 - Steinmetz, Matthias A1 - Adorf, Hans-Martin A1 - Beck-Ratzka, Alexander A1 - Breitling, Frank A1 - Brüsemeister, Thomas A1 - Carlson, Arthur A1 - Ensslin, Torsten A1 - Högqvist, Mikael A1 - Nickelt, Iliya A1 - Radke, Thomas A1 - Reinefeld, Alexander A1 - Reiser, Angelika A1 - Scholl, Tobias A1 - Spurzem, Rainer A1 - Steinacker, Jürgen A1 - Voges, Wolfgang A1 - Wambsganß, Joachim A1 - White, Steve T1 - AstroGrid-D: Grid technology for astronomical science JF - New Astronomy Y1 - 2011 UR - http://www.sciencedirect.com/science/article/pii/S1384107610000837 U6 - https://doi.org/10.1016/j.newast.2010.07.005 VL - 16 IS - 2 SP - 79 EP - 93 ER - TY - JOUR A1 - Golas, Ulrike A1 - Biermann, E. A1 - Ehrig, Hartmut A1 - Ermel, Claudia T1 - A Visual Interpreter Semantics for Statecharts Based on Amalgamated Graph Transformation JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/645 VL - 39 SP - 1 EP - 24 ER - TY - CHAP A1 - Gesing, Sandra A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Krüger, Jens A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin A1 - Kohlbacher, Oliver T1 - A Science Gateway for Molecular Simulations T2 - EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts Y1 - 2011 SP - 94 EP - 95 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science JF - Journal of Cheminformatics 2011 Y1 - 2011 UR - http://www.jcheminf.com/content/3/S1/P14 U6 - https://doi.org/10.1186/1758-2946-3-S1-P14 VL - 3 IS - Suppl 1 ER - TY - CHAP A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, Andre A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - The MoSGrid Community – From National to International Scale T2 - EGI Community Forum 2012 Y1 - 2012 ER - TY - JOUR A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Orejas, Fernando T1 - Attributed Graph Transformation with Inheritance JF - Theoretical Computer Science Y1 - 2012 U6 - https://doi.org/10.1016/j.tcs.2012.01.032 VL - 424 SP - 46 EP - 68 ER - TY - CHAP A1 - Soboll, T. A1 - Golas, Ulrike ED - Filipe, J. ED - Fred, A. T1 - A Local-Global Model for Multiagent Systems - Sheaves on the Category MAS T2 - Proceedings of ICAART 2012 Y1 - 2012 VL - 2 SP - 331 EP - 334 PB - SciTePress ER - TY - CHAP A1 - Kindermann, S. A1 - Schintke, Florian A1 - Fritzsch, B. T1 - A Collaborative Data Management Infrastructure for Climate Data Analysis T2 - Geophysical Research Abstracts Y1 - 2012 UR - http://meetingorganizer.copernicus.org/EGU2012/EGU2012-10569.pdf U6 - https://doi.org/10013/epic.39635.d001 VL - 14, EGU2012-10569 ER - TY - CHAP A1 - Schäfer, Patrick A1 - Högqvist, Mikael T1 - SFA : a symbolic fourier approximation and index for similarity search in high dimensional datasets T2 - Proceedings of the 15th International Conference on Extending Database Technology Y1 - 2012 UR - http://doi.acm.org/10.1145/2247596.2247656 U6 - https://doi.org/10.1145/2247596.2247656 SP - 516 EP - 527 PB - ACM CY - New York, NY, USA ER - TY - GEN ED - Golas, Ulrike ED - Soboll, T. T1 - Proceedings of ACCAT 2012 T2 - Electronic Proceedings in Theoretical Computer Science 93 Y1 - 2012 U6 - https://doi.org/10.4204/EPTCS.93 ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 2 JF - Fundamenta Informaticae Y1 - 2012 U6 - https://doi.org/10.3233/FI-2012-705 VL - 118 IS - 1-2 SP - 35 EP - 63 ER - TY - JOUR A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - Energy consumption of CUDA kernels with varying thread topology JF - Computer Science - Research and Development Y1 - 2012 UR - http://dx.doi.org/10.1007/s00450-012-0230-4 U6 - https://doi.org/10.1007/s00450-012-0230-4 SP - 1 EP - 9 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - An Analysis of SMP Memory Allocators T2 - Proceedings of the 41st International Conference on Parallel Processing Workshops (Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2)) Y1 - 2012 U6 - https://doi.org/10.1109/ICPPW.2012.10 SP - 48 EP - 54 PB - IEEE Computer Society ER - TY - CHAP A1 - Heckel, R. A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Hermann, Frank ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Parallelism and Concurrency of Stochastic Graph Transformations T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_7 VL - 7562 SP - 96 EP - 110 PB - Springer ER - TY - CHAP A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Giese, H. ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Towards Bridging the Gap between Formal Foundations and Current Practice for Triple Graph Grammars - Flexible Relations between Source and Target Elements T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_10 VL - 7562 SP - 141 EP - 155 PB - Springer ER - TY - CHAP A1 - Golas, Ulrike ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - A General Attribution Concept for Models in M-Adhesive Transformation Systems T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_13 VL - 7562 SP - 187 EP - 202 PB - Springer ER - TY - JOUR A1 - Enke, Harry A1 - Partl, Adrian A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Handling Big Data in Astronomy and Astrophysics JF - Datenbank-Spektrum Y1 - 2012 UR - http://dx.doi.org/10.1007/s13222-012-0099-1 U6 - https://doi.org/10.1007/s13222-012-0099-1 VL - 12 IS - 3 SP - 173 EP - 181 PB - Springer-Verlag ER - TY - CHAP A1 - Grunzke, Richard A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Kruse, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Steinke, Thomas A1 - Zink, Andreas T1 - A Data Driven Science Gateway for Computational Workflows T2 - Proceedings of the UNICORE Summit Y1 - 2012 CY - Dresden, Germany ER - TY - JOUR A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Wewior, Martin A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Herres-Pawlis, Sonja A1 - Breuers, Sebastian A1 - Balasko, Akos A1 - Kozlovszky, Miklos A1 - Szikszay Fabri, Anna A1 - Packschies, Lars A1 - Kacsuk, Peter A1 - Blunk, Dirk A1 - Steinke, Thomas A1 - Brinkmann, André A1 - Fels, Gregor A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Kohlbacher, Oliver T1 - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics JF - Journal of Grid Computing Y1 - 2012 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment JF - Journal of Cheminformatics Y1 - 2012 UR - http://www.jcheminf.com/content/4/S1/P21 U6 - https://doi.org/10.1186/1758-2946-4-S1-P21 VL - 4 IS - Suppl 1 SP - 21 ER - TY - CHAP A1 - Peter, Kathrin A1 - Sobe, Peter T1 - Application of Regenerating Codes for Fault Tolerance in Distributed Storage Systems T2 - Network Computing and Applications (NCA), 2012 11th IEEE International Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/NCA.2012.35 SP - 67 EP - 70 ER - TY - JOUR A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - A Science Gateway Getting Ready for Serving the International Molecular Simulation Community JF - Proceedings of Science Y1 - 2012 UR - http://pos.sissa.it/archive/conferences/162/050/EGICF12-EMITC2_050.pdf VL - PoS(EGICF12-EMITC2)050 ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering T2 - Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/SAAHPC.2012.12 SP - 74 EP - 83 ER - TY - CHAP A1 - Peter, Kathrin A1 - Reinefeld, Alexander T1 - Consistency and fault tolerance for erasure-coded distributed storage systems T2 - Proceedings of the fifth international workshop on Data-Intensive Distributed Computing Date Y1 - 2012 UR - http://doi.acm.org/10.1145/2286996.2287002 U6 - https://doi.org/10.1145/2286996.2287002 SP - 23 EP - 32 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Flik, T. A1 - Reinefeld, Alexander ED - Czichos, Horst ED - Hennecke, Manfred T1 - Rechnerorganisation T2 - Hütte – Das Ingenieurwissen Y1 - 2012 SP - J6 EP - J124 PB - Springer-Verlag Berlin ET - 34 ER - TY - THES A1 - Högqvist, Mikael T1 - Consistent Key-Based Routing in Decentralized and Reconfigurable Data Services Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:11-100206145 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=39763 ER - TY - THES A1 - Kolbeck, Björn T1 - A fault-tolerant and scalable protocol for replication in distributed file systems Y1 - 2012 ER - TY - CHAP A1 - Enke, Harry A1 - Fiedler, Norman A1 - Fischer, Thomas A1 - Gnadt, Timo A1 - Ketzan, Erik A1 - Ludwig, Jens A1 - Rathmann, Torsten A1 - Stöckle, Gabriel A1 - Schintke, Florian ED - Enke, Harry ED - Ludwig, Jens T1 - Leitfaden zum Forschungsdaten-Management T2 - Leitfaden zum Forschungsdaten-Management Y1 - 2013 PB - Verlag Werner Hülsbusch, Glückstadt ER - TY - JOUR A1 - Berlin, Michael T1 - Consistent and Partition-Tolerant File Replication in the Cloud File System Xtreem FS JF - Praxis der Informationsverarbeitung und Kommunikation Y1 - 2013 UR - http://dx.doi.org/10.1515/pik-2012-0144 U6 - https://doi.org/10.1515/pik-2012-0144 VL - 36 IS - 1 SP - 39 ER - TY - CHAP A1 - Orejas, Fernando A1 - Boronat, Artur A1 - Golas, Ulrike A1 - Mylonakis, Nikos ED - Pfenning, Frank T1 - Checking Bisimilarity for Attributed Graph Transformation T2 - Foundations of Software Science and Computation Structures. Proceedings of FOSSACS 2013 Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-37075-5_8 VL - 7794 SP - 113 EP - 128 PB - Springer ER - TY - JOUR A1 - Schintke, Florian T1 - XtreemFS & Scalaris JF - Science & Technology Y1 - 2013 IS - 6 SP - 54 EP - 55 PB - Pan European Networks ER - TY - THES A1 - Sobe, Kathrin T1 - Consistency and Fault Tolerance of Distributed Storage Systems Y1 - 2013 UR - http://www.epubli.de/shop/buch/Consistency-and-Fault-Tolerance-of-Distributed-Storage-Systems-Kathrin-Sobe-9783844258899/27831 ER - TY - THES A1 - Stender, Jan T1 - Snapshots in Large-Scale Distributed File Systems Y1 - 2013 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=39839 ER - TY - CHAP A1 - Stender, Jan A1 - Berlin, Michael A1 - Reinefeld, Alexander ED - Kyriazis, D. ED - Voulodimos, A. ED - Gogouvitis, S. ED - Varvarigou, Theodora A. T1 - XtreemFS – a File System for the Cloud T2 - Data Intensive Storage Services for Cloud Environments Y1 - 2013 UR - http://dx.doi.org/10.4018/978-1-4666-3934-8 U6 - https://doi.org/10.4018/978-1-4666-3934-8 PB - IGI Global ER - TY - JOUR A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Döbbelin, Robert T1 - MR-search: massively parallel heuristic search JF - Concurrency and Computation: Practice and Experience Y1 - 2011 U6 - https://doi.org/10.1002/cpe.1833 VL - 25 IS - 1 SP - 40 EP - 54 ER - TY - CHAP A1 - Schütt, Thorsten A1 - Döbbelin, Robert A1 - Reinefeld, Alexander T1 - Forward Perimeter Search with Controlled Use of Memory T2 - International Joint Conference on Artificial Intelligence, IJCAI-13, Beijing Y1 - 2013 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - Automated Analysis of Complex Data Objects T2 - 28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013 Y1 - 2013 N1 - Posterbeitrag ER - TY - CHAP A1 - Ries, F. A1 - Ditze, M. A1 - Piater, A. A1 - Singer, E. A1 - Fäßler, V. A1 - Dreßler, Sebastian A1 - Soddemann, T. T1 - Tool-Supported Integration of Hardware Acceleration in Automotive CFD-Simulations T2 - NAFEMS 2013 Proceedings Y1 - 2013 ER - TY - CHAP A1 - Schäfer, Patrick A1 - Dreßler, Sebastian T1 - Shooting Audio Recordings of Insects with SFA T2 - AmiBio Workshop, Bonn, Germany Y1 - 2013 ER - TY - CHAP A1 - Orlowski, Sebastian A1 - Werner, Axel A1 - Wessäly, Roland ED - Klatte, Diethart ED - Lüthi, Hans-Jakob ED - Schmedders, Karl T1 - Estimating trenching costs in FTTx network planning T2 - Operations Research Proceedings 2011 Y1 - 2012 SP - 89 EP - 94 PB - Springer Verlag ER - TY - JOUR A1 - Werner, Axel T1 - Kombinatorische Optimierung und die 40-Punkte-Regel JF - Mitteilungen der DMV Y1 - 2011 VL - 19 SP - 153 EP - 157 ER - TY - JOUR A1 - Werner, Axel A1 - Wotzlaw, Ronald T1 - On linkages in polytope graphs JF - Adv. Geom. Y1 - 2011 U6 - https://doi.org/10.1515/ADVGEOM.2011.015 VL - 11 IS - 3 SP - 411 EP - 427 ER - TY - CHAP A1 - Bentz, Winfried A1 - Eckel, Klaus A1 - Louchet, Hadrien A1 - Orlowski, Sebastian A1 - Patzak, Erwin A1 - Seibel, Julia A1 - Werner, Axel A1 - Wessäly, Roland T1 - Schätze heben bei der Planung von FTTx-Netzen T2 - Breitbandversorgung in Deutschland Y1 - 2011 VL - 227 PB - VDE-Verlag ER - TY - CHAP A1 - Bentz, Winfried A1 - Martens, Maren A1 - Orlowski, Sebastian A1 - Werner, Axel A1 - Wessäly, Roland T1 - FTTx-PLAN T2 - Breitbandversorgung in Deutschland Y1 - 2010 VL - 220 PB - VDE-Verlag ER - TY - THES A1 - Werner, Axel T1 - Linear constraints on face numbers of polytopes Y1 - 2009 UR - http://opus.kobv.de/tuberlin/volltexte/2009/2263 ER - TY - JOUR A1 - Sanyal, Raman A1 - Werner, Axel A1 - Ziegler, Günter T1 - On Kalai’s conjectures concerning centrally symmetric polytopes. JF - Discrete Comput. Geom. Y1 - 2009 U6 - https://doi.org/10.1007/s00454-008-9104-8 VL - 41 IS - 2 SP - 183 EP - 198 ER - TY - JOUR A1 - Paffenholz, Andreas A1 - Werner, Axel T1 - Constructions for 4-polytopes and the cone of flag vectors. JF - Contemporary Mathematics Y1 - 2006 VL - 423 SP - 283 EP - 303 PB - Algebraic and geometric combinatorics. Euroconference in mathematics, algebraic and geometric combinatorics, Anogia, Crete, Greece, August 20–26, 2005. Providence, RI: American Mathematical Society (AMS) ER - TY - GEN A1 - Werner, Axel T1 - Smallest non-trivial 2s2s-polytope Y1 - 2005 UR - http://www.eg-models.de/2005.12.001 PB - EG Model, online ER - TY - CHAP A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - Improved destination call elevator control algorithms for up peak traffic T2 - Operations Research Proceedings 2010 Y1 - 2010 PB - Springer ER - TY - CHAP A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - Improving the performance of elevator systems using exact reoptimization algorithms T2 - Proceedings of MAPSP Y1 - 2009 UR - http://opus.kobv.de/zib/volltexte/2009/1161/ SP - 224 EP - 226 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Krumke, Sven A1 - Saliba, Sleman A1 - Tuchscherer, Andreas T1 - Randomized Online Algorithms for Dynamic Multi-Period Routing Problems T2 - Proceedings of MAPSP Y1 - 2009 SP - 71 EP - 73 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Tuchscherer, Andreas ED - Kalcsics, Jörg ED - Nickel, Stefan T1 - Real-Time Destination-Call Elevator Group Control on Embedded Microcontrollers T2 - Operations Research Proceedings Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2007/1025/ SP - 357 EP - 362 PB - Springer ER - TY - JOUR A1 - Heinz, Stefan A1 - Kaibel, Volker A1 - Peinhardt, Matthias A1 - Rambau, Jörg A1 - Tuchscherer, Andreas T1 - LP-Based Local Approximation for Markov Decision Problems Y1 - 2006 IS - 343 PB - Matheon ER - TY - CHAP A1 - Tuchscherer, Andreas ED - Fleuren, Hein ED - den Hertog, Dick ED - Kort, Peter T1 - Dynamical configuration of transparent optical telecommunication networks T2 - Operations Research Proceedings Y1 - 2004 SP - 25 EP - 32 PB - Springer ER - TY - CHAP A1 - Heinz, Stefan A1 - Krumke, Sven A1 - Megow, Nicole A1 - Rambau, Jörg A1 - Tuchscherer, Andreas A1 - Vredeveld, Tjark ED - Erlebach, Thomas ED - Persiano, Giuseppe T1 - The Online Target Date Assignment Problem T2 - Proc. 3rd Workshop on Approximation and Online Algorithms Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2005/894/ VL - 3879 SP - 230 EP - 243 PB - Springer ER - TY - CHAP A1 - Hülsermann, Ralf A1 - Jäger, Monika A1 - Poensgen, Diana A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Tuchscherer, Andreas ED - Cinkler, Tibor ED - Jakab, Tivadar ED - Tapolcai, Jànos ED - Gàspàr, Csaba T1 - Dynamic routing algorithms in transparent optical networks T2 - Proceedings of the 7th IFIP Working Conference on Optical Network Design & Modelling (ONDM 2003) Y1 - 2003 UR - http://opus.kobv.de/zib/volltexte/2002/703/ SP - 293 EP - 312 PB - Kluwer Academic Press ER - TY - JOUR A1 - Hartvigsen, D. A1 - Hell, P. A1 - Szabó, Jácint T1 - The k-piece packing problem JF - Journal of Graph Theory Y1 - 2006 VL - 52 IS - 4 SP - 267 EP - 293 PB - John Wiley & Sons ER - TY - JOUR A1 - Janata, M. A1 - Szabó, Jácint T1 - The superstar packing problem JF - Combinatorica Y1 - 2009 VL - 29 IS - 1 SP - 27 EP - 48 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Upgrading edge-disjoint paths in a ring JF - Discrete Optimization Y1 - 2010 PB - Elsevier BV ER - TY - JOUR A1 - Janata, M. A1 - Loebl, M. A1 - Szabó, Jácint T1 - A Gallai-Edmonds type theorem for the k-piece packing problem JF - Electron. J. Combin Y1 - 2005 VL - 12 SP - 1 ER - TY - JOUR A1 - Szabó, Jácint T1 - Good characterizations for some degree constrained subgraphs JF - Journal of Combinatorial Theory, Series B Y1 - 2009 VL - 99 IS - 2 SP - 436 EP - 446 PB - Elsevier ER - TY - JOUR A1 - Szabó, Jácint T1 - Packing Trees with Constraints on the Leaf Degree JF - Graphs and Combinatorics Y1 - 2008 VL - 24 IS - 5 SP - 485 EP - 494 PB - Springer ER - TY - JOUR A1 - Király, Z. A1 - Szabó, Jácint T1 - Induced graph packing problems JF - Graphs and Combinatorics Y1 - 2010 VL - 26 IS - 2 SP - 243 EP - 257 PB - Springer ER - TY - JOUR A1 - Makai, M. A1 - Szabó, Jácint T1 - The parity problem of polymatroids without double circuits JF - Combinatorica Y1 - 2008 VL - 28 IS - 6 SP - 679 EP - 692 PB - Springer ER - TY - JOUR A1 - Király, T. A1 - Szabó, Jácint T1 - A note on parity constrained orientations JF - Combinatorica Y1 - 2009 VL - 29 IS - 5 SP - 619 EP - 628 PB - Springer ER - TY - JOUR A1 - Makai, M. A1 - Pap, G. A1 - Szabó, Jácint T1 - Matching problems in polymatroids without double circuits JF - Integer Programming and Combinatorial Optimization Y1 - 2007 SP - 167 EP - 181 PB - Springer ER - TY - JOUR A1 - Recski, A. A1 - Szabó, Jácint T1 - On the generalization of the matroid parity problem JF - Graph Theory in Paris Y1 - 2007 SP - 347 EP - 354 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Matroid parity and jump systems JF - SIAM Journal on Discrete Mathematics Y1 - 2008 VL - 22 SP - 854 ER - TY - JOUR A1 - Frank, A. A1 - Chi Lau, L. A1 - Szabó, Jácint T1 - A note on degree-constrained subgraphs JF - Discrete Mathematics Y1 - 2008 VL - 308 IS - 12 SP - 2647 EP - 2648 PB - Elsevier ER - TY - JOUR A1 - Bíró, István A1 - Szabó, Jácint T1 - Latent Dirichlet Allocation for Automatic Document Categorization JF - Machine Learning and Knowledge Discovery in Databases Y1 - 2009 SP - 430 EP - 441 PB - Springer ER - TY - CHAP A1 - Liebchen, Christian A1 - Swarat, Elmar ED - Fischetti, Matteo ED - Widmayer, Peter T1 - The Second Chvatal Closure Can Yield Better Railway Timetables T2 - ATMOS 2008 - 8th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0030-drops-15802 UR - http://drops.dagstuhl.de/opus/volltexte/2008/1580 PB - Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany CY - Dagstuhl, Germany ER - TY - GEN A1 - Stephan, Rüdiger T1 - An extension of disjunctive programming and its impact for compact tree formulations Y1 - 2010 PB - Center for Operations Research and Econometrics, Université catholique de Louvain, Discussion paper 2010/45 ER - TY - THES A1 - Stephan, Rüdiger T1 - Polyhedral aspects of cardinality constrained combinatorial optimization problems Y1 - 2009 ER - TY - JOUR A1 - Stephan, Rüdiger A1 - Spiegelberg, Ingo T1 - On cardinality constrained polymatroids JF - Electronic Notes in Discrete Mathematics Y1 - 2010 UR - http://www.sciencedirect.com/science/article/B75GV-50JJF7F-4K/2/2761e6edfcb262af0ba4856767d82a42 U6 - https://doi.org/DOI: 10.1016/j.endm.2010.05.129 VL - 36 SP - 1017 EP - 1024 ER - TY - JOUR A1 - Stephan, Rüdiger T1 - Cardinality constrained combinatorial optimization JF - Discrete Optim. Y1 - 2010 VL - 7 IS - 3 SP - 99 EP - 113 ER - TY - JOUR A1 - Stephan, Rüdiger T1 - Facets of the (s,t)-p-path polytope JF - Discrete Appl. Math. Y1 - 2009 U6 - https://doi.org/10.1016/j.dam.2009.06.003 VL - 157 IS - 14 SP - 3119 EP - 3132 ER - TY - GEN A1 - Maurras, Jean A1 - Stephan, Rüdiger T1 - On the cardinality constrained matroid polytope Y1 - 2009 ER - TY - BOOK A1 - Stephan, Rüdiger T1 - Polytopes associated with length restricted directed circuits Y1 - 2005 PB - diploma thesis, Technische Universität Berlin ER - TY - JOUR A1 - Kaibel, Volker A1 - Stephan, Rüdiger T1 - On cardinality constrained cycle and path polytopes JF - Math. Program. Y1 - 2010 U6 - https://doi.org/10.1007/s10107-008-0257-2 VL - 123 IS - 2 (A) SP - 371 EP - 394 ER - TY - JOUR A1 - Balas, Egon A1 - Stephan, Rüdiger T1 - On the cycle polytope of a directed graph and its relaxations JF - Networks Y1 - 2009 U6 - https://doi.org/10.1002/net.20303 VL - 54 IS - 1 SP - 47 EP - 55 ER - TY - CHAP A1 - Schlechte, Thomas A1 - Tanner, Andreas T1 - Railway capacity auctions with dual prices T2 - Selected Proceedings of the 12th World Conference on Transport Research Y1 - 2010 UR - http://opus.kobv.de/zib/volltexte/2010/1233/ ER - TY - CHAP A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Gross, James A1 - Puñal, Oscar A1 - Schweiger, Jonas T1 - A Two-Stage Approach to WLAN Planning T2 - Proc. of the 8th International Symposium on Modeling and Optimization in Mobile, Ad Hoc, and Wireless Networks (WiOpt’10) Y1 - 2010 SP - 232 EP - 241 CY - Avignon, France ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimizing the Simplon railway corridor JF - Annals of Operations Research Y1 - 2012 UR - http://dx.doi.org/10.1007/s10479-012-1260-9 U6 - https://doi.org/10.1007/s10479-012-1260-9 VL - 218 IS - 1 SP - 93 EP - 106 PB - Springer US ET - Annals of Operations Research ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Schlechte, Thomas ED - Hansen, I. ED - Wendler, E. ED - Weidmann, U. ED - Lüthi, M. ED - Rodriguez, J. ED - Ricci, S. ED - Kroon, Leo T1 - Optimization of macroscopic train schedules via TS-OPT T2 - Proceedings of the 3rd International Seminar on Railway Operations Modelling and Analysis - Engineering and Optimisation Approaches Y1 - 2009 CY - Zürich, Switzerland ER - TY - CHAP A1 - Erol, Berkan A1 - Klemenz, Marc A1 - Schlechte, Thomas A1 - Schultz, Sören A1 - Tanner, Andreas ED - Tomii, A. ED - Allan, J. ED - Arias, E. ED - Brebbia, C. ED - Goodman, C. ED - Rumsey, A. ED - Sciutto, G. T1 - TTPlib 2008 - A Library for Train Timetabling Problems T2 - Computers in Railways XI Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2008/1102/ PB - WIT Press ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schlechte, Thomas ED - Ehrgott, Matthias ED - Naujoks, Boris ED - Stewart, Theo ED - Wallenius, Jyrki T1 - Balancing Efficiency and Robustness T2 - MCDM for Sustainable Energy and Transportation Systems Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2008/1105/ PB - Lecture Notes in Economics and Mathematical Systems ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schlechte, Thomas ED - Liebchen, Christian ED - Ahuja, Ravindra ED - Mesa, Juan T1 - Models for Railway Track Allocation T2 - ATMOS 2007 - 7th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems Y1 - 2007 VL - 07001 PB - Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany ER - TY - THES A1 - Schlechte, Thomas T1 - Das Resource-Constraint-Shortest-Path-Problem und seine Anwendung in der ÖPNV-Dienstplanung Y1 - 2003 UR - http://www.zib.de/groetschel/students/Diplom-Schlechte-0311.pdf ER - TY - THES A1 - Raack, Christian T1 - Employing Mixed-Integer Rounding in Telecommunication Network Design Y1 - 2005 UR - http://www.zib.de/groetschel/students/masterstudents.html ER - TY - CHAP A1 - Orlowski, Sebastian A1 - Koster, Arie M.C.A. A1 - Raack, Christian A1 - Wessäly, Roland T1 - Two-layer Network Design by Branch-and-Cut featuring MIP-based Heuristics T2 - Proceedings of the INOC 2007, Spa, Belgium, also ZIB Report ZR-06-47 Y1 - 2007 UR - http://www.zib.de/Publications/abstracts/ZR-06-47 PB - International Network Optimization Conference CY - Spa, Belgium ER - TY - CHAP A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Baier, Georg A1 - Engel, Thomas T1 - Single-layer Cuts for Multi-Layer Network Design Problems T2 - Telecommunications Modeling Policy and Technology, also ZIB Report ZR-07-21 Y1 - 2008 UR - http://dx.doi.org/10.1007/978-0-387-77780-1_1 SP - 1 EP - 23 PB - Springer CY - College Park, MD, U.S.A. ER - TY - CHAP A1 - Raack, Christian A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - Capacitated network design using general flow-cutset inequalities T2 - Proceedings of the INOC 2007, Spa, Belgium, also ZIB Report ZR-07-14 Y1 - 2007 UR - http://www.zib.de/Publications/abstracts/ZR-07-14 PB - International Network Optimization Conference CY - Spa, Belgium ER - TY - CHAP A1 - Bley, Andreas A1 - Menne, Ulrich A1 - Klähne, Roman A1 - Raack, Christian A1 - Wessäly, Roland T1 - Multi-layer network design – A model-based optimization approach T2 - Proceedings of the PGTS 2008, Berlin, Germany Y1 - 2008 SP - 107 EP - 116 PB - Polish-German Teletraffic Symposium CY - Berlin, Germany ER - TY - CHAP A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Baier, Georg A1 - Engel, Thomas A1 - Belotti, Pietro T1 - Branch-and-cut techniques for solving realistic two-layer network design problems T2 - Graphs and Algorithms in Communication Networks Y1 - 2009 UR - http://www.springerlink.com/content/g3rt54x5w4110240 SP - 95 EP - 118 PB - Springer Berlin Heidelberg ER - TY - CHAP A1 - Idzikowski, Filip A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Woesner, Hagen A1 - Wolisz, Adam T1 - Saving energy in IP-over-WDM networks by switching off line cards in low-demand scenarios T2 - Proceedings of the 14th conference on Optical network design and modeling Y1 - 2010 UR - http://portal.acm.org/citation.cfm?id=1834075.1834085 SP - 42 EP - 47 PB - IEEE Press CY - Piscataway, NJ, USA ER - TY - CHAP A1 - Koster, Arie M.C.A. A1 - Raack, C. T1 - A packing integer program arising in two-layer network design T2 - Proceedings of the INOC 2009, Pisa, Italy Y1 - 2009 PB - International Network Optimization Conference CY - Pisa, Italy ER - TY - JOUR A1 - Idzikowski, Filip A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Woesner, Hagen A1 - Wolisz, Adam T1 - Dynamic routing at different layers in IP-over-WDM networks – Maximizing energy savings JF - Optical Switching and Networking, Special Issue on Green Communications Y1 - 2011 UR - http://opus.kobv.de/zib/volltexte/2010/1230/ ER - TY - JOUR A1 - Achterberg, Tobias A1 - Raack, Christian T1 - The MCF-Separator – Detecting and Exploiting Multi-Commodity Flows in MIPs JF - Mathematical Programming C Y1 - 2010 UR - http://www.springerlink.com/content/383250gmx3184126/ IS - 2 SP - 125 EP - 165 ER - TY - JOUR A1 - Raack, Christian A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - On cut-based inequalities for capacitated network design polyhedra JF - Networks Y1 - 2011 UR - http://onlinelibrary.wiley.com/doi/10.1002/net.20395/abstract VL - 57 IS - 2 SP - 141 EP - 156 ER - TY - CHAP A1 - Koster, Arie M.C.A. A1 - Kutschka, Manuel A1 - Raack, Christian T1 - Towards Robust Network Design using Integer Linear Programming Techniques T2 - Proceedings of the NGI 2010, Paris, France Y1 - 2010 UR - http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5534462 PB - Next Generation Internet CY - Paris, France ER - TY - JOUR A1 - Dash, Sanjeeb A1 - Günlük, Oktay A1 - Raack, Christian T1 - A note on the MIR closure and basic relaxations of polyhedra JF - Optimization Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/12/2853.html VL - 39 IS - 3 SP - 198 EP - 199 ER - TY - THES A1 - Miltenberger, Matthias T1 - Die IDR(s)-Methode zur Lösung von parametrisierten Gleichungssystemen Y1 - 2009 ER - TY - GEN A1 - Koch, Thorsten ED - Achterberg, Tobias ED - Beck, J. Christopher T1 - Which mixed integer programs could a million CPUs solve? T2 - CPAIOR 2011 – Late Breaking Abstracts Y1 - 2011 UR - http://opus4.kobv.de/opus4-zib/files/1294/ZR-11-20.pdf IS - 11-20 SP - 17 EP - 18 PB - Zuse Institute Berlin CY - Takustr. 7, Berlin ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Junglas, Daniel A1 - Koch, Thorsten A1 - Kürner, T. A1 - Martin, Alexander T1 - Final Report on Automatic Planning and Optimisation Y1 - 2003 UR - http://momentum.zib.de/paper/momentum-d47.pdf IS - D4.7 PB - IST-2000-28088 MOMENTUM ER - TY - RPRT A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Türke, Ulrich T1 - MOMENTUM Public Planning Scenarios and their XML Format Y1 - 2003 IS - TD(03) 167 PB - COST 273 CY - Prague, Czech Republic ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Fledderus, E. A1 - Geerdes, Hans-Florian A1 - Heideck, B. A1 - Junglas, Daniel A1 - Koch, Thorsten A1 - Kürner, T. A1 - Martin, Alexander ED - Martin, Alexander T1 - Mathematical Methods for Automatic Optimization of UMTS Radio Networks Y1 - 2003 UR - http://momentum.zib.de/paper/momentum-d43.pdf IS - D4.3 PB - IST-2000-28088 MOMENTUM ER - TY - RPRT A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Türke, Ulrich T1 - Describing UMTS Radio Networks using XML Y1 - 2003 PB - MOMENTUM ER - TY - JOUR A1 - Koch, Thorsten A1 - Ralphs, Ted A1 - Shinano, Yuji T1 - Could we use a million cores to solve an integer program? JF - Mathematical Methods of Operations Research Y1 - 2012 U6 - https://doi.org/10.1007/s00186-012-0390-9 VL - 76 IS - 1 SP - 67 EP - 93 ER - TY - CHAP A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten ED - Bischof, Christian ED - Hegering, Heinz-Gerd ED - Nagel, Wolfgang ED - Wittum, Gabriel T1 - ParaSCIP: a parallel extension of SCIP T2 - Competence in High Performance Computing 2010 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-24025-6_12 SP - 135 EP - 148 PB - Springer ER - TY - CHAP A1 - Dorndorf, Ulrich A1 - Droste, Stefan A1 - Koch, Thorsten ED - Kallrath, Josef T1 - Using ZIMPL for Modeling Production Planning Problems T2 - Algebraic Modeling Systems Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23592-4 SP - 145 EP - 158 PB - Springer ER - TY - CHAP A1 - Martin, Alexander A1 - Geißler, Björn A1 - Heyn, Christine A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Morsi, Antonio A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Steinbach, Marc A1 - Willert, Bernhard T1 - Optimierung Technischer Kapazitäten in Gasnetzen T2 - Optimierung in der Energiewirtschaft Y1 - 2011 SP - 105 EP - 114 PB - VDI-Verlag, Düsseldorf ER - TY - CHAP A1 - Koch, Thorsten A1 - Leövey, Hernan A1 - Mirkov, Radoslava A1 - Römisch, Werner A1 - Wegner-Specht, Isabel T1 - Szenariogenerierung zur Modellierung der stochastischen Ausspeiselasten in einem Gastransportnetz T2 - Optimierung in der Energiewirtschaft Y1 - 2011 UR - http://www2.mathematik.hu-berlin.de/%7Eromisch/papers/SzengenVDI11.pdf SP - 115 EP - 125 PB - VDI-Verlag, Düsseldorf ER - TY - CHAP A1 - Cook, William A1 - Koch, Thorsten A1 - Steffy, Daniel A1 - Wolter, Kati ED - Günlük, Oktay ED - Woeginger, Gerhard T1 - An Exact Rational Mixed-Integer Programming Solver T2 - IPCO 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-20807-2_9 VL - 6655 SP - 104 EP - 116 ER - TY - JOUR A1 - Koch, Thorsten A1 - Achterberg, Tobias A1 - Andersen, Erling A1 - Bastert, Oliver A1 - Berthold, Timo A1 - Bixby, Robert E. A1 - Danna, Emilie A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Lodi, Andrea A1 - Mittelmann, Hans A1 - Ralphs, Ted A1 - Salvagnin, Domenico A1 - Steffy, Daniel A1 - Wolter, Kati T1 - MIPLIB 2010 JF - Mathematical Programming Computation Y1 - 2011 UR - http://mpc.zib.de/index.php/MPC/article/view/56 U6 - https://doi.org/10.1007/s12532-011-0025-9 VL - 3 IS - 2 SP - 103 EP - 163 ER - TY - JOUR A1 - Cook, William A1 - Koch, Thorsten T1 - Mathematical Programming Computation: A New MPS Journal JF - Optima Y1 - 2008 UR - http://www.mathopt.org/Optima-Issues/optima78.pdf IS - 78 SP - 1,7 EP - 8,11 PB - Mathematical Programming Society & University of Florida ER - TY - CHAP A1 - Bley, Andreas A1 - Koch, Thorsten T1 - Integer programming approaches to access and backbone IP-network planning T2 - Modeling, Simulation and Optimization of Complex Processes, Proceedings of the 3rd International Conference on High Performance Scientific Computing, March 6-10, Hanoi, Vietnam Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2002/709/ SP - 87 EP - 110 PB - Springer ER - TY - CHAP A1 - Achterberg, Tobias A1 - Heinz, Stefan A1 - Koch, Thorsten ED - Perron, Laurent ED - Trick, Michael T1 - Counting Solutions of Integer Programs Using Unrestricted Subtree Detection T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 5th International Conference, CPAIOR 2008 Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2008/1092/ VL - 5015 SP - 278 EP - 282 PB - Springer ER - TY - CHAP A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Koch, Thorsten A1 - Wolter, Kati ED - Perron, Laurent ED - Trick, Michael T1 - Constraint Integer Programming: A New Approach to Integrate CP and MIP T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 5th International Conference, CPAIOR 2008 Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-68155-7_4 VL - 5015 SP - 6 EP - 20 PB - Springer ER - TY - JOUR A1 - Froyland, Gary A1 - Koch, Thorsten A1 - Megow, Nicole A1 - Duane, Emily A1 - Wren, Howard T1 - Optimizing the Landside Operation of a Container Terminal JF - OR Spectrum Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2006/900/ U6 - https://doi.org/10.1007/s00291-007-0082-7 VL - 30 IS - 1 SP - 53 EP - 75 ER - TY - CHAP A1 - Koch, Thorsten ED - Haasis, Hans-Dietrich ED - Kopfer, Herbert ED - Schönberger, Jörn T1 - Rapid Mathematical Programming or How to Solve Sudoku Puzzles in a few Seconds T2 - Operations Research Proceedings 2005 Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2005/884/ SP - 21 EP - 26 ER - TY - JOUR A1 - Kaibel, Volker A1 - Koch, Thorsten T1 - Mathematik für den Volkssport JF - Mitteilungen der DMV Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2006/922/ VL - 14 IS - 2 SP - 93 EP - 96 ER - TY - JOUR A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Martin, Alexander T1 - MIPLIB 2003 JF - Operations Research Letters Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2005/862/ U6 - https://doi.org/10.1016/j.orl.2005.07.009 VL - 34 IS - 4 SP - 361 EP - 372 PB - Elsevier / North-Holland ER - TY - JOUR A1 - Koch, Thorsten T1 - Mathematische Programmierung auf der Überholspur JF - OR News Y1 - 2006 IS - 26 SP - 36 EP - 37 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Wessäly, Roland T1 - UMTS Radio Network Evaluation and Optimization beyond Snapshots JF - Mathematical Methods of Operations Research Y1 - 2005 UR - http://opus.kobv.de/zib/volltexte/2004/791/ U6 - https://doi.org/10.1007/s00186-005-0002-z VL - 63 IS - 1 SP - 1 EP - 29 ER - TY - THES A1 - Koch, Thorsten T1 - Rapid Mathematical Programming Y1 - 2004 UR - http://opus.kobv.de/zib/volltexte/2005/834/ ER - TY - JOUR A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Branching Rules Revisited JF - Operations Research Letters Y1 - 2005 UR - http://opus.kobv.de/zib/volltexte/2004/789/ U6 - https://doi.org/10.1016/j.orl.2004.04.002 VL - 33 IS - 1 SP - 42 EP - 54 PB - Elsevier / North-Holland ER - TY - CHAP A1 - Koch, Thorsten A1 - Wessäly, Roland ED - Elmer, Carl-Friedrich ED - von Hirschhausen, Christian T1 - Hierarchical Infrastructure Planning in Networks T2 - Proceedings of the 3rd Conference on Applied Infrastructure Research, 9. October 2004, Berlin Y1 - 2004 UR - http://opus.kobv.de/zib/volltexte/2004/818/ ER - TY - CHAP A1 - Bley, Andreas A1 - Koch, Thorsten A1 - Wessäly, Roland ED - Kaindl, H. T1 - Large-Scale hierarchical networks: How to compute an optimal architecture? T2 - Networks 2004 Y1 - 2004 SN - 3-8007-2840-0 SP - 429 EP - 434 PB - VDE Verlag CY - Berlin ER - TY - JOUR A1 - Koch, Thorsten T1 - The final NETLIB-LP results JF - Operations Research Letters Y1 - 2004 UR - http://opus.kobv.de/zib/volltexte/2003/728/ U6 - https://doi.org/10.1016/S0167-6377(03)00094-4 VL - 32 IS - 2 SP - 138 EP - 142 PB - Elsevier / North-Holland ER - TY - CHAP A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Geerdes, Hans-Florian A1 - Junglas, Daniel A1 - Koch, Thorsten A1 - Martin, Alexander ED - Ahr, Dino ED - Fahrion, Roland ED - Oswald, Marcus ED - Reinelt, Gerhard T1 - Optimisation Methods for UMTS Radio Network Planning T2 - Operation Research Proceedings 2003 Y1 - 2003 U6 - https://doi.org/10.1007/978-3-642-17022-5_5 SP - 31 EP - 38 PB - Springer ER - TY - CHAP A1 - Eisenblätter, Andreas A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Achterberg, Tobias A1 - Fügenschuh, Armin A1 - Koster, Arie M.C.A. A1 - Wegel, Oliver A1 - Wessäly, Roland ED - Anandalingam, G. ED - Raghavan, S. T1 - Modelling Feasible Network Configurations for UMTS T2 - Telecommunications Network Design and Management Y1 - 2003 UR - http://opus.kobv.de/zib/volltexte/2002/684/ PB - Kluver ER - TY - JOUR A1 - Rosenberg, Marjorie A1 - Agarwala, Richa A1 - Bouffard, Gerard A1 - Davis, Joie A1 - Fiermonte, Giuseppe A1 - Hilliard, Mark A1 - Koch, Thorsten A1 - Kalikin, Linda A1 - Makalowska, Izabela A1 - Morton, D. A1 - Petty, Elizabeth A1 - Weber, James A1 - Palmieri, Ferdinando A1 - Kelley, Richard A1 - Schäffer, Alejandro A1 - Biesecker, Leslie T1 - Mutant deoxynucleotide carrier DNC is associated with congenital microcephaly JF - Nature Genetics Y1 - 2002 U6 - https://doi.org/10.1038/ng948 VL - 32 IS - 1 SP - 175 EP - 179 ER - TY - CHAP A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Voß, Stefan ED - Du, D.-Z. ED - Cheng, X. T1 - SteinLib: An Updated Library on Steiner Tree Problems in Graphs T2 - Steiner Trees in Industry Y1 - 2001 U6 - https://doi.org/10.1007/978-1-4613-0255-1_9 SP - 285 EP - 325 PB - Kluwer ER - TY - JOUR A1 - Bley, Andreas A1 - Koch, Thorsten T1 - Optimierung des G-WiN JF - DFN-Mitteilungen Y1 - 2000 UR - http://www.dfn.de/content/fileadmin/5Presse/DFNMitteilungen/heft54.pdf IS - 54 SP - 13 EP - 15 ER - TY - JOUR A1 - Johnston, Jennifer A1 - Kelley, Richard A1 - Crawford, Thomas A1 - Morton, D. A1 - Agarwala, Richa A1 - Koch, Thorsten A1 - Schäffer, Alejandro A1 - Francomano, Clair A1 - Biesecker, Leslie T1 - A novel nemaline myopathy in the Amish caused by a mutation in troponin T1 JF - American Journal of Human Genetics Y1 - 2000 UR - http://www.journals.uchicago.edu/AJHG/journal/issues/v67n4/002057/002057.html VL - 67 SP - 814 EP - 821 ER - TY - JOUR A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Solving Steiner tree problems in graphs to optimality JF - Networks Y1 - 1998 UR - http://opus.kobv.de/zib/volltexte/1996/253/ U6 - https://doi.org/10.1002/(SICI)1097-0037(199810)32:3%3C207::AID-NET5%3E3.0.CO;2-O VL - 32 SP - 207 EP - 232 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc ED - Barnhart, Cynthia ED - Clausen, Uwe ED - Lauther, Ulrich ED - Möhring, Rolf T1 - Line Planning and Connectivity T2 - Models and Algorithms for Optimization in Logistics Y1 - 2009 IS - 09261 PB - Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany CY - Dagstuhl, Germany ER - TY - CHAP A1 - Neumann, Marika ED - Waldmann, Karl-Heinz ED - Stocker, Ulrike T1 - Fare Planning for Public Transport T2 - Operations Research Proceedings 2006 Y1 - 2007 UR - {http://opus.kobv.de/zib/volltexte/2009/1160/} SP - 61 EP - 66 PB - Springer-Verlag ER - TY - JOUR A1 - Neumann, Marika T1 - Mathematische Preisplanung im ÖPNV JF - OR News Y1 - 2007 IS - 30 SP - 29 EP - 31 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc ED - Haasis, Hans-Dietrich ED - Kopfer, Herbert ED - Schönberger, Jörn T1 - Optimal Fares for Public Transport T2 - Operations Research Proceedings 2005 Y1 - 2006 UR - {http://opus.kobv.de/zib/volltexte/2005/869/} SP - 29 EP - 36 PB - Springer-Verlag ER - TY - THES A1 - Neumann, Marika T1 - Mathematische Preisplanung im ÖPNV Y1 - 2005 UR - http://www.zib.de/groetschel/students/Diplom-Neumann.pdf ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung T1 - Determining Fair Ticket Prices in Public Transport by Solving a Cost Allocation Problem T2 - Appeared in: Modeling, Simulation and Optimization of Complex Processes, Proceedings of the Fourth International Conference on High Performance Scientific Computing, March 2-6, 2009, Hanoi, Vietnam Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-25707-0_5 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin A1 - Koch, Thorsten A1 - Hoang, Nam-Dung ED - Biermann, Katja ED - Grötschel, Martin ED - Lutz-Westphal, Brigitte T1 - Lagenwechsel minimieren – oder das Bohren von Löchern in Leiterplatten T2 - Besser als Mathe Y1 - 2010 U6 - https://doi.org/10.1007/978-3-658-01004-1_19 SP - 161 EP - 174 PB - Vieweg+Teubner ER - TY - CHAP A1 - Heuveline, Vincent A1 - Hoang, Nam-Dung ED - Kunisch, Karl ED - Leugering, Günter ED - Sprekels, Jürgen ED - Tröltzsch, Fredi T1 - On two numerical approaches for the boundary control stabilization of semi-linear parabolic systems: a comparison T2 - Control of Coupled Partial Differential Equations, International Series of Numerical Mathematics, Vol. 155 Y1 - 2007 U6 - https://doi.org/10.1007/978-3-7643-7721-2_5 SP - 95 EP - 118 PB - Birkhäuser ER - TY - GEN A1 - Hiller, Benjamin T1 - Hochlastvarianten des Algorithmus ZIBDIP für die automatische Disposition von ADAC-Einsatzfahrzeugen Y1 - 2003 PB - Studienarbeit TU Ilmenau\,/\,Konrad-Zuse-Zentrum für Informationstechnik Berlin ER - TY - CHAP A1 - Berberich, Eric A1 - Hagen, Matthias A1 - Hiller, Benjamin A1 - Moser, Hannes ED - Müller-Hannemann, Matthias ED - Schirra, Stefan T1 - Experiments T2 - Algorithm Engineering Y1 - 2010 VL - 5971 SP - 325 EP - 388 PB - Springer ER - TY - CHAP A1 - Geyer, Markus A1 - Hiller, Benjamin A1 - Meinert, Sascha ED - Müller-Hannemann, Matthias ED - Schirra, Stefan T1 - Modeling T2 - Algorithm Engineering Y1 - 2010 VL - 5971 SP - 16 EP - 57 PB - Springer ER - TY - JOUR A1 - Hiller, Benjamin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Reoptimization Gaps versus Model Errors in Online-Dispatching of Service Units for ADAC JF - DISAM Y1 - 2006 VL - 154 IS - 13 SP - 1897 EP - 1907 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Probabilistic alternatives for competitive analysis JF - Computer Science - Research and Development Y1 - 2012 U6 - https://doi.org/10.1007/s00450-011-0149-1 VL - 27 IS - 3 SP - 189 EP - 196 PB - Springer ER - TY - CHAP A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Stochastic dominance analysis of online bin coloring algorithms T2 - 9th Workshop on Models and Algorithms for Planning and Scheduling Problems Y1 - 2009 ER - TY - CHAP A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Probabilistic analysis of Online Bin Coloring algorithms via Stochastic Comparison T2 - Proceedings of the 16th esa Y1 - 2008 VL - 5193 SP - 528 EP - 539 PB - Springer ER - TY - CHAP A1 - Hiller, Benjamin A1 - Tuchscherer, Andreas T1 - Real-Time Destination-Call Elevator Group Control on Embedded Microcontrollers T2 - Operations Research Proceedings 2007 Y1 - 2008 SP - 357 EP - 362 PB - Springer ER - TY - CHAP A1 - Hiller, Benjamin A1 - Krumke, Sven A1 - Rambau, Jörg ED - Liebling, T. ED - Duran, G. ED - Matamala, M. T1 - Reoptimization Gaps versus Model Errors in Online-Dispatching of Service Units for ADAC T2 - Latin-American Conference on Combinatorics, Graphs and Applications, Santiago de Chile 2004 Y1 - 2004 VL - 18 SP - 157 EP - 163 ER - TY - THES A1 - Hiller, Benjamin T1 - Online Optimization Y1 - 2009 ER - TY - THES A1 - Hiller, Benjamin T1 - Bad Guys are Rare Y1 - 2004 ER - TY - BOOK ED - Grötschel, Martin ED - Lucas, Klaus ED - Mehrmann, Volker T1 - Production Factor Mathematics Y1 - 2010 UR - http://www.springer.com/math/book/978-3-540-89434-6 SN - 978-3-642-11247-8 U6 - https://doi.org/10.1007/978-3-642-11248-5 PB - acatech – Deutsche Akademie der Technikwissenschaften und Springer ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas ED - Aigner, Martin ED - Behrends, Ehrhard T1 - The Quickest Path to the Goal JF - Mathematics Everywhere Y1 - 2010 UR - http://www.ams.org/bookstore-getitem/item=MBK-72 SP - 27 EP - 51 PB - American Mathematical Society CY - Providence, Rhode Iland, USA ER - TY - BOOK ED - Biermann, Katja ED - Grötschel, Martin ED - Lutz-Westphal, Brigitte T1 - Besser als Mathe - Moderne angewandte Mathematik aus dem Matheon zum Mitmachen Y1 - 2010 UR - http://www.viewegteubner.de/index.php;do=show/site=v/book_id=18692 SN - 978-3-8348-0733-5 PB - Vieweg + Teubner ER - TY - CHAP A1 - Grötschel, Martin A1 - Hiller, Benjamin A1 - Tuchscherer, Andreas ED - Lucas, Klaus ED - Roosen, Peter T1 - Structuring a Dynamic Environment T2 - Emergence, Analysis and Evolution of Structures. Concepts and Strategies Across Disciplines Y1 - 2009 UR - http://www.springer.com/engineering/book/978-3-642-00869-6 U6 - https://doi.org/10.1007/978-3-642-00870-2 SP - 199 EP - 214 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - Lutz-Westphal, Brigitte T1 - Diskrete Mathematik und ihre Anwendungen JF - Jahresbericht der Deutschen Mathematiker-Vereinigung Y1 - 2009 VL - 111 IS - 1 SP - 3 EP - 22 PB - Vieweg+Teubner ER - TY - CHAP A1 - Grötschel, Martin ED - der Wissenschaften, Berlin-Brandenburgische T1 - Ohne x is nix T2 - Berichte und Abhandlungen Y1 - 2008 VL - 14 SP - 195 EP - 219 PB - Akademie-Verlag CY - Berlin ER - TY - CHAP A1 - Grötschel, Martin ED - der Wissenschaften, Berlin-Brandenburgische T1 - Geistiges Eigentum – Eine Zusammenfassung der vorgetragenen Standpunkte T2 - Geistiges Eigentum – Streitgespräche in den Wissenschaftlichen Sitzungen der Versammlung der Berlin-Brandenburgischen Akademie der Wissenschaften Y1 - 2008 VL - Heft 7 SP - 89 EP - 95 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - CHAP A1 - Grötschel, Martin ED - der Wissenschaften, Berlin-Brandenburgische T1 - Geistiges Eigentum – Einführung in das Thema T2 - Geistiges Eigentum – Streitgespräche in den Wissenschaftlichen Sitzungen der Versammlung der Berlin-Brandenburgischen Akademie der Wissenschaften Y1 - 2008 VL - Heft 7 SP - 9 EP - 14 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Grötschel, Martin T1 - Planning UMTS Radio Networks JF - OR/MS Today Y1 - 2008 UR - http://www.lionhrtpub.com/orms/orms-12-08/frradio.html VL - 35 IS - 6 SP - 40 EP - 46 ER - TY - BOOK ED - Grötschel, Martin ED - Lucas, Klaus ED - Mehrmann, Volker T1 - PRODUKTIONSFAKTOR MATHEMATIK – Wie Mathematik Technik und Wirtschaft bewegt T3 - acatech DISKUTIERT Y1 - 2008 UR - http://www.springer.com/math/book/978-3-540-89434-6 SN - 978-3-540-89434-6 U6 - https://doi.org/10.1007/978-3-540-89435-3 PB - acatech – Deutsche Akademie der Technikwissenschaften und Springer ER - TY - CHAP A1 - Grötschel, Martin ED - Hecht, Hartmut ED - Mikosch, Regina ED - Schwarz, Ingo ED - Siebert, Harald ED - Werther, Romy T1 - Tiefensuche T2 - Kosmos und Zahl - Beiträge zur Mathematik- und Astronomiegeschichte, zu Alexander von Humboldt und Leibniz Y1 - 2008 UR - http://www.steiner-verlag.de/titel/56734.html VL - 58 SP - 331 EP - 346 PB - Franz Steiner Verlag ER - TY - BOOK ED - Grötschel, Martin ED - Katona, Gyula T1 - Building Bridges - Between Mathematics and Computer Science T3 - Bolyai Society Mathematical Studies Y1 - 2008 UR - http://www.springer.com/math/numbers/book/978-3-540-85218-6 SN - 3-540-85218-6 PB - Springer ER - TY - JOUR A1 - Abboud, Nadine A1 - Grötschel, Martin A1 - Koch, Thorsten T1 - Mathematical methods for physical layout of printed circuit boards: an overview JF - OR Spectrum Y1 - 2008 U6 - https://doi.org/10.1007/s00291-007-0080-9 VL - 30 IS - 3 SP - 453 EP - 468 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim ED - Keil, Reinhard ED - Kerres, Michael ED - Schulmeister, Rolf T1 - Die Wissenschaftsgalaxis T2 - eUniversity - Update Bologna Y1 - 2007 UR - http://opus.kobv.de/zib/volltexte/2007/1014/ SP - 335 EP - 354 PB - Waxmann Verlag ER - TY - GEN A1 - Grötschel, Martin ED - Hußmann, Stephan ED - Lutz-Westphal, Brigitte T1 - Das Problem mit der Komplexität T2 - Kombinatorische Optimierung erleben – In Studium und Unterricht Y1 - 2007 U6 - https://doi.org/10.1007/978-3-8348-9120-4_9 SP - 265 EP - 274 PB - Vieweg CY - Wiesbaden ER - TY - CHAP A1 - Grötschel, Martin ED - Hußmann, Stephan ED - Lutz-Westphal, Brigitte T1 - Schnelle Rundreisen T2 - Kombinatorische Optimierung erleben – In Studium und Unterricht Y1 - 2007 UR - http://www.viewegteubner.de/index.php;do=show/site=v/book_id=6158 SP - 95 EP - 128 PB - Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - A Column-Generation Approach to Line Planning in Public Transport JF - Transportation Science (INFORMS) Y1 - 2007 U6 - https://doi.org/10.1287/trsc.1060.0161 VL - 41 IS - 1 SP - 123 EP - 132 ER - TY - JOUR A1 - Achterberg, Tobias A1 - Grötschel, Martin A1 - Koch, Thorsten T1 - Teaching MIP Modeling and Solving JF - OR/MS Today Y1 - 2006 UR - http://www.lionhrtpub.com/orms/orms-12-06/freducation.html VL - 33 IS - 6 SP - 14 EP - 15 ER - TY - JOUR A1 - Grötschel, Martin A1 - Hinrichs, Hinrich A1 - Schröer, Klaus A1 - Tuchscherer, Andreas T1 - Ein gemischt-ganzzahliges lineares Optimierungsmodell für ein Laserschweißproblem im Karosseriebau JF - Zeitschrift für wirtschaftlichen Fabrikbetrieb (ZWF) Karosseriebau Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2006/915/ VL - 101 IS - 5 SP - 260 EP - 264 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Lukac, Sascha A1 - Mitusch, Kay A1 - Schlechte, Thomas A1 - Schultz, Sören A1 - Tanner, Andreas T1 - An Auctioning Approach to Railway Slot Allocation JF - Competition and Regulation in Network Industries Y1 - 2006 VL - 1 IS - 2 SP - 163 EP - 196 ER - TY - CHAP A1 - Grötschel, Martin ED - der Wissenschaften, Berlin-Brandenburgische T1 - Der junge Albring und Schwelm T2 - Der Forscher und der Zweifler - Werner Albring zum 90. Geburtstag Y1 - 2005 SP - 11 EP - 35 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - CHAP A1 - Grötschel, Martin T1 - In der Mathematik sind sich alle einig und die Gesellschaft hat von ihr nichts zu befürchten T2 - Wissenschaft Kontrovers Y1 - 2005 VL - 2 PB - Chronos, Edition Collegium Helveticum CY - Zürich ER - TY - JOUR A1 - Grötschel, Martin T1 - Telota baut das elektronische Hirn der Akademie zusammen JF - Circular der BBAW Y1 - 2005 IS - 31 SP - 34 EP - 35 ER - TY - JOUR A1 - Grötschel, Martin T1 - Matheon JF - Jahresbericht der DMV Y1 - 2005 VL - 107 IS - 4 SP - 173 EP - 196 PB - B. G. Teubner ER - TY - JOUR A1 - Bosse, Hartwig A1 - Grötschel, Martin A1 - Henk, Martin T1 - Polynomial inequalities representing polyhedra JF - Mathematical Programming Y1 - 2005 U6 - https://doi.org/10.1007/s10107-004-0563-2 VL - 103 IS - 1 SP - 35 EP - 44 ER - TY - CHAP A1 - Grötschel, Martin ED - Grötschel, Martin T1 - Cardinality Homogeneous Set Systems, Cycles in Matroids, and Associated Polytopes T2 - The Sharpest Cut Y1 - 2004 SP - 99 EP - 120 PB - MPS-SIAM ER - TY - BOOK ED - Grötschel, Martin T1 - The Sharpest Cut: The Impact of Manfred Padberg and His Work Y1 - 2004 SN - 0-89871-552-0 U6 - https://doi.org/10.1137/1.9780898718805 PB - SIAM ER - TY - JOUR A1 - Grötschel, Martin T1 - Das elektronische Leben der Akademie JF - Circular der BBAW Y1 - 2003 IS - 28 SP - 14 EP - 15 ER - TY - GEN A1 - Grötschel, Martin A1 - Borndörfer, Ralf A1 - Löbel, Andreas ED - Jäger, Willi ED - Krebs, Hans-Joachim T1 - Duty Scheduling in Public Transit T2 - MATHEMATICS – Key Technology for the Future Y1 - 2003 U6 - https://doi.org/10.1007/978-3-642-55753-8_50 SP - 653 EP - 674 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - Henk, Martin T1 - The Representation of Polyhedra by Polynomial Inequalities JF - Discrete & Computational Geometry Y1 - 2003 U6 - https://doi.org/10.1007/s00454-003-0782-y VL - 29 IS - 4 SP - 485 EP - 504 ER - TY - CHAP A1 - Grötschel, Martin ED - der Berliner Mathematischen Gesellschaft, Vorstand T1 - The DFG research center “Mathematics for key technologies” T2 - DFG Research Center – Mathematics for Key Technologies Y1 - 2002 SP - 3 EP - 8 PB - Berliner Mathematische Gesellschaft ER - TY - CHAP A1 - Grötschel, Martin ED - von Kathrin Künzel, Sonja T1 - Telota T2 - Berlin-Brandenburgische Akademie der Wissenschaften, Jahrbuch 2001 Y1 - 2002 SP - 439 EP - 445 PB - Akademie-Verlag CY - Berlin ER - TY - JOUR A1 - Grötschel, Martin T1 - P=NP? JF - Elemente der Mathematik, Eine Zeitschrift der Schweizerischen Mathematischen Gesellschaft Y1 - 2002 VL - 57 IS - 3 SP - 96 EP - 102 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Torres, Luis Miguel T1 - Making the Yellow Angels Fly JF - SIAM News Y1 - 2002 VL - 35 IS - 4 SP - 1,10,11 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequency Planning and Ramifications of Coloring JF - Discussiones Mathematicae, Graph Theory Y1 - 2002 IS - 22 SP - 51 EP - 88 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequenzplanung im Mobilfunk JF - DMV-Mitteilungen Y1 - 2002 IS - 1 SP - 18 EP - 25 ER - TY - JOUR A1 - Grötschel, Martin T1 - Mein digitaler Traum JF - Gegenworte der BBAW Y1 - 2001 IS - 8 SP - 10 EP - 16 ER - TY - JOUR A1 - Grötschel, Martin T1 - Telota - Was soll das? JF - Circular der BBAW Y1 - 2001 IS - 23 SP - 3 EP - 7 ER - TY - JOUR A1 - Grötschel, Martin T1 - Empfehlungen des Wissenschaftsrates zur digitalen Informationsversorgung durch Hochschulbibliotheken JF - DMV-Mitteilungen Y1 - 2001 VL - 4 SP - 40 EP - 43 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Le stanze del TSP JF - AIROnews Y1 - 2001 VL - VI IS - 3 SP - 6 EP - 9 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - The Optimized Odyssey JF - AIROnews Y1 - 2001 VL - VI IS - 2 SP - 1 EP - 7 ER - TY - JOUR A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lill, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) JF - Bibliothek, Forschung und Praxis Y1 - 2001 VL - 25 IS - 1 SP - 55 EP - 65 ER - TY - CHAP A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Winter, Thomas A1 - Zimmermann, Uwe ED - Grötschel, Martin ED - Krumke, Sven ED - Rambau, Jörg T1 - Combinatorial Online Optimization in Real Time T2 - Online Optimization of Large Scale Systems Y1 - 2001 SP - 679 EP - 704 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg ED - Grötschel, Martin ED - Krumke, Sven ED - Rambau, Jörg T1 - Online Optimization of Complex Transportation Systems T2 - Online Optimization of Large Scale Systems Y1 - 2001 SP - 705 EP - 729 PB - Springer ER - TY - BOOK ED - Grötschel, Martin ED - Krumke, Sven ED - Rambau, Jörg T1 - Online Optimization of Large Scale Systems Y1 - 2001 SN - 3-540-42459-8 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin T1 - Copyright und elektronisches Publizieren JF - DMV-Mitteilungen Y1 - 2001 VL - 3 SP - 8 EP - 10 ER - TY - CHAP A1 - Grötschel, Martin T1 - Mathematik in der Industrie T2 - Berufs- und Karriere-Planer, Mathematik 2001, Schlüsselqualifikation für Technik, Wirtschaft und IT Y1 - 2001 SP - 43 EP - 48 PB - Vieweg ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - Solving the Asymmetric Travelling Salesman Problem with time windows by branch-and-cut JF - Mathematical Programming, Series A Y1 - 2001 VL - 90 IS - 3 SP - 475 EP - 506 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin A1 - Fonseca, Irene A1 - Davis, Mark ED - Casacuberta, Carles ED - Miró-Roig, Rosa ED - Ortega, Joaquín ED - Xambó-Descamps, Sebastià T1 - The Impact of Mathematical Research on Industry and Vice Versa T2 - Mathematical Glimpses into the 21st Century Y1 - 2001 SP - 35 EP - 53 PB - Societat Catalana de Matemàtiques and Centro Internacional de Métodos Numéricos en Ingeniería CY - Barcelona, Spain ET - First ER - TY - CHAP A1 - Grötschel, Martin ED - Kapoor, Sanjiv ED - Prasad, Sanjiva T1 - Frequency Assignment in Mobile Phone Systems T2 - FST TCS 2000 Y1 - 2000 VL - 1974 SP - 81 EP - 86 PB - Springer ER - TY - CHAP A1 - Bley, Andreas A1 - Grötschel, Martin A1 - Wessäly, Roland ED - Dean, Nathaniel ED - Hsu, D. ED - Ravi, R. T1 - Design of broadband virtual private networks: Model and Heuristics for the B–WiN T2 - Robust communication networks: Interconnection and survivability. DIMACS workshop, Princeton, NJ, USA, 1998 at Rutgers University Y1 - 2000 VL - 53 SP - 1 EP - 16 PB - American Mathematical Society CY - Providence, RI ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - A Polyhedral Study of the Asymmetric Traveling Salesman Problem with Time Windows JF - Networks Y1 - 2000 VL - 36 IS - 2 SP - 69 EP - 79 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Die optimierte Odyssee JF - Spektrum der Wissenschaft, Digest Y1 - 1999 VL - 2 SP - 32 EP - 41 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Die optimierte Odyssee JF - Spektrum der Wissenschaft Y1 - 1999 VL - 4 SP - 76 EP - 85 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim ED - Gaul, Wolfgang ED - Loracek-Junge, H. T1 - Scientific Information Systems and Metadata T2 - Classification in the Information Age Y1 - 1999 SP - 3 EP - 20 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg JF - ABI Technik – Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen Y1 - 1999 VL - 19 IS - 4 SP - 350 EP - 367 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Wo bleibt der Aufzug? JF - OR News Y1 - 2006 VL - Sonderausgabe SP - 70 EP - 72 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Wo bleibt der Aufzug? JF - OR News Y1 - 1999 VL - 5 SP - 11 EP - 13 ER - TY - CHAP A1 - Grötschel, Martin ED - Hömberg, Dietmar T1 - Verkehrsplanung T2 - FORSCHUNGSPOLITISCHE DIALOGE IN BERLIN Y1 - 1999 SP - 11 EP - 22 PB - Veranstaltungsforum der Verlagsgruppe Georg von Holtzbrinck GmbH ER - TY - JOUR A1 - Grötschel, Martin T1 - My Favorite Theorem JF - OPTIMA Y1 - 1999 VL - 62 SP - 2 EP - 5 ER - TY - CHAP A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg ED - Kall, Peter ED - Lüthi, Hans-Jakob T1 - Combinatorial Online Optimization T2 - Operations Research Proceedings 1998. Selected Papers of the International Conference on Operations Research Zurich, August 31 – September 3, 1998 Y1 - 1999 SP - 21 EP - 37 PB - Springer ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Abdel-Hamid, Atef Abdel-Aziz T1 - Order picking in an automatic warehouse JF - Mathematical Methods of Operations Research Y1 - 1999 VL - 49 IS - 3 SP - 501 EP - 515 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Winczewski, Vincent T1 - Mathe im Netz - Math-Net JF - DFN-Mitteilungen Y1 - 1998 VL - Heft 48 SP - 4 EP - 6 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas ED - Butzer, Paul Leo ED - Jongen, Hubertus ED - Oberschelp, Walter T1 - Alcuin’s Transportation Problems and Integer Programming T2 - Charlemagne and his Heritage. 1200 Years of Civilization and Science in Europe. Karl der Grosse und sein Nachwirken . 1200 Jahre Kultur und Wissenschaft in Europa Y1 - 1998 VL - 2 SP - 379 EP - 409 PB - Brepols Publisher CY - Turnhout ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Martin, Alexander T1 - Frequency assignment in cellular phone networks JF - Annals of Operations Research Y1 - 1998 U6 - https://doi.org/10.1023/A:1018908907763 VL - 76 SP - 73 EP - 93 PB - J. C. Baltzer AG, Science Publishers ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Kamin, Nicola A1 - Rambau, Jörg T1 - Combinatorial online optimization in practice JF - OPTIMA Y1 - 1998 VL - 57 SP - 1 EP - 6 ER - TY - JOUR A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - Cost-efficient network synthesis from leased lines JF - Annals of Operations Research Y1 - 1998 VL - 76 SP - 1 EP - 20 ER - TY - JOUR A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Jonas, Peter A1 - Paul, Uwe A1 - Wessäly, Roland T1 - Survivable Mobile Phone Network Architectures JF - IEEE Communications Magazine Y1 - 1998 SP - 88 EP - 93 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - The Steiner tree packing problem in VLSI design JF - Mathematical Programming Y1 - 1997 VL - 78 IS - 2 SP - 265 EP - 281 ER - TY - CHAP A1 - Grötschel, Martin A1 - Löbel, Andreas A1 - Völker, Manfred ED - Hoffmann, Karl-Heinz ED - Jäger, Willi ED - Lohmann, Thomas ED - Schunck (Hrsg.), Hermann T1 - Optimierung des Fahrzeugumlaufs im Öffentlichen Nahverkehr T2 - Mathematik Y1 - 1997 SP - 609 EP - 624 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin T1 - Der Weg der Mathematik in die Informationsgesellschaft – Teil I JF - DMV-Mitteilungen Y1 - 1997 VL - 3 SP - 48 EP - 57 ER - TY - JOUR A1 - Grötschel, Martin T1 - Der Weg der Mathematik in die Informationsgesellschaft – Teil II JF - DMV-Mitteilungen Y1 - 1997 VL - 4 SP - 43 EP - 48 ER - TY - CHAP A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim ED - Sydow, Achim T1 - Information Services for Mathematics in the Internet (Math-Net) T2 - 15th IMACS World Congress 1997 on Scientific Computation, Modelling and Applied Mathematics, Volume IV Y1 - 1997 SP - 773 EP - 778 PB - Wissenschaft und Technik CY - Berlin ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Berliner Telebussystem bietet Mobilität für Behinderte JF - Der Nahverkehr Y1 - 1997 VL - 1/2 SP - 20 EP - 22 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Optimierung des Berliner Behindertenfahrdienstes JF - DMV-Mitteilungen Y1 - 1997 VL - 2 SP - 38 EP - 43 ER - TY - CHAP A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland ED - Barceló, Jaime T1 - Capacity and Survivability Models for Telecommunication Networks T2 - Proceedings of the EURO XV/INFORMS XXXIV Meeting, Barcelona June 1997 Y1 - 1997 PB - Universitat Politècnica de Catalunya CY - Barcelona, Spanien ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner trees: a cutting plane algorithm and computational results JF - Mathematical Programming, Series A Y1 - 1996 U6 - https://doi.org/10.1007/BF02592086 VL - 72 IS - 2 SP - 125 EP - 145 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner trees: Polyhedral Investigations JF - Mathematical Programming, Series A Y1 - 1996 U6 - https://doi.org/10.1007/BF02592085 VL - 72 IS - 2 SP - 101 EP - 123 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Optimum Path Packing on Wheels JF - Computers and Mathematics with Applications Y1 - 1996 VL - 31 IS - 11 SP - 23 EP - 35 PB - Elsevier ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Separation Algorithms JF - SIAM Journal on Discrete Mathematics Y1 - 1996 U6 - https://doi.org/10.1137/S0895480193258716 VL - 9 IS - 2 SP - 233 EP - 257 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Further Facets JF - European Journal of Combinatorics Y1 - 1996 U6 - https://doi.org/10.1006/eujc.1996.0004 VL - 17 IS - 1 SP - 39 EP - 52 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Neue Produkte für die digitale Bibliothek T2 - Die unendliche Bibliothek Y1 - 1996 SP - 38 EP - 67 PB - Harrassowitz-Verlag CY - Wiesbaden ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Information und Kommunikation im Umbruch JF - Forschung & Lehre, Mitteilungen des Deutschen Hochschulverbandes Y1 - 1996 VL - 4 SP - 194 EP - 198 ER - TY - JOUR A1 - Grötschel, Martin T1 - Den Kohl heile rüberbringen … – Mathematische Methoden der Transportoptimierung JF - Unsere-Duisburger-Hochschule-Zeitschrift Y1 - 1996 VL - 48 IS - 1 SP - 15 EP - 17 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Polyhedral and Computational Investigations for Designing Communication Networks with High Survivability Requirements JF - Operations Research Y1 - 1995 VL - 43 IS - 6 SP - 1012 EP - 1024 ER - TY - CHAP A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild ED - Ball, Michael ED - Magnanti, Thomas ED - Monma, Clyde ED - Nemhauser, George T1 - Design of Survivable Networks T2 - Network Models Y1 - 1995 VL - 7 SP - 617 EP - 672 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Routing in Grid Graphs by Cutting Planes JF - ZOR - Mathematical Methods of Operations Research Y1 - 1995 VL - 41 IS - 3 SP - 255 EP - 275 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Zimmermann, Uwe T1 - Wissenschaftliche Information am Wendepunkt? T2 - Referate/4. Weinheimer Bibliothekartreffen, 20-21. April 1995 Y1 - 1995 SP - 15 EP - 23 PB - Verlag Chemie CY - Weinheim ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Kommunikation am Wendepunkt - Bibliotheken im Zeitalter globaler elektronischer Netze JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 1995 VL - 42 IS - 3 SP - 287 EP - 312 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Aufbau elektronischer Informations- und Kommunikationsstrukturen JF - Newsletter der Gesellschaft für Mathematik, Ökonomie und Operations Research Y1 - 1995 VL - 3/4 SP - 24 EP - 66 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Die Zukunft wissenschaftlicher Kommunikation aus Sicht der Mathematik JF - Spektrum der Wissenschaft Y1 - 1995 SP - 39 EP - 43 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lovász, Lászlo ED - Graham, Ronald ED - Grötschel, Martin ED - Lovász, Lászlo T1 - Combinatorial Optimization T2 - Handbook of Combinatorics, Volume II Y1 - 1995 SP - 1541 EP - 1597 PB - Elsevier (North-Holland) ER - TY - BOOK ED - Graham, Ronald ED - Grötschel, Martin ED - Lovász, Lászlo T1 - Handbook of Combinatorics, Volume II Y1 - 1995 SN - 0-444-82351-4 (Volume 2) (Elsevier); 0-262-07171-1 (Volume 2) (MIT); 0-444-88002-X (Set of vols 1 and 2) (ELsevier); 0-262-07169-X (Sets of vols 1 and 2) (MIT) PB - Elsevier (North-Holland); The MIT Press, Cambridge, Massachusetts ER - TY - BOOK ED - Graham, Ronald ED - Grötschel, Martin ED - Lovász, Lászlo T1 - Handbook of Combinatorics, Volume I Y1 - 1995 SN - 0-444-82346-8 (Elsevier); 0-262-07170-3 (MIT) PB - Elsevier (North-Holland); The MIT Press, Cambridge, Massachusetts ER - TY - CHAP A1 - Godsil, Chris A1 - Grötschel, Martin A1 - Welsh, Dominic ED - Graham, Ronald ED - Grötschel, Martin ED - Lovász, Lászlo T1 - Combinatorics in Statistical Physics T2 - Handbook of combinatorics, Volume II, Part IV Y1 - 1995 SP - 1925 EP - 1954 PB - Elsevier (North-Holland) CY - Amsterdam ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Verteiltes Informationssystem für die Mathematik JF - Mitteilungen der Deutschen Mathematiker-Vereinigung Y1 - 1995 VL - 1 SP - 52 EP - 54 ER - TY - CHAP A1 - Abdel-Hamid, Atef Abdel-Aziz A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Schorer, Herbert ED - Bachem, Achim ED - Jünger, Michael ED - Schrader, Rainer T1 - Simulation und Optimierung einer PC-Fertigung unter Echtzeitbedingungen T2 - Mathematik in der Praxis. Fallstudien aus Industrie, Wirtschaft, Naturwissenschaften und Medizin Y1 - 1995 SP - 261 EP - 277 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram ED - Chatterji, S. ED - Fuchssteiner, Benno ED - Kulisch, Ulrich ED - Liedl, Roman T1 - Wissenschaftliches Publizieren und Elektronische Fachinformation im Umbruch T2 - Jahrbuch 1994 Überblicke Mathematik Y1 - 1994 SP - 154 EP - 174 PB - Vieweg CY - Braunschweig/Wiesbaden ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - New Perspectives of a Distributed Electronic Information System for Mathematics, Part II JF - European Mathematical Society Newsletter Y1 - 1994 VL - 14 SP - 6 EP - 14 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - New Perspectives of a Distributed Electronic Information System for Mathematics, Part I JF - European Mathematical Society Newsletter Y1 - 1994 VL - 13 SP - 6 EP - 17 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Neue Wege für die Fachinformation JF - DFN-Mitteilungen Y1 - 1994 VL - 34 SP - 4 EP - 7 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Neue Perspektiven eines Informationssystems für die Mathematik JF - Rundbrief der Gesellschaft für Angewandte Mathematik und Mechanik Y1 - 1994 VL - 3 SP - 4 EP - 7 ER - TY - CHAP A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert ED - Rinaldi, Giovanni ED - Wolsey, Laurence T1 - Routing in grid graphs by cutting planes T2 - Integer Programming and Combinatorial Optimization. Proceedings of a Conference held at Centro Ettore Majorana, Erice, Italy, April 29 - May 1, 1993 Y1 - 1993 SP - 447 EP - 461 PB - Librarian CORE CY - Louvain-la-Neuve ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - DMV-Projekt “Fachinformation” JF - DMV-Mitteilungen Y1 - 1993 VL - 2 SP - 21 EP - 28 ER - TY - BOOK A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Geometric Algorithms and Combinatorial Optimization T3 - Algorithms and Combinatorics Y1 - 1993 SN - 3-540-56740-2, 0-387-56740-2 (U.S.) VL - 2 PB - Springer ET - Second corrected edition ER - TY - JOUR A1 - Ferreira, Carlos A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert A1 - Kiefl, Stefan A1 - Krispenz, Ludwig T1 - Some Integer Programs Arising in the Design of Main Frame Computers JF - ZOR - Methods and Models of Operations Research Y1 - 1993 VL - 38 IS - 1 SP - 77 EP - 100 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Escudero, Laureano A1 - Grötschel, Martin A1 - Stoer, Mechthild T1 - A Cutting Plane Approach to the Sequential Ordering Problem (with Applications to Job Scheduling in Manufacturing) JF - SIAM Journal on Optimization Y1 - 1993 VL - 3 IS - 1 SP - 25 EP - 42 ER - TY - JOUR A1 - Grötschel, Martin A1 - Win, Zaw T1 - A cutting plane algorithm for the windy postman problem JF - Mathematical Programming, Series A Y1 - 1992 VL - 55 IS - 3 SP - 339 EP - 358 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Facets for polyhedra arising in the design of communication networks with low-connectivity constraints JF - SIAM Journal on Optimization Y1 - 1992 VL - 2 IS - 3 SP - 474 EP - 504 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Computational Results with a Cutting Plane Algorithm for Designing Communication Networks with Low-Connectivity Constraints JF - Operations Research Y1 - 1992 VL - 40 IS - 2 SP - 309 EP - 330 ER - TY - CHAP A1 - Grötschel, Martin ED - Frederickson, Greg T1 - Theoretical and practical aspects of combinatorial problem solving T2 - Proceedings of the third annual ACM-SIAM symposium on discrete algorithms,held January 27-29, 1992, in Orlando, FL, USA Y1 - 1992 SP - 195 PB - SIAM CY - Philadelphia, PA ER - TY - JOUR A1 - Deza, Michel A1 - Grötschel, Martin A1 - Laurent, Monique T1 - Clique-Web Facets for Multicut Polytopes JF - Mathematics of Operations Research Y1 - 1992 VL - 17 IS - 4 SP - 981 EP - 1000 ER - TY - CHAP A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild ED - Roberts, Fred ED - Hwang, Frank ED - Monma, Clyde T1 - Polyhedral Approaches to Network Survivability T2 - Reliability of Computer and Communication Networks, Proc. Workshop 1989, New Brunswick, NJ/USA Y1 - 1991 VL - 5 SP - 121 EP - 141 PB - American Mathematical Society ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Optimal Control of Plotting and Drilling Machines JF - Zeitschrift für Operations Research Y1 - 1991 VL - 35 IS - 1 SP - 61 EP - 84 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - Solution of large-scale symmetric travelling salesman problems JF - Mathematical Programming, Series A Y1 - 1991 VL - 51 IS - 2 SP - 141 EP - 202 ER - TY - CHAP A1 - Grötschel, Martin ED - O’Malley, Robert T1 - Discrete Mathematics in Manufacturing T2 - ICIAM 1991 Y1 - 1991 SP - 119 EP - 145 PB - SIAM ER - TY - CHAP A1 - Deza, Michel A1 - Grötschel, Martin A1 - Laurent, Monique ED - Gritzmann, Peter ED - Sturmfels, Bernd T1 - Complete descriptions of small multicut polytopes T2 - Applied Geometry and Discrete Mathematics, The Victor Klee Festschrift Y1 - 1991 VL - 4 SP - 221 EP - 252 PB - AMS ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - Facets of the clique partitioning polytope JF - Mathematical Programming, Series A Y1 - 1990 VL - 47 IS - 3 SP - 367 EP - 387 ER - TY - CHAP A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko ED - Bodendiek, Rainer ED - Henn, Rudolf T1 - Composition of facets of the clique partitioning polytope T2 - Topics in combinatorics and graph theory. Essays in honour of Gerhard Ringel Y1 - 1990 SP - 271 EP - 284 PB - Physica-Verlag CY - Heidelberg ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde T1 - Integer Polyhedra Arising from Certain Network Design Problems with Connectivity Constraints JF - SIAM Journal on Discrete Mathematics Y1 - 1990 VL - 3 IS - 4 SP - 502 EP - 523 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - A cutting plane algorithm for a clustering problem JF - Mathematical Programming, Series B Y1 - 1989 VL - 45 SP - 59 EP - 96 PB - Mathematical Programming, Series B ER - TY - CHAP A1 - Ascheuer, Norbert A1 - Escudero, Laureano A1 - Grötschel, Martin A1 - Stoer, Mechthild ED - Kannan, Ravi ED - Pulleyblank, William T1 - On Identifying in Polynomial Time Violated Subtour Elimination and Precedence Forcing Constraints for the Sequential Ordering Problem T2 - Integer Programming and Combinatorial Optimization, Proceeedings of a Conference held at the University of Waterloo, May 28-30, 1990 Y1 - 1990 SP - 19 EP - 28 PB - University of Waterloo Press ER - TY - JOUR A1 - Grötschel, Martin A1 - Truemper, Klaus T1 - Master Polytopes for Cycles of Binary Matroids JF - Linear Algebra and its Applications Y1 - 1989 VL - 114/115 SP - 523 EP - 540 ER - TY - JOUR A1 - Grötschel, Martin A1 - Truemper, Klaus T1 - Decomposition and Optimization over Cycles in Binary Matroids JF - Journal of Combinatorial Theory, Series B Y1 - 1989 VL - 46 IS - 3 SP - 306 EP - 337 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Via Minimization with Pin Preassignments and Layer Preference JF - ZAMM – Zeitschrift für Angewandte Mathematik und Mechanik Y1 - 1989 VL - 69 IS - 11 SP - 393 EP - 399 ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - An application of combinatorial optimization to statistical physics and circuit layout design JF - Operations Research Y1 - 1988 VL - 36 IS - 3 SP - 493 EP - 513 ER - TY - BOOK A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Geometric Algorithms and Combinatorial Optimization T3 - Algorithms and Combinatorics Y1 - 1988 SN - 3-540-13624-X, 0-387-13624-X (U.S.) VL - 2 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard ED - van Hemmen, J. ED - Morgenstern, I. T1 - Calculating Exact Ground States of Spin Glasses T2 - Proceedings of the Heidelberg Colloquium on “Glassy Dynamics”, Lecture Notes in Physics 275 Y1 - 1987 SP - 325 EP - 353 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - Pulleyblank, William T1 - Clique tree inequalities and the symmetric travelling salesman problem JF - Mathematics of Operations Research Y1 - 1986 VL - 11 IS - 4 SP - 537 EP - 569 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - A Cutting Plane Algorithm for Minimum Perfect 2-Matchings JF - Computing Y1 - 1987 VL - 39 SP - 327 EP - 344 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Relaxations of Vertex Packing JF - Journal of Combinatorial Theory, Series B Y1 - 1986 VL - 40 SP - 330 EP - 343 ER - TY - CHAP A1 - Grötschel, Martin ED - Kerber, Adalbert T1 - Polyedrische Kombinatorik und Schnittebenenverfahren, Tagungsbericht 2. Sommerschule Diskrete Strukturen, Bayreuth 1985 T2 - Diskrete Strukturen, algebraische Methoden und Anwendungen Y1 - 1986 VL - 21 SP - 69 EP - 100 PB - Institut für Mathematik, Universität Bayreuth ER - TY - CHAP A1 - Grötschel, Martin ED - Krelle, Wilhelm T1 - Fortschritte in der polyedrischen Kombinatorik T2 - Ökonomische Prognose-, Entscheidungs- und Gleichgewichtsmodelle, Abschlußberichte des SFB 21 Y1 - 1986 SP - 341 EP - 367 PB - Verlag Chemie CY - Weinheim ER - TY - RPRT A1 - Barahona, Francisco A1 - Grötschel, Martin T1 - The Travelling Salesman Problem for Graphs not Contractible to K_5 - e Y1 - 1985 IS - 77 PB - Mathematisches Institut, Universität Augsburg ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin T1 - On the Cycle Polytope of a Binary Matroid JF - Journal of Combinatorial Theory, Series B Y1 - 1986 VL - 40 SP - 40 EP - 62 ER - TY - CHAP A1 - Padberg, Manfred A1 - Grötschel, Martin ED - Lawler, Eugene ED - Lenstra, Jan ED - Kan, Alexander ED - Shmoys, David T1 - Polyhedral computations T2 - The Traveling Salesman Problem. A Guided Tour of Combinatorial Optimization Y1 - 1985 SP - 307 EP - 360 PB - Wiley ER - TY - CHAP A1 - Grötschel, Martin A1 - Padberg, Manfred ED - Lawler, Eugene ED - Lenstra, Jan ED - Kan, Alexander ED - Shmoys, David T1 - Polyhedral theory T2 - The Traveling Salesman Problem. A Guided Tour of Combinatorial Optimization Y1 - 1985 SP - 251 EP - 306 PB - Wiley ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - On the acyclic subgraph polytope JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 1 SP - 28 EP - 42 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Facets of the linear ordering polytope JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 1 SP - 43 EP - 60 PB - North-Holland ER - TY - CHAP A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard ED - Rival, Ivan T1 - Acyclic subdigraphs and linear orderings T2 - Graphs and Order. The Role of Graphs in the Theory of Ordered Sets and its Applications, Proceedings of NATO ASI, Ser. C 147, Banff/Canada 1984 Y1 - 1985 SP - 217 EP - 264 PB - D. Reidel Publishing Company ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin A1 - Mahjoub, Ali T1 - Facets of the Bipartite Subgraph Polytope JF - Mathematics of Operations Research Y1 - 1985 VL - 10 SP - 340 EP - 358 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - Solving matching problems with linear programming JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 3 SP - 243 EP - 259 ER - TY - CHAP A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko ED - Cottle, Richard ED - Kelmanson, Milton ED - Korte, Bernhard T1 - Constructions of hypotraceable digraphs T2 - Mathematical Programming. Proceedings of the International Congress on Mathematical Programming, Rio de Janeiro, Brazil, 6-8 April 1981 Y1 - 1984 SP - 147 EP - 175 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Corrigendum to our paper “The ellipsoid method and its consequences in combinatorial optimization” JF - Combinatorica Y1 - 1984 VL - 4 IS - 4 SP - 291 EP - 295 ER - TY - JOUR A1 - Grötschel, Martin A1 - Nemhauser, George T1 - A polynomial algorithm for the max-cut problem on graphs without long odd cycles JF - Mathematical Programming Y1 - 1984 VL - 29 IS - 1 SP - 28 EP - 40 PB - North-Holland ER - TY - CHAP A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander ED - Berge, Claude ED - Chvátal, Vašek T1 - Polynomial algorithms for perfect graphs T2 - Topics on perfect graphs Y1 - 1984 VL - 21 SP - 325 EP - 356 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Optimal triangulation of large real world input-output matrices JF - Statistische Hefte Y1 - 1984 VL - 25 SP - 261 EP - 295 ER - TY - CHAP A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander ED - Pulleyblank, William T1 - Geometric Methods in Combinatorial Optimization T2 - Progress in Combinatorial Optimization, (Conference Waterloo/Ontario 1982) Y1 - 1984 SP - 167 EP - 183 PB - Academic Press ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - A Cutting Plane Algorithm for the Linear Ordering Problem JF - Operations Research Y1 - 1984 VL - 32 IS - 6 SP - 1195 EP - 1220 ER - TY - CHAP A1 - Grötschel, Martin ED - O’Heigeartaigh, Michael ED - Lenstra, Jan ED - Kan, Alexander T1 - Polyhedral Combinatorics T2 - COMBINATORIAL OPTIMIZATION Y1 - 1984 SP - 1 EP - 10 PB - Wiley ER - TY - RPRT A1 - Grötschel, Martin T1 - Polyedrische Kombinatorik und Schnittebenenverfahren Y1 - 1984 IS - 231 PB - Forschungszentrum Graz, Österreich ER - TY - CHAP A1 - Grötschel, Martin ED - Jäger, Willi ED - Moser, J. ED - Remmert, R. T1 - Developments in combinatorial optimization T2 - Perspectives in Mathematics (Anniversary of Oberwolfach 1984) Y1 - 1984 SP - 249 EP - 294 PB - Birkhäuser CY - Basel ER - TY - CHAP A1 - Grötschel, Martin ED - Bollobás, Béla T1 - On Intersections of Longest Cycles T2 - Graph Theory and Combinatorics Y1 - 1984 SP - 171 EP - 189 PB - Academic Press ER - TY - BOOK ED - Bachem, Achim ED - Grötschel, Martin ED - Korte, Bernhard T1 - Mathematical Programming. The State of the Art, Bonn 1982 Y1 - 1983 SN - 3-540-12082-3 PB - Springer ER - TY - CHAP A1 - Grötschel, Martin ED - Korte, Bernhard T1 - Approaches to Hard Combinatorial Optimization Problems T2 - Modern Applied Mathematics, Optimization and Operations Research, Lect. Summer Sch., Bonn 1979 Y1 - 1982 SP - 437 EP - 515 PB - North-Holland ER - TY - CHAP A1 - Grötschel, Martin ED - der Universität Bonn, Der T1 - Kombinatorische Optimierung T2 - Forschungsbericht 1978-1980 der Rheinischen Friedrich-Wilhelms-Universität Y1 - 1982 SP - 45 EP - 54 PB - Bouvier CY - Bonn ER - TY - BOOK ED - Bachem, Achim ED - Grötschel, Martin ED - Korte, Bernhard T1 - Bonn Workshop on Combinatorial Optimization T3 - Annals of Discrete Mathematics, 16. North-Holland Mathematics Studies 66 Y1 - 1982 SN - 0-444-86366-4 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - On the structure of the monotone asymmetric travelling salesman polytope II JF - Mathematical Programming Study Y1 - 1981 VL - 14 SP - 77 EP - 97 ER - TY - CHAP A1 - Bachem, Achim A1 - Grötschel, Martin ED - Korte, Bernhard T1 - New aspects of polyhedral theory T2 - Modern Applied Mathematics Y1 - 1982 SP - 51 EP - 106 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Pulleyblank, William T1 - Weakly bipartite graphs and the max-cut problem JF - Operations Research Letters Y1 - 1981 VL - 1 IS - 1 SP - 23 EP - 27 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - On the structure of the monotone asymmetric travelling salesman polytope I JF - Discrete Mathematics Y1 - 1981 VL - 34 SP - 43 EP - 59 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - The ellipsoid method and its consequences in combinatorial optimization JF - IIASA Collab. Proceedings Ser. CP-81-S1 Y1 - 1981 SP - 511 EP - 546 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - The ellipsoid method and its consequences in combinatorial optimization JF - Combinatorica Y1 - 1981 VL - 1 IS - 2 SP - 169 EP - 197 ER - TY - CHAP A1 - Bachem, Achim A1 - Grötschel, Martin ED - König, Heinz ED - Korte, Bernhard ED - Ritter, Klaus T1 - Characterizations of adjacency of faces of polyhedra T2 - Mathematical Programming at Oberwolfach Y1 - 1981 VL - 14 SP - 1 EP - 22 PB - North-Holland ER - TY - JOUR A1 - Bachem, Achim A1 - Grötschel, Martin T1 - Homogenization of polyhedra JF - Methods of Operations Research Y1 - 1981 VL - 40 SP - 215 EP - 219 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - Hypohamiltonian digraphs JF - Methods of Operations Research Y1 - 1980 VL - 36 SP - 99 EP - 119 ER - TY - BOOK A1 - Bachem, Achim A1 - Butz, Lothar A1 - Grötschel, Martin A1 - (Bearb.), Rainer A1 - Leitung), Bernhard T1 - Input-Output-Analyse bei unternehmensgrößenspezifischen Fragestellungen Y1 - 1981 PB - Institut für Mittelstandsforschung CY - Bonn ER - TY - JOUR A1 - Grötschel, Martin A1 - Thomassen, Carsten A1 - Wakabayashi, Yoshiko T1 - Hypotraceable digraphs JF - Journal of Graph Theory Y1 - 1980 VL - 4 SP - 377 EP - 381 ER - TY - JOUR A1 - Grötschel, Martin T1 - On the symmetric travelling salesman problem JF - Mathematical Programming Study Y1 - 1980 VL - 12 SP - 61 EP - 77 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin T1 - On the monotone symmetric travelling salesman problem JF - Mathematics of Operations Research Y1 - 1980 VL - 5 IS - 2 SP - 285 EP - 292 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - On the symmetric travelling salesman problem I JF - Mathematical Programming Y1 - 1979 VL - 16 SP - 265 EP - 280 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - On the symmetric travelling salesman problem II JF - Mathematical Programming Y1 - 1979 VL - 16 SP - 281 EP - 302 ER - TY - JOUR A1 - Grötschel, Martin A1 - Harary, Frank T1 - The Graphs for which All Strong Orientations Are Hamiltonian JF - Journal of Graph Theory Y1 - 1979 VL - 3 SP - 221 EP - 223 ER - TY - JOUR A1 - Grötschel, Martin T1 - On minimal strong blocks JF - Journal of Graph Theory Y1 - 1979 VL - 3 SP - 213 EP - 219 ER - TY - CHAP A1 - Grötschel, Martin ED - Collatz, Lothar ED - Meinardus, G. ED - Wetterling (Hrsg.), W. T1 - Strong blocks and the optimum branching problem T2 - Numerische Methoden bei graphentheoretischen und kombinatorischen Problemen, Bd. 2, Tagung in Oberwolfach 1978 Y1 - 1979 VL - 46 SP - 112 EP - 121 PB - Birkhäuser CY - Basel ER - TY - CHAP A1 - Grötschel, Martin A1 - Padberg, Manfred ED - Henn, Rudolf ED - Korte, Bernhard ED - Oettli, W. T1 - On the symmetric travelling salesman problem T2 - Optimization and operations research, Proc. Workshop, Bonn 1977 Y1 - 1978 VL - 157 SP - 105 EP - 115 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin A1 - von Randow, Rabe T1 - A property of continuous unbounded algorithms JF - Mathematical Programming Y1 - 1978 VL - 14 SP - 373 EP - 377 ER - TY - JOUR A1 - Grötschel, Martin T1 - Hypo-Hamiltonian Facets of the Symmetric Travelling Salesman Polytope JF - Zeitschrift für Angewandte Mathematik und Mechanik Y1 - 1978 VL - 58 SP - T469 EP - T471 ER - TY - CHAP A1 - Grötschel, Martin A1 - Korte, Bernhard ED - Albach, Horst ED - Helmstädter, Ernst ED - Henn, Rudolf T1 - Bemerkungen zur Optimierung ökonomischer Modelle T2 - Quantitative Wirtschaftsforschung, Willhelm Krelle zum 60. Geburtstag Y1 - 1977 SP - 457 EP - 467 PB - J. C. B. Mohr CY - Tübingen ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Lineare Charakterisierungen von Travelling Salesman Problemen JF - Zeitschrift für Operations Research, Series A Y1 - 1977 VL - 21 IS - 1 SP - 33 EP - 64 PB - Physica-Verlag ER - TY - CHAP A1 - Grötschel, Martin T1 - The monotone 2-matching polytope on a complete graph T2 - Operations Research Verfahren XXIV, Symposium in Mannheim Y1 - 1977 SP - 72 EP - 84 ER - TY - CHAP A1 - Grötschel, Martin T1 - Facetten von Matroid-Polytopen T2 - Operations Research Verfahren XXV, Symposium Heidelberg 1976 Y1 - 1977 SP - 306 EP - 313 ER - TY - BOOK A1 - Grötschel, Martin T1 - Polyedrische Charakterisierungen kombinatorischer Optimierungsprobleme T3 - Mathematical Systems in Economics Y1 - 1977 SN - 3-445-01537-6 VL - 36 PB - Verlag Anton Hain CY - Meisenheim am Glan ER - TY - CHAP A1 - Grötschel, Martin ED - Hammer, Peter ED - Johnson, Ellis ED - Korte, Bernhard ED - Nemhauser, George T1 - Graphs with cycles containing given paths T2 - Studies in Integer Programming Y1 - 1977 VL - 1 SP - 233 EP - 245 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Partial linear characterizations of the asymmetric travelling salesman polytope JF - Mathematical Programming Y1 - 1975 VL - 8 SP - 378 EP - 381 ER - TY - CHAP A1 - Grötschel, Martin ED - Kohlas, Jürg ED - Seifert, Olaf ED - Zimmermann, H. T1 - Über Graphen mit Kreisen, die gegebene Wege enthalten T2 - Proceedings in Operations Research Y1 - 1976 VL - 5 SP - 119 EP - 121 PB - Physica-Verlag CY - Würzburg ER - TY - THES A1 - Grötschel, Martin T1 - Der Satz von Frobenius für konvergente Potenzreihen Y1 - 1973 ER - TY - THES A1 - Gleixner, Ambros T1 - Solving Large-scale Open Pit Mining Production Scheduling Problems by Integer Programming Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2009/1187/ ER - TY - JOUR A1 - Boland, Natashia A1 - Dumitrescu, Irina A1 - Froyland, Gary A1 - Gleixner, Ambros T1 - LP-based disaggregation approaches to solving the open pit mining production scheduling problem with block processing selectivity JF - Computers & Operations Research Y1 - 2009 VL - 36 SP - 1064 EP - 1089 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Buehler, Jörg T1 - Optimal Control of a Single Queue with Retransmissions JF - IEEE Trans. on Wireless Communications Y1 - 2009 VL - 8, no. 7 SP - 3736 EP - 3746 ER - TY - JOUR A1 - Wiese, M. A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard T1 - Optimal Power Allocation Policies for the Reliable Transmission of a Single Packet via ARQ Protocols JF - Asilomar Conf. on Sign. Sys. and Comp. Y1 - 2008 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger A1 - Stefanov, Stoycho T1 - Optimal Control of Transmission Errors with Power Allocation and Stability in ARQ Downlink JF - CISS’08, Princeton, USA Y1 - 2008 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger T1 - An Optimal Stopping Approach to ARQ Protocols with Variable Success Probabilities per Retransmission JF - 45th Ann. Allerton Conf. Y1 - 2007 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger T1 - A short-term throughput measure for communications using ARQ protocols JF - Proc. 7th ITG Conf. on SCC Y1 - 2008 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Stanczak, Slawomir T1 - Stability and Distributed Power Control in MANETs with per Hop Retransmissions JF - IEEE Trans. on Communications Y1 - 2011 ER - TY - CHAP A1 - Giovanidis, Anastasios A1 - Stanczak, Slawomir T1 - Conditions for the Stability of Wireless ARQ Protocols and Reliable Communications T2 - 15th European Wireless Conference, Aalborg, Denmark Y1 - 2009 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Stanczak, Slawomir T1 - Retransmission Aware Congestion Control and Distributed Power Allocation in MANETs JF - Proc. 5th Int. Workshop on Resource Allocation, Cooperation and Competition in Wireless Networks (RAWNET/WNC3), Seoul, Korea Y1 - 2009 ER - TY - CHAP A1 - Giovanidis, Anastasios A1 - Sezgin, A. A1 - Mönich, U. A1 - Kim, D. T1 - Dynamic User Grouping and Shared Frequency Resource Assignment Strategies for OFDMA T2 - IEEE 65th Vehicular Technology Conference VTC2007-Spring, Dublin, Ireland Y1 - 2007 ER - TY - CHAP A1 - Giovanidis, Anastasios A1 - Haustein, T. A1 - Jorswieck, E. A1 - Kim, D. T1 - Maximization of the Single User Rate in OFDMA Assuming Equal Power on Allocated Subcarriers T2 - IEEE 65th Vehicular Technology Conference VTC2007-Spring, Dublin, Ireland Y1 - 2007 ER - TY - BOOK A1 - Giovanidis, Anastasios T1 - ARQ protocols in wireless communications Y1 - 2010 SN - 978-3-8381-2055-3 PB - SVH Verlag ER - TY - CHAP A1 - Giovanidis, Anastasios A1 - Haustein, T. A1 - Hadisusanto, Y. A1 - Sezgin, A. A1 - Kim, D. T1 - Multiuser Scheduling using Equal Power in Allocated Subcarriers for OFDM Uplink T2 - 40th Annual Asilomar Conference on Signals, Systems and Computers, Monterey, USA Y1 - 2006 ER - TY - GEN A1 - Fügenschuh, Armin T1 - Proteinfaltung Y1 - 2001 PB - Mathematische Modellierung mit Schülern - Die Modellierungswoche im Kloster Höchst. M. Kiehl, A. Schich, S. Purpus (Hrsg.). Zentrum für Mathematik, Bensheim ER - TY - GEN A1 - Fügenschuh, Armin T1 - Einsatzplanung von ÖPNV-Bussen Y1 - 2002 PB - Mathematische Modellierung mit Schülern - Die Modellierungswoche im Kloster Höchst. M. Kiehl, A. Schich, S. Purpus (Hrsg.). Zentrum für Mathematik, Bensheim ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Mathematische Modelle zur betrieblichen Optimierung JF - Z! - das Zukunftsmagazin Y1 - 2006 VL - 1 SP - 3 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Optimal verknüpft - Schulanfangszeiten und öffentlicher Personennahverkehr JF - thema forschung Y1 - 2006 VL - 1 SP - 82 EP - 85 ER - TY - GEN A1 - Fügenschuh, Armin T1 - Optimale Schulanfangszeiten Y1 - 2006 PB - Bild der Wissenschaft 11/2006, Sonderbeilage zum Klaus-Tschira-Preis ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Huhn, Petra A1 - Klamroth, Kathrin A1 - Saliba, Sleman A1 - Tammer, Christiane T1 - EURO Summer Institute 2006 in Wittenberg JF - OR News Y1 - 2006 VL - 28 SP - 71 EP - 72 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Optimierte Schulanfangszeiten JF - OR News Y1 - 2006 VL - 28 SP - 25 EP - 27 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Bestes Blech – Der hochkomplexe unsichtbare Weg zum präzisen und belastbaren Bauteil JF - hoch$^3$ Y1 - 2007 VL - 2 SP - 20 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Spalten am Stück – Maschinenbauer, Materialwissenschaftler und Mathematiker erfinden die Blechbearbeitung neu JF - hoch$^3$ Y1 - 2007 VL - 2 SP - 19 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Scheduling School Starting Times and Public Buses JF - SIAG/OPT Views-and-News Y1 - 2009 VL - 20 IS - 1 SP - 1 EP - 6 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Türke, Ulrich A1 - Meijerink, Ellen T1 - XML Data Specification and Documentation Y1 - 2003 PB - IST-2000-28088 MOMENTUM Technical Report ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Verfahren und Vorrichtung zur automatischen Optimierung von Schulanfangszeiten und des öffentlichen Personenverkehrs und entsprechendes Computerprogramm JF - Deutsche Patentanmeldung Y1 - 2004 VL - DE 10 2004 020 786.0 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Ulbrich, Stefan T1 - Verfahren und Vorrichtung zum Auswuchten von wellenelastischen Rotoren JF - Deutsche Patentanmeldung Y1 - 2006 VL - DE 10 2006 060 583.7 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Schabel, Samuel A1 - Schönberger, Christine A1 - Villforth, Klaus T1 - Verfahren zum Einstellen und/oder Optimieren einer einen Gutstoff von einem Schlechtstoff trennenden Sortieranlage und Sortieranlage JF - Deutsches Patent Y1 - 2008 VL - DE 10 2008 013 034 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Schabel, Samuel A1 - Schönberger, Christine A1 - Villforth, Klaus T1 - Steuerung einer Sortieranlage, z.B. für Altpapier JF - Europäische Patentanmeldung Y1 - 2010 VL - EP 09 718 564.9 ER - TY - CHAP A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Koch, Thorsten A1 - Koster, Arie M.C.A. A1 - Martin, Alexander A1 - Pfender, Tobias A1 - Wegel, Oliver A1 - Wessäly, Roland ED - G. Anandalingam, S. T1 - Mathematical Model of Feasible Network Configurations for UMTS T2 - Telecommunications network design and management Y1 - 2002 SP - 1 EP - 24 PB - Kluwer ER - TY - CHAP A1 - Fügenschuh, Armin ED - Görts, W. T1 - Von Mikrochips, Proteinen und Schulbussen – Projektproseminare im Mathematikstudium T2 - Projektveranstaltungen in Mathematik, Informatik und Ingenieurwissenschaften Y1 - 2003 SP - 21 EP - 43 PB - UVW UniversitätsVerlagWebler, Bielefeld ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Martin, Alexander ED - Aardal, Karen I. ED - Nemhauser, George ED - Weismantel, R. T1 - Computational Integer Programming and Cutting Planes T2 - Handbooks in Operations Research and Management Science, Vol. 12 Y1 - 2005 SP - 69 EP - 122 PB - North-Holland ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Stöveken, Peter ED - Bixby, Robert E. ED - Simchi-Levi, D. ED - Martin, Alexander ED - Zimmermann, U. T1 - Integrated Optimization of School Starting Times and Public Bus Services T2 - Mathematics in the Supply Chain Y1 - 2004 ER - TY - CHAP A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Geerdes, Hans-Florian A1 - Junglas, Daniel A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Integer Programming Methods for UMTS Radio Network Planning T2 - Proceedings of the WiOpt’04, Cambridge, UK Y1 - 2004 ER - TY - CHAP A1 - Fügenschuh, Armin ED - Jaszkiewicz, A. ED - Kaczmarek, M. ED - Zak, J. ED - Kubiak, M. T1 - Scheduling Buses in Rural Areas T2 - Advanced OR and AI Methods in Transportation, 10th EWGT / 16th Mini-Euro Conference Proceedings, Poznan Y1 - 2005 SP - 706 EP - 711 ER - TY - CHAP A1 - Fügenschuh, Armin ED - Aguilera, María J. ED - Blum, Christian ED - Roli, Andrea ED - Sampels, Michael T1 - Parametrized Greedy Heuristics in Theory and Practice T2 - Hybrid Metaheuristics, Second International Workshop, HM 2005, Barcelona Y1 - 2005 SP - 21 EP - 31 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Stöveken, Peter T1 - Integrierte Optimierung der Schulanfangszeit und des Nahverkehrs-Angebots T2 - Tagungsband der Heureka’05 – Optimierung in Verkehr und Transport Y1 - 2005 SP - 265 EP - 278 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Mehlert, Christian A1 - Stöveken, Peter ED - Günther, H.-O. ED - Mattfeld, D. ED - Suhl, L. T1 - Ein Planungstool zur Schulzeitstaffelung T2 - Supply Chain Management und Logistik Y1 - 2005 SP - 419 EP - 436 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Stöveken, Peter ED - Fleuren, Hein ED - den Hertog, Dick ED - Kort, Peter T1 - Integrated Optimization of School Starting Times and Public Bus Services T2 - Operations Research Proceedings Y1 - 2005 SP - 150 EP - 157 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Huck, Andreas A1 - Martin, Alexander ED - Jacob, R. ED - Müller-Hannemann, Matthias T1 - Locomotive and Wagon Scheduling in Freight Transport T2 - Proceedings of the ATMOS06 Y1 - 2006 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Höfler, Benjamin ED - Gottlieb, J. ED - Raidl, G. T1 - Parametrized GRASP Heuristics for Three-Index Assignment T2 - Evolutionary Computation in Combinatorial Optimization Y1 - 2006 SP - 61 EP - 72 ER - TY - CHAP A1 - Birkhofer, Herbert A1 - Fügenschuh, Armin A1 - Günther, Ute A1 - Junglas, Daniel A1 - Martin, Alexander A1 - Sauer, Thorsten A1 - Ulbrich, Stefan A1 - Wäldele, Martin A1 - Walter, Stephan ED - Haasis, Hans-Dietrich ED - Kopfer, Herbert ED - Schönberger, Jörn T1 - Topology- and shape-optimization of branched sheet metal products T2 - Operations Research Proceedings Y1 - 2006 SP - 327 EP - 336 ER - TY - CHAP A1 - Fügenschuh, Armin ED - Waldmann, Karl-Heinz ED - Stocker, Ulrike T1 - Scheduling Buses and School Starting Times T2 - Operations Research Proceedings Y1 - 2007 SP - 17 EP - 22 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Hess, Wolfgang A1 - Martin, Alexander A1 - Ulbrich, Stefan ED - Groche, P. T1 - Diskrete und kontinuierliche Modelle zur Topologie- und Geometrie-Optimierung von Blechprofilen T2 - Sonderforschungsbereich 666 Y1 - 2007 SP - 37 EP - 47 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael ED - Oberweis, A. ED - Weinhardt, C. ED - Gimpel, H. ED - Koschmider, A. ED - Pankratius, V. ED - Schnizler, B. T1 - Water Contamination Detection T2 - eOrganisation Y1 - 2007 SP - 501 EP - 518 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael ED - Günther, H.-O. ED - Mattfeld, D. ED - Suhl, L. T1 - A new modeling approach for an integrated simulation and optimization of production networks T2 - Management logistischer Netzwerke Y1 - 2007 SP - 45 EP - 60 ER - TY - CHAP A1 - Birkhofer, Herbert A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Wäldele, Martin T1 - Algorithmenbasierte Produktentwicklung für integrale Blechbauweisen höherer Verzweigungsordnung T2 - Optimierung in der Produktentwicklung, 5. Geimeinsames Kolloquium Konstruktionstechnik Y1 - 2007 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Prick, Matthias A1 - Stöveken, Peter T1 - Ausschreibung von Linienbündeln versus Schulzeitkoordinierung? T2 - VWT Conference e-Proceedings Y1 - 2007 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Mixed-integer models for topology optimization in sheet metal design T2 - Sixth International Congress on Industrial Applied Mathematics (ICIAM07) and GAMM Annual Meeting, Zürich 2007 Y1 - 2007 SP - 2060049 EP - 2060050 ER - TY - CHAP A1 - Balaprakash, Prasanna A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Schoch, Michael A1 - Stützle, Thomas A1 - Yuan, Zhi ED - Aguilera, María J. T1 - Iterated Greedy Algorithms for a Real-World Cyclic Train Scheduling Problem T2 - Hybrid Metaheuristics, 4th International Workshop, HM 2008, Malaga, Spain, October 8-9, 2008 Y1 - 2008 SP - 21 EP - 31 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Hess, Wolfgang A1 - Schewe, Lars A1 - Martin, Alexander A1 - Ulbrich, Stefan ED - Groche, P. T1 - Verfeinerte Modelle zur Topologie- und Geometrie-Optimierung von Blechprofilen mit Kammern T2 - Sonderforschungsbereich 666 Y1 - 2008 SP - 17 EP - 28 ER - TY - CHAP A1 - Dsoki, Chalid A1 - Fügenschuh, Armin A1 - Hanselka, Holger A1 - Hochbaum, Dorit A1 - Hernandez-Magallanes, Irma A1 - Moreno-Centeno, Erick A1 - Peter, Andrea ED - Groche, P. T1 - Das ANSLC-Programm und das SDM im Vergleich T2 - Sonderforschungsbereich 666 Y1 - 2008 SP - 97 EP - 106 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - ler, Björn A1 - Martin, Alexander A1 - Morsi, Antonio ED - Barnhart, Cynthia ED - Clausen, Uwe ED - Lauther, Ulrich ED - Möhring, Rolf T1 - The Transport PDE and Mixed-Integer Linear Programming T2 - Dagstuhl Seminar Proceedings 09261, Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Deutschland Y1 - 2009 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Schülldorf, Hanno ED - Barnhart, Cynthia ED - Clausen, Uwe ED - Lauther, Ulrich ED - Möhring, Rolf T1 - Single Car Routing in Rail Freight Transport T2 - Dagstuhl Seminar Proceedings 09261, Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Deutschland Y1 - 2009 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Defterli, Özlem A1 - Weber, Gehard-Wilhelm T1 - New Discretization and Optimization Techniques with Results in the Dynamics of Gene-Environment Networks T2 - 3rd Global Conference on Power Control and Optimization (PCO 2010) Y1 - 2010 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Gausemeier, Pia A1 - Seliger, Günther A1 - Severengiz, Semih ED - Dangelmaier, W. T1 - Scenario Technique with Integer Programming for Sustainability in Manufacturing T2 - 8th International Heinz Nixdorf Symposium, Changing Paradigms Y1 - 2010 SP - 320 EP - 331 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Schülldorf, Hanno A1 - Vigerske, Stefan ED - Rodrigues, H. T1 - Mixed-Integer Nonlinear Problems in Transportation Applications T2 - Proceedings of the 2nd International Conference on Engineering Optimization (+CD-rom) Y1 - 2010 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Stöveken, Peter T1 - Integrierte Optimierung des ÖPNV-Angebots und der Schulanfangszeiten JF - Straß enverkehrstechnik Y1 - 2005 VL - 49 IS - 6 SP - 281 EP - 287 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Herty, Michael A1 - Klar, Axel A1 - Martin, Alexander T1 - Combinatorial and Continuous Models and Optimization for Traffic Flow on Networks JF - SIAM Journal on Optimization Y1 - 2006 VL - 16 IS - 4 SP - 1155 EP - 1176 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Welche Gemeinsamkeiten haben Jugendliche und Groß banken? JF - mathematiklehren Y1 - 2006 VL - 129 SP - 50 EP - 54 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - The Vehicle Routing Problem with Coupled Time Windows JF - Central European Journal of Operations Research Y1 - 2006 VL - 14 IS - 2 SP - 157 EP - 176 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - A Multicriterial Approach for Optimizing Bus Schedules and School Starting Times JF - Annals of Operations Research Y1 - 2006 VL - 147 IS - 1 SP - 199 EP - 216 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael A1 - Klar, Alexander A1 - Martin, Alexander T1 - A Discrete Optimization Approach to Large Scale Supply Networks Based on Partial Differential Equations JF - SIAM Journal on Scientific Computing Y1 - 2008 VL - 30 IS - 3 SP - 1490 EP - 1507 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Fügenschuh, Marzena T1 - Integer Linear Programming Models for Topology Optimization in Sheet Metal Design JF - Mathematical Methods of Operations Research Y1 - 2008 VL - 68 IS - 2 SP - 313 EP - 331 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Huck, Andreas A1 - Martin, Alexander A1 - Yuan, Zhi T1 - Scheduling Locomotives and Car Transfers in Freight Transport JF - Transportation Science Y1 - 2008 VL - 42 IS - 4 SP - 1 EP - 14 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Solving a School Bus Scheduling Problem with Integer Programming JF - European Journal of Operational Research Y1 - 2009 VL - 193 IS - 3 SP - 867 EP - 884 ER - TY - JOUR A1 - Dittel, Agnes A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael T1 - MIP Presolve Techniques for a PDE-based Supply Chain Model JF - Optimization Methods & Software Y1 - 2009 VL - 24 IS - 3 SP - 427 EP - 445 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Kirchner, Claus A1 - Herty, Michael A1 - Martin, Alexander T1 - Efficient Reformulation and Solution of a Nonlinear PDE-Controlled Flow Network Model JF - Computing Y1 - 2009 VL - 85 IS - 3 SP - 245 EP - 265 ER - TY - JOUR A1 - Frank, Martin A1 - Fügenschuh, Armin A1 - Herty, Michael A1 - Schewe, Lars T1 - The Coolest Path Problem JF - Networks and Heterogeneous Media Y1 - 2010 VL - 5 IS - 1 SP - 143 EP - 162 ER - TY - THES A1 - Fügenschuh, Armin T1 - Zur Bergman-Vollständigkeit hyperkonvexer Gebiete Y1 - 2000 ER - TY - BOOK A1 - Fügenschuh, Armin T1 - The Integrated Optimization of School Starting Times and Public Bus Services Y1 - 2005 PB - Logos Verlag Berlin ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Cardonha, Carlos T1 - A set partitioning approach to shunting T2 - LAGOS 09 V Latin-American Algorithms, Graphs and Optimization Symposium Y1 - 2009 SP - 359 EP - 364 PB - Elsevier ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the distribution of the number of packets in the fluid flow approximation of packet arrival streams JF - Queueing Syst. Y1 - 1994 VL - 17 SP - 275 EP - 315 ER - TY - CHAP A1 - Brandt, Andreas A1 - Brandt, Manfred A1 - Spahl, G. A1 - Weber, D. T1 - Modelling and optimization of call distribution systems T2 - Proc. 15th Int. Teletraffic Cong. (ITC 15) Y1 - 1997 SP - 133 EP - 144 CY - Washington D.C., USA ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the sojourn times for many-queue head-of-the-line processor-sharing systems with permanent customers JF - Math. Methods Oper. Res. Y1 - 1998 VL - 47 SP - 181 EP - 220 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On a two-queue priority system with impatience and its application to a call center JF - Methodol. Comput. Appl. Probab. Y1 - 1999 VL - 1 SP - 191 EP - 210 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the $M(n)/M(n)/s$ queue with impatient calls JF - Perform. Eval. Y1 - 1999 VL - 35 SP - 1 EP - 18 ER - TY - CHAP A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the computation of the probability of a system failure T2 - Proc. ESREL’99 10th European Conf. on Safety and Reliability, G.I. Schuëller, P. Kafka (eds.), Balkema Rotterdam Y1 - 1999 SP - 457 EP - 461 CY - München-Garching ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - A note on the stability of the many-queue head-of-the-line processor-sharing system with permanent customers JF - Queueing Syst. Y1 - 1999 VL - 32 SP - 363 EP - 381 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Approximation for overflow moments of a multiservice link with trunk reservation JF - Perform. Eval. Y1 - 2001 VL - 43 SP - 259 EP - 268 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Asymptotic results and a Markovian approximation for the $M(n)/M(n)/s+GI$ system JF - Queueing Syst. Y1 - 2002 VL - 41 SP - 73 EP - 94 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the moments of overflow and freed carried traffic for the $GI/M/C/0$ system JF - Methodol. Comput. Appl. Probab. Y1 - 2002 VL - 4 SP - 69 EP - 82 ER - TY - CHAP A1 - Brandt, Andreas A1 - Brandt, Manfred A1 - Rugel, S. A1 - Weber, D. T1 - Admission control for realtime traffic T2 - Proc. IEEE Wireless Communications & Networking Conference WCNC 2005 Y1 - 2005 CY - New Orleans, USA ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the two-class $M/M/1$ system under preemptive resume and impatience of the prioritized customers JF - Queueing Syst. Y1 - 2004 VL - 47 SP - 147 EP - 168 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Individual overflow and freed carried traffics for a link with trunk reservation JF - Telecommunication Syst. Y1 - 2005 VL - 29 SP - 283 EP - 308 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - A sample path relation for the sojourn times in $G/G/1-PS$ systems and its applications JF - Queueing Syst. Y1 - 2006 VL - 52 SP - 281 EP - 286 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Waiting times for $M/M$ systems under state-dependent processor sharing JF - Queueing Syst. Y1 - 2008 VL - 59 SP - 297 EP - 319 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the stability of the multi-queue multi-server processor sharing with limited service JF - Queueing Syst. Y1 - 2007 VL - 56 SP - 1 EP - 8 ER - TY - JOUR A1 - Brandt, Manfred A1 - Brandt, Andreas T1 - On sojourn times in $M/GI$ systems under state-dependent processor sharing JF - Queueing Syst. Y1 - 2010 VL - 64 SP - 167 EP - 201 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Insensitive bounds for the moments of the sojourn times in $M/GI$ systems under state-dependent processor sharing JF - Adv. Appl. Probab. Y1 - 2010 VL - 42 SP - 246 EP - 267 ER - TY - CHAP A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Martin, Alexander T1 - Leitwegeplanung T2 - Mathematik für Innovationen in Industrie und Dienstleistungen Y1 - 2007 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas A1 - Weider, Steffen T1 - Integrierte Umlauf- und Dienstplanung im öffentlichen Nahverkehr T2 - Neue Mathematische Verfahren in Industrie und Dienstleistungen Y1 - 2001 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Dienstplanung im öffentlichen Nahverkehr T2 - Mathematische Verfahren zur Lösung von Problemstellungen in Industrie und Wirtschaft Y1 - 1997 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Umlaufplanung im öffentlichen Nahverkehr T2 - Anwendungsorientierte Verbundprojekte auf dem Gebiet der Mathematik Y1 - 1994 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Erlebach, Thomas ED - Lübbecke, Marco T1 - Railway Track Allocation by Rapid Branching T2 - Proceedings of the 10th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems Y1 - 2010 UR - http://drops.dagstuhl.de/opus/volltexte/2010/2746 U6 - https://doi.org/http://dx.doi.org/10.4230/OASIcs.ATMOS.2010.13 VL - 14 SP - 13 EP - 23 PB - Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - BOOK A1 - Borndörfer, Ralf T1 - Mathematical Optimization and Public Transportation Y1 - 2010 PB - TU Berlin ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Mura, Annette A1 - Schlechte, Thomas ED - Fleischmann, Bernhard ED - Borgwardt, Karl ED - Klein, Robert ED - Tuma, Axel T1 - Vickrey Auctions for Railway Tracks T2 - Operations Research Proceedings 2008 Y1 - 2009 UR - http://opus.kobv.de/zib/volltexte/2008/1122/ SP - 551 EP - 556 PB - Springer-Verlag ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc ED - Fleischmann, Bernhard ED - Borgwardt, Karl ED - Klein, Robert ED - Tuma, Axel T1 - The Line Connectivity Problem T2 - Operations Research Proceedings 2008 Y1 - 2009 UR - http://opus.kobv.de/zib/volltexte/2008/1117/ SP - 557 EP - 562 PB - Springer-Verlag ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Cardonha, Carlos T1 - A Set Partitioning Approach to Shunting JF - Electronic Notes in Discrete Mathematics Y1 - 2009 UR - http://opus.kobv.de/zib/volltexte/2009/1181/ U6 - https://doi.org/10.1016/j.endm.2009.11.059 SP - 359 EP - 364 ER - TY - CHAP A1 - Torres, Luis Miguel A1 - Torres, Ramiro A1 - Borndörfer, Ralf A1 - Pfetsch, Marc ED - Fischetti, Matteo ED - Widmayer, Peter T1 - Line Planning on Paths and Tree Networks with Applications to the Quito Trolebus System T2 - ATMOS 2008 - 8th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems Y1 - 2008 UR - http://drops.dagstuhl.de/opus/volltexte/2008/1580 PB - Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany CY - Dagstuhl, Germany ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schlechte, Thomas ED - Kalcsics, Jörg ED - Nickel, Stefan T1 - Solving Railway Track Allocation Problems T2 - Operations Research Proceedings 2007 Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2007/974/ SP - 117 EP - 122 PB - Springer-Verlag ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - Angebotsplanung im öffentlichen Nahverkehr T2 - HEUREKA’08 Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2008/1084/ PB - FGSV Verlag ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Weider, Steffen ED - Hickman, Mark ED - Mirchandani, Pitu ED - Voß, Stefan T1 - A Bundle Method for Integrated Multi-Depot Vehicle and Duty Scheduling in Public Transit T2 - Computer-aided Systems in Public Transport Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2004/790/ VL - 600 SP - 3 EP - 24 PB - Springer-Verlag ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Liebchen, Christian ED - Kalcsics, Jörg ED - Nickel, Stefan T1 - When Periodic Timetables are Suboptimal T2 - Operations Research Proceedings 2007 Y1 - 2008 SP - 449 EP - 454 PB - SPRINGER ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc ED - Hickman, Mark ED - Mirchandani, Pitu ED - Voß, Stefan T1 - Models for Line Planning in Public Transport T2 - Computer-aided Systems in Public Transport (CASPT 2004) Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-73312-6_18 VL - 600 SP - 363 EP - 378 PB - Springer-Verlag ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Jaeger, Ulrich ED - Grötschel, Martin ED - Lucas, Klaus ED - Mehrmann, Volker T1 - Planungsprobleme im öffentlichen Verkehr T2 - PRODUKTIONSFAKTOR MATHEMATIK – Wie Mathematik Technik und Wirtschaft bewegt Y1 - 2008 UR - http://opus.kobv.de/zib/volltexte/2008/1103/ SP - 127 EP - 153 PB - acatech – Deutsche Akademie der Technikwissenschaften und Springer ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Schelten, Uwe A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Haasis, Hans-Dietrich T1 - A Column Generation Approach to Airline Crew Scheduling T2 - Operations Research Proceedings 2005 Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2005/871/ SP - 343 EP - 348 PB - Springer-Verlag ER - TY - CHAP A1 - Pfetsch, Marc A1 - Borndörfer, Ralf ED - Haasis, Hans-Dietrich T1 - Routing in Line Planning for Public Transportation T2 - Operations Research Proceedings 2005 Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2005/870/ SP - 405 EP - 410 PB - Springer-Verlag ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - Public transport to the fORe JF - OR/MS Today Y1 - 2006 UR - http://www.lionhrtpub.com/orms/orms-4-06/frtransport.html SP - 30 EP - 40 ER - TY - GEN A1 - Borndörfer, Ralf ED - Grötschel, Martin T1 - Combinatorial Packing Problems T2 - The Sharpest Cut – The Impact of Manfred Padberg and His Work Y1 - 2004 UR - http://opus.kobv.de/zib/volltexte/2003/726/ SP - 19 EP - 32 PB - SIAM CY - Philadelphia ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Weider, Steffen T1 - Integrierte Umlauf- und Dienstplanung im Öffentlichen Verkehr T2 - Heureka ’02 Y1 - 2002 UR - http://opus.kobv.de/zib/volltexte/2002/678/ SP - 77 EP - 98 PB - Forschungsgesellschaft für Straßen- und Verkehrswesen CY - Köln ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Weismantel, Robert T1 - Discrete Relaxations of Combinatorial Programs JF - Discrete Appl. Math. Y1 - 2001 UR - http://opus.kobv.de/zib/volltexte/1997/324/ VL - 112 IS - 1–3 SP - 11 EP - 26 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Weismantel, Robert T1 - Set Packing Relaxations of Some Integer Programs JF - Math. Programming Y1 - 2000 UR - http://opus.kobv.de/zib/volltexte/1997/300/ VL - 88 SP - 425 EP - 450 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas ED - Aigner, Martin ED - Behrends, Ehrhard T1 - Der schnellste Weg zum Ziel T2 - Alles Mathematik Y1 - 2000 U6 - https://doi.org/10.1007/978-3-322-96366-6_5 SP - 45 EP - 76 PB - Vieweg Verlag CY - Braunschweig/Wiesbaden ER - TY - GEN A1 - Borndörfer, Ralf A1 - Löbel, Andreas T1 - Dienstplanoptimierung im ÖPNV Y1 - 2000 UR - http://www.uni-duisburg.de/FB11/PUBL/PRPLIST/prp00.html ER - TY - GEN A1 - Borndörfer, Ralf T1 - Optimierung im Nahverkehr Y1 - 2000 UR - http://www.kompetenznetze.de/inhaltnf\_b1\_c2\_s2\_e1\_d0\_t102\_g14\_n11\_t102\_n11.htm PB - Forschungs- und Anwendungsverbund Verkehr & Initiativgemeinschaft Außeruniversitärer Forschungseinrichtungen in Adlershof e.V. ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Strubbe, Uwe A1 - Völker, Manfred T1 - Zielorientierte Dienstplanoptimierung T2 - Heureka ’99 Y1 - 1999 UR - http://opus.kobv.de/zib/volltexte/1998/385/ SP - 171 EP - 194 PB - Forschungsgesellschaft für Strassen- und Verkehrswesen CY - Köln ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian ED - Wilson, Nigel T1 - Telebus Berlin: Vehicle Scheduling in a Dial-a-Ride System T2 - Proceedings of the 7th International Workshop on Computer-Aided Transit Scheduling Y1 - 1999 U6 - https://doi.org/10.1007/978-3-642-85970-0_19 SP - 391 EP - 422 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Ferreira, Carlos A1 - Martin, Alexander T1 - Decomposing Matrices into Blocks JF - SIAM J. Optim. Y1 - 1998 UR - http://opus.kobv.de/zib/volltexte/1997/285/ VL - 9 IS - 1 SP - 236 EP - 269 ER - TY - THES A1 - Borndörfer, Ralf T1 - Aspects of Set Packing, Partitioning, and Covering Y1 - 1998 UR - http://opus.kobv.de/zib/volltexte/1998/1028/ ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Telebus Berlin – Mobilität für Behinderte JF - Der Nahverkehr Y1 - 1997 UR - http://opus.kobv.de/zib/volltexte/1996/251/ VL - 1–2 SP - 20 EP - 22 ER - TY - CHAP A1 - Borndörfer, Ralf A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Martin, Alexander T1 - Stable-Set and Other Techniques for Frequency Assignment Problems T2 - Anais da I Oficina Nacional em Problemas de Corte & Empacotamento Y1 - 1996 SP - 17 EP - 21 PB - Universidade de São Paulo, Instituto de Matemática e Estatística ER - TY - THES A1 - Borndörfer, Ralf T1 - Mengenpartitionen und ihre Anwendung auf ein Maschinenbelegungsproblem Y1 - 1991 ER - TY - THES A1 - Berthold, Timo T1 - Primal Heuristics for Mixed Integer Programs Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2007/1054/ ER - TY - JOUR A1 - Achterberg, Tobias A1 - Berthold, Timo T1 - Improving the Feasibility Pump JF - Discrete Optimization Y1 - 2007 VL - Special Issue 4 IS - 1 SP - 77 EP - 86 ER - TY - JOUR A1 - Berthold, Timo T1 - Heuristiken im Branch-and-Cut-Framework SCIP JF - OR News Y1 - 2008 IS - 32 SP - 24 EP - 25 ER - TY - CHAP A1 - Berthold, Timo ED - Kalcsics, Jörg ED - Nickel, Stefan T1 - Heuristics of the Branch-Cut-and-Price-Framework SCIP T2 - Operations Research Proceedings 2007 Y1 - 2008 SP - 31 EP - 36 PB - Springer-Verlag ER - TY - CHAP A1 - Achterberg, Tobias A1 - Berthold, Timo ED - van Hoeve, Willem ED - Hooker, John T1 - Hybrid Branching T2 - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 6th International Conference, CPAIOR 2009 Y1 - 2009 VL - 5547 SP - 309 EP - 311 PB - Springer ER - TY - CHAP A1 - Berthold, Timo A1 - Pfetsch, Marc ED - Fleischmann, Bernhard ED - Borgwardt, Karl ED - Klein, Robert ED - Tuma, Axel T1 - Detecting Orbitopal Symmetries T2 - Operations Research Proceedings 2008 Y1 - 2009 SP - 433 EP - 438 PB - Springer-Verlag ER - TY - CHAP A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Pfetsch, Marc ED - Kullmann, Oliver T1 - Nonlinear pseudo-Boolean optimization T2 - Theory and Applications of Satisfiability Testing – SAT 2009 Y1 - 2009 VL - 5584 SP - 441 EP - 446 PB - Springer ER - TY - CHAP A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Lübbecke, Marco A1 - Möhring, Rolf A1 - Schulz, Jens ED - Lodi, Andrea ED - Milano, Michela ED - Toth, Paolo T1 - A Constraint Integer Programming Approach for Resource-Constrained Project Scheduling T2 - Proc. of CPAIOR 2010 Y1 - 2010 VL - 6140 SP - 313 EP - 317 PB - Springer ER - TY - CHAP A1 - Berthold, Timo A1 - Feydy, Thibaut A1 - Stuckey, Peter ED - Lodi, Andrea ED - Milano, Michela ED - Toth, Paolo T1 - Rapid Learning for Binary Programs T2 - Proc. of CPAIOR 2010 Y1 - 2010 VL - 6140 SP - 51 EP - 55 PB - Springer ER - TY - JOUR A1 - Scharkoi, Olga A1 - Fackeldey, Konstantin A1 - Merkulow, Igor A1 - Andrae, Karsten A1 - Weber, Marcus A1 - Nehls, Irene T1 - Conformational Analysis of Alternariol on the Quantum Level JF - J. Mol. Model. Y1 - 2013 U6 - https://doi.org/10.1007/s00894-013-1803-2 VL - 19 IS - 6 SP - 2567 EP - 2572 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - A Square Root Approximation of Transition Rates for a Markov State Model JF - SIAM. J. Matrix Anal. Appl. Y1 - 2013 U6 - https://doi.org/10.1137/120899959 VL - 34 IS - 2 SP - 738 EP - 756 ER - TY - JOUR A1 - Hansen, Poul-Erik A1 - Burger, Sven T1 - Investigation of microstructured fiber geometries by scatterometry JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2020526 VL - 8789 SP - 87890R ER - TY - JOUR A1 - Soltwisch, Victor A1 - Burger, Sven A1 - Scholze, Frank T1 - Scatterometry sensitivity analysis for conical diffraction versus in-plane diffraction geometry with respect to the side wall angle JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2020487 VL - 8789 SP - 878905 ER - TY - JOUR A1 - Endres, Johannes A1 - Burger, Sven A1 - Wurm, Matthias A1 - Bodermann, Bernd T1 - Numerical investigations of the influence of different commonly applied approximations in scatterometry JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2022108 VL - 8789 SP - 878904 ER - TY - JOUR A1 - Wulkow, Michael A1 - Gerstlauer, A. A1 - Nieken, U. T1 - Modeling of Crystallization Processes using PARSIVAL JF - Chem. Eng. Sci. Y1 - 2001 VL - 56 SP - 2575 EP - 2588 ER - TY - JOUR A1 - Wulkow, Michael A1 - Busch, Markus A1 - Davis, Thomas P. A1 - Barner-Kowollik, Christopher T1 - Implementing the Reversible Addition Fragmentation Chain Transfer (RAFT) Process in Predici. JF - Journal of Polymer Science Y1 - 2004 VL - 42 SP - 1441 ER - TY - JOUR A1 - Wulkow, Michael T1 - Feature article - The Simulation of Molecular Weight Distributions in Polyreaction Kinetics by Discrete Galerkin Methods JF - Macromol. Theory Simul. Y1 - 1996 VL - 5 SP - 393 EP - 416 ER - TY - JOUR A1 - Wulkow, Michael T1 - Feature article - Computer Aided Modeling of Polymer Reaction Engineering - The Status of Predici, 1 - Simulation JF - Macromol. React. Eng. Y1 - 2008 VL - 2 SP - 461 EP - 494 ER - TY - JOUR A1 - Teichmann, L. A1 - Liebelt, U. A1 - Reuschenbach, P. A1 - Wulkow, Michael A1 - Horn, H. T1 - Two dimensional simulation of mass transport and nitrification in the river Rhine JF - Eng. Life Sci. Y1 - 2001 VL - 1 IS - 4 SP - 145 EP - 149 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics JF - Macromol. React. Eng. Y1 - 2010 VL - 4 SP - 562 EP - 577 ER - TY - JOUR A1 - Schmidt, Christian-Ulrich A1 - Busch, Markus A1 - Lilge, Dieter A1 - Wulkow, Michael T1 - Detailed Molecular Structure Modeling – A Path Forward to Designing Application Properties of ldPE JF - Macromolecular Materials and Engineering Y1 - 2005 VL - 290 SP - 404 ER - TY - JOUR A1 - Reynhout, X. A1 - Meuldijk, J. A1 - Drinkenburg, B. A1 - Iedema, P. A1 - Wulkow, Michael T1 - A Novel Method to Model Emulsion Polymerization Kinetics JF - Polymer-Plastics Tech. Eng. Y1 - 2005 VL - 44 IS - 4 SP - 707 EP - 740 ER - TY - JOUR A1 - Reuter, H. A1 - Krause, G. A1 - Wulkow, Michael A1 - Mönig, A. A1 - Horn, H. T1 - A water quality management tool for river basins JF - Wat. Sci. Techn. Y1 - 2003 VL - 48 IS - 10 SP - 47 EP - 53 ER - TY - JOUR A1 - Ochoa, J.G. A1 - Wulkow, Michael T1 - DNA damages as a Depolymerization Process JF - International Journal of Modern Physics C Y1 - 2012 VL - 23 IS - 03 SP - 1250018 EP - 1 ER - TY - JOUR A1 - Müller, A. A1 - Yan, D. A1 - Wulkow, Michael T1 - Molecular Parameters of Hyperbranched Polymers Made by Self-condensing Vinyl Polymerization, 1. Molecular weight distribution JF - Macromolecules Y1 - 1997 VL - 30 SP - 7015 ER - TY - JOUR A1 - Lin, P.-J. A1 - Grimm, L. A1 - Wulkow, Michael A1 - Hempel, D. A1 - Krull, R. T1 - Population Balance Modeling of the Conidial Aggregation of Aspergillus niger JF - Biotechnology and Bioengineering Y1 - 2008 VL - 99 IS - 2 SP - 341 EP - 350 ER - TY - JOUR A1 - Katzer, J. A1 - Pauer, W. A1 - Moritz, H.-U. A1 - Wulkow, Michael T1 - Thermal polymerization of styrene Part B JF - Macromol. React. Eng Y1 - 2012 VL - 6 SP - 225 EP - 238 ER - TY - JOUR A1 - Iedema, P. A1 - Wulkow, Michael A1 - Hoefsloot:, H. T1 - Modeling Molecular Weight and Degree of Branching Distribution of low density Polyethylene JF - Macromolecules Y1 - 2000 VL - 33 SP - 7173 EP - 7184 ER - TY - JOUR A1 - Iedema, P. A1 - Wulkow, Michael A1 - Hoefsloot, H. T1 - Conditional Monte Carlo sampling to find branching architectures of polymers from radical polymerizations with transfer to polymer and recombination termination JF - Polymer Y1 - 2007 VL - 48 IS - 6 SP - 1770 EP - 1784 ER - TY - JOUR A1 - Hungenberg, K.-D. A1 - Knoll, K. A1 - Wulkow, Michael T1 - Absolute Propagation Rate Coefficients in Radical Polymerization from Gel Permeation Chromatography of Polymers Produced by Intermittent Initiation JF - Macromol. Theory Simul. Y1 - 1997 VL - 6 ER - TY - JOUR A1 - Hungenberg, K.-D. A1 - Chen, C.-C. A1 - Zhang, F. A1 - Wulkow, Michael A1 - Stubbe, G. A1 - Nieken, U. T1 - Design of Polymer Processes Using the Coupling of Commercial Simulation Packages Polymers Plus and PREDICI JF - DECHEMA Monographs Y1 - 2001 VL - 137 SP - 237 EP - 245 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Telgmann, R. A1 - Wulkow, Michael T1 - The virtual lab approach to pharmacokinetic JF - Drug Discov Today Y1 - 2006 VL - 11 SP - 800 EP - 805 ER - TY - JOUR A1 - Horn, H. A1 - Wulkow, Michael T1 - Modellierung von Einleitungen in kleine Fließgewässer JF - gwf Wasser Abwasser Y1 - 1996 VL - 137 ER - TY - JOUR A1 - Horn, H. A1 - Wulkow, Michael T1 - Simulation von Wachstum und Abtrag der Biomasse – Eine exemplarische Betrachtung für eine 2D-Modellierung JF - Chem. Ing. Technik Y1 - 2005 VL - 77 IS - 4 SP - 418 EP - 424 ER - TY - JOUR A1 - Horn, H. A1 - Neu, T. A1 - Wulkow, Michael T1 - Modelling the Structure and Function of Extracellular Polymeric Substances in Biofilms with new Numerical Techniques JF - Wat. Sci. Techn. Y1 - 2001 VL - 43 IS - ´6 SP - 121 EP - 127 ER - TY - JOUR A1 - Grosch, R. A1 - Briesen, Heiko A1 - Wulkow, Michael A1 - Marquardt, Wolfgang T1 - Generalization and numerical investigation of QMOM for crystallization processes JF - AIChE J. Y1 - 2007 VL - 53 SP - 207 EP - 227 ER - TY - JOUR A1 - Busch, Markus A1 - Wulkow, Michael T1 - Modellierung differenzierter mikrostruktureller Eigenschaften JF - Chem. Ing. Tech. Y1 - 2003 VL - 75 SP - 1027 ER - TY - JOUR A1 - Busch, Markus A1 - Müller, M. A1 - Wulkow, Michael T1 - The use of Simulation Techniques in Developing Kinetic Models for Polymerizations JF - Chem. Eng. Technol. Y1 - 2003 VL - 26 SP - 1031 ER - TY - JOUR A1 - Brüggemann, Stefan A1 - Bauer, Nanette A1 - Fuchs, Eberhard A1 - Polt, Axel A1 - Wagner, Bernhard A1 - Wulkow, Michael T1 - Support of Strategic Business Decisions at BASF’s Largest Integrated Production Site Based on Site-Wide Verbund Simulation JF - Computer Aided Chem. Eng. Y1 - 2008 VL - 25 SP - 925 EP - 930 ER - TY - JOUR A1 - Bockhorn, Henning A1 - Hornung, Andreas A1 - Hornung, Ursel A1 - Jakobströer, Petra A1 - Wulkow, Michael T1 - Modeling of Thermal Degradation of Polymers JF - Proceedings of the Workshop Scientific Computing in Chemical Engineering II Y1 - 1999 VL - 1 ER - TY - JOUR A1 - Appel, Jörg A1 - Bockhorn, Henning A1 - Wulkow, Michael T1 - Numerical Simulation of Soot Particle Size Distributions with a Discrete Galerkin Method JF - Proceedings of the Workshop Scientific Computing in Chemical Engineering II Y1 - 1999 VL - 2 ER - TY - JOUR A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Becker, Christiane A1 - Ruske, Florian A1 - Schmidt, Frank A1 - Rech, Bernd T1 - Optical properties and Limits of a Large-Area Periodic Nanophotonic Light Trapping Design for Polycrystalline Silicon Thin Film Solar Cells JF - MRS Proceedings Y1 - 2013 U6 - https://doi.org/10.1557/opl.2013.28 VL - 1493 SP - 59 EP - 64 ER - TY - JOUR A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Becker, Christiane A1 - Rudigier-Voigt, Eveline A1 - Schmidt, Frank A1 - Rech, Bernd T1 - Nanophotonic light trapping in 3-dimensional thin-film silicon architectures JF - Opt. Express Y1 - 2013 U6 - https://doi.org/10.1364/OE.21.000A42 VL - 21 SP - A42 ER - TY - JOUR A1 - Sontheimer, Tobias A1 - Rudigier-Voigt, Eveline A1 - Bockmeyer, Matthias A1 - Lockau, Daniel A1 - Klimm, Carola A1 - Becker, Christiane A1 - Rech, Bernd T1 - Light harvesting architectures for electron beam evaporated solid phase crystallized Si thin film solar cells JF - Journal of Non-Crystalline Solids Y1 - 2012 U6 - https://doi.org/10.1016/j.jnoncrysol.2011.10.025 VL - 358 IS - 17 SP - 2303 EP - 2307 ER - TY - JOUR A1 - Becker, Christiane A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Schubert-Bischoff, Peter A1 - Rudigier-Voigt, Eveline A1 - Bockmeyer, Matthias A1 - Schmidt, Frank A1 - Rech, Bernd T1 - Large-area 2D periodic crystalline silicon nanodome arrays on nanoimprinted glass exhibiting photonic band structure effects JF - Nanotechnology Y1 - 2012 U6 - https://doi.org/10.1088/0957-4484/23/13/135302 VL - 23 IS - 13 SP - 135302 ER - TY - JOUR A1 - Tyminski, Jacek A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Flagello, Donis A1 - Matsuyama, Tomiyuki T1 - Topographic mask modeling with reduced basis finite element method JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2011613 VL - 8683 SP - 86831C ER - TY - JOUR A1 - Bock, Martin A1 - Skibina, Julia A1 - Fischer, Dorit A1 - Bretschneider, Mario A1 - Wedell, Reiner A1 - Grunwald, Rüdiger A1 - Burger, Sven A1 - Beloglazov, Valentin A1 - Steinmeyer, Günter T1 - Nanostructured fibers for sub-10 fs optical pulse delivery JF - Laser & Photonics Reviews Y1 - 2013 U6 - https://doi.org/10.1002/lpor.201300006 VL - 7 SP - 566 EP - 570 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. JF - preprint Y1 - 1992 UR - http://publications.imp.fu-berlin.de/109/ ER - TY - JOUR A1 - Schütte, Christof T1 - A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation JF - Impact of Computing in Sci. Eng. Y1 - 1993 UR - http://publications.imp.fu-berlin.de/108/ U6 - https://doi.org/10.1006/icse.1993.1008 VL - 5 IS - 3 SP - 176 EP - 200 ER - TY - JOUR A1 - Manz, Jörn A1 - Paramonov, G. A1 - Polasek, M. A1 - Schütte, Christof T1 - Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D JF - Isr. J. Chem. Y1 - 1994 UR - http://publications.imp.fu-berlin.de/107/ VL - 34 IS - 1 SP - 115 EP - 125 ER - TY - JOUR A1 - Schütte, Christof A1 - Dinand, Manfred T1 - Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers JF - J. Lightw. Techn. Y1 - 1995 UR - http://publications.imp.fu-berlin.de/106/ VL - 13 IS - 1 SP - 14 EP - 23 ER - TY - GEN A1 - Schütte, Christof T1 - Smoothed Molecular Dynamics for Thermally Embedded Systems Y1 - 1995 UR - http://publications.imp.fu-berlin.de/105/ ER - TY - JOUR A1 - Schütte, Christof A1 - Zumbusch, Gerhard A1 - Brinkmann, Ralf T1 - Dynamics of Erbium-doped Waveguide Lasers JF - preprint Y1 - 1995 UR - http://publications.imp.fu-berlin.de/104/ ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Nettesheim, Peter A1 - Schütte, Christof T1 - Quantum-classical molecular dynamics as an approximation to full quantum dynamics JF - J. Chem. Phys. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/103/ U6 - https://doi.org/10.1063/1.471952 VL - 105 IS - 3 SP - 1074 EP - 1083 ER - TY - JOUR A1 - Nettesheim, Peter A1 - Bornemann, Folkmar A. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics JF - Chem. Phys. Lett. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/101/ U6 - https://doi.org/10.1016/0009-2614(96)00471-X VL - 256 IS - 6 SP - 581 EP - 588 ER - TY - JOUR A1 - Nettesheim, Peter A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - Chebyshev-Approximation for Wavepacket-Dynamics JF - preprint Y1 - 1996 UR - http://publications.imp.fu-berlin.de/102/ ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Homogenization of Hamiltonian Systems with a Strong Constraining Potential JF - Physica D Y1 - 1997 UR - http://publications.imp.fu-berlin.de/100/ U6 - https://doi.org/10.1016/S0167-2789(96)00245-X VL - 102 IS - 1-2 SP - 57 EP - 77 ER - TY - JOUR A1 - Schütte, Christof A1 - Bornemann, Folkmar A. T1 - Homogenization Approach to Smoothed Molecular Dynamics JF - Nonlinear Analysis Y1 - 1997 UR - http://publications.imp.fu-berlin.de/99/ U6 - https://doi.org/10.1016/S0362-546X(97)00216-2 VL - 30 IS - 3 SP - 1805 EP - 1814 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble JF - J. Comp. Chem. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/97/ U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - A mathematical investigation of the Car-Parrinello Method JF - Num. Math. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/96/ U6 - https://doi.org/10.1007/s002110050316 VL - 78 IS - 3 SP - 359 EP - 376 ER - TY - THES A1 - Schütte, Christof T1 - Partial Wigner transforms and the quantum-classical Liouville equation Y1 - 1999 UR - http://publications.imp.fu-berlin.de/95/ ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - On the Singular Limit of the Quantum-Classical Molecular Dynamics Model JF - J. Appl. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/94/ U6 - https://doi.org/10.1137/S0036139997318834 VL - 59 IS - 4 SP - 1208 EP - 1224 ER - TY - CHAP A1 - Nettesheim, Peter A1 - Schütte, Christof ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Numerical Integrators for Quantum-Classical Molecular Dynamics T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.imp.fu-berlin.de/137/ VL - 4 SP - 396 EP - 411 PB - Springer ER - TY - CHAP A1 - Schütte, Christof A1 - Nettesheim, Peter ED - Keil, F. ED - Mackens, W. ED - Voss, H. ED - Werther, J. T1 - Nonadiabatic Effects in Quantum-Classical Molecular Dynamics T2 - Scientific Computing in Chemical Engineering II Y1 - 1999 UR - http://publications.imp.fu-berlin.de/136/ SP - 42 EP - 56 PB - Springer ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature choice JF - Comp. Phys. Comm. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/93/ U6 - https://doi.org/10.1016/S0010-4655(99)00274-X VL - 121 SP - 37 EP - 39 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/92/ U6 - https://doi.org/10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo JF - J. Comp. Phys Y1 - 1999 UR - http://publications.imp.fu-berlin.de/87/ U6 - https://doi.org/10.1006/jcph.1999.6231 VL - 151 IS - 1 SP - 146 EP - 168 ER - TY - JOUR A1 - Schütte, Christof T1 - Conformational Dynamics JF - preprint Y1 - 1999 UR - http://publications.imp.fu-berlin.de/89/ ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dellnitz, M. A1 - Junge, Oliver A1 - Schütte, Christof ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Computation of Essential Molecular Dynamics by Subdivision Techniques T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.mi.fu-berlin.de/135/ VL - 4 SP - 98 EP - 115 PB - Springer ER - TY - CHAP A1 - Schütte, Christof A1 - Bornemann, Folkmar A. ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.imp.fu-berlin.de/134/ VL - 4 SP - 380 EP - 395 PB - Springer ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Adaptive Accuracy Control for Car-Parrinello Simulations JF - Num. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/88/ U6 - https://doi.org/10.1007/s002110050445 VL - 83 IS - 2 SP - 179 EP - 186 ER - TY - CHAP A1 - Schütte, Christof A1 - Cordes, Frank ED - Esser, R. ED - Grassberger, P. ED - Grotendorst, J. ED - Lewerenz, M. T1 - On Dynamical Transitions between Conformational Ensembles T2 - Molecular Dynamics on Parallel Computers Y1 - 2000 UR - http://publications.imp.fu-berlin.de/132/ U6 - https://doi.org/10.1142/9789812793768_0002 SP - 32 EP - 45 PB - World Scientific ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Fiedler, B. ED - Grger, K. ED - Sprekels, Jürgen T1 - On Conformational Dynamics induced by Langevin Processes T2 - Equadiff 99 Y1 - 2000 UR - http://publications.imp.fu-berlin.de/131/ U6 - https://doi.org/10.1142/9789812792617_0234 VL - 2 SP - 1247 EP - 1262 PB - World Scientific ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2000 UR - http://publications.imp.fu-berlin.de/84/ U6 - https://doi.org/10.1016/S0024-3795(00)00095-1 VL - 315 IS - 1-3 SP - 39 EP - 59 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Sreenivas, R. ED - Jones, D. T1 - Biomolecular Conformations as Metastable Sets of Markov Chains T2 - Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA Y1 - 2000 UR - http://publications.imp.fu-berlin.de/130/ SP - 1106 EP - 1115 PB - University of Illinois at Urbana-Champaign ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - Fiedler, B. T1 - Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems T2 - Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems Y1 - 2001 UR - http://publications.imp.fu-berlin.de/129/ SP - 191 EP - 223 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - A Theoretical Model for Molecules Interacting with Intense Laser Pulses JF - J. Chem. Phys. Y1 - 2001 UR - http://publications.imp.fu-berlin.de/79/ U6 - https://doi.org/10.1063/1.1398577 VL - 115 IS - 13 SP - 5733 EP - 5743 ER - TY - JOUR A1 - Horenko, Illia A1 - Salzmann, Ch. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Quantum-Classical Liouville Approach to Molecular Dynamics JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/75/ U6 - https://doi.org/10.1063/1.1522712 VL - 117 IS - 24 SP - 11075 EP - 11088 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/73/ U6 - https://doi.org/10.1063/1.1498467 VL - 117 IS - 10 SP - 4643 EP - 4650 ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://publications.imp.fu-berlin.de/128/ VL - 24 SP - 235 EP - 259 PB - Springer ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Meyn, S. ED - Namachchivaya, N. ED - Lin, Y. T1 - Metastability of Diffusion Processes T2 - Nonlinear Stochastic Dynamics Y1 - 2003 UR - http://publications.imp.fu-berlin.de/127/ VL - 110 SP - 71 EP - 81 PB - Springer ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Schütte, Christof A1 - Stuart, Andrew T1 - Extracting Macroscopic Stochastic Dynamics JF - Comm. Pure Appl. Math. Y1 - 2003 UR - http://publications.imp.fu-berlin.de/72/ U6 - https://doi.org/10.1002/cpa.10057 VL - 56 IS - 2 SP - 234 EP - 269 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Ciarlet, P. ED - Le Bris, Claude T1 - Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics T2 - Special Volume Y1 - 2003 UR - http://publications.imp.fu-berlin.de/126/ VL - X SP - 699 EP - 744 PB - Elsevier ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Meyn, S. A1 - Schütte, Christof T1 - Phase Transitions and Metastability in Markovian and Molecular Systems JF - Ann. Appl. Prob. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/67/ U6 - https://doi.org/10.1214/aoap/1075828057 VL - 14 IS - 1 SP - 419 EP - 458 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Schütte, Christof ED - Hill, James ED - Moore, Ross T1 - Molecular Conformation Dynamics and Computational Drug Design T2 - Applied Mathematics Entering the 21st Century Y1 - 2004 UR - http://publications.imp.fu-berlin.de/125/ VL - 116 SP - 91 EP - 119 PB - SIAM ER - TY - JOUR A1 - Horenko, Illia A1 - Weiser, Martin A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Fully Adaptive Propagation of the Quantum-Classical Liouville Equation JF - J. Chem. Phys. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/65/ U6 - https://doi.org/10.1063/1.1691015 VL - 120 IS - 19 SP - 8913 EP - 8923 ER - TY - JOUR A1 - Preis, R. A1 - Dellnitz, M. A1 - Hessel, M. A1 - Schütte, Christof A1 - Meerbach, E. T1 - Dominant Paths Between Almost Invariant Sets of Dynamical Systems JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/64/ ER - TY - JOUR A1 - Schütte, Christof A1 - Walter, J. A1 - Hartmann, Carsten A1 - Huisinga, Wilhelm T1 - An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations JF - Multiscale Model. Simul. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/62/ U6 - https://doi.org/10.1137/030600308 VL - 2 IS - 3 SP - 501 EP - 526 ER - TY - JOUR A1 - Walter, J. A1 - Schütte, Christof A1 - Pavliotis, G. A1 - Stuart, Andrew T1 - Averaging of Stochastic Differential Equations JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/63/ ER - TY - CHAP A1 - Schütte, Christof A1 - Forster, R. A1 - Meerbach, E. A1 - Fischer, Alexander ED - Kornhuber, Ralf ED - Hoppe, Ronald H. W. ED - PÃ\copyrightriaux, J. ED - Pironneau, O. ED - Widlund, Olof ED - Xu, J. T1 - Uncoupling-Coupling Techniques for Metastable Dynamical Systems T2 - Domain Decomposition Methods in Science and Engineering Y1 - 2005 UR - http://publications.imp.fu-berlin.de/124/ VL - 40 SP - 115 EP - 129 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Schütte, Christof T1 - Reduced Stochastic Models for Complex Molecular Systems JF - Comp. Vis. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/59/ U6 - https://doi.org/10.1007/s00791-006-0021-1 VL - 9 IS - 2 SP - 89 EP - 102 ER - TY - JOUR A1 - Dellnitz, M. A1 - Neumann, M. A1 - Schütte, Christof T1 - Special Issue on Matrices and Mathematical Biology JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/60/ U6 - https://doi.org/10.1016/j.laa.2004.12.006 VL - 398 SP - 1 EP - 245 ER - TY - JOUR A1 - Antony, Jens A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes JF - J. Chem. Phys. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/57/ U6 - https://doi.org/10.1063/1.1829057 VL - 122 IS - 1 SP - 014309 ER - TY - BOOK ED - Chipot, C. ED - Elber, R. ED - Laaksonen, A. ED - Leimkuhler, Benedict ED - Mark, A. ED - Schlick, T. ED - Schütte, Christof ED - Skeel, R. T1 - New Algorithms for Macromolecular Simulation T3 - Lecture Notes in Computational Science and Engineering Y1 - 2005 UR - http://publications.imp.fu-berlin.de/139/ VL - 49 PB - Springer ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof A1 - Fischer, Alexander T1 - Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/54/ U6 - https://doi.org/10.1016/j.laa.2004.10.018 VL - 398 SP - 141 EP - 160 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Geometric Approach to Constrained Molecular Dynamics and Free Energy JF - Comm. Math. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/48/ VL - 3 IS - 1 SP - 1 EP - 20 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables JF - Z. Angew. Math. Mech. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/47/ U6 - https://doi.org/10.1002/zamm.200410218 VL - 85 IS - 10 SP - 700 EP - 710 ER - TY - JOUR A1 - Horenko, Illia A1 - Lorenz, S. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics JF - J. Comp. Chem. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/49/ U6 - https://doi.org/10.1002/jcc.20234 VL - 26 IS - 9 SP - 941 EP - 948 ER - TY - CHAP A1 - Horenko, Illia A1 - Schmidt-Ehrenberg, Johannes A1 - Schütte, Christof ED - Berthold, Michael R. ED - Glen, Robert C. ED - Fischer, Ingrid T1 - Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models T2 - Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006 Y1 - 2006 UR - http://publications.imp.fu-berlin.de/121/ U6 - https://doi.org/10.1007/11875741_8 VL - 4216 SP - 74 EP - 85 PB - Springer ER - TY - CHAP A1 - Meerbach, E. A1 - Dittmer, E. A1 - Horenko, Illia A1 - Schütte, Christof ED - Ferrario, Mauro ED - Ciccotti, Giovanni ED - Binder, Kurt T1 - Multiscale Modelling in Molecular Dynamics T2 - Computer Simulations in Condensed Matter Y1 - 2006 UR - http://publications.imp.fu-berlin.de/119/ VL - 703 SP - 475 EP - 497 PB - Springer ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Illustration of Transition Path Theory on a Collection of Simple Examples JF - J. Chem. Phys. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/45/ U6 - https://doi.org/10.1063/1.2335447 VL - 125 IS - 8 SP - 084110 ER - TY - CHAP A1 - Dellnitz, M. A1 - Molo, M. A1 - Metzner, Ph. A1 - Preis, R. A1 - Schütte, Christof ED - Mielke, A. T1 - Graph Algorithms for Dynamical Systems T2 - Analysis, Modeling and Simulation of Multiscale Problems Y1 - 2006 UR - http://publications.imp.fu-berlin.de/118/ U6 - https://doi.org/10.1007/3-540-35657-6_23 SP - 619 EP - 645 PB - Springer ER - TY - CHAP A1 - Walter, J. A1 - Schütte, Christof ED - Mielke, A. T1 - Conditional Averaging for Diffusive Fast-Slow Systems T2 - Analysis, Modeling and Simulation of Multiscale Problems Y1 - 2006 UR - http://publications.imp.fu-berlin.de/117/ U6 - https://doi.org/10.1007/3-540-35657-6_24 SP - 647 EP - 682 PB - Springer ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Hagehülsmann, Andre A1 - Diederichs, Elmar A1 - Baumann, Sven A1 - Thiery, Joachim A1 - Schütte, Christof T1 - Beating the Noise JF - Lecture Notes in Computer Science Y1 - 2006 UR - http://publications.imp.fu-berlin.de/5/ VL - 4216 SP - 119 EP - 128 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Automated Model Reduction for Complex Systems exhibiting Metastability JF - Mult. Mod. Sim. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/44/ U6 - https://doi.org/10.1137/050623310 VL - 5 IS - 3 SP - 802 EP - 827 ER - TY - JOUR A1 - Noé, Frank A1 - Smith, J. A1 - Schütte, Christof T1 - A network-based approach to biomolecular dynamics JF - From Computational Biophysics to Systems Biology (CBSB07). Editors Y1 - 2007 UR - http://publications.imp.fu-berlin.de/319/ VL - NIC Series 36 PB - John von Neumann Institute for Computing, Jülich ER - TY - CHAP A1 - Meerbach, E. A1 - Schütte, Christof A1 - Horenko, Illia A1 - Schmidt, Burkhard ED - Kühn, O. ED - Wöste, L. T1 - Metastable Conformational Structure and Dynamics T2 - Analysis and Control of Ultrafast Photoinduced Reactions Y1 - 2007 UR - http://publications.imp.fu-berlin.de/114/ U6 - https://doi.org/10.1007/978-3-540-68038-3_9 VL - 87 SP - 796 EP - 806 PB - Springer CY - Berlin ER - TY - JOUR A1 - Fischer, Alexander A1 - Waldhausen, S. A1 - Horenko, Illia A1 - Meerbach, E. A1 - Schütte, Christof T1 - Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/38/ U6 - https://doi.org/10.1002/jcc.20692 VL - 28 IS - 15 SP - 2453 EP - 2464 ER - TY - JOUR A1 - Horenko, Illia A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/31/ U6 - https://doi.org/10.1103/PhysRevE.76.016706 VL - 76 IS - 01 SP - 016706 ER - TY - CHAP A1 - Held, M. A1 - Meerbach, E. A1 - Hinderlich, S. A1 - Reutter, W. A1 - Schütte, Christof ED - Hansmann, U. ED - Meinke, J. ED - Mohanty, S. ED - Zimmermann, O. T1 - Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity T2 - From Computational Biophysics to Systems Biology Y1 - 2007 UR - http://publications.imp.fu-berlin.de/113/ VL - 36 SP - 145 EP - 148 PB - John von Neumann Institut for Computing ER - TY - JOUR A1 - Lorenz, S. A1 - Diederichs, Elmar A1 - Telgmann, R. A1 - Schütte, Christof T1 - Discrimination of Dynamical System Models for Biological and Chemical Processes JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/33/ U6 - https://doi.org/10.1002/jcc.20674 VL - 28 IS - 8 SP - 1384 EP - 1399 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Comment on Two Distinct Notions of Free Energy JF - Physica D Y1 - 2007 UR - http://publications.imp.fu-berlin.de/30/ U6 - https://doi.org/10.1016/j.physd.2007.02.006 VL - 228 IS - 1 SP - 59 EP - 63 ER - TY - JOUR A1 - Noé, Frank A1 - Horenko, Illia A1 - Schütte, Christof A1 - Smith, J. T1 - Hierarchical Analysis of Conformational Dynamics in Biomolecules JF - J. Chem. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/37/ U6 - https://doi.org/10.1063/1.2714539 VL - 126 IS - 15 SP - 155102 ER - TY - JOUR A1 - Metzner, Ph. A1 - Horenko, Illia A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/36/ U6 - https://doi.org/10.1103/PhysRevE.76.066702 VL - 76 IS - 06 SP - 066702 ER - TY - JOUR A1 - Metzner, Ph. A1 - Dittmer, E. A1 - Jahnke, Tobias A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes JF - J. Comp. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/35/ U6 - https://doi.org/10.1016/j.jcp.2007.07.032 VL - 227 IS - 1 SP - 353 EP - 375 ER - TY - CHAP A1 - Gräfe, Ch. A1 - Schütte, Christof A1 - Nordmeier, V. T1 - Spielend lernen - ein Online-Computerspiel zur Moleküldynamik T2 - Didaktik der Physik ? Y1 - 2008 UR - http://publications.imp.fu-berlin.de/811/ PB - Lehmanns Media CY - Berlin ER - TY - JOUR A1 - Diederichs, Elmar A1 - Juditski, A. A1 - Spokoiny, V. A1 - Schütte, Christof T1 - Sparse Non-Gaussian Component Analysis JF - IEEE Transactions on Information Theory, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/42/ ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Journal of Multivariate Analysis, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/24/ ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Lankas, F. A1 - Maddocks, J. A1 - Metzner, Ph. A1 - Schütte, Christof T1 - Macroscopic Dynamics of Complex Metastable Systems JF - J. Appl. Dyn. Syst. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/56/ U6 - https://doi.org/10.1137/050630064 VL - 7 IS - 2 SP - 532 EP - 560 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/39/ U6 - https://doi.org/10.1137/070687451 VL - 7 IS - 2 SP - 731 EP - 773 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications JF - Adv. Data Anal. Class., submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/32/ ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Balancing of partially-observed stochastic differential equations JF - 47th IEEE Conference on Decision and Control Y1 - 2008 UR - http://publications.imp.fu-berlin.de/16/ U6 - https://doi.org/10.1109/CDC.2008.4739161 SP - 4867 EP - 4872 ER - TY - JOUR A1 - Horenko, Illia A1 - Klein, Rupert A1 - Dolaptchiev, S. A1 - Schütte, Christof T1 - Automated Generation of Reduced Stochastic Weather Models I JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/15/ U6 - https://doi.org/10.1137/060670535 VL - 6 IS - 4 SP - 1125 EP - 1145 ER - TY - JOUR A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion JF - J. Phys. Chem. A Y1 - 2008 UR - http://publications.imp.fu-berlin.de/13/ U6 - https://doi.org/10.1021/jp711545s VL - 112 IS - 27 SP - 6125 EP - 6133 ER - TY - CHAP A1 - Gräfe, Ch. A1 - Schütte, Christof A1 - Nordmeier, V. T1 - "Learner as creator" - SchülerInnen generieren eigene Lernspiele T2 - Didaktik der Physik - Bochum 2009 Y1 - 2009 UR - http://publications.imp.fu-berlin.de/806/ PB - Lehmanns Media CY - Berlin ER - TY - JOUR A1 - Metzner, Ph. A1 - Noé, Frank A1 - Schütte, Christof T1 - Estimating the Sampling Error JF - Phys. Rev. E Y1 - 2009 UR - http://publications.imp.fu-berlin.de/17/ U6 - https://doi.org/10.1103/PhysRevE.80.021106 VL - 80 IS - 2 SP - 021106 PB - American Physical Society ER - TY - JOUR A1 - Gräfe, Ch. A1 - Nordmeier, V. A1 - Schütte, Christof T1 - Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels JF - Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/163/ VL - 1 SP - 77 EP - 79 PB - LIT VERLAG Dr. W. Hopf ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Transition Path Theory for Markov Jump Processes JF - Mult. Mod. Sim. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/43/ U6 - https://doi.org/10.1137/070699500 VL - 7 IS - 3 SP - 1192 EP - 1219 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Kalibaeva, G. A1 - Pierro, M. A1 - Ciccotti, Giovanni T1 - Fast Simulation of Polymer Chains JF - J. Chem. Phys. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/18/ U6 - https://doi.org/10.1063/1.3110603 VL - 130 SP - 144101 ER - TY - JOUR A1 - Fiedler, Georg Martin A1 - Leichtle, Alexander Benedikt A1 - Kase, Julia A1 - Baumann, Sven A1 - Ceglarek, Uta A1 - Felix, Klaus A1 - Conrad, Tim A1 - Witzigmann, Helmut A1 - Weimann, Arved A1 - Schütte, Christof A1 - Hauss, Johann A1 - Büchler, Markus A1 - Thiery, Joachim T1 - Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer JF - Clinical Cancer Research Y1 - 2009 UR - http://publications.imp.fu-berlin.de/155/ U6 - https://doi.org/10.1158/1078-0432.CCR-08-2701 VL - 15 IS - 11 SP - 3812 EP - 3819 PB - American Association for Cancer Research, ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Meerbach, E. A1 - Metzner, Ph. A1 - Hartmann, Carsten T1 - Conformation Dynamics JF - Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), Y1 - 2009 UR - http://publications.imp.fu-berlin.de/110/ U6 - https://doi.org/10.4171/056-1/15 SP - 297 EP - 335 PB - EMS publishing house ER - TY - JOUR A1 - Schütte, Christof A1 - Jahnke, Tobias T1 - Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation JF - Mathematical Modelling and Numerical Analysis (ESAIM) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/26/ U6 - https://doi.org/10.1051/m2an/2009027 VL - 43 IS - 4 SP - 721 EP - 742 PB - EDP Sciences ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Optimal Fuzzy Aggregation of Networks JF - Multiscale Modeling and Simulation Y1 - 2010 U6 - https://doi.org/10.1137/090758519 VL - 8 IS - 4 SP - 1535 EP - 1561 ER - TY - JOUR A1 - Noé, Frank A1 - Schütte, Christof A1 - Vanden-Eijnden, E. A1 - Reich, L. A1 - Weikl, T. T1 - Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations JF - Proc. Natl. Acad. Sci. USA Y1 - 2009 UR - http://publications.imp.fu-berlin.de/826/ U6 - https://doi.org/10.1073/pnas.0905466106 VL - 106 IS - 45 SP - 19011 EP - 19016 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Ciccotti, Giovanni T1 - On the linear response of mechanical systems with constraints JF - J. Chem. Phys. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/794/ U6 - https://doi.org/10.1063/1.3354126 VL - 132 IS - 11 SP - 111103 ER - TY - CHAP A1 - Djurdjevac Conrad, Natasa A1 - Sarich, Marco A1 - Schütte, Christof T1 - On Markov State Models for Metastable Processes T2 - Proceedings of the International Congress of Mathematics, Hyderabad, India, Section Invited Talks. (ICM) 2010 Y1 - 2010 UR - http://publications.imp.fu-berlin.de/991/ ER - TY - JOUR A1 - Sarich, Marco A1 - Noé, Frank A1 - Schütte, Christof T1 - On the Approximation Quality of Markov State Models JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/771/ U6 - https://doi.org/10.1137/090764049 VL - 8 IS - 4 SP - 1154 EP - 1177 ER - TY - JOUR A1 - Marsalek, Ondrej A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Bradforth, Stephen E. A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Hydrogen Forms in Water by Proton Transfer to a Distorted Electron JF - J. Phys. Chem. B Y1 - 2010 UR - http://publications.imp.fu-berlin.de/818/ U6 - https://doi.org/10.1021/jp908986z VL - 114 IS - 2 SP - 915 EP - 920 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics JF - Macromol. React. Eng. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/956/ U6 - https://doi.org/10.1002/mren.200900073 VL - 4 IS - 9-10 SP - 562 EP - 577 ER - TY - JOUR A1 - Latorre, J. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Free energy computation by controlled Langevin processes JF - Procedia Computer Science Y1 - 2010 UR - http://publications.imp.fu-berlin.de/801/ U6 - https://doi.org/10.1016/j.procs.2010.04.179 VL - 1 IS - 1 SP - 1591 EP - 1600 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - On metastable conformational analysis of non-equilibrium biomolecular time series JF - Multiscale Modeling & Simulation Y1 - 2010 UR - http://publications.imp.fu-berlin.de/146/ U6 - https://doi.org/10.1137/080744347 VL - 8 IS - 2 SP - 701 EP - 716 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Vulcanov, V.-M. A1 - Schütte, Christof T1 - Balanced Truncation of Second Order Systems JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/28/ U6 - https://doi.org/10.1137/080732717 VL - 8 IS - 4 SP - 1348 EP - 1367 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Daskalaki, A. ED - Lazakidou, A. T1 - From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis T2 - Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine Y1 - 2010 UR - http://publications.imp.fu-berlin.de/945/ PB - Hershey, PA: Medical Information Science Reference ER - TY - JOUR A1 - Latorre, J. A1 - Metzner, Ph. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Structure-preserving numerical discretization of reversible diffusions JF - Commun. Math. Sci. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/896/ VL - 9 IS - 4 SP - 1051 EP - 1072 ER - TY - JOUR A1 - Frank, M. A1 - von Kleist, Max A1 - Kunz, A. A1 - Harms, G. A1 - Schütte, Christof A1 - Kloft, Ch. T1 - Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1 JF - Antimicrob. Agents Chemother. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1093/ VL - 55 IS - 12 SP - 5529 EP - 5540 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Knets, I. ED - Brebbia, C. ED - Miftahof, R. ED - Kasyanov, V. ED - Popov, V. T1 - Statistical parameter estimation and signal classification in cardiovascular diagnosis T2 - Modelling in Medicine and Biology Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1070/ VL - IX IS - 15 PB - WIT Press CY - Southampton & Boston ER - TY - JOUR A1 - von Kleist, Max A1 - Menz, Stephan A1 - Stocker, Hartmut A1 - Arasteh, Keikawus A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - HIV Quasispecies Dynamics during Pro-active Treatment Switching JF - Plos One Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1051/ U6 - https://doi.org/10.1371/journal.pone.0018204 VL - 6 IS - 3 SP - e18204 PB - Public Library of Science ER - TY - JOUR A1 - Prinz, J.-H. A1 - Wu, Hao A1 - Sarich, Marco A1 - Keller, B. A1 - Fischbach, M. A1 - Held, M. A1 - Chodera, J. A1 - Schütte, Christof A1 - Noé, Frank T1 - Markov models of molecular kinetics JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/944/ U6 - https://doi.org/10.1063/1.3565032 VL - 134 SP - 174105 ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Lu, Jianfeng A1 - Sarich, Marco A1 - Vanden-Eijnden, E. T1 - Markov State Models Based on Milestoning JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1022/ U6 - https://doi.org/10.1063/1.3590108 VL - 134 IS - 20 SP - 204105 ER - TY - JOUR A1 - Meerbach, E. A1 - Latorre, J. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Multicale Model. Sim. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1123/ U6 - https://doi.org/10.1137/110850621 VL - 10 IS - 4 SP - 1263 EP - 1291 ER - TY - JOUR A1 - Schäfer-Bung, B. A1 - Hartmann, Carsten A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Dimension reduction by balanced truncation JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1023/ VL - 135 IS - 1 SP - 014112 ER - TY - JOUR A1 - von Kleist, Max A1 - Metzner, Ph. A1 - Marquet, R. A1 - Schütte, Christof T1 - Polymerase Inhibition by Nucleoside Analogs JF - Plos Computational Biology Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1087/ U6 - https://doi.org/10.1371/journal.pcbi.1002359 VL - 8 IS - 1 SP - e1002359 ER - TY - JOUR A1 - Duwal, Sulav A1 - Schütte, Christof A1 - von Kleist, Max T1 - Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. JF - PLoS One Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1130/ U6 - https://doi.org/10.1371/journal.pone.0040382 VL - 7 IS - 7 SP - e40382 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - A pH-dependent coarse-grained model of peptides JF - Soft Matter Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1192/ U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control with Rare State Observation JF - International Journal of Biomathematics and Biostatistics Y1 - 2012 UR - http://publications.mi.fu-berlin.de/1177/ ER - TY - JOUR A1 - Menz, Stephan A1 - Latorre, J. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation JF - SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1039/ U6 - https://doi.org/10.1137/110825716 VL - 10 IS - 4 SP - 1232 EP - 1262 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation JF - Communications in Mathematical Sciences Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1176/ VL - 12 IS - 859 ER - TY - JOUR A1 - Rath, Barbara A1 - Yousef, Kaveh A1 - Katzenstein, D. A1 - Shafer, R. A1 - Schütte, Christof A1 - von Kleist, Max A1 - Merigan, T. T1 - HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitor Induced Selective Pressure in vitro JF - PLoS ONE Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1178/ U6 - https://doi.org/10.1371/journal.pone.0061102 VL - 8 IS - 4 PB - Public Library of Science ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Sarich, Marco A1 - Schütte, Christof T1 - Estimating the eigenvalue error of Markov State Models JF - Multiscale Modeling & Simulation Y1 - 2012 UR - http://publications.imp.fu-berlin.de/914/ U6 - https://doi.org/10.1137/100798910 VL - 10 IS - 1 SP - 61 EP - 81 ER - TY - JOUR A1 - Senne, M. A1 - Trendelkamp-Schroer, B. A1 - Mey, A. A1 - Schütte, Christof A1 - Noé, Frank T1 - EMMA - A software package for Markov model building and analysis JF - Journal of Chemical Theory and Computation Y1 - 2012 U6 - https://doi.org/10.1021/ct300274u VL - 8 SP - 2223 EP - 2238 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1182/ U6 - https://doi.org/10.1021/ct3003354 VL - 8 IS - 8 SP - 2878 EP - 2887 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Stefanie A1 - Conrad, Tim A1 - Schütte, Christof T1 - Random Walks on Complex Modular Networks JF - Journal of Numerical Analysis, Industrial and Applied Mathematics Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1090/ VL - 6 IS - 1-2 SP - 29 EP - 50 PB - European Society of Computational Methods in Sciences and Engineering ER - TY - JOUR A1 - Weiss, Maximilian A1 - Paulus, Florian A1 - Steinhilber, D. A1 - Nikitin, Anatoly A1 - Haag, Rainer A1 - Schütte, Christof T1 - Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures JF - MACROMOLECULAR THEORY and SIMULATIONS Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1142/ U6 - https://doi.org/10.1002/mats.201200003 VL - 21 IS - 7 SP - 470 EP - 481 ER - TY - JOUR A1 - Aiche, Stephan A1 - Reinert, Knut A1 - Schütte, Christof A1 - Hildebrand, Diana A1 - Schlüter, Hartmut A1 - Conrad, Tim T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs JF - PLoS ONE Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1143/ U6 - https://doi.org/10.1371/journal.pone.0040656 VL - 7 IS - 7 SP - e40656 PB - Public Library of Science ER - TY - JOUR A1 - Wang, Han A1 - Zhang, P. A1 - Schütte, Christof T1 - On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1181/ U6 - https://doi.org/10.1021/ct300343y VL - 8 IS - 9 SP - 3243 EP - 3256 ER - TY - JOUR A1 - Schütte, Christof A1 - Winkelmann, Stefanie A1 - Hartmann, Carsten T1 - Optimal control of molecular dynamics using Markov state models JF - Math. Program. (Series B) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1107/ U6 - https://doi.org/10.1007/s10107-012-0547-6 VL - 134 IS - 1 SP - 259 EP - 282 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Zhang, P. T1 - Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems JF - Phys. Rev. E Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1125/ U6 - https://doi.org/10.1103/PhysRevE.86.026704 VL - 86 IS - 02 SP - 026704 ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof T1 - Approximating Selected Non-dominant Timescales by Markov State Models JF - Comm. Math. Sci. Y1 - 2012 U6 - https://doi.org/10.4310/CMS.2012.v10.n3.a14 VL - 10 IS - 3 SP - 1001 EP - 1013 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Efficient rare event simulation by optimal nonequilibrium forcing JF - J. Stat. Mech. Theor. Exp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1153/ U6 - https://doi.org/10.1088/1742-5468/2012/11/P11004 VL - 2012 SP - P11004 ER - TY - JOUR A1 - Sarich, Marco A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Sharon A1 - Conrad, Tim A1 - Schütte, Christof T1 - Modularity revisited: A novel dynamics-based concept for decomposing complex networks JF - Journal of Computational Dynamics Y1 - 2014 UR - http://publications.mi.fu-berlin.de/1127/ U6 - https://doi.org/10.3934/jcd.2014.1.191 VL - 1 IS - 1 SP - 191 EP - 212 ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique JF - Phys. Rev. X Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevX.3.011018 VL - 3 SP - 011018 ER - TY - JOUR A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Bodermann, Bernd T1 - Fast simulation method for parameter reconstruction in optical metrology JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2011154 VL - 8681 SP - 868119 ER - TY - JOUR A1 - Maes, Bjorn A1 - Petráček, Jiří A1 - Burger, Sven A1 - Kwiecien, Pavel A1 - Luksch, Jaroslav A1 - Richter, Ivan T1 - Simulations of high-Q optical nanocavities with a gradual 1D bandgap JF - Opt. Express Y1 - 2013 U6 - https://doi.org/10.1364/OE.21.006794 VL - 21 SP - 6794 EP - 6806 PB - OSA ER - TY - CHAP A1 - Taylor, William R. A1 - Fröhlich, Annika A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Witaschek, Tom A1 - Duda, Georg ED - Kersting, Uwe ED - Morlock, Michael ED - Jirova-Enzmann, Daniela ED - Dremstrup, Kim T1 - Metacarpophalangeal joint stiffness is reduced in patients affected by rheumatoid arthritis after glucocorticoid medication T2 - Proceedings of the ESM-2012, Aalborg Y1 - 2012 SP - 39 PB - Department of Health Science and Technology, Aalborg University ER - TY - JOUR A1 - Kratzenstein, Stefan A1 - Kornaropoulos, Evgenios I. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Pöpplau, Berry M. A1 - Taylor, William R. T1 - Effective marker placement for functional identification of the centre of rotation at the hip JF - Gait & Posture Y1 - 2012 U6 - https://doi.org/http://dx.doi.org/10.1016/j.gaitpost.2012.04.011 VL - 36 IS - 3 SP - 482 EP - 486 ER - TY - JOUR A1 - Fasting, Carlo A1 - Schalley, Christoph A. A1 - Weber, Marcus A1 - Seitz, Oliver A1 - Hecht, Stefan A1 - Koksch, Beate A1 - Dernedde, Jens A1 - Graf, Christina A1 - Knapp, Ernst-Walter A1 - Haag, Rainer T1 - Multivalency as a Chemical Organization and Action Principle JF - Angew. Chem. Int. Ed. Y1 - 2012 VL - 51 IS - 42 SP - 10472 EP - 10498 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Bujotzek, Alexander A1 - Weber, Marcus T1 - A meshless discretization method for Markov state models applied to explicit water peptide folding simulations T2 - Meshfree Methods for Partial Differential Equations VI Y1 - 2012 VL - 89 SP - 141 EP - 154 PB - Springer ER - TY - JOUR A1 - Weber, Marcus A1 - Bujotzek, Alexander A1 - Haag, Rainer T1 - Quantifying the rebinding effect in multivalent chemical ligand-receptor systems JF - J. Chem. Phys. Y1 - 2012 VL - 137 IS - 5 SP - 054111 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Becker, Roland T1 - How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers JF - Journal of Molecular Modeling Y1 - 2012 U6 - https://doi.org/10.1007/s00894-011-1239-5 VL - 18 SP - 2399 EP - 2408 ER - TY - JOUR A1 - Köppen, Robert A1 - Riedel, Juliane A1 - Proske, Matthias A1 - Drzymala, Sarah A1 - Rasenko, Tatjana A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Koch, Matthias T1 - Photochemical trans-/cis-isomerization and quantification of zearalenone in edible oils JF - J. Agric. Food Chem. Y1 - 2012 U6 - https://doi.org/10.1021/jf3037775 VL - 60 SP - 11733 EP - 11740 ER - TY - JOUR A1 - Kewes, Günter A1 - Schell, Andreas W. A1 - Henze, Rico A1 - Schonfeld, Rolf S. A1 - Burger, Sven A1 - Busch, Kurt A1 - Benson, Oliver T1 - Design and numerical optimization of an easy-to-fabricate photon-to-plasmon coupler for quantum plasmonics JF - Applied Physics Letters Y1 - 2013 U6 - https://doi.org/10.1063/1.4790824 VL - 102 SP - 051104 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Lockau, Daniel A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schwanke, Christoph A1 - Kirner, Simon A1 - Calnan, Sonya A1 - Stannowski, Bernd A1 - Rech, Bernd T1 - FEM-based optical modeling of silicon thin-film tandem solar cells with randomly textured interfaces in 3D JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2001789 VL - 8620 SP - 86201H ER - TY - JOUR A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Blome, Mark A1 - Schmidt, Frank T1 - Advanced finite-element methods for design and analysis of nano-optical structures: Applications JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2001094 VL - 8642 SP - 864205 ER - TY - JOUR A1 - Arellano, Cristina A1 - Mingaleev, Sergei F. A1 - Koltchanov, Igor A1 - Richter, Andre A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Efficient design of photonic integrated circuits (PICs) by combining device- and circuit- level simulation tools JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2004378 VL - 8627 SP - 862711 ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Greiner, Horst A1 - Burger, Sven A1 - Schmidt, Frank T1 - Numerical analysis of nanostructures for enhanced light extraction from OLEDs JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2001132 VL - 8641 SP - 86410B ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Klimm, Martina A1 - Weber, Marcus T1 - A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules JF - Journal of Mathematical Chemistry Y1 - 2012 VL - 5 IS - 9 SP - 2623 EP - 2635 ER - TY - CHAP A1 - Fackeldey, Konstantin T1 - Multiscale Methods in Time and Space T2 - Progress in Industrial Mathematics at ECMI 2010 Y1 - 2012 VL - 17 SP - 619 EP - 626 ER - TY - THES A1 - Durmaz, Vedat T1 - Theoretical Investigations on HBCD and PBCD Y1 - 2009 ER - TY - THES A1 - Scharkoi, O. T1 - Conformation Dynamics Design of Pain Relief Drugs Y1 - 2009 ER - TY - JOUR A1 - Weber, Marcus A1 - Durmaz, Vedat A1 - Becker, Roland A1 - Esslinger, Susanne T1 - Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR JF - Organohalogen Compounds Y1 - 2009 VL - 71 SP - 247 EP - 252 ER - TY - CHAP A1 - Weber, Marcus ED - Dunemann, L. ED - Schmoll, O. T1 - Spurenstoffe im Trinkwasser - Risikoqualifizierung im Rechner? T2 - Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene Y1 - 2009 ER - TY - JOUR A1 - Bujotzek, Alexander A1 - Weber, Marcus T1 - Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach JF - Journal of Bioinformatics and Computational Biology Y1 - 2009 VL - 7(5) SP - 811 EP - 831 ER - TY - JOUR A1 - Köppen, Robert A1 - Becker, Roland A1 - Weber, Marcus A1 - Durmaz, Vedat A1 - Nehls, Irene T1 - HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota JF - Organohalogen Compounds Y1 - 2009 VL - 70 SP - 910 EP - 913 ER - TY - JOUR A1 - Dahlke, S. A1 - Fornasier, M. A1 - Rauhut, H. A1 - Steidl, G. A1 - Teschke, G. T1 - Generalized Coorbit Theory, Banach Frames, and the Relations to α–Modulation Spaces JF - under review Y1 - 2005 ER - TY - GEN A1 - Kellermann, R. A1 - Weber, Marcus A1 - Bujotzek, Alexander T1 - Vom Dietrich zum Sicherheitsschlüssel – Mathematiker des Matheon simulieren neuen Wirkstoff für die Diabetes-Behandlung Y1 - 2007 IS - 2 PB - DFG-Forschungszentrum Matheon ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Reflectivity Densities in a Narrowband Regime JF - IEEE Transactions on Antennas and Propagation Y1 - 2004 VL - 52 IS - 6 SP - 1603 EP - 1606 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Wideband Reflectivity Densities by Wavelet Transforms JF - Advances in Computational Mathematics Y1 - 2003 VL - 2-4 IS - 18 SP - 189 EP - 209 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Interpolating Scaling Functions with Duals JF - Journal of Computational Analysis and Applications Y1 - 2004 VL - 1 IS - 6 SP - 19 EP - 29 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Reflectivity Densities by Wavelet Transforms JF - Technical Report 01-10, ISSN 1435-7968 Y1 - 2007 ER - TY - JOUR A1 - Dahlke, S. A1 - Lehmann, V. A1 - Teschke, G. T1 - Applications of Wavelet Methods to the Analysis of Meteorological Radar Data - An Overview JF - (invited paper) Arabian Journal of Science and Engineering Y1 - 2003 VL - 28 IS - 1C SP - 3 EP - 44 ER - TY - JOUR A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi A1 - Weiser, Martin T1 - The convergence of an interior point method for an elliptic control problem with mixed control-state constraints JF - Comput. Optim. Appl. Y1 - 2008 VL - 39 IS - 2 SP - 183 EP - 218 ER - TY - JOUR A1 - Kube, Susanna A1 - Lasser, Caroline A1 - Weber, Marcus T1 - Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics JF - Journal of Computational Physics Y1 - 2008 U6 - https://doi.org/10.1016/j.jcp.2008.11.016 VL - 228 IS - 6 SP - 1947 EP - 1962 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Jahnke, Tobias A1 - Wulkow, Michael T1 - Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation JF - SIAM J. Sci. Comput Y1 - 2008 VL - 30 IS - 6 SP - 2990 EP - 3011 ER - TY - THES A1 - Schräer, Ingo T1 - Modellreduktion in der Hyperthermie mittels POD Y1 - 2008 CY - Fachbereich Mathematik ER - TY - JOUR A1 - Schiela, Anton T1 - State constrained optimal control problems with states of low regularity JF - SIAM J. on Control and Optimization Y1 - 2009 VL - 48 IS - 4 SP - 2407 EP - 2432 ER - TY - JOUR A1 - Schiela, Anton T1 - Barrier Methods for Optimal Control Problems with State Constraints JF - SIAM J. on Optimization Y1 - 2009 VL - 20 IS - 2 SP - 1002 EP - 1031 ER - TY - CHAP A1 - Schiela, Anton T1 - An Extended Mathematical Framework for Barrier Methods in Function Space T2 - Domain Decomposition Methods in Science and Engineering XVIII Y1 - 2009 VL - 70 ER - TY - THES A1 - Schiela, Anton T1 - The Control Reduced Interior Point Method. A Function Space Oriented Algorithmic Approach Y1 - 2006 CY - Fachbereich Mathematik ER - TY - JOUR A1 - Schiela, Anton T1 - A Simplified Approach to Semismooth Newton Methods in Function Space JF - SIAM J. on Optimization Y1 - 2008 VL - 19 IS - 3 SP - 369 EP - 393 ER - TY - JOUR A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi T1 - An interior point method for a parabolic optimal control problem with regularized pointwise state constraints JF - ZAMM Y1 - 2007 UR - http://www.math.tu-berlin.de/~pruefert/Publicat/index_en.html U6 - https://doi.org/10.1002/zamm.200610337 VL - 87 IS - 8–9 SP - 564 EP - 589 CY - Berlin ER - TY - JOUR A1 - Prüfert, Uwe A1 - Schiela, Anton T1 - The Minimization of a maximum-norm functional subject to an elliptic PDE and state constraints JF - Z. angew. Math. Mech. Y1 - 2009 VL - 89 IS - 7 SP - 536 EP - 551 ER - TY - THES A1 - Massing, Andre T1 - 1D-Reduktion thermal signifikanter Aderstränge in der Hyperthermie-Modellierung Y1 - 2007 CY - Fachbereich Mathematik ER - TY - JOUR A1 - Meyer, Christian A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi T1 - On two numerical methods for state-constrained elliptic control problems JF - Optimization Methods and Software Y1 - 2007 UR - http://www.math.tu-berlin.de/~pruefert/Publicat/index_en.html UR - /homes/numerik/pruefert/WWW/Publicat/on2numerical.pdf VL - 22 IS - 6 SP - 871 EP - 899 ER - TY - JOUR A1 - Hinze, Michael A1 - Schiela, Anton T1 - Discretization of Interior Point Methods for State Constrained Elliptic Optimal Control Problems: optimal error estimates and parameter adjustment JF - Comp. Opt. and Appl. Y1 - 2011 U6 - https://doi.org/10.1007/s10589-009-9278-x VL - 48 IS - 3 SP - 581 EP - 600 PB - Springer ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Schmidt, Frank ED - Horiuchi, Toshiyuki T1 - Finite element simulation of light propagation in non-periodic mask patterns T2 - Photomask and Next-Generation Lithography Mask Technology XV Y1 - 2008 UR - http://arxiv.org/pdf/0804.2587v1 VL - 7028 PB - SPIE ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank T1 - A new finite element realization of the Perfectly Matched Layer Method for Helmholtz scattering problems on polygonal domains in 2D JF - J. Comput. Appl. Math. Y1 - 2006 U6 - https://doi.org/10.1016/j.cam.2005.03.047 VL - 188 SP - 12 EP - 32 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Greiner, Horst A1 - Pomplun, Jan A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schmidt, Frank T1 - FEM simulations of light extraction from nanostructured organic light-emitting diodes T2 - Renewable Energy and the Environment Optics and Photonics Congress Y1 - 2012 U6 - https://doi.org/10.1364/SOLED.2012.LT2B.5 SP - LT2B.5 PB - Optical Society of America ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schädle, Achim A1 - Schmidt, Frank T1 - Domain decomposition method for electromagnetic scattering problems: application to EUV lithography T2 - Proceedings of the 5th International Conference on Numerical Simulation of Optoelectronic devices Y1 - 2005 U6 - https://doi.org/10.1109/NUSOD.2005.1518132 SP - 55 EP - 56 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schädle, Achim A1 - Schmidt, Frank ED - Levinson, Harry ED - Dusa, Mircea T1 - A rigorous finite-element domain decomposition method for electromagnetic near field simulations T2 - Optical Microlithography XXI Y1 - 2008 U6 - https://doi.org/10.1117/12.771989 VL - 6924 PB - SPIE ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank ED - Sidorin, Y. ED - Waechter, Ch. T1 - Goal oriented adaptive finite element method for precise simulation of optical components T2 - Proc. SPIE, Integrated Optics Y1 - 2007 UR - http://arxiv.org/pdf/physics/0702128 VL - 6475 SP - 64750H ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank ED - Sidorin, Y. ED - Wächter, Christoph T1 - JCMmode: an adaptive finite element solver for the computation of leaky modes T2 - Integrated Optics: Devices, Materials, and Technologies IX Y1 - 2005 U6 - https://doi.org/10.1117/12.590372 VL - 5728 SP - 192 EP - 202 PB - Proc. SPIE ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Kettner, Benjamin A1 - Schmidt, Frank T1 - Advanced Finite Element Method for Nano-Resonators T2 - Proc. SPIE Y1 - 2006 U6 - https://doi.org/10.1117/12.646252 VL - 6115 SP - 611515 ER - TY - JOUR A1 - Zhao, J. A1 - Frank, B. A1 - Burger, Sven A1 - Giessen, H. T1 - Large-Area High-Quality Plasmonic Oligomers Fabricated by Angle-Controlled Colloidal Nanolithography JF - ACS Nano Y1 - 2011 U6 - https://doi.org/10.1021/nn203177s VL - 5 IS - 11 SP - 9009 ER - TY - JOUR A1 - Zeilhofer, Hans-Florian A1 - Zachow, Stefan A1 - Fairley, Jeffrey A1 - Sader, Robert A1 - Deuflhard, Peter T1 - Treatment Planning and Simulation in Craniofacial Surgery with Virtual Reality Techiques JF - Journal of Cranio-Maxillofacial Surgery Y1 - 2000 VL - 28 (Suppl. 1) SP - 82 ER - TY - CHAP A1 - Zachow, Stefan A1 - Weiser, Martin A1 - Deuflhard, Peter ED - Niederlag, Wolfgang ED - Lemke, Heinz ED - Meixensberger, Jürgen ED - Baumann, Michael T1 - Modellgestützte Operationsplanung in der Kopfchirurgie T2 - Modellgestützte Therapie Y1 - 2008 SP - 140 EP - 156 PB - Health Academy ER - TY - CHAP A1 - Zachow, Stefan A1 - Weiser, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Payan, Y. T1 - Soft Tissue Prediction in Computer Assisted Maxillofacial Surgery Planning T2 - Biomechanics Applied to Computer Assisted Surgery Y1 - 2005 SP - 277 EP - 298 PB - Research Signpost ER - TY - JOUR A1 - Stötzel, Claudia A1 - Plöntzke, Julia A1 - Heuwieser, Wolfgang A1 - Röblitz, Susanna T1 - Advances in modelling of the bovine estrous cycle: Synchronization with PGF2alpha JF - Theriogenology Y1 - 2012 U6 - https://doi.org/10.1016/j.theriogenology.2012.04.017 VL - 78 SP - 1415 EP - 1428 ER - TY - JOUR A1 - Röblitz, Susanna A1 - Stötzel, Claudia A1 - Deuflhard, Peter A1 - Jones, Hannah M. A1 - Azulay, David-Olivier A1 - van der Graaf, Piet A1 - Martin, Steven T1 - A mathematical model of the human menstrual cycle for the administration of GnRH analogues JF - Journal of Theoretical Biology Y1 - 2013 U6 - https://doi.org/10.1016/j.jtbi.2012.11.020 VL - 321 SP - 8 EP - 27 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Röblitz, Susanna A1 - Wade, Moritz A1 - Deuflhard, Peter T1 - Parameter identification in large kinetic networks with BioPARKIN JF - CoRR - Computing Research Repository - arXiv.org Y1 - 2013 UR - arxiv.org/abs/1303.4928v2 VL - abs/1303.4928 ER - TY - RPRT A1 - Deuflhard, Peter A1 - Fiedler, B. A1 - Kunkel, P. T1 - Efficient numerical pathfollowing beyond critical points Y1 - 1984 IS - 278 PB - Universität Heidelberg ER - TY - JOUR A1 - Yevick, David A1 - Yu, J. A1 - Schmidt, Frank T1 - Analytic Studies of Absorbing and Impedance-Matched Boundary Layers JF - IEEE Photonics Technology Letters Y1 - 1997 U6 - https://doi.org/10.1109/68.554499 VL - 9 SP - 73 EP - 75 ER - TY - JOUR A1 - Yevick, David A1 - Friese, T. A1 - Schmidt, Frank T1 - A Comparison of Transparent Boundary Conditions for the Fresnel Equation JF - J. Comput. Phys. Y1 - 2001 VL - 168 IS - 2 SP - 433 EP - 444 ER - TY - JOUR A1 - Yan, Hong-Dan A1 - Lemmens, Peter A1 - Ahrens, Johannes A1 - Bröring, Martin A1 - Burger, Sven A1 - Daum, Winfried A1 - Lilienkamp, Gerhard A1 - Korte, Sandra A1 - Lak, Aidin A1 - Schilling, Meinhard T1 - High-density array of Au nanowires coupled by plasmon modes JF - Acta Phys. Sin. Y1 - 2012 U6 - https://doi.org/10.7498/aps.61.237105 VL - 61 IS - 23 SP - 237105 ER - TY - JOUR A1 - Wust, Peter A1 - Seebass, Martin A1 - Nadobny, Johanna A1 - Deuflhard, Peter A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Simulation studies promote technological development of radiofrequency phased array hyperthermia JF - Int J Hyperthermia Y1 - 1996 VL - 12 IS - 4 SP - 477 EP - 494 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Gellermann, Johanna A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Influence of patient models and numerical methods on predicted power deposition patterns JF - Int. J. Hyperthermia Y1 - 1999 VL - 15 IS - 6 SP - 519 EP - 540 ER - TY - CHAP A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Gellermann, Johanna A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Budach, Volker A1 - Felix, Roland T1 - Patient Models and Algorithms for Hyperthermia Planning T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 75 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Felix, Roland A1 - Deuflhard, Peter A1 - Louis, Alfred A1 - John, W. T1 - Strategies for optimized application of annular-phased-array systems in clinical hyperthermia JF - Int J Hyperthermia Y1 - 1991 VL - 7 SP - 157 EP - 173 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Felix, Roland A1 - Deuflhard, Peter A1 - John, W. A1 - Louis, Alfred T1 - Numerical approaches to treatment planning in deep RF-hyperthermia JF - Strahlenther Onkol Y1 - 1989 VL - 165 IS - 10 SP - 751 EP - 757 ER - TY - JOUR A1 - Wust, Peter A1 - Gellermann, Johanna A1 - Beier, Jürgen A1 - Wegner, S. A1 - Tilly, Wolfgang A1 - Troger, J. A1 - Stalling, Detlev A1 - Oswald, H. A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Evaluation of segmentation algorithms for generation of patient models in radiofrequency hyperthermia JF - Phys Med Biol Y1 - 1998 VL - 43 SP - 3295 EP - 3307 ER - TY - GEN A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter T1 - Künstliches Fieber gegen Krebs Y1 - 1999 PB - Spektrum der Wissenschaft, pp. 78-84 (December 1999). ER - TY - JOUR A1 - Wust, Peter A1 - Fahling, Horst A1 - Wlodarczyk, Waldemar A1 - Seebass, Martin A1 - Gellermann, Johanna A1 - Deuflhard, Peter A1 - Nadobny, Johanna T1 - Antenna arrays in the SIGMA-eye applicator JF - Med Phys Y1 - 2001 VL - 28 IS - 8 SP - 1793 EP - 1805 ER - TY - CHAP A1 - Wulkow, Michael A1 - Deuflhard, Peter ED - Fatunla, S. T1 - Towards an Efficient Computational Treatment of Heterogeneous Polymer Reactions T2 - Computational Ordinary Differential Equations Y1 - 1992 SP - 287 EP - 306 PB - University Press, Nigeria ER - TY - CHAP A1 - Wong, G. A1 - Kang, M. A1 - Lee, H. A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Biancalana, F. A1 - Russell, P. T1 - Strongly Twisted Solid-Core PCF: A One-Dimensional Chiral Metamaterial T2 - Frontiers in Optics Y1 - 2011 U6 - https://doi.org/10.1364/FIO.2011.FMG3 SP - FMG3 PB - Optical Society of America ER - TY - CHAP A1 - Wlodarczyk, Waldemar A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Mönich, Gerhard A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Systematic design of antennas for cylindrical 3D phased array hyperthermia applicator T2 - Proc. IEEE Antennas Propagat. Soc. Intern. Symposium, July 11-16, 1999, Orlando, FL, USA, Y1 - 1999 SP - 1004 EP - 1007 ER - TY - JOUR A1 - Wix, A. A1 - Schaber, Karlheinz A1 - Ofenloch, O. A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Simulation of Aerosol Formation in Gas-Liquid Contact Devices JF - Chem. Eng. Comm. Y1 - 2007 VL - 194 SP - 565 EP - 577 ER - TY - JOUR A1 - Weiser, Martin T1 - Interior point methods in function space JF - SIAM J. Control Optimization Y1 - 2005 VL - 44 IS - 5 SP - 1766 EP - 1786 ER - TY - JOUR A1 - Weihrauch, Mirko A1 - Wust, Peter A1 - Weiser, Martin A1 - Nadobny, Johanna A1 - Eisenhardt, Steffen A1 - Budach, Volker A1 - Gellermann, Johanna T1 - Adaptation of antenna profiles for control of MR guided hyperthermia (HT) in a hybrid MR-HT system JF - Medical Physics Y1 - 2007 VL - 34 IS - 12 SP - 4717 EP - 4725 ER - TY - JOUR A1 - Weiser, Martin A1 - Deuflhard, Peter A1 - Erdmann, Bodo T1 - Affine conjugate adaptive Newton methods for nonlinear elastomechanics JF - Opt. Meth. Softw. Y1 - 2007 VL - 22 IS - 3 SP - 413 EP - 431 ER - TY - JOUR A1 - Weiser, Martin T1 - Pointwise Nonlinear Scaling for Reaction-Diffusion Equations JF - Appl. Num. Math. Y1 - 2009 VL - 59 IS - 8 SP - 1858 EP - 1869 ER - TY - JOUR A1 - Weiser, Martin T1 - Optimization and Identification in Regional Hyperthermia JF - Int. J. Appl. Electromagn. and Mech. Y1 - 2009 VL - 30 SP - 265 EP - 275 ER - TY - JOUR A1 - Weiser, Martin A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Asymptotic Mesh Independence of Newton’s Method Revisited JF - SIAM J. Num. Anal. Y1 - 2005 VL - 42 IS - 5 SP - 1830 EP - 1845 ER - TY - JOUR A1 - Weber, Marcus A1 - Kube, Susanna A1 - Walter, Lionel A1 - Deuflhard, Peter T1 - Stable Computation of Probability Densities of Metastable Dynamical Systems JF - SIAM J. Multiscale Model. Simul. Y1 - 2007 VL - 6 IS - 2 SP - 396 EP - 416 ER - TY - CHAP A1 - Kube, Susanna A1 - Weber, Marcus T1 - Preserving the Markov Property of Reduced Reversible Markov Chains T2 - Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008 Y1 - 2008 VL - 1048 SP - 593 EP - 596 ER - TY - JOUR A1 - Förster, C. A1 - Brauer, Arnd B. E. A1 - Fürste, J. A1 - Betzel, C. A1 - Weber, Marcus A1 - Cordes, Frank A1 - Erdmann, V. T1 - Visualization of the tRNA(Ser) acceptor step binding site in the seryl-tRNA synthetase JF - BBRC Y1 - 2007 VL - 362 IS - 2 SP - 415 EP - 418 ER - TY - JOUR A1 - Weber, Marcus A1 - Becker, Roland A1 - Köppen, Robert A1 - Durmaz, Vedat T1 - Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane JF - Journal of Molecular Simulation Y1 - 2008 VL - 34 IS - 7 SP - 727 EP - 736 ER - TY - JOUR A1 - Weber, Marcus A1 - Bujotzek, Alexander A1 - Andrae, Karsten A1 - Weinhart, M. A1 - Haag, Rainer T1 - Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces JF - J. Mol. Sim. Y1 - 2011 ER - TY - JOUR A1 - Weber, Marcus A1 - Andrae, Karsten T1 - A simple method for the estimation of entropy differences JF - MATCH Commun. Math. Comp. Chem. 2010 Y1 - 2010 VL - 63(2) SP - 319 EP - 332 ER - TY - JOUR A1 - Weiser, Martin A1 - Schiela, Anton T1 - Function space interior point methods for PDE constrained optimization JF - PAMM Y1 - 2004 VL - 4 IS - 1 SP - 43 EP - 46 ER - TY - CHAP A1 - Weber, Marcus A1 - Rungsarityotin, Wasinee A1 - Schliep, Alexander ED - Spiliopoulou, Myra ED - Kruse, Rudolf ED - Borgelt, Christian ED - Nürnberger, Andreas ED - Gaul, Wolfgang T1 - An Indicator for the Number of Clusters T2 - From Data and Information Analysis to Knowledge Engineering Y1 - 2006 UR - http://dx.doi.org/10.1007/3-540-31314-1_11 SP - 103 EP - 110 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Weiser, Martin A1 - Gänzler, Tobias A1 - Schiela, Anton T1 - A control reduced primal interior point method for a class of control constrained optimal control problems JF - Comput. Optim. Appl. Y1 - 2007 VL - 41 IS - 1 SP - 127 EP - 145 ER - TY - THES A1 - Weber, Marcus T1 - Meshless Methods in Conformation Dynamics Y1 - 2006 ER - TY - RPRT A1 - Volkwein, S. A1 - Weiser, Martin T1 - Optimality Conditions for a Constrained Parameter Identification Problem in Hyperthermia Y1 - 2004 IS - 305 PB - University of Graz, SFB F003 CY - Graz, Austria ER - TY - JOUR A1 - Volkwein, S. A1 - Weiser, Martin T1 - Affine Invariant Convergence Analysis for Inexact Augmented Lagrangian SQP Methods JF - SIAM J. Control Optim. Y1 - 2002 VL - 41 IS - 3 SP - 875 EP - 899 ER - TY - CHAP A1 - Tyminski, Jacek A1 - Popescu, Raluca A1 - Burger, Sven A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Matsuyama, Tomoyuki A1 - Noda, Tomoya ED - Conley, W. T1 - Finite element models of lithographic mask topography T2 - Proc. SPIE Y1 - 2012 U6 - https://doi.org/10.1117/12.916957 VL - 8326 SP - 83261B ER - TY - JOUR A1 - Teschke, G. T1 - Frames, Sparsity, and Nonlinear InverseProblems JF - Oberwolfach Reports Y1 - 2006 ER - TY - JOUR A1 - Teschke, G. A1 - Ramlau, R. T1 - An Iterative Algorithm for Nonlinear InverseProblems with Joint Sparsity Constraints in Vector Valued Regimes and an Application to Color Image Inpainting JF - under review Y1 - 2007 ER - TY - JOUR A1 - Teschke, G. T1 - A new frame-based statistical strategy for bird migration clutter removal in wind profiler radar data JF - preprint Y1 - 2006 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - A new intermittent clutter filtering algorithm for radar wind profiler JF - Proc. ISTP Boulder Y1 - 2006 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - Wavelet based methods for improved wind profiler signal processing JF - Annales Geophysicae Y1 - 2001 IS - 19 SP - 825 EP - 836 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - Advanced Intermittent Clutter Filtering for Radar Wind Profiler JF - under review Y1 - 2007 ER - TY - JOUR A1 - Teschke, G. A1 - Görsdorf, U. A1 - Körner, P. A1 - Trede, D. T1 - A New Approach for Target Classification in Ka-Band Radar Data JF - Proc. ERAD Barcelona Y1 - 2006 ER - TY - JOUR A1 - Boeth, Heide A1 - Duda, Georg A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Doyscher, Ralf A1 - Jung, Tobias A1 - Moewis, Philippe A1 - Scheffler, Sven A1 - Taylor, William R. T1 - Anterior cruciate ligament-deficient patients with passive knee joint laxity have a decreased range of anterior-posterior motion during active movements JF - The American Journal of Sports Medicine Y1 - 2013 U6 - https://doi.org/10.1177/0363546513480465 VL - 41 IS - 5 SP - 1051 EP - 7 ER - TY - JOUR A1 - Taylor, William R. A1 - Pöpplau, Berry M. A1 - König, Christian A1 - Ehrig, Rainald A1 - Zachow, Stefan A1 - Duda, Georg A1 - Heller, Markus O. T1 - The medial-lateral force distribution in the ovine stifle joint during walking JF - Journal of Orthopaedic Research Y1 - 2011 U6 - https://doi.org/10.1002/jor.21254 VL - 29 IS - 4 SP - 567 EP - 571 ER - TY - CHAP A1 - Taylor, William R. A1 - Kassi, J.-P. A1 - Schwarzkopf, J. A1 - Ehrig, Rainald A1 - Schell, H. A1 - Duda, G. T1 - The Profile of Mechanical Loading is Independent of Fracture Fixation Principle T2 - Proceedings of the 51th Annual Meeting of the Orthopedic Society Y1 - 2005 CY - Washington ER - TY - CHAP A1 - Taylor, William R. A1 - König, Christian A1 - Speirs, A. A1 - Ehrig, Rainald A1 - Duda, G. A1 - Heller, Markus O. T1 - Die medio-laterale Kraftverteilung im Schafsknie T2 - Deutscher Kongress für Orthpädie und Unfallchirurgie, Berlin Y1 - 2006 ER - TY - CHAP A1 - Taylor, William R. A1 - König, Christian A1 - Speirs, A. A1 - Ehrig, Rainald A1 - Duda, G. A1 - Heller, Markus O. T1 - The medio-lateral force distribution in the sheep knee during walking T2 - 5. World Congress of Biomechanics, Munich, Journal of Biomechanics Y1 - 2006 IS - 39, Suppl. 1 SP - S491 ER - TY - CHAP A1 - Taylor, William R. A1 - Kornaropoulos, Evgenios I. A1 - Kratzenstein, Stefan A1 - Ehrig, Rainald A1 - Plank, F. A1 - Heller, Markus O. T1 - Targeted Marker Placement for the Functional Identification of the Hip Joint Centre T2 - Transactions Vol. 36, 2011 Annual Meeting of the Orthopedic Society Y1 - 2011 CY - Long Beach ER - TY - CHAP A1 - Taylor, William R. A1 - Kratzenstein, Stefan A1 - Kornaropoulos, Evgenios I. A1 - Ehrig, Rainald A1 - Moewis, Philippe A1 - Heller, Markus O. T1 - Non-invasive Assessment of Skeletal Kinematics T2 - Measurement and Sensing in Medicine and Health Y1 - 2009 CY - London ER - TY - CHAP A1 - Taylor, William R. A1 - Kornaropoulos, Evgenios I. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Duda, Georg T1 - Reproducibility of a functional approach to gait analysis T2 - Annual meeting of the ESMAC 2009 Y1 - 2009 CY - London ER - TY - JOUR A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Seebeck, P. A1 - Duda, G. T1 - Tibio-femoral Joint Contact Forces in Sheep JF - Journal of Biomechanics Y1 - 2006 IS - 39 SP - 791 EP - 798 ER - TY - CHAP A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Seebeck, P. A1 - Duda, G. T1 - Animal Models for Knee Injury Frequently Underestimate the Mechanical Conditions of the Clinical Situation T2 - Proceedings of the 51th Annual Meeting of the Orthopedic Society Y1 - 2005 CY - Washington ER - TY - JOUR A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Klein, P. A1 - Duda, G. T1 - On the Influence of Soft Tissue Coverage in the Determination of Bone Kinematics using Bone Markers JF - Journal of Orthopedic Research Y1 - 2005 IS - 23 SP - 726 EP - 734 ER - TY - CHAP A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Duda, G. T1 - Can Skin Markers Determine the Kinematics of Underlying Bones? T2 - Proceedings of the 50th Annual Meeting of the Orthopedic Society Y1 - 2004 CY - San Francisco ER - TY - CHAP A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Duda, G. A1 - Heller, Markus O. T1 - The Symmetrical Axis of Rotation Approach (SARA) for Determination of Joint Axes in Clinical Gait Analysis T2 - 1st Joint ESMAC-GCMAS Meeting, Amsterdam Y1 - 2006 ER - TY - CHAP A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Duda, G. A1 - Heller, Markus O. T1 - The determination of joint axes T2 - 5. World Congress of Biomechanics, Munich, Journal of Biomechanics Y1 - 2006 IS - 39, Suppl. 1 SP - S571 EP - S572 ER - TY - CHAP A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Hege, Hans-Christian A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland ED - Franconi, Cafiero T1 - HyperPlan - an integrated system for treatment planning in regional hyperthermia T2 - Proc. of the 7th Int. Congress on Hyperthermic Oncology, Rome, Italy, April 1996 Y1 - 1996 VL - 2 SP - 552 EP - 554 ER - TY - JOUR A1 - Soares, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Regularization for Nonlinear Diffusion Equations in a Multiresolution Framework JF - Mathematical Methods in Applied Sciences Y1 - 2007 ER - TY - JOUR A1 - Sreenivasa, G. A1 - Gellermann, Johanna A1 - Nadobny, Johanna A1 - Schlag, P. A1 - Deuflhard, Peter A1 - Felix, Roland A1 - Wust, Peter T1 - Clinical Use of the Hyperthermia Treatment Planning System Hyperplan to Predict Effectiveness and Toxicity JF - Int. J. Oncology Biol. Phys. Y1 - 2003 VL - 55 IS - 2 SP - 407 EP - 419 ER - TY - JOUR A1 - Soares, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Wavelet Regularization for Nonlinear Diffusion Equations JF - Technical Report 04-12, ISSN 1435-7968 Y1 - 2004 ER - TY - JOUR A1 - Siegel, D. A1 - Andrae, Karsten A1 - Proske, Matthias A1 - Kochan, C. A1 - Koch, Matthias A1 - Weber, Marcus A1 - Nehls, Irene T1 - Dynamic covalent hydrazine chemistry as a specific extraction and cleanup technique for the quantification of the Fusarium mycotoxin zearalenone in edible oils JF - Journal of Chromatography A Y1 - 2010 VL - 1217(15) SP - 2206 EP - 15 ER - TY - THES A1 - Sim, I. T1 - Analysis und Numerik der Resonanzen des Schrödinger-Operators in 1D Y1 - 2005 ER - TY - THES A1 - Schmidt, Frank T1 - Untersuchung heteronomer Differentialgleichungen mit Hilfe des Analogrechners Y1 - 1986 ER - TY - CHAP A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Zöckler, M. A1 - Hege, Hans-Christian A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter T1 - Surface Mesh Generation for Numerical Simulations of Hyperthermia Treatments T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 146 ER - TY - CHAP A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Felix, Roland A1 - Deuflhard, Peter ED - Franconi, Cafiero T1 - Three-Dimensional Finite Element Mesh Generation for Numerical Simulations of Hyperthermia Treatments T2 - Proc. of the 7th Int. Congress on Hyperthermic Oncology, Rome, Italy, April 1996 Y1 - 1996 VL - 2 SP - 547 EP - 548 ER - TY - THES A1 - Schräer, Ingo T1 - Modellreduktion in der regionalen Hyperthermie mittels POD Y1 - 2008 CY - Fachbereich Mathematik ER - TY - CHAP A1 - Schmidt, Frank A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Fast online simulation of 3D nanophotonic structures by the reduced basis method T2 - Integrated Optics: Devices, Materials, and Technologies XV Y1 - 2011 U6 - https://doi.org/10.1117/12.874726 VL - 7941 SP - 79410G PB - Proc. SPIE ER - TY - CHAP A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Hiremath, Kirankumar A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, Shaul A1 - Richter, Marten T1 - Combining nanooptical fields and coherent spectroscopy on systems with delocalized excitons T2 - Proc. SPIE Y1 - 2012 U6 - https://doi.org/10.1117/12.906671 VL - 8260 SP - 82601V ER - TY - CHAP A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, Shaul A1 - Richter, Marten T1 - Coherent Nonlinear Spectroscopy with Spatiotemporally Controlled Fields T2 - CLEO/QELS Y1 - 2012 U6 - https://doi.org/10.1364/QELS.2012.QF3D.6 SP - QF3D.6 PB - Optical Society of America ER - TY - JOUR A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, S. A1 - Richter, Marten T1 - Ultrafast nonlinear spectroscopy with spatially confined fields JF - AIP Conference Proceedings Y1 - 2011 U6 - https://doi.org/10.1063/1.3644223 VL - 1398 SP - 94 EP - 96 PB - AIP ER - TY - JOUR A1 - Schädle, Achim A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Klose, Roland A1 - Schmidt, Frank T1 - Domain Decomposition Method for Maxwell’s Equations JF - J. Comput. Phys. Y1 - 2007 U6 - https://doi.org/10.1016/j.jcp.2007.04.017 VL - 226 SP - 477 EP - 493 ER - TY - JOUR A1 - Scheibe, Ch. A1 - Bujotzek, Alexander A1 - Dernedde, Jens A1 - Weber, Marcus A1 - Seitz, O. T1 - DNA-programmed spatial screening of carbohydrate-lectin interactions JF - Chem. Sci. Y1 - 2011 VL - 2 SP - 770 EP - 775 ER - TY - CHAP A1 - Schädle, Achim A1 - Zschiedrich, Lin ED - Widlund, Olof ED - Keyes, David T1 - Additive Schwarz method for scattering problems using the PML method at interfaces T2 - Domain Decomposition Methods in Science and Engineering XVI Y1 - 2007 VL - 55 SP - 205 EP - 212 PB - Springer ER - TY - CHAP A1 - Schmidt, Frank A1 - Yevick, David T1 - Discrete Transparent Boundary Conditions for the Fresnel Equation T2 - Proceedings of the 8th European Conference on Integrated Optics Y1 - 1997 SP - 222 EP - 225 CY - Royal Institute of Technology, Stockholm, Sweden ER - TY - JOUR A1 - Schmidt, Frank A1 - Yevick, David T1 - Discrete Transparent Boundary Conditions for Schrödinger-Type Equations JF - J. Comput. Phys. Y1 - 1997 U6 - https://doi.org/10.1006/jcph.1997.5675 VL - 134 IS - 1 SP - 96 EP - 107 ER - TY - CHAP A1 - Schädle, Achim A1 - Ruprecht, Daniel A1 - Schmidt, Frank ED - et.al., N. Biggs T1 - Transparent boundary conditions - the pole condition approach T2 - Proceedings of Waves 2007 Y1 - 2007 SP - 301 EP - 303 ER - TY - JOUR A1 - Schaber, Karlheinz A1 - Ofenloch, Oliver A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Aerosolbildung in Gas/Flüssigkeits-Kontaktapparaten - Modellierungsstrategien und Simulation JF - Chemie Ingenieur Technik Y1 - 2004 VL - 76 IS - 9 SP - 1358 EP - 1359 ER - TY - CHAP A1 - Schmidt, Frank A1 - Nolting, Hans-Peter T1 - An Adaptive Approach to a Beam Propagation Method T2 - Integrated Photonics Research Y1 - 1992 SP - 302 EP - 303 CY - New Orleans, Louisiana, USA ER - TY - JOUR A1 - Schmidt, Frank A1 - Nolting, Hans-Peter T1 - Adaptive Multilevel Beam Propagation Method JF - IEEE Photonics Technology Letter Y1 - 1992 VL - 4 SP - 1381 EP - 1383 ER - TY - JOUR A1 - Schmidt, Frank A1 - März, Reinhard T1 - On the Reference Wave Vector of Paraxial Helmholtz Equations JF - IEEE Journal of Lightwave Technology Y1 - 1996 VL - 14 SP - 2395 EP - 2400 ER - TY - JOUR A1 - Schädle, Achim A1 - López-Fernández, María A1 - Lubich, Christian T1 - Fast and oblivious convolution quadrature JF - SIAM J. Sci. Comput. Y1 - 2006 U6 - https://doi.org/http://dx.doi.org/10.1137/050623139 VL - 28 IS - 2 SP - 421 EP - 438 ER - TY - CHAP A1 - Scholze, Frank A1 - Laubis, Christian A1 - Dersch, Uwe A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank ED - Bosse, Harald T1 - The influence of line edge roughness and CD uniformity on EUV scatterometry for CD characterization of EUV masks T2 - Modeling Aspects in Optical Metrology Y1 - 2007 VL - 6617 SP - 66171A PB - Proc. SPIE ER - TY - JOUR A1 - Schaber, Karlheinz A1 - Koerber, Jens A1 - Ofenloch, O. A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Aerosol Formation in Gas-Liquid Contact Devices- Nucleation, Growth and Particle Dynamics JF - Chem.Eng.Sci. Y1 - 2002 VL - 57 SP - 4345 EP - 4356 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - Fiedler, Bernold T1 - Transfer operator approach to conformational dynamics in biomolecular systems T2 - Ergodic theory, analysis, and efficient simulation of dynamical systems Y1 - 2001 SP - 191 EP - 223 PB - Berlin: Springer ER - TY - JOUR A1 - Schmidt, Frank A1 - Hohage, Thorsten A1 - Klose, Roland A1 - Schädle, Achim A1 - Zschiedrich, Lin T1 - Pole condition: A numerical method for Helmholtz-type scattering problems with inhomogeneous exterior domain JF - J. Comput. Appl. Math. Y1 - 2008 U6 - https://doi.org/10.1016/j.cam.2007.04.046 VL - 218 IS - 1 SP - 61 EP - 69 ER - TY - JOUR A1 - Schmidt, Frank A1 - Gottschling, K. T1 - Improved Method of Mode Determination in Planar Optical Waveguides Using Line Transmission Approach JF - J. Opt. Commun. Y1 - 1992 VL - 12 IS - 3 SP - 112 EP - 114 ER - TY - JOUR A1 - Schiela, Anton A1 - Günther, Andreas T1 - An Interior Point Algorithm with Inexact Step Computation in Function Space for State Constrained Optimal Control JF - Numer. Math. Y1 - 2011 U6 - https://doi.org/10.1007/s00211-011-0381-4 VL - 119 IS - 2 SP - 373 EP - 407 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Schmidt, Frank A1 - Friese, T. A1 - Zschiedrich, Lin A1 - Deuflhard, Peter T1 - Adaptive Multigrid Methods for the Vectorial Maxwell Eigenvalue Problem for Optical Waveguide Design T2 - Mathematics - Key Technology for the Future Y1 - 2003 UR - http://www.zib.de/Publications/Reports/ZR-00-54.pdf SP - 270 EP - 292 PB - Springer ER - TY - JOUR A1 - Schmidt, Frank A1 - Friese, T. A1 - Yevick, David T1 - Transparent Boundary Conditions for Split-Step Padé Approximations of the One-Way Helmholtz equation JF - J. Comp. Phys Y1 - 2001 VL - 170 SP - 696 EP - 719 ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo JF - J. Comput. Phys. Y1 - 1999 UR - http://www.zib.de/PaperWeb/abstracts/SC-98-45 VL - 151 SP - 146 EP - 168 ER - TY - JOUR A1 - Schmidt, Frank T1 - Construction of Discrete Transparent Boundary Conditions for Schrödinger-Type equations JF - Surv. Math. Ind. Y1 - 1999 VL - 9 SP - 87 EP - 100 ER - TY - CHAP A1 - Schmidt, Frank T1 - Simulation of Scattering and Reflection Problems via Solution of the 2D Helmholtz Equation T2 - Integrated Photonics Research Y1 - 1998 VL - 4 SP - 408 EP - 410 ER - TY - JOUR A1 - Schmidt, Frank T1 - Computation of Discrete Transparent Boundary Conditions for the 2D Helmholtz equation JF - Optical and Quantum Electronics Y1 - 1998 VL - 30 IS - 5,6 SP - 427 EP - 441 ER - TY - CHAP A1 - Schmidt, Frank ED - G. C. Righini, D. T1 - Phase-adaptive basis functions for a multilevel finite element solution of the paraxial wave equation T2 - Euro-Opto Series Y1 - 1994 SP - 57 EP - 61 CY - Lindau, Germany ER - TY - JOUR A1 - Schmidt, Frank T1 - An Adaptive Approach to the Numerical Solution of Fresnel’s Wave Equation. JF - IEEE Journal of Lightwave Technology Y1 - 1993 VL - 11 IS - 9 SP - 1425 EP - 1435 ER - TY - JOUR A1 - Schmidt, Frank T1 - Simulation und Herstellung von Faserschleifkopplern JF - Wissenschaftliche Zeitschrift der Humboldt-Universität zu Berlin, R. Math./Naturwiss. Y1 - 1990 VL - 39 IS - 2 SP - 115 EP - 118 ER - TY - THES A1 - Schmidt, Frank T1 - Ingenieurmäßige Berechnung der Feldausbreitung in optischen Bauelementen der Lichtwellenleitertechnik Y1 - 1989 ER - TY - JOUR A1 - Schmidt, Frank T1 - Pole Condition: A new Approach to Solve Scattering Problems JF - Oberwolfach Report Y1 - 2004 VL - 1 IS - 1 SP - 615 EP - 617 PB - Mathematisches Forschungsinstitut Oberwolfach ER - TY - THES A1 - Schmidt, Frank T1 - Solution of Interior-Exterior Helmholtz-Type Problems Based on the Pole Condition Concept Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-02-45 ER - TY - CHAP A1 - Schmidt, Frank ED - Bermúdez, A. ED - Gómez, D. ED - Hazard, C. ED - Joly, P. ED - Roberts, J. T1 - Discrete Nonreflecting Boundary Conditions for the Helmholtz equation T2 - Fifth International Conference on Mathematical and Numerical Aspects of Wave Propagation Y1 - 2000 UR - http://www.zib.de/Publications/Reports/ZR-00-06.pdf SP - 921 EP - 925 CY - Waves 2000, Santiago de Compostella, Spain ER - TY - JOUR A1 - Schmidt, Frank A1 - Deuflhard, Peter T1 - Discrete Transparent Boundary Conditions for the Numerical Solution of Fresnel’s Equation. JF - Comput. Math. Appl. Y1 - 1995 VL - 29 SP - 53 EP - 76 ER - TY - CHAP A1 - Schmidt, Frank A1 - Deuflhard, Peter T1 - Discrete Transparent Boundary Conditions for Fresnel’s Equation T2 - Integrated Photonics Research Y1 - 1994 SP - 45 EP - 47 CY - San Francisco, California, USA ER - TY - CHAP A1 - Schöpf, R. A1 - Deuflhard, Peter ED - et al. Bulirsch, R. T1 - OCCAL. A mixed symbolic-numeric optimal control calculator T2 - Computational optimal control Y1 - 1994 VL - 115 SP - 269 EP - 278 PB - Birkhäuser Verlag Basel ER - TY - CHAP A1 - Schmidt, Frank A1 - Burger, Sven A1 - Schädle, Achim A1 - Klose, Roland T1 - Finite element methods for optical device design T2 - Proceedings of the 5th International Conference on Numerical Simulation of Optoelectronic devices Y1 - 2005 U6 - https://doi.org/10.1109/NUSOD.2005.1518133 SP - 57 EP - 58 ER - TY - CHAP A1 - Schmidt, Frank A1 - Burger, Sven A1 - Pomplun, Jan A1 - Zschiedrich, Lin ED - Greiner, Christoph ED - Wächter, Christoph T1 - Advanced FEM analysis of optical waveguides: algorithms and applications T2 - Integrated Optics Y1 - 2008 U6 - https://doi.org/10.1117/12.765720 VL - 6896 SP - 689602 PB - SPIE ER - TY - JOUR A1 - Schiela, Anton A1 - Weiser, Martin T1 - Superlinear convergence of the Control Reduced Interior Point Method for PDE Constrained Optimization JF - Computational Optimization and Applications Y1 - 2008 VL - 39 IS - 3 SP - 369 EP - 393 ER - TY - JOUR A1 - Schlegel, Martin A1 - Marquardt, Wolfgang A1 - Ehrig, Rainald A1 - Nowak, Ulrich T1 - Sensitivity analysis of linearly-implicit differential-algebraic systems by one-step extrapolation JF - Applied Numerical Mathematics Y1 - 2004 IS - 48 SP - 83 EP - 102 ER - TY - JOUR A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Transparent boundary conditions for time-dependent problems JF - SIAM J. Sci. Comput. Y1 - 2008 U6 - https://doi.org/10.1137/070692637 VL - 30 IS - 5 SP - 2358 EP - 2385 ER - TY - THES A1 - Ruprecht, Daniel T1 - Konstruktion transparenter Randbedingungen für die Wellengleichung mit Hilfe der Polbedingung Y1 - 2005 ER - TY - CHAP A1 - Rozova, Maria A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Burger, Sven T1 - 3D finite element simulation of optical modes in VCSELs T2 - Proc. SPIE Y1 - 2012 U6 - https://doi.org/10.1117/12.906372 VL - 8255 SP - 82550K ER - TY - JOUR A1 - Richter, Marten A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, Shaul T1 - Reconstruction of the wave functions of coupled nanoscopic emitters using a coherent optical technique JF - Phys. Rev. B Y1 - 2012 U6 - https://doi.org/10.1103/PhysRevB.86.085308 VL - 86 SP - 085308 ER - TY - THES A1 - Reinecke, Isabel T1 - Mathematical modeling and simulation of the female menstrual cycle Y1 - 2009 ER - TY - JOUR A1 - Reinecke, Isabel A1 - Deuflhard, Peter T1 - A Complex Mathematical Model of the Human Menstrual Cycle JF - Journal of Theoretical Biology Y1 - 2007 VL - 247 IS - 2 SP - 303 EP - 330 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - A Projection Iteration for Nonlinear Operator Equations with Sparsity Constraints JF - Numerische Mathematik Y1 - 2006 VL - 104 SP - 177 EP - 203 ER - TY - CHAP A1 - Reinecke, Isabel A1 - Deuflhard, Peter ED - Daskalaki, A. T1 - Model Development and Decomposition in Physiology T2 - Handbook of Research on Systems Biology Applications in Medicine Y1 - 2008 VL - 2 SP - 759 EP - 797 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Regularization of Sobolev Embedding Operators and Applications Part II JF - Sampling Theory in Signal and Image Processing Y1 - 2004 VL - 3 IS - 3 SP - 225 EP - 246 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Tikhonov Replacement Functionals for Iteratively Solving Nonlinear Operator Equations JF - InverseProblems Y1 - 2005 VL - 21 SP - 1571 EP - 1592 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Regularization of Sobolev Embedding Operators and Applications Part I JF - Sampling Theory in Signal and Image Processing Y1 - 2004 VL - 3 IS - 2 SP - 175 EP - 196 ER - TY - CHAP A1 - Roitzsch, Rainer A1 - Lang, Jens A1 - Erdmann, Bodo T1 - The Benefits of Modularization T2 - Proc. 14th GAMM-Seminar Kiel on ’Concepts of Numerical Software Y1 - 1998 PB - did not appear ER - TY - JOUR A1 - Rätsch, M. A1 - Romdhani, S. A1 - Teschke, G. A1 - Vetter, T. T1 - Wavelet Frame Accelerated Reduced Support Vector Machine JF - to appaer in: Y1 - 2006 ER - TY - JOUR A1 - Teschke, G. A1 - Zhariy, M. A1 - Maass, Peter A1 - Sassen, K. T1 - Extraction and Analysis of Structural Features in Cloud Radar and Lidar Data Using Wavelet Based Methods JF - Proceedings of ERAD Y1 - 2002 ER - TY - THES A1 - Riemer, Alexander T1 - Accuracy, stability, convergence of rigorous thermodynamic sampling methods Y1 - 2006 ER - TY - CHAP A1 - Pomplun, Jan A1 - Wenzel, Hans A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Rozova, Maria A1 - Schmidt, Frank A1 - Crump, Paul A1 - Ekhteraei, Hossein A1 - Schultz, Christoph M. A1 - Erbert, Götz T1 - Thermo-optical simulation of high-power diode lasers T2 - Proc. SPIE Y1 - 2012 U6 - https://doi.org/10.1117/12.909330 VL - 8255 SP - 825510 ER - TY - CHAP A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Reduced basis method for real-time inverse scatterometry T2 - Modelling Aspects in Optical Metrology III Y1 - 2011 U6 - https://doi.org/10.1117/12.889892 VL - 8083 SP - 808308 PB - Proc. SPIE ER - TY - JOUR A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schmidt, Frank A1 - Burger, Sven T1 - Finite element simulation of radiation losses in photonic crystal fibers JF - phys. stat. sol. (a) Y1 - 2007 U6 - https://doi.org/10.1002/pssa.200776414 VL - 204 IS - 11 SP - 3822 EP - 3837 ER - TY - CHAP A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Burger, Sven A1 - Zschiedrich, Lin T1 - Adaptive Reduced Basis Method for Optical Scattering Problems T2 - Integrated Photonics Research, Silicon and Nanophotonics Y1 - 2010 U6 - https://doi.org/10.1364/IPRSN.2010.IWD4 SP - IWD4 PB - OSA ER - TY - CHAP A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Reduced Basis Method for Nano Optical Simulations T2 - Integrated Photonics and Nanophotonics Research and Applications Y1 - 2008 SP - IWD7 PB - Optical Society of America ER - TY - CHAP A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Reduced Basis Method for Electromagnetic Field Computations T2 - Scientific Computing in Electrical Engineering SCEE 2008 Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-12294-1_12 SP - 85 PB - Springer Berlin Heidelberg ER - TY - CHAP A1 - Pomplun, Jan A1 - Holzlöhner, Ronald A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank ED - Adibi, Ali ED - Scherer, Axel ED - Lin, Shawn-Yu T1 - FEM investigation of leaky modes in hollow core photonic crystal fibers T2 - Proc. SPIE, Photonic Crystal Materials and Devices VI Y1 - 2007 UR - http://arxiv.org/pdf/physics/0702165 VL - 6480 SP - 64800M ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Adaptive finite element method for simulation of optical nano structures JF - Phys. Status Solidi B Y1 - 2007 U6 - https://doi.org/10.1002/pssb.200743192 VL - 244 SP - 3419 EP - 3434 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schliwa, Andrei A1 - Bimberg, Dieter A1 - Pietrzak, Agnieszka A1 - Wenzel, Hans A1 - Erbert, Götz T1 - Finite element simulation of the optical modes of semiconductor lasers JF - Phys. Status Solidi B Y1 - 2010 U6 - https://doi.org/10.1002/pssb.200945451 VL - 247 SP - 846 EP - 853 ER - TY - CHAP A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank A1 - Scholze, Frank A1 - Laubis, Christian A1 - Dersch, Uwe ED - Bosse, Harald T1 - Finite element analysis of EUV lithography T2 - Modeling Aspects in Optical Metrology Y1 - 2007 U6 - https://doi.org/10.1117/12.726156 VL - 6617 SP - 661718 PB - Proc. SPIE ER - TY - CHAP A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin A1 - Scholze, Frank ED - Martin, P. ED - Naber, R. T1 - Rigorous FEM-Simulation of EUV-Masks: Influence of shape and material parameters T2 - Photomask Technology Y1 - 2006 U6 - https://doi.org/10.1117/12.686828 VL - 6349 SP - 63493D PB - Proc. SPIE ER - TY - CHAP A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank A1 - Scholze, Frank A1 - Laubis, Christian A1 - Dersch, Uwe ED - Horiuchi, Toshiyuki T1 - Metrology of EUV masks by EUV-scatterometry and finite element analysis T2 - Photomask and Next-Generation Lithography Mask Technology XV Y1 - 2008 VL - 7028 PB - SPIE ER - TY - CHAP A1 - Scholze, Frank A1 - Laubis, Christian A1 - Ulm, Gerhard A1 - Dersch, Uwe A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank ED - Schellenberg, Frank T1 - Evaluation of EUV scatterometry for CD characterization of EUV masks using rigorous FEM-simulation T2 - Emerging Lithographic Technologies XII Y1 - 2008 VL - 6921 PB - SPIE ER - TY - THES A1 - Pollok, T. T1 - Separabilität von Helmholtz- und Maxwellgleichungen über unbeschränkten heterogenen Gebieten Y1 - 2007 UR - http://www.zib.de/Numerik/NanoOptics/publications/PubText/Pollok07.pdf ER - TY - CHAP A1 - Philippow, E. A1 - Schmidt, Frank T1 - Besondere Lösungen in harmonisch erregten Ferroresonanz-Kreisen T2 - 4. Internationales Symposium Theoretische Elektrotechnik Ilmenau Y1 - 1987 VL - 2 SP - 26 EP - 32 ER - TY - THES A1 - Pomplun, Jan T1 - Rigorous FEM-Simulation of Maxwell’s Equations for EUV-Lithography Y1 - 2006 UR - http://www.zib.de/Numerik/NanoOptics/publications/PubText/Pomplun06.pdf ER - TY - CHAP A1 - Petracek, Jiri A1 - Luksch, Jaroslav A1 - Maes, Bjorn A1 - Burger, Sven A1 - Kwiecien, Pavel A1 - Richter, Ivan ED - Ferrari, M. ED - Marciniak, M. ED - Righini, G. ED - Szoplik, T. ED - Varas, S. T1 - Simulation of photonic crystal nanocavities using a bidirectional eigenmode propagation algorithm: a comparative study T2 - Micro- and nanophotonic materials and devices Y1 - 2012 SN - 9788377980200 SP - 109 EP - 112 PB - IFN-CNR, Trento, Italy ER - TY - CHAP A1 - Petracek, Jiri A1 - Maes, Bjorn A1 - Burger, Sven A1 - Luksch, Jaroslav A1 - Kwiecien, Pavel A1 - Richter, Ivan T1 - Simulation of high-Q nanocavities with 1D photonic gap T2 - Transparent Optical Networks (ICTON) Y1 - 2012 U6 - https://doi.org/10.1109/ICTON.2012.6253762 SP - 1 EP - 4 PB - IEEE ER - TY - JOUR A1 - Pearce, G. J. A1 - Wiederhecker, G. S. A1 - Poulton, Christopher G. A1 - Burger, Sven A1 - Russell, P. St. J. T1 - Models for guidance in kagome-structured hollow-core photonic crystal fibres JF - Optics Express Y1 - 2007 U6 - https://doi.org/10.1364/OE.15.012680 VL - 15 SP - 12680 ER - TY - JOUR A1 - Pedri, P. A1 - Pitaevskii, L. A1 - Stringari, S. A1 - Fort, C. A1 - Burger, Sven A1 - Cataliotti, F. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo T1 - Expansion of a Coherent Array of Bose-Einstein Condensates JF - Physical Review Letters Y1 - 2001 VL - 87 SP - 220401 ER - TY - CHAP A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for computational lithography T2 - Photomask Technology Y1 - 2009 U6 - https://doi.org/10.1117/12.829639 VL - 7488 SP - 74882B PB - Proc. SPIE ER - TY - CHAP A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Reduced basis method for fast and robust simulation of electromagnetic scattering problems T2 - Numerical Methods in Optical Metrology Y1 - 2009 U6 - https://doi.org/10.1117/12.827588 VL - 7390 SP - 73900I PB - Proc. SPIE ER - TY - JOUR A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Accelerated a posteriori error estimation for the reduced basis method with application to 3D electromagnetic scattering problems JF - SIAM J. Sci. Comput. Y1 - 2010 U6 - https://doi.org/10.1137/090760271 VL - 32 SP - 498 EP - 520 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Roitzsch, Rainer A1 - Lines, Glenn Terje T1 - Adaptive Finite Element Simulation of Ventricular Dynamics JF - J. Computing and Visualization in Science Y1 - 2009 VL - 12 SP - 201 EP - 205 ER - TY - JOUR A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Numerical Identification of Selected Rate Constants in Large Chemical Reaction Systems JF - Appl. Numer. Math. Y1 - 1985 VL - 1 SP - 59 EP - 75 ER - TY - THES A1 - Scharkoi, O. T1 - Simulation von Opioiden unter Hinzunahme von Temperatur und pH-Wert Y1 - 2007 ER - TY - CHAP A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Towards Parameter Identification for Large Chemical Reaction Systems T2 - Numerical Treatment of Inverse Problems in Differential and Integral Equations Y1 - 1983 VL - 2 SP - 13 EP - 26 PB - Boston: Birkhäuser ER - TY - CHAP A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Davidov, D. ED - Mastorakis, N. T1 - Localized resonant states and transmission in a two- dimensional photonic quasicrystal T2 - Proc. of the 5th International Conference on Applied Mathematics, Simulation, Modelling (ASM ’II), Corfu, 2011 Y1 - 2011 SN - 978-1-61804-016-9 VL - 1 SP - 178 EP - 182 ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Lifshitz, R. A1 - Davidov, D. T1 - Negative Refraction and Omni Directionality in 2D Photonic Quasicrystal Superstructure JF - AIP Conference Proceedings Y1 - 2010 U6 - https://doi.org/10.1063/1.3498134 VL - 1281 SP - 1622 PB - AIP ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Davidov, D. T1 - Resonant Transmission of Electromagnetic Waves through 2D Photonic Quasicrystals JF - J. Appl. Phys. Y1 - 2010 U6 - https://doi.org/10.1063/1.3329542 VL - 107 SP - 063105 ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Davidov, D. T1 - Fast Light and Focusing in 2D Photonic Quasicrystals JF - PIERS Online Y1 - 2009 U6 - https://doi.org/10.2529/PIERS081223080021 VL - 5 SP - 451 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Wlodarczyk, Waldemar A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland ED - Franconi, Cafiero T1 - Simulation Studies for Combination of Hyperthermia and Magnetic Resonance Systems T2 - Proc. of the 7th Int. Congress on Hyperthermic Oncology, Rome, Italy, April 1996 Y1 - 1996 VL - 2 SP - 549 EP - 551 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Quantitative Comparison between the VSIE and the FDTD method using Electrically Equivalent Patient and Antenna Models T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 145 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Volume-Surface Integral Method for Solving Maxwell’s Equations in Electrically Inhomogeneous Media Using Tetrahedral Grids JF - IEEE Transactions on Microwave Theory and Techniques Y1 - 1996 VL - 44 IS - 4 SP - 543 EP - 554 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland ED - Simunic, D. T1 - The Use of the Volume-Surface Integral Equation Method (VSIE) for Antenna Problems T2 - Proc. COST 244 meeting on Reference Models for Bioelectromagnetic Test of Mobile Communication Systems, Roma, November 1994 Y1 - 1995 SP - 67 EP - 74 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Wlodarczyk, Waldemar A1 - Deuflhard, Peter A1 - Mönich, Gerhard A1 - Wust, Peter ED - Stuchly, M. ED - Shannon, D. T1 - Numerical and Experimental Investigations of Different Antenna Types for Deep Body Hyperthermia T2 - Proc. 2001 URSI International Symposium on electromagnetic Theory Y1 - 2001 SP - 473 EP - 475 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Sullivan, Dennis A1 - Wust, Peter A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A High Resolution Interpretation at Arbitrary Interfaces for the FDTD Method T2 - IEEE Transactions on Microwave Theory and Techniques Y1 - 1998 VL - 46 IS - 11 SP - 1759 EP - 1766 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Sullivan, Dennis A1 - Wlodarczyk, Waldemar A1 - Deuflhard, Peter A1 - Wust, Peter T1 - A 3-D Tensor FDTD-Formulation for Treatment of Sloped Interfaces in Electrically Inhomogeneous Media JF - IEEE Transactions on Antennas and Propagation Y1 - 2003 VL - 51 IS - 8 SP - 1760 EP - 1770 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Pontalti, R. A1 - Sullivan, Dennis A1 - Wlodarczyk, Waldemar A1 - Vaccari, A. A1 - Deuflhard, Peter A1 - Wust, Peter T1 - A Thin-Rod Approximation for the Improved Modeling of Bare and Insulated Cylindrical Antennas Using the FDTD Method JF - IEEE Transactions on Antennas and Propagation Y1 - 2003 VL - 51 IS - 8 SP - 1780 EP - 1796 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Fähling, Horst A1 - Hagmann, M. A1 - Turner, P. A1 - Wlodarczyk, Waldemar A1 - Gellermann, Johanna A1 - Deuflhard, Peter A1 - Wust, Peter T1 - Experimental and numerical investigation of feed-point parameters in a 3-D hyperthermia applicator using different FDTD models of feed networks JF - IEEE Trans Biomed Eng Y1 - 2002 VL - 49 IS - 11 SP - 1348 EP - 1359 ER - TY - CHAP A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Roitzsch, Rainer ED - Mackens, W. ED - Rump, S. T1 - Eine graphische Oberfläche für numerische Programme T2 - Software Engineering im Scientific Computing Y1 - 1996 SP - 264 EP - 278 PB - Vieweg ER - TY - CHAP A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Roitzsch, Rainer A1 - Sukrow, B. ED - Mackens, W. ED - Rump, S. T1 - Formale Spezifikation des ZIB-GUI mit Hilfe von Graph-Grammatiken T2 - Software Engineering im Scientific Computing Y1 - 1996 SP - 290 EP - 296 PB - Vieweg ER - TY - CHAP A1 - Nowak, Ulrich A1 - Ehrig, Rainald A1 - Oeverdieck, Lars ED - Sloot, P. ED - Bubak, Marian ED - Hertzberger, B. T1 - Parallel Extrapolation Methods and Their Application in Chemical Engineering T2 - High-Performance Computing and Networking Y1 - 1998 VL - 1401 SP - 419 EP - 428 PB - Springer ER - TY - JOUR A1 - Muschinski, A. A1 - Lehmann, V. A1 - Justen, L. A1 - Teschke, G. T1 - Advanced Radar Wind Profiling JF - Meteorologische Zeitschrift Y1 - 2005 VL - 5 IS - 14 SP - 609 EP - 626 ER - TY - JOUR A1 - Michaelis, D. A1 - Wächter, Christoph A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Bräuer, Andreas T1 - Micro-optically assisted high index waveguide coupling JF - Appl. Opt. Y1 - 2006 U6 - https://doi.org/10.1364/AO.45.001831 VL - 45 SP - 1831 EP - 1838 ER - TY - JOUR A1 - Metzner, Ph. A1 - Weber, Marcus A1 - Schütte, Christof T1 - Observation uncertainty in reversible Markov chains JF - Phys. Rev. E Y1 - 2010 U6 - https://doi.org/10.1103/PhysRevE.82.031114 VL - 82 IS - 3 SP - 031114 PB - American Physical Society ER - TY - JOUR A1 - Rätsch, M. A1 - Romdhani, S. A1 - Teschke, G. A1 - Vetter, T. T1 - Overcomplete Wavelet Approximation of a Support Vector Machine for Efficient Classification JF - Springer Lecture Notes in Computer Science Y1 - 2005 SP - 351ff ER - TY - JOUR A1 - Holschneider, M. A1 - Teschke, G. T1 - Existence and Computation of Optimally Localized Coherent States JF - Journal of Mathematical Physics Y1 - 2006 VL - 47 SP - 123503 ER - TY - THES A1 - Massing, Andre T1 - 1D-Reduktion thermal signifikanter Aderstränge in der Hyperthermie-Modellierung Y1 - 2007 ER - TY - CHAP A1 - März, Reinhard A1 - Burger, Sven A1 - Golka, S. A1 - Forchel, A. A1 - Herrmann, Christian A1 - Jamois, C. A1 - Michaelis, D. A1 - Wandel, K. T1 - Planar High Index-Contrast Photonic Crystals for Telecom Applications T2 - Photonic Crystals - Advances in Design, Fabrication and Characterization Y1 - 2006 U6 - https://doi.org/10.1002/3527602593.ch16 SP - 308 EP - 329 PB - Wiley-VCH ER - TY - CHAP A1 - März, Reinhard A1 - Burger, Sven A1 - Forchel, A. A1 - Heidrich, H. A1 - Hess, O. A1 - Michaelis, D. A1 - Wandel, K. A1 - Wehrspohn, R. ED - Lipson, M. T1 - High-contrast planar photonic crystals T2 - Nanophotonics for Communication Y1 - 2004 U6 - https://doi.org/10.1117/12.580070 VL - 5597 SP - 68 EP - 81 PB - Proc. SPIE ER - TY - CHAP A1 - Maass, Peter A1 - Ende, M. A1 - Kayser, D. A1 - Osten, W. A1 - Teschke, G. ED - Osten, W. T1 - Continuous Wavelet Methods in Signal Processing T2 - Invited paper in Y1 - 2001 PB - Elsevier Verlag, ISBN: 2-84299-318-7 CY - Paris ER - TY - JOUR A1 - Maaß, P. A1 - Teschke, G. A1 - Willmann, W. A1 - Wollmann, G. T1 - Detection and Classification of Material Attributes - A Practical Application of Wavelet Analysis JF - IEEE Transactions on Signal Processing Y1 - 2000 VL - 48 IS - 08 SP - 2432 EP - 2438 ER - TY - THES A1 - Marwitz, Ch. T1 - Numerische Berechnung von modifizierten Blochmoden in der Bandlücke periodischer Strukturen Y1 - 2005 UR - http://www.zib.de/Numerik/NanoOptics/publications/PubText/Marwitz05.pdf ER - TY - CHAP A1 - Lockau, D. A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schmidt, Frank A1 - Ruske, F. A1 - Rech, Bernd T1 - Rigorous optical simulation of light management in crystalline silicon thin film solar cells with rough interface textures T2 - Physics and Simulation of Optoelectronic Devices XIX Y1 - 2011 U6 - https://doi.org/10.1117/12.874967 VL - 7933 SP - 79330M PB - Proc. SPIE ER - TY - CHAP A1 - Lockau, D. A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Burger, Sven A1 - Rech, Bernd T1 - Efficient simulation of plasmonic structures for solar cells T2 - International Workshop on Optical Waveguide Theory and Numerical Modelling Y1 - 2009 VL - XVIII SP - 48 PB - Fraunhofer Institute for Applied Optics and Precision Engineering ER - TY - JOUR A1 - Lopez-Fernandez, Maria A1 - Palencia, Cesar A1 - Schädle, Achim T1 - A spectral order method for inverting sectorial Laplace transforms JF - SIAM J. Numer. Anal. Y1 - 2006 U6 - https://doi.org//10.1137/050629653 VL - 44 IS - 3 SP - 1332 EP - 1350 ER - TY - JOUR A1 - Lockau, D. A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Accurate simulation of light transmission through subwavelength apertures in metal films JF - J. Opt. A Y1 - 2009 U6 - https://doi.org/10.1088/1464-4258/11/11/114013 VL - 11 SP - 114013 ER - TY - JOUR A1 - Lopez-Fernandez, Maria A1 - Lubich, Christian A1 - Schädle, Achim T1 - Adaptive, Fast and Oblivious Convolution in Evolution Equations with Memory JF - SIAM J. Sci. Comput. Y1 - 2008 U6 - https://doi.org//10.1137/060674168 VL - 30 IS - 2 SP - 1015 EP - 1037 ER - TY - JOUR A1 - López-Fernández, Maria A1 - Lubich, Christian A1 - Palencia, Cesar A1 - Schädle, Achim T1 - Fast Runge-Kutta approximation of inhomogeneous parabolic equations JF - Numer. Math. Y1 - 2005 U6 - https://doi.org/http://dx.doi.org/10.1007/s00211-005-0624-3 VL - 102 SP - 277 EP - 291 ER - TY - JOUR A1 - Linden, S. A1 - Enkrich, Christian A1 - Dolling, G. A1 - Klein, M. A1 - Zhou, J. A1 - Koschny, T. A1 - Soukoulis, C. A1 - Burger, Sven A1 - Schmidt, Frank A1 - Wegener, M. T1 - Photonic metamaterials: Magnetism at Optical Frequencies JF - IEEE Journal of Selected Topics in Quantum Electronics Y1 - 2006 U6 - https://doi.org/10.1109/JSTQE.2006.880600 VL - 12 IS - 6 SP - 1097 EP - 1105 ER - TY - CHAP A1 - Lamecker, Hans A1 - Seebass, Martin A1 - Lange, Thomas A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Westwood, J. T1 - Visualization of the variability of 3D statistical shape models by animation T2 - Proc. Medicine Meets Virtual Reality Y1 - 2004 VL - 98 SP - 190 EP - 196 PB - IOS Press ER - TY - CHAP A1 - Lamecker, Hans A1 - Seebaß, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Fitzpatrick, J. ED - Sonka, Milan T1 - A 3d statistical shape model of the pelvic bone for segmentation T2 - Proc. SPIE Medical Imaging 2004 Y1 - 2004 VL - 5370 SP - 1341 EP - 1351 ER - TY - JOUR A1 - Lasser, Caroline A1 - Röblitz, Susanna T1 - Computing expectation values for molecular quantum dynamics JF - SIAM Journal on Scientific Computing Y1 - 2010 U6 - https://doi.org//10.1137/090770461 VL - 32 IS - 3 SP - 1465 EP - 1483 ER - TY - CHAP A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Kober, Cornelia A1 - Deuflhard, Peter A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian ED - Alt, Walter ED - Hermann, Martin T1 - Effiziente und zuverlässige Finite-Elemente-Methoden zur Simulation des menschlichen Unterkiefers T2 - Berichte des IZWR - Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Y1 - 2003 VL - 1 SP - 49 EP - 57 PB - Universität Jena CY - Germany ER - TY - CHAP A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Roitzsch, Rainer ED - Sydow, Achim T1 - Adaptive Time-Space Discretization for Combustion Problems T2 - 15th IMACS World Congress on Scientific Computation, Modelling and Applied Mathematics, Vol. 2, Numerical Mathematics Y1 - 1997 SP - 49 EP - 155 PB - Wissenschaft und Technik Verlag, Berlin ER - TY - CHAP A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Roitzsch, Rainer ED - Lewis, R. T1 - Three-Dimensional Fully Adaptive Solution of Thermo-Diffusive Flame Propagation Problems T2 - Numerical Methods in Thermal Problems Y1 - 1997 SP - 857 EP - 862 PB - Pineridge Press, Swansea, UK ER - TY - JOUR A1 - Kümmel, S. A1 - Andrae, Karsten A1 - Reinhard, P.-G. T1 - Collectivity in the optical response. of small metal clusters JF - Applied Physics B Y1 - 2001 UR - http://dx.doi.org/10.1007/s003400100679 VL - 73 IS - 4 SP - 293 EP - 297 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Kube, Susanna A1 - Weber, Marcus T1 - A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations JF - Journal of Chemical Physics Y1 - 2007 U6 - https://doi.org/10.1063/1.2404953 VL - 126 IS - 2 ER - TY - CHAP A1 - Kube, Susanna A1 - Weber, Marcus T1 - Computation of equilibrium densities in metastable dynamical systems by domain decomposition T2 - Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008 Y1 - 2008 VL - 1048 SP - 339 EP - 342 PB - AIP Conference Proceedings ER - TY - JOUR A1 - Koerber, Jens A1 - Schaber, Karlheinz A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Modelling and simulation of aerosol formation in absorption processes JF - J. Aerosol Sci Y1 - 1998 VL - 29 SP - 579 EP - 580 ER - TY - CHAP A1 - Kober, C. A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Deuflhard, Peter ED - Capasso, Vincenzo T1 - An Individual Anisotropic and Inhomogeneous Material Description of the Human Mandible T2 - Mathematical Modelling and Computing in Biology and Medicine Y1 - 2003 SP - 103 EP - 109 PB - ESTMB ER - TY - CHAP A1 - Kleemann, B. A1 - Kurz, J. A1 - Hetzler, J. A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Fast online inverse scattering with Reduced Basis Method (RBM) for a 3D phase grating with specific line roughness T2 - Modelling Aspects in Optical Metrology III Y1 - 2011 U6 - https://doi.org/10.1117/12.889364 VL - 8083 SP - 808309 PB - Proc. SPIE ER - TY - THES A1 - Klapproth, Corinna T1 - Adaptive numerical integration for dynamical contact problems Y1 - 2012 ER - TY - JOUR A1 - Klapproth, Corinna A1 - Deuflhard, Peter A1 - Schiela, Anton T1 - A Perturbation Result for Dynamical Contact Problems JF - Numer. Math Y1 - 2009 VL - 2 SP - 237 EP - 257 ER - TY - JOUR A1 - Klimm, Martina A1 - Bujotzek, Alexander A1 - Weber, Marcus T1 - Direct Reweighting Strategies in Conformation Dynamics JF - MATCH Commun. Math. Comp. Chem. Y1 - 2011 VL - 65(2) SP - 333 EP - 346 ER - TY - CHAP A1 - Klose, Roland A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - A multilevel method for the computation of eigenmodes in 3D photonic crystals T2 - Proceedings of the 5th International Conference on Numerical Simulation of Optoelectronic Devices Y1 - 2005 U6 - https://doi.org/10.1109/NUSOD.2005.1518135 SP - 61 EP - 62 ER - TY - CHAP A1 - Kettner, Benjamin A1 - Schmidt, Frank T1 - The pole condition as transparent boundary condition for resonance problems T2 - Physics and Simulation of Optoelectronic Devices XIX Y1 - 2011 U6 - https://doi.org/10.1117/12.874752 VL - 7933 SP - 79331B PB - Proc. SPIE ER - TY - THES A1 - Kettner, Benjamin T1 - Ein Algorithmus zur prismatoidalen Diskretisierung von unbeschränkten Außenräumen in 2D und 3D unter Einhaltung von Nebenbedingungen Y1 - 2006 UR - http://www.zib.de/Numerik/NanoOptics/publications/PubText/Kettner06.pdf ER - TY - JOUR A1 - Karl, M. A1 - Kettner, Benjamin A1 - Burger, Sven A1 - Schmidt, Frank A1 - Kalt, H. A1 - Hetterich, M. T1 - Dependencies of micro-pillar cavity quality factors calculated with finite element methods JF - Optics Express Y1 - 2009 UR - http://dx.doi.org/10.1364/OE.17.001144 U6 - https://doi.org/10.1364/OE.17.001144 VL - 17 SP - 1144 ER - TY - JOUR A1 - Kalkbrenner, T. A1 - Hakanson, U. A1 - Schädle, Achim A1 - Burger, Sven A1 - Henkel, C. A1 - Sandoghdar, V. T1 - Optical microscopy using the spectral modifications of a nano-antenna JF - Phys. Rev. Lett. Y1 - 2005 U6 - https://doi.org/10.1103/PhysRevLett.95.200801 VL - 95 SP - 200801 ER - TY - CHAP A1 - Weber, Marcus A1 - Kube, Susanna T1 - Robust Perron Cluster Analysis for Various Applications in Computational Life Science T2 - Computational Life Sciences Y1 - 2005 SP - 57 EP - 66 ER - TY - CHAP A1 - Kassi, J.-P. A1 - Taylor, William R. A1 - Schwarzkopf, J. A1 - Schell, H. A1 - Duda, G. A1 - Ehrig, Rainald T1 - Wie sind Osteosynthesesysteme und Defektzonen in vivo belastet? T2 - 68. Jahrestagung der Deutschen Gesellschaft für Unfallchirurgie in Verbindung mit dem Deutschen Orthopädenkongress Y1 - 2004 CY - Berlin ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. T1 - Reduction of the influence of skin marker artefacts using the optimal common shape technique T2 - Annual meeting of the ESMAC 2009 Y1 - 2009 CY - London ER - TY - JOUR A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Matziolis, Georg A1 - Müller, Michael A1 - Wassilew, Georgi A1 - Asbach, Patrick A1 - Perka, Carsten A1 - Heller, Markus O. T1 - Frontal plane alignment: An imageless method to predict the mechanical femoral–tibial angle (mFTA) based on functional determination of joint centres and axes JF - Gait & Posture Y1 - 2010 U6 - https://doi.org/10.1016/j.gaitpost.2009.10.006 VL - 31 IS - 2 SP - 204 EP - 208 ER - TY - CHAP A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Matziolis, Georg A1 - Müller, Michael A1 - Wassilew, Georgi A1 - Asbach, Patrick A1 - Perka, Carsten A1 - Heller, Markus O. T1 - An imageless method to quantify the mechanical femoral-tibial angle based on the functional determination of joint centers and axes T2 - Annual meeting of the ESMAC 2009 Y1 - 2009 CY - London ER - TY - JOUR A1 - Kober, C. A1 - Stübinger, S. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Radtke, Thomas A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Finite element simulation of the human mandible JF - Int. Poster J. Dent. Oral Med. Y1 - 2006 ER - TY - JOUR A1 - Kober, C. A1 - Stübinger, S. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Radtke, Thomas A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Finite element simulation of the human mandible JF - Int. Poster J. Dent. Oral Med. Y1 - 2006 ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Wassilew, Georgi A1 - Duda, Georg A1 - Taylor, William R. T1 - A new approach for optimally reducing skin marker artifact allows determination of the hip joint center within 3mm T2 - Transactions Vol. 35, 2010 Annual Meeting of the Orthopedic Society Y1 - 2010 CY - New Orleans ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Taylor, William R. T1 - The Hip Joint Centre can be determined to within 3 mm T2 - 17th Congress of the European Society of Biomechanics Y1 - 2010 CY - Edinburgh ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Taylor, William R. T1 - The Residual: A Reliable Measure of Accuracy in the Determination of Joint Centers T2 - Transactions Vol. 35, 2010 Annual Meeting of the Orthopedic Society Y1 - 2010 CY - New Orleans ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Schröder, Jörg H. A1 - Taylor, William R. T1 - Der Vergleich von nicht-invasiven Techniken zur Bestimmung der Hüftgelenksposition T2 - Annual meeting of the German Society of Orthopaedics and Trauma Surgery Y1 - 2009 CY - Berlin ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Schröder, Jörg H. A1 - Taylor, William R. T1 - Die Bestimmung der Genauigkeit nicht-invasiver Techniken zur Ermittlung der Hüftgelenksposition in-vivo T2 - 6th annual meeting of the German Society for Biomechanics (DGfB) Y1 - 2009 CY - Münster ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - An Application of Adaptive Finite Element Techniques in Biomechanics T2 - 22. CAD-FEM Users Meeting - Internationale FEM Technologietage Y1 - 2004 CY - Dresden, Germany ER - TY - JOUR A1 - Kober, C. A1 - Erdmann, Bodo A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Belastungssimulation beim menschlichen Biss im Vergleich mit der Dichtestruktur im Unterkieferknochen JF - Biomedizinische Technik Y1 - 2003 VL - 48 IS - Ergänzungsband 1 SP - 268 EP - 269 ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Simulation of the Human Mandible T2 - Proceedings of 10th Workshop on The Finite Element Method in Biomedical Engineering, Biomechanics and Related Fields Y1 - 2003 CY - Ulm, Germany ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Adaptive Finite Element Simulation of the Human Mandible Using a New Physiological Model of the Masticatory Muscles T2 - Proc. of 75th Annual Meeting of the GAMM Y1 - 2004 VL - 4 IS - 1 SP - 332 EP - 333 ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Sensitivity of the Temporomandibular Joint Capsule for the Structural Behaviour of the Human Mandible T2 - Proc. BMT 2004 Y1 - 2004 VL - 49-2 SP - 372 EP - 373 CY - Ilmenau, Deutschland ER - TY - JOUR A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Validation of interdependency between inner structure visualization and structural mechanics simulation JF - Int. Poster J. Dent. Oral Med. Y1 - 2006 ER - TY - JOUR A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Validation of interdependency between inner structure visualization and structural mechanics simulation JF - Int. Poster J. Dent. Oral Med. Y1 - 2006 ER - TY - JOUR A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Consideration of anisotropic elasticity minimizes volumetric rather than shear deformation in human mandible JF - Comp. Meth. Biomech. Biomed. Eng. Y1 - 2006 VL - 9(2) SP - 91 EP - 101 ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian ED - CADFEM GmbH, Grafing T1 - The Influence of the Periodontal Ligament on Overall Stress/Strain Profiles of a Human Mandible T2 - Proc. of 23rd CADFEM Users’ Meeting, Int. Congress on FEM Technology, Biomechanics Y1 - 2005 SP - 1 EP - 10 CY - Bonn, Germany ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian ED - Boenick, U. ED - Bolz, A. T1 - Consideration of Bone Inhomogeneity and Anisotropy in Deformation Analysis of a Human Mandible T2 - Proc. of BMT2005, 39th Annual Congress of the German Society of Biomedical Engineering, Nuremberg, Germany Y1 - 2005 VL - 1 SP - 814 EP - 815 PB - VDE CY - Nuremberg, Germany ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Anisotropic Simulation of the Human Mandible T2 - Proc. of 17th ASCE Engineering Mechanics Conference Y1 - 2004 PB - Univ. of Delaware ER - TY - CHAP A1 - Kober, C. A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Geiger, M. A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian ED - Davidovitch, Z. ED - Mah, J. ED - Suthanarak, S. T1 - How does the periodontal ligament influence overall stress/strain profiles of a partially edentulous mandible? T2 - Proc. of 8th Int. Conference on Biological Mechanisms of Tooth Eruption, Resorption and Movement, Phuket, Thailand Y1 - 2005 CY - Harvard Society of the Advancement of Orthodontics, Boston, Massachusetts, USA ER - TY - CHAP A1 - Kratzenstein, Stefan A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Duda, Georg A1 - Taylor, William R. T1 - A Quantification of Accuracy in Estimating Joint Centers T2 - 17th Congress of the European Society of Biomechanics Y1 - 2010 CY - Edinburgh ER - TY - JOUR A1 - Kato, Akiko A1 - Burger, Sven A1 - Scholze, Frank T1 - Analytical modeling and 3D finite element simulation of line edge roughness in scatterometry JF - Appl. Optics Y1 - 2012 U6 - https://doi.org/10.1364/AO.51.006457 VL - 51 SP - 6457 EP - 6464 ER - TY - JOUR A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Solving Time-Harmonic Scattering Problems Based on the Pole Condition II: Convergence of the PML Method JF - SIAM J. Math. Anal. Y1 - 2003 U6 - https://doi.org/10.1137/S0036141002406485 VL - 35 IS - 3 SP - 547 EP - 560 ER - TY - JOUR A1 - Justen, L. A1 - Teschke, G. A1 - Lehmann, V. T1 - Wavelet-based methods for clutter removal from radar wind profiler data JF - Proc. SPIE Vol. 5266, p. 157-168, Wavelet Applications in Industrial Processing; Frederic Truchetet; Ed. Y1 - 2004 ER - TY - JOUR A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Solving Time-Harmonic Scattering Problems Based on the Pole Condition I: Theory JF - SIAM J. Math. Anal. Y1 - 2003 U6 - https://doi.org/10.1137/S0036141002406473 VL - 35 IS - 1 SP - 183 EP - 210 ER - TY - CHAP A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin ED - Michielsen, Bas ED - Decavèle, Francine T1 - A new method for the solution of scattering problems T2 - Proceedings of the JEE’02 Symposium Y1 - 2002 SP - 251 EP - 256 PB - ONERA CY - Toulouse ER - TY - CHAP A1 - Hoffmann, Johannes A1 - Hafner, Christian A1 - Leidenberger, P. A1 - Hesselbarth, J. A1 - Burger, Sven T1 - Comparison of electromagnetic field solvers for the 3D analysis of plasmonic nano antennas T2 - Numerical Methods in Optical Metrology Y1 - 2009 UR - http://dx.doi.org/10.1117/12.828036 U6 - https://doi.org/10.1117/12.828036 VL - 7390 SP - 73900J PB - Proc. SPIE ER - TY - JOUR A1 - Hochmuth, Reinhard A1 - Deuflhard, Peter T1 - On the thermoregulation in the human microvascular system JF - PAMM Y1 - 2003 VL - 3 SP - 378 EP - 379 ER - TY - JOUR A1 - Holzlöhner, Ronald A1 - Burger, Sven A1 - Roberts, P. A1 - Pomplun, Jan T1 - Efficient optimization of hollow-core photonic crystal fiber design using the finite-element method JF - J. Eur. Opt. Soc.-Rapid Y1 - 2006 U6 - https://doi.org/10.2971/jeos.2006.06011 VL - 1 SP - 06011 ER - TY - JOUR A1 - Hiptmair, Ralf A1 - Schädle, Achim T1 - Non-reflecting boundary conditions for Maxwell’s equations JF - Computing Y1 - 2003 UR - http://dx.doi.org/10.1007/s00607-003-0026-2 VL - 71 IS - 3 ER - TY - JOUR A1 - Haack, Fiete A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Schmidt, Burkhard A1 - Weber, Marcus T1 - Adaptive Spectral Clustering for Conformation Analysis JF - AIP Conference Proceedings Y1 - 2010 UR - http://link.aip.org/link/?APC/1281/1585/1 U6 - https://doi.org/10.1063/1.3498116 VL - 1281 IS - 1 SP - 1585 EP - 1588 PB - AIP ER - TY - JOUR A1 - Heller, Markus O. A1 - König, Christian A1 - Graichen, F. A1 - Hinterwimmer, S. A1 - Ehrig, Rainald A1 - Duda, G. A1 - Taylor, William R. T1 - A new model to predict in vivo human knee kinematics under physiological-like muscle activation JF - Journal of Biomechanics Y1 - 2007 SP - 45 EP - 53 ER - TY - JOUR A1 - Heller, Markus O. A1 - Kratzenstein, Stefan A1 - Ehrig, Rainald A1 - Wassilew, Georgi A1 - Duda, Georg A1 - Taylor, William R. T1 - The weighted optimal common shape technique improves identification of the hip joint centre of rotation in vivo JF - Journal of Orthopedic Research Y1 - 2011 VL - 29 SP - 1470 EP - 5 ER - TY - JOUR A1 - Hellmich, Christian A1 - Kober, Cornelia A1 - Erdmann, Bodo T1 - Micromechanics-based conversion of CT data into anisotropic elasticity tensors, applied to FE simulations of a mandible JF - Annals of Biomedical Engineering Y1 - 2008 U6 - https://doi.org/10.1007/s10439-007-9393-8 VL - 36 IS - 1 SP - 108 EP - 122 ER - TY - JOUR A1 - Hiremath, Kirankumar A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Numerical solution of nonlocal hydrodynamic Drude model for arbitrary shaped nano-plasmonic structures using Nedelec finite elements JF - J. Comp. Phys. Y1 - 2012 U6 - https://doi.org/10.1016/j.jcp.2012.05.013 VL - 231 IS - 17 SP - 5890 EP - 5896 ER - TY - CHAP A1 - Heller, Markus O. A1 - Duda, G. A1 - König, Christian A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Hinterwimmer, S. A1 - Graichen, H. T1 - Validation of a New Model of Human Knee Kinematics against in Vivo Data under Physiologic Neuromuscular Activation Patterns T2 - Proceedings of the 51th Annual Meeting of the Orthopedic Society Y1 - 2005 CY - Washington ER - TY - JOUR A1 - Heller, Markus O. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Schell, H. A1 - Seebeck, P. A1 - Taylor, William R. T1 - Muskuloskeletale Belastungen im Schafshinterlauf JF - Materialwissenschaft und Werkstofftechnik Y1 - 2005 IS - 36 SP - 775 EP - 780 ER - TY - JOUR A1 - Hochmuth, Reinhard A1 - Deuflhard, Peter T1 - Multiscale Analysis for the Bio-Heat-Transfer Equation - The Nonisolated Case JF - Mathematical Models and Methods in Applied Sciences (M$^3$AS) Y1 - 2004 VL - 14 IS - 11 SP - 1621 EP - 1634 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - THES A1 - Gürler, A. T1 - Selection and flexible optimization of binding modes from conformation ensembles. Y1 - 2006 ER - TY - CHAP A1 - Hammerschmidt, Martin A1 - Lockau, Daniel A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schwanke, Christoph A1 - Kirner, Simon A1 - Calnan, Sonya A1 - Stannowski, Bernd A1 - Rech, Bernd T1 - 3D optical modeling of thin-film a-Si/mc-Si tandem solar cells with random textured interfaces using FEM T2 - Renewable Energy and the Environment Optics and Photonics Congress Y1 - 2012 U6 - https://doi.org/10.1364/E2.2012.JM5A.15 SP - JM5A.15 PB - Optical Society of America ER - TY - JOUR A1 - Guerler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2008 UR - http://www.sciencedirect.com/science/article/pii/S0303264707001670 U6 - https://doi.org/DOI: 10.1016/j.biosystems.2007.11.004 VL - 92 IS - 1 SP - 42 EP - 48 ER - TY - CHAP A1 - Gladilin, Evgeny T1 - A contour based approach for invariant shape description T2 - SPIE Medical Imaging Conference Y1 - 2004 VL - 5370 SP - 1282 EP - 1291 CY - San Diego, USA ER - TY - JOUR A1 - Gürler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2007 ER - TY - THES A1 - Gladilin, Evgeny T1 - Biomechanical Modeling of Soft Tissue and Facial Expressions for Craniofacial Surgery Planning Y1 - 2003 CY - Germany ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Meiler, M. ED - Saupe, D. ED - Krugel, F. ED - Handels, H. ED - Lehmann, T. T1 - Biomechanisches Modell zur Abschätzung der individuellen Gesichtsmimik T2 - Proc.of Workshop Bildverarbeitung für die Medizin (BVM) Y1 - 2002 SP - 25 EP - 28 CY - Leipzig, Germany ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Biomechanical modeling of individual facial emotion expressions T2 - Proc. of Visualization, Imaging, and Image Processing (VIIP) Y1 - 2002 SP - 7 EP - 11 CY - Malaga, Spain ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - A nonlinear soft tissue model for craniofacial surgery simulations T2 - Proc. of Modeling and Simulation for Computer-aided Medicine and Surgery (MS4CMS Y1 - 2002 PB - INRIA CY - Paris, France ER - TY - JOUR A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - A nonlinear elastic soft tissue model for craniofacial surgery simulations JF - ESAIM, Proc. Y1 - 2002 U6 - https://doi.org/10.1051/proc:2002011 VL - 12 SP - 61 EP - 66 ER - TY - JOUR A1 - Teschke, G. T1 - Operator Equations, Mixed Constraints, Frame Based Iterative Concepts and Application JF - Habilitation thesis, Bremen Y1 - 2005 ER - TY - JOUR A1 - Teschke, G. T1 - Waveletkonstruktion über Unschärferelationen und Anwendungen in der Signalanalyse JF - PhD thesis, Bremen Y1 - 2001 ER - TY - JOUR A1 - Teschke, G. T1 - Construction of Generalized Uncertainty Principles and Wavelets in Bessel Potential Spaces JF - International Journal of Wavelets, Multiresolution and Information Processing Y1 - 2005 VL - 3 IS - 2 SP - 189 EP - 209 ER - TY - JOUR A1 - Teschke, G. T1 - Multi-Frames in Thresholding Iterations for Nonlinear Operator Equations with Mixed Sparsity Constraints JF - DFG-SPP-1114 preprint 131 Y1 - 2005 ER - TY - JOUR A1 - Teschke, G. T1 - Multi-Frame Representations in Linear InverseProblems with Mixed Multi-Constraints JF - Applied and Computational Harmonic Analysis Y1 - 2007 VL - 22 SP - 43 EP - 60 ER - TY - JOUR A1 - Gellermann, Johanna A1 - Weihrauch, Mirko A1 - Cho, C. A1 - Wlodarczyk, Waldemar A1 - Fähling, Horst A1 - Felix, Roland A1 - Budach, Volker A1 - Weiser, Martin A1 - Nadobny, Johanna A1 - Wust, Peter T1 - Comparison of MR-thermography and planning calculations in phantoms JF - Medical Physics Y1 - 2006 VL - 33 SP - 3912 EP - 3920 ER - TY - CHAP A1 - Gellermann, Johanna A1 - Wust, Peter A1 - Stalling, Detlev A1 - Tilly, Wolfgang A1 - Nadobny, Johanna A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland A1 - Budach, Volker T1 - First Clinical Experiences with the Hyperthermia Planning System HyperPlan T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 79 ER - TY - JOUR A1 - Gellermann, Johanna A1 - Wust, Peter A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Nadobny, Johanna A1 - Beck, Rudolf A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Clinical evaluation and verification of the hyperthermia treatment planning system hyperplan JF - Int J Radiat Oncol Biol Phys Y1 - 2000 VL - 47 IS - 4 SP - 1145 EP - 1156 ER - TY - JOUR A1 - Gansel, J. A1 - Wegener, M. A1 - Burger, Sven A1 - Linden, S. T1 - Gold helix photonic metamaterials: a numerical parameter study JF - Opt. Express Y1 - 2010 U6 - https://doi.org/10.1364/OE.18.001059 VL - 18 SP - 1059 EP - 1069 ER - TY - CHAP A1 - Galliat, Tobias A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - H. Bothe, R. T1 - Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification T2 - Neural Computation, ICSC Academic Press Y1 - 2000 SP - 227 EP - 232 ER - TY - CHAP A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Automatic Identification of Metastable Conformations via Self-Organized Neural Networks T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-00-51 IS - 24 PB - Springer ER - TY - JOUR A1 - Griesse, Roland A1 - Weiser, Martin T1 - On the Interplay Between Interior Point Approximation and Parametric Sensitivities in Optimal Control JF - Journal of Mathematical Analysis and Applications Y1 - 2008 SP - 771 EP - 793 ER - TY - JOUR A1 - Gänzler, Tobias A1 - Volkwein, S. A1 - Weiser, Martin T1 - SQP methods for parameter identification problems arising in hyperthermia JF - Optim. Methods Softw. Y1 - 2006 VL - 21 IS - 6 SP - 869 EP - 887 ER - TY - RPRT A1 - Gladilin, Evgeny A1 - Peckar, W. A1 - Rohr, K. A1 - Stiehl, H. T1 - A Comparsion Between BEM and FEM for Elastic Registration of Medical Images Y1 - 1999 IS - FBI-HH-M-287/99 PB - FB Informatik CY - Hamburg, Germany ER - TY - CHAP A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank T1 - Automatic identification of metastable conformations via self-organized neural networks T2 - Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling Y1 - 2002 ER - TY - JOUR A1 - Friese, T. A1 - Schmidt, Frank A1 - Yevick, David T1 - Transparent boundary conditions for a wide-angle approximation of the one-way Helmholtz equation JF - J. Comput. Phys. Y1 - 2000 U6 - https://doi.org/10.1006/jcph.2000.6637 VL - 165 IS - 2 SP - 645 EP - 659 ER - TY - CHAP A1 - Friese, T. A1 - Deuflhard, Peter A1 - Schmidt, Frank ED - Lai, Choi-Hong ED - Bjørstad, Petter E. ED - Cross, Mark ED - Widlund, Olof T1 - A Multigrid Method for the Complex Helmholtz Eigenvalue Problem T2 - Procs. Eleventh International Conference on Domain Decomposition Methods in Sciences and Engineering (DD11), UK Y1 - 1999 SP - 19 EP - 26 PB - DDM.org ER - TY - CHAP A1 - Fröhlich, Jochen A1 - Deuflhard, Peter ED - Neunzert, H. T1 - An adaptive Galerkin method for the PDF transport equation of turbulent reactive flows T2 - Progress in Industrial Mathematics, Proc. 8th Conference of the European Consortium for Mathematics in Industry (ECMI 94) Y1 - 1996 SP - 176 EP - 184 PB - Wiley & Teubner ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-01-03 IS - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in Mixed–Canonical Ensemble: Efficient conformational analysis of RNA JF - J. Comp. Chem. Y1 - 1998 U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - JOUR A1 - Ferlaino, F. A1 - Maddaloni, P. A1 - Burger, Sven A1 - Cataliotti, F. A1 - Fort, C. A1 - Modugno, M. A1 - Inguscio, Massimo T1 - Dynamics of a Bose-Einstein condensate at finite temperature in an atom-optical coherence filter JF - Phys. Rev. A Y1 - 2002 VL - 66 SP - 11604 ER - TY - JOUR A1 - Fackeldey, Konstantin T1 - Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach JF - IJPAM Y1 - 2011 VL - 69 IS - 2 SP - 185 EP - 202 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf A1 - Schweitzer, M. ED - Griebel, Michael ED - Schweitzer, M. T1 - Stability of Energy Transfer in the Weak Coupling Method T2 - Meshfree Methods for Partial Differential Equations IV Y1 - 2008 VL - 65 SP - 111 EP - 121 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf A1 - Lenzen, Christoph T1 - Coupling Molecular Dynamics and Continua with Weak Constraints JF - SIAM Multiscale Model. Simul. Y1 - 2011 U6 - https://doi.org//10.1137/100782097 N1 - also as MATHEON Preprint VL - 9 SP - 1459 EP - 1494 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf ED - Griebel, Michael ED - Schweitzer, M. T1 - Numerical Validation of Constraints Based Multiscale Methods T2 - Lecture Notes in Computational Science and Engineering Y1 - 2010 SP - 141 EP - 154 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf T1 - Weak Coupling Algorithms in Multiscale Simulations T2 - Proceedings of the third Inter. Confer. on Comp. Meth. for Coupled Problems in Science and Engrg Y1 - 2009 SP - 1023pp ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf T1 - Quadrature and Implementation of the Weak Coupling Method T2 - MMM 2008: Proceedings of the 4th International Conference on Multiscale Materials Modelling, 27-31 October 2008, Tallahassee, Fla. Y1 - 2008 SP - 62 EP - 65 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach T2 - Proc. Appl. Math. Mech. Y1 - 2008 VL - 8 IS - 1 SP - 10495pp ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - Weak coupling in function space T2 - Proc. Appl. Math. Mech. Y1 - 2007 VL - 7 IS - 1 SP - 2020113pp ER - TY - JOUR A1 - Faustino, Nelson A1 - Kaehler, U. A1 - Teschke, G. T1 - A Wavelet Galerkin Scheme for the Navier Stokes Equations JF - under review Y1 - 2006 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf ED - Widlund, Olof T1 - Solving Frictional Contact Problems with Multigrid Efficiency T2 - Proc.of the 16th International Conference on Domain Decomposition Methods Y1 - 2007 VL - 50 SP - 547 EP - 554 ER - TY - THES A1 - Fackeldey, Konstantin T1 - The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics Y1 - 2009 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics JF - International Journal for Numerical Methods in Engineering Y1 - 2009 U6 - https://doi.org/10.1002/nme.2626 VL - 79 IS - 12 SP - 1517 EP - 1535 ER - TY - CHAP A1 - Erdmann, Bodo A1 - Kober, C. A1 - Lang, Jens A1 - Deuflhard, Peter A1 - Zeilhofer, J. A1 - Sader, Robert T1 - Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible T2 - proceedings of 9th Workshop on The Finite Element Method in Biomedical Engineering, Biomechanics and Related Fields Y1 - 2002 CY - Ulm, Germany ER - TY - JOUR A1 - Enkrich, Christian A1 - Wegener, M. A1 - Linden, S. A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Zhou, C. A1 - Koschny, T. A1 - Soukoulis, C. T1 - Magnetic metamaterials at telecommunication and visible frequencies JF - Phys. Rev. Lett. Y1 - 2005 U6 - https://doi.org/10.1103/PhysRevLett.95.203901 VL - 95 SP - 203901 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Ofenloch, O. A1 - Schaber, Karlheinz A1 - Deuflhard, Peter T1 - Modelling and Simulation of Aerosol Formation by Heterogeneous Nucleation in Gas-Liquid Contact Devices JF - Chem.Eng.Sci. Y1 - 2002 VL - 57 IS - 7 SP - 1151 EP - 1163 ER - TY - CHAP A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Oeverdieck, Lars A1 - Deuflhard, Peter ED - H.-J. Bungartz, F. T1 - Advanced Extrapolation Methods for Large Scale Differential Algebraic Problems T2 - High Performance Scientific and Engineering Computing Y1 - 1999 VL - 8 SP - 233 EP - 244 PB - Springer Verlag ER - TY - CHAP A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Deuflhard, Peter ED - Khoroshevsky, V. T1 - Massively Parallel Simulation in Chemical Engineering by Extrapolation Algorithms T2 - Procs. 16th International Workshop on Distributed Data Processing, Novosibirsk, Russia Y1 - 1998 SP - 1 EP - 6 ER - TY - BOOK ED - Ebert, K. ED - Deuflhard, Peter ED - Jäger, Willi T1 - Modelling of Chemical Reaction Systems T3 - Series in Chemical Physics Y1 - 1981 IS - 18 PB - Springer Verlag ER - TY - JOUR A1 - Ehrig, Rainald A1 - Taylor, William R. A1 - Duda, Georg A1 - Heller, Markus O. T1 - A Survey for Formal Methods for Determining Functional Joint Axes JF - Journal of Biomechanics Y1 - 2007 SP - 2150 EP - 2157 ER - TY - CHAP A1 - Ehrig, Rainald A1 - Taylor, William R. A1 - Duda, G. A1 - Heller, Markus O. T1 - A New Approach for the Determination of Joint Axes T2 - Proceedings of the 52th Annual Meeting of the Orthopedic Society Y1 - 2006 CY - Chicago ER - TY - JOUR A1 - Ehrig, Rainald A1 - Taylor, William R. A1 - Duda, G. A1 - Heller, Markus O. T1 - A Survey for Formal Methods for Determining the Centre of Ball Joints JF - Journal of Biomechanics Y1 - 2006 IS - 39 SP - 2798 EP - 2809 ER - TY - JOUR A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Seebass, Martin T1 - The Impact of a Nonlinear Heat Transfer Model for Temperature Control in Regional Hyperthermia JF - IEEE Transactions on Biomedical Engineering Y1 - 1999 VL - 49 IS - 9 SP - 1129 EP - 1138 ER - TY - CHAP A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Seebass, Martin ED - Diller, K. T1 - Optimization of Temperature Distributions for Regional Hyperthermia based on a Nonlinear Heat Transfer Model T2 - Biotransport Y1 - 1998 VL - 858 SP - 36 EP - 46 ER - TY - CHAP A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Seebass, Martin ED - de Vahl Davis, G. ED - Leonardi, E. T1 - Adaptive Solutions of Nonlinear Parabolic Equations with Application to Hyperthermia Treatments T2 - CHT’97 Y1 - 1997 SP - 103 EP - 110 CY - Cesme, Turkey ER - TY - CHAP A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Roitzsch, Rainer A1 - Lourenco, Maria José A1 - Rosa, S. A1 - de Castro, C.A. A1 - Albuquerque, C. ED - Kim, M. ED - Ro, S. T1 - Simulation of the Transient Heating in an Unsymmetrical Coated Hot-Strip Sensor With a Self-Adaptive Finite Element Method T2 - Proc. 5th Asian Thermophysical Properties Conference Y1 - 1998 VL - 1 SP - 91 EP - 94 CY - Seoul, South Corea ER - TY - JOUR A1 - Erdmann, Bodo A1 - Ljubijankic, M. A1 - Nytsch-Geusen, C. T1 - Entwicklung einer Toolbox zur zwei- und dreidimensionalen instationären thermischen Bauteilsimulation mit KARDOS JF - Bauphsik Y1 - 2007 VL - 29 IS - 1 SP - 33 EP - 39 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Kratzenstein, Stefan A1 - Duda, Georg A1 - Trepczynski, Adam A1 - Taylor, William R. T1 - The SCoRE residual: A quality index to assess the accuracy of joint estimations JF - Journal of Biomechanics Y1 - 2011 U6 - https://doi.org/10.1016/j.jbiomech.2010.12.009 VL - 44 IS - 7 SP - 1400 EP - 1404 ER - TY - CHAP A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Weber, Marcus ED - Mode, Ch. T1 - A rapidly Mixing Monte Carlo Method for the Simulation of Slow Molecular Processes T2 - Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science Y1 - 2011 PB - InTech ER - TY - JOUR A1 - Dolling, G. A1 - Wegener, M. A1 - Schädle, Achim A1 - Burger, Sven A1 - Linden, S. T1 - Observation of magnetization waves in negative-index photonic metamaterials JF - Appl. Phys. Lett. Y1 - 2006 U6 - https://doi.org/10.1063/1.2403905 VL - 89 SP - 231118 ER - TY - JOUR A1 - Dolling, G. A1 - Klein, M. A1 - Wegener, M. A1 - Schädle, Achim A1 - Burger, Sven A1 - Linden, S. T1 - Negative beam displacement for negative-index photonic metamaterials JF - Optics Express Y1 - 2007 U6 - https://doi.org/10.1364/OE.15.014219 VL - 15 IS - 21 SP - 14219 EP - 14227 ER - TY - GEN A1 - Teschke, G. T1 - Komplexwertige Wavelets und Phaseninformation, Anwendungen in der Signalverarbeitung Y1 - 1998 PB - Universität Potsdam CY - Potsdam ER - TY - GEN ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Mark, A. ED - Reich, Sebastian ED - Skeel, B. T1 - Computational Molecular Dynamics: Challenges, Methods, Ideas T2 - Lecture Notes in Computational Science and Engineering Y1 - 1999 U6 - https://doi.org/10.1007/978-3-642-58360-5 VL - 4 PB - Springer ER - TY - JOUR A1 - Decker, Manuel A1 - Burger, Sven A1 - Linden, S. A1 - Wegener, M. T1 - Magnetization waves in split-ring-resonator arrays JF - Phys. Rev. B Y1 - 2009 UR - http://dx.doi.org/10.1103/PhysRevB.80.193102 U6 - https://doi.org/10.1103/PhysRevB.80.193102 VL - 80 IS - 19 SP - 193102 ER - TY - CHAP A1 - Deuflhard, Peter T1 - Painters, Murderers, Mathematicians T2 - Mathematics and Culture in Europe. Mathematics in Art, Technology, Cinema, and Theatre Y1 - 2007 SP - 141 EP - 152 PB - Springer-Verlag ER - TY - CHAP A1 - Deuflhard, Peter A1 - Wulkow, Michael ED - et al. Bachem, Achim T1 - Simulationsverfahren für die Polymerchemie T2 - Mathematik in der Praxis. Fallstudien aus Industrie, Wirtschaft, Naturwissenschaften und Medizin Y1 - 1995 SP - 117 EP - 136 PB - Berlin: Springer-Verlag ER - TY - JOUR A1 - Deuflhard, Peter A1 - Wulkow, Michael T1 - Computational treatment of polyreaction kinetics by orthogonal polynomials of a discrete variable JF - IMPACT Comput. Sci. Eng. Y1 - 1989 VL - 1 IS - 3 SP - 269 EP - 301 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Zachow, Stefan T1 - Mathematics in Facial Surgery JF - AMS Notices Y1 - 2006 VL - 53 IS - 9 SP - 1012 EP - 1016 ER - TY - BOOK A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Adaptive numerical solution of PDEs Y1 - 2012 PB - de Gruyter CY - Berlin ER - TY - BOOK A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Numerische Mathematik 3 Y1 - 2011 PB - de Gruyter, Berlin ER - TY - JOUR A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Seebass, Martin T1 - A new nonlinear elliptic multilevel FEM in clinical cancer therapy planning JF - Comput. Vis. Sci. Y1 - 2000 VL - 3 SP - 115 EP - 120 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Weiser, Martin ED - et al. Hackbusch, Wolfgang T1 - Global inexact Newton multilevel FEM for nonlinear elliptic problems T2 - Multigrid methods V. proceedings of the 5th European multigrid conference, held in Stuttgart, Germany, October 1–4, 1996. Y1 - 1998 VL - 3 SP - 71 EP - 89 PB - Berlin: Springer ER - TY - CHAP A1 - Deuflhard, Peter A1 - Weiser, Martin ED - et al. Bristeau, M.-O. T1 - Local inexact Newton multilevel FEM for nonlinear elliptic problems T2 - Computational science for the 21st century Y1 - 1997 SP - 129 EP - 138 PB - Chichester: John Wiley & Sons. ER - TY - CHAP A1 - Deuflhard, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Beck, Rudolf A1 - Hege, Hans-Christian ED - Sydow, Achim T1 - Hyperthermia Treatment Planning in Clinical Cancer Therapy:Modelling, Simulation, and Visualization T2 - Computational Physics, Chemistry and Biology Y1 - 1997 VL - 3 PB - Wissenschaft und Technik Verlag CY - Plenary keynote talk, 15th IMACS World Congress 1997 on Scientific Computation, Modelling and Applied Mathematics ER - TY - CHAP A1 - Deuflhard, Peter A1 - Seebass, Martin ED - Lai, Choi-Hong ED - Bjørstad, Petter E. ED - Cross, Mark ED - Widlund, Olof T1 - Adaptive Multilevel FEM as Decisive Tools in the Clinical Cancer Therapy Hyperthermia T2 - Procs. Eleventh International Conference on Domain Decomposition Methods Y1 - 1999 SP - 403 EP - 414 PB - DDM-org Press,Bergen ER - TY - GEN A1 - Deuflhard, Peter A1 - Schütte, Christof A1 - Cordes, Frank A1 - Müller-Kurth, L. T1 - Konformationsdynamik. Mathematischer Entwurf hochspezifischer Biomoleküle Y1 - 1999 PB - In: D. Hömberg (ed.), 8. Veranstaltungsreihe Forschungspolitische Dialoge in Berlin: Angewandte Mathematik - die verborgene Schlüsseltechnologie, 30. April 1999, Konrad-Zuse-Zentrum Berlin, pp. 30-34 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Schütte, Christof ED - Hill, James ED - Moore, Ross T1 - Molecular Conformation Dynamics and Computational Drug Design T2 - Applied Mathematics Entering the 21st Century Y1 - 2004 UR - ftp://ftp.zib.de/pub/zib-publications/reports/ZR-03-20.pdf IS - 116 SP - 91 EP - 119 PB - SIAM ER - TY - JOUR A1 - Deuflhard, Peter A1 - Sautter, W. T1 - On Rank-Deficient Pseudoinverses JF - Lin. Alg. Appl. Y1 - 1980 VL - 29 SP - 91 EP - 111 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Pesch, H.-J. A1 - Rentrop, P. T1 - A Modified Continuation Method for the Numerical Solution of Nonlinear Two-Point Boundary Value Problems by Shooting Techniques JF - Numer. Math. Y1 - 1976 VL - 26 SP - 327 EP - 343 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Potra, Florian T1 - Asymptotic Mesh Independence for Newton-Galerkin Methods via a Refined Mysovskii Theorem JF - SIAM J. Numer. Anal. Y1 - 1992 VL - 29 IS - 5 SP - 1395 EP - 1412 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Wulkow, Michael T1 - Recent Developments in Chemical Computing JF - Computers in Chemical Engineering Y1 - 1990 VL - 14 SP - 1249 EP - 1258 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Nowak, Ulrich ED - Deuflhard, Peter ED - Engquist, B. T1 - Extrapolation integrators for quasilinear implicit ODEs. T2 - Large scale scientific computing, Proc. Meet., Oberwolfach/FRG 1985, Y1 - 1987 VL - 7 SP - 37 EP - 50 PB - Boston-Basel-Stuttgart: Birkhäuser ER - TY - GEN A1 - Deuflhard, Peter A1 - Mehrmann, Volker T1 - Numerical analysis and scientific computing in key technologies Y1 - 2002 SP - 9 EP - 19 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Lipnikov, Konstantin T1 - Domain decomposition with subdomain CCG for material jump elliptic problems JF - East-West J. Numer. Math. Y1 - 1998 VL - 6 IS - 2 SP - 81 EP - 100 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Leinen, P. A1 - Yserentant, H. T1 - Concepts of an adaptive hierarchical finite element code JF - IMPACT Comput. Sci. Eng. Y1 - 1989 VL - 1 IS - 1 SP - 3 EP - 35 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Lang, Jens A1 - Nowak, Ulrich ED - Neunzert, H. T1 - Recent Progress in Dynamical Process Simulation T2 - Progress in Industrial Mathematics, Proc. 8th Conference of the European Consortium for Mathematics in Industry (ECMI 94) Y1 - 1996 SP - 122 EP - 137 PB - Wiley & Teubner ER - TY - JOUR A1 - Deuflhard, Peter A1 - Krause, Rolf A1 - Ertel, Susanne T1 - A Contact-Stabilized Newmark Method for Dynamical Contact Problems JF - International Journal for Numerical Methods in Engineering Y1 - 2007 VL - 73 IS - 9 SP - 1274 EP - 1290 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2000 VL - 315 SP - 39 EP - 59 ER - TY - BOOK A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Numerical analysis. A 1st course in scientific computation. Transl. from the German by F. A. Potra and F. Schulz Y1 - 1995 PB - de Gruyter Textbook. Berlin: De Gruyter ER - TY - BOOK A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Numerische Mathematik I. Eine algorithmisch orientierte Einführung Y1 - 1991 PB - de Gruyter Lehrbuch,Berlin ER - TY - JOUR A1 - Deuflhard, Peter A1 - Hochmuth, Reinhard T1 - Multiscale analysis of thermoregulation in the human microvascular system JF - Math. Methods Appl. Sci. Y1 - 2004 VL - 27 IS - 8 SP - 971 EP - 989 PB - Wiley Verlag ER - TY - BOOK A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Numerical analysis in modern scientific computing. An introduction. 2nd revised ed. T3 - Texts in Applied Mathematics Y1 - 2003 VL - 43 PB - New York, NY: Springer ER - TY - BOOK A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Numerische Mathematik. I Y1 - 2002 PB - de Gruyter Lehrbuch. Berlin: de Gruyter ET - 3 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin ED - Grönemeyer, W. T1 - Progress Towards a Combined MRI Hyperthermia System T2 - Proc. Second Int. Congress HIGH CARE 2000, Bochum Y1 - 2000 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Heroth, Jörg A1 - Maas, Ulrich T1 - Towards Dynamic Dimension Reduction in Reactive Flow Problems T2 - Proc. 3rd Workshop on Modelling of Chemical Reaction Systems Y1 - 1996 CY - Heidelberg ER - TY - CHAP A1 - Deuflhard, Peter A1 - Heroth, Jörg ED - et al. Keil, Frerich T1 - Dynamic dimension reduction in ODE models T2 - Scientific computing in chemical engineering Y1 - 1996 SP - 29 EP - 43 PB - Berlin: Springer-Verlag ER - TY - JOUR A1 - Deuflhard, Peter A1 - Heindl, G. T1 - Affine Invariant Convergence Theorems for Newton’s Method and Extensions to Related Methods JF - SIAM J. Numer. Anal. Y1 - 1979 VL - 16 SP - 1 EP - 10 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Hairer, E. A1 - Zugck, J. T1 - One-step and extrapolation methods for differential-algebraic systems JF - Numer. Math. Y1 - 1987 VL - 51 SP - 501 EP - 516 ER - TY - CHAP ED - Deuflhard, Peter ED - Hairer, E. T1 - Numerical treatment of inverse problems in differential and integral equations. proceedings of an International Workshop, Heidelberg, Fed. Rep. of Germany, August 30 - September 3, 1982 T2 - Progress in Scientific Computing Y1 - 1983 VL - 2 PB - Boston-Basel-Stuttgart:Birkhäuser ER - TY - JOUR A1 - Deuflhard, Peter A1 - Freund, R. A1 - Walter, Artur T1 - Fast secant methods for the iterative solution of large nonsymmetric linear systems JF - IMPACT Comput. Sci. Eng. Y1 - 1990 VL - 2 SP - 244 EP - 276 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Friese, T. A1 - Schmidt, Frank A1 - März, Reinhard A1 - Nolting, Hans-Peter ED - et al. Hoffmann, K.-H. T1 - Effiziente Eigenmodenberechnung für den Entwurf integriert-optischer Chips T2 - Mathematik - Schlüsseltechnologie für die Zukunft Y1 - 1996 SP - 267 EP - 279 PB - Springer Verlag ER - TY - CHAP A1 - Deuflhard, Peter A1 - Fiedler, B. A1 - Kunkel, P. T1 - Numerical Pathfollowing Beyond Critical Points in ODE Models T2 - Large Scale Scientific Computing Y1 - 1987 SP - 97 EP - 113 PB - Birkhäuser/Boston ER - TY - JOUR A1 - Deuflhard, Peter A1 - Fiedler, P. A1 - Kunkel, P. T1 - Efficient numerical pathfollowing beyond critical points JF - SIAM J. Numer. Anal. Y1 - 1987 VL - 24 SP - 912 EP - 927 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Engl, H. A1 - Scherzer, O. T1 - A convergence analysis of iterative methods for the solution of nonlinear ill-posed problems under affinely invariant conditions JF - Inverse Probl. Y1 - 1998 VL - 14 SP - 1081 EP - 1106 ER - TY - CHAP ED - Deuflhard, Peter ED - Engquist, B. T1 - Large scale scientific computing. (proceedings of a Meeting on Large Scale Scientific Computing held at the Oberwolfach Mathematical Insitute, Oberwolfach, FRG, July 14-19, 1985) T2 - Progress in Scientific Computing Y1 - 1987 VL - 7 PB - Boston-Basel-Stuttgart: Birkhäuser ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dellnitz, M. A1 - Junge, Oliver A1 - Schütte, Christof ED - Deuflhard, Peter T1 - Computation of essential molecular dynamics by subdivision techniques T2 - Computational molecular dynamics Y1 - 1998 VL - 4 SP - 98 EP - 115 PB - Berlin: Springer. ER - TY - BOOK A1 - Deuflhard, Peter A1 - Bornemann, Folkmar A. T1 - Numerische Mathematik. II Y1 - 2002 PB - de Gruyter Lehrbuch. Berlin: de Gruyter ET - 2 ER - TY - BOOK A1 - Deuflhard, Peter A1 - Bornemann, Folkmar A. T1 - Scientific computing with ordinary differential equations. Transl. from the German by Werner C. Rheinboldt T3 - Texts in Applied Mathematics Y1 - 2002 VL - 42 PB - New York, NY: Springer ER - TY - CHAP A1 - Deuflhard, Peter A1 - Bader, G. T1 - Multiple Shooting Techniques Revisited T2 - Numerical Treatment of Inverse Problems in Differential and Integral Equations Y1 - 1983 VL - 2 SP - 74 EP - 94 PB - Boston: Birkhäuser ER - TY - CHAP A1 - Deuflhard, Peter A1 - Bader, G. A1 - Nowak, Ulrich T1 - LARKIN - a Software Package for the Numerical Simulation of LARge Systems Arising in Chemical Reaction KINetics T2 - Modelling of Chemical Reaction Systems Y1 - 1981 VL - 18 SP - 38 EP - 55 PB - Springer Verlag ER - TY - CHAP A1 - Deuflhard, Peter A1 - Apostolescu, Victor T1 - A Study of the Gauss-Newton Method for the Solution of Nonlinear Least Squares Problems T2 - Special Topics of Applied Mathematics Y1 - 1980 SP - 129 EP - 150 PB - Amsterdam: North-Holland Publ. ER - TY - CHAP A1 - Deuflhard, Peter A1 - Ackermann, Jörg ED - et al. Dikshit, H. T1 - Adaptive discrete Galerkin methods for macromolecular processes T2 - proceedings of the conference on advances in computational mathematics, held at New Delhi, India, January 5-9, 1993. Singapore Y1 - 1994 SP - 59 EP - 72 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Ackermann, Jörg ED - Dikshit, H. ED - Michelli, C. T1 - Adaptive Discrete Galerkin-Methods for Macromolecular Processes T2 - Advances in Computational Mathematics Y1 - 1994 SP - 59 EP - 72 PB - World Scientific Publishing Co. Inc. ER - TY - CHAP A1 - Deuflhard, Peter ED - Davis, W. ED - Chu, M. ED - Dolan, P. ED - McConnell, J. ED - Noris, L. ED - Ortiz, E. ED - Plemmons, R. ED - Ridgeway, D. ED - Stewart, W. ED - York, Jr., J. ED - Doggett, W. ED - Gellai, B. ED - Gsponer, A. ED - Prioli, C. T1 - Commentary on Cornelius Lanczos’s Solution of Ordinary Differential Equations by Trigonometric Interpolation T2 - Cornelius Lanczos Collected Published Papers with Commentaries Y1 - 1999 VL - VI SP - 3 EP - 667–3–669 PB - North Carolina State University, Raleigh ER - TY - CHAP A1 - Deuflhard, Peter ED - Davis, W. ED - Chu, M. ED - Dolan, P. ED - McConnell, J. ED - Noris, L. ED - Ortiz, E. ED - Plemmons, R. ED - Ridgeway, D. ED - Stewart, W. ED - York, Jr., J. ED - Doggett, W. ED - Gellai, B. ED - Gsponer, A. ED - Prioli, C. T1 - Commentary on Cornelius Lanczos’s Extended Boundary Value Problems T2 - Cornelius Lanczos Collected Published Papers with Commentaries Y1 - 1999 VL - VI SP - 3 EP - 650–3–653 PB - North Carolina State University, Raleigh ER - TY - GEN A1 - Deuflhard, Peter ED - et al. Begehr, H. T1 - Fast algorithms, fast computers: The Konrad-Zuse-Zentrum Berlin (ZIB) T2 - Mathematics in Berlin Y1 - 1998 SP - 183 EP - 184 PB - Basel: Birkhäuser ER - TY - CHAP A1 - Deuflhard, Peter ED - Sydow, Achim T1 - Computational Mathematics as Key Technology T2 - Systems Analysis Modelling Simulation (SAMS),Proc. IMACS Symposium on Systems Analysis and Simulation, Berlin, 26-30 June 1995 Y1 - 1995 VL - 18-19 SP - 19 EP - 26 PB - Gordon and Breach Science Publishers SA ER - TY - CHAP A1 - Deuflhard, Peter ED - et al. Keyes, David T1 - Cascadic conjugate gradient methods for elliptic partial differential equations T2 - Domain decomposition methods in scientific and engineering computing Y1 - 1994 VL - 180 SP - 29 EP - 42 PB - Providence, RI: American Mathematical Society ER - TY - CHAP A1 - Deuflhard, Peter ED - Platen, E. T1 - Stochastic Versus Deterministic Numerical ODE Integration T2 - Proc. 1st Workshop on Stochastic Numerics, Berlin Y1 - 1992 SP - 16 EP - 20 ER - TY - JOUR A1 - Deuflhard, Peter T1 - Global inexact Newton methods for very large scale nonlinear problems JF - IMPACT Comput. Sci. Eng. Y1 - 1991 VL - 3 SP - 366 EP - 393 ER - TY - CHAP A1 - Deuflhard, Peter ED - Griffiths, D. ED - Watson, G. T1 - Uniqueness Theorems for Stiff ODE Initial Value Problems T2 - Numerical analysis 1989, proceedings 13th Biennial Conference on Numerical Analysis 1989, Y1 - 1990 SP - 74 EP - 205 PB - Dundee, Longman Scientific & Technical, Harlow, Essex, UK, ER - TY - JOUR A1 - Deuflhard, Peter T1 - Numerical Treatment of Implicit Differential Equations and Differential Algebraic Systems JF - ZAMM Y1 - 1989 VL - 69 IS - 4 SP - T32 ER - TY - JOUR A1 - Deuflhard, Peter T1 - Recent Progress in Extrapolation Methods for Ordinary Differential Equations JF - SIAM Rev. Y1 - 1985 VL - 27 SP - 505 EP - 535 ER - TY - JOUR A1 - Deuflhard, Peter T1 - Order and Stepsize Control in Extrapolation Methods JF - Numer. Math. Y1 - 1983 VL - 41 SP - 399 EP - 422 ER - TY - JOUR A1 - Deuflhard, Peter T1 - Computation of Periodic Solutions of Nonlinear ODEs JF - BIT Y1 - 1984 VL - 24 SP - 456 EP - 466 ER - TY - JOUR A1 - Deuflhard, Peter T1 - Kepler discretization in regular celestial mechanics JF - Celestial Mech. Y1 - 1980 VL - 21 SP - 213 EP - 223 ER - TY - JOUR A1 - Bader, G. A1 - Deuflhard, Peter T1 - A semi-implicit mid-point rule for stiff systems of ordinary differential equations JF - Numer. Math. Y1 - 1983 VL - 41 SP - 373 EP - 398 ER - TY - CHAP A1 - Deuflhard, Peter T1 - Recent Advances in Multiple Shooting Techniques T2 - Computational Techniques for Ordinary Differential Equations Y1 - 1980 SP - 217 EP - 272 PB - London: Academic Press ER - TY - JOUR A1 - Deuflhard, Peter T1 - A study of extrapolation methods based on multistep schemes without parasitic solutions JF - J.App.Math.Phys.(ZAMP) Y1 - 1979 VL - 30 SP - 177 EP - 189 ER - TY - JOUR A1 - Deuflhard, Peter T1 - A Stepsize Control for Continuation Methods and its Special Application to Multiple Shooting Techniques JF - Numer. Math. Y1 - 1979 VL - 33 SP - 115 EP - 146 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Apostolescu, Victor ED - Stoer, J. T1 - An Underrelaxed Gauss-Newton Method for Equality Constrained Nonlinear Least Squares Problems T2 - Optimization Techniques, Proc. 8th IFIP Conf., Würzburg 1977, part 2 Y1 - 1978 VL - 7 SP - 22 EP - 32 PB - Springer ER - TY - CHAP A1 - Deuflhard, Peter ED - Childs, B. T1 - Nonlinear Equation Solvers in Boundary Value Problem Codes T2 - Proc. Working Conf. on Codes for BVPs in ODEs, Houston/Texas 1978 Y1 - 1979 VL - 74 SP - 40 EP - 66 PB - Springer ER - TY - JOUR A1 - Deuflhard, Peter T1 - A Summation Technique for Minimal Solutions of Linear Homogeneous Difference Equations JF - Computing Y1 - 1977 VL - 18 SP - 1 EP - 13 ER - TY - CHAP A1 - Deuflhard, Peter T1 - A Relaxation Strategy for the Modified Newton Method T2 - Optimization and Optimal Control Y1 - 1975 VL - 477 SP - 59 EP - 73 PB - Springer ER - TY - JOUR A1 - Deuflhard, Peter T1 - On Algorithms for the Summation of Certain Special Functions JF - Computing Y1 - 1976 VL - 17 SP - 37 EP - 48 ER - TY - JOUR A1 - Deuflhard, Peter T1 - A Modified Newton Method for the Solution of Ill-Conditioned Systems of Nonlinear Equations with Application to Multiple Shooting JF - Numer. Math. Y1 - 1974 VL - 22 SP - 289 EP - 315 ER - TY - BOOK A1 - Deuflhard, Peter T1 - Newton Methods for Nonlinear Problems. Affine Invariance and Adaptive Algorithms T3 - Springer Series in Computational Mathematics Y1 - 2004 PB - Springer ER - TY - BOOK A1 - Deuflhard, Peter T1 - Newton Methods for Nonlinear Problems. Affine Invariance and Adaptive Algorithms T3 - Springer Series in Computational Mathematics Y1 - 2006 PB - Springer ER - TY - JOUR A1 - Deuflhard, Peter T1 - bookreview JF - Annual Report DMV Y1 - 2004 VL - 106 SP - 43 ER - TY - CHAP A1 - Deuflhard, Peter ED - et al. Kirkilionis, Markus T1 - From Molecular Dynamics to Conformational Dynamics in Drug Design T2 - Trends in Nonlinear Analysis Y1 - 2003 SP - 269 EP - 288 PB - Springer Verlag Berlin ER - TY - CHAP A1 - Deuflhard, Peter T1 - A Comparison of Related Concepts in Computational Chemistry and Mathematics T2 - Chemisty and Mathematics Y1 - 2003 VL - 88 IS - 330 SP - 51 EP - 66 ER - TY - CHAP A1 - Deuflhard, Peter T1 - Differential Equations in Technology and Medicine. Computational Concepts, Adaptive Algorithms, and Virtual Labs T2 - Computational Mathematics Driven by Industrial Applications Y1 - 2000 VL - 1739 SP - 69 EP - 125 PB - Springer-Verlag ER - TY - GEN A1 - Deuflhard, Peter A1 - Felix, Roland A1 - Wust, Peter T1 - Wärme für das Leben. Mathematische Hyperthermieplanung am virtuellen Krebspatienten Y1 - 1999 PB - In: D. Hömberg (ed.), 8. Veranstaltungsreihe Forschungspolitische Dialoge in Berlin: Angewandte Mathematik - die verborgene Schlüsseltechnologie, 30. April 1999, Konrad-Zuse-Zentrum Berlin, pp. 23-29 ER - TY - GEN A1 - Deuflhard, Peter ED - et al. Begehr, H. T1 - Mathematics in Berlin Y1 - 1998 SP - 183 EP - 184 PB - Basel: Birkhäuser ER - TY - GEN A1 - Deuflhard, Peter T1 - Pittori, assassini, matematici Y1 - 2005 UR - http://www.zib.de/deuflhard/pub/mmm-english.pdf PB - M. Manaresi (ed.), Matematica e Cultura in Europa. Springer-Verlag Italia, pp. 145-155 ER - TY - GEN A1 - Deuflhard, Peter T1 - Linear and nonlinear least squares computing in view of control applications Y1 - 1980 SP - 85 EP - 92 PB - Sonderforschungsbereich 123, Stochastische Mathematische Modelle. Universität Heidelberg ER - TY - GEN A1 - Deuflhard, Peter T1 - Maler, Mörder, Mathematiker Y1 - 2003 PB - Gegenworte: Der Mythos und die Wissenschaft. Berlin-Brandenburgische Akademie der Wissenschaften (BBAW), 12. Heft, pp. 25-30 ER - TY - GEN A1 - Deuflhard, Peter T1 - Maler, Mörder, Mathematiker Y1 - 2003 PB - Mitteilungen der Deutschen MathematikerVereinigung (DMV), pp. 16-21, Heft 4 ER - TY - THES A1 - Deuflhard, Peter T1 - A Stepsize Control for Continuation Methods with Special Application to Multiple Shooting Techniques Y1 - 1976 CY - Math. Institute, Munich University of Technology ER - TY - GEN A1 - Deuflhard, Peter T1 - Therapieplanung an virtuellen Krebspatienten Y1 - 2000 PB - M. Aigner, E. Behrends (eds.): Alles Mathematik. Von Pythagoras zum CD-Player. Vieweg Verlag, pp. 22-30 ER - TY - THES A1 - Deuflhard, Peter T1 - Stimulierte Brillouinstreuung in Germanium bei 10.6 μ Y1 - 1968 CY - Physics Dept. ER - TY - THES A1 - Deuflhard, Peter T1 - Ein Newton-Verfahren bei fastsingulärer Funktionalmatrix zur Lösung von nichtlinearen Randwertaufgaben mit der Mehrzielmethode Y1 - 1972 CY - Math. Institute University of Cologne ER - TY - JOUR A1 - Daubechies, I. A1 - Teschke, G. T1 - Variational image restoration by means of wavelets JF - Applied and Computational Harmonic Analysis Y1 - 2005 VL - 19 IS - 1 SP - 1 EP - 16 ER - TY - JOUR A1 - Daubechies, I. A1 - Teschke, G. A1 - Vese, Luminita T1 - Iteratively solving linear inverse problems with general convex constraints JF - InverseProblems and Imaging Y1 - 2007 VL - 1 IS - 1 SP - 29 EP - 46 ER - TY - JOUR A1 - Daubechies, I. A1 - Teschke, G. T1 - Wavelet–based image decomposition by variational functionals JF - Proc. SPIE Vol. 5266, p. 94-105, Wavelet Applications in Industrial Processing; Frederic Truchetet; Ed. Y1 - 2004 ER - TY - JOUR A1 - Dahlke, S. A1 - Steidl, G. A1 - Teschke, G. T1 - Frames and Coorbit Theory on Homogeneous Spaces with a Special Guidance on the Sphere JF - Special Issue Y1 - 2007 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Weber, Marcus T1 - Robust Perron Cluster Analysis in Conformation Dynamics T2 - Lin. Alg. Appl. – Special Issue on Matrices and Mathematical Biology Y1 - 2005 VL - 398 SP - 161 EP - 184 PB - Elsevier Journals CY - Germany ER - TY - JOUR A1 - Dahlke, S. A1 - Steidl, G. A1 - Teschke, G. T1 - Weighted Coorbit Spaces and Banach Frames on Homogeneous Spaces JF - Journal of Fourier Analysis and Applications Y1 - 2004 VL - 5 IS - 10 SP - 507 EP - 539 ER - TY - JOUR A1 - Dahlke, S. A1 - Steidl, G. A1 - Teschke, G. T1 - Coorbit Spaces and Banach Frames on Homogeneous Spaces with Applications to Analyzing Functions on Spheres JF - Adv. Comput.Math. Y1 - 2004 VL - 1-2 IS - 21 SP - 147 EP - 180 ER - TY - JOUR A1 - Dahlke, S. A1 - Kutyniok, Gitta A1 - Steidl, G. A1 - Teschke, G. T1 - Shearlet coorbit spaces and associated Banach frames JF - Bericht Nr. 2007-5, Philipps-Universität Marburg Y1 - 2007 ER - TY - JOUR A1 - Dahlke, S. A1 - Lorenz, Dirk A. A1 - Maass, Peter A1 - Sagiv, C. A1 - Teschke, G. T1 - The Canonical Coherent states associated with Quotients of the Affine Weyl–Heisenberg Group JF - to appear Y1 - 2007 ER - TY - JOUR A1 - Dahlke, S. A1 - Kutyniok, Gitta A1 - Maass, Peter A1 - Sagiv, C. A1 - Stark, H.-G. A1 - Teschke, G. T1 - The Uncertainty Principle Associated with the Continuous Shearlet Transform JF - to appear Y1 - 2006 ER - TY - JOUR A1 - Cataliotti, F. A1 - Burger, Sven A1 - Fort, C. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Trombettoni, A. A1 - Smerzi, A. A1 - Inguscio, Massimo T1 - Josephson Junction Arrays with Bose-Einstein condensates JF - Science Y1 - 2001 VL - 293 SP - 843 EP - 846 ER - TY - CHAP A1 - Cataliotti, F. A1 - Burger, Sven A1 - Natale, P. A1 - Fort, C. A1 - Giusfredi, G. A1 - Inguscio, Massimo A1 - Minardi, F. A1 - Pastor, P. A1 - Pavone, F. ED - Figger, H. ED - Meschede, D. ED - Zimmermann, C. T1 - From Atoms to Single Biomolecules Through Bose-Einstein Condensates T2 - Laser Physics at the Limits Y1 - 2002 PB - Springer Verlag CY - Heidelberg ER - TY - JOUR A1 - Carr, L. A1 - Brand, J. A1 - Burger, Sven A1 - Sanpera, Anna T1 - Dark-soliton creation in Bose-Einstein condensates JF - Phys. Rev. A Y1 - 2001 U6 - https://doi.org/10.1103/PhysRevA.63.051601 VL - 63 SP - 051601 ER - TY - JOUR A1 - Cerejeiras, P. A1 - Dahlke, S. A1 - Soares, M. A1 - Kaehler, U. A1 - Lindemann, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Wavelet-Galerkin Scheme for Nonlinear Elliptic Partial Differential Equations JF - in preparation Y1 - 2004 ER - TY - JOUR A1 - Cerejeiras, P. A1 - Dahlke, S. A1 - Soares, M. A1 - Kaehler, U. A1 - Lindemann, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Wavelet Based Numerical Method for Nonlinear Elliptic Partial Differential Equations JF - IKM Proceedings Y1 - 2004 ER - TY - JOUR A1 - Colli Franzone, Piero A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Pavarino, Luca Franco T1 - Adaptivity in Space and Time for Reaction-Diffusion Systems in Electrocardiology JF - SIAM J. Sc. Comp. Y1 - 2006 VL - 28 SP - 942 EP - 962 ER - TY - CHAP A1 - Burger, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Finite-element method simulations of high-Q nanocavities with 1D photonic bandgap T2 - Physics and Simulation of Optoelectronic Devices XIX Y1 - 2011 U6 - https://doi.org/10.1117/12.875044 VL - 7933 SP - 79330T PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Kato, Akiko A1 - Laubis, Christian A1 - Scholze, Frank T1 - Investigation of 3D Patterns on EUV Masks by Means of Scatterometry and Comparison to Numerical Simulations T2 - Photomask Technology 2011 Y1 - 2011 U6 - https://doi.org/10.1117/12.896839 VL - 8166 SP - 81661Q PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank ED - Bodermann, Bernd T1 - Rigorous simulations of 3D patterns on extreme ultraviolet lithography masks T2 - Modelling Aspects in Optical Metrology III Y1 - 2011 U6 - https://doi.org/10.1117/12.889831 VL - 8083 SP - 80831B PB - Proc. SPIE ER - TY - JOUR A1 - Bujotzek, Alexander A1 - Shan, Min A1 - Haag, Rainer A1 - Weber, Marcus T1 - Towards a rational spacer design for bivalent inhibition of estrogen receptor JF - J. Comput.-Aided Mol. Des. Y1 - 2011 VL - 25(3) SP - 253 EP - 262 ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Evanschitzky, Peter A1 - Erdmann, Andreas ED - Kawahira, H. ED - Zurbrick, L. S. T1 - Benchmark of rigorous methods for electromagnetic field simulation T2 - Photomask Technology Y1 - 2008 UR - http://dx.doi.org/10.1117/12.801248 U6 - https://doi.org/10.1117/12.801248 VL - 7122 SP - 71221 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Köhle, Roderick A1 - Küchler, Bernd A1 - Nölscher, Christoph T1 - EMF Simulations of Isolated and Periodic 3D Photomask Patterns T2 - Photomask Technology Y1 - 2007 UR - http://arxiv.org/pdf/0709.3934 VL - 6730 SP - 6630 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Köhle, Roderick A1 - Henkel, Thomas A1 - Küchler, Bernd A1 - Nölscher, Christoph ED - Bosse, Harald T1 - 3D simulations of electromagnetic fields in nanostructures using the time-harmonic finite-element method T2 - Modeling Aspects in Optical Metrology Y1 - 2007 U6 - https://doi.org/10.1117/12.726236 VL - 6617 SP - 66170V PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schädle, Achim A1 - Klose, Roland A1 - Kettner, Benjamin A1 - Pomplun, Jan A1 - Pollok, T. A1 - Schmidt, Frank T1 - Advanced FEM Analysis of Nano-Optical Devices T2 - Proc. Symposium on Photonics Technologies for the 7th Framework Programme Y1 - 2006 ER - TY - JOUR A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - FEM Simulation of Plasmon Laser Resonances JF - AIP Conference Proceedings Y1 - 2010 U6 - https://doi.org/10.1063/1.3498131 VL - 1281 SP - 1613 EP - 1616 PB - AIP ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - JCMsuite: An Adaptive FEM Solver for Precise Simulations in Nano-Optics T2 - Integrated Photonics and Nanophotonics Research and Applications Y1 - 2008 U6 - https://doi.org/10.1364/IPNRA.2008.ITuE4 SP - ITuE4 PB - Optical Society of America ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Finite element method for accurate 3D simulation of plasmonic waveguides T2 - Integrated Optics: Devices, Materials, and Technologies XIV Y1 - 2010 U6 - https://doi.org/10.1117/12.841995 VL - 7604 SP - 76040F PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Pomplun, Jan A1 - Schmidt, Frank A1 - Kettner, Benjamin A1 - Lockau, D. T1 - 3D Finite-Element Simulations of Enhanced Light Transmission Through Arrays of Holes in Metal Films T2 - Numerical Methods in Optical Metrology Y1 - 2009 U6 - https://doi.org/10.1117/12.827543 VL - 7390 SP - 73900H PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Enkrich, Christian A1 - Linden, S. A1 - Wegener, M. A1 - Soukoulis, C. ED - Szoplik, T. ED - Özbay, E. ED - Soukoulis, C. ED - Zheludev, N. T1 - Numerical Investigation of Light Scattering off Split-Ring Resonators T2 - Metamaterials Y1 - 2005 U6 - https://doi.org/10.1117/12.622184 VL - 5955 SP - 18 EP - 26 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Kettner, Benjamin A1 - Schmidt, Frank ED - Hergert, W. ED - Wriedt, T. T1 - FEM simulation of light scattering by nonspherical objects T2 - Mie Theory 1908 – 2008 Y1 - 2008 SP - 82 EP - 83 PB - Universität Bremen ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin ED - Chigrin, Dmitry T1 - Numerical Investigation of Silicon-on-Insulator 1D Photonic Crystal Microcavities T2 - Theoretical and computational nanooptics Y1 - 2009 U6 - https://doi.org/10.1063/1.3253915 VL - 1176 SP - 43 EP - 45 PB - AIP ER - TY - CHAP A1 - Burger, Sven A1 - Schädle, Achim A1 - Zschiedrich, Lin A1 - Schmidt, Frank ED - Andrews, David L. ED - Nunzi, Jean-Michel ED - Ostendorf, Andreas T1 - Advanced FEM Analysis of Nano-Optical Devices T2 - Nanophotonics Y1 - 2006 U6 - https://doi.org/10.1117/12.662942 VL - 6195 SP - 72 EP - 82 PB - Proc. SPIE ER - TY - CHAP A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Schmidt, Frank A1 - Tyminski, Jacek A1 - Flagello, Donis A1 - Toshiharu, N. T1 - Reduced basis method for source mask optimization T2 - Photomask Technology Y1 - 2010 U6 - https://doi.org/10.1117/12.866101 VL - 7823 SP - 78230E PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Numerical Investigation of Photonic Crystal Microcavities in Silicon-on-Insulator Waveguides T2 - Photonic and Phononic Crystal Materials and Devices X Y1 - 2010 U6 - https://doi.org/10.1117/12.841867 VL - 7609 SP - 76091Q PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Numerical investigation of optical resonances in circular grating resonators T2 - Silicon Photonics V Y1 - 2010 U6 - https://doi.org/10.1117/12.842061 VL - 7606 SP - 760610 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin ED - Jena, Friedrich-Schiller-Universität T1 - FEM simulation of resonances in low-Q cavities for plasmon lasers T2 - International Workshop on Photonic Nanomaterials Y1 - 2010 SN - 978-3-00-031358-5 SP - 36 ER - TY - CHAP A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - 3D FEM Simulations of High-Q Resonances in Photonic Crystal Microcavities T2 - Integrated Photonics Research, Silicon and Nanophotonics Y1 - 2010 U6 - https://doi.org/10.1364/IPRSN.2010.IWB7 SP - IWB7 PB - OSA ER - TY - CHAP A1 - Burger, Sven A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - A fast and efficient Finite-Element Solver for 2D and 3D Photonic Band-Gap Problems T2 - Dig. LEOS/IEEE 2003 Summer Topicals Y1 - 2003 U6 - https://doi.org/10.1109/LEOSST.2003.1224282 SP - 75 ER - TY - CHAP A1 - Burger, Sven A1 - Pomplun, Jan A1 - Schmidt, Frank ED - Bhushan, B. T1 - Finite Element Methods for Computational Nano-optics T2 - Encyclopedia of Nanotechnology Y1 - 2012 U6 - https://doi.org/10.1007/978-90-481-9751-4_17 SP - 837 EP - 843 PB - Springer Netherlands ER - TY - CHAP A1 - Burger, Sven A1 - Lockau, D. A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Finite-element simulations of light propagation through subwavelength apertures in metal films T2 - International Workshop on Optical Waveguide Theory and Numerical Modelling Y1 - 2009 VL - XVIII SP - 59 PB - Fraunhofer Institute for Applied Optics and Precision Engineering ER - TY - CHAP A1 - Burger, Sven A1 - Köhle, Roderick A1 - Zschiedrich, Lin A1 - Gao, W. A1 - Schmidt, Frank A1 - März, Reinhard A1 - Nölscher, Christoph ED - Weed, J. ED - Martin, P. T1 - Benchmark of FEM, Waveguide and FDTD Algorithms for Rigorous Mask Simulation T2 - Photomask Technology Y1 - 2005 U6 - https://doi.org/10.1117/12.631696 VL - 5992 SP - 378 EP - 389 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Köhle, Roderick A1 - Zschiedrich, Lin A1 - Nguyen, H. A1 - Schmidt, Frank A1 - März, Reinhard A1 - Nölscher, Christoph ED - Martin, P. ED - Naber, R. T1 - Rigorous Simulation of 3D Masks T2 - Photomask Technology Y1 - 2006 UR - http://arxiv.org/pdf/physics/0610218 VL - 6349 SP - 63494Z PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Kleemann, B. A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Finite-Element Simulations of Light Propagation through Circular Subwavelength Apertures T2 - Microtechnologies for the New Millenium Y1 - 2009 U6 - https://doi.org/10.1117/12.822828 VL - 7366 SP - 736621 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Adaptive FEM solver for the computation of electromagnetic eigenmodes in 3D photonic crystal structures T2 - Scientific Computing in Electrical Engineering Y1 - 2006 U6 - https://doi.org/10.1007/978-3-540-32862-9_24 SP - 169 EP - 175 PB - Springer Verlag ER - TY - CHAP A1 - Burger, Sven A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin ED - Sidorin, Y. ED - Wächter, Christoph T1 - FEM modelling of 3D photonic crystals and photonic crystal waveguides T2 - Integrated Optics : Devices, Materials and Technologies IX Y1 - 2005 U6 - https://doi.org/10.1117/12.585895 VL - 5728 SP - 164 EP - 173 PB - Proc. SPIE ER - TY - CHAP A1 - Burger, Sven A1 - Klose, Roland A1 - März, Reinhard A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Efficient Finite Element Methods for the Design of Microoptical Components T2 - Proc. Microoptics Conf. 2004 Y1 - 2004 ER - TY - JOUR A1 - Burger, Sven A1 - Carr, L. A1 - Öhberg, P. A1 - Sengstock, Klaus A1 - Sanpera, Anna T1 - Generation and interaction of solitons in Bose-Einstein condensates JF - Phys. Rev. A Y1 - 2002 VL - 65 SP - 043611 ER - TY - BOOK ED - Burkard, Rainer E. ED - Deuflhard, Peter ED - Jameson, A. ED - Strang, Gilbert ED - Lions, J. ED - Capasso, Vincenzo ED - Engl, H. ED - Periaux, J. T1 - Computational Mathematics Driven by Industrial Problems T3 - Lecture Notes in Mathematics Y1 - 2000 VL - 1739 PB - Springer ER - TY - CHAP A1 - Burger, Sven A1 - Cataliotti, F. A1 - Fort, C. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo ED - Chu, S. T1 - Coherent Dynamics of Bose-Einstein condensates in an Optical Lattice T2 - Laser Spectroscopy XV Y1 - 2002 PB - World Scientific ER - TY - JOUR A1 - Burger, Sven A1 - Cataliotti, F. A1 - Fort, C. A1 - Minardi, F. A1 - Inguscio, Massimo A1 - Chiofalo, M. A1 - Tosi, M. T1 - Superfluid and Dissipative Dynamics of a Bose-Einstein Condensate in a Periodic Optical Potential JF - Phys. Rev. Lett. Y1 - 2001 VL - 86 IS - 20 SP - 4447 EP - 4450 ER - TY - CHAP A1 - Burger, Sven A1 - Cataliotti, F. A1 - Ferlaino, F. A1 - Fort, C. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo ED - Martini, F. ED - Monroe, C. T1 - Bose-Einstein Condensates in an Optical Lattice T2 - Experimental Quantum Computation and Information Y1 - 2002 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Burger, Sven A1 - Bongs, Kai A1 - Dettmer, Stefanie A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus A1 - Sanpera, Anna A1 - Shlyapnikov, Gora A1 - Lewenstein, Maciej T1 - Dark Solitons in Bose-Einstein Condensates JF - Phys. Rev. Lett. Y1 - 1999 U6 - https://doi.org/10.1103/PhysRevLett.83.5198 VL - 83 IS - 25 SP - 5198 EP - 5201 ER - TY - THES A1 - Burger, Sven T1 - Erzeugung und Untersuchung dunkler Solitonen in Bose-Einstein Kondensaten Y1 - 2000 ER - TY - JOUR A1 - Burger, Sven T1 - Simulation method improves accuracy for optical metrology and nanooptics design JF - SPIE Newsroom Y1 - 2009 U6 - https://doi.org/10.1117/2.1200905.1629 ER - TY - JOUR A1 - Bredies, Kristian A1 - Lorenz, Dirk A. A1 - Maass, Peter A1 - Teschke, G. T1 - A partial differential equation for continuous non-linear shrinkage filtering and its application for analyzing MMG data JF - Proc. SPIE Vol. 5266, p. 84-93, Wavelet Applications in Industrial Processing; Frederic Truchetet; Ed. Y1 - 2004 ER - TY - JOUR A1 - Braess, Dietrich A1 - Deuflhard, Peter A1 - Lipnikov, Konstantin T1 - A Subspace Cascadic Multigrid Method for Mortar Elements JF - Computing Y1 - 2002 VL - 69 SP - 205 EP - 225 ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Apri, Mochamad A1 - Molenaar, Jaap A1 - Stötzel, Claudia A1 - Veerkamp, Roel F. A1 - Woelders, Henri T1 - Candidate mechanisms underlying atypical progesterone profiles as deduced from parameter perturbations in a mathematical model of the bovine estrous cycle JF - Journal of Dairy Science Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S0022030212003621 U6 - https://doi.org/10.3168/jds.2011-5241 VL - 95 IS - 7 SP - 3837 EP - 3851 ER - TY - CHAP A1 - Boer, H. Marike T. A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Woelders, Henri T1 - A differential equation model to investigate the dynamics of the bovine estrous cycle T2 - Advances in Systems Biology Y1 - 2012 U6 - https://doi.org/10.1007/978-1-4419-7210-1_35 VL - 736 SP - 597 EP - 606 ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Röblitz, Susanna A1 - Stötzel, Claudia A1 - Veerkamp, Roel F. A1 - Kemp, Bas A1 - Woelders, Henri T1 - Mechanisms regulating follicle wave patterns in the bovine estrous cycle investigated with a mathematical model JF - Journal of Dairy Science Y1 - 2011 U6 - https://doi.org/10.3168/jds.2011-4400 VL - 94 IS - 12 SP - 5987 EP - 6000 ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Deuflhard, Peter A1 - Veerkamp, Roel F. A1 - Woelders, Henri T1 - A simple mathematical model of the bovine estrous cycle JF - Journal of Theoretical Biology Y1 - 2011 U6 - https://doi.org/10.1016/j.jtbi.2011.02.021 VL - 278 IS - 1 SP - 20 EP - 31 ER - TY - CHAP A1 - Bodermann, Bernd A1 - Hansen, Poul-Erik A1 - Burger, Sven A1 - Henn, Mark-Alexander A1 - Gross, Hermann A1 - Bär, Markus A1 - Scholze, Frank A1 - Endres, Johannes A1 - Wurm, Matthias T1 - First steps towards a scatterometry reference standard T2 - Proc. SPIE Y1 - 2012 U6 - https://doi.org/10.1117/12.929903 VL - 8466 SP - 84660E ER - TY - JOUR A1 - Bodermann, Bernd A1 - Buhr, Egbert A1 - Danzebrink, Hans-Ulrich A1 - Bär, Markus A1 - Scholze, Frank A1 - Krumrey, Michael A1 - Wurm, Matthias A1 - Klapetek, Petr A1 - Hansen, Poul-Erik A1 - Korpelainen, Virpi A1 - van Veghel, Marijn A1 - Yacoot, Andrew A1 - Siitonen, Samuli A1 - El Gawhary, Omar A1 - Burger, Sven A1 - Saastamoinen, Toni T1 - Joint Research on Scatterometry and AFM Wafer Metrology JF - AIP Conference Proceedings Y1 - 2011 U6 - https://doi.org/10.1063/1.3657910 VL - 1395 IS - 1 SP - 319 EP - 323 PB - AIP ER - TY - CHAP A1 - Bock, Martin A1 - Skibina, Julia A1 - Fischer, Dorit A1 - Grunwald, Rüdiger A1 - Burger, Sven A1 - Beloglazov, Valentin A1 - Steinmeyer, Günter T1 - 10-fs pulse delivery through a fiber T2 - CLEO Y1 - 2012 U6 - https://doi.org/10.1364/CLEO_SI.2012.CTh3G.3 SP - CTh3G.3 PB - Optical Society of America ER - TY - JOUR A1 - Böck, J. A1 - Deuflhard, Peter A1 - Hoeft, A. A1 - Korb, H. A1 - Steinmann, J. A1 - Wolpers, H. A1 - Hellige, G. T1 - Evaluation of monoexponential extrapolation of transpulmonary thermal-dye kinetics by use of a new model-free deconvolution algorithm JF - Med Instrum Y1 - 1988 VL - 22 IS - 1 SP - 20 EP - 28 ER - TY - JOUR A1 - Böck, J. A1 - Deuflhard, Peter A1 - Hoeft, A. A1 - Korb, H. A1 - Wolpers, H. A1 - Steinmann, J. A1 - Hellige, G. T1 - Thermal recovery after passage of the pulmonary circulation assessed by deconvolution JF - J. Appl. Physiol. Y1 - 1988 VL - 64 IS - 3 SP - 1210 EP - 1216 ER - TY - CHAP A1 - Bornemann, Folkmar A. A1 - Deuflhard, Peter ED - Glowinski, J. R. ED - Widlund, Olof T1 - Cascadic Multigrid Methods T2 - Domain Decomposition Methods in Sciences and Engineering Y1 - 1996 SP - 205 EP - 212 PB - John Wiley & Sons Ltd ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Deuflhard, Peter T1 - The cascadic multigrid method for elliptic problems JF - Numer. Math. Y1 - 1996 VL - 75 SP - 135 EP - 152 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang T1 - Manipulation of Bose-Einstein condensates by dipole potentials JF - J. Mod. Opt. Y1 - 2000 U6 - https://doi.org/10.1080/09500340008232190 VL - 47 SP - 2697 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Hellweg, D. A1 - Arlt, J. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus T1 - Waveguide for Bose-Einstein condensates JF - Phys. Rev. A Y1 - 2001 VL - 63 SP - 31602 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Birkl, G. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang A1 - Rzazewski, K. A1 - Sanpera, Anna A1 - Lewenstein, Maciej T1 - Coherent Evolution of Bouncing Bose-Einstein Condensates JF - Phys. Rev. Lett. Y1 - 1999 VL - 83 IS - 18 SP - 3577 EP - 3580 ER - TY - JOUR A1 - Blome, Mark A1 - McPeak, Kevin A1 - Burger, Sven A1 - Schmidt, Frank A1 - Norris, David T1 - Back-reflector design in thin-film silicon solar cells by rigorous 3D light propagation modeling JF - COMPEL: Int. J. Comput. Mathem. Electr. Electron. Eng. Y1 - 2014 U6 - https://doi.org/10.1108/COMPEL-12-2012-0367 VL - 33 IS - 4 SP - 1282 EP - 1295 ER - TY - JOUR A1 - Bethge, Jens A1 - Steinmeyer, Günter A1 - Burger, Sven A1 - Lederer, Falk A1 - Iliew, Rumen T1 - Guiding properties of chirped photonic crystal fibers JF - Journal of Lightwave Technology Y1 - 2009 U6 - https://doi.org/10.1109/JLT.2009.2021583 VL - 27 SP - 1698 ER - TY - CHAP A1 - Beck, Rudolf A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland ED - Franconi, Cafiero T1 - Adaptive finite element codes for numerical calculations in hyperthermia treatment planning T2 - Proc. of the 7th Int. Congress on Hyperthermic Oncology, Rome, Italy, April 1996 Y1 - 1996 VL - 2 SP - 515 EP - 517 ER - TY - CHAP A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Wust, Peter A1 - Felix, Roland T1 - Electromagnetic Field Calculations by Finite Elements T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 77 ER - TY - JOUR A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hiptmair, Ralf A1 - Hoppe, Ronald H. W. A1 - Wohlmuth, Barbara T1 - Adaptive multilevel methods for edge element discretizations of Maxwell’s equations JF - Surv. Math. Ind. Y1 - 1999 VL - 8 IS - 3-4 SP - 271 EP - 312 ER - TY - CHAP A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Numerical Algorithms and Visualization in Medical Treament Planning T2 - Visualization and Mathematics Y1 - 1997 SP - 303 EP - 328 PB - Springer-Verlag ER - TY - JOUR A1 - Babicheva, Viktoriia E. A1 - Vergeles, Sergey S. A1 - Vorobev, Petr E. A1 - Burger, Sven T1 - Localized surface plasmon modes in a system of two interacting metallic cylinders JF - J. Opt. Soc. Am. B Y1 - 2012 U6 - https://doi.org/10.1364/JOSAB.29.001263 VL - 29 IS - 6 SP - 1263 EP - 1269 ER - TY - CHAP A1 - Bader, G. A1 - Nowak, Ulrich A1 - Deuflhard, Peter ED - Aiken, R. T1 - An Advanced Simulation Package for Large Chemical Reaction Systems T2 - Stiff Computation. Proc. Intern. Conf. Park City, Utah/USA Y1 - 1985 PB - Oxford University Press ER - TY - JOUR A1 - Bergmann, G. A1 - Graichen, F. A1 - Rohlmann, A. A1 - Bender, Alwina A1 - Ehrig, Rainald A1 - Westerhoff, P. A1 - Heinlein, B. T1 - Design and calibration of load sensing orthopaedic implants JF - Journal Biomech. Eng. Y1 - 2008 SP - 02109 EP - 1–02109–9 ER - TY - CHAP A1 - Beck, Rudolf A1 - Erdmann, Bodo A1 - Roitzsch, Rainer ED - Arge, Erlend ED - Bruaset, Are Magnus ED - Langtangen, Hans Petter T1 - An Object-Oriented Adaptive Finite Element Code T2 - Modern Software Tools for Scientific Computing Y1 - 1997 SP - 105 EP - 124 PB - Birkhäuser, Boston ER - TY - JOUR A1 - Asam, P. A1 - Deuflhard, Peter A1 - Kaiser, Wolfgang T1 - Intensity Limiting and Stimulated Brillouin Scattering in Germanium JF - Physics Letters Y1 - 1968 VL - 27 A SP - 78 EP - 79 ER - TY - JOUR A1 - Andrae, Karsten A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Systematics of spin-polarized small Na clusters JF - Annals of the European Academy of Science Y1 - 2007 ER - TY - JOUR A1 - Andrae, Karsten A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Crossed Beam Pump and Probe Dynamics in Metal Clusters JF - Phys. Rev. Lett. Y1 - 2004 U6 - https://doi.org/10.1103/PhysRevLett.92.173402 VL - 92 IS - 17 SP - 173402 PB - American Physical Society ER - TY - JOUR A1 - Andrae, Karsten A1 - Dinh, P. A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Pump and probe analysis of metal cluster dynamics JF - Computational Materials Science Y1 - 2006 UR - http://www.sciencedirect.com/science/article/pii/S0927025605001163 U6 - https://doi.org/DOI: 10.1016/j.commatsci.2004.09.062 VL - 35 IS - 3 SP - 169 EP - 173 ER - TY - JOUR A1 - Antoine, Xavier A1 - Arnold, Anton A1 - Besse, Christophe A1 - Ehrhardt, Matthias A1 - Schädle, Achim T1 - A Review of Transparent and Artificial Boundary Conditions Techniques for Linear and Nonlinear Schrödinger Equations JF - Commun. Comput. Phys. Y1 - 2008 UR - http://www.global-sci.com/openaccess/v4_729.pdf VL - 4 SP - 729 EP - 796 ER - TY - JOUR A1 - Abendroth, Frank A1 - Bujotzek, Alexander A1 - Shan, Min A1 - Haag, Rainer A1 - Weber, Marcus A1 - Seitz, Oliver T1 - DNA-controlled bivalent presentation of ligands for the estrogen receptor JF - Angew. Chem. Int. Ed. Y1 - 2011 ER - TY - JOUR A1 - Ackermann, Jörg A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - A self-adaptive multilevel finite element method for the stationary Schrödinger equation in three space dimensions JF - J. Chem. Phys. Y1 - 1994 VL - 101 SP - 7643 EP - 7650 ER - TY - JOUR A1 - Casas, E. A1 - de Los Reyes, J. A1 - Tröltzsch, Fredi T1 - Sufficient second-order optimality conditions for semilinear control problems with pointwise state constraints JF - SIAM Journal on Optimization Y1 - 2007 U6 - https://doi.org/10.1137/07068240X VL - 19 IS - 2 SP - 616 EP - 643 ER - TY - JOUR A1 - Weiser, Martin A1 - Deuflhard, Peter T1 - Inexact central path following algorithms for optimal control problems JF - SIAM J. Control Opt. Y1 - 2007 VL - 46 IS - 3 SP - 792 EP - 815 ER - TY - GEN A1 - Volkwein, S. A1 - Tröltzsch, Fredi T1 - POD a-posteriori error estimates for linear-quadratic optimal control problems Y1 - 2007 IS - SFB-Report 2007-008 PB - SFB Research Center "Mathematical Optimization and Applications in Biomedical Sciences", Karl-Franzens-Universität Graz ER - TY - JOUR A1 - Schenk, O. A1 - Wächter, Andreas A1 - Weiser, Martin T1 - Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization JF - SIAM J. Sci. Comp. Y1 - 2008 VL - 31 IS - 2 SP - 939 EP - 960 ER - TY - JOUR A1 - Neitzel, Ira A1 - Prüfert, Uwe A1 - Slawig, Thomas T1 - Strategies for time-dependent PDE control using an integrated modeling and simulation environment. Part two Y1 - 2007 IS - 24-02 PB - SPP 1253 ER - TY - JOUR A1 - Neitzel, Ira A1 - Prüfert, Uwe A1 - Slawig, Thomas T1 - Strategies for time-dependent PDE control using an integrated modeling and simulation environment. Part one Y1 - 2007 IS - 408 PB - Matheon CY - Berlin ER - TY - BOOK A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Numerische Mathematik I. Eine algorithmisch orientierte Einführung.(Numerical mathematics I. An algorithmically oriented introduction) Y1 - 1993 PB - de Gruyter Lehrbuch. Berlin: Walter de Gruyter, ET - 2 ER - TY - BOOK A1 - Deuflhard, Peter A1 - Bornemann, Folkmar A. T1 - Numerische Mathematik. II Y1 - 1994 PB - De Gruyter Lehrbuch. Berlin: de Gruyter ER - TY - GEN A1 - Borndörfer, Ralf A1 - Fügenschuh, Armin A1 - Klug, Torsten A1 - Schang, Thilo A1 - Schlechte, Thomas A1 - Schülldorf, Hanno T1 - The Freight Train Routing Problem N2 - We consider the following freight train routing problem (FTRP). Given is a transportation network with fixed routes for passenger trains and a set of freight trains (requests), each defined by an origin and destination station pair. The objective is to calculate a feasible route for each freight train such that a sum of all expected delays and all running times is minimal. Previous research concentrated on microscopic train routings for junctions or inside major stations. Only recently approaches were developed to tackle larger corridors or even networks. We investigate the routing problem from a strategic perspective, calculating the routes in a macroscopic transportation network of Deutsche Bahn AG. Here macroscopic refers to an aggregation of complex real-world structures are into fewer network elements. Moreover, the departure and arrival times of freight trains are approximated. The problem has a strategic character since it asks only for a coarse routing through the network without the precise timings. We give a mixed-integer nonlinear programming~(MINLP) formulation for FTRP, which is a multi-commodity flow model on a time-expanded graph with additional routing constraints. The model's nonlinearities are due to an algebraic approximation of the delays of the trains on the arcs of the network by capacity restraint functions. The MINLP is reduced to a mixed-integer linear model~(MILP) by piecewise linear approximation. The latter is solved by a state of the art MILP solver for various real-world test instances. T3 - ZIB-Report - 13-36 KW - Mixed-Integer Nonlinear Programming KW - multi-commodity flows KW - freight train routing Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18991 ER - TY - GEN A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Linear response theory and optimal control for a molecular system under nonequilibrium conditions N2 - In this paper, we propose a straightforward generalization of linear response theory to systems in nonequilibrium that are subject to nonequilibrium driving. We briefly revisit the standard linear response result for equilibrium systems, where we consider Langevin dynamics as a special case, and then give an alternative derivation using a change-of-measure argument that does not rely on any stationarity or reversibility assumption. This procedure moreover easily enables us to calculate the second order correction to the linear response formula (which may or may not be useful in practice). Furthermore, we outline how the novel nonequilibirum linear response formula can be used to compute optimal controls of molecular systems for cases in which one wants to steer the system to maximize a certain target expectation value. We illustrate our approach with simple numerical examples. T3 - ZIB-Report - 13-33 KW - nonequilibrium molecular dynamics KW - linear response KW - Girsanov transformation KW - stochastic control Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18944 ER - TY - GEN A1 - Scheumann, René A1 - Vierhaus, Ingmar A1 - Chang, Ya-Ju A1 - Fügenschuh, Armin A1 - Finkbeiner, Matthias T1 - Identification of trade-offs for sustainable manufacturing of a Bamboo Bike by System Dynamics N2 - We develop a generic System Dynamic model to simulate the production, machines, employees, waste, and capital flows of a manufacturing company. In a second step, this model is specialised by defining suit-able input data to represent a bicycle manufacturing company in a developing country. We monitor a set of sustainability indicators to understand the social, environmental and economic impact of the company, and to estimate managerial decisions to be taken in order to improve on these criteria. We show that the social and environmental situation can be improved over time without sacrificing the economic success of the company's business. T3 - ZIB-Report - 13-32 KW - System Dynamics KW - Modelling KW - Life Cycle Sustainability Assessment KW - Sustainability Indicators Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18895 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Humpola, Jesco T1 - A Unified View on Relaxations for a Nonlinear Network Flow Problem N2 - We consider a nonlinear nonconvex network flow problem that arises, for example, in natural gas or water transmission networks. Given is such network with active and passive components, that is, valves, compressors, pressure regulators (active) and pipelines (passive), and a desired amount of flow at certain specified entry and exit nodes of the network. Besides flow conservation constraints in the nodes the flow must fulfill nonlinear nonconvex pressure loss constraints on the arcs subject to potential values (i.e., pressure levels) in both end nodes of each arc. The problem is how to numerically compute this flow and pressures. We review an existing approach of Maugis (1977) and extend it to the case of networks with active elements (for example, compressors). We further examine different ways of relaxations for the nonlinear network flow model. We compare different approaches based on nonlinear optimization numerically on a set of test instances. T3 - ZIB-Report - 13-31 KW - Nonlinear Network Flow KW - Mixed-Integer Nonlinear Programming KW - Relaxations Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18857 ER - TY - GEN A1 - Weiser, Martin T1 - Faster SDC convergence on non-equidistant grids by DIRK sweeps N2 - Spectral deferred correction methods for solving stiff ODEs are known to converge rapidly towards the collocation limit solution on equidistant grids, but show a much less favourable contraction on non-equidistant grids such as Radau-IIa points. We interprete SDC methods as fixed point iterations for the collocation system and propose new DIRK-type sweeps for stiff problems based on purely linear algebraic considerations. Good convergence is recovered also on non-equidistant grids. The properties of different variants are explored on a couple of numerical examples. T3 - ZIB-Report - 13-30 KW - spectral deferred correction Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18662 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Raack, Christian A1 - Werner, Axel T1 - Towards optimizing the deployment of optical access networks N2 - In this paper we study the cost-optimal deployment of optical access networks considering variants of the problem such as fiber to the home (FTTH), fiber to the building (FTTB), fiber to the curb (FTTC), or fiber to the neighborhood (FTTN). We identify the combinatorial structures of the most important sub-problems arising in this area and model these, e.g., as capacitated facility location, concentrator location, or Steiner tree problems. We discuss modeling alternatives as well. We finally construct a “unified” integer programming model that combines all sub-models and provides a global view of all these FTTx problems. We also summarize computational studies of various special cases. T3 - ZIB-Report - 13-11 KW - FTTx, FTTH, FTTB, FTTC, FTTN, telecommunications, access networks, passive optical networks, network design, routing, energy efficiency Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18627 SN - 1438-0064 ER - TY - GEN A1 - Leitner, Markus A1 - Ljubic, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - On the Two-Architecture Connected Facility Location Problem N2 - We introduce a new variant of the connected facility location problem that allows for modeling mixed deployment strategies (FTTC/FTTB/FTTH) in the design of local access telecommunication networks. Several mixed integer programming models and valid inequalities are presented. Computational studies on realistic instances from three towns in Germany are provided. T3 - ZIB-Report - 13-29 KW - Connected Facility Location, Branch-and-Cut, FTTx Deployment Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18610 SN - 1438-0064 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Vierhaus, Ingmar T1 - A Global Approach to the Optimal Control of System Dynamics Models N2 - The System Dynamics (SD) methodology is a framework for modeling and simulating the dynamic behavior of socioeconomic systems. Characteristic for the description of such systems is the occurrence of feedback loops together with stocks and flows. The mathematical equations that describe the system are usually ordinary differential equations and nonlinear algebraic constraints. Therefore seemingly simple systems can show a nonintuitive, unpredictable behavior over time. Controlling a dynamical system means to specify potential interventions from outside that should keep the system on the desired track, and to define an evaluation schema to compare different controls among each other, so that a "best" control can be defined in a meaningful way. The central question is how to compute such globally optimal control for a given SD model, that allows the transition of the system into a desired state with minimum effort. We propose a mixed-integer nonlinear programming (MINLP) reformulation of the System Dynamics Optimization (SDO) problem. MINLP problems can be solved by linear programming based branch-and-bound approach. We demonstrate that standard MINLP solvers are not able to solve SDO problem. To overcome this obstacle, we introduce a special-tailored bound propagation method. We apply our new method to a predator-prey model with additional hunting activity as control, and to a mini-world model with the consumption level as control. Numerical results for these test cases are presented. T3 - ZIB-Report - 13-28 KW - System Dynamics KW - Global Optimal Control KW - Mixed-Integer Nonlinear Optimization KW - Bounds Strengthening Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18600 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy Compression for PDE-constrained Optimization: Adaptive Error Control N2 - For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the ad-joint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances. T3 - ZIB-Report - 13-27 KW - optimal control KW - semilinear parabolic PDEs KW - Newton-CG KW - trajectory storage KW - lossy compression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18575 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Nagaiah, Chamakuri A1 - Kunisch, Karl A1 - Weiser, Martin T1 - Lossy Compression in Optimal Control of Cardiac Defibrillation N2 - This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples. T3 - ZIB-Report - 13-26 KW - monodomain model KW - defibrillation KW - optimal control KW - Newton-CG KW - trajectory storage KW - compression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18566 SN - 1438-0064 ER - TY - GEN T1 - Jahresbericht 2012 T1 - Annual 2012 T3 - Jahresbericht - 2012 KW - Annual Report Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18510 SN - 0934-5892 VL - 2012 ER - TY - GEN A1 - Fügenschuh, Armin A1 - van Veldhuizen, Roel A1 - Vierhaus, Ingmar T1 - Production Planning for Non-Cooperating Companies with Nonlinear Optimization N2 - We consider a production planning problem where two competing companies are selling their items on a common market. Moreover, the raw material used in the production is a limited non-renewable resource. The revenue per item sold depends on the total amount of items produced by both players. If they collaborate they could apply a production strategy that leads to the highest combined revenue. Usually the formation of such syndicates is prohibited by law; hence we assume that one company does not know how much the other company will produce. We formulate the problem for company A to find an optimal production plan without information on the strategy of company B as a nonlinear mathematical optimization problem. In its naive formulation the model is too large, making its solution practically impossible. After a reformulation we find a much smaller model, which we solve by spatial branch-and-cut methods and linear programming. We discuss the practical implications of our solutions. T3 - ZIB-Report - 13-25 KW - Non-Cooperative Two-Person Games; Mixed-Integer Nonlinear Optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18163 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/4026 SN - 1438-0064 ER - TY - GEN A1 - Brose, Achim A1 - Fügenschuh, Armin A1 - Gausemeier, Pia A1 - Vierhaus, Ingmar A1 - Seliger, Günther T1 - A System Dynamic Enhancement for the Scenario Technique N2 - The Scenario Technique is a strategic planning method that aims to describe and analyze potential developments of a considered system in the future. Its application consists of several steps, from an initial problem analysis over an influence analysis to projections of key factors and a definition of the scenarios to a final interpretation of the results. The technique itself combines qualitative and quantitative methods and is an enhancement of the standard Scenario Technique. We use the numerical values gathered during the influence analysis, and embed them in a System Dynamics framework. This yields a mathematically rigorous way to achieve predictions of the system‘s future behavior from an initial impulse and the feedback structure of the factors. The outcome of our new method is a further way of projecting the present into the future, which enables the user of the Scenario Technique to obtain a validation of the results achieved by the standard method. T3 - ZIB-Report - 13-24 KW - Scenario Technique; System Dynamics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18150 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/4026 SN - 1438-0064 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Vierhaus, Ingmar T1 - System Dynamic Optimization in the Sustainability Assessment of a World-Model N2 - The System Dynamics (SD) methodology is a framework for modeling and simulating the dynamic behavior of socioeconomic systems. Characteristic for the description of such systems is the occurrence of feedback loops together with stocks and flows. The mathematical equations that describe the system are usually nonlinear. Therefore seemingly simple systems can show a nonintuitive, nonpredictable behavior over time. Controlling a dynamical system means to define a desired final state in which the system should be, and to specify potential interventions from outside that should keep the system on the right track. The central question is how to compute such globally optimal control for a given SD model. We propose a branch-and-bound approach that is based on a bound propagation method, primal heuristics, and spatial branching. We apply our new SD-control method to a small System Dynamics model, that describes the evolution of a social-economic system over time. We examine the problem of steering this system on a sustainable consumption path. T3 - ZIB-Report - 13-23 KW - System Dynamics; Mixed-Integer Nonlinear Optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18148 UR - http://opus4.kobv.de/opus4-tuberlin/frontdoor/index/index/docId/4026 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - 制約整数計画ソルバ SCIP の並列化 T1 - Parallelizing the Constraint Integer Programming Solver SCIP N2 - 制約整数計画(CIP: Constraint Integer Programming)は,制約プログラミング(CP: Constraint Programming),混合整数計画(MIP: Mixed Integer Programming), 充足可能性問題(SAT: Satisfiability Problems)の研究分野におけるモデリング技術と解法を統合している.その結果,制約整数計画は,広いクラスの最適化問題を扱うことができる.SCIP (Solving Constraint Integer Programs)は,CIPを解くソルバとして実装され,Zuse Institute Berlin (ZIB)の研究者を中心として継続的に拡張が続けられている.本論文では,著者らによって開発されたSCIP に対する2種類の並列化拡張を紹介する. 一つは,複数計算ノード間で大規模に並列動作するParaSCIP である. もう一つは,複数コアと共有メモリを持つ1台の計算機上で(スレッド)並列で動作するFiberSCIP である. ParaSCIP は,HLRN IIスーパーコンピュータ上で, 一つのインスタンスを解くために最大7,168 コアを利用した動作実績がある.また,統計数理研究所のFujitsu PRIMERGY RX200S5上でも,最大512コアを利用した動作実績がある.統計数理研究所のFujitsu PRIMERGY RX200S5上 では,これまでに最適解が得られていなかったMIPLIB2010のインスタンスであるdg012142に最適解を与えた. N2 - The paradigm of Constraint Integer Programming (CIP) combines modeling and solving techniques from the fields of Constraint Programming (CP), Mixed Integer Programming (MIP) and Satisfiability Problems (SAT). The paradigm allows us to address a wide range of optimization problems. SCIP is an implementation of the idea of CIP and is now continuously extended by a group of researchers centered at Zuse Institute Berlin (ZIB). This paper introduces two parallel extensions of SCIP. One is ParaSCIP, which is intended to run on a large scale distributed memory computing environment, and the other is FiberSCIP, intended to run on shared memory computing environments. ParaSCIP has successfully been run on the HLRN II supercomputer utilizing up to 7,168 cores to solve a single difficult MIP. It has also been tested on an ISM supercomputer (Fujitsu PRIMERGY RX200S5 using up to 512 cores). The previously unsolved instance dg012142 from MIPLIB2010 was solved by using the ISM supercomputer. T2 - Parallelizing the Constraint Integer Programming Solver SCIP T3 - ZIB-Report - 13-22 KW - Mixed Integer Programming KW - Constraint Integer Programming KW - Parallel Computing KW - Distributed Memory Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18130 SN - 1438-0064 ER - TY - GEN A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle N2 - The performance of heuristic search algorithms depends crucially on the effectiveness of the heuristic. A pattern database (PDB) is a powerful heuristic in the form of a pre-computed lookup table. Larger PDBs provide better bounds and thus allow more cut-offs in the search process. Today, the largest PDB for the 24-puzzle is a 6-6-6-6 PDB with a size of 486 MB. We created 8-8-8, 9-8-7 and 9-9-6 PDBs that are three orders of magnitude larger (up to 1.4 TB) than the 6-6-6-6 PDB. We show how to compute such large PDBs and we present statistical and empirical data on their efficiency. The largest single PDB gives on average an 8-fold improvement over the 6-6-6-6 PDB. Combining several large PDBs gives on average an 12-fold improvement. T3 - ZIB-Report - 13-21 KW - heuristic search KW - pattern databases Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18095 SN - 1438-0064 ER - TY - GEN A1 - Wiebel, Alexander A1 - Preis, Philipp A1 - Vos, Frans M. A1 - Hege, Hans-Christian T1 - Computation and Application of 3D Strokes on Visible Structures in Direct Volume Rendering N2 - In this paper we describe VisiTrace, a novel technique to draw 3D lines in 3D volume rendered images. It allows to draw strokes in the 2D space of the screen to produce 3D lines that run on top or in the center of structures actually visible in the volume rendering. It can handle structures that only shortly occlude the structure that has been visible at the starting point of the stroke and is able to ignore such structures. For this purpose a shortest path algorithm finding the optimal curve in a specially designed graph data structure is employed. We demonstrate the usefulness of the technique by applying it to MRI data from medicine and engineering, and show how the method can be used to mark or analyze structures in the example data sets, and to automatically obtain good views toward the selected structures. T3 - ZIB-Report - 13-20 KW - DVR KW - interaction Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18070 SN - 1438-0064 ER - TY - GEN A1 - Raack, Christian A1 - Raymond, Annie A1 - Werner, Axel A1 - Schlechte, Thomas T1 - Integer Programming and Sports Rankings N2 - Sports rankings are obtained by applying a system of rules to evaluate the performance of the participants in a competition. We consider rankings that result from assigning an ordinal rank to each competitor according to their performance. We develop an integer programming model for rankings that allows us to calculate the number of points needed to guarantee a team the ith position, as well as the minimum number of points that could yield the ith place. The model is very general and can thus be applied to many types of sports. We discuss examples coming from football (soccer), ice hockey, and Formula~1. We answer various questions and debunk a few myths along the way. Are 40 points enough to avoid relegation in the Bundesliga? Do 95 points guarantee the participation of a team in the NHL playoffs? Moreover, in the season restructuration currently under consideration in the NHL, will it be easier or harder to access the playoffs? Is it possible to win the Formula~1 World Championship without winning at least one race or without even climbing once on the podium? Finally, we observe that the optimal solutions of the aforementioned model are associated to extreme situations which are unlikely to happen. Thus, to get closer to realistic scenarios, we enhance the model by adding some constraints inferred from the results of the previous years. T3 - ZIB-Report - 13-19 KW - sport ranking KW - integer programming Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18068 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros T1 - Undercover Branching N2 - In this paper, we present a new branching strategy for nonconvex MINLP that aims at driving the created subproblems towards linearity. It exploits the structure of a minimum cover of an MINLP, a smallest set of variables that, when fixed, render the remaining system linear: whenever possible, branching candidates in the cover are preferred. Unlike most branching strategies for MINLP, Undercover branching is not an extension of an existing MIP branching rule. It explicitly regards the nonlinearity of the problem while branching on integer variables with a fractional relaxation solution. Undercover branching can be naturally combined with any variable-based branching rule. We present computational results on a test set of general MINLPs from MINLPLib, using the new strategy in combination with reliability branching and pseudocost branching. The computational cost of Undercover branching itself proves negligible. While it turns out that it can influence the variable selection only on a smaller set of instances, for those that are affected, significant improvements in performance are achieved. T3 - ZIB-Report - 13-14 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18030 SN - 1438-0064 ER - TY - GEN A1 - Harrod, Steven A1 - Schlechte, Thomas T1 - A Direct Comparison of Physical Block Occupancy Versus Timed Block Occupancy in Train Timetabling Formulations N2 - Two fundamental mathematical formulations for railway timetabling are compared on a common set of sample problems, representing both multiple track high density services in Europe and single track bidirectional operations in North America. One formulation, ACP, enforces against conflicts by constraining time intervals between trains, while the other formulation, HGF, monitors physical occupation of controlled track segments. The results demonstrate that both ACP and HGF return comparable solutions in the aggregate, with some significant differences in select instances, and a pattern of significant differences in performance and constraint enforcement overall. T3 - ZIB-Report - 13-18 KW - Railway Scheduling KW - Train Timetabling KW - Track Allocation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17946 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo T1 - Measuring the impact of primal heuristics N2 - In modern MIP solvers, primal heuristics play a major role in finding and improving feasible solutions early in the solution process. However, classical performance measures such as time to optimality or number of branch-and-bound nodes reflect the impact of primal heuristics on the overall solving process badly. This article discusses the question of how to evaluate the effect of primal heuristics. Therefore, we introduce a new performance measure, the "primal integral" which depends on the quality of solutions found during the solving process as well as on the points in time when they are found. Our computational results reveal that heuristics improve the performance of MIP solvers in terms of the primal bound by around 80%. Further, we compare five state-of-the-art MIP solvers w.r.t. the newly proposed measure. T3 - ZIB-Report - 13-17 KW - mixed integer programming KW - primal heuristic KW - performance measure Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17887 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Witzig, Jakob T1 - Reoptimization in branch-and-bound algorithms with an application to elevator control N2 - We consider reoptimization (i.e. the solution of a problem based on information available from solving a similar problem) for branch-and-bound algorithms and propose a generic framework to construct a reoptimizing branch-and-bound algorithm. We apply this to an elevator scheduling algorithm solving similar subproblems to generate columns using branch-and-bound. Our results indicate that reoptimization techniques can substantially reduce the running times of the overall algorithm. T3 - ZIB-Report - 13-15 KW - reoptimization KW - branch-and-bound KW - column generation KW - elevator control Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17876 SN - 1438-0064 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Gollmer, Ralf A1 - Hayn, Christine A1 - Henrion, Rene A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Mirkov, Radoslava A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Willert, Bernhard T1 - Mathematical Optimization for Challenging Network Planning Problems in Unbundled Liberalized Gas Markets N2 - The recently imposed new gas market liberalization rules in Germany lead to a change of business of gas network operators. While previously network operator and gas vendor where united, they were forced to split up into independent companies. The network has to be open to any other gas trader at the same conditions, and free network capacities have to be identified and publicly offered in a non-discriminatory way. We show that these new paradigms lead to new and challenging mathematical optimization problems. In order to solve them and to provide meaningful results for practice, all aspects of the underlying problems, such as combinatorics, stochasticity, uncertainty, and nonlinearity, have to be addressed. With such special-tailored solvers, free network capacities and topological network extensions can, for instance, be determined. T3 - ZIB-Report - 13-13 KW - Gas Market Liberalization KW - Entry-Exit Model KW - Gas Network Access Regulation KW - Mixed-Integer Nonlinear Nonconvex Stochastic Optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17821 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the Minimal Rebinding Effect Included in a Given Kinetics N2 - The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory. T3 - ZIB-Report - 13-12 KW - Rebinding KW - Molecular Kinetics KW - Conformation Dynamics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17796 SN - 1438-0064 ER - TY - GEN A1 - Humpola, Jesco A1 - Fügenschuh, Armin T1 - A New Class of Valid Inequalities for Nonlinear Network Design Problems N2 - We consider a nonlinear nonconvex network design problem that arises in the extension of natural gas transmission networks. Given is such network with active and passive components, that is, valves, compressors, pressure regulators (active) and pipelines (passive), and a desired amount of flow at certain specified entry and exit nodes of the network. Besides flow conservation constraints in the nodes the flow must fulfill nonlinear nonconvex pressure loss constraints on the arcs subject to potential values (i.e., pressure levels) in both end nodes of each arc. Assume that there does not exist a feasible flow that fulfills all physical constraints and meets the desired entry and exit amounts. Then a natural question is where to extend the network by adding pipes in the most economic way such that this flow becomes feasible. Answering this question is computationally demanding because of the difficult problem structure. We use mixed-integer nonlinear programming techniques that rely on an outer approximation of the overall problem, and a branching on decision variables. We formulate a new class of valid inequalities (or cutting planes) which reduce the overall solution time when added to the formulation. We demonstrate the computational merits of our approach on test instances. T3 - ZIB-Report - 13-06 KW - Network Design KW - Mixed-Integer Nonlinear Programming KW - Cutting Planes Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17771 SN - 1438-0064 ER - TY - GEN A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Olany, Amiya A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - Modeling potassium balance in dairy cows N2 - Potassium is fundamental for cell functioning including signal transduction, acid-base- and water-metabolism. Since diet of dairy cows is generally rich in potassium, hypokalemia was not in the focus of research for long time. Furthermore, hypokalemia was not frequently diagnosed because blood potassium content is difficult to measure. In recent years, measurement methods have been improved. Nowadays hypokalemia is increasingly diagnosed in cows with disorders such as abomasal displacement, ketosis or down cow syndrome, calling for intensified research on this topic. In this report we describe the development of a basic mechanistic, dynamic model of potassium balance based on ordinary differential and algebraic equations. Parameter values are obtained from data of a clinical trial in which potassium balance and the influence of therapeutic intervention in glucose and electrolyte metabolism on potassium balance in non-lactating dairy cows were studied. The model is formulated at a high abstraction level and includes information and hypotheses from literature. This work represents a first step towards the understanding and design of effective prophylactic feed additives and treatment strategies. T3 - ZIB-Report - 13-09 KW - systems biology KW - differential equations KW - metabolism Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17749 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Vigerske, Stefan T1 - Analyzing the computational impact of MIQCP solver components N2 - We provide a computational study of the performance of a state-of-the-art solver for nonconvex mixed-integer quadratically constrained programs (MIQCPs). Since successful general-purpose solvers for large problem classes necessarily comprise a variety of algorithmic techniques, we focus especially on the impact of the individual solver components. The solver SCIP used for the experiments implements a branch-and-cut algorithm based on a linear relaxation to solve MIQCPs to global optimality. Our analysis is based on a set of 86 publicly available test instances. T3 - ZIB-Report - 13-08 KW - mixed-integer quadratically constrained programming KW - mixed-integer programming KW - branch-and-cut KW - nonconvex KW - global optimization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17754 SN - 1438-0064 ER - TY - GEN A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions N2 - We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar. The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage. The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer. The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network". T3 - ZIB-Report - 13-07 KW - HCI KW - Cultural Heritage KW - Kiosk application KW - iPad Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17731 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald T1 - Improving strong branching by propagation N2 - Strong branching is an important component of most variable selection rules in branch-and-bound based mixed-integer linear programming solvers. It predicts the dual bounds of potential child nodes by solving auxiliary LPs and thereby helps to keep the branch-and-bound tree small. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Computational experiments on standard MIP instances indicate that this is beneficial in three aspects: It helps to reduce the average number of LP iterations per strong branching call, the number of branch-and-bound nodes, and the overall solving time. T3 - ZIB-Report - 12-46 KW - mixed-integer programming KW - branch-and-bound KW - branching rule KW - strong branching KW - domain propagation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17701 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Ku, Wen-Yang A1 - Beck, J. Christopher T1 - Recent improvements using constraint integer programming for resource allocation and scheduling N2 - Recently, we compared the performance of mixed-integer programming (MIP), constraint programming (CP), and constraint integer programming (CIP) to a state-of-the-art logic-based Benders manual decomposition (LBBD) for a resource allocation/scheduling problem. For a simple linear relaxation, the LBBD and CIP models deliver comparable performance with MIP also performing well. Here we show that algorithmic developments in CIP plus the use of an existing tighter relaxation substantially improve one of the CIP approaches. Furthermore, the use of the same relaxation in LBBD and MIP models significantly improves their performance. While such a result is known for LBBD, to the best of our knowledge, the other results are novel. Our experiments show that both CIP and MIP approaches are competitive with LBBD in terms of the number of problems solved to proven optimality, though MIP is about three times slower on average. Further, unlike the LBBD and CIP approaches, the MIP model is able to obtain provably high-quality solutions for all problem instances. T3 - ZIB-Report - 13-05 KW - constraint integer programming KW - constraint programming KW - cumulative constraint KW - mixed integer programming KW - optional activities Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17676 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Weltge, Stefan T1 - Learning and Propagating Lagrangian Variable Bounds for Mixed-Integer Nonlinear Programming N2 - Optimization-based bound tightening (OBBT) is a domain reduction technique commonly used in nonconvex mixed-integer nonlinear programming that solves a sequence of auxiliary linear programs. Each variable is minimized and maximized to obtain the tightest bounds valid for a global linear relaxation. This paper shows how the dual solutions of the auxiliary linear programs can be used to learn what we call Lagrangian variable bound constraints. These are linear inequalities that explain OBBT's domain reductions in terms of the bounds on other variables and the objective value of the incumbent solution. Within a spatial branch-and-bound algorithm, they can be learnt a priori (during OBBT at the root node) and propagated within the search tree at very low computational cost. Experiments with an implementation inside the MINLP solver SCIP show that this reduces the number of branch-and-bound nodes and speeds up solution times. T3 - ZIB-Report - 13-04 KW - MINLP KW - optimization-based bound tightening KW - optimality-based bound tightening KW - OBBT KW - propagation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17631 SN - 1438-0064 ER - TY - GEN A1 - Ballerstein, Martin A1 - Michaels, Dennis A1 - Vigerske, Stefan T1 - Linear Underestimators for bivariate functions with a fixed convexity behavior N2 - This is a technical report for the SCIP constraint handler cons_bivariate. We describe a cut-generation algorithm for a class of bivariate twice continuously differentiable functions with fixed convexity behavior over a box. Computational results comparing our cut-generation algorithms with state-of-the-art global optimization software on a series of randomly generated test instances are reported and discussed. T3 - ZIB-Report - 13-02 KW - bivariate functions KW - convex envelope KW - global optimization KW - linear underestimator Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17641 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Hendel, Gregor T1 - Shift-And-Propagate N2 - For mixed integer programming, recent years have seen a growing interest in the design of general purpose primal heuristics for use inside complete solvers. Many of these heuristics rely on an optimal LP solution. Finding this may itself take a significant amount of time. The presented paper addresses this issue by the introduction of the Shift-And-Propagate heuristic. Shift-And-Propagate is a pre-root primal heuristic that does not require a previously found LP solution. It applies domain propagation techniques to quickly drive a variable assignment towards feasibility. Computational experiments indicate that this heuristic is a powerful supplement of existing rounding and propagation heuristics. T3 - ZIB-Report - 13-03 KW - primal heuristic KW - mixed integer programming KW - domain propagation KW - rounding Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17596 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume T1 - On the semidefinite representations of real functions applied to symmetric matrices N2 - We present a new semidefinite representation for the trace of a real function f applied to symmetric matrices, when a semidefinite representation of the convex function f is known. Our construction is intuitive, and yields a representation that is more compact than the previously known one. We also show with the help of matrix geometric means and the Riemannian metric of the set of positive definite matrices that for a rational number p in the interval (0,1], the matrix X raised to the exponent p is the largest element of a set represented by linear matrix inequalities. We give numerical results for a problem inspired from the theory of experimental designs, which show that the new semidefinite programming formulation yields a speed-up factor in the order of 10. T3 - ZIB-Report - 12-50 KW - semidefinite representability KW - optimal experimental designs KW - SDP KW - matrix geometric mean Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17511 SN - 1438-0064 VL - 439 SP - 2829 EP - 2843 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Buwaya, Julia A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - Optimizing Toll Enforcement in Transportation Networks: a Game-Theoretic Approach N2 - We present a game-theoretic approach to optimize the strategies of toll enforcement on a motorway network. In contrast to previous approaches, we consider a network with an arbitrary topology, and we handle the fact that users may choose their Origin-Destination path; in particular they may take a detour to avoid sections with a high control rate. We show that a Nash equilibrium can be computed with an LP (although the game is not zero-sum), and we give a MIP for the computation of a Stackelberg equilibrium. Experimental results based on an application to the enforcement of a truck toll on German motorways are presented. T3 - ZIB-Report - 12-47 KW - Stackelberg Equilibrium KW - Game Theory KW - Mixed Integer Programming Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17401 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume T1 - Picos Documentation. Release 0.1.1. N2 - PICOS is a user friendly interface to several conic and integer programming solvers, very much like YALMIP under MATLAB. The main motivation for PICOS is to have the possibility to enter an optimization problem as a high level model, and to be able to solve it with several different solvers. Multidimensional and matrix variables are handled in a natural fashion, which makes it painless to formulate a SDP or a SOCP. This is very useful for educational purposes, and to quickly implement some models and test their validity on simple examples. Furthermore, with PICOS you can take advantage of the python programming language to read and write data, construct a list of constraints by using python list comprehensions, take slices of multidimensional variables, etc. T3 - ZIB-Report - 12-48 KW - mathematical programming KW - SDP KW - SOCP KW - python Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17396 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Salvagnin, Domenico T1 - Cloud branching N2 - Branch-and-bound methods for mixed-integer programming (MIP) are traditionally based on solving a linear programming (LP) relaxation and branching on a variable which takes a fractional value in the (single) computed relaxation optimum. In this paper we study branching strategies for mixed-integer programs that exploit the knowledge of multiple alternative optimal solutions (a cloud) of the current LP relaxation. These strategies naturally extend state-of-the-art methods like strong branching, pseudocost branching, and their hybrids. We show that by exploiting dual degeneracy, and thus multiple alternative optimal solutions, it is possible to enhance traditional methods. We present preliminary computational results, applying the newly proposed strategy to full strong branching, which is known to be the MIP branching rule leading to the fewest number of search nodes. It turns out that cloud branching can reduce the mean running time by up to 30% on standard test sets. T3 - ZIB-Report - 13-01 KW - mixed integer programming KW - branching rule KW - search strategy KW - dual degeneracy Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17301 SN - 1438-0064 ER - TY - GEN A1 - Cook, William A1 - Koch, Thorsten A1 - Steffy, Daniel A1 - Wolter, Kati T1 - A Hybrid Branch-and-Bound Approach for Exact Rational Mixed-Integer Programming N2 - We present an exact rational solver for mixed-integer linear programming that avoids the numerical inaccuracies inherent in the floating-point computations used by existing software. This allows the solver to be used for establishing theoretical results and in applications where correct solutions are critical due to legal and financial consequences. Our solver is a hybrid symbolic/numeric implementation of LP-based branch-and-bound, using numerically-safe methods for all binding computations in the search tree. Computing provably accurate solutions by dynamically choosing the fastest of several safe dual bounding methods depending on the structure of the instance, our exact solver is only moderately slower than an inexact floating-point branch-and-bound solver. The software is incorporated into the SCIP optimization framework, using the exact LP solver QSopt_ex and the GMP arithmetic library. Computational results are presented for a suite of test instances taken from the MIPLIB and Mittelmann libraries and for a new collection of numerically difficult instances. T3 - ZIB-Report - 12-49 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17171 SN - 1438-0064 ER - TY - GEN A1 - Betker, Andreas A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Pfeuffer, Frank A1 - Raack, Christian A1 - Werner, Axel T1 - Energy efficiency in extensive multilayer core and regional networks with protection N2 - Energy-efficient operation of large telecommunication networks is an important issue today and in the near future. Given that the energy consumption rises with the ever increasing demand for capacity and network speed, there is a growing interest in strategies for a sustainable network management. It is a well-known fact that traffic demands vary significantly over time, most notably in day/night- and in weekly cycles. This provides the main potential for energy-saving strategies. We study the question of how much power is necessary to operate a network with state-of-the-art hardware during peak or low-traffic times. The study respects realistic side constraints, such as protection requirements and routing schemes, and takes the special structure of an extensive nation-wide optical network, including backbone and regional sections, into account. We formulate mixed integer programming models for the corresponding optimization problems using predictions for traffic matrices, as well as state-of-the-art hardware and power models. We address questions as the following: How much energy is spent in the core and in metro regions of the network and how big are the savings in low-demand scenarios if we always assume the system power-minimum in these situations? What is the influence of different hardware on the overall energy consumption? How much do different routing schemes or protection scenarios restrict potential energy savings? T3 - ZIB-Report - 12-45 KW - telecommunications KW - network design KW - routing KW - energy efficiency Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17154 SN - 1438-0064 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Hayn, Christine A1 - Michaels, Dennis T1 - Mixed-Integer Linear Methods for Layout-Optimization of Screening Systems in Recovered Paper Production N2 - The industrial treatment of waste paper in order to regain valuable fibers from which recovered paper can be produced, involves several steps of preparation. One important step is the separation of stickies that are normally attached to the paper. If not properly separated, remaining stickies reduce the quality of the recovered paper or even disrupt the production process. For the mechanical separation process of fibers from stickies a separator screen is used. This machine has one input feed and two output streams, called the accept and the reject. In the accept the fibers are concentrated, whereas the reject has a higher concentration of stickies. The machine can be controlled by setting its reject rate. But even when the reject rate is set properly, after just a single screening step, the accept still has too many stickies, or the reject too many fibers. To get a proper separation, several separators have to be assembled into a network. From a mathematical point of view this problem can be seen as a multi-commodity network flow design problem with a nonlinear, controllable distribution function at each node. We present a nonlinear mixed-integer programming model for the simultaneous selection of a subset of separators, the network's topology, and the optimal setting of each separator. Numerical results are obtained via different types of linearization of the nonlinearities and the use of mixed-integer linear solvers, and compared with state-of-the-art global optimization software. T3 - ZIB-Report - 12-44 KW - Mixed-Integer Linear Programming KW - Nonlinear Programming KW - Piecewise Linear Approximation KW - Topology Optimization KW - Network Design Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16862 SN - 1438-0064 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric intensity models for accurate simulation of X-ray images N2 - We present an efficient GPU-based method to generate virtual X-ray images from tetrahedral meshes which are associated with attenuation values. In addition, a novel approach is proposed that performs the model deformation on the GPU. The tetrahedral grids are derived from volumetric statistical shape and intensity models (SSIMs) and describe anatomical structures. Our research targets at reconstructing 3D anatomical shapes by comparing virtual X-ray images generated using our novel approach with clinical data while varying the shape and density of the SSIM in an optimization process. We assume that a deformed SSIM adequately represents an anatomy of interest when the similarity between the virtual and the clinical X-ray image is maximized. The OpenGL implementation presented here generates accurate (virtual) X-ray images at interactive rates, thus qualifying it for its use in the reconstruction process. T3 - ZIB-Report - 12-40 KW - Digitally Reconstructed Radiograph (DRR), Anatomy Reconstruction, Statistical Shape and Intensity Model (SSIM), GPU acceleration Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16580 SN - 1438-0064 ER - TY - GEN A1 - Pfetsch, Marc A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Geißler, Nina A1 - Gollmer, Ralf A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Vigerske, Stefan A1 - Willert, Bernhard T1 - Validation of Nominations in Gas Network Optimization: Models, Methods, and Solutions N2 - In this article we investigate methods to solve a fundamental task in gas transportation, namely the validation of nomination problem: Given a gas transmission network consisting of passive pipelines and active, controllable elements and given an amount of gas at every entry and exit point of the network, find operational settings for all active elements such that there exists a network state meeting all physical, technical, and legal constraints. We describe a two-stage approach to solve the resulting complex and numerically difficult mixed-integer non-convex nonlinear feasibility problem. The first phase consists of four distinct algorithms facilitating mixed-integer linear, mixed-integer nonlinear, reduced nonlinear, and complementarity constrained methods to compute possible settings for the discrete decisions. The second phase employs a precise continuous nonlinear programming model of the gas network. Using this setup, we are able to compute high quality solutions to real-world industrial instances whose size is significantly larger than networks that have appeared in the literature previously. T3 - ZIB-Report - 12-41 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16531 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - An Exact Reoptimization Algorithm for the Scheduling of Elevator Groups N2 - The task of an elevator control is to schedule the elevators of a group such that small waiting and travel times for the passengers are obtained. We present an exact reoptimization algorithm for this problem. A reoptimization algorithm computes a new schedule for the elevator group each time a new passenger arrives. Our algorithm uses column generation techniques and is, to the best of our knowledge, the first exact reoptimization algorithms for a group of passenger elevators. To solve the column generation problem, we propose a Branch & Bound method. T3 - ZIB-Report - 12-43 KW - elevator control, online optimization, reoptimization algorithms, column generation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16485 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Stochastic dominance analysis of Online Bin Coloring algorithms N2 - This paper proposes a new method for probabilistic analysis of online algorithms. It is based on the notion of stochastic dominance. We develop the method for the online bin coloring problem introduced by Krumke et al (2008). Using methods for the stochastic comparison of Markov chains we establish the result that the performance of the online algorithm GreedyFit is stochastically better than the performance of the algorithm OneBin for any number of items processed. This result gives a more realistic picture than competitive analysis and explains the behavior observed in simulations. T3 - ZIB-Report - 12-42 KW - online algorithms, stochastic dominance, algorithm analysis, Markov chains Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16502 SN - 1438-0064 ER - TY - GEN A1 - Reuther, Markus A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - Integrated Optimization of Rolling Stock Rotations for Intercity Railways N2 - This paper provides a highly integrated solution approach for rolling stock planning problems in the context of intercity passenger traffic. The main contributions are a generic hypergraph based mixed integer programming model and an integrated algorithm for the considered rolling stock rotation planning problem. The new developed approach is able to handle a very large set of industrial railway requirements, such as vehicle composition, maintenance constraints, infrastructure capacity, and regularity aspects. By the integration of this large bundle of technical railway aspects, we show that our approach has the power to produce implementable rolling stock rotations for our industrial cooperation partner DB Fernverkehr. This is the first time that the rolling stock rotations at DB Fernverkehr could be optimized by an automated system utilizing advanced mathematical programming techniques. T3 - ZIB-Report - 12-39 KW - Mixed Integer Programming KW - Railway Optimization KW - Rolling Stock Rostering Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16424 SN - 1438-0064 ER - TY - GEN A1 - Schlechte, Thomas T1 - Railway Track Allocation N2 - This article gives an overview of the results of the author's PhD thesis. The thesis deals with the mathematical optimization for the efficient use of railway infrastructure. We address the optimal allocation of the available railway track capacity - the track allocation problem. This track allocation problem is a major challenge for a railway company, independent of whether a free market, a private monopoly, or a public monopoly is given. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense sizes of the problem instances. Mathematical models and optimization techniques can result in huge gains for both railway customers and operators, e.g., in terms of cost reductions or service quality improvements. We tackle this challenge by developing novel mathematical models and associated innovative algorithmic solution methods for large scale instances. We made considerable progress on solving track allocation problems by two main features - a novel modeling approach for the macroscopic track allocation problem and algorithmic improvements based on the utilization of the bundle method. This allows us to produce for the first time reliable solutions for a real world instance, i.e., the Simplon corridor in Switzerland. T3 - ZIB-Report - 12-38 KW - large-scale integer programming KW - network aggregation KW - configuration models KW - rapid branching Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16402 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros T1 - Factorization and update of a reduced basis matrix for the revised simplex method N2 - In this paper, we describe a method to enhance the FTRAN and BTRAN operations in the revised simplex algorithm by using a reduced basis matrix defined by basic columns and nonbasic rows. This submatrix of the standard basis matrix is potentially much smaller, but may change its dimension dynamically from iteration to iteration. For the classical product form update ("eta update"), the idea has been noted already by Zoutendijk, but only preliminarily tested by Powell in the early 1970s. We extend these ideas to Forrest-Tomlin type update formulas for an LU factorization of the reduced basis matrix, which are suited for efficient implementation within a state-of-the-art simplex solver. The computational advantages of the proposed method apply to pure LP solving as well as to LP-based branch-and-cut algorithms. It can easily be integrated into existing simplex codes. T3 - ZIB-Report - 12-36 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16349 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Schulz, Jens A1 - Beck, J. Christopher T1 - Using dual presolving reductions to reformulate cumulative constraints N2 - Dual presolving reductions are a class of reformulation techniques that remove feasible or even optimal solutions while guaranteeing that at least one optimal solution remains, as long as the original problem was feasible. Presolving and dual reductions are important components of state-of-the-art mixed-integer linear programming solvers. In this paper, we introduce them both as unified, practical concepts in constraint programming solvers. Building on the existing idea of variable locks, we formally define and justify the use of dual information for cumulative constraints during a presolving phase of a solver. In particular, variable locks are used to decompose cumulative constraints, detect irrelevant variables, and infer variable assignments and domain reductions. Since the computational complexity of propagation algorithms typically depends on the number of variables and/or domain size, such dual reductions are a source of potential computational speed-up. Through experimental evidence on resource constrained project scheduling problems, we demonstrate that the conditions for dual reductions are present in well-known benchmark instances and that a substantial proportion of them can be solved to optimality in presolving -- without search. While we consider this result very promising, we do not observe significant change in overall run-time from the use of our novel dual reductions. T3 - ZIB-Report - 12-37 KW - dual reductions KW - cumulative constraints KW - presolving KW - variable locks Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16321 SN - 1438-0064 ER - TY - GEN A1 - Anco, Stephen A1 - Mohiuddin, Mohammad A1 - Wolf, Thomas T1 - Travelling waves and conservation laws for complex mKdV-type equations N2 - Travelling waves and conservation laws are studied for a wide class of $U(1)$-invariant complex mKdV equations containing the two known integrable generalizations of the ordinary (real) mKdV equation. The main results on travelling waves include deriving new complex solitary waves and kinks that generalize the well-known mKdV $\sech$ and $\tanh$ solutions. The main results on conservation laws consist of explicitly finding all 1st order conserved densities that yield phase-invariant counterparts of the well-known mKdV conserved densities for momentum, energy, and Galilean energy, and a new conserved density describing the angular twist of complex kink solutions. T3 - ZIB-Report - 12-34 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16124 SN - 1438-0064 ER - TY - GEN A1 - Anco, Stephen A1 - MacNaughton, Steven A. A1 - Wolf, Thomas T1 - Conservation laws and symmetries of quasilinear radial wave equations in multi-dimensions N2 - Symmetries and conservation laws are studied for two classes of physically and analytically interesting radial wave equations with power nonlinearities in multi-dimensions. The results consist of two main classifications: all symmetries of point type and all conservation laws of a general energy-momentum type are explicitly determined, including those such as dilations, inversions, similarity energies and conformal energies that exist only for special powers or dimensions. In particular, all variational cases (when a Lagrangian formulation exists) and non-variational cases (when no Lagrangian exists) for these wave equations are considered. As main results, the classification yields generalized energies and radial momenta in certain non-variational cases, which are shown to arise from a new type of Morawetz dilation identity that produces conservation laws for each of the two classes of wave equations in a different way than Noether's theorem. T3 - ZIB-Report - 12-33 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16111 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas A1 - Schrüfer, Eberhard A1 - Webster, Kenneth T1 - Solving large linear algebraic systems in the context of integrable non-abelian Laurent ODEs N2 - The paper reports on a computer algebra program {\sc LSSS} (Linear Selective Systems Solver) for solving linear algebraic systems with rational coefficients. The program is especially efficient for very large sparse systems that have a solution in which many variables take the value zero. The program is applied to the symmetry investigation of a non-abelian Laurent ODE introduced recently by M.\ Kontsevich. The computed symmetries confirmed that a Lax pair found for this system earlier generates all first integrals of degree at least up to 14. T3 - ZIB-Report - 12-32 KW - linear algebraic systems, integrability, Lax pairs, noncommutative ODE, Laurent ODE Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16102 SN - 1438-0064 ER - TY - GEN A1 - Odesskii, Alexander A1 - Wolf, Thomas T1 - Compatible quadratic Poisson brackets related to a family of elliptic curves N2 - We construct nine pairwise compatible quadratic Poisson structures such that a generic linear combination of them is associated with an elliptic algebra in $n$ generators. Explicit formulas for Casimir elements of this elliptic Poisson structure are obtained. T3 - ZIB-Report - 12-31 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16097 SN - 1438-0064 ER - TY - GEN A1 - Euler, Marianna A1 - Euler, Norbert A1 - Wolf, Thomas T1 - The Two-Component Camassa-Holm Equations CH(2,1) and CH(2,2): First-Order Integrating Factors and Conservation Laws N2 - Recently, Holm and Ivanov, proposed and studied a class of multi-component generalisations of the Camassa-Holm equations [D D Holm and R I Ivanov, Multi-component generalizations of the CH equation: geometrical aspects, peakons and numerical examples, {\it J. Phys A: Math. Theor} {\bf 43}, 492001 (20pp), 2010]. We consider two of those systems, denoted by Holm and Ivanov by CH(2,1) and CH(2,2), and report a class of integrating factors and its corresponding conservation laws for these two systems. In particular, we obtain the complete sent of first-order integrating factors for the systems in Cauchy-Kovalevskaya form and evaluate the corresponding sets of conservation laws for CH(2,1) and CH(2,2). T3 - ZIB-Report - 12-30 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16087 SN - 1438-0064 ER - TY - GEN A1 - Tunga, Burcu A1 - Weber, Marcus T1 - Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration N2 - This work aims to develop a new algorithm to calculate the free energy of water molecules by using a deterministic way. For this purpose, we assume a closed system confined to a physical volume, having water molecules in gas phase. To calculate the free energy of this sytem we utilized Mayer cluster expansion and the fluctuation free integration method. T3 - ZIB-Report - 12-35 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16031 SN - 1438-0064 ER - TY - GEN T1 - Jahresbericht 2011 T1 - Annual 2011 T3 - Jahresbericht - 2011 KW - Annual Report Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15867 SN - 0934-5892 VL - 2011 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika ED - Delling, Daniel ED - Liberti, Leo T1 - A Direct Connection Approach to Integrated Line Planning and Passenger Routing T2 - ATMOS 2012 - 12th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems N2 - The treatment of transfers is a major challenge in line planning. Existing models either route passengers and lines sequentially, and hence disregard essential degrees of freedom, or they are of extremely large scale, and seem to be computationally intractable. We propose a novel direct connection approach that allows an integrated optimization of line and passenger routing, including accurate estimates of the number of direct travelers, for large-scale real-world instances. T3 - ZIB-Report - 12-29 KW - combinatorial optimization KW - integer programming KW - line planning KW - transfers Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15812 SN - 1438-0064 VL - 25 SP - 47 EP - 57 PB - Schloss Dagstuhl - Leibniz-Zentrum für Informatik ER - TY - GEN A1 - Scheumann, Rene A1 - Fügenschuh, Armin A1 - Schenker, Sebastian A1 - Vierhaus, Ingmar A1 - Borndörfer, Ralf A1 - Finkbeiner, Matthias T1 - Global Manufacturing: How to Use Mathematical Optimisation Methods to Transform to Sustainable Value Creation N2 - It is clear that a transformation to sustainable value creation is needed, because business as usual is not an option for preserving competitive advantages of leading industries. What does that mean? This contribution proposes possible approaches for a shift in existing manufacturing paradigms. In a first step, sustainability aspects from the German Sustainability Strategy and from the tools of life cycle sustainability assessment are chosen to match areas of a value creation process. Within these aspects are indicators, which can be measured within a manufacturing process. Once these data are obtained they can be used to set up a mathematical linear pulse model of manufacturing in order to analyse the evolution of the system over time, that is the transition process, by using a system dynamics approach. An increase of technology development by a factor of 2 leads to an increase of manufacturing but also to an increase of climate change. Compensation measures need to be taken. This can be done by e.g. taking money from the GDP (as an indicator of the aspect ``macroeconomic performance''). The value of the arc from that building block towards climate change must then be increased by a factor of 10. The choice of independent and representative indicators or aspects shall be validated and double-checked for their significance with the help of multi-criteria mixed-integer programming optimisation methods. T3 - ZIB-Report - 12-28 KW - Multi-Criteria Optimisation KW - Sustainability Indicator KW - System Dynamics KW - Value Creation Process Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15703 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - Solving mixed integer linear and nonlinear problems using the SCIP Optimization Suite N2 - This paper introduces the SCIP Optimization Suite and discusses the capabilities of its three components: the modeling language Zimpl, the linear programming solver SoPlex, and the constraint integer programming framework SCIP. We explain how these can be used in concert to model and solve challenging mixed integer linear and nonlinear optimization problems. SCIP is currently one of the fastest non-commercial MIP and MINLP solvers. We demonstrate the usage of Zimpl, SCIP, and SoPlex by selected examples, we give an overview of available interfaces, and outline plans for future development. T3 - ZIB-Report - 12-27 KW - LP, MIP, CIP, MINLP, modeling, optimization, SCIP, SoPlex, Zimpl Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15654 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - SCIP Optimization Suite を利用した 混合整数(線形/非線形) 計画問題の解法 T1 - Solving mixed integer linear and nonlinear problems using the SCIP Optimization Suite N2 - この論文ではソフトウェア・パッケージSCIP Optimization Suite を紹介し,その3つの構成要素:モデリン グ言語Zimpl, 線形計画(LP: linear programming) ソルバSoPlex, そして,制約整数計画(CIP: constraint integer programming) に対するソフトウェア・フレームワークSCIP, について述べる.本論文では,この3つの 構成要素を利用して,どのようにして挑戦的な混合整数線形計画問題(MIP: mixed integer linear optimization problems) や混合整数非線形計画問題(MINLP: mixed integer nonlinear optimization problems) をモデル化 し解くのかを説明する.SCIP は,現在,最も高速なMIP,MINLP ソルバの1つである.いくつかの例により, Zimpl, SCIP, SoPlex の利用方法を示すとともに,利用可能なインタフェースの概要を示す.最後に,将来の開 発計画の概要について述べる. N2 - This paper introduces the SCIP Optimization Suite and discusses the capabilities of its three components: the modeling language Zimpl, the linear programming solver SoPlex, and the constraint integer programming framework SCIP. We explain how in concert these can be used to model and solve challenging mixed integer linear and nonlinear optimization problems. SCIP is currently one of the fastest non-commercial MIP and MINLP solvers. We demonstrate the usage of Zimpl, SCIP, and SoPlex by selected examples, we give an overview over available interfaces, and outline plans for future development. T3 - ZIB-Report - 12-24 KW - SCIP, MIP, MINLP, CIP, LP, modeling, optimization Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15598 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Held, Harald A1 - Huang, Wei A1 - Vigerske, Stefan T1 - Towards globally optimal operation of water supply networks N2 - This paper is concerned with optimal operation of pressurized water supply networks at a fixed point in time. We use a mixed-integer nonlinear programming (MINLP) model incorporating both the nonlinear physical laws and the discrete decisions such as switching pumps on and off. We demonstrate that for instances from our industry partner, these stationary models can be solved to ε-global optimality within small running times using problem-specific presolving and state-of-the-art MINLP algorithms. In our modeling, we emphasize the importance of distinguishing between what we call real and imaginary flow, i.e., taking into account that the law of Darcy-Weisbach correlates pressure difference and flow along a pipe if and only if water is available at the high pressure end of a pipe. Our modeling solution extends to the dynamic operative planning problem. T3 - ZIB-Report - 12-25 KW - MINLP, global optimization, operative planning, water supply networks Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15603 SN - 1438-0064 ER - TY - GEN A1 - Bondouy, Manon A1 - Röblitz, Susanna T1 - Mathematical modeling of follicular development in bovine estrous cycles N2 - Normal follicular growth is a prerequisite for successful fertilization of dairy cows. However, submission rates have been decreasing during the last decades because animals are not ovulating at the planned time of mating or insemination. In this study we use a mathematical model to investigate mechanisms that lead to anestrus. This model is derived by coupling two previously published models: a small model for the development of multiple follicles (Smith et al., 2004), and a large estrous cycle model (St\"otzel et al., 2012). We first investigate the influence of synchronization protocols on the time-shift of ovulation. In a second scenario we simulate an extended period of anestrus as it typically occurs after calving. T3 - ZIB-Report - 12-26 KW - ordinary differential equations KW - systems biology KW - reproduction KW - dairy cows Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15585 SN - 1438-0064 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - A Novel Hybrid Approach to Automatically Determine Kernel Interface Data Volumes N2 - Scheduling algorithms for heterogeneous platforms make scheduling decisions based on several metrics. One of these metrics is the amount of data to be transferred from and to the accelerator. However, the automated determination of this metric is not a simple task. A few schedulers and runtime systems solve this problem by using regression models, which are imprecise though. Our novel approach for the determination of data volumes removes this limitation and thus provides a solution to obtain exact information. T3 - ZIB-Report - 12-23 KW - function parameter analysis KW - function parameter sizes KW - heterogeneous systems KW - scheduling metrics KW - tool flow Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15569 SN - 1438-0064 ER - TY - GEN A1 - Golas, Ulrike T1 - A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version N2 - Attributes are an important concept for modeling data in practical applications. Up to now there is no adequate way to define attributes for different kinds of models used in M-adhesive transformation systems, which are a special kind of graph transformation systems based on M-adhesive categories. Especially a proper representation and definition of attributes and their values as well as a suitable handling of the data does not fit well with other graph transformation formalisms. In this paper, we propose a new method to define attributes in a natural, but still formally precise and widely applicable way. We define a new kind of adhesive category, called W-adhesive, that can be used for transformations of attributes, while the underlying models are still M-adhesive ones. As a result, attributed models can be used as they are intended to be, but with a formal background and proven well-behavior. T3 - ZIB-Report - 12-22 KW - graph transformation KW - attribution KW - adhesive categories Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15547 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - A Case Study on Optimizing Toll Enforcements on Motorways N2 - In this paper we present the problem of computing optimal tours of toll inspectors on German motorways. This problem is a special type of vehicle routing problem and builds up an integrated model, consisting of a tour planning and a duty rostering part. The tours should guarantee a network-wide control whose intensity is proportional to given spatial and time dependent traffic distributions. We model this using a space-time network and formulate the associated optimization problem by an integer program (IP). Since sequential approaches fail, we integrated the assignment of crews to the tours in our model. In this process all duties of a crew member must fit in a feasible roster. It is modeled as a Multi-Commodity Flow Problem in a directed acyclic graph, where specific paths correspond to feasible rosters for one month. We present computational results in a case-study on a German subnetwork which documents the practicability of our approach. T3 - ZIB-Report - 12-21 KW - Vehicle Routing Problem KW - Duty Rostering KW - Integer Programming KW - Operations Research Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15498 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Improving the Accuracy of Linear Programming Solvers with Iterative Refinement N2 - We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the objective function, right-hand side, and variable bounds. Exact computation is used to compute and store the exact representation of the transformed problems, while numeric computation is used for solving LPs. At all steps of the algorithm the LP bases encountered in the transformed problems correspond directly to LP bases in the original problem description. We demonstrate that this algorithm is effective in practice for computing extended precision solutions and that this leads to direct improvement of the best known methods for solving LPs exactly over the rational numbers. T3 - ZIB-Report - 12-19 KW - Linear programming KW - Iterative refinement KW - Exact linear programming Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15451 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo T1 - RENS – the optimal rounding N2 - This article introduces RENS, the relaxation enforced neighborhood search, a large neighborhood search algorithm for mixed integer nonlinear programming (MINLP) that uses a sub-MINLP to explore the set of feasible roundings of an optimal solution x' of a linear or nonlinear relaxation. The sub-MINLP is constructed by fixing integer variables x_j with x'_j in Z and bounding the remaining integer variables to x_j in {floor(x'_j), ceil(x'_j)}. We describe two different applications of RENS: as a standalone algorithm to compute an optimal rounding of the given starting solution and as a primal heuristic inside a complete MINLP solver. We use the former to compare different kinds of relaxations and the impact of cutting planes on the roundability of the corresponding optimal solutions. We further utilize RENS to analyze the performance of three rounding heuristics implemented in the branch-cut-and-price framework SCIP. Finally, we study the impact of RENS when it is applied as a primal heuristic inside SCIP. All experiments were performed on three publically available test sets of mixed integer linear programs (MIPs), mixed integer quadratically constrained programs (MIQCPs), and MINLPs, using solely software which is available in source code. It turns out that for these problem classes 60% to 70% of the instances have roundable relaxation optima and that the success rate of RENS does not depend on the percentage of fractional variables. Last but not least, RENS applied as primal heuristic complements nicely with existing root node heuristics in SCIP and improves the overall performance. T3 - ZIB-Report - 12-17 KW - Primal Heuristic KW - Mixed-Integer Nonlinear Programming KW - Large Neighborhood Search KW - Mixed-Integer Quadratically Constrained Programming KW - Mixed-Intger Programming Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15203 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Maierhofer, Christiane A1 - Richter, Regina T1 - Data Enhancement for Active Thermography N2 - Pulse thermography is a non-destructive testing method based on infrared imaging of transient thermal patterns. Heating the surface of the structure under test for a short period of time generates a non-stationary temperature distribution and thus a thermal contrast between the defect and the sound material. Due to measurement noise, preprocessing of the experimental data is necessary, before reconstruction algorithms can be applied. We propose a decomposition of the measured temperature into Green's function solutions to eliminate noise. T3 - ZIB-Report - 12-20 KW - data enhancement KW - active thermography KW - quantitative reconstruction KW - Green's functions Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15243 UR - http://qirt.gel.ulaval.ca/archives/qirt2012/papers/QIRT-2012-167.pdf SN - 1438-0064 ER - TY - GEN A1 - Klapproth, Corinna T1 - The Contact-Stabilized Newmark Method - Consistency Error of a Spatiotemporal Discretization N2 - The paper considers an improved variant of the contact-stabilized Newmark method by Deuflhard et al., which provides a spatiotemporal numerical integration of dynamical contact problems between viscoelastic bodies in the frame of the Signorini condition. Up no now, the question of consistency in the case of contact constraints has been discussed for time integrators in function space under the assumption of bounded total variation of the solution. Here, interest focusses on the consistency error of the Newmark scheme in physical energy norm after discretization both in time and in space. The resulting estimate for the local discretization error allows to prove global convergence of the Newmark scheme under an additional assumption on the active contact boundaries. T3 - ZIB-Report - 12-18 KW - dynamical contact problems, contact-stabilized Newmark method, consistency error Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15198 SN - 1438-0064 ER - TY - GEN A1 - Szabó, Jácint T1 - The set of solutions to nomination validation in passive gas transportation networks with a generalized flow formula N2 - In this paper we give an analytical description on the structure of solutions to the gas nomination validation problem in gas transportation networks. These networks are assumed to contain no active devices, only certain hypothetical pipelines, where the flow of gas is modeled by a generalized version of the quadratic Weymouth's equation. The purpose of considering generalized flow formulas is to be able to adapt our results to various gas network optimization problems involving gas flow formulas beyond Weymouth's equation. Such formulas can appear in leaves of branch and bound trees, or they can stem from discretization and linearization carried out at active devices. We call a balanced supply-demand vector a nomination, and the passive nomination validation problem is to decide whether there exist pressures at the nodes generating a given nomination. We prove that in our setup the pressure square vectors generating a given nomination form a one-dimensional connected and continuous curve in the pressure square space, and this curve is a line for the classical Weymouth's equation. We also present a visual approach for the easy comprehension of how this solution curve arises; we give a short investigation of the set of feasible nominations; and finally we give a proof that the nomination validation problem in gas networks with active devices is NP-complete. T3 - ZIB-Report - 11-44 KW - pressure drop equation KW - gas networks KW - generalized flow formula Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15151 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Probabilistic alternatives for competitive analysis N2 - In the last 20 years competitive analysis has become the main tool for analyzing the quality of online algorithms. Despite of this, competitive analysis has also been criticized: It sometimes cannot discriminate between algorithms that exhibit significantly different empirical behavior, or it even favors an algorithm that is worse from an empirical point of view. Therefore, there have been several approaches to circumvent these drawbacks. In this survey, we discuss probabilistic alternatives for competitive analysis. T3 - ZIB-Report - 11-55 KW - online algorithms KW - probabilistic analysis KW - competitive analysis KW - survey Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15131 SN - 1438-0064 ER - TY - GEN A1 - Martin, Alexander A1 - Geißler, Björn A1 - Hayn, Christine A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Morsi, Antonio A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Steinbach, Marc A1 - Willert, Bernhard T1 - Optimierung Technischer Kapazitäten in Gasnetzen N2 - Die mittel- und längerfristige Planung für den Gastransport hat sich durch Änderungen in den regulatorischen Rahmenbedingungen stark verkompliziert. Kernpunkt ist die Trennung von Gashandel und -transport. Dieser Artikel diskutiert die hieraus resultierenden mathematischen Planungsprobleme, welche als Validierung von Nominierungen und Buchungen, Bestimmung der technischen Kapazität und Topologieplanung bezeichnet werden. Diese mathematischen Optimierungsprobleme werden vorgestellt und Lösungsansätze skizziert. T3 - ZIB-Report - 11-56 KW - Gasnetzplanung KW - Technische Kapazitäten KW - Nominierungsvalidierung KW - Buchungsvalidierung KW - Topologieplanung Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15121 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Omont, Bertrand A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - A Stackelberg game to optimize the distribution of controls in transportation networks N2 - We propose a game theoretic model for the spatial distribution of inspectors on a transportation network. The problem is to spread out the controls so as to enforce the payment of a transit toll. We formulate a linear program to find the control distribution which maximizes the expected toll revenue, and a mixed integer program for the problem of minimizing the number of evaders. Furthermore, we show that the problem of finding an optimal mixed strategy for a coalition of $N$ inspectors can be solved efficiently by a column generation procedure. Finally, we give experimental results from an application to the truck toll on German motorways. T3 - ZIB-Report - 12-15 KW - Stackelberg game KW - Polymatrix game KW - Controls in transportation networks Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14995 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - A cubic regularization algorithm for nonconvex optimization in function space (in preparation) N2 - We propose a cubic regularization algorithm that is constructed to deal with nonconvex minimization problems in function space. It allows for a flexible choice of the regularization term and thus accounts for the fact that in such problems one often has to deal with more than one norm. Global and local convergence results are established in a general framework. Moreover, several variants of step computations are compared. In the context of nonlinear elasticity it turns out the a cg method applied to an augmented Hessian is more robust than truncated cg. T3 - ZIB-Report - 12-16 KW - nonconvex optimization KW - optimization in function space KW - nonlinear elasticity Y1 - 2012 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume T1 - Approximation of a Maximum-Submodular-Coverage problem involving spectral functions, with application to Experimental Design N2 - We study a family of combinatorial optimization problems defined by a parameter $p\in[0,1]$, which involves spectral functions applied to positive semidefinite matrices, and has some application in the theory of optimal experimental design. This family of problems tends to a generalization of the classical maximum coverage problem as $p$ goes to $0$, and to a trivial instance of the knapsack problem as $p$ goes to $1$. In this article, we establish a matrix inequality which shows that the objective function is submodular for all $p\in[0,1]$, from which it follows that the greedy approach, which has often been used for this problem, always gives a design within $1-1/e$ of the optimum. We next study the design found by rounding the solution of the continuous relaxed problem, an approach which has been applied by several authors. We prove an inequality which generalizes a classical result from the theory of optimal designs, and allows us to give a rounding procedure with an approximation factor which tends to $1$ as $p$ goes to $1$. T3 - ZIB-Report - 11-53 KW - Maximum Coverage KW - Optimal Experimental Design KW - Polynomial Time Approximability KW - Kiefer's p-criterion Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14956 SN - 1438-0064 VL - 151 IS - 1--2 SP - 258 EP - 276 ER - TY - GEN A1 - Sagnol, Guillaume T1 - Network-related problems in Optimal Experimental Design and Second Order Cone Programming N2 - In the past few years several applications of optimal experimental designs have emerged to optimize the measurements in communication networks. The optimal design problems arising from this kind of applications share three interesting properties: (i) measurements are only available at a small number of locations of the network; (ii) each monitor can simultaneously measure several quantities, which can be modeled by ``multiresponse experiments"; (iii) the observation matrices depend on the topology of the network. In this paper, we give an overview of these experimental design problems and recall recent results for the computation of optimal designs by Second Order Cone Programming (SOCP). New results for the network-monitoring of a discrete time process are presented. In particular, we show that the optimal design problem for the monitoring of an AR1 process can be reduced to the standard form and we give experimental results. T3 - ZIB-Report - 11-52 KW - Optimal Experimental Design KW - Second Order Cone Programming KW - Network measurements Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14942 SN - 1438-0064 VL - 51 IS - 51 SP - 161 EP - 171 ER - TY - GEN A1 - Sagnol, Guillaume T1 - A Class of Semidefinite Programs with rank-one solutions N2 - We show that a class of semidefinite programs (SDP) admits a solution that is a positive semidefinite matrix of rank at most $r$, where $r$ is the rank of the matrix involved in the objective function of the SDP. The optimization problems of this class are semidefinite packing problems, which are the SDP analogs to vector packing problems. Of particular interest is the case in which our result guarantees the existence of a solution of rank one: we show that the computation of this solution actually reduces to a Second Order Cone Program (SOCP). We point out an application in statistics, in the optimal design of experiments. T3 - ZIB-Report - 11-51 KW - SDP KW - Semidefinite Packing Problem KW - rank 1-solution KW - Low-rank solutions KW - SOCP KW - Optimal Experimental Design KW - Multiresponse experiments Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14933 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Stephan, Rüdiger T1 - Characterization of Facets of the Hop Constrained Chain Polytope via Dynamic Programming N2 - In this paper, we study the hop constrained chain polytope, that is, the convex hull of the incidence vectors of (s,t)-chains using at most k arcs of a given digraph, and its dominant. We use extended formulations (implied by the inherent structure of the Moore-Bellman-Ford algorithm) to derive facet defining inequalities for these polyhedra via projection. Our findings result into characterizations of all facet defining {0,+1,-1}-inequalities for the hop constrained chain polytope and all facet defining {0,1}-inequalities for its dominant. Although the derived inequalities are already known, such classifications were not previously given to the best of our knowledge. Moreover, we use this approach to generalize so called jump inequalities, which have been introduced in a paper of Dahl and Gouveia in 2004. T3 - ZIB-Report - 11-54 KW - hop constraints KW - chains KW - dynamic programming KW - facets Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14914 SN - 1438-0064 ER - TY - THES A1 - Schlechte, Thomas T1 - Railway Track Allocation: Models and Algorithms N2 - This thesis is about mathematical optimization for the efficient use of railway infrastructure. We address the optimal allocation of the available railway track capacity - the track allocation problem. This track allocation problem is a major challenge for a railway company, independent of whether a free market, a private monopoly, or a public monopoly is given. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense sizes of the problem instances. Mathematical models and optimization techniques can result in huge gains for both railway customers and operators, e.g., in terms of cost reductions or service quality improvements. We tackle this challenge by developing novel mathematical models and associated innovative algorithmic solution methods for large scale instances. This allows us to produce for the first time reliable solutions for a real world instance, i.e., the Simplon corridor in Switzerland. The opening chapter gives a comprehensive overview on railway planning problems. This provides insights into the regulatory and technical framework, it discusses the interaction of several planning steps, and identifies optimization potentials in railway transportation. The remainder of the thesis is comprised of two major parts. The first part is concerned with modeling railway systems to allow for resource and capacity analysis. Railway capacity has basically two dimensions, a space dimension which are the physical infrastructure elements as well as a time dimension that refers to the train movements, i.e., occupation or blocking times, on the physical infrastructure. Railway safety systems operate on the same principle all over the world. A train has to reserve infrastructure blocks for some time to pass through. Two trains reserving the same block of the infrastructure within the same point in time is called block conflict. Therefore, models for railway capacity involve the definition and calculation of reasonable running and associated reservation and blocking times to allow for a conflict free allocation. In the second and main part of the thesis, the optimal track allocation problem for macroscopic models of the railway system is considered. The literature for related problems is surveyed. A graph-theoretic model for the track allocation problem is developed. In that model optimal track allocations correspond to conflict-free paths in special time-expanded graphs. Furthermore, we made considerable progress on solving track allocation problems by two main features - a novel modeling approach for the macroscopic track allocation problem and algorithmic improvements based on the utilization of the bundle method. Finally, we go back to practice and present in the last chapter several case studies using the tools netcast and tsopt. We provide a computational comparison of our new models and standard packing models used in the literature. Our computational experience indicates that our approach, i.e., ``configuration models'', outperforms other models. Moreover, the rapid branching heuristic and the bundle method enable us to produce high quality solutions for very large scale instances, which has not been possible before. In addition, we present results for a theoretical and rather visionary auction framework for track allocation. We discuss several auction design questions and analyze experiments of various auction simulations. The highlights are results for the Simplon corridor in Switzerland. We optimized the train traffic through this tunnel using our models and software tools. To the best knowledge of the author and confirmed by several railway practitioners this was the first time that fully automatically produced track allocations on a macroscopic scale fulfill the requirements of the originating microscopic model, withstand the evaluation in the microscopic simulation tool OpenTrack, and exploit the infrastructure capacity. This documents the success of our approach in practice and the usefulness and applicability of mathematical optimization to railway track allocation. KW - railway track allocation KW - large-scale integer programming KW - network aggregation KW - rapid branching Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-34272 UR - http://opus.kobv.de/tuberlin/volltexte/2012/3427/pdf/schlechte_thomas.pdf SN - 978-3-8381-3222-8 PB - Südwestdeutscher Verlag für Hochschulschriften CY - Saarbrücken, Germany ER - TY - GEN A1 - Orlowski, Sebastian A1 - Werner, Axel A1 - Wessäly, Roland T1 - Estimating trenching costs in FTTx network planning N2 - In this paper we assess to which extent trenching costs of an FTTx network are unavoidable, even if technical side constraints are neglected. For that purpose we present an extended Steiner tree model. Using a variety of realistic problem instances we demonstrate that the total trenching cost can only be reduced by about 5 percent in realistic scenarios. This work has been funded by BMBF (German Federal Ministry of Education and Research) within the program "KMU-innovativ". T3 - ZIB-Report - 11-49 KW - Optical access networks KW - Optimization KW - Steiner trees Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14884 SN - 1438-0064 ER - TY - GEN A1 - Werner, Axel T1 - Kombinatorische Optimierung und die 40-Punkte-Regel N2 - Wieviele Punkte braucht eine Mannschaft in der Fußball-Bundesliga mindestens, um sicher dem Abstieg zu entgehen? Wir benutzen kombinatorische Optimierung, um diese und ähnliche Fragen zu beantworten. T3 - ZIB-Report - 11-48 KW - Kombinatorische Optimierung KW - Sport KW - Bundesliga Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14871 SN - 1438-0064 ER - TY - GEN A1 - Wessäly, Roland A1 - Werner, Axel A1 - Eckel, Klaus A1 - Seibel, Julia A1 - Orlowski, Sebastian A1 - Louchet, Hadrien A1 - Patzak, Erwin A1 - Bentz, Winfried T1 - Schätze heben bei der Planung von FTTx-Netzen: optimierte Nutzung von existierenden Leerrohren - eine Praxisstudie N2 - Das vom BMBF geförderte Projekt FTTX-PLAN entwickelt mathematische Modelle und Optimierungsverfahren, um automatisiert kostenoptimierte FTTx-Netze berechnen zu können. Wir zeigen anhand einer Praxisstudie in Zusammenarbeit mit der Regensburger R-KOM, wie ein Planer von diesen Verfahren profitieren kann, um die Auswirkungen bestimmter Entscheidungen auf die Netzstruktur und -kosten zu untersuchen. Wir illustrieren dies am Beispiel eines FTTB/FTTH-Vergleichs, der Variation von Kundenanbindungsraten und der gezielten Ausnutzung existierender Leerrohre, um Tiefbau zu vermeiden. T3 - ZIB-Report - 11-47 KW - Praxisstudie KW - Optische Zugangsnetze KW - Optimierung Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14861 UR - http://www.vde-verlag.de/buecher/453339/breitbandversorgung-in-deutschland-itg-fb-227.html SN - 1438-0064 ER - TY - GEN A1 - Menne, Ulrich A1 - Raack, Christian A1 - Wessäly, Roland A1 - Kharitonov, Daniel T1 - Optimal Degree of Optical Circuit Switching in IP-over-WDM Networks N2 - In this paper, we study the influence of technology, traffic properties and price trends on optimized design of a reference IP-over-WDM network with rich underlying fiber topology. In each network node, we investigate the optimal degree of traffic switching in an optical (lambda) domain versus an electrical (packet) domain, also known as measure of \emph{node transparency}. This measure is studied in connection to changes in traffic volume, demand affinity, optical circuit speeds and equipment cost. By applying variable design constraints, we assess the relative roles of the two distinct equipment groups, IP routers and optical cross-connects, with respect to resulting changes in cost-sensitive network architectures. T3 - ZIB-Report - 11-50 KW - IP-over-WDM KW - Circuit Switching KW - Opacity Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14843 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Heismann, Olga T1 - The Hypergraph Assignment Problem N2 - The hypergraph assignment problem (HAP) is the generalization of assignments from directed graphs to directed hypergraphs. It serves, in particular, as a universal tool to model several train composition rules in vehicle rotation planning for long distance passenger railways. We prove that even for problems with a small hyperarc size and hypergraphs with a special partitioned structure the HAP is NP-hard and APX-hard. Further, we present an extended integer linear programming formulation which implies, e. g., all clique inequalities. T3 - ZIB-Report - 12-14 KW - directed hypergraphs KW - hyperassignment KW - assignment Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14822 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Neumann, Gerald T1 - 10 Jahre TELOTA N2 - Das TELOTA-Projekt - zunächst nur für zwei Jahre gestartet - feierte am 15. Juni 2011 sein 10-jähriges Bestehen im Rahmen eines Workshops mit einem abschließenden Festvortrag von Richard Stallmann zum Thema „Copyright versus community in the age of computer networks“. Diese Veranstaltung zeigte, wie aktuell die TELOTA-Themen weiterhin sind und dass diese eine große Resonanz in der allgemeinen Öffentlichkeit finden. Die TELOTA-Aktivitäten haben sich als wichtiger Bestandteil der IT-Infrastruktur der BBAW erwiesen, gehen aber weit über reinen Service hinaus. Sie beeinflussen die Forschung selbst und führen zu neuen interessanten wissenschaftlichen Fragestellungen. Der Rückblick auf die ersten zehn Jahre der TELOTA-Initiative in diesem Artikel soll einen kleinen Eindruck von dem geben, was bisher geleistet wurde. T3 - ZIB-Report - 12-13 KW - BBAW KW - Telota Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14799 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus T1 - The funnel trap paradox N2 - In this article, an illustrative example is given for the coarse-graining of a Markov process which leads to a shift in the statistical weights of a two-states-system. The example is based on a 2D-funnel trap. The funnel trap is constructed in such a way, that the area inside and outside of the trap is identical. However, observing the flight of the insect as a Markov process, the probability for being “in the trap” is higher. This example can be transferred to several kinds of processes (like receptor-ligandbinding processes in chemistry) and describes the influence of “re-entering events”. T3 - ZIB-Report - 12-12 KW - Markov process KW - Robust Perron Cluster Analysis KW - Conformation Dynamics Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14765 SN - 1438-0064 ER - TY - GEN A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An optimal control problem in polyconvex hyperelasticity N2 - We consider a shape implant design problem that arises in the context of facial surgery. We introduce a reformulation as an optimal control problem, where the control acts as a boundary force. The state is modelled as a minimizer of a polyconvex hyperelastic energy functional. We show existence of optimal solutions and derive - on a formal level - first order optimality conditions. Finally, preliminary numerical results are presented. T3 - ZIB-Report - 12-08 KW - polyconvex elasticity KW - implant design KW - optimal control Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14745 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - Vehicle Rotation Planning for Intercity Railways N2 - This paper provides a generic formulation for rolling stock planning problems in the context of intercity passenger traffic. The main contributions are a graph theoretical model and a Mixed-Integer-Programming formulation that integrate all main requirements of the considered Vehicle-Rotation-Planning problem (VRPP). We show that it is possible to solve this model for real-world instances provided by our industrial partner DB Fernverkehr AG using modern algorithms and computers. T3 - ZIB-Report - 12-11 KW - rolling-stock-planning KW - mixed-integer-programming KW - hypergraphs KW - column generation KW - rapid branching Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14731 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - Rapid Branching N2 - We propose rapid branching (RB) as a general branch-and-bound heuristic for solving large scale optimization problems in traffic and transport. The key idea is to combine a special branching rule and a greedy node selection strategy in order to produce solutions of controlled quality rapidly and efficiently. We report on three successful applications of the method for integrated vehicle and crew scheduling, railway track allocation, and railway vehicle rotation planning. T3 - ZIB-Report - 12-10 KW - large scale optimization KW - rapid branching KW - column generation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14728 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Langenhan, Andreas A1 - Löbel, Andreas A1 - Schulz, Christof A1 - Weider, Steffen T1 - Duty Scheduling Templates N2 - We propose duty templates as a novel concept to produce similar duty schedules for similar days of operation in public transit. Duty templates can conveniently handle various types of similarity requirements, and they can be implemented with ease using standard algorithmic techniques. They have produced good results in practice. T3 - ZIB-Report - 12-09 KW - duty scheduling KW - duty templates Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14699 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Beck, J. Christopher T1 - Reconsidering Mixed Integer Programming and MIP-based Hybrids for Scheduling N2 - Despite the success of constraint programming (CP) for scheduling, the much wider penetration of mixed integer programming (MIP) technology into business applications means that many practical scheduling problems are being addressed with MIP, at least as an initial approach. Furthermore, there has been impressive and well-documented improvements in the power of generic MIP solvers over the past decade. We empirically demonstrate that on an existing set of resource allocation and scheduling problems standard MIP and CP models are now competitive with the state-of-the-art manual decomposition approach. Motivated by this result, we formulate two tightly coupled hybrid models based on constraint integer programming (CIP) and demonstrate that these models, which embody advances in CP and MIP, are able to out-perform the CP, MIP, and decomposition models. We conclude that both MIP and CIP are technologies that should be considered along with CP for solving scheduling problems. T3 - ZIB-Report - 12-05 KW - constraint integer programming KW - constraint programming KW - cumulative constraint KW - mixed integer programming KW - optional activities Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14660 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros T1 - Undercover: a primal MINLP heuristic exploring a largest sub-MIP N2 - We present Undercover, a primal heuristic for nonconvex mixed-integer nonlinear programming (MINLP) that explores a mixed-integer linear subproblem (sub-MIP) of a given MINLP. We solve a vertex covering problem to identify a minimal set of variables that need to be fixed in order to linearize each constraint, a so-called cover. Subsequently, these variables are fixed to values obtained from a reference point, e.g., an optimal solution of a linear relaxation. We apply domain propagation and conflict analysis to try to avoid infeasibilities and learn from them, respectively. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. We present computational results on a test set of mixed-integer quadratically constrained programs (MIQCPs) and general MINLPs from MINLPLib. It turns out that the majority of these instances allow for small covers. Although general in nature, the heuristic appears most promising for MIQCPs, and complements nicely with existing root node heuristics in different state-of-the-art solvers. T3 - ZIB-Report - 12-07 KW - Primal Heuristic KW - Mixed-Integer Nonlinear Programming KW - Large Neighborhood Search KW - Mixed-Integer Quadratically Constrained Programming KW - Nonconvex Optimization Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14631 SN - 1438-0064 ER - TY - GEN A1 - Hoang, Nam-Dung A1 - Koch, Thorsten T1 - Steiner Tree Packing Revisited N2 - The Steiner tree packing problem (STPP) in graphs is a long studied problem in combinatorial optimization. In contrast to many other problems, where there have been tremendous advances in practical problem solving, STPP remains very difficult. Most heuristics schemes are ineffective and even finding feasible solutions is already NP-hard. What makes this problem special is that in order to reach the overall optimal solution non-optimal solutions to the underlying NP-hard Steiner tree problems must be used. Any non-global approach to the STPP is likely to fail. Integer programming is currently the best approach for computing optimal solutions. In this paper we review some “classical” STPP instances which model the underlying real world application only in a reduced form. Through improved modelling, including some new cutting planes, and by emplyoing recent advances in solver technology we are for the first time able to solve those instances in the original 3D grid graphs to optimimality. T3 - ZIB-Report - 12-02 KW - Steiner tree packing KW - Integer Programming KW - grid graphs Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14625 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Heismann, Olga T1 - Minimum Cost Hyperassignments with Applications to ICE/IC Rotation Planning N2 - Vehicle rotation planning is a fundamental problem in rail transport. It decides how the railcars, locomotives, and carriages are operated in order to implement the trips of the timetable. One important planning requirement is operational regularity, i.e., using the rolling stock in the same way on every day of operation. We propose to take regularity into account by modeling the vehicle rotation planning problem as a minimum cost hyperassignment problem (HAP). Hyperassignments are generalizations of assignments from directed graphs to directed hypergraphs. Finding a minimum cost hyperassignment is NP-hard. Most instances arising from regular vehicle rotation planning, however, can be solved well in practice. We show that, in particular, clique inequalities strengthen the canonical LP relaxation substantially. T3 - ZIB-Report - 11-46 KW - hyperassignments KW - vehicle rotation planning Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14564 UR - http://link.springer.com/chapter/10.1007%2F978-3-642-29210-1_10 SN - 1438-0064 ER - TY - GEN A1 - Sander, Oliver A1 - Klapproth, Corinna A1 - Youett, Jonathan A1 - Kornhuber, Ralf A1 - Deuflhard, Peter T1 - Towards an Efficient Numerical Simulation of Complex 3D Knee Joint Motion N2 - We present a time-dependent finite element model of the human knee joint of full 3D geometric complexity. Its efficient numerical simulation requires advanced numerical algorithms that have been developed just recently. Up to now, the model comprises bones, cartilage, and the major ligaments (patella and menisci are still missing). Bones (femur, tibia, and fibula) are modelled by linear elastic materials, cartilage by viscoelastic materials, ligaments by one-dimensional so-called Cosserat rods. In order to capture the dynamical contact problems correctly, we solve the full PDEs of elasticity in the presence of strict contact inequalities. For the total spatio-temporal discretization we apply a method of layers approach (first time, then space discretization). For the time discretization of the elastic and viscoelastic parts, we apply a new contact-stabilized Newmark method, while for the Cosserat rods we choose an energy-momentum method. For the space discretization, we use linear finite elements for the elastic and viscoelastic parts and novel geodesic finite elements for the Cosserat rods. The coupled system is solved by a Dirichlet-Neumann method, and the arising large algebraic systems are solved by a recent fast multigrid solver, the truncated non-smooth Newton multigrid method. T3 - ZIB-Report - 12-06 KW - contact problem KW - contact-stabilized Newmark method KW - domain decomposition KW - energy-momentum method KW - geodesic finite elements KW - knee model Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14512 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Friedow, Isabel A1 - Karbstein, Marika T1 - Optimierung des Linienplans 2010 in Potsdam N2 - Im Zuge der Übernahme von 6 Linien der Havelbus Verkehrsgesellschaft mbH durch die ViP Verkehr in Potsdam GmbH ergab sich 2009 die Notwendigkeit der Entwicklung eines neuen Linien- und Taktplans für das Jahr 2010. Das Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) entwickelt in einem Projekt des DFG-Forschungszentrums Matheon ein Verfahren zur mathematischen Linienoptimierung. Dieses Tool wurde bei der Optimierung des ViP Linienplans 2010 in einer projektbegleitenden Studie eingesetzt, um Alternativen bei verschiedenen Planungs- und Zielvorgaben auszuloten. In dem Artikel wird eine Auswertung der Ergebnisse mit dem Verkehrsanalysesystem Visum der PTV AG beschrieben. Die Auswertungen bestätigen, dass mit Hilfe von mathematischer Optimierung eine weitere Verkürzung der Reisezeit um 1%, eine als um 6% verkürzt empfundene Reisezeit, 10% weniger Fahrzeit im Fahrzeug und eine gleichzeitige Kostenreduktion um 5% möglich sind. T3 - ZIB-Report - 12-04 KW - Fallstudie KW - Linienplan KW - Optimierung Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14486 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - A Note on Menger's Theorem for Hypergraphs N2 - We prove the companion Theorem to Menger's Theorem for hypergraphs. This result gives rise to a new class of blocking pairs of ideal matrices, that generalize the incidence matrices of cuts and paths. T3 - ZIB-Report - 12-03 KW - ideal matrices Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14471 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin T1 - Einblicke in die Diskrete Mathematik N2 - „Diskrete Mathematik, was ist das?“, ist eine typische Frage von Lehrern mit traditioneller Mathematikausbildung, denn dort kam und kommt diskrete Mathematik kaum vor. Die etwas Aufgeschlosseneren fragen: „Wenn (schon wieder) etwas Neues unterrichtet werden soll, was soll denn dann im Lehrplan gestrichen werden?“ Auf die zweite Frage wird hier nicht eingegangen. Das Ziel dieses Aufsatzes ist es, in diskrete Mathematik einzuführen, Interesse an diesem Fachgebiet zu wecken und dazu anzuregen, dieses auch im Schulunterricht (ein wenig) zu berücksichtigen. Die Schüler und Schülerinnen werden dafür dankbar sein – eine Erfahrung, die in vielen Unterrichtsreihen gemacht wurde. T3 - ZIB-Report - 12-01 KW - diskrete Mathematik Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14399 SN - 1438-0064 ER - TY - GEN A1 - Wiebel, Alexander A1 - Vos, Frans M. A1 - Hege, Hans-Christian T1 - Perception-Oriented Picking of Structures in Direct Volumetric Renderings N2 - Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques. T3 - ZIB-Report - 11-45 KW - DVR KW - picking KW - pointing KW - direct volume rendering Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14343 SN - 1438-0064 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Workload and busy period for M/GI/1 with a general impatience mechanism N2 - The paper deals with the workload and busy period for the M/GI/1 system under FCFS discipline, where the customers may become impatient during their waiting for service with generally distributed maximal waiting times and also during their service with generally distributed maximal service times depending on the time waited for service. This general impatience mechanism, originally introduced by Kovalenko (1961) and considered by Daley (1965), too, covers the special cases of impatience on waiting times as well as impatience on sojourn times, for which Boxma et al. (2010), (2011) gave new results and outlined special cases recently. Our unified approach bases on the vector process of workload and busy time. Explicit representations for the LSTs of workload and busy period are given in case of phase-type distributed impatience. T3 - ZIB-Report - 11-43 KW - impatient customers KW - workload KW - busy period KW - waiting time dependent service Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14304 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - An IP Approach to Toll Enforcement Optimization on German Motorways N2 - This paper proposes the first model for toll enforcement optimization on German motorways. The enforcement is done by mobile control teams and our goal is to produce a schedule achieving network-wide control, proportional to spatial and time-dependent traffic distributions. Our model consists of two parts. The first plans control tours using a vehicle routing approach with profits and some side constraints. The second plans feasible rosters for the control teams. Both problems can be modeled as Multi-Commodity Flow Problems. Adding additional coupling constraints produces a large-scale integrated integer programming formulation. We show that this model can be solved to optimality for real world instances associated with a control area in East Germany. T3 - ZIB-Report - 11-42 KW - Toll Enforcement KW - Vehicle Routing Problem KW - Duty Roster Planning KW - Integer Programming Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14299 SN - 1438-0064 ER - TY - GEN A1 - Clasen, Malte A1 - Paar, Philip A1 - Prohaska, Steffen T1 - Level of Detail for Trees Using Clustered Ellipsoids N2 - We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts. T3 - ZIB-Report - 11-41 KW - level of detail KW - rendering KW - natural scene KW - Gaussian mixture model Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14251 SN - 1438-0064 ER - TY - GEN A1 - Koch, Thorsten A1 - Ralphs, Ted A1 - Shinano, Yuji T1 - What could a million CPUs do to solve Integer Programs? N2 - Given the steady increase in cores per CPU, it is only a matter of time until supercomputers will have a million or more cores. In this article, we investigate the opportunities and challenges that will arise when trying to utilize this vast computing power to solve a single integer linear optimization problem. We also raise the question of whether best practices in sequential solution of ILPs will be effective in massively parallel environments. T3 - ZIB-Report - 11-40 Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14222 SN - 1438-0064 ER - TY - GEN A1 - Deuflhard, Peter A1 - Schiela, Anton A1 - Weiser, Martin T1 - Mathematical Cancer Therapy Planning in Deep Regional Hyperthermia N2 - This paper surveys the required mathematics for a typical challenging problem from computational medicine, the cancer therapy planning in deep regional hyperthermia. In the course of many years of close cooperation with clinics, the medical problem gave rise to quite a number of subtle mathematical problems, part of which had been unsolved when the common project started. Efficiency of numerical algorithms, i.e. computational speed and monitored reliability, play a decisive role for the medical treatment. Off-the-shelf software had turned out to be not sufficient to meet the requirements of medicine. Rather, new mathematical theory as well as new numerical algorithms had to be developed. In order to make our algorithms useful in the clinical environment, new visualization software, a virtual lab, including 3D geometry processing of individual virtual patients had to be designed and implemented. Moreover, before the problems could be attacked by numerical algorithms, careful mathematical modelling had to be done. Finally, parameter identification and constrained optimization for the PDEs had to be newly analyzed and realized over the individual patient's geometry. Our new techniques had an impact on the specificity of the individual patients' treatment and on the construction of an improved hyperthermia applicator. T3 - ZIB-Report - 11-39 KW - hyperthermia therapy planning KW - mathematical modelling KW - Maxwell equations KW - state constraints KW - parameter identification Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14204 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Schlechte, Thomas A1 - Stephan, Rüdiger A1 - Winkler, Michael T1 - Solving steel mill slab design problems N2 - The steel mill slab design problem from the CSPLIB is a combinatorial optimization problem motivated by an application of the steel industry. It has been widely studied in the constraint programming community. Several methods were proposed to solve this problem. A steel mill slab library was created which contains 380 instances. A closely related binpacking problem called the multiple knapsack problem with color constraints, originated from the same industrial problem, was discussed in the integer programming community. In particular, a simple integer program for this problem has been given by Forrest et al. The aim of this paper is to bring these different studies together. Moreover, we adapt the model of Forrest et al. for the steel mill slab design problem. Using this model and a state-of-the-art integer program solver all instances of the steel mill slab library can be solved efficiently to optimality. We improved, thereby, the solution values of 76 instances compared to previous results. Finally, we consider a recently introduced variant of the steel mill slab design problem, where within all solutions which minimize the leftover one is interested in a solution which requires a minimum number of slabs. For that variant we introduce two approaches and solve all instances of the steel mill slab library with this slightly changed objective function to optimality. T3 - ZIB-Report - 11-38 KW - steel mill slab design problem KW - multiple knapsack problem with color constraints KW - integer programming KW - set partitioning KW - binpacking with side constraints Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14089 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton A1 - Hintermüller, Michael T1 - On the Length of the Primal-Dual Path in Moreau-Yosida-based Path-following for State Constrained Optimal Control: Analysis and Numerics N2 - We derive a-priori estimates on the length of the primal-dual path that results from a Moreau-Yosida approximation of the feasible set for state constrained optimal control problems. These bounds depend on the regularity of the state and the dimension of the problem. Comparison with numerical results indicates that these bounds are sharp and are attained for the case of a single active point. T3 - ZIB-Report - 11-37 KW - state constraints KW - PDE constrained optimization KW - path-following Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14071 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - A Hypergraph Model for Railway Vehicle Rotation Planning N2 - We propose a model for the integrated optimization of vehicle rotations and vehicle compositions in long distance railway passenger transport. The main contribution of the paper is a hypergraph model that is able to handle the challenging technical requirements as well as very general stipulations with respect to the ``regularity'' of a schedule. The hypergraph model directly generalizes network flow models, replacing arcs with hyperarcs. Although NP-hard in general, the model is computationally well-behaved in practice. High quality solutions can be produced in reasonable time using high performance Integer Programming techniques, in particular, column generation and rapid branching. We show that, in this way, large-scale real world instances of our cooperation partner DB Fernverkehr can be solved. T3 - ZIB-Report - 11-36 KW - Rolling Stock Planning, Hypergraph Modeling, Integer Programming, Column Generation, Rapid Branching Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0030-drops-32746 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Railway Track Allocation - Simulation, Aggregation, and Optimization N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway company. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market in Europe. This leads to more potential conflicts between trains caused by an increasing demand of train paths. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. In order to make best use of the infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithms can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and an associated concept for track allocation, that consists of three important parts, simulation, aggregation, and optimization. Furthermore, we present results of our general framework for real world data. T3 - ZIB-Report - 11-35 KW - railway models, railway capacity, track allocation framework Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14031 SN - 1438-0064 ER - TY - THES A1 - Weber, Marcus T1 - A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator N2 - Supercomputers can simulate complex molecular systems. However, there is a very large gap between the fastest oscillations of covalent bonds of a molecule and the time-scale of the dominant processes. In order to extract the dominant time-scales and to identify the dominant processes, a clustering of information is needed. This thesis shows that only the subspace-based Robust Perron Cluster Analysis (PCCA+) can solve this problem correctly by the construction of a Markov State Model. PCCA+ allows for time-extrapolation in molecular kinetics. This thesis shows the difference between molecular dynamics and molecular kinetics. Only in the molecular kinetics framework a definition of transition rates is possible. In this context, the existence of an infinitesimal generator of the dynamical processes is discussed. If the existence is assumed, the Theorem of Gauß can be applied in order to compute transition rates efficiently. Molecular dynamics, however, is not able to provide a suitable statistical basis for the determination of the transition pattern. KW - Conformation Dynamics KW - Molecular Kinetics KW - Transition Rates KW - Markov State Models Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14025 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Kutschka, Manuel A1 - Raack, Christian T1 - Robust Network Design: Formulations, Valid Inequalities, and Computations N2 - Traffic in communication networks fluctuates heavily over time. Thus, to avoid capacity bottlenecks, operators highly overestimate the traffic volume during network planning. In this paper we consider telecommunication network design under traffic uncertainty, adapting the robust optimization approach of Bertsimas and Sim [2004]. We present three different mathematical formulations for this problem, provide valid inequalities, study the computational implications, and evaluate the realized robustness. To enhance the performance of the mixed-integer programming solver we derive robust cutset inequalities generalizing their deterministic counterparts. Instead of a single cutset inequality for every network cut, we derive multiple valid inequalities by exploiting the extra variables available in the robust formulations. We show that these inequalities define facets under certain conditions and that they completely describe a projection of the robust cutset polyhedron if the cutset consists of a single edge. For realistic networks and live traffic measurements we compare the formulations and report on the speed up by the valid inequalities. We study the "price of robustness" and evaluate the approach by analyzing the real network load. The results show that the robust optimization approach has the potential to support network planners better than present methods. T3 - ZIB-Report - 11-34 KW - robust network design KW - cutset inequalities Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13890 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin T1 - Mathematik, Politik und Recht N2 - Politiker müssten doch in der Lage sein, faire Wahlverfahren, rationale gesellschaftliche Entscheidungsprozesse und schlupflochfreie Marktregulierungen zu finden. Und wenn sie sich nicht einigen können, so denkt fast jeder, dann sollen das eben unsere Gerichte regeln. Dies ist im Allgemeinen unerfüllbares Wunschdenken. Die Gründe dafür sind oft mathematischer Natur. Man kann z. B. mathematisch beweisen, dass es (in einem präzisierbaren Sinn) gar keine „fairen“ Wahlverfahren und nur in seltenen Fällen „rationale“ Entscheidungsprozesse gibt. Ein anderer Sachverhalt liegt z. B. bei Regulierungs- oder Deregulierungsmaßnahmen vor. Die dabei zu berücksichtigenden technischen Restriktionen sind häufig so kompliziert (man denke u. a. an die technischen Vorschriften im Schienen- oder Luftverkehr oder zum Betrieb von Pipelines), dass sie einfach nicht in juristischer Sprache formuliert werden können. Gut gemeinte Verordnungen sind nicht selten mathematisch widersprüchlich, führen auf praktisch unlösbare Probleme oder überfordern das Verständnis aller Beteiligten. Diese Beispiele legen nahe, dass bei einigen Gesetzgebungsprozessen und Verordnungen mathematischer Sachverstand erforderlich ist. Dieser wird derzeit aber nur sehr selten genutzt. T3 - ZIB-Report - 11-33 KW - Mathematik als Entscheidungshilfe KW - Spieltheorie KW - Kostenaufteilungsprobleme KW - Wahlverfahren und Mathematik Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13845 SN - 1438-0064 ER - TY - THES A1 - Borndörfer, Ralf T1 - Mathematical Optimization and Public Transportation N2 - This cumulative thesis collects the following six papers for obtaining the habilitation at the Technische Universität Berlin, Fakultät II – Mathematik und Naturwissenschaften: (1) Set packing relaxations of some integer programs. (2) Combinatorial packing problems. (3) Decomposing matrices into blocks. (4) A bundle method for integrated multi-depot vehicle and duty scheduling in public transit. (5) Models for railway track allocation. (6) A column-generation approach to line planning in public transport. Some changes were made to the papers compared to the published versions. These pertain to layout unifications, i.e., common numbering, figure, table, and chapter head layout. There were no changes with respect to notation or symbols, but some typos have been eliminated, references updated, and some links and an index was added. The mathematical content is identical. The papers are about the optimization of public transportation systems, i.e., bus networks, railways, and airlines, and its mathematical foundations, i.e., the theory of packing problems. The papers discuss mathematical models, theoretical analyses, algorithmic approaches, and computational aspects of and to problems in this area. Papers 1, 2, and 3 are theoretical. They aim at establishing a theory of packing problems as a general framework that can be used to study traffic optimization problems. Indeed, traffic optimization problems can often be modelled as path packing, partitioning, or covering problems, which lead directly to set packing, partitioning, and covering models. Such models are used in papers 4, 5, and 6 to study a variety of problems concerning the planning of line systems, buses, trains, and crews. The common aim is always to exploit as many degrees of freedom as possible, both at the level of the individual problems by using large-scale integer programming techniques, as well as on a higher level by integrating hitherto separate steps in the planning process. KW - set packing KW - set partitioning KW - set covering KW - polyhedral combinatorics KW - public transport KW - railways Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13613 ER - TY - GEN A1 - Schlechte, Thomas T1 - Railway Track Allocation - Simulation and Optimization N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway infrastructure provider. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market. This leads to an increase of slot requests and then it is natural that conflicts occur among them. Furthermore, railway infrastructure networks consist of very expensive assets, even more they are rigid due to the long-term upgrade process. In order to make best use of these valuable infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithmic methodology can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and a general framework to support the integration of simulation and optimization for railway capacity allocation. T3 - ZIB-Report - 11-32 KW - railway models KW - railway capacity KW - track allocation framework Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13632 SN - 1438-0064 ER - TY - THES A1 - Heismann, Olga T1 - Minimum Cost Hyperassignments N2 - Vehicle rotation planning for long distance passenger railways is a fundamental problem in rail transport. It deals with the allocation of vehicles to trips in a cyclic weekly schedule. Its result is an assignment of each trip to a follow-on trip which will be serviced by the same vehicle. To take so-called regularity, which is an important requirement, into account, vehicle rotation planning can be modeled as a hyperassignment problem. This is a generalization of the assignment problem to directed hypergraphs we propose. We prove that the hyperassignment problem is NP-hard for the practically relevant cases and that the canonical integer linear programming (ILP) formulation results in large integrality gaps and arbitrarily high basis matrix determinants. Our main contribution is an extended ILP formulation, which provably implies important classes of inequalities, e. g., all clique inequalities. Clique inequalities are of great importance, because as calculations with practical data show they highly reduce the LP-IP gap. The extended formulation can be solved by column generation. We propose fast combinatorial algorithms for the pricing subproblem. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13371 ER - TY - GEN A1 - Giovanidis, Anastasios A1 - Pulaj, Jonad T1 - The Multiperiod Network Design Problem: Lagrangian-based Solution Approaches N2 - We present and prove a theorem which gives the optimal dual vector for which a Lagrangian dual problem in the Single Period Design Problem (SPDP) is maximized. Furthermore we give a straightforward generalization to the Multi-Period Design Problem (MPDP). Based on the optimal dual values derived we compute the solution of the Lagrangian relaxation and compare it with the linear relaxation and optimal IP values. T3 - ZIB-Report - 11-31 KW - Network Design KW - Lagrangian Relaxation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13367 ER - TY - THES A1 - Hendel, Gregor T1 - New Rounding and Propagation Heuristics for Mixed Integer Programming N2 - Die vorliegende Arbeit befasst sich mit Primalheuristiken für gemischt-ganzzahlige, lineare Optimierungsprobleme (engl.: mixed integer program MIP). Zahlreiche Optimierungsprobleme aus der Praxis lassen sich als MIP modellieren, Beispiele hierfür sind u. a. Optimierungsprobleme im öffentlichen Nah- und Fernverkehr, bei logistischen Fragestellungen oder im Bereich der Chip-Verifikation. Das Lösen von MIP ist NP-schwer und wird heutzutage meistens mit Hilfe von Branch-and-Bound-basierenden Algorithmen versucht. Das Branch-and-Bound-Ver\-fah\-ren profitiert unter Umständen von bereits frühzeitig zur Verfügung stehenden Lösungen, daher sind wir sehr an heuristischen Verfahren interessiert, die in der Praxis schnell eine gute Lösung für eine große Zahl an MIPs liefern und somit die Lösezeit des Branch-and-Bound-Verfahrens erheblich beschleunigen können. Primalheuristiken sind Suchverfahren zum Auffinden zulässiger Lösungen eines MIP. Verschiedene Typen von Primalheuristiken sollen dabei den jeweiligen Bedarf des Anwenders zu unterschiedlichen Zeiten während der Branch-and-Bound-Suche decken. Während Start- und Rundeheuristiken zu Beginn des Löseprozesses eine große Rolle bei der Suche nach der ersten zulässigen Lösung haben, arbeiten Verbesserungs-heuristiken auf schon bekannten Lösungen, um neue, bessere Lösungen zu produzieren. Diese Arbeit beschäftigt sich mit Primalheuristiken, welche Teil des MIP-Lösers SCIP sind. Im ersten Kapitel werden nach der Erarbeitung grundlegender Definitionen viele der durch Tobias Achterberg und Timo Berthold in SCIP integrierten heuristischen Verfahren vorgestellt und kategorisiert. Auf dieser Grundlage bauen dann die Kapitel 2-4 der Arbeit auf. In diesen werden drei zusätzliche Heuristiken vorgestellt, im Einzelnen sind dies ZI Round, eine Rundeheuristik, welche zuerst von Wallace beschrieben wurde, außerdem eine 2-Opt-Heuristik für MIP und eine neue Startheuristik, Shift-And-Propagate. Großer Wert wird in jedem Kapitel auf die algorithmische Beschreibung der Heuristiken gelegt, die stets anhand von motivierenden Beispielen eingeführt und anhand von Pseudocode-Algorithmen begleitet werden. Zusätzlich enthält jedes Kapitel Auswertungen der mit den neuen Heuristiken gemessenen Ergebnisse von SCIP. Eine kurze Zusammenfassung in Kapitel 5 schließt diese Arbeit ab. N2 - Many practically relevant problems can be formulated in terms of a mixed integer programming (MIP) model. MIP denotes the optimization of a linear objective function under a certain number of linear side constraints including the need for some of the involved variables to take integral solution values. Applications of MIP based optimization can be found in the area of public transit, scheduling, automatic vehicle routing, network design, etc. From a complexity point of view, MIP solving is known to be NP-hard and most commonly tried to be solved via Branch-and-Bound based algorithms. Branch-and-Bound algorithms benefit from early and good feasible solutions of a MIP in various ways. Primal heuristics are aimed at finding new solutions during the MIP solving process. There are different types of primal heuristics: while start heuristics are particularly valuable to find an early solution, improvement heuristics hopefully drive a given solution further towards optimality. This thesis focusses on primal heuristics which are part of the MIP-solving framework SCIP. The first chapter comes with basic definitions and a brief description of SCIP and the test set which we used. The remainder of the first chapter is an overview of the existing heuristics in SCIP which have been implemented by Achterberg and Berthold. In the following chapters we introduce three new heuristics which apply rounding or propagation techniques for their specific purpose, namely the new rounding heuristic ZI Round, taken from Wallace, a 2-Opt improvement heuristic for MIP and the propagation heuristic Shift-and-Propagate. It is characteristic of all three heuristics that they mainly apply computationally inexpensive algorithms. Each of them is presented in an own chapter, starting with an algorithmic description, followed by implementational details. All chapters close with a discussion of the computational results obtained with the respective implementations in SCIP. KW - Primal Heuristics, MIP, mixed integer programming, ZI Round, Shift-and-Propagate, optimization Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13322 ER - TY - GEN A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Hendel, Gregor T1 - Rounding and Propagation Heuristics for Mixed Integer Programming N2 - Primal heuristics are an important component of state-of-the-art codes for mixed integer programming. In this paper, we focus on primal heuristics that only employ computationally inexpensive procedures such as rounding and logical deductions (propagation). We give an overview of eight different approaches. To assess the impact of these primal heuristics on the ability to find feasible solutions, in particular early during search, we introduce a new performance measure, the primal integral. Computational experiments evaluate this and other measures on MIPLIB~2010 benchmark instances. T3 - ZIB-Report - 11-29 KW - primal heuristic KW - mixed integer programming KW - domain propagation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13255 ER - TY - GEN A1 - Gottwald, Susanne T1 - Recommender Systeme für den Einsatz in Bibliotheken N2 - In diesem Report wird ein Überblick über Recommender Systeme (RS) im Bibliotheksbereich gegeben, welche Eigenschaften RS haben und welche Bedeutung sie damit für Bibliotheken besitzen. Es existieren semantische und nicht-semantische Lösungen, die dem Benutzer aus einer Menge von Publikationen die für ihn relevantesten empfehlen. Diese Arbeiten sowie eine Einleitung in das Thema werden präsentiert und mit den gewonnenen Kenntnissen ein Ausblick auf mögliche Entwicklungen gegeben. T3 - ZIB-Report - 11-30 KW - Semantic Web KW - Recommender Systems Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13261 ER - TY - GEN A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Symmetry analysis and exact solutions of semilinear heat flow in multi-dimensions N2 - A symmetry group method is used to obtain exact solutions for a semilinear radial heat equation in $n&gt;1$ dimensions with a general power nonlinearity. The method involves an ansatz technique to solve an equivalent first-order PDE system of similarity variables given by group foliations of this heat equation, using its admitted group of scaling symmetries. This technique yields explicit similarity solutions as well as other explicit solutions of a more general (non-similarity) form having interesting analytical behavior connected with blow up and dispersion. In contrast, standard similarity reduction of this heat equation gives a semilinear ODE that cannot be explicitly solved by familiar integration techniques such as point symmetry reduction or integrating factors. T3 - ZIB-Report - 11-26 KW - semilinear heat equation, similarity reduction, exact solutions, group foliation, symmetry Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13213 ER - TY - GEN A1 - Manfred, Brandt A1 - Andreas, Brandt T1 - On sojourn times for an infinite-server system in random environment and its application to processor sharing systems N2 - We deal with an infinite-server system where the service speed is governed by a stationary and ergodic process with countably many states. Applying a random time transformation such that the service speed becomes one, the sojourn time of a class of virtual requests with given required service time is equal in distribution to an additive functional defined via a stationary version of the time-changed process. Thus bounds for the expectation of functions of additive functionals yield bounds for the expectation of functions of virtual sojourn times, in particular bounds for fractional moments and the distribution function. Interpreting the $GI(n)/GI(n)/\infty$ system or equivalently the $GI(n)/GI$ system under state-dependent processor sharing as an infinite-server system with random states given by the number $n$ of requests in the system provides results for sojourn times of virtual requests. In case of $M(n)/GI(n)/\infty$, the sojourn times of arriving and added requests are equal in distribution to sojourn times of virtual requests in modified systems, which yields many results for the sojourn times of arriving and added requests. In case of integer moments, the bounds generalize earlier results for $M/GI(n)/\infty$. In particular, the mean sojourn times of arriving and added requests in $M(n)/GI(n)/\infty$ are proportional to the required service time, generalizing Cohen's famous result for $M/GI(n)/\infty$. T3 - ZIB-Report - 11-28 KW - infinite-server KW - random environment KW - time transformation KW - sojourn times KW - state-dependent processor sharing Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13190 ER - TY - GEN A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Weber, Marcus T1 - Soft Versus Hard Metastable Conformations in Molecular Simulations N2 - Particle methods have become indispensible in conformation dynamics to compute transition rates in protein folding, binding processes and molecular design, to mention a few. Conformation dynamics requires at a decomposition of a molecule's position space into metastable conformations. In this paper, we show how this decomposition can be obtained via the design of either ``soft'' or ``hard'' molecular conformations. We show, that the soft approach results in a larger metastabilitiy of the decomposition and is thus more advantegous. This is illustrated by a simulation of Alanine Dipeptide. T3 - ZIB-Report - 11-27 KW - Proteins, Conformation Space, Meshfree Methods Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13189 ER - TY - GEN A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Exact solutions of nonlinear partial differential equations by the method of group foliation reduction N2 - A novel symmetry method for finding exact solutions to nonlinear PDEs is illustrated by applying it to a semilinear reaction-diffusion equation in multi-dimensions. The method is based on group foliation reduction and employs a separation ansatz to solve an equivalent first-order group foliation system whose independent and dependent variables respectively consist of the invariants and differential invariants of a given one-dimensional group of point symmetries for the reaction-diffusion equation. With this method, solutions of the reaction-diffusion equation are obtained in an explicit form, including group-invariant similarity solutions and travelling-wave solutions, as well as dynamically interesting solutions that are not invariant under any of the point symmetries admitted by this equation. T3 - ZIB-Report - 11-25 KW - semilinear heat equation, similarity reduction, exact solutions, group foliation, symmetry Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13171 ER - TY - GEN T1 - Jahresbericht 2010 T1 - Annual 2010 T3 - Jahresbericht - 2010 KW - Annual Report Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13165 ER - TY - GEN A1 - Wolf, Thomas A1 - Efimovskaya, Olga T1 - On integrability of the Kontsevich non-abelian ODE system N2 - We consider systems of ODEs with the right hand side being Laurent polynomials in several non-commutative unknowns. In particular, these unknowns could be matrices of arbitrary size. An important example of such a system was proposed by M. Kontsevich. We prove the integrability of the Kontsevich system by finding a Lax pair, corresponding first integrals and commuting flows. We also provide a pre-Hamiltonian operator which maps gradients of integrals for the Kontsevich system to symmetries. T3 - ZIB-Report - 11-24 KW - integrability, Lax pairs, noncommutative ODE, Laurent ODE Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13113 ER - TY - GEN A1 - Schiela, Anton A1 - Wachsmuth, Daniel T1 - Convergence Analysis of Smoothing Methods for Optimal Control of Stationary Variational Inequalities N2 - In the article an optimal control problem subject to a stationary variational inequality is investigated. The optimal control problem is complemented with pointwise control constraints. The convergence of a smoothing scheme is analyzed. There, the variational inequality is replaced by a semilinear elliptic equation. It is shown that solutions of the regularized optimal control problem converge to solutions of the original one. Passing to the limit in the optimality system of the regularized problem allows to prove C-stationarity of local solutions of the original problem. Moreover, convergence rates with respect to the regularization parameter for the error in the control are obtained. These rates coincide with rates obtained by numerical experiments, which are included in the paper. T3 - ZIB-Report - 11-23 KW - Variational inequalities KW - optimal control KW - control constraints KW - path-following KW - C-stationarity Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13125 ER - TY - GEN A1 - Günther, Andreas A1 - Lamecker, Hans A1 - Weiser, Martin T1 - Direct LDDMM of Discrete Currents with Adaptive Finite Elements N2 - We consider Large Deformation Diffeomorphic Metric Mapping of general $m$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete $m$-current attributes. T3 - ZIB-Report - 11-22 KW - Large Deformation KW - Diffeomorphic Registration KW - Matching KW - Currents KW - Adaptive Finite Elements Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13090 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Pfetsch, Marc A1 - Vigerske, Stefan T1 - Large Neighborhood Search beyond MIP N2 - Large neighborhood search (LNS) heuristics are an important component of modern branch-and-cut algorithms for solving mixed-integer linear programs (MIPs). Most of these LNS heuristics use the LP relaxation as the basis for their search, which is a reasonable choice in case of MIPs. However, for more general problem classes, the LP relaxation alone may not contain enough information about the original problem to find feasible solutions with these heuristics, e.g., if the problem is nonlinear or not all constraints are present in the current relaxation. In this paper, we discuss a generic way to extend LNS heuristics that have been developed for MIP to constraint integer programming (CIP), which is a generalization of MIP in the direction of constraint programming (CP). We present computational results of LNS heuristics for three problem classes: mixed-integer quadratically constrained programs, nonlinear pseudo-Boolean optimization instances, and resource-constrained project scheduling problems. Therefore, we have implemented extended versions of the following LNS heuristics in the constraint integer programming framework SCIP: Local Branching, RINS, RENS, Crossover, and DINS. Our results indicate that a generic generalization of LNS heuristics to CIP considerably improves the success rate of these heuristics. T3 - ZIB-Report - 11-21 KW - Large Neighborhood Search KW - Primal Heuristic KW - MIP KW - MIQCP KW - Pseudo-Boolean Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12989 ER - TY - GEN ED - Achterberg, Tobias ED - Beck, J. Christopher T1 - CPAIOR 2011 - Late Breaking Abstracts N2 - As part of the CPAIOR 2011 a call was made for late breaking abstracts for presentation at the conference. These abstracts were meant to represent work in process, recent work, or work appearing in other academic areas but of interest to the CPAIOR community. A total of 19 submissions were received of which 16 were selected by the program chairs for presentation. This document is a compilation of the presented abstracts. T3 - ZIB-Report - 11-20 KW - CPAIOR KW - Late Breaking Abstracts Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12947 ER - TY - GEN A1 - Koch, Thorsten A1 - Achterberg, Tobias A1 - Andersen, Erling A1 - Bastert, Oliver A1 - Berthold, Timo A1 - Bixby, Robert E. A1 - Danna, Emilie A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Lodi, Andrea A1 - Mittelmann, Hans A1 - Ralphs, Ted A1 - Salvagnin, Domenico A1 - Steffy, Daniel A1 - Wolter, Kati T1 - MIPLIB 2010 N2 - This paper reports on the fifth version of the Mixed Integer Programming Library. The MIPLIB 2010 is the first MIPLIB release that has been assembled by a large group from academia and from industry, all of whom work in integer programming. There was mutual consent that the concept of the library had to be expanded in order to fulfill the needs of the community. The new version comprises 361 instances sorted into several groups. This includes the main benchmark test set of 87 instances, which are all solvable by today's codes, and also the challenge test set with 164 instances, many of which are currently unsolved. For the first time, we include scripts to run automated tests in a predefined way. Further, there is a solution checker to test the accuracy of provided solutions using exact arithmetic. T3 - ZIB-Report - 10-31 KW - Mixed Integer Programming KW - Problem Instances KW - IP KW - MIP KW - MIPLIB Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12953 ER - TY - GEN A1 - Stötzel, Claudia A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Advances in modelling of the bovine estrous cycle: Administration of PGF2alpha N2 - Our model of the bovine estrous cycle is a set of ordinary differential equations which generates hormone profiles of successive estrous cycles with several follicular waves per cycle. It describes the growth and decay of the follicles and the corpus luteum, as well as the change of the key substances over time. In this work we describe recent improvements of this model, including the introduction of new components, and elimination of time delays. We validate our model by showing that the simulations agree with observations from synchronization studies and with measured progesterone data after a single dose administration of synthetic prostaglandin F2alpha. T3 - ZIB-Report - 11-17 KW - cow KW - reproduction KW - hormone patterns KW - differential equations KW - systems biology Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12740 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Schulz, Jens T1 - An approximative Criterion for the Potential of Energetic Reasoning N2 - Energetic reasoning is one of the most powerful propagation algorithms in cumulative scheduling. In practice, however, it is not commonly used because it has a high running time and its success highly depends on the tightness of the variable bounds. In order to speed up energetic reasoning, we provide an easy-to-check necessary condition for energetic reasoning to detect infeasibilities. We present an implementation of energetic reasoning that employs this condition and that can be parametrically adjusted to handle the trade-off between solving time and propagation overhead. Computational results on instances from the PSPLIB are provided. These results show that using this condition decreases the running time by more than a half, although more search nodes need to be explored. T3 - ZIB-Report - 11-12 KW - conflict analysis KW - constraint integer programming KW - cumulative constraint KW - resource-constrained project scheduling KW - energetic reasoning Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12655 ER - TY - GEN A1 - Heinz, Stefan A1 - Beck, J. Christopher T1 - Solving Resource Allocation/Scheduling Problems with Constraint Integer Programming N2 - Constraint Integer Programming (CIP) is a generalization of mixed-integer programming (MIP) in the direction of constraint programming (CP) allowing the inference techniques that have traditionally been the core of \P to be integrated with the problem solving techniques that form the core of complete MIP solvers. In this paper, we investigate the application of CIP to scheduling problems that require resource and start-time assignments to satisfy resource capacities. The best current approach to such problems is logic-based Benders decomposition, a manual decomposition method. We present a CIP model and demonstrate that it achieves performance competitive to the decomposition while out-performing the standard MIP and CP formulations. T3 - ZIB-Report - 11-14 KW - constraint integer programming KW - cumulative constraint KW - optional resources KW - mixed integer programming KW - constraint programming Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12691 ER - TY - GEN A1 - Heinz, Stefan A1 - Schulz, Jens T1 - Explanations for the Cumulative Constraint: an Experimental Study N2 - In cumulative scheduling, conflict analysis seems to be one of the key ingredients to solve such problems efficiently. Thereby, the computational complexity of explanation algorithms plays an important role. Even more when we are faced with a backtracking system where explanations need to be constructed on the fly. In this paper we present extensive computational results to analyze the impact of explanation algorithms for the cumulative constraint in a backward checking system. The considered explanation algorithms differ in their quality and computational complexity. We present results for the domain propagation algorithms time-tabling, edge-finding, and energetic reasoning. T3 - ZIB-Report - 11-13 KW - conflict analysis KW - constraint integer programming KW - cumulative constraint KW - resource-constrained project scheduling KW - propagation algorithms Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12668 ER - TY - GEN A1 - Giovanidis, Anastasios A1 - Brueck, Stefan A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Hartanto Tanzil, Vicky T1 - A 0-1 Program for Minimum Clustering in Downlink Base Station Cooperation N2 - Base station cooperation in the downlink of cellular systems has been recently suggested as a promising concept towards a better exploitation of the communication system physical resources. It may offer a high gain in capacity through interference mitigation. This however, comes at a cost of high information exchange between cooperating entities and a high computational burden. Clustering of base stations into subgroups is an alternative to guarantee such cooperation benefits in a lower scale. The optimal definition of clusters, however, and a systematic way to find a solution to such problem is not yet available. In this work, we highlight the combinatorial nature of the problem, exploit this to describe the system of users and base stations as a graph and formulate a pure 0-1 program. Its solution suggests a cost optimal way to form clusters and assign user subsets to them. T3 - ZIB-Report - 11-19 KW - Wireless Communications KW - Base Station Cooperation KW - 0-1 Program Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12776 ER - TY - GEN A1 - Giovanidis, Anastasios A1 - Liao, Qi A1 - Stanczak, Slawomir T1 - Measurement Based Self-Optimization in Random Access Communications N2 - The current work considers random access communications within a single cell and provides an algorithmic suggestion for the almost optimal coordination of user actions. In the scenario considered, an access effort is successful if (a) the signal is detected at the receiver and (b) no collision occurs. The first event is controlled by the user transmission power and the second by the choice of access (back-off) probability. These constitute the user action pair. The algorithm aims at exploiting information from measurements and user reports, in order to estimate current values of the system situation. Based on these, two optimization problems can be formulated and solved for the so called contention level and transmission power level at the base station side. The methodology to find the optimal values is based on minimization of a drift function. The two values are broadcast in order to help the users update their actions ``almost optimally``. In this way the wireless cell can achieve self-optimization, without outside coordination, by relying on such intelligent information exchange and parameter estimation. Numerical results illustrate the great benefits of the suggested algorithm, compared to scenarios where the actions remain fixed, at a very low or even zero cost in power expenditure and delay. T3 - ZIB-Report - 11-18 KW - Random Access Channel KW - Self Organizing Networks (SONs) KW - Dynamic Programming KW - Drift Minimization KW - ALOHA Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12764 ER - TY - GEN A1 - Röblitz, Susanna A1 - Stötzel, Claudia A1 - Deuflhard, Peter A1 - Jones, Hannah M. A1 - Azulay, David-Olivier A1 - van der Graaf, Piet A1 - Martin, Steven T1 - A mathematical model of the human menstrual cycle for the administration of GnRH analogues N2 - This study presents a differential equation model for the feedback mechanisms between Gonadotropin-releasing Hormone (GnRH), Follicle-Stimulating Hormone (FSH), Luteinizing Hormone (LH), development of follicles and corpus luteum, and the production of estradiol (E2), progesterone (P4), inhibin A (IhA), and inhibin B (IhB) during the female menstrual cycle. In contrast to other models, this model does not involve delay differential equations and is based on deterministic modelling of the GnRH pulse pattern, which allows for faster simulation times and efficient parameter identification. These steps were essential to tackle the task of developing a mathematical model for the administration of GnRH analogues. The focus of this paper is on model development for GnRH receptor binding and the integration of a pharmacokinetic/pharmacodynamic model for the GnRH agonist Nafarelin and the GnRH antagonist Cetrorelix into the menstrual cycle model. The final mathematical model describes the hormone profiles (LH, FSH, P4, E2) throughout the menstrual cycle in 12 healthy women. Moreover, it correctly predicts the changes in the cycle following single and multiple dose administration of Nafarelin or Cetrorelix at different stages in the cycle. T3 - ZIB-Report - 11-16 KW - human menstrual cycle KW - systems biology KW - mathematical modelling KW - GnRH analogues KW - differential equations Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12732 ER - TY - GEN A1 - Dierkes, Thomas A1 - Wade, Moritz A1 - Nowak, Ulrich A1 - Röblitz, Susanna T1 - BioPARKIN - Biology-related Parameter Identification in Large Kinetic Networks N2 - Modelling, parameter identification, and simulation play an important rôle in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years. T3 - ZIB-Report - 11-15 KW - systems biology KW - ordinary differential equations KW - sensitivity analysis KW - parameter identification KW - affine invariant Gauss-Newton algorithm KW - numerical library KW - graphical user interface Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12706 ER - TY - GEN A1 - Dittel, Agnes A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Polyhedral Aspects of Self-Avoiding Walks N2 - In this paper, we study self-avoiding walks of a given length on a graph. We consider a formulation of this problem as a binary linear program. We analyze the polyhedral structure of the underlying polytope and describe valid inequalities. Proofs for their facial properties for certain special cases are given. In a variation of this problem one is interested in optimal configurations, where an energy function measures the benefit if certain path elements are placed on adjacent vertices of the graph. The most prominent application of this problem is the protein folding problem in biochemistry. On a set of selected instances, we demonstrate the computational merits of our approach. T3 - ZIB-Report - 11-11 KW - Polyhedral Combinatorics KW - Integer Programming KW - Self-Avoiding Path KW - Protein Folding Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12576 ER - TY - GEN A1 - Kratz, Andrea A1 - Reininghaus, Jan A1 - Hadwiger, Markus A1 - Hotz, Ingrid T1 - Adaptive Screen-Space Sampling for Volume Ray-Casting N2 - This work is concerned with adaptive screen-space sampling for volume ray-casting. The goal is to reduce the number of rays being cast into the scene and, thus, the overall number of sampling points. We guarantee reliable images through explicit error control using an error estimator that is founded in the field of finite element methods (FEM). FEM theory further provides a well-founded theory to prove the efficiency of the presented algorithm via convergence analysis. We, therefore, compare the convergence behavior of our method against uniform subdivisions and a refinement scheme that was presented in the context of CPU volume ray-casting. Minimizing the number of sampling points is of interest for rendering large datasets where each evaluation might need an expensive decompression. Furthermore, with increasing screen resolutions high-resolution images are created more efficiently with our method. T3 - ZIB-Report - 11-04 Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12446 ER - TY - GEN A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Valid Linear Programming Bounds for Exact Mixed-Integer Programming N2 - Fast computation of valid linear programming (LP) bounds serves as an important subroutine for solving mixed-integer programming problems exactly. We introduce a new method for computing valid LP bounds designed for this application. The algorithm corrects approximate LP dual solutions to be exactly feasible, giving a valid bound. Solutions are repaired by performing a projection and a shift to ensure all constraints are satisfied; bound computations are accelerated by reusing structural information through the branch-and-bound tree. We demonstrate this method to be widely applicable and faster than solving a sequence of exact LPs. Several variations of the algorithm are described and computationally evaluated in an exact branch-and-bound algorithm within the mixed-integer programming framework SCIP. T3 - ZIB-Report - 11-08 KW - linear programming bounds KW - mixed integer programming KW - branch-and-bound KW - exact computation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12332 ER - TY - GEN A1 - Fügenschuh, Armin A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Szabó, Jácint T1 - Gas Network Topology Optimization for Upcoming Market Requirements N2 - Gas distribution networks are complex structures that consist of passive pipes, and active, controllable elements such as valves and compressors. Controlling such network means to find a suitable setting for all active components such that a nominated amount of gas can be transmitted from entries to exits through the network, without violating physical or operational constraints. The control of a large-scale gas network is a challenging task from a practical point of view. In most companies the actual controlling process is supported by means of computer software that is able to simulate the flow of the gas. However, the active settings have to be set manually within such simulation software. The solution quality thus depends on the experience of a human planner. When the gas network is insufficient for the transport then topology extensions come into play. Here a set of new pipes or active elements is determined such that the extended network admits a feasible control again. The question again is how to select these extensions and where to place them such that the total extension costs are minimal. Industrial practice is again to use the same simulation software, determine extensions by experience, add them to the virtual network, and then try to find a feasible control of the active elements. The validity of this approach now depends even more on the human planner. Another weakness of this manual simulation-based approach is that it cannot establish infeasibility of a certain gas nomination, unless all settings of the active elements are tried. Moreover, it is impossible to find a cost-optimal network extension in this way. In order to overcome these shortcomings of the manual planning approach we present a new approach, rigorously based on mathematical optimization. Hereto we describe a model for finding feasible controls and then extend this model such that topology extensions can additionally and simultaneously be covered. Numerical results for real-world instances are presented and discussed. T3 - ZIB-Report - 11-09 KW - Mathematical Optimization KW - Gas Distribution Networks KW - Topology Planning Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12348 ER - TY - GEN A1 - Cook, William A1 - Koch, Thorsten A1 - Steffy, Daniel A1 - Wolter, Kati T1 - An Exact Rational Mixed-Integer Programming Solver N2 - We present an exact rational solver for mixed-integer linear programming that avoids the numerical inaccuracies inherent in the floating-point computations used by existing software. This allows the solver to be used for establishing theoretical results and in applications where correct solutions are critical due to legal and financial consequences. Our solver is a hybrid symbolic/numeric implementation of LP-based branch-and-bound, using numerically-safe methods for all binding computations in the search tree. Computing provably accurate solutions by dynamically choosing the fastest of several safe dual bounding methods depending on the structure of the instance, our exact solver is only moderately slower than an inexact floating-point branch-and-bound solver. The software is incorporated into the SCIP optimization framework, using the exact LP solver QSopt_ex and the GMP arithmetic library. Computational results are presented for a suite of test instances taken from the MIPLIB and Mittelmann collections. T3 - ZIB-Report - 11-07 KW - mixed integer programming KW - branch-and-bound KW - exact computation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12329 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Schweiger, Jonas T1 - Multistage Stochastic Programming in Strategic Telecommunication Network Planning N2 - Mobile communication is nowadays taken for granted. Having started primarily as a service for speech communication, data service and mobile Internet access are now driving the evolution of network infrastructure. Operators are facing the challenge to match the demand by continuously expanding and upgrading the network infrastructure. However, the evolution of the customer's demand is uncertain. We introduce a novel (long-term) network planning approach based on multistage stochastic programming, where demand evolution is considered as a stochastic process and the network is extended as to maximize the expected profit. The approach proves capable of designing large-scale realistic UMTS networks with a time-horizon of several years. Our mathematical optimization model, the solution approach, and computational results are presented in this paper. T3 - ZIB-Report - 11-06 KW - UMTS KW - Network Evolution KW - Multistage KW - Stochastic Programming Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12232 ER - TY - THES A1 - Schweiger, Jonas T1 - Application of Multistage Stochastic Programming in Strategic Telecommunication Network Planning N2 - Telecommunication is fundamental for the information society. In both, the private and the professional sector, mobile communication is nowadays taken for granted. Starting primarily as a service for speech communication, data service and mobile Internet access are now driving the evolution of network infrastructure. In the year 2009, 19 million users generated over 33 million GB of traffic using mobile data services. The 3rd generation networks (3G or UMTS) in Germany comprises over 39,000 base stations with some 120,000 cells. From 1998 to 2008, the four network operators in Germany invested over 33 billion Euros in their infrastructure. A careful allocation of the resources is thus crucial for the profitability for a network operator: a network should be dimensioned to match customers demand. As this demand evolves over time, the infrastructure has to evolve accordingly. The demand evolution is hard to predict and thus constitutes a strong source of uncertainty. Strategic network planning has to take this uncertainty into account, and the planned network evolution should adapt to changing market conditions. The application of superior planning methods under the consideration of uncertainty can improve the profitability of the network and creates a competitive advantage. Multistage stochastic programming is a suitable framework to model strategic telecommunication network planning. We present mathematical models and effective optimization procedures for strategic cellular network design. The demand evolution is modeled as a continuous stochastic process which is approximated by a discrete scenario tree. A tree-stage approach is used for the construction of non-uniform scenario trees that serve as input of the stochastic program. The model is calibrated by historical traffic observations. A realistic system model of UMTS radio cells is used that determines coverage areas and cell capacities and takes signal propagation and interferences into account. The network design problem is formulated as a multistage stochastic mixed integer linear program, which is solved using state-of-the-art commercial MIP solvers. Problem specific presolving is proposed to reduce the problem size. Computational results on realistic data is presented. Optimization for the expected profit and the conditional value at risk are performed and compared. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12206 ER - TY - GEN A1 - Reininghaus, Jan A1 - Kasten, Jens A1 - Weinkauf, Tino A1 - Hotz, Ingrid T1 - Combinatorial Feature Flow Fields: Tracking Critical Points in Discrete Scalar Fields N2 - We propose a combinatorial algorithm to track critical points of 2D time-dependent scalar fields. Existing tracking algorithms such as Feature Flow Fields apply numerical schemes utilizing derivatives of the data, which makes them prone to noise and involve a large number of computational parameters. In contrast, our method is robust against noise since it does not require derivatives, interpolation, and numerical integration. Furthermore, we propose an importance measure that combines the spatial persistence of a critical point with its temporal evolution. This leads to a time-aware feature hierarchy, which allows us to discriminate important from spurious features. Our method requires only a single, easy-to-tune computational parameter and is naturally formulated in an out-of-core fashion, which enables the analysis of large data sets. We apply our method to a number of data sets and compare it to the stabilized continuous Feature Flow Field tracking algorithm. T3 - ZIB-Report - 11-02 KW - data analysis KW - feature detection KW - time-varying data KW - topology-based techniques Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12151 ER - TY - GEN A1 - Poss, Michael A1 - Raack, Christian T1 - Affine recourse for the robust network design problem: between static and dynamic routing N2 - Affinely-Adjustable Robust Counterparts provide tractable alternatives to (two-stage) robust programs with arbitrary recourse. We apply them to robust network design with polyhedral demand uncertainty, introducing the affine routing principle. We compare the affine routing to the well-studied static and dynamic routing schemes for robust network design. All three schemes are embedded into the general framework of two-stage network design with recourse. It is shown that affine routing can be seen as a generalization of the widely used static routing still being tractable and providing cheaper solutions. We investigate properties on the demand polytope under which affine routings reduce to static routings and also develop conditions on the uncertainty set leading to dynamic routings being affine. We show however that affine routings suffer from the drawback that (even totally) dominated demand vectors are not necessarily supported by affine solutions. Uncertainty sets have to be designed accordingly. Finally, we present computational results on networks from SNDlib. We conclude that for these instances the optimal solutions based on affine routings tend to be as cheap as optimal network designs for dynamic routings. In this respect the affine routing principle can be used to approximate the cost for two-stage solutions with free recourse which are hard to compute. T3 - ZIB-Report - 11-03 KW - robust optimization KW - network design KW - recourse KW - affine adjustable robust counterparts KW - affine routing Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12122 ER - TY - THES A1 - Tuchscherer, Andreas T1 - Local Evaluation of Policies for Discounted Markov Decision Problems N2 - Providing realistic performance indicators of online algorithms for a given online optimization problem is a difficult task in general. Due to significant drawbacks of other concepts like competitive analysis, Markov decision problems (MDPs) may yield an attractive alternative whenever reasonable stochastic information about future requests is available. However, the number of states in MDPs emerging from real applications is usually exponential in the original input parameters. Therefore, the standard methods for analyzing policies, i.e., online algorithms in our context, are infeasible. In this thesis we propose a new computational tool to evaluate the behavior of policies for discounted MDPs locally, i.e., depending on a particular initial state. The method is based on a column generation algorithm for approximating the total expected discounted cost of an unknown optimal policy, a concrete policy, or a single action (which assumes actions at other states to be made according to an optimal policy). The algorithm determines an $\varepsilon$-approximation by inspecting only relatively small local parts of the total state space. We prove that the number of states required for providing the approximation is independent of the total number of states, which underlines the practicability of the algorithm. The approximations obtained by our algorithm are typically much better than the theoretical bounds obtained by other approaches. We investigate the pricing problem and the structure of the linear programs encountered in the column generation. Moreover, we propose and analyze different extensions of the basic algorithm in order to achieve good approximations fast. The potential of our analysis tool is exemplified for discounted MDPs emerging from different online optimization problems, namely online bin coloring, online target date assignment, and online elevator control. The results of the experiments are quite encouraging: our method is mostly capable to provide performance indicators for online algorithms that much better reflect observations made in simulations than competitive analysis does. Moreover, the analysis allows to reveal weaknesses of the considered online algorithms. This way, we developed a new online algorithm for the online bin coloring problem that outperforms existing ones in our analyses and simulations. KW - Markov decision problem KW - online optimization KW - linear programming KW - column generation KW - performance guarantees Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11963 ER - TY - GEN A1 - Meyer, Christian A1 - Panizzi, Lucia A1 - Schiela, Anton T1 - Uniqueness criteria for solutions of the adjoint equation in state-constrained optimal control N2 - The paper considers linear elliptic equations with regular Borel measures as inhomogeneity. Such equations frequently appear in state-constrained optimal control problems. By a counter-example of Serrin, it is known that, in the presence of non-smooth data, a standard weak formulation does not ensure uniqueness for such equations. Therefore several notions of solution have been developed that guarantee uniqueness. In this note, we compare different definitions of solutions, namely the ones of Stampacchia and the two notions of solutions of Casas and Alibert-Raymond, and show that they are the same. As side results, we reformulate the solution in the sense of Stampacchia, and prove the existence and uniqueness of solutions in in case of mixed boundary conditions. T3 - ZIB-Report - 10-28 KW - optimal control KW - elliptic partial differential equations KW - state constraints KW - measure right hand sides Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11933 ER - TY - GEN A1 - Stephan, Rüdiger A1 - Maurras, Jean A1 - Nedev, Roumen T1 - On the connectivity of k-clique polytopes N2 - In this paper, we study the neighbourlicity of the polytope $P_{k n}^2$ constituted by the $k$-cliques of the complete graph $K_n$ on $n$ vertices. We prove that this polytope is $3$-, but not $4$-neighbourly. Following a remark of Pierre Duchet, we partially generalize this result to the $k$-clique polytopes of $r$-uniform complete hypergraphs, $P_{kn}^r$. We show that the neighbourlicity of $P_{kn}^r$ is between $r$ and $2^r-1$ whenever $k\geq r+1$ and $n\geq k+r+1$. Computational results indicate that the upper bound is tight. T3 - ZIB-Report - 10-29 KW - clique polytope KW - connectivity Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11949 ER - TY - GEN A1 - Stephan, Rüdiger T1 - Smaller compact formulation for lot-sizing with constant batches N2 - We consider a variant of the classical lot-sizing problem in which the capacity in each period is an integer multiple of some basic batch size. Pochet and Wolsey (Math. Oper. Res. 18, 1993) presented an O(n^2 min{n,C}) algorithm to solve this problem and a linear program with O(n^3) variables and inequalities, where n is the number of periods and C the batch size. We provide a linear program of size O(n^2 min{n,C}), that is, in case that C < n, our formulation is smaller. T3 - ZIB-Report - 10-30 KW - compact formulation KW - lot-sizing KW - constant batch size Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11956 ER - TY - GEN A1 - Kratz, Andrea A1 - Meyer, Björn A1 - Hotz, Ingrid T1 - A Visual Approach to Analysis of Stress Tensor Fields N2 - We present a visual approach for the exploration of stress tensor fields. Therefore, we introduce the idea of multiple linked views to tensor visualization. In contrast to common tensor visualization methods that only provide a single view to the tensor field, we pursue the idea of providing various perspectives onto the data in attribute and object space. Especially in the context of stress tensors, advanced tensor visualization methods have a young tradition. Thus, we propose a combination of visualization techniques domain experts are used to with statistical views of tensor attributes. The application of this concept to tensor fields was achieved by extending the notion of shape space. It provides an intuitive way of finding tensor invariants that represent relevant physical properties. Using brushing techniques, the user can select features in attribute space, which are mapped to displayable entities in a three-dimensional hybrid visualization in object space. Volume rendering serves as context, while glyphs encode the whole tensor information in focus regions. Tensorlines can be included to emphasize directionally coherent features in the tensor field. We show that the benefit of such a multi-perspective approach is manifold. Foremost, it provides easy access to the complexity of tensor data. Moreover, including wellknown analysis tools, such as Mohr diagrams, users can familiarize themselves gradually with novel visualization methods. Finally, by employing a focus-driven hybrid rendering, we significantly reduce clutter, which was a major problem of other three-dimensional tensor visualization methods. T3 - ZIB-Report - 10-26 KW - Visualisierung KW - Datenanalyse KW - Tensorfelder Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11915 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten T1 - ParaSCIP - a parallel extension of SCIP N2 - Mixed integer programming (MIP) has become one of the most important techniques in Operations Research and Discrete Optimization. SCIP (Solving Constraint Integer Programs) is currently one of the fastest non-commercial MIP solvers. It is based on the branch-and-bound procedure in which the problem is recursively split into smaller subproblems, thereby creating a so-called branching tree. We present ParaSCIP, an extension of SCIP, which realizes a parallelization on a distributed memory computing environment. ParaSCIP uses SCIP solvers as independently running processes to solve subproblems (nodes of the branching tree) locally. This makes the parallelization development independent of the SCIP development. Thus, ParaSCIP directly profits from any algorithmic progress in future versions of SCIP. Using a first implementation of ParaSCIP, we were able to solve two previously unsolved instances from MIPLIB2003, a standard test set library for MIP solvers. For these computations, we used up to 2048 cores of the HLRN~II supercomputer. T3 - ZIB-Report - 10-27 KW - massive parallization KW - mixed integer programming KW - ParaSCIP KW - branch-and-cut KW - branch-and-bound Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11921 UR - http://www.springerlink.com/content/t2160206253v7661/ ER - TY - GEN A1 - Berg, Mascha A1 - Ritter, Julia A1 - Röblitz, Susanna T1 - A mathematical model for the Zinc response of young pigs N2 - In a number of studies the feeding of pharmacological levels of Zinc to weanling pigs was examined. The publications agree in the fact that the achieved performance increase of the pigs depends on the amount of Zinc as well as on the type of mineral complex used as feed additive. The results are based on measurements of the animals' body weight and the Zinc concentration in the blood within the first two weeks of the experiments. From the measurement values, conclusions are drawn about adequate Zinc doses, but a deeper understanding of the physiological processes that influence the Zinc distribution in the organism is still missing. In this report, we want to close this gap by using a systems biology approach. We present a small mathematical model that describes the organic feedback mechanisms with the help of differential equations. The simulation results not only match with measurement values, but also give insight into non-measurable processes, which will hopefully contribute to animal experiments being organized in a more selective and reduced way. T3 - ZIB-Report - 11-05 KW - systems biology KW - ordinary differential equations KW - feeding study KW - weanling pigs Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12191 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Vigerske, Stefan T1 - On the computational impact of MIQCP solver components N2 - We provide a computational study of the performance of a state-of-the-art solver for nonconvex mixed-integer quadratically constrained programs (MIQCPs). Since successful general-purpose solvers for large problem classes necessarily comprise a variety of algorithmic techniques, we focus especially on the impact of the individual solver components. The solver SCIP used for the experiments implements a branch-and-cut algorithm based on linear outer approximation to solve MIQCPs to global optimality. Our analysis is based on a set of 86 publicly available test instances. T3 - ZIB-Report - 11-01 KW - MIQCP KW - MIP KW - mixed-integer quadratically constrained programming KW - computational KW - nonconvex Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11998 ER - TY - GEN A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Schiela, Anton T1 - Solving Optimal Control Problems with the Kaskade 7 Finite Element Toolbox N2 - This paper presents concepts and implementation of the finite element toolbox Kaskade 7, a flexible C++ code for solving elliptic and parabolic PDE systems. Issues such as problem formulation, assembly and adaptivity are discussed at the example of optimal control problems. Trajectory compression for parabolic optimization problems is considered as a case study. T3 - ZIB-Report - 10-25 KW - partial differential equations KW - optimal control KW - finite elements KW - generic programming KW - adaptive methods Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11909 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimizing the Simplon Railway Corridor N2 - This paper presents a case study on a railway timetable optimization for the very dense Simplon corridor, a major railway connection in the Alps between Switzerland and Italy. Starting from a detailed microscopic network as it is used in railway simulation, the data is transformed by an automatic procedure to a less detailed macroscopic network, that is sufficient for the purpose of capacity planning and amenable to state-of-the-art integer programming optimization methods. In this way, the macroscopic railway network is saturated with trains. Finally, the corresponding timetable is re-transformed to the microscopic level in such a way that it can be operated without any conflicts among the slots. Using this integer programming based micro-macro aggregation-disaggregation approach, it becomes for the first time possible to generate a profit maximal and conflict free timetable for the complete Simplon corridor over an entire day by a simultaneous optimization of all trains requests. This also allows to to undertake a sensitivity analysis of various problem parameters. T3 - ZIB-Report - 10-24 KW - Trassenallokation KW - Netzwerkaggregation KW - Fallstudie KW - Simplon Korridor KW - railway track allocation KW - network aggregation KW - case study KW - Simplon corridor Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11892 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Aggregation Methods for Railway Networks N2 - In this paper a bottom-up approach of automatic simplification of a railway network is presented. Starting from a very detailed, microscopic level, as it is used in railway simulation, the network is transformed by an algorithm to a less detailed level (macroscopic network), that is sufficient for long-term planning and optimization. In addition running and headway times are rounded to a pre-chosen time discretization by a special cumulative method, which we will present and analyse in this paper. After the transformation we fill the network with given train requests to compute an optimal slot allocation. Then the optimized schedule is re-transformed into the microscopic level and can be simulated without any conflicts occuring between the slots. The algorithm is used to transform the network of the very dense Simplon corridor between Swiss and Italy. With our aggregation it is possible for the first time to generate a profit maximal and conflict free timetable for the corridor across a day by a simultaneously optimization run. T3 - ZIB-Report - 10-23 KW - makroskopische Bahnmodellierung KW - Netzwerkaggregation KW - macroscopic railway modeling KW - network aggregation Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11881 UR - http://www.sciencedirect.com/science/article/pii/S2210970611000047 SN - 1438-0064 ER - TY - THES A1 - Orlowski, Sebastian T1 - Optimal Design of Survivable Multi-layer Telecommunication Networks N2 - Telecommunication transport networks consist of a stack of technologically different subnetworks, so-called layers, which are strongly interdependent. For example, one layer may correspond to an Internet (IP) backbone network whose links are realized by lightpath connections in an underlying optical fiber layer. To ensure that the network can fulfill its task of routing all communication requests, the inter-layer dependencies have to be taken into account already in the planning phase of the network. This is particularly important with survivability constraints, where connections in one layer have to be protected against cable cuts or equipment failures in another layer. The traditional sequential planning approach where one layer is optimized after the other cannot properly take care of the inter-layer dependencies; this can only be achieved with an integrated planning of several network layers at the same time. This thesis provides mathematical models and algorithmic techniques for the integrated optimization of two network layers with survivability constraints. We describe a multi-layer network design problem which occurs in various technologies, and model it mathematically using mixed-integer programming (MIP) formulations. The presented models cover many important practical side constraints from different technological contexts. In contrast to previous models from the literature, they can be used to design large two-layer networks with survivability requirements. We discuss modeling alternatives for various aspects of a multi-layer network and compare different routing formulations under multi-layer survivability constraints. We solve our models using a branch-and-cut-and-price approach with various problemspecific enhancements. This includes a presolving technique based on linear programming to reduce the problem size, combinatorial and sub-MIP-based primal heuristics to compute feasible network configurations, cutting planes which take the multi-layer survivability constraints into account to improve the lower bound on the optimal network cost, and column generation to generate flow variables dynamically during the algorithm. We develop techniques to speed up computations in a Benders decomposition approach and compare this approach to the standard formulation with a single MIP. We use the developed techniques to design large survivable two-layer networks by means of linear and integer programming methods. On realistic test instances with up to 67 network nodes and survivability constraints, we investigate the algorithmic impact of our techniques and show how to use them to compute good network configurations with quality guarantees. Most of the smaller test instances with up to 17 nodes can be solved to near-optimality. Moreover, we can compute feasible solutions and dual bounds even for large networks with survivability constraints, which has not been possible before. KW - Telekommunikationsnetze KW - Multi-layer-Netzen Ausfallsicherheit KW - gemischt-ganzzahlige Optimierung KW - Branch-and-cut-and-price KW - telecommunication networks KW - survivable multi-layer network design KW - mixed-integer programming KW - branch-and-cut-and-price Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11876 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - Railway Track Allocation by Rapid Branching N2 - The track allocation problem, also known as train routing problem or train timetabling problem, is to find a conflict-free set of train routes of maximum value in a railway network. Although it can be modeled as a standard path packing problem, instances of sizes relevant for real-world railway applications could not be solved up to now. We propose a rapid branching column generation approach that integrates the solution of the LP relaxation of a path coupling formulation of the problem with a special rounding heuristic. The approach is based on and exploits special properties of the bundle method for the approximate solution of convex piecewise linear functions. Computational results for difficult instances of the benchmark library TTPLIB are reported. T3 - ZIB-Report - 10-22 KW - Trassenallokationsproblem KW - Ganzzahlige Programmierung KW - Rapid-Branching-Heuristik KW - Proximale Bündelmethode KW - Optimization KW - Railway Track Allocation KW - Bundle Method KW - Rapid Branching Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11864 SN - 1438-0064 ER - TY - THES A1 - Ruprecht, Daniel T1 - Analysis of a multi-scale asymptotic model for internal gravity waves in a moist atmosphere N2 - The thesis presents the analysis of a reduced model for modulation of internal gravity waves by deep convective clouds. The starting point for the derivation are conservation laws for mass, momentum and energy coupled with a bulk micro-physics model describing the evolution of mixing ratios of water vapor, cloud water and rain water. A reduced model for the identified scales of the regime is derived, using multi-scale asymptotics. The closure of the model employs conditional averaging over the horizontal scale of the convective clouds. The resulting reduced model is an extension of the anelastic equations, linearized around a constant background state, which are well-known from meteorology. The closure of the model is achieved purely by analytical means and involves no additional physically motivated assumptions. The essential new parameter arising from the coupling to a micro-physics model is the area fraction of saturated regions on the horizontal scale of the convective clouds. It turns out that this parameter is constant on the employed short timescale. Hence the clouds constitute a constant background, modulating the characteristics of propagation of internal waves. The model is then investigated by analytical as well as numerical means. Important results are, among others, that in the model moisture (i) inhibits propagation of internal waves by reducing the modulus of the group velocity, (ii) reduces the angle between the propagation direction of a wave-packet and the horizontal, (iii) causes critical layers and (iv) introduces a maximum horizontal wavelength beyond which waves are no longer propagating but become evanescent. The investigated examples of orographically generated gravity waves also feature a significant reduction of vertical momentum flux by moisture. The model is extended by assuming systematically small under-saturation, that is saturation at leading order. The closure is similar to the original case but requires additional assumptions. The saturated area fraction in the obtained model is no longer constant but now depends nonlinearly on vertical displacement and thus on vertical velocity. KW - gravity-waves KW - moisture KW - multiscale KW - reduced model KW - deep convective clouds Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000018355-1 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - The Quickest Path to the Goal N2 - We provide an introduction into the mathematics of and with paths. Not on the shortest, but hopefully on an entertaining path! T3 - ZIB-Report - 10-21 KW - shortest paths KW - combinatorial optimization KW - operations research Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11840 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika T1 - Linienoptimierung - reif für die Praxis? N2 - Wir stellen in dieser Arbeit ein mathematisches Optimierungsmodell zur Bestimmung eines optimalen Linienplans vor, das sowohl die Fahrzeiten und die Anzahl der Umstiege berücksichtigt als auch die Kosten des Liniennetzes. Dieses Modell deckt wichtige praktische Anforderungen ab, die in einem gemeinsamen Projekt mit den Verkehrsbetrieben in Potsdam (ViP) formuliert wurden. In diesem Projekt wurde der Linienplan 2010 für Potsdam entwickelt. Unsere Berechnungen zeigen, dass die mathematische Optimierung in nichts einer "Handplanung" des Liniennetzes nachsteht. Im Gegenteil, mit Hilfe des Optimierungsprogramms ist es möglich, durch Veränderung der Parameter mehrere verschiedene Szenarien zu berechnen, miteinander zu vergleichen und Aussagen über minimale Kosten und Fahrzeiten zu machen. T3 - ZIB-Report - 10-20 KW - Linienplanung KW - Optimierung Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11832 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - Positions in the Game of Go as Complex Systems N2 - The paper gathers evidence showing different dimensions of the game of Go: the continuous and discrete nature of the game and different types of relations between state variables happening on ultra local, local, regional, and global scales. Based on these observations a new continuous local model for describing a board position is introduced. This includes the identification of the basic variables describing a board position and the formulation and solution of a dynamical system for their computation. To be usable as a static evaluation function for a game playing program at least group-wide (regional)aspects will have to be incorporated. T3 - ZIB-Report - 10-19 KW - Computer Go KW - static evaluation KW - discrete dynamical systems Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11823 SN - 1438-0064 ER - TY - GEN T1 - Jahresbericht 2009 T1 - Annual 2009 T3 - Jahresbericht - 2009 KW - Annual Report Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11814 SN - 0934-5892 ER - TY - GEN A1 - Wolf, Thomas A1 - Efimovskaya, Olya V. T1 - Classification of integrable quadratic Hamiltonians on e(3) N2 - Linear Poisson brackets on e(3) typical of rigid body dynamics are considered. All quadratic Hamiltonians of Kowalevski type having additional first integral of fourth degree are found. Quantum analogs of these Hamiltonians are listed. T3 - ZIB-Report - 10-18 KW - Linear Poisson brackets on e(3) KW - rigid body dynamics KW - Kowalevski type Hamiltonians KW - first integrals Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11807 SN - 1438-0064 ER - TY - GEN A1 - Kiselev, A. V. A1 - Wolf, Thomas T1 - Classification of integrable super-systems using the SsTools environment N2 - A classification problem is proposed for supersymmetric %scaling\/-\/in\-va\-ri\-ant evolutionary PDE that satisfy the assumptions of nonlinearity, nondegeneracy, and homogeneity. Four classes of nonlinear coupled boson\/-\/fermion systems are discovered under the weighting assumption $|f|=|b|=|D_t|=\oh$. The syntax of the \Reduce\ package \SsTools, which was used for intermediate computations, and the applicability of its procedures to the calculus of super\/-\/PDE are described. T3 - ZIB-Report - 10-17 KW - Integrable super-systems KW - symmetries KW - recursions KW - classifiaction Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11792 SN - 1438-0064 ER - TY - GEN A1 - Hussin, V. A1 - Kiselev, A. V. A1 - Krutov, A.O. A1 - Wolf, Thomas T1 - N=2 supersymmetric a=4-KdV hierarchy derived via Gardner's deformation of Kaup-Boussinesq equation N2 - We consider the problem of constructing Gardner's deformations for the $N{=}2$ supersymmetric $a{=}4$--\/Korteweg\/--\/de Vries equation; such deformations yield recurrence relations between the super\/-\/Hamiltonians of the hierarchy. We prove the non\/-\/existence %P.~Mathieu's Open problem on constructing for of supersymmetry\/-\/invariant %Gardner's deformations that %solutions, retract to Gardner's formulas for the KdV equation %whenever it is assumed that, under the %respective component reduction. % in the $N{=}2$ super\/-\/field. the solutions . At the same time, we propose a two\/-\/step scheme for the recursive production of the integrals of motion for the $N{=}2$,\ $a{=}4$--\/SKdV. First, we find a new Gardner's deformation of the Kaup\/--\/Boussinesq equation, which is contained in the bosonic limit of the super\/-\/%$N{=}2$,\ $a{=}4$--\/SKdV hierarchy. This yields the recurrence relation between the Hamiltonians of the limit, whence we determine the bosonic super\/- /Hamiltonians of the full $N{=}2$, $a{=}4$--\/SKdV hierarchy. T3 - ZIB-Report - 10-16 KW - Korteweg-de Vries equation KW - Kaup-Boussinesq equation KW - supersymmetry KW - Gardner's deformations KW - bi-Hamilltonian hierarchies Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11787 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - A Dynamical Systems Approach for Static Evaluation in Go N2 - In the paper arguments are given why the concept of static evaluation (SE) has the potential to be a useful extension to Monte Carlo tree search. A new concept of modeling SE through a dynamical system is introduced and strengths and weaknesses are discussed. The general suitability of this approach is demonstrated. A Remark: Among users of the Internet Go server KGS the abbreviation SE is used for 'Score Estimator'. Although different from 'Static Evaluation' a score estimator is easily obtained from static evaluation by adding up probabilities of chains to be alive at the end of the game or points to be owned by White or Black T3 - ZIB-Report - 10-15 KW - discrete dynamical systems KW - Computer Go KW - static evaluation Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11771 SN - 1438-0064 ER - TY - GEN A1 - Bouchareb, Adel A1 - Clément, Gérard A1 - Chen, Chiang-Mei A1 - Wolf, Thomas A1 - Gal'tsov, Dmitri V. A1 - Scherbluk, Nikolai G. T1 - G_2 generating technique for minimal D=5 supergravity and black rings N2 - A solution generating technique is developed for $D=5$ minimal supergravity with two commuting Killing vectors based on the $G_2$ U-duality arising in the reduction of the theory to three dimensions. The target space of the corresponding 3-dimensional sigma-model is the coset $G_{2(2)}/(SL(2,R)\times SL(2,R))$. Its isometries constitute the set of solution generating symmetries. These include two electric and two magnetic Harrison transformations with the corresponding two pairs of gauge transformations, three $SL(2,R) \; S$-duality transformations, and the three gravitational scale, gauge and Ehlers transformations (altogether 14). We construct a representation of the coset in terms of $7\times 7$ matrices realizing the automorphisms of split octonions. Generating a new solution amounts to transforming the coset matrices by one-parametric subgroups of $G_{2(2)}$ and subsequently solving the dualization equations. Using this formalism we derive a new charged black ring solution with two independent parameters of rotation. T3 - ZIB-Report - 10-14 KW - supergravity KW - black rings KW - Killing vectors KW - duality Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11732 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - Merging solutions of non-linear algebraic systems N2 - In solving large polynomial algebraic systems that are too big for standard Gröbner basis techniques one way to make progress is to introduce case distinctions. This divide and conquer technique can be beneficial if the algorithms and computer programs know how to take advantage of inequalities. A further hurdle is the form of the resulting general solutions which often have unnecessarily many branches. In this paper we discuss a procedure to merge solutions by dropping inequalities which are associated with them and, if necessary, by re-parametrizing solutions. In the appendix the usefulness of the procedure is demonstrated in the classification of quadratic Hamiltonians with a Lie-Poisson bracket $e(3)$. This application required the solution of algebraic systems with over 200 unknowns, 450 equations and between 5000 and 9000 terms. T3 - ZIB-Report - 10-13 KW - computer algebra KW - polynomial systems KW - Lie-Poisson brackets KW - quadratic Hamiltonians Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11769 SN - 1438-0064 ER - TY - GEN A1 - Fackeldey, Konstantin T1 - Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach N2 - In contrast to the well known meshbased methods like the finite element method, meshfree methods do not rely on a mesh. However besides their great applicability, meshfree methods are rather time consuming. Thus, it seems favorable to combine both methods, by using meshfree methods only in a small part of the domain, where a mesh is disadvantageous, and a meshbased method for the rest of the domain. We motivate, that this coupling between the two simulation techniques can be considered as saddle point problem and show the stability of this coupling. Thereby a novel transfer operator is introduced, which interacts in the transition zone, where both methods coexist. T3 - ZIB-Report - 10-12 KW - Gitterlose Methoden KW - inf-sup-Bedingung KW - Kopplung KW - meshfree KW - meshbased KW - inf-sup-Condition Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11755 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika T1 - Models for Line Planning with Transfers N2 - We propose a novel integer programming approach to transfer minimization for line planning problems in public transit. The idea is to incorporate penalties for transfers that are induced by “connection capacities” into the construction of the passenger paths. We show that such penalties can be dealt with by a combination of shortest and constrained shortest path algorithms such that the pricing problem for passenger paths can be solved efficiently. Connection capacity penalties (under)estimate the true transfer times. This error is, however, not a problem in practice. We show in a computational comparison with two standard models on a real-world scenario that our approach can be used to minimize passenger travel and transfer times for large-scale line planning problems with accurate results. T3 - ZIB-Report - 10-11 KW - Linienplanung KW - Umsteigen KW - Ganzzahlige Programmierung KW - Kombinatorische Optimierung KW - line planning KW - transfers KW - integer programming KW - combinatorial optimization Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11742 SN - 1438-0064 ER - TY - GEN A1 - Schlechte, Thomas A1 - Tanner, Andreas T1 - Railway capacity auctions with dual prices N2 - Railway scheduling is based on the principle of the construction of a conflict-free timetable. This leads to a strict definition of capacity: in contrast with road transportation, it can be said in advance whether a given railway infrastructure can accommodate - at least in theory - a certain set of train requests. Consequently, auctions for railway capacity are modeled as auctions of discrete goods -- the train slots. We present estimates for the efficiency gain that may be generated by slot auctioning in comparison with list price allocation. We introduce a new class of allocation and auction problems, the feasible assignment problem, that is a proper generalization of the well-known combinatorial auction problem. The feasible assignment class was designed to cover the needs for an auction mechanism for railway slot auctions, but is of interest in its own right. As a practical instance to state and solve the railway slot allocation problem, we present an integer programming formulation, briefly the ACP, which turns out to be an instance of the feasible assignment problem and whose dual problem yields prices that can be applied to define a useful activity rule for the linearized version of the Ausubel Milgrom Proxy auction. We perform a simulation aiming to measure the impact on efficiency and convergence rate. T3 - ZIB-Report - 10-10 KW - Combinatorial Auction Problem KW - Railway Track Allocation KW - Ausubel Milgrom Proxy Auction Mechanism Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11729 SN - 1438-0064 ER - TY - GEN A1 - Klapproth, Corinna A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Adaptive Timestep Control for the Contact-Stabilized Newmark Method N2 - The aim of this paper is to devise an adaptive timestep control in the contact--stabilized Newmark method (CONTACX) for dynamical contact problems between two viscoelastic bodies in the framework of Signorini's condition. In order to construct a comparative scheme of higher order accuracy, we extend extrapolation techniques. This approach demands a subtle theoretical investigation of an asymptotic error expansion of the contact--stabilized Newmark scheme. On the basis of theoretical insight and numerical observations, we suggest an error estimator and a timestep selection which also cover the presence of contact. Finally, we give a numerical example. T3 - ZIB-Report - 10-09 KW - dynamical contact problems KW - contact--stabilized Newmark method KW - extrapolation methods KW - adaptivity KW - timestep control Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11714 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Dovica, Ivan A1 - Nowak, Ivo A1 - Schickinger, Thomas T1 - Robust Tail Assignment N2 - We propose an efficient column generation method to minimize the probability of delay propagations along aircraft rotations. In this way, delay resistant schedules can be constructed. Computational results for large-scale real-world problems demonstrate substantial punctuality improvements. The method can be generalized to crew and integrated scheduling problems. T3 - ZIB-Report - 10-08 KW - Flugzeugumlaufplanung KW - robuste Optimierung KW - Spaltenerzeugung KW - Tail Assignment KW - Robust Optimization KW - Column Generation Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11707 SN - 1438-0064 ER - TY - GEN A1 - Idzikowski, Filip A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Woesner, Hagen A1 - Wolisz, Adam T1 - Dynamic routing at different layers in IP-over-WDM networks -- Maximizing energy savings N2 - We estimate potential energy savings in IP-over-WDM networks achieved by switching off router line cards in low-demand hours. We compare three approaches to react on dynamics in the IP traffic over time, FUFL, DUFL and DUDL. They provide different levels of freedom in adjusting the routing of lightpaths in the WDM layer and the routing of demands in the IP layer. Using MILP models based on three realistic network topologies as well as realistic demands, power, and cost values, we show that already a simple monitoring of the lightpath utilization in order to deactivate empty line cards (FUFL) brings substantial benefits. The most significant savings, however, are achieved by rerouting traffic in the IP layer (DUFL), which allows emptying and deactivating lightpaths together with the corresponding line cards. A sophisticated reoptimization of the virtual topologies and the routing in the optical domain for every demand scenario (DUDL) yields nearly no additional profits in the considered networks. These results are independent of the ratio between the demand and capacity granularities, the time scale and the network topology, and show little dependency on the demand structure. T3 - ZIB-Report - 10-07 KW - network design KW - energy efficiency KW - power consumption KW - multi-layer KW - multi-hour KW - multi-period Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11692 SN - 1438-0064 ER - TY - GEN A1 - Boer, H. Marike T. A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Deuflhard, Peter A1 - Veerkamp, Roel F. A1 - Woelders, Henri T1 - A simple mathematical model of the bovine estrous cycle: follicle development and endocrine interactions N2 - Bovine fertility is the subject of extensive research in animal sciences, especially because fertility of dairy cows has declined during the last decades. The regulation of estrus is controlled by the complex interplay of various organs and hormones. Mathematical modeling of the bovine estrous cycle could help in understanding the dynamics of this complex biological system. In this paper we present a mathematical model of the bovine estrous cycle that includes the processes of follicle and corpus luteum development and the key hormones that interact to control these processes. Focus in this paper is on development of the model, but also some simulation results are presented, showing that a set of equations and parameters is obtained that describes the system consistent with empirical knowledge. Even though the majority of the mechanisms that are included are only known qualitatively as stimulatory or inhibitory effects, the model surprisingly well features quantitative observations made in reality. This model of the bovine estrous cycle could be used as a basis for more elaborate models with the ability to study effects of external manipulations and genetic differences. T3 - ZIB-Report - 10-06 KW - cow KW - reproduction KW - hormone patterns KW - ordinary differential equations KW - systems biology Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11682 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin A1 - Götschel, Sebastian T1 - State Trajectory Compression for Optimal Control with Parabolic PDEs N2 - In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and quasi-Newton methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy coding maintaining an error bound is sufficient. T3 - ZIB-Report - 10-05 KW - optimal control KW - adjoint gradient computation KW - trajectory storage Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11676 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Feydy, Thibaut A1 - Stuckey, Peter T1 - Rapid Learning for Binary Programs N2 - Learning during search allows solvers for discrete optimization problems to remember parts of the search that they have already performed and avoid revisiting redundant parts. Learning approaches pioneered by the SAT and CP communities have been successfully incorporated into the SCIP constraint integer programming platform. In this paper we show that performing a heuristic constraint programming search during root node processing of a binary program can rapidly learn useful nogoods, bound changes, primal solutions, and branching statistics that improve the remaining IP search. T3 - ZIB-Report - 10-04 KW - Ganzzahlige Programmierung KW - Constraintprogrammierung KW - Primalheuristik KW - Konfliktanalyse KW - constraint programming KW - integer programming KW - primal heuristic KW - conflict learning Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11663 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Lübbecke, Marco A1 - Möhring, Rolf A1 - Schulz, Jens T1 - A Constraint Integer Programming Approach for Resource-Constrained Project Scheduling N2 - We propose a hybrid approach for solving the resource-constrained project scheduling problem which is an extremely hard to solve combinatorial optimization problem of practical relevance. Jobs have to be scheduled on (renewable) resources subject to precedence constraints such that the resource capacities are never exceeded and the latest completion time of all jobs is minimized. The problem has challenged researchers from different communities, such as integer programming (IP), constraint programming (CP), and satisfiability testing (SAT). Still, there are instances with 60 jobs which have not been solved for many years. The currently best known approach, lazyFD, is a hybrid between CP and SAT techniques. In this paper we propose an even stronger hybridization by integrating all the three areas, IP, CP, and SAT, into a single branch-and-bound scheme. We show that lower bounds from the linear relaxation of the IP formulation and conflict analysis are key ingredients for pruning the search tree. First computational experiments show very promising results. For five instances of the well-known PSPLIB we report an improvement of lower bounds. Our implementation is generic, thus it can be potentially applied to similar problems as well. T3 - ZIB-Report - 10-03 KW - constraint integer programming KW - cumulative constraint KW - scheduling KW - conflict analysis KW - resource-constrained project Scheduling Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11180 SN - 1438-0064 ER - TY - GEN A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Stender, Jan A1 - Hupfeld, Felix T1 - Fault-Tolerant and Decentralized Lease Coordination in Distributed Systems N2 - Applications which need exclusive access to a shared resource in distributed systems require a fault-tolerant and scalable mechanism to coordinate this exclusive access. Examples of such applications include distributed file systems and master/slave data replication. We present Flease, an algorithm for decentralized and fault-tolerant lease coordination in distributed systems. Our algorithm allows the processes competing for a resource to coordinate exclusive access through leases among themselves without a central component. The resulting system easily scales with an increasing number of nodes and resources. We prove that Flease ensures exclusive access, i.e. guarantees that there is at most one valid lease at any time. T3 - ZIB-Report - 10-02 Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11658 SN - 1438-0064 ER - TY - GEN A1 - Neun, Winfried A1 - Sturm, Thomas A1 - Vigerske, Stefan T1 - Supporting Global Numerical Optimization of Rational Functions by Generic Symbolic Convexity Tests N2 - Convexity is an important property in nonlinear optimization since it allows to apply efficient local methods for finding global solutions. We propose to apply symbolic methods to prove or disprove convexity of rational functions over a polyhedral domain. Our algorithms reduce convexity questions to real quantifier elimination problems. Our methods are implemented and publicly available in the open source computer algebra system REDUCE. Our long term goal is to integrate REDUCE as a workhorse'' for symbolic computations into a numerical solver. T3 - ZIB-Report - 10-01 KW - Nonlinear Global Optimization KW - Hybrid Symbolic-Numeric Computation KW - Convex Functions KW - Real Quantifier Elimination Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11644 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Gleixner, Ambros T1 - Undercover – a primal heuristic for MINLP based on sub-MIPs generated by set covering N2 - We present Undercover, a primal heuristic for mixed-integer nonlinear programming (MINLP). The heuristic constructs a mixed-integer linear subproblem (sub-MIP) of a given MINLP by fixing a subset of the variables. We solve a set covering problem to identify a minimal set of variables which need to be fixed in order to linearise each constraint. Subsequently, these variables are fixed to approximate values, e.g. obtained from a linear outer approximation. The resulting sub-MIP is solved by a mixed-integer linear programming solver. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. Although general in nature, the heuristic seems most promising for mixed-integer quadratically constrained programmes (MIQCPs). We present computational results on a general test set of MIQCPs selected from the MINLPLib. T3 - ZIB-Report - 09-40 KW - MINLP KW - MIQCP KW - Primalheuristik KW - Nachbarschaftssuche KW - Mengenüberdeckung KW - mixed-integer nonlinear programming KW - MIQCP KW - primal heuristic KW - large neighborhood search KW - set covering Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11632 SN - 1438-0064 ER - TY - THES A1 - Röblitz, Thomas T1 - Co-Reservation of Resources in the Grid N2 - Executing applications in the Grid often requires access to multiple geographically distributed resources. In a Grid environment, these resources belong to different administrative domains, each employing its own scheduling policy. That is, at which time an activity (e.g., compute job, data transfer) is started, is decided by the resource's local management system. In such an environment, the coordinated execution of distributed applications requires guarantees on the quality of service (QoS) of the needed resources. Reserving resources in advance is an accepted means to obtain QoS guarantees from a single provider. The challenge, however, is to coordinate advance reservations of multiple resources. This work presents a system architecture and mechanisms to coordinate multiple advance reservations -- called co-reservations -- for delivering QoS guarantees to complex applications. We formally define the co-reservation problem as an optimization problem. The presented model supports three dimensions of freedom: the start time, the duration and the service level of a reservation. Requests and resources are described in a simple language. After matching the static properties and requirements of either side in a mapping, the reservation mechanism probes information about the future status of the resources. The versatile design of the probing step allows the efficient processing of requests, but also lets the resources express their preferences among the myriads of reservation candidates. Next, the best mapping is found through an implementation of the formal co-reservation model. Then, the mapping has to be secured, i.e., resources need to be allocated to a co-reservation candidate with all-or-nothing semantics. We study several goal-driven sequential and concurrent allocation mechanisms and define schemes for handling allocation failures. Finally, we introduce the concept of virtual resources for seamlessly embedding co-reservations into Grid resource management. N2 - Die Ausführung von Anwendungen erfordert oft mehrere, geographisch verteilte Ressourcen. In Grid-Umgebungen gehören diese Ressourcen zu verschiedenen administrativen Organisationen, wobei jede ihre eigene Schedulingregeln verwendet. Das bedeutet, zu welcher Zeit eine Aktivität gestartet wird (z.B. ein Rechenjob), wird vom lokalen Ressourcenmanagementsystem entschieden. Die koordinierte Ausführung von verteilten Anwendungen erfordert Dienstgütegarantien für die benötigten Ressourcen. Das Reservieren von Ressourcen im Voraus ist ein Mittel, um Dienstgütegarantien von einem einzelnen Ressourcenanbieter zu erhalten. Die Herausforderung in dieser Arbeit ist, Vorausreservierungen von mehreren Ressourcen zu koordinieren. Es wird ein System für die Koordinierung mehrerer Vorausreservierungen -- Co-Reservierungen genannt -- für die Bereitstellung von Dienstgütegarantien vorgestellt. Wir definieren das Co-Reservierungsproblem als Optimierungsproblem. Das vorgestellte Modell unterstützt drei Freiheitsgrade: die Startzeit, die Dauer und die Dienstgüte einer Reservierung. Anfragen und Ressourcen werden in einer einfachen Sprache beschrieben. Nachdem statische Eigenschaften und Anforderungen beider Seiten überprüft wurden, ermittelt der Reservierungsmechanismus Informationen über den zukünftigen Zustand der Ressourcen. Dieser Schritt ist so allgemein gehalten, daß er sowohl ein effizientes Bearbeiten der Anfragen erlaubt als auch den Ressourcen ermöglicht ihre Präferenzen auszudrücken. Im Anschluss wird die optimale Zuweisung von Anfragen zu Ressourcen ermittelt. Im letzten Schritt muss diese Zuweisung umgesetzt werden, d.h., entweder alle oder keine Ressource wird allokiert. Es werden mehrere sequentielle und parallele Allokationsverfahren vorgestellt sowie deren Auswirkung auf verschiedene Metriken untersucht. Die Einbettung von Co-Reservierungen in das Grid-Ressourcenmanagement wird anhand des Konzeptes der virtuellen Ressource dargestellt. KW - Ressourcen-Verwaltung KW - Reservierung KW - Verteilte Systeme KW - Grid Computing KW - resource management KW - reservation KW - distributed systems KW - grid computing Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11626 SN - 978-3-86853-137-4 ER - TY - GEN A1 - Gottwald, Susanne T1 - Die Wissensberechnungsmaschine Wolfram|Alpha T1 - The computational knowledge engine Wolfram|Alpha N2 - Im Mai 2009 wurde Wolfram|Alpha gestartet, ein Service, der seinen Namen von seinem Entwickler, dem britischen Mathematiker Stephen Wolfram, ableitet. Dem Benutzer soll nicht nur eine Liste von Webseiten als Ergebnis auf Anfragen geliefert werden, sondern Antworten auf konkrete Fragen geben. In diesem Report soll gezeigt werden, warum sichWolframjAlpha von Suchmaschinen abgrenzt und was die Berechnung von Antworten auf natürlichsprachliche Fragen möglich machen kann. N2 - Wolfram|Alpha was started in May 2009 and it's a service whose name derives from the british mathematician Stephen wolfram. As a result for a request the user is not just supported with a list of websites but with answers for concrete questions. In this report it will be shown why Wolfram|Alpha seperates from search engines and moreover what makes the computation of answers for natural language queries possible. T3 - ZIB-Report - 09-39 KW - natürlichsprachlich KW - Suchmaschine KW - Fakten KW - Mathematica KW - natural language KW - search engine KW - facts KW - Mathematica Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11614 SN - 1438-0064 ER - TY - THES A1 - Zschiedrich, Lin T1 - Transparent boundary conditions for Maxwell's equations: Numerical concepts beyond the PML method N2 - Optical technologies are ubiquitously used in hi-tech devices. As a common feature of such devices one finds structures with dimensions in the order of the wavelength of the used light. To design and produce such devices, the wave nature of light must be taken into account. Accordingly, robust simulation tools are required which are based on rigorously solving Maxwell's equations, the governing equations of light propagation within macroscopic media. This thesis contributes to the modeling and the numerical computation of light scattering problems: Light scattering problems are typically posed on the entire space. The Perfectly-Matched -Layer method (PML) is widely used to restrict the simulation problem onto a bounded computational domain. We propose an adaptive PML method which exhibits a good convergence even for critical problems where standard PML implementations fail. Besides the computation of the near field, that is the electromagnetic field within the computational domain, it is of major interest to evaluate the electromagnetic field in the exterior domain and to compute the far field. So far, this was numerically only possible for simple geometries such as homogeneous exterior domains or layered media. To deal with more complicated devices, for example with waveguide inhomogeneities, we develop an evaluation formula based on the PML solution which allows for an exterior domain field evaluation in a half space above the device. Finally, we generalize the PML method to problems with multiply structured exterior domains. The term “multiply structured exterior domain” is defined in this thesis and means that the exterior domain exhibits several half-infinite structures. Mathematically, this gives rise to various complications. For example, no analytical solutions to Maxwell's equations for standard light sources are available in the exterior domain, which are needed to describe the incoming field in a light scattering problem. To tackle this we propose a new light scattering problem formulation which fits well into the PML method framework and which may be regarded as an extension of classical contributions by Sommerfeld, Wiener and Hopf. An exterior domain evaluation formula for multiply structured exterior domains with an extended illumination is derived as well. KW - transparent boundary conditions KW - electromagnetic scattering KW - Maxwell's equations KW - perfectly matched layers KW - PML KW - Wiener-Hopf techniques Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000013994-8 ER - TY - GEN A1 - Achterberg, Tobias A1 - Raack, Christian T1 - The MCF-Separator -- Detecting and Exploiting Multi-Commodity Flow Structures in MIPs N2 - Given a general mixed integer program (MIP), we automatically detect block structures in the constraint matrix together with the coupling by capacity constraints arising from multi-commodity-flow formulations. We identify the underlying graph and generate cutting planes based on cuts in the detected network. Our implementation adds a separator to the branch-and-cut libraries of SCIP and CPLEX. We make use of the complemented mixed integer rounding framework (cMIR) but provide a special purpose aggregation heuristic that exploits the network structure. Our separation scheme speeds-up the computation for a large set of MIPs coming from network design problems by a factor of two on average. T3 - ZIB-Report - 09-38 KW - mixed integer programming KW - network detection KW - cut-based inequalities KW - cplex KW - scip Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11592 SN - 1438-0064 ER - TY - THES A1 - Wölk, Bertram T1 - Generierung hybrider Gitter für die Strömungssimulation auf komplexen anatomischen Geometrien T1 - Generation of hybrid grids for flow simulation on complex anatomical geometries N2 - Basierend auf einem vorhandenen Ansatz zur Einführung von anisotropen Tetraedern im Randbereich eines reinen Tetraedergitters wird ein Gittergenerator für hybride Gitter implementiert. Das hybride Gitter besteht in Randnähe primär aus anisotropen Prismen und im Inneren der Geometrie aus isotropen Tetraedern. Eine erhöhte Auflösung im Randbereich soll zu besseren Ergebnissen von numerischen Strömungssimulationen führen, für welche eine problemangepasste Diskretisierung des zu untersuchenden Gebietes benötigt wird. In dem zuvor genannten Ansatz wird eine Reihe von Übergangselementen vorgeschlagen, die an scharfen Kanten der Oberfläche platziert werden sollen. Im Rahmen dieser Diplomarbeit wird die Idee der Übergangselemente aufgegriffen und bei hybriden Gittern eingesetzt, um auch komplexe Eingabegeometrien vergittern zu können. Der ursprüngliche Gittergenerierungprozess wird überarbeitet und erweitert. Eine neue Menge an Übergangselementen wird eingeführt, es werden gekrümmte Extrusionsvektoren verwendet und es wird die Auswertung der medialen Oberfläche vorgenommen, um Überschneidungen im hybriden Gitter zu vermeiden. Der Gittergenerator wird als Modul in das Visualisierungs- und Analyseprogramm Amira implementiert und die erstellten hybriden Gitter werden auf ihre Elementqualität und die Güte der Strömungssimulationsergebnisse hin überprüft. N2 - Based on an existing approach for the introduction of anisotropic tetrahedra near the surface boundary of a tetrahedral grid a grid generator for hybrid grids is implemented. The hybrid grid consists near the surface boundary primarily of anisotropic prisms and inside the geometry of isotropic tetrahedra. An increased resolution near the boundary should lead to better results of numerical flow simulations, which needs a problem specific discretization of the analyzed domain. In the aforementioned approach a set of transition elements is suggested, which should be placed at sharp surface corners. As a part of this diploma thesis the concept of using transition elements is applied for creating hybrid grids even for very complex input geometries. The initial grid generation process is revised and enhanced. A new set of transition elements is introduced, curved extrusion vectors are used and the medial surface is evaluated to avoid intersections in the hybrid grid. The grid generator is implemented as a module for the visualization and analysis tool Amira and the element quality of the generated hybrid grids and the quality of flow simulations performed on the grids are tested. KW - Gittergenerierung KW - Hybrid KW - Randschicht KW - Anisotrope Prismen KW - Strömungssimulation KW - hybrid KW - mesh KW - grid KW - generation KW - boundary layer Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11588 ER - TY - GEN A1 - Frank, Martin A1 - Fügenschuh, Armin A1 - Herty, Michael A1 - Schewe, Lars T1 - The Coolest Path Problem N2 - We introduce the coolest path problem, which is a mixture of two well-known problems from distinct mathematical fields. One of them is the shortest path problem from combinatorial optimization. The other is the heat conduction problem from the field of partial differential equations. Together, they make up a control problem, where some geometrical object traverses a digraph in an optimal way, with constraints on intermediate or the final state. We discuss some properties of the problem and present numerical solution techniques. We demonstrate that the problem can be formulated as a linear mixed-integer program. Numerical solutions can thus be achieved within one hour for instances with up to 70 nodes in the graph. T3 - ZIB-Report - 09-37 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11571 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton A1 - Weiser, Martin T1 - Barrier methods for a control problem from hyperthermia treatment planning N2 - We consider an optimal control problem from hyperthermia treatment planning and its barrier regularization. We derive basic results, which lay the groundwork for the computation of optimal solutions via an interior point path-following method. Further, we report on a numerical implementation of such a method and its performance at an example problem. T3 - ZIB-Report - 09-36 KW - hyperthermia treatment planning KW - optimal control KW - barrier methods Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11567 SN - 1438-0064 ER - TY - THES A1 - Mauter, Daniel T1 - Ein eingebettetes Hauptspeicher-Datenbanksystem mit Snapshot-Reads T1 - An embedded main memory database with snapshot-reads N2 - Entwurf und Entwicklung eines eingebetteten Hauptspeicher-Datenbanksystems mit Snapshot-Reads. N2 - Design and implementation of an embedded main memory database with snapshot reads. KW - Datenbank KW - Hauptspeicher KW - Snapshot-Reads KW - database KW - main memory KW - snapshot-read Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11552 ER - TY - GEN A1 - Kuberek, Monika T1 - Strategien für die Zukunft der regionalen Informationsinfrastruktur - der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) N2 - Eines der Hauptanliegen bei der Initiierung des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) war die Schaffung einer modernen, leistungsfähigen Informationsinfrastruktur unter Einbeziehung möglichst aller Bibliotheken der in ihrer Dichte und Vielfalt in Deutschland einmaligen Bibliothekslandschaft. Sie wurde beim Aufbau des KOBV durch die Wahl des Verbundmodelles mit seinen offenen, integrativen Strukturen befördert. Die Ziele und Strategien des KOBV leiten sich aus dem Grundauftrag der Bibliotheken her, ihre NutzerInnen optimal mit Medien und Informationen zu versorgen. Mit dem KOBV haben die Bibliotheken eine gemeinsame Plattform und ein regionales Netzwerk geschaffen, mit deren Hilfe sie die Informationsinfrastruktur in Berlin und Brandenburg zusammen aufgebaut und grundlegend verbessert haben. Nach rund elf Jahren ist der KOBV in eine neue Phase eingetreten, indem er – unter Wahrung seiner institutionellen Eigenständigkeit – eine Strategische Allianz mit dem Bibliotheksverbund Bayern (BVB) eingegangen ist und die bislang auf die Region bezogene Kooperation der Bibliotheken überregional ausgeweitet hat. Wenn auch die Universalbibliotheken des KOBV in dieser Zusammenarbeit einen Kurswechsel zur zentralen Katalogisierung vollziehen, bedeutet dies für den KOBV insgesamt keinen Paradigmenwechsel: Er bleibt ein dezentraler Verbund und wird sein flexibles technisches Mischkonzept von verteilter und zentraler Datenhaltung fortführen. Dieses lässt den Bibliotheken die Freiheit zu entscheiden, ob sie zentral oder dezentral katalogisieren möchten. Die KOBV-Zentrale, die im KOBV keine Aufgaben in der Katalogisierung wahrnimmt, wird wie bislang allen Mitgliedsbibliotheken die ASP-Dienste und weiteren Angebote gleichermaßen zur Verfügung stellen und die Dienstleistungen für NutzerInnen und Bibliotheken weiter ausbauen. Mit dem vorhandenen Know How, der eingesetzten modernen Technologie und der strategischen Entscheidung, Ressourcen und Kompetenzen mit dem BVB zu bündeln und durch verbundübergreifende arbeitsteilige Verfahren Synergien zu gewinnen, ist der KOBV gut aufgestellt, um die Herausforderungen der kommenden Jahre anzugehen und das Leistungsspektrum der KOBV-Bibliotheken durch die Entwicklung neuer Dienste auszuweiten. T3 - ZIB-Report - 09-35 KW - Bibliotheksverbund KW - Informationsinfrastruktur KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11546 SN - 1438-0064 ER - TY - GEN A1 - Moser, Monika A1 - Haridi, Seif A1 - Shafaat, Tallat A1 - Schütt, Thorsten A1 - Högqvist, Mikael A1 - Reinefeld, Alexander T1 - Transactional DHT Algorithms N2 - We present a framework for transactional data access on data stored in a DHT. It allows to atomically read and write items and to run distributed transactions consisting of a sequence of read and write operations on the items. Items are symmetrically replicated in order to achieve durability of data stored in the SON. To provide availability of items despite the unavailability of some replicas, operations on items are quorum-based. They make progress as long as a majority of replicas can be accessed. Our framework processes transactions optimistically with an atomic commit protocol that is based on Paxos atomic commit. We present algorithms for the whole framework with an event based notation. Additionally we discuss the problem of lookup inconsistencies and its implications on the one-copy serializability property of the transaction processing in our framework. T3 - ZIB-Report - 09-34 KW - Distributed System KW - DHT KW - Paxos KW - Algorithms KW - Storage Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11532 SN - 1438-0064 ER - TY - GEN A1 - Gottwald, Susanne A1 - Tolksdorf, Robert T1 - Planning Teams with Semantic Web Technologies N2 - When planning teams for projects with specific goals, employees of a company have to group together so well, that all necessary knowledge for conquering the project’s challenges are met within the member’s skills. A tool that facilitates semantic web technologies can support the team recruiter, who is responsible for chosing the members of the team, in terms of finding the most efficient combinations of the company’s employees based on their expertises. T3 - ZIB-Report - 09-33 KW - Teamplanung KW - Projektarbeit KW - Teams KW - semantische Technologien KW - Semantic Web KW - Knowledge Management KW - teamplanning KW - teams Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11523 SN - 1438-0064 ER - TY - THES A1 - Kruber, Nico T1 - DHT Load Balancing with Estimated Global Information N2 - One of the biggest impacts on the performance of a Distributed Hash Table (DHT), once established, is its ability to balance load among its nodes. DHTs supporting range queries for example suffer from a potentially huge skew in the distribution of their items since techniques such as consistent hashing can not be applied. Thus explicit load balancing schemes need to be deployed. Several such schemes have been developed and are part of recent research, most of them using only information locally available in order to scale to arbitrary systems. Gossiping techniques however allow the retrieval of fairly good estimates of global information with low overhead. Such information can then be added to existing load balancing algorithms that can use the additional knowledge to improve their performance. Within this thesis several schemes are developed that use global information like the average load and the standard deviation of the load among the nodes to primarily reduce the number of items an algorithm moves to achieve a certain balance. Two novel load balancing algorithms have then been equipped with implementations of those schemes and have been simulated on several scenarios. Most of these variants show better balance results and move far less items than the algorithms they are based on. The best of the developed algorithms achieves a 15-30% better balance and moves only about 50-70% of the number of items its underlying algorithm moves. This variation is also very robust to erroneous estimates and scales linearly with the system size and system load. Further experiments with self-tuning algorithms that set an algorithm’s parameter according to the system’s state show that even more improvements can be gained if additionally applied. Such a variant based on the algorithm described by Karger and Ruhl shows the same balance improvements of 15-30% as the variant above but reduces the number of item movements further to 40-65%. KW - Peer-to-Peer KW - Verteilte Hashtabelle (DHT) KW - Lastverteilung KW - Gossiping KW - Peer-to-Peer KW - Distributed Hash Table (DHT) KW - Load Balancing KW - Gossiping Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11514 ER - TY - GEN A1 - Bley, Andreas A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Vigerske, Stefan T1 - Comparing MIQCP solvers to a specialised algorithm for mine production scheduling N2 - In this paper we investigate the performance of several out-of-the box solvers for mixed-integer quadratically constrained programmes (MIQCPs) on an open pit mine production scheduling problem with mixing constraints. We compare the solvers BARON, Couenne, SBB, and SCIP to a problem-specific algorithm on two different MIQCP formulations. The computational results presented show that general-purpose solvers with no particular knowledge of problem structure are able to nearly match the performance of a hand-crafted algorithm. T3 - ZIB-Report - 09-32 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11507 SN - 1438-0064 ER - TY - THES A1 - Prollius, Christian von T1 - Ein Peer-to-Peer System mit Bereichsabfragen in PlanetLab T1 - A Peer-to-Peer System with Range Queries in PlanetLab N2 - Aktuelle Entwicklungen zeigen, dass Peer-to-Peer (P2P) Anwendungen wie Skype oder Bittorrent im Internet immer mehr an Bedeutung gewinnen. In den letzten Jahren hat es einen explosionsartigen Anstieg an Nutzern und Daten in solchen Netzen gegeben. Dabei stellt der eigentliche Dateitransfer zwischen zwei Rechnern kein großes Problem mehr dar und auch der Speicherbedarf für die große Menge an Daten kann durch die Weiterentwicklung der Hardware gut gedeckt werden. Das eigentliche Problem liegt vielmehr darin, den Rechner zu finden, der die gewünschten Daten hat. Client-Server Architekturen, wie zum Beispiel Napster, haben sich als ungünstig herausgestellt. Wenige Server, die eine große Anzahl an Clients bedienen müssen, sind einerseits sehr anfällig gegenüber Angriffen und Ausfällen (Single Point of Failure)und kommen auch nicht mit der ständig wachsenden Anzahl an Nutzern zurecht. Verteilte Hashtabellen (DHT) bieten hier einen guten Lösungsansatz, der mit einer großen Anzahl an Nutzern skaliert und ausfallsicher ist. Andere dezentrale Lösungen, wie zum Beispiel das P2P Netzwerk Gnutella haben zwar das Problem des Single Point of Failure gelöst, jedoch haben sie starke Nachteile bei der Suche nach Keys. Bei einer Suche wird ein Broadcast verwendet (jeder schickt die Anfrage an jeden weiter) und damit ein enormer Netzwerkverkehr erzeugt. In "Why Gnutella Can't Scale. No, Really" wird erklärt, dass eine Suchanfrage bei Standardeinstellungen in der Clientsoftware einen Netzwerkverkehr von 17MB erzeugt. Deswegen wird zusätzlich eine Lösung benötigt, die Keys und Values geordnet verteilt, damit sie gezielt gesucht werden können. Aus diesem Grund beschäftigt sich die folgende Arbeit mit einer völlig dezentralen Architektur, die außerdem eine sinnvolle Platzierung der Keys vornimmt. Die dezentrale Architektur hat den Vorteil, dass die Endgeräte den Hauptteil des Dienstes selbst erbringen und damit jeder zusätzliche Teilnehmer seine eigenen Ressourcen beisteuert. Diese Arbeit präsentiert Chord#, eine dezentrale, skalierbare und selbstorganisierende verteilte Hashtabelle. Chord# wurde ausgewählt, da in dieser Arbeit auch Wert auf Bereichsabfragen gelegt wurde. Diese sind zum Beispiel bei dem Chord Algorithmus nicht möglich, da dieser eine Hashfunktion für die Keys verwendet und somit die Daten zwar gleichmäßig aber unsortiert auf die Teilnehmer verteilt. Es wird in dieser Arbeit gezeigt, dass mit Hilfe von Chord# auch ohne die Hashfunktion gute Ergebnisse erzielt werden. Außerdem können durch den Verzicht auf die Hashfunktion Bereichsabfragen ermöglicht werden. Dafür wird der Chord# Algorithmus in Java implementiert (ca. 1500 Zeilen Code) und in dem Forschungsnetz PlanetLab ausführlich auf Laufzeiten, Instandhaltungskosten und Skalierung getestet. N2 - Recent developments show that peer-to-peer (p2p) applications, such as Skype or Bittorrent have become increasingly important in the internet. Over the last years there has been a rapid growth of both users and data in such networks. However, the actual file transfer between two peers is not really an issue anymore. The same holds true for data storage, since the new hardware grants users enough space to store their data. The real problem is finding the peers that possess the desired data. Client-server architectures like Napster have proven to be ineffective addressing that problem. One or few servers being responsible for many peers are vulnerable to attacks or failures (single point of failure). Additionally, they are unable to cope with the rapidly growing number of peers. Distributed hashtables (DHT) are a good approach to solve these problems, since they scale nicely with large numbers of peers and provide a high tolerance for errors. Other decentralized solutions like the p2p network Gnutella solved the problem of Single Point of Failure but show considerable disadvantages when searching for keys. The peers in Gnutella use a broadcast (sending the message to all peers they know)resulting in massive traffic. According to "Why Gnutella Can't Scale. No, Really.", each search using standard client settings yields 17MB traffc. This calls for a different solution, distributing keys and values to peers quickly and efficiently so they can be found fast. For that reason this thesis focuses on a fully distributed architecture using organized key placement. One major advantage of distributed architecture is the fact, that the peers do most of the work themselves. This way, new peers joining the network add resources to it. This thesis presents Chord#, a scalable, self-organizing and completely decentralized DHT. It has been chosen due to its capability to allow range queries. The regular Chord algorithm does not support range queries, because of the hashfunction it uses to evenly distribute the keys among the peers. This results in similar or logical coherent keys most likely not being close together in the network. This thesis shows Chord# achieving same results as Chord - regarding performance costs - without the hashfunction. In dropping the hashfunction this algorithm allows the use of range queries. The Chord# algorithm is implemented in Java (about 1500 lines of code) and thoroughly tested in the research network PlanetLab. The results are evaluated regarding performance, maintenance and scalability. KW - Peer-to-Peer KW - Bereichsabfragen KW - peer-to-peer KW - range queries Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11492 ER - TY - THES A1 - Tuschl, Roland T1 - Ein Userspace-Dateisystem zur Verwaltung von Grid-Daten T1 - A Userspace Filesystem for the Management of Grid Data N2 - Das Ziel dieser Arbeit ist die Schaffung einer Zugriffs-Komponente für das Grid-Datenmanagement-System ZIB-DMS, das dessen transparente Einbindung in den Verzeichnisbaum eines Linux-Systems erlaubt. Dazu wird unter Verwendung des FUSE-Rahmenwerkes ein Userspace-Dateisystem mit Anbindung an das ZIB-DMS konzipiert und implementiert. Im Fokus stehen dabei die Abbildung der erweiterten Verwaltungsmechanismen des Systems auf die limitierte Schnittstelle hierarchischer Dateisysteme und die dazu notwendigen Änderungen am ZIB-DMS. N2 - The goal of this work is to create an access component for the Grid data management system ZIB-DMS, that allows a transparent integration into the directory tree of a Linux system. For this purpose the FUSE framework is used to design and implement a userspace file system with connections to the ZIB-DMS. The focus is on the mapping of the extended management mechanisms of the system to the limited interface of hierarchical file systems and the therefore necessary changes to ZIB-DMS. KW - Dateisystem KW - Grid KW - Datenmanagement KW - filesystem KW - Grid KW - data management Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11483 ER - TY - GEN A1 - Schmidt, Heiko A1 - Jimenéz, Carmen T1 - Numerical study of the direct pressure effect of acoustic waves in planar premixed flames N2 - Recently the unsteady response of 1-D premixed flames to acoustic pressure waves for the range of frequencies below and above the inverse of the flame transit time was investigated experimentally by Wangher et al. using OH chemiluminescence. They compared the frequency dependence of the measured response to the prediction of an analytical model proposed by Clavin et al., derived from the standard flame model (one-step Arrhenius kinetics). Discrepancies between the experimental results and the model led to the conclusion that the standard model does not provide an adequate description of the unsteady response of real flames and that it is necessary to investigate more realistic chemical models. Here we follow exactly this suggestion and perform numerical studies of the reponse of lean methane flames using different reaction mechanisms. We find that the global flame response obtained with both detailed chemistry (GRI3.0) and a reduced multi-step model by Peters lies slightly above the predictions of the analytical model, but is close to experimental results. We additionally used an irreversible one-step reaction model which yields good results at least for frequencies close to the inverse flame transit time. T3 - ZIB-Report - 09-31 KW - Druckeffekt KW - Akustik KW - Flammenantwort KW - inkompressibel KW - Direct pressure effect KW - acoustics KW - flame response KW - incompressible Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11476 SN - 1438-0064 ER - TY - GEN A1 - Lasser, Caroline A1 - Röblitz, Susanna T1 - Computing expectation values for molecular quantum dynamics N2 - We compute expectation values for the solution of the nuclear Schrödinger equation. The proposed particle method consists of three steps: sampling of the initial Wigner function, classical transport of the sampling points, weighted phase space summation for the final computation of the expectation values. The Egorov theorem guarantees that the algorithm is second order accurate with respect to the semiclassical parameter. We present numerical experiments for a two-dimensional torsional potential with three different sets of initial data and for a six-dimensional Henon-Heiles potential. By construction, the computing times scale linearly with the number of initial sampling points and range between three seconds and one hour. T3 - ZIB-Report - 09-30 KW - time dependent Schrödinger equation KW - molecular quantum dynamics KW - expectation values KW - Wigner functions Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11461 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - E-Learning and the Working Mathematician N2 - Eigentlich war der erste Autor nur zu einem Grußwort zur Tagung „GML² 2009 - Grundfragen Multi¬medialen Lehrens und Lernens“ eingeladen. Daraus wurde ein E-Learning-bezogener Vortrag, der – basierend auf Erfahrungen im Fach Mathematik – einen kritischen Blick auf die E-Learning-Szene in Deutschland wirft und diese mit entsprechenden Aktivitäten weltweit vergleicht. Dies ist die in seinen mathematischen Teilen gekürzte, in den E-Learning-Anteilen ein wenig erweiterte schriftliche Fassung des Vortrags. Der Artikel stammt nicht von E-Learning-Spezialisten sondern von Personen, die sich seit fast zwanzig Jahren mit elektronischer Information und Kommunikation (kurz: IuK) – insbesondere in der Mathematik – beschäftigen. Nach einer Definition von Michael Kerres kennzeichnet der Begriff E-Learning (electronic learning – elektronisch unterstütztes Lernen) alle Formen von Lernen, bei denen digitale Medien für die Präsentation und Distribution von Lernmaterialien und/oder zur Unterstützung zwischenmenschlicher Kommunikation zum Einsatz kommen, siehe z.B. http://de.wikipedia.org/wiki/E-Learning. IuK und E-Learning haben nach dieser Begriffsbildung viele Berührungspunkte. Deswegen wagen wir es, unsere positiven und negativen Erfahrungen im Bereich IuK in diesem Eröffnungsvortrag zu berichten, einige Entwicklungslinien zu vergleichen und eine eigene Kurzversion der Definition von E-Learning (besser E-Teaching and -Learning) voranzustellen: „Lehren und Lernen mit Unterstützung elektronischer Hilfsmittel“. T3 - ZIB-Report - 09-29 KW - E-Learning KW - elektronisches Lehren und Lernen KW - e-learning KW - electronic learning Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11455 UR - http://www.gml-2009.de/media/tagungsbandgml2009.pdf SN - 1438-0064 ER - TY - GEN A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Haridi, Seif A1 - Schütt, Thorsten T1 - Enhanced Paxos Commit for Transactions on DHTs N2 - Key/value stores which are built on structured overlay networks often lack support for atomic transactions and strong data consistency among replicas. This is unfortunate, because consistency guarantees and transactions would allow a wide range of additional application domains to benefit from the inherent scalability and fault-tolerance of DHTs. The Scalaris key/value store supports strong data consistency and atomic transactions. It uses an enhanced Paxos Commit protocol with only four communication steps rather than six. This improvement was possible by exploiting information from the replica distribution in the DHT. Scalaris enables implementation of more reliable and scalable infrastructure for collaborative Web services that require strong consistency and atomic changes across multiple items. T3 - ZIB-Report - 09-28 KW - Paxos KW - Transaktionen KW - DHT KW - strenge Konsistenz KW - Paxos KW - transactions KW - DHT KW - strong consistency Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11448 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus T1 - A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator N2 - Supercomputers can simulate complex molecular systems. However, there is a very large gap between the fastest oscillations of covalent bonds of a molecule and the time-scale of the dominant processes. In order to extract the dominant time-scales and to identify the dominant processes, a clustering of information is needed. This thesis shows that only the subspace-based Robust Perron Cluster Analysis (PCCA+) can solve this problem correctly by the construction of a Markov State Model. PCCA+ allows for time-extrapolation in molecular kinetics. This thesis shows the difference between molecular dynamics and molecular kinetics. Only in the molecular kinetics framework a definition of transition rates is possible. In this context, the existence of an infinitesimal generator of the dynamical processes is discussed. If the existence is assumed, the Theorem of Gauß can be applied in order to compute transition rates efficiently. Molecular dynamics, however, is not able to provide a suitable statistical basis for the determination of the transition pattern. T3 - ZIB-Report - 09-27 KW - Robuste Perron Cluster Analyse KW - Molekülkinetik KW - Übergangsraten KW - Robust Perron cluster analysis KW - molecular kinetics KW - transition rates Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11432 SN - 1438-0064 ER - TY - GEN A1 - Franck, Hildegard A1 - Klein, Thoralf A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Maiwald, Gunar T1 - Automatisierte Fernleihe im KOBV - Handbuch für Bibliotheken - 3. Auflage N2 - Im Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) wird für die automatisierte Fernleihe der Zentrale-Fernleihserver (ZFL-Server) der Firma Sisis eingesetzt. Die Software ist in der KOBV-Zentrale installiert. Der ZFL-Server dient im KOBV sowohl für die Bestellung von Monographien als auch für die Bestellung von Aufsatzkopien aus Zeitschriften. Prinzipiell gibt es zwei Verfahren, mit denen sich Bibliotheken an der automatisierten Fernleihe beteiligen können: das E-Mail-Verfahren und das SLNP-Verfahren. Auf beide wird im Handbuch eingegangen. Die automatisierte Fernleihe wurde im KOBV eingeführt, um die Fernleihe für die Benutzer zu beschleunigen, das Verfahren für die Bibliotheksmitarbeiter zu vereinfachen und den Arbeitsaufwand zu reduzieren. Sie basiert darauf, dass eine Bestellung anhand eines gefundenen Treffers ausgelöst wird – d.h. die bibliographischen Daten sind bereits verifiziert und in einem Katalog nachgewiesen. Anschließend wird die Bestellung über den ZFL-Server automatisch ausgeführt und verwaltet – sowohl in der regionalen KOBV-Fernleihe als auch in der verbundübergreifenden Fernleihe mit den deutschen Bibliotheksverbünden. Der ZFL-Server besteht aus verschiedenen technischen Komponenten. Eine dieser Komponenten ist das Bibliothekskonto, eine Internetanwendung, in der die Bestellverwaltung des ZFL-Servers für die Bibliotheksbediensteten transparent abläuft. Dazu hat jede Bibliothek im Bibliothekskonto eine eigene, Passwort-geschützte Dienstoberfläche. Im Laufe des Jahres 2009 hat die KOBV-Zentrale das Bibliothekskonto grundlegend überarbeitet; die neue Version wurde im September 2009 freigegeben. Neben der Überabeitung des Interfaces – so wird den Bibliotheken auf der Startseite nun eine Übersicht ihrer laufenden Bestellungen angezeigt und dient als direkter Einstieg in die Bearbeitung – wurde das Bibliothekskonto um folgende Funktionen erweitert: Bestellung zurücklegen (HOLD), Vormerkungen, Bestellungen zur Anfrage, Abbruch des Leitweges (auch verbundübergreifend), erweiterte Kommentarfunktion, Bestellnummernsuche in allen Verbünden. Das Handbuch, das die Vorgänge der Bestellverwaltung im Bibliothekskonto beschreibt, wurde in der nun vorliegenden 3. Auflage um die Beschreibung der neuen Funktionen ergänzt. An dieser Stelle ein Dank an die Kolleginnen und Kollegen aus den KOBV-Bibliotheken – Frau Bruske (UB der Freien Universität Berlin), Frau Ebert (UB der Europa-Universität Viadrina Frankfurt (Oder)), Frau Preuß (UB der Technischen Universität Berlin) und Herrn Ringmayer (Zentral- und Landesbibliothek Berlin) – für die tatkräftige Unterstützung bei der Entwicklung der neuen Funktionen. T3 - ZIB-Report - 09-26 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11429 SN - 1438-0064 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Approximations for the second moments of sojourn times in M/GI systems under state-dependent processor sharing N2 - We consider a system with Poisson arrivals and general service times, where the requests are served according to the State-Dependent Processor Sharing (SDPS) discipline (Cohen's generalized processor sharing discipline), where each request receives a service capacity which depends on the actual number of requests in the system. For this system, denoted by $M/GI/SDPS$, we derive approximations for the squared coefficients of variation of the conditional sojourn time of a request given its service time and of the unconditional sojourn time by means of two-moment fittings of the service times. The approximations are given in terms of the squared coefficients of variation of the conditional and unconditional sojourn time in related $M/D/SDPS$ and $M/M/SDPS$ systems, respectively. The numerical results presented for $M/GI/m-PS$ systems illustrate that the proposed approximations work well. T3 - ZIB-Report - 09-25 KW - state-dependent processor sharing KW - M/GI/m-PS KW - sojourn time KW - moments KW - approximations Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11414 SN - 1438-0064 ER - TY - THES A1 - Massing, André T1 - 1D-Reduktion thermal signifikanter Aderstränge in der Hyperthermie-Modellierung T1 - 1D-Reduction of Thermal Significant Blood Vessels in the Context of Hyperthermia-Modelling N2 - In dieser Arbeit wird ein neuer Ansatz zur Modellierung von thermal signifikanten Gefäßsträngen im Hyperthermie-Kontext betrachtet. Ausgehend von einer Konvektions-Diffusions-Gleichung wird durch Reskalierung des Massenflussterms eine Reduktion des Adergebietes auf eine 1D-Struktur erreicht. Nach numerischen Vorbetrachtungen wird die Grenzgleichung innerhalb einer verallgemeinerten Sobolev-Algebra formuliert. Die Untersuchung der Lösungsfamilie in klassischen Funktionenräumen zeigt, dass deren schwacher Grenzwert die Lösung der korrespondierenden Diffusions-Gleichung ist. Die Diskretisierung einer formalen Grenzgleichung mit Linienstromanteil stellt jedoch eine gute Approximation an die Diskretisierung des ursprünglichen Problems dar, wenn man die lokale Maschenweite an die Gefäßradien koppelt und bei erhöhtem Genauigkeitsbedarf auf ein vollständiges 3D-Modell umschaltet. KW - Finite Elemente Methode KW - Mehrskalen-Modellierung KW - Bio-Heat-Transer-Equation KW - Asymptotische Analysis KW - Finite Element Method KW - Multiscale-Modelling KW - Bio-Heat-Transer-Equation KW - Asymptotic Analysis Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11407 ER - TY - GEN A1 - Luce, Robert A1 - Duintjer Tebbens, Jurjen A1 - Liesen, Jörg A1 - Nabben, Robert A1 - Grötschel, Martin A1 - Koch, Thorsten A1 - Schenk, Olaf T1 - On the Factorization of Simplex Basis Matrices N2 - In the simplex algorithm, solving linear systems with the basis matrix and its transpose accounts for a large part of the total computation time. We investigate various methods from modern numerical linear algebra to improve the computation speed of the basis updates arising in LPs. The experiments are executed on a large real-world test set. The most widely used solution technique is sparse LU factorization, paired with an updating scheme that allows to use the factors over several iterations. Clearly, small number of fill-in elements in the LU factors is critical for the overall performance. Using a wide range of LPs we show numerically that after a simple permutation the non-triangular part of the basis matrix is so small, that the whole matrix can be factorized with (relative) fill-in close to the optimum. This permutation has been exploited by simplex practitioners for many years. But to our knowledge no systematic numerical study has been published that demonstrates the effective reduction to a surprisingly small non-triangular problem, even for large scale LPs. For the factorization of the non-triangular part most existing simplex codes use some variant of dynamic Markowitz pivoting, which originated in the late 1950s. We also show numerically that, in terms of fill-in and in the simplex context, dynamic Markowitz is quite consistently superior to other, more recently developed techniques. T3 - ZIB-Report - 09-24 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11392 SN - 1438-0064 ER - TY - THES A1 - Gleixner, Ambros T1 - Solving Large-scale Open Pit Mining Production Scheduling Problems by Integer Programming N2 - Since the initial application of mathematical optimisation methods to mine planning in 1965, the Lerchs-Grossmann algorithm for computing the ultimate pit limit, operations researchers have worked on a variety of challenging problems in the area of open pit mining. This thesis focuses on the open pit mining production scheduling problem: Given the discretisation of an orebody as a block model, determine the sequence in which the blocks should be removed from the pit, over the lifespan of the mine, such that the net present value of the mining operation is maximised. In practise, when some material has been removed from the pit, it must be processed further in order to extract the valuable elements contained therein. If the concentration of valuable elements is not sufficiently high, the material is discarded as waste or stockpiled. Realistically-sized block models can contain hundreds of thousands of blocks. A common approach to render these problem instances computationally tractable is the aggregation of blocks to larger scheduling units. The thrust of this thesis is the investigation of a new mixed-integer programming formulation for the open pit mining production scheduling problem, which allows for processing decisions to be made at block level, while the actual mining schedule is still computed at aggregate level. A drawback of this model in its full form is the large number of additional variables needed to model the processing decisions. One main result of this thesis shows how these processing variables can be aggregated efficiently to reduce the problem size significantly, while practically incurring no loss in net present value. The second focus is on the application of lagrangean relaxation to the resource constraints. Using a result of Möhring et al. (2003) for project scheduling, the lagrangean relaxation can be solved efficiently via minimum cut computations in a weighted digraph. Experiments with a bundle algorithm implementation by Helmberg showed how the lagrangean dual can be solved within a small fraction of the time required by standard linear programming algorithms, while yielding practically the same dual bound. Finally, several problem-specific heuristics are presented together with computational results: two greedy sub-MIP start heuristics and a large neighbourhood search heuristic. A combination of a lagrangean-based start heuristic followed by a large neighbourhood search proved to be effective in generating solutions with objective values within a 0.05% gap of the optimum. Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11389 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Vigerske, Stefan T1 - Extending a CIP framework to solve MIQCPs N2 - This paper discusses how to build a solver for mixed integer quadratically constrained programs (MIQCPs) by extending a framework for constraint integer programming (CIP). The advantage of this approach is that we can utilize the full power of advanced MIP and CP technologies. In particular, this addresses the linear relaxation and the discrete components of the problem. For relaxation, we use an outer approximation generated by linearization of convex constraints and linear underestimation of nonconvex constraints. Further, we give an overview of the reformulation, separation, and propagation techniques that are used to handle the quadratic constraints efficiently. We implemented these methods in the branch-cut-and-price framework SCIP. Computational experiments indicates the potential of the approach. T3 - ZIB-Report - 09-23 KW - mixed integer quadratically constrained programming KW - constraint integer programming KW - convex relaxation KW - nonconvex Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11371 SN - 1438-0064 ER - TY - GEN A1 - Brandt, Manfred A1 - Brandt, Andreas T1 - On sojourn times in M/GI systems under state-dependent processor sharing N2 - We consider a system with Poisson arrivals and i.i.d. service times. The requests are served according to the state-dependent processor sharing discipline, where each request receives a service capacity which depends on the actual number of requests in the system. The linear systems of PDEs describing the residual and attained sojourn times coincide for this system, which provides time reversibility including sojourn times for this system, and their minimal non negative solution gives the LST of the sojourn time $V(\tau)$ of a request with required service time $\tau$. For the case that the service time distribution is exponential in a neighborhood of zero, we derive a linear system of ODEs, whose minimal non negative solution gives the LST of $V(\tau)$, and which yields linear systems of ODEs for the moments of $V(\tau)$ in the considered neighborhood of zero. Numerical results are presented for the variance of $V(\tau)$. In case of an M/GI/2-PS system, the LST of $V(\tau)$ is given in terms of the solution of a convolution equation in the considered neighborhood of zero. For bounded from below service times, surprisingly simple expressions for the LST and variance of $V(\tau)$ in this neighborhood of zero are derived, which yield in particular the LST and variance of $V(\tau)$ in M/D/2-PS. T3 - ZIB-Report - 09-22 KW - state-dependent processor sharing KW - locally exponential service time KW - sojourn time KW - M/D/2-PS Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11366 SN - 1438-0064 ER - TY - GEN A1 - Ruprecht, Daniel A1 - Klein, Rupert A1 - Majda, Andrew J. T1 - Moisture-Gravity Wave Interactions in a Multiscale Environment N2 - Starting from the conservation laws for mass, momentum and energy together with a three species, bulk microphysic model, a model for the interaction of internal gravity waves and deep convective hot towers is derived by using multiscale asymptotic techniques. From the resulting leading order equations, a closed model is obtained by applying weighted averages to the smallscale hot towers without requiring further closure approximations. The resulting model is an extension of the linear, anelastic equations, into which moisture enters as the area fraction of saturated regions on the microscale with two way coupling between the large and small scale. Moisture reduces the effective stability in the model and defines a potential temperature sourceterm related to the net effect of latent heat release or consumption by microscale up- and downdrafts. The dispersion relation and group velocity of the system is analyzed and moisture is found to have several effects: It reduces energy transport by waves, increases the vertical wavenumber but decreases the slope at which wave packets travel and it introduces a lower horizontal cutoff wavenumber, below which modes turn into evanescent. Further, moisture can cause critical layers. Numerical examples for steadystate and timedependent mountain waves are shown and the effects of moisture on these waves are investigated. T3 - ZIB-Report - 09-21 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11358 SN - 1438-0064 ER - TY - GEN A1 - Münch, Matthias A1 - Kilian, Susanne T1 - A new generalized domain decomposition strategy for the efficient parallel solution of the FDS-pressure equation. Part II: Verification and Validation N2 - Because CFD programs, like FDS, generally consist of a large number of different components representing the variety of participating numerical algorithms and chemical / physical processes, it is nearly impossible to verify such codes in their entirety, for example with comparisons of fire tests. Instead, a careful verification and validation with respect to the underlying mathematical conditions and applied numerical schemes is indispensable. In particular, error cancelations between single program components can only be detected by such detailed component-level tests. In part I of this article series a conceptual deficiency of the FDS program package with regard to multi-mesh computations was illustrated and an alternative domain decomposition strategy FDS-ScaRC was introduced. In this second part we will present the structure of a comprehensive test concept and the needs for a more mathematically and numerically orientated test procedure that is much more suited for a reliable evaluation than only a simple visual comparison of the numerical results with experimental fire tests. After a general introduction of our test concept we will demonstrate the high potential of the new FDS-\scarc{} technique compared to the FDS-FFT technique which is used in the FDS program package as yet. Based on this concept, we will present a comprehensive set of analytical and numerical test results. T3 - ZIB-Report - 09-20 KW - Fire Dynamics Simulator (FDS) KW - domain decomposition KW - Verification and Validation KW - fire safety engineering Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11340 SN - 1438-0064 ER - TY - GEN A1 - Kilian, Susanne A1 - Münch, Matthias T1 - A new generalized domain decomposition strategy for the efficient parallel solution of the FDS-pressure equation. Part I: Theory, Concept and Implementation N2 - A world-wide used program for the simulation of fire-induced flows is the Fire Dynamics Simulator (FDS) which originally was developed for a purely serial execution on single-processor computing systems. Due to steadily increasing problem sizes and accuracy requirements as well as restrictions in storage capacity and computing power on single-processor systems, the efficient simulation of the considered fire scenarios can only be achieved on modern high-performance systems based on multi-processor architectures. The transition to those systems requires the elaborate parallelization of the underlying numerical methods which must guarantee the same result for a given problem as the corresponding serial execution. Unfortunately, one fundamental serial serial solver of FDS, the pressure solver, only possesses a low degree of inherent parallelizm. Its current parallelization may cause additional numerical errors, casually leading to significant losses of accuracy or even numerical instabilities. In order to ensure that the parallelization errors are limited by the leading error of the numerical scheme such that second order convergence for the whole method can be acchieved, optimized parallelization concepts must be designed. With respect to these considerations this articles gives an overview of the current parallel pressure solver as well as the problems related to it and presents an alternative method, SCARC, to overcome the existing complicacies. Part I explains the theory, concept and implementation of this new strategy, whereas Part II describes a series of validation and verification tests to proof its correctness. T3 - ZIB-Report - 09-19 KW - Fire Dynamics Simulator (FDS) KW - Zero-Mach number KW - domain decomposition KW - pressure-solver KW - fire safety engineering Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11332 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Cardonha, Carlos T1 - A Set Partitioning Approach to Shunting N2 - The Vehicle Positioning Problem (VPP) is a classical combinatorial optimization problem in public transport planning. A number of models and approaches have been suggested in the literature, which work for small problems, but not for large ones. We propose in this article a novel set partitioning model and an associated column generation solution approach for the VPP. The model provides a tight linear description of the problem. The pricing problem, and hence the LP relaxation itself, can be solved in polynomial resp. pseudo-polynomial time for some versions of the problems. T3 - ZIB-Report - 09-18 KW - integer programming KW - set partitioning KW - combinatorial packing KW - vehicle positioning Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11326 SN - 1438-0064 ER - TY - THES A1 - Röblitz, Susanna T1 - Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics N2 - The understanding of geometric structures and dynamical properties of molecular conformations gives insight into molecular long-term behavior. The identification of metastable conformations together with their life times and transition patterns is the intention of conformation dynamics. Conformation dynamics is a multi-scale approach that leads to a reduced description of the dynamical system in terms of a stochastic transition probability matrix. The present thesis deals with the error analysis of computed matrices and the resulting matrix functions. Since conformational membership vectors, as they are computed by the Robust Perron Cluster Analysis (PCCA+), form an invariant subspace of the transition matrix, subspace-based error estimators are of particular interest. The decomposition of the state space into basis functions and the approximation of integrals by Monte-Carlo quadrature give rise to row-wise correlated random matrices, for which stochastic norms are computed. Together with an appropriate statistical model for the distribution of matrix rows, this allows for the calculation of error bounds and error distributions of the invariant subspace and other variables of interest. Equilibration of errors among the basis functions can be achieved by enhanced sampling in regions where the trajectories are mixing slowly. Hierarchical refinement of such basis functions systematically improves the clustering into metastable conformations by reducing the error in the corresponding invariant subspace. These techniques allow for an evaluation of simulation results and pave the way for the analysis of larger molecules. Moreover, the extension of PCCA+ to non-reversible Markov chains, verified by the corresponding perturbation theory, and the modification of the objective function for the case of soft membership vectors represent a further generalization of the clustering method, thus continuing the development from PCCA over PCCA+ to PCCA++. The methods developed in this thesis are useful for but not limited to conformation dynamics. In fact, they are applicable to a broader class of problems which combine domain decomposition with Monte-Carlo quadrature. Possible application areas may include the chemical master equation or quantum dynamical systems. N2 - Das Verständnis von geometrischen Strukturen und dynamischen Eigenschaften molekularer Konformationen ist essentiell für die Vorhersage des Langzeitverhaltens von Molekülen. Die Identifikation metastabiler Konformationen sowie die Bestimmung von Übergangswahrscheinlichkeiten und Haltezeiten sind Bestandteil der Konformationdynamik. Dabei handelt es sich um eine Mehrskalenmethode, die auf eine reduzierte Beschreibung des Systems mittels einer stochastischen Übergangsmatrix führt. In der vorliegenden Dissertation wurde untersucht, wie man die Genauigkeit der Matrizen sowie der daraus berechneten Größen quantifizieren kann. Im Mittelpunkt stehen dabei Fehlerschätzer für den invarianten Unterraum, da die rechten Eigenvektoren als Grundlage der Robusten Perron Cluster Analyse (PCCA+) zur Identifizierung der metastabilen Konformationen dienen. Die Zerlegung des Zustandsraumes in Basisfunktionen sowie die Approximation der Matrixeinträge mittels Monte-Carlo-Quadratur führen zu zeilenweise korrelierten Zufallsmatrizen. Mit Hilfe einer stochastischen Norm sowie einem geeigneten statistischen Modell für die Verteilung der Matrixzeilen können u.a. Fehlerschranken und -verteilungen für den invarianten Unterraum brechnet werden. Eine Equilibrierung des Fehlers zwischen den Basisfunktionen kann durch erweitertes Sampling in solchen Regionen erreicht werden, in denen die Trajektorien nur langsam mischen.Eine hierarchische Zerlegung dieser Basisfunktionen verbessert systematisch die Zerlegung in metastabile Konformationen, indem sie den Fehler im invarianten Unterraum reduziert. Diese Techniken gestatten eine Evaluierung der Simulationsergebnisse und ebnen den Weg zur Behandlung komplexerer Moleküle. Desweiteren wurden Verallgemeinerungen der PCCA+ untersucht. Die Erweiterung der PCCA+ auf nicht-reversible Markov-Ketten sowie die Modifizierung der Zielfunktion für den Fall der weichen Clusterung setzen die Entwicklung von der PCCA über PCCA+ zu PCCA++ fort. Somit können neue Anwendungsfelder für dieses Cluster-Verfahren erschlossen werden. Die Methoden wurden zwar in Rahmen der Konformationsdynamik entwickelt, jedoch lassen sie sich auf eine weite Problemklasse anwenden, in der Gebietszerlegungsverfahren mit Monte-Carlo-Quadratur kombiniert werden. Mögliche Anwendungsgebiete umfassen die chemische Master-Gleichung oder quantenchemische Systeme. KW - Konformationsdynamik KW - Metastabilität KW - gitterfreie Methoden KW - Monte-Carlo-Quadratur KW - Perron-Cluster-Analyse KW - conformation dynamics KW - metastability KW - mesh-free methods KW - Monte Carlo quadrature KW - Perron cluster analysis Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000008079-9 ER - TY - GEN T1 - Jahresbericht 2008 T1 - Annual 2008 T3 - Jahresbericht - 2008 KW - Annual Report Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11307 SN - 0934-5892 ER - TY - GEN A1 - Tsarev, Sergey A1 - Wolf, Thomas T1 - Hyperdeterminants as integrable discrete systems N2 - We give the basic definitions and some theoretical results about hyperdeterminants, introduced by A.~Cayley in 1845. We prove integrability (understood as $4d$-consistency) of a nonlinear difference equation defined by the $2 \times 2 \times 2$ - hyperdeterminant. This result gives rise to the following hypothesis: the difference equations defined by hyperdeterminants of any size are integrable. We show that this hypothesis already fails in the case of the $2\times 2\times 2\times 2$ - hyperdeterminant. T3 - ZIB-Report - 09-17 KW - hyper determinants KW - integrable systems KW - discrete equations KW - large polynomial systems KW - computer algebra KW - Form KW - Reduce KW - Singular Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11292 SN - 1438-0064 ER - TY - GEN A1 - Maiwald, Gunar A1 - Peters-Kottig, Wolfgang T1 - Ergebnisse aus dem BVB-KOBV-Entwicklungsprojekt "Literaturverwaltungsprogramme": Handreichung für Bibliotheken T1 - Results of the BVB-KOBV project "Literaturverwaltungsprogramme": Handout for Libraries N2 - Zwischen dem Bibliotheksverbund Bayern (BVB) und dem Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) besteht seit Ende 2007 eine Strategische Allianz, die auf zwei Säulen beruht: einer langfristigen Entwicklungspartnerschaft einerseits und der Kooperation im Dienstleistungsbereich mit der Integration der Verbundkataloge andererseits. Ende 2008 wurde das erste Entwicklungsprojekt "Literaturverwaltungsprogramme" abgeschlossen, dessen Ergebnisse in dieser Handreichung in Form von Handlungsempfehlungen für Bibliotheken vorgestellt werden. Ziel des Projekts war es, den Datenaustausch zwischen den Bibliotheks- und Verbundkatalogen des BVB und KOBV und gängigen Literaturverwaltungsprogrammen zu optimieren. Neben Handlungsempfehlungen für die Implementierung neuer Exportschnittstellen und die Verbesserung bestehender Exportmöglichkeiten werden Hinweise auf verbesserte Nutzerführung gegeben. Die Empfehlungen beziehen sich vorwiegend auf den Datenaustausch zwischen den Bibliothekssystemen Aleph 500, MetaLib und WebOPAC/InfoGuide und den Literaturverwaltungsprogrammen Citavi, EndNote, RefWorks und Zotero. T3 - ZIB-Report - 09-16 KW - Literaturverwaltungsprogramm KW - Online-Katalog KW - reference management software KW - online library catalog Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11285 SN - 1438-0064 ER - TY - GEN A1 - Bley, Andreas T1 - On the Hardness of Finding Small Shortest Path Routing Conflicts N2 - Nowadays most data networks use shortest path protocols such as OSPF or IS-IS to route traffic. Given administrative routing lengths for the links of a network, all data packets are sent along shortest paths with respect to these lengths from their source to their destination. One of the most fundamental problems in planning shortest path networks is to decide whether a given set of routing paths forms a valid routing and, if this is not the case, to find a small subset of the given paths that cannot be shortest paths simultaneously for any routing lengths. In this paper we show that it is NP-hard to approximate the size of the smallest shortest path conflict by a factor less than 7/6. T3 - ZIB-Report - 09-15 KW - shortest path routing KW - computational complexity Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11276 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Stephan, Rüdiger A1 - Schlechte, Thomas T1 - Solving Steel Mill Slab Problems with Branch and Price N2 - The steel mill slab design problem from the CSPLib is a binpacking problem that is motivated by an application of the steel industry and that has been widely studied in the constraint programming community. Recently, several people proposed new models and methods to solve this problem. A steel mill slab library was created which contains 380 instances. A closely related binpacking problem called multiple knapsack problem with color constraints, originated from the same industrial problem, were discussed in the integer programming community. In particular, a simple integer programming for this problem has been given by Forrest et al. [3]. The aim of this paper is to bring these different studies together. Moreover, we adopt the model of [3] for the steel mill slab problem. Using a state of the art integer program solver, this model is capable to solve all instances of the steel mill slab library, mostly in less than one second, to optimality. We improved, thereby, the solution value of 76 instances. T3 - ZIB-Report - 09-14 KW - steel mill slab problem KW - branch-and-price KW - integer programming Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11260 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Jaeger, Ulrich T1 - Planning Problems in Public Transit N2 - Every day, millions of people are transported by buses, trains, and airplanes in Germany. Public transit (PT) is of major importance for the quality of life of individuals as well as the productivity of entire regions. Quality and efficiency of PT systems depend on the political framework (state-run, market oriented) and the suitability of the infrastructure (railway tracks, airport locations), the existing level of service (timetable, flight schedule), the use of adequate technologies (information, control, and booking systems), and the best possible deployment of equipment and resources (energy, vehicles, crews). The decision, planning, and optimization problems arising in this context are often gigantic and “scream” for mathematical support because of their complexity. This article sketches the state and the relevance of mathematics in planning and operating public transit, describes today’s challenges, and suggests a number of innovative actions. The current contribution of mathematics to public transit is — depending on the transportation mode — of varying depth. Air traffic is already well supported by mathematics. Bus traffic made significant advances in recent years, while rail traffic still bears significant opportunities for improvements. In all areas of public transit, the existing potentials are far from being exhausted. For some PT problems, such as vehicle and crew scheduling in bus and air traffic, excellent mathematical tools are not only available, but used in many places. In other areas, such as rolling stock rostering in rail traffic, the performance of the existing mathematical algorithms is not yet sufficient. Some topics are essentially untouched from a mathematical point of view; e.g., there are (except for air traffic) no network design or fare planning models of practical relevance. PT infrastructure construction is essentially devoid of mathematics, even though enormous capital investments are made in this area. These problems lead to questions that can only be tackled by engineers, economists, politicians, and mathematicians in a joint effort. Among other things, the authors propose to investigate two specific topics, which can be addressed at short notice, are of fundamental importance not only for the area of traffic planning, should lead to a significant improvement in the collaboration of all involved parties, and, if successful, will be of real value for companies and customers: • discrete optimal control: real-time re-planning of traffic systems in case of disruptions, • model integration: service design in bus and rail traffic. Work on these topics in interdisciplinary research projects could be funded by the German ministry of research and education (BMBF), the German ministry of economics (BMWi), or the German science foundation (DFG). T3 - ZIB-Report - 09-13 KW - öffentlicher Verkehr KW - diskrete Optimierung KW - ganzzahlige Programmierung KW - public transit KW - discrete optimization KW - integer programming Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11252 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Cardonha, Carlos T1 - A Binary Quadratic Programming Approach to the Vehicle Positioning Problem N2 - The Vehicle Positioning Problem (VPP) consists of the assignment of vehicles (buses, trams or trains) of a public transport or railway company to parking positions in a depot and to timetabled trips. Such companies have many different types of vehicles, and each trip can be performed only by vehicles of some of these types. These assignments are non-trivial due to the topology of depots. The parking positions are organized in tracks, which work as one- or two-sided stacks or queues. If a required type of vehicle is not available in the front of any track, shunting movements must be performed in order to change vehicles' positions, which is undesirable and should be avoided. In this text we present integer linear and non-linear programming formulations for some versions of the problem and compare them from a theoretical and a computational point of view. T3 - ZIB-Report - 09-12 KW - quadratic programming KW - integer programming KW - nonlinear programming KW - vehicle positioning Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11242 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Pfetsch, Marc T1 - Nonlinear pseudo-Boolean optimization: relaxation or propagation? N2 - Pseudo-Boolean problems lie on the border between satisfiability problems, constraint programming, and integer programming. In particular, nonlinear constraints in pseudo-Boolean optimization can be handled by methods arising in these different fields: One can either linearize them and work on a linear programming relaxation or one can treat them directly by propagation. In this paper, we investigate the individual strengths of these approaches and compare their computational performance. Furthermore, we integrate these techniques into a branch-and-cut-and-propagate framework, resulting in an efficient nonlinear pseudo-Boolean solver. T3 - ZIB-Report - 09-11 KW - Pseudo-Boolean KW - constraint integer programming KW - linear relaxation KW - separation algorithm KW - domain propagation Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11232 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Veränderungen der Publikations- und Kommunikationswelt: Open Access, Google, etc. T1 - Changes in the world of publishing and communication: Open Access, Google etc. N2 - Vorbemerkung Beim Schreiben dieses Artikels, der auf Veränderungen der Kommunikations- und Publikationstechniken und ihre Bedeutung hinweist, ist uns mehr als je zuvor bewusst geworden, wie beschränkt das Medium Papier ist. Es gibt z. B. keine Hyperlinks, durch die man unmittelbar das Erwähnte erleben oder überprüfen kann. Ein schneller Wechsel vom Wort zum Bild, zum Ton oder Video ist nicht möglich. Wer will schon lange URLs abtippen und Medienbrüche erleiden? Wir haben uns daher entschlossen, eine textidentische Version dieses Artikels mit allen URLs – sie liegt Ihnen hier vor – elektronisch anzubieten und in der für die "Gegenworte" (BBAW) gekürzten Fassung nur durch [URL] anzudeuten, dass der Leser an dieser Stelle einfach in der elektronischen Version einen Klick ins Internet machen sollte. Und damit sind wir bereits mitten im Thema. T3 - ZIB-Report - 09-10 KW - Publikations- und Kommunikationstechniken KW - Open Access KW - techniques of publishing and communication KW - Open Access Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11223 SN - 1438-0064 ER - TY - GEN A1 - Schmidt, Heiko A1 - Oevermann, Michael A1 - Bastiaans, Rob J.M. A1 - Kerstein, Alan R. T1 - A Priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds, Extended to Incorporate Strain Effects N2 - In this paper we revisit the a priori turbulent flame speed tabulation (TFST) technique for a given parameter space within the region of flamelet combustion-regimes. It can be used as a subgrid-scale (SGS) model in Large Eddy Simulation (LES). In a first step, stationary laminar flamelets are computed and stored over the progress variable following the ideas of flamelet generated manifolds (FGM). In a second step, the incompressible one-dimensional Navier-Stokes equations supplemented by the equation for the progress variable are solved on a grid that resolves all turbulent scales. Additionally, turbulent transport is implemented via the linear eddy model (LEM). The turbulent flame structures are solved until a statistically stationary mean value of the turbulent flame speed has been reached. The results are stored in a table that could be used by large scale premixed combustion models, e.g. front tracking schemes. First results are compared quantitatively with direct numerical simulations (DNS) taken from literature. Then it is illustrated in one example how the new method could help to fix constants in algebraic models for turbulent flame speeds. Further it is shown how the technique can be extended to incorporate turbulent strain effects. Finally we investigate the effect of the use of detailed and tabulated chemistry under unsteady conditions. T3 - ZIB-Report - 09-09 KW - Turbulente Verbrennung KW - Flammenstrukturen KW - Linear Eddy Model KW - FGM KW - Turbulente Brenngeschwindigkeit KW - Streckungseffekte KW - turbulent premixed combustion KW - flame structures KW - linear eddy model KW - flamelet generated manifolds KW - turbulent flame speed tabulation KW - strain effects Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11214 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf T1 - Discrete Optimization in Public Transportation N2 - The mathematical treatment of planning problems in public transit has made significant advances in the last decade. Among others, the classical problems of vehicle and crew scheduling can nowadays be solved on a routine basis using combinatorial optimization methods. This is not yet the case for problems that pertain to the design of public transit networks, and for the problems of operations control that address the implementation of a schedule in the presence of disturbances. The article gives a sketch of the state and important developments in these areas, and it addresses important challenges. The vision is that mathematical tools of computer aided scheduling (CAS) will soon play a similar role in the design and operation of public transport systems as CAD systems in manufacturing. N2 - Die mathematische Behandlung von Planungsproblemen im öffentlichen Verkehr hat im letzten Jahrzehnt große Fortschritte gemacht. Klassische Probleme wie die Umlauf- und die Dienstplanung können heutzutage routinemäßig mit kombinatorischen Optimierungsmethoden gelöst werden. Die Behandlung von Problemen der Angebotsplanung und der Betriebssteuerung sind dagegen noch nicht ganz auf diesem Stand. Dieser Artikel gibt einen Überblick über den Stand der Forschung, über wichtige Entwicklungen und einige Herausforderungen in diesem Gebiet. Die Vision ist, dass mathematische Planungswerkzeuge im öffentlichen Verkehr (Computer Aided Scheduling, CAS) in Zukunft eine ähnliche Rolle spielen werden wie CAD-Systeme in der industriellen Fertigung. T3 - ZIB-Report - 08-56 KW - Öffentlicher Verkehr KW - Nahverkehr KW - Optimierung KW - Public Transit KW - Optimization Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11207 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin T1 - On goal-oriented adaptivity for elliptic optimal control problems N2 - The paper proposes goal-oriented error estimation and mesh refinement for optimal control problems with elliptic PDE constraints using the value of the reduced cost functional as quantity of interest. Error representation, hierarchical error estimators, and greedy-style error indicators are derived and compared to their counterparts when using the all-at-once cost functional as quantity of interest. Finally, the efficiency of the error estimator and generated meshes are demonstrated on numerical examples. T3 - ZIB-Report - 09-08 KW - optimal control KW - error estimation KW - adaptive mesh refinement Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11192 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - The Steiner Connectivity Problem N2 - The Steiner connectivity problem is a generalization of the Steiner tree problem. It consists in finding a minimum cost set of simple paths to connect a subset of nodes in an undirected graph. We show that polyhedral and algorithmic results on the Steiner tree problem carry over to the Steiner connectivity problem, namely, the Steiner cut and the Steiner partition inequalities, as well as the associated polynomial time separation algorithms, can be generalized. Similar to the Steiner tree case, a directed formulation, which is stronger than the natural undirected one, plays a central role. T3 - ZIB-Report - 09-07 KW - Steiner Tree KW - Partition Inequalities KW - Paths KW - Connectivity KW - Generalization Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11171 SN - 1438-0064 ER - TY - GEN A1 - Klapproth, Corinna A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Consistency Results for the Contact-Stabilized Newmark Method N2 - The paper considers the time integration of frictionless dynamical contact problems between viscoelastic bodies in the frame of the Signorini condition. Among the numerical integrators, interest focuses on the contact-stabilized Newmark method recently suggested by Deuflhard et al., which is compared to the classical Newmark method and an improved energy dissipative version due to Kane et al. In the absence of contact, any such variant is equivalent to the Störmer-Verlet scheme, which is well-known to have consistency order 2. In the presence of contact, however, the classical approach to discretization errors would not show consistency at all because of the discontinuity at the contact. Surprisingly, the question of consistency in the constrained situation has not been solved yet. The present paper fills this gap by means of a novel proof technique using specific norms based on earlier perturbation results due to the authors. The corresponding estimation of the local discretization error requires the bounded total variation of the solution. The results have consequences for the construction of an adaptive timestep control, which will be worked out subsequently in a forthcoming paper. T3 - ZIB-Report - 09-06 KW - Dynamical contact problems KW - viscoelasticity KW - Signorini condition KW - consistency KW - Newmark method Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11164 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - Improving the performance of elevator systems using exact reoptimization algorithms N2 - This extended abstract is about algorithms for controlling elevator systems employing destination hall calls, i.e. the passenger provides his destination floor when calling an elevator. We present the first exact algorithm for controlling a group of elevators and report on simulation results indicating that destination hall call systems outperform conventional systems. T3 - ZIB-Report - 09-05 KW - Aufzugssteuerung KW - Onlineoptimierung KW - Exakte Reoptimierung KW - elevator control KW - online optimization KW - exact reoptimation Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11155 SN - 1438-0064 ER - TY - GEN A1 - Neumann, Marika T1 - Fare Planning for Public Transport N2 - In this paper we investigate the fare planning model for public transport, which consists in designing a system of fares maximizing the revenue. We discuss a discrete choice model in which passengers choose between different travel alternatives to express the demand as a function of fares. Furthermore, we give a computational example for the city of Potsdam and discuss some theoretical aspects. T3 - ZIB-Report - 09-04 KW - fares KW - descrete choice Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11144 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Krumke, Sven A1 - Saliba, Sleman A1 - Tuchscherer, Andreas T1 - Randomized Online Algorithms for Dynamic Multi-Period Routing Problems N2 - The Dynamic Multi-Period Routing Problem DMPRP introduced by Angelelli et al. gives a model for a two-stage online-offline routing problem. At the beginning of each time period a set of customers becomes known. The customers need to be served either in the current time period or in the following. Postponed customers have to be served in the next time period. The decision whether to postpone a customer has to be done online. At the end of each time period, an optimal tour for the customers assigned to this period has to be computed and this computation can be done offline. The objective of the problem is to minimize the distance traveled over all planning periods assuming optimal routes for the customers selected in each period. We provide the first randomized online algorithms for the DMPRP which beat the known lower bounds for deterministic algorithms. For the special case of two planning periods we provide lower bounds on the competitive ratio of any randomized online algorithm against the oblivious adversary. We identify a randomized algorithm that achieves the optimal competitive ratio of $\frac{1+\sqrt{2}}{2}$ for two time periods on the real line. For three time periods, we give a randomized algorithm that is strictly better than any deterministic algorithm. T3 - ZIB-Report - 09-03 KW - Online-Optimierung KW - Randomisierte Algorithmen KW - Zweistufiges Problem KW - Traveling-Salesman-Problem KW - online optimization KW - randomized algorithm KW - two-stage problem KW - traveling salesman problem Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11132 SN - 1438-0064 ER - TY - THES A1 - Achterberg, Tobias T1 - Constraint Integer Programming N2 - This thesis introduces the novel paradigm of "constraint integer programming" (CIP), which integrates constraint programming (CP) and mixed integer programming (MIP) modeling and solving techniques. It is supplemented by the software SCIP, which is a solver and framework for constraint integer programming that also features SAT solving techniques. SCIP is freely available in source code for academic and non-commercial purposes. Our constraint integer programming approach is a generalization of MIP that allows for the inclusion of arbitrary constraints, as long as they turn into linear constraints on the continuous variables after all integer variables have been fixed. The constraints, may they be linear or more complex, are treated by any combination of CP and MIP techniques: the propagation of the domains by constraint specific algorithms, the generation of a linear relaxation and its solving by LP methods, and the strengthening of the LP by cutting plane separation. The current version of SCIP comes with all of the necessary components to solve mixed integer programs. In the thesis, we cover most of these ingredients and present extensive computational results to compare different variants for the individual building blocks of a MIP solver. We focus on the algorithms and their impact on the overall performance of the solver. In addition to mixed integer programming, the thesis deals with chip design verification, which is an important topic of electronic design automation. Chip manufacturers have to make sure that the logic design of a circuit conforms to the specification of the chip. Otherwise, the chip would show an erroneous behavior that may cause failures in the device where it is employed. An important subproblem of chip design verification is the property checking problem, which is to verify whether a circuit satisfies a specified property. We show how this problem can be modeled as constraint integer program and provide a number of problem-specific algorithms that exploit the structure of the individual constraints and the circuit as a whole. Another set of extensive computational benchmarks compares our CIP approach to the current state-of-the-art SAT methodology and documents the success of our method. N2 - Diese Arbeit stellt einen integrierten Ansatz aus "Constraint Programming" (CP) und Gemischt-Ganzzahliger Programmierung ("Mixed Integer Programming", MIP) vor, den wir "Constraint Integer Programming" (CIP) nennen. Sowohl Modellierungs- als auch Lösungstechniken beider Felder fließen in den neuen integrierten Ansatz ein, um die unterschiedlichen Stärken der beiden Gebiete zu kombinieren. Als weiteren Beitrag stellen wir der wissenschaftlichen Gemeinschaft die Software SCIP zur Verfügung, die ein Framework für Constraint Integer Programming darstellt und zusätzlich Techniken des SAT-Lösens beinhaltet. SCIP ist im Source Code für akademische und nicht-kommerzielle Zwecke frei erhältlich. Unser Ansatz des Constraint Integer Programming ist eine Verallgemeinerung von MIP, die zusätzlich die Verwendung beliebiger Constraints erlaubt, solange sich diese durch lineare Bedingungen ausdrücken lassen falls alle ganzzahligen Variablen auf feste Werte eingestellt sind. Die Constraints werden von einer beliebigen Kombination aus CP- und MIP-Techniken behandelt. Dies beinhaltet insbesondere die "Domain Propagation", die Relaxierung der Constraints durch lineare Ungleichungen, sowie die Verstärkung der Relaxierung durch dynamisch generierte Schnittebenen. Die derzeitige Version von SCIP enthält alle Komponenten, die für das effiziente Lösen von Gemischt-Ganzzahligen Programmen benötigt werden. Die vorliegende Arbeit liefert eine ausführliche Beschreibung dieser Komponenten und bewertet verschiedene Varianten in Hinblick auf ihren Einfluß auf das Gesamt-Lösungsverhalten anhand von aufwendigen praktischen Experimenten. Dabei wird besonders auf die algorithmischen Aspekte eingegangen. Ein weiterer Hauptteil der Arbeit befasst sich mit der Chip-Design-Verifikation, die ein wichtiges Thema innerhalb des Fachgebiets der "Electronic Design Automation" darstellt. Chip-Hersteller müssen sicherstellen, dass der logische Entwurf einer Schaltung der gegebenen Spezifikation entspricht. Andernfalls würde der Chip fehlerhaftes Verhalten aufweisen, dass zu Fehlfunktionen innerhalb des Gerätes führen kann, in dem der Chip verwendet wird. Ein wichtiges Teilproblem in diesem Feld ist das Eigenschafts-Verifikations-Problem, bei dem geprüft wird, ob der gegebene Schaltkreisentwurf eine gewünschte Eigenschaft aufweist. Wir zeigen, wie dieses Problem als Constraint Integer Program modelliert werden kann und geben eine Reihe von problemspezifischen Algorithmen an, die die Struktur der einzelnen Constraints und der Gesamtschaltung ausnutzen. Testrechnungen auf Industrie-Beispielen vergleichen unseren Ansatz mit den bisher verwendeten SAT-Techniken und belegen den Erfolg unserer Methode. KW - Ganzzahlige Programmierung KW - Constraint Programmierung KW - SAT KW - Chip-Verifikation KW - Mathematische Programmierung KW - Integer Programming KW - Constraint Programming KW - SAT KW - Chip Verification KW - Mathematical Programming Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11129 ER - TY - GEN A1 - Lügger, Joachim T1 - Zum Nutzen des Web 2.0 für „Die kleine Kollaboration“ in den Wissenschaften T1 - Utilisation of the Web 2.0 for the "Small Collaboration" in the Sciences N2 - Gemeinsame Web-Auftritte zu organisieren, die sich über mehrere Institutionen und Fachgebiete erstrecken, ist eine anspruchsvolle und faszinierende Aufgabe, die auf verschiedene Weise gelingen, aber auch scheitern kann. Wer sich daran versucht, tut gut daran, sich über bestimmte Prinzipien und technische Mittel zu informieren, die das fortgeschrittene Web ihm heute bietet. Das Internet, das World Wide Web und das moderne Web 2.0 sind in einer fast zwanzig Jahre dauernden Kollaboration einer globalen Gemeinschaft von Entwicklern und Anwendern entstanden. Es enthält heute eine Fülle sofort einsetzbarer Komponenten, von der „Benutzerdefinierten Google-Suche Beta“ mit Google‘s PageRanking auf ausgewählten Web-Seiten bis hin zum automatisierten Web-Server mit Content-Management für das „Mitmach-Web“. Der Artikel stellt nur eine kleine Auswahl solcher Lösungen vor und macht den Versuch, einige Prinzipien des Web 2.0 so herauszuarbeiten, dass die notwendige Kommunikation zwischen Managern, Technikern, Redakteuren und Organisatoren in der kleinen Kollaboration unterstützt wird. „Kleine Kollaboration“ bedeutet hier, dass es nicht um die globale Vernetzung von technischen Großgeräten der e-Science gehen soll, auch nicht um die Super-Suchmaschine in Europa, sondern um die Unterstützung der Zusammenarbeit und Kommunikation von Wissenschaftlern und Museumsfachleuten mit Ihren Nutzern. T3 - ZIB-Report - 08-55 KW - Web 2.0 KW - Kollaboration Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11114 SN - 1438-0064 ER - TY - THES A1 - Lamecker, Hans T1 - Variational and statistical shape modeling for 3D geometry reconstruction N2 - The reconstruction of geometric shapes plays an important role in many biomedical applications. One example is the patient-specific, computer-aided planning of complex interventions, which requires the generation of explicitly represented geometric models of anatomical structures from medical image data. Only solutions that require minimal interaction by medical personnel are likely to enter clinical routine. Another example is the planning of surgical corrections of deformities where the target shape is unknown. Surgeons are often forced to resort to subjective criteria. These applications still pose highly challenging reconstruction problems, which are addressed in this thesis. The fundamental hypothesis, pursued in this thesis, is that the problems can be solved by incorporating a-priori knowledge about shape and other application-specific characteristics. Here, we focus mainly on the aspect of geometric shape analysis. The basic idea is to capture the most essential variations of a certain class of geometric objects via statistical shape models, which model typical features contained in a given population, and restrict the outcome of a reconstruction algorithm (more or less) to the space spanned by such models. A fundamental prerequisite for performing statistical shape analysis on a set of different objects is the identification of corresponding points on their associated surfaces. This problem is particularly difficult to solve if the shapes stem from different individuals. The reason lies in the basic difficulty of defining suitable measures of similarity. In this thesis, we divide the correspondence problem into feature and non-feature matching. The feature part depends on the application, while the non-feature part can be characterized by a purely geometric description. We propose two different approaches. The first approach has proved useful in many applications. Yet, it suffers from some practical limitations and does not yield a measure of similarity. Our second, variational, approach is designed to overcome these limitations. In it, we propose to minimize an invariant stretching measure, constrained by previously computed features. An important property, which sets our method apart from previous work, is that it does not require the computation of a global surface parameterization. KW - correspondence problem KW - surface matching KW - image segmentation KW - model-based shape reconstruction KW - 2d-3d shape reconstruction Y1 - 2008 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000005805 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Insensitivity bounds for the moments of the sojourn times in M/GI systems under state-dependent processor sharing N2 - We consider a system with Poisson arrivals and i.i.d. service times and where the requests are served according to the state-dependent (Cohen's generalized) processor sharing discipline, where each request in the system receives a service capacity which depends on the actual number of requests in the system. For this system we derive asymptotically tight upper bounds for the moments of the conditional sojourn time of a request with given required service time. The bounds generalize corresponding results, recently given for the single-server processor sharing system by Cheung et al. and for the state-dependent processor sharing system with exponential service times by the authors. Analogous results hold for the waiting times. T3 - ZIB-Report - 09-02 KW - state-dependent processor sharing KW - sojourn time KW - moments KW - bounds KW - M/GI/m-PS Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11092 SN - 1438-0064 ER - TY - GEN A1 - Allalen, Mohammed A1 - Brehm, Matthias A1 - Stüben, Hinnerk T1 - Performance of Quantum Chromodynamics (QCD) Simulations on the SGI Altix N2 - We study performance and scaling of the Berlin Quantum Chromodynamics Program (BQCD) on the SGI Altix 4700 at Leibniz Supercomputing Centre (LRZ). We employ different communication methods (MPI, MPI with two OpenMP threads per process, as well as the shmem library) and run the MPI version on the two types of nodes of that machine. For comparison with other machines we made performance measurements on an IBM p690 cluster and a Cray XT4. T3 - ZIB-Report - 08-54 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11086 SN - 1438-0064 ER - TY - GEN A1 - Torres, Luis Miguel A1 - Torres, Ramiro A1 - Borndörfer, Ralf A1 - Pfetsch, Marc T1 - Line Planning on Paths and Tree Networks with Applications to the Quito Trolebus System (Extended Abstract) N2 - Line planning is an important step in the strategic planning process of a public transportation system. In this paper, we discuss an optimization model for this problem in order to minimize operation costs while guaranteeing a certain level of quality of service, in terms of available transport capacity. We analyze the problem for path and tree network topologies as well as several categories of line operation that are important for the Quito Trolebus system. It turns out that, from a computational complexity worst case point of view, the problem is hard in all but the most simple variants. In practice, however, instances based on real data from the Trolebus System in Quito can be solved quite well, and significant optimization potentials can be demonstrated. T3 - ZIB-Report - 08-53 KW - line planning KW - computational complexity KW - public transport KW - integer programming Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11076 SN - 1438-0064 ER - TY - GEN A1 - Torres, Luis Miguel A1 - Torres, Ramiro A1 - Borndörfer, Ralf A1 - Pfetsch, Marc T1 - On the Line Planning Problem in Tree Networks N2 - We introduce an optimization model for the line planning problem in a public transportation system that aims at minimizing operational costs while ensuring a given level of quality of service in terms of available transport capacity. We discuss the computational complexity of the model for tree network topologies and line structures that arise in a real-world application at the Trolebus Integrated System in Quito. Computational results for this system are reported. T3 - ZIB-Report - 08-52 KW - line planning KW - computational complexity KW - public transport optimization Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11069 SN - 1438-0064 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Pióro, Michal T1 - On the complexity of column generation in survivable network design with path-based survivability mechanisms N2 - This survey concerns optimization problems arising in the design of survivable communication networks. It turns out that such problems can be modeled in a natural way as non-compact linear programming formulations based on multicommodity flow network models. These non-compact formulations involve an exponential number of path flow variables, and therefore require column generation to be solved to optimality. We consider several path-based survivability mechanisms and present results, both known and new, on the complexity of the corresponding column generation problems (called the pricing problems). We discuss results for the case of the single link (or node) failures scenarios, and extend the considerations to multiple link failures. Further, we classify the design problems corresponding to different survivability mechanisms according to the structure of their pricing problem. Finally, we show that almost all encountered pricing problems are hard to solve for scenarios admitting multiple failures. T3 - ZIB-Report - 08-51 KW - Netzplanung KW - Dimensionierung KW - Spaltengenerierung KW - Mehrfachausfälle KW - survivable network design KW - routing KW - column generation KW - pricing KW - complexity Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11058 SN - 1438-0064 ER - TY - GEN A1 - Mellado, Juan Pedro A1 - Stevens, Bjorn A1 - Schmidt, Heiko A1 - Peters, Norbert T1 - Buoyancy-reversal in cloud-top mixing layers N2 - A theoretical and numerical small-scale study of the evaporative cooling phenomenon that might appear in the stratocumulus-topped boundary layers is presented. An ideal configuration of a cloud-top mixing layer is considered as defined by two nonturbulent horizontal layers, stably stratified and with buoyancy reversal within a certain range of mixture fractions due to the evaporative cooling. Linear stability analysis of the shear-free configuration is employed to provide a new interpretation of the buoyancy reversal parameter, namely, in terms of a time-scale ratio between the unstable and the stable modes of the system. An incompressible high-order numerical algorithm to perform direct numerical simulation of the configuration is described and two-dimensional simulations of single-mode perturbations are discussed. These simulations confirm the role of the different parameters identified in the linear stability analysis and show that convoluted flow patterns can be generated by the evaporative cooling even for the low levels of buoyancy reversal found in stratocumulus clouds. They also show that there is no enhancement of entrainment of upper layer fluid in the shear-free configuration, and mixing enhancement by the evaporative cooling is restricted to the lower layer. T3 - ZIB-Report - 08-50 KW - Stratocumulus Wolken KW - freie Konvektion KW - turbulente Strömungen KW - stratocumulus KW - free convection KW - free turbulent flows Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11046 SN - 1438-0064 ER - TY - GEN A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian T1 - Dual Streamline Seeding - Method and Implementation N2 - This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces. N2 - In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist. T3 - ZIB-Report - 08-49 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11032 SN - 1438-0064 ER - TY - GEN A1 - Stephan, Rüdiger T1 - Cardinality Constrained Combinatorial Optimization: Complexity and Polyhedra N2 - Given a combinatorial optimization problem and a subset $N$ of natural numbers, we obtain a cardinality constrained version of this problem by permitting only those feasible solutions whose cardinalities are elements of $N$. In this paper we briefly touch on questions that addresses common grounds and differences of the complexity of a combinatorial optimization problem and its cardinality constrained version. Afterwards we focus on polytopes associated with cardinality constrained combinatorial optimization problems. Given an integer programming formulation for a combinatorial optimization problem, by essentially adding Grötschel's cardinality forcing inequalities, we obtain an integer programming formulation for its cardinality restricted version. Since the cardinality forcing inequalities in their original form are mostly not facet defining for the associated polyhedra, we discuss possibilities to strengthen them. T3 - ZIB-Report - 08-48 KW - Combinatorial Optimization KW - Cardinality Constraints KW - Matroids KW - Cardinality Forcing Inequalities Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11026 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton A1 - Wollner, Winnifried T1 - Barrier Methods for Optimal Control Problems with Convex Nonlinear Gradient Constraints N2 - In this paper we are concerned with the application of interior point methods in function space to gradient constrained optimal control problems, governed by partial differential equations. We will derive existence of solutions together with first order optimality conditions. Afterwards we show continuity of the central path, together with convergence rates depending on the interior point parameter. T3 - ZIB-Report - 08-47 KW - interior point method KW - necessary optimality conditions KW - convergence of the central path KW - gradient constrained optimization Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11014 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton A1 - Günther, Andreas T1 - Interior Point Methods in Function Space for State Constraints - Inexact Newton and Adaptivity N2 - We consider an interior point method in function space for PDE constrained optimal control problems with state constraints. Our emphasis is on the construction and analysis of an algorithm that integrates a Newton path-following method with adaptive grid refinement. This is done in the framework of inexact Newton methods in function space, where the discretization error of each Newton step is controlled by adaptive grid refinement in the innermost loop. This allows to perform most of the required Newton steps on coarse grids, such that the overall computational time is dominated by the last few steps. For this purpose we propose an a-posteriori error estimator for a problem suited norm. T3 - ZIB-Report - 09-01 KW - interior point methods KW - function space KW - adaptivity KW - state constraints Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11007 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung T1 - Fair Ticket Prices in Public Transport N2 - Ticket pricing in public transport usually takes a welfare or mnemonics maximization point of view. These approaches do not consider fairness in the sense that users of a shared infrastructure should pay for the costs that they generate. We propose an ansatz to determine fair ticket prices that combines concepts from cooperative game theory and integer programming. An application to pricing railway tickets for the intercity network of the Netherlands demonstrates that, in this sense, prices that are much fairer than standard ones can be computed in this way. T3 - ZIB-Report - 08-46 KW - Ticket prices KW - cost allocation game Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10999 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin A1 - Röllig, Mathias A1 - Arndt, Ralf A1 - Erdmann, Bodo T1 - Development and test of a numerical model for pulse thermography in civil engineering N2 - Pulse thermography of concrete structures is used in civil engineering for detecting voids, honeycombing and delamination. The physical situation is readily modeled by Fourier's law. Despite the simplicity of the PDE structure, quantitatively realistic numerical 3D simulation faces two major obstacles. First, the short heating pulse induces a thin boundary layer at the heated surface which encapsulates all information and therefore has to be resolved faithfully. Even with adaptive mesh refinement techniques, obtaining useful accuracies requires an unsatisfactorily fine discretization. Second, bulk material parameters and boundary conditions are barely known exactly. We address both issues by a semi-analytic reformulation of the heat transport problem and by parameter identification. Numerical results are compared with measurements of test specimens. T3 - ZIB-Report - 08-45 KW - finite element model KW - KARDOS KW - pulse thermography KW - civil engineering KW - inverse solution Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10980 SN - 1438-0064 ER - TY - THES A1 - Prohaska, Steffen T1 - Skeleton-based visualization of massive voxel objects with network-like architecture T1 - Skelettbasierte Visualisierung großer Voxel-Objekte mit netzwerkartiger Architektur N2 - This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation. N2 - Die vorliegende Arbeit führt I/O-effiziente Algorithmen und Standard-Algorithmen zur Berechnung von Voxel-Skeletten aus großen Voxel-Objekten mit komplexer, netzwerkartiger Struktur und zur Umwandlung solcher Voxel-Skelette in stückweise-lineare Geometrie ein. Die vorgestellten Techniken werden zur Visualisierung und Analyse komplexer drei-dimensionaler Bilddaten, beispielsweise aus Biologie und Medizin, eingesetzt. Abschnitt 2.3.1 leistet mit der Diskussion von topologischem Thinning im Grid-Cell-Modell einen Beitrag zu den theoretischen Grundlagen von Thinning-Algorithmen. Im Grid-Cell-Modell wird ein Voxel-Objekt als Zellkomplex dargestellt, der aus den Ecken, Kanten, Flächen und den eingeschlossenen Volumina der Voxel gebildet wird. Topologisch unklare Situationen an Verzweigungen und blockierte Voxel-Kombinationen werden aufgelöst. Die Charakterisierung von Zellpaaren, die im Thinning-Prozess entfernt werden dürfen, ist einfacher als bekannte Charakterisierungen von so genannten "Simple Voxels". Eine wesentliche Schlussfolgerung ist, dass das Grid-Cell-Modell atomaren Voxeln überlegen ist, wenn Algorithmen detaillierte Kontrolle über Topologie benötigen. Abschnitt 2.3.2 präsentiert ein rauschunempfindliches Maß, das den geodätischen Abstand entlang der Oberfläche verwendet, um zweidimensionale Skelette zu berechnen, welche dünne, aber geometrisch bedeutsame, Strukturen des Objekts rauschunempfindlich abbilden. Das Maß wird im weiteren mit Thinning kombiniert, um die Erosion von Voxeln auf Linien zuzusteuern, die zentriert in plattenförmigen Strukturen liegen. Maße, die auf dem geodätischen Abstand aufbauen, scheinen sehr geeignet zu sein, um ein- und zwei-dimensionale Skelette bei vorhandenem Rauschen zu identifizieren. Eine theoretische Begründung für diese Beobachtung steht noch aus. In Abschnitt 6 werden die diskutierten Methoden zur Visualisierung von Knochenfeinstruktur eingesetzt. Abschnitt 3 beschreibt eine Methode, um Voxel-Skelette durch kontrollierte Retraktion in eine stückweise-lineare geometrische Darstellung umzuwandeln, die als Eingabe für Geometrieverarbeitung und effizientes Rendering von Voxel-Skeletten dient. Es zeigt sich, dass eine detaillierte Betrachtung der topologischen Eigenschaften eines Voxel-Skeletts einer Betrachtung von allgemeinen Voxel-Konfigurationen für die Umwandlung zu einer geometrischen Darstellung überlegen ist. Die diskutierte Methode bildet die Grundlage für die Anwendungen, die in Abschnitt 6 diskutiert werden. Abschnitt 5 führt einen I/O-effizienten Algorithmus für Thinning ein. Die vorgestellte Methode erweitert bekannte Algorithmen zur Berechung von Chamfer-Distanztransformationen und Thinning so, dass diese effizient ausführbar sind, wenn die Eingabedaten den verfügbaren Hauptspeicher übersteigen. Der Einfluss der Blockgrenzen auf die Algorithmen wurde analysiert, um global korrekte Ergebnisse sicherzustellen. Eine detaillierte Analyse ist einer naiven Zerlegung, die die Einflüsse von Blockgrenzen vernachlässigt, überlegen. In Abschnitt 6 wird, aufbauend auf den I/O-effizienten Algorithmen, ein Verfahren zur quantitativen Analyse von Mikrogefäßnetzwerken diskutiert. KW - Visualisierung KW - Bilddatenanalyse KW - Skelettberechnung KW - Geometrieerzeugung KW - I/O-effiziente Algorithmen KW - visualization KW - image data analysis KW - skeletonization KW - geometry generation KW - external memory algorithms Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-14888 UR - http://opus.kobv.de/ubp/volltexte/2007/1488/ ER - TY - GEN A1 - Carqué, Gunter A1 - Schmidt, Heiko A1 - Stevens, Bjorn A1 - Klein, Rupert T1 - Plausibility Check of an Asymptotic Column Model for Deep Convective Clouds N2 - By use of asymptotic analysis Carqué et al. [ZIB-Report 08-03] derived an asymptotic column model for deep convective clouds based on the three dimensional compressible flow equations and a bulk microphysics parameterization. In the present study we check the plausibility of the reduced model equations by comparing implications of the model for the scaling of various terms in the governing equations with those extracted from large eddy simulation data based on the computational model UCLA-LES1.1. This code solves an anelastic system of equations with complete droplet based microphysics and LES closures. We observe that the simulation data corroborate the basic assumptions of the asymptotic analysis and the main conclusions implied by the asymptotically reduced model. The code output reflects the scales of space and time: The deep convective clouds show an anisotropic structure where the horizontal scale is considerably narrower than the vertical scale; with a period of about 20 min, from emergence to breakup, the life cycle of one particular deep convective cloud corresponds exactly to the reference time of the reduced model. The characteristic properties of dynamics as predicted by the reduced model are also reflected in the simulation data: The horizontal flow is controlled by the pressure field; the vertical velocity develops freely independent of pressure over the depth of the convective column; the vertical velocity is directly determined by the buoyancy induced by the potential temperature deviation relative to the background stratification. With respect to grid resolution we observe that refining the spatial step size of the equidistant computational grid from 125 m to 62.5 m does not influence the results: Even with the coarser grid the relevant physical phenomena are sufficiently resolved. Somewhat surprisingly, the Coriolis term involving vertical velocity and acting on the horizontal (east-west) velocity component appears at leading order in the asymptotics. Accordingly, we expected to find a nontrivial impact of this Coriolis effect on the horizontal flow velocity components within columns of updrafts. However, switching the term on and off in subsequent simulations did not sizeably affect the results. T3 - ZIB-Report - 08-44 KW - atmospheric moist convection KW - deep convection KW - precipitating clouds KW - asymptotic analysis KW - Large Eddy Simulation Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10967 SN - 1438-0064 ER - TY - GEN A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Wolter, Kati T1 - Constraint Integer Programming: Techniques and Applications N2 - This article introduces constraint integer programming (CIP), which is a novel way to combine constraint programming (CP) and mixed integer programming (MIP) methodologies. CIP is a generalization of MIP that supports the notion of general constraints as in CP. This approach is supported by the CIP framework SCIP, which also integrates techniques for solving satisfiability problems. SCIP is available in source code and free for noncommercial use. We demonstrate the usefulness of CIP on three tasks. First, we apply the constraint integer programming approach to pure mixed integer programs. Computational experiments show that SCIP is almost competitive to current state-of-the-art commercial MIP solvers. Second, we demonstrate how to use CIP techniques to compute the number of optimal solutions of integer programs. Third, we employ the CIP framework to solve chip design verification problems, which involve some highly nonlinear constraint types that are very hard to handle by pure MIP solvers. The CIP approach is very effective here: it can apply the full sophisticated MIP machinery to the linear part of the problem, while dealing with the nonlinear constraints by employing constraint programming techniques. T3 - ZIB-Report - 08-43 KW - constraint programming KW - mixed integer programming KW - branch-and-cut KW - optimization software KW - chip verification Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10950 SN - 1438-0064 ER - TY - GEN A1 - Haack, Fiete T1 - Properties of Reduced Reversible Markov Chains N2 - The enormous time lag between fast atomic motion and complex pro- tein folding events makes it almost impossible to compute molecular dy- namics on a high resolution. A common way to tackle this problem is to model the system dynamics as a Markov process. Yet for large molec- ular systems the resulting Markov chains can hardly be handled due to the curse of dimensionality. Coarse graining methods can be used to re- duce the dimension of a Markov chain, but it is still unclear how far the coarse grained Markov chain resembles the original system. In order to answer this question, two different coarse-graining methods were analysed and compared: a classical set-based reduction method and an alternative subspace-based approach, which is based on membership vectors instead of sets. On the basis of a small toy system, it could be shown, that in con- trast to the subset-based approach, the subspace-based reduction method preserves the Markov property as well as the essential dynamics of the original system. T3 - ZIB-Report - 08-42 KW - Markov Chain KW - PCCA+ KW - Conformation dynamics Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10941 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Deuflhard, Peter T1 - On Efficiency and Accuracy in Cardioelectric Simulation N2 - Reasons for the failure of adaptive methods to deliver improved efficiency when integrating monodomain models for myocardiac excitation are discussed. Two closely related techniques for reducing the computational complexity of linearly implicit integrators, deliberate sparsing and splitting, are investigated with respect to their impact on computing time and accuracy. T3 - ZIB-Report - 08-41 KW - elektrische Herzanregung KW - Diskretisierungsfehler KW - splitting KW - mass lumping KW - cardioelectric excitation KW - discretization error KW - splitting KW - mass lumping Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10934 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin T1 - Optimization and Identification in Regional Hyperthermia N2 - Regional hyperthermia is a cancer therapy aiming at heating tumors using phased array applicators. This article provides an overview over current mathematical challenges of delivering individually optimal treatments. The focus is on therapy planning and identification of technical as well as physiological quantities from MR thermometry measurements. T3 - ZIB-Report - 08-40 KW - Hyperthermie-Therapieplanung KW - Identifizierung KW - MR-Thermometrie KW - Innere-Punkte-Methoden KW - hyperthermia treatment planning KW - identification KW - MR thermometry KW - interior point methods Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10916 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - On the optimality of Least Recently Used N2 - It is well known that competitive analysis yields too pessimistic results when applied to the paging problem and it also cannot make a distinction between many paging strategies. Many deterministic paging algorithms achieve the same competitive ratio, ranging from inefficient strategies as flush-when-full to the good performing least-recently-used (LRU). In this paper, we study this fundamental online problem from the viewpoint of stochastic dominance. We show that when sequences are drawn from distributions modelling locality of reference, LRU is stochastically better than any other online paging algorithm. T3 - ZIB-Report - 08-39 KW - Paging KW - locality of reference KW - LRU KW - Onlinealgorithmen KW - Stochastische Dominanz KW - paging KW - locality of reference KW - LRU KW - online algorithms KW - stochastic dominance Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10928 SN - 1438-0064 ER - TY - GEN A1 - Oevermann, Michael A1 - Scharfenberg, Carsten A1 - Klein, Rupert T1 - A sharp interface finite volume method for elliptic equations on Cartesian grids N2 - We present a second order sharp interface finite volume method for the solution of the three-dimensional poisson equation with variable coefficients on Cartesian grids. In particular, we focus on interface problems with discontinuities in the coefficient, the source term, the solution, and the fluxes across the interface. The method uses standard piecewiese trilinear finite elements for normal cells and a double piecewise trilinear ansatz for the solution on cells intersected by the interface resulting always in a compact 27-point stencil. Singularities associated with vanishing partial volumes of intersected grid cells are removed by a two-term asymptotic approach. In contrast to the 2D method presented by two of the authors in [M.~Oevermann, R.~Klein: A Cartesian grid finite volume method for elliptic equations with variable coefficients and embedded interfaces, J.~Comp.~Phys.~219 (2006)] we use a minimization technique to determine the unknown coefficients of the double trilinear ansatz. This simplifies the treatment of the different cut-cell types and avoids additional special operations for degenerated interface topologies. The resulting set of linear equations has been solved with a BiCGSTAB solver preconditioned with an algebraic multigrid. In various testcases -- including large coefficient ratios and non-smooth interfaces -- the method achieves second order of accuracy in the L_inf and L_2 norm. T3 - ZIB-Report - 08-38 KW - elliptische Gleichungen KW - Finite Volumen KW - eingebettete Ränder KW - variable und diskontinuierliche Koeffizienten KW - diskontinuierliche Lösung KW - Elliptic equations KW - finite volume methods KW - embedded interface KW - variable and discontinuous coefficients KW - discontinuous solution Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10900 SN - 1438-0064 ER - TY - GEN A1 - Herm, Karin A1 - Volz, Sibylle T1 - The Library Search Engine: A Smart Solution for Integrating Resources Beyond Library Holdings N2 - The Cooperative Library Network Berlin-Brandenburg (KOBV), Germany, addresses the problem of how to integrate resources found outside the library and library holdings into a single discovery tool. It presents a solution that uses open source technology to develop a next-generation catalog interface called the Library Search Engine. This pilot project was launched in 2007 with the library of Albert Einstein Science Park, Potsdam. The idea was to design and develop a fast and convenient search tool, integrating local holdings (books, journals, journal articles) as well as relevant scientific subject information such as open access publications and bibliographies. T3 - ZIB-Report - 08-37 KW - Suchmaschinentechnologie KW - Bibliothekskatalog KW - search engine technology KW - library catalogue Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10893 SN - 1438-0064 ER - TY - THES A1 - Kinder, Mathias T1 - Models for Periodic Timetabling N2 - We investigate the computation of periodic timetables for public transport by mixed integer programming. After introducing the problem, we describe two mathematical models for periodic timetabling, the PERIODIC EVENT SCHEDULING PROBLEM (PESP) and the QUADRATIC SEMI-ASSIGNMENT PROBLEM. Specifically, we give an overview of existing integer programming (IP) formulations for both models. An important contribution of our work are new IP formulations for the PESP based on time discretization. We provide an analytical comparison of these formulations and describe different techniques that allow a more efficient solution by mixed integer programming. In a preliminary computational study, on the basis of standard IP solvers, we compare different formulations for computing periodic timetables. Our results justify a further investigation of the time discretization approach. Typically the timetable is optimized for the current traffic situation. The main difficulty with this approach is that after introducing the new timetable the passengers’ travel behavior may differ from that assumed for the computation. Motivated by this problem, we examine an iterative timetabling procedure that is a combination of timetable computation and passenger routing. We discuss the algorithmic issues of the passenger routing and study properties of the computed timetables. Finally, we confirm our theoretical results on the basis of an own implementation. N2 - Wir untersuchen die Berechnung von Taktfahrplänen für den öffentlichen Verkehr mit gemischt-ganzzahliger Programmierung (MIP). Im Anschluss an die Problembeschreibung, stellen wir zwei mathematische Modellierungen vor, das PERIODIC EVENT SCHEDULING PROBLEM (PESP) und das QUADRATIC SEMI-ASSIGNMENT PROBLEM. Wichtiger Bestandteil ist ein Überblick über existierende ganzzahlige Formulierungen beider Modelle. Wir entwickeln neue ganzzahlige Formulierungen für das PESP auf der Basis von Zeitdiskretisierung. Diese werden analytisch miteinander verglichen und wir beschreiben verschiedene Techniken, die eine effizientere Lösung der Formulierungen mit gemischt-ganzzahliger Programmierung ermöglichen. In einer ersten Rechenstudie, unter Verwendung gängiger MIP-Löser, vergleichen wir verschiedene ganzzahlige Formulierungen zur Berechnung von Taktfahrplänen. Unsere Ergebnisse rechtfertigen eine weitere Untersuchung des Zeitdiskretisierungsansatzes. In der Regel werden Fahrpläne mit Bezug auf die gegenwärtige Verkehrssituation optimiert. Dies birgt jedoch folgendes Problem. Wenn der neue Fahrplan eingeführt wird, ist es möglich, dass die Passagiere ein anderes Fahrverhalten zu Tage legen, als für die Berechnung des Fahrplans angenommen wurde. Vor diesem Hintergrund behandeln wir ein iteratives Verfahren zur Berechnung von Taktfahrplänen. Dieses ist eine Kombination aus Fahrplanberechnung und Passagierrouting. Neben den algorithmischen Details des Passagierroutings untersuchen wir Eigenschaften der berechneten Fahrpläne. Abschließend bestätigen wir unsere theoretischen Ergebnisse auf Grundlage einer eigenen Implementierung des Verfahrens. KW - Taktfahrplanung KW - PESP KW - iterative Fahrplanung KW - gemischt-ganzzahlige Programmierung KW - periodic timetabling KW - PESP KW - iterative timetabling KW - mixed integer programming Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10887 ER - TY - GEN A1 - Weber, Marcus T1 - An efficient analysis of rare events in canonical ensemble dynamics N2 - For an analysis of a molecular system from a computational statistical thermodynamics point of view, extensive molecular dynamics simulations are very inefficient. During this procedure, at lot of redundant data is generated. Whereas the algorithms spend most of the computing time for a sampling of configurations within the basins of the potential energy landscape of the molecular system, the important information about the long-time behaviour of the molecules is given by transition regions and barriers between the basins, which are sampled rarely only. Thinking of molecular dynamics trajectories, researchers try to figure out which kind of dynamical model is suitable for an efficient simulation. This article suggests to change the point of view from extensive simulation of molecular dynamics trajectories to more efficient sampling strategies of the conformation dynamics approach. T3 - ZIB-Report - 08-36 KW - Moleküldynamik KW - Kanonische Gesamtheit KW - Metastabilität KW - molecular dynamics KW - canonical ensemble KW - metastability Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10871 SN - 1438-0064 ER - TY - GEN A1 - Torres, Luis Miguel A1 - Torres, Ramiro A1 - Borndörfer, Ralf A1 - Pfetsch, Marc T1 - Line Planning on Paths and Tree Networks with Applications to the Quito Trolebus System N2 - Line planning is an important step in the strategic planning process of a public transportation system. In this paper, we discuss an optimization model for this problem in order to minimize operation costs while guaranteeing a certain level of quality of service, in terms of available transport capacity. We analyze the problem for path and tree network topologies as well as several categories of line operation that are important for the Quito Trolebus system. It turns out that, from a computational complexity worst case point of view, the problem is hard in all but the most simple variants. In practice, however, instances based on real data from the Trolebus System in Quito can be solved quite well, and significant optimization potentials can be demonstrated. T3 - ZIB-Report - 08-35 KW - line planning KW - computational complexity KW - public transport KW - integer programming Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10869 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Mura, Annette A1 - Schlechte, Thomas T1 - Vickrey Auctions for Railway Tracks N2 - We consider an auction of slots to run trains through a railway network. In contrast to the classical setting for combinatorial auctions, there is not only competition for slots, but slots can mutually exclude each other, such that general conflict constraints on bids arise. This turns the winner determination problem associated with such an auction into a complex combinatorial optimization problem. It also raises a number of auction design questions, in particular, on incentive compatibilty. We propose a single-shot second price auction for railway slots, the Vickrey Track Auction (VTA). We show that this auction is incentive compatible, i.e., rational bidders are always motivated to bid their true valuation, and that it produces efficient allocations, even in the presence of constraints on allocations. These properties are, however, lost when rules on the submission of bids such as, e.g., lowest bids, are imposed. Our results carry over to generalized" Vickrey auctions with combinatorial constraints. T3 - ZIB-Report - 08-34 KW - Vickrey Auktion KW - Fahrplanung KW - Vickrey Auction KW - Track Allocation Problem Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10855 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Pfetsch, Marc T1 - Detecting Orbitopal Symmetries N2 - Orbitopes can be used to handle symmetries which arise in integer programming formulations with an inherent assignment structure. We investigate the detection of symmetries appearing in this approach. We show that detecting so-called orbitopal symmetries is graph-isomorphism hard in general, but can be performed in linear time if the assignment structure is known. T3 - ZIB-Report - 08-33 KW - Symmetrie-Erkennung KW - Orbitope KW - Ganzzahlige Programmierung KW - Symmetrie-Brechung KW - Graphenisomorphie KW - symmetry detection KW - orbitopes KW - integer programming KW - symmetry breaking KW - graph ismorphism Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10842 SN - 1438-0064 ER - TY - GEN A1 - Heinz, Stefan A1 - Sachenbacher, Martin T1 - Using Model Counting to Find Optimal Distinguishing Tests N2 - Testing is the process of stimulating a system with inputs in order to reveal hidden parts of the system state. In the case of non-deterministic systems, the difficulty arises that an input pattern can generate several possible outcomes. Some of these outcomes allow to distinguish between different hypotheses about the system state, while others do~not. In this paper, we present a novel approach to find, for non-deterministic systems modeled as constraints over variables, tests that allow to distinguish among the hypotheses as good as possible. The idea is to assess the quality of a test by determining the ratio of distinguishing (good) and not distinguishing (bad) outcomes. This measure refines previous notions proposed in the literature on model-based testing and can be computed using model counting techniques. We propose and analyze a greedy-type algorithm to solve this test optimization problem, using existing model counters as a building block. We give preliminary experimental results of our method, and discuss possible improvements. T3 - ZIB-Report - 08-32 KW - zählen KW - automatische Test Generierung KW - counting KW - automated test generation KW - constraint programming Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10832 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - The Line Connectivity Problem N2 - This paper introduces the "line connectivity problem", a generalization of the Steiner tree problem and a special case of the line planning problem. We study its complexity and give an IP formulation in terms of an exponential number of constraints associated with "line cut constraints". These inequalities can be separated in polynomial time. We also generalize the Steiner partition inequalities. T3 - ZIB-Report - 08-31 KW - Steiner Tree Generalization Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10820 SN - 1438-0064 ER - TY - GEN A1 - Bley, Andreas T1 - An Integer Programming Algorithm for Routing Optimization in IP Networks N2 - Most data networks nowadays use shortest path protocols to route the traffic. Given administrative routing lengths for the links of the network, all data packets are sent along shortest paths with respect to these lengths from their source to their destination. In this paper, we present an integer programming algorithm for the minimum congestion unsplittable shortest path routing problem, which arises in the operational planning of such networks. Given a capacitated directed graph and a set of communication demands, the goal is to find routing lengths that define a unique shortest path for each demand and minimize the maximum congestion over all links in the resulting routing. We illustrate the general decomposition approach our algorithm is based on, present the integer and linear programming models used to solve the master and the client problem, and discuss the most important implementational aspects. Finally, we report computational results for various benchmark problems, which demonstrate the efficiency of our algorithm. T3 - ZIB-Report - 08-30 KW - Shortest Path Routing KW - Integer Programming Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10814 SN - 1438-0064 ER - TY - GEN A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Tuchscherer, Andreas T1 - On the Effects of Minor Changes in Model Formulations N2 - Starting with the description of the Traveling Salesmen Problem formulation as given by van Vyve and Wolsey in the article Approximate extended formulations'', we investigate the effects of small variations onto the performance of contemporary mixed integer programming solvers. We will show that even minor changes in the formulation of the model can result in performance difference of more than a factor of 1000. As the results show it is not obvious which changes will result in performance improvements and which not. T3 - ZIB-Report - 08-29 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10808 SN - 1438-0064 ER - TY - GEN A1 - Bley, Andreas A1 - Koch, Thorsten A1 - Niu, Lingfeng T1 - Experiments with nonlinear extensions to SCIP N2 - This paper describes several experiments to explore the options for solving a class of mixed integer nonlinear programming problems that stem from a real-world mine production planning project. The only type of nonlinear constraints in these problems are bilinear equalities involving continuous variables, which enforce the ratios between elements in mixed material streams. A branch-and-bound algorithm to handle the integer variables has been tried in another project. However, this branch-and-bound algorithm is not effective for handling the nonlinear constraints. Therefore state-of-the-art nonlinear solvers are utilized to solve the resulting nonlinear subproblems in this work. The experiments were carried out using the NEOS server for optimization. After finding that current nonlinear programming solvers seem to lack suitable preprocessing capabilities, we preprocess the instances beforehand and use an heuristic approach to solve the nonlinear subproblems. In the appendix, we explain how to add a polynomial constraint handler that uses IPOPT as embedded nonlinear programming solver for the constraint programming framework SCIP. This is one of the crucial steps for implementing our algorithm in SCIP. We briefly described our approach and give an idea of the work involved. T3 - ZIB-Report - 08-28 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8300 SN - 1438-0064 ER - TY - GEN A1 - Klapproth, Corinna A1 - Deuflhard, Peter A1 - Schiela, Anton T1 - A Perturbation Result for Dynamical Contact Problems N2 - This paper is intended to be a first step towards the continuous dependence of dynamical contact problems on the initial data as well as the uniqueness of a solution. Moreover, it provides the basis for a proof of the convergence of popular time integration schemes as the Newmark method. We study a frictionless dynamical contact problem between both linearly elastic and viscoelastic bodies which is formulated via the Signorini contact conditions. For viscoelastic materials fulfilling the Kelvin-Voigt constitutive law, we find a characterization of the class of problems which satisfy a perturbation result in a non-trivial mix of norms in function space. This characterization is given in the form of a stability condition on the contact stresses at the contact boundaries. Furthermore, we present perturbation results for two well-established approximations of the classical Signorini condition: The Signorini condition formulated in velocities and the model of normal compliance, both satisfying even a sharper version of our stability condition. T3 - ZIB-Report - 08-27 KW - Dynamical contact problems KW - stability KW - (visco-)elasticity KW - Signorini condition KW - Newmark method Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10793 SN - 1438-0064 ER - TY - GEN A1 - Ridder, Johanna T1 - Wegeprobleme der Graphentheorie T1 - Path problems in graph theory N2 - Den kürzesten Weg in einem Graphen zu finden ist ein klassisches Problem der Graphentheorie. Über einen Vortrag zu diesem Thema beim Tag der Mathematik 2007 von R. Borndörfer kam ich in Kontakt mit dem Konrad-Zuse-Zentrum (ZIB), das sich u.a. mit Wegeoptimierung beschäftigt. Ein Forschungsschwerpunkt dort ist im Rahmen eines Projekts zur Chipverifikation das Zählen von Lösungen, das, wie wir sehen werden, eng mit dem Zählen von Wegen zusammenhängt. Anhand von zwei Fragen aus der Graphentheorie soll diese Facharbeit unterschiedliche Lösungsmethoden untersuchen. Wie bestimmt man den kürzesten Weg zwischen zwei Knoten in einem Graphen und wie findet man alle möglichen Wege? Nach einer Einführung in die Graphentheorie und einer Konkretisierung der Probleme wird zunächst für beide eine Lösung mit auf Graphen basierenden Algorithmen vorgestellt. Während der Algorithmus von Dijkstra sehr bekannt ist, habe ich für das Zählen von Wegen einen eigenen Algorithmus auf der Basis der Tiefensuche entwickelt. Im zweiten Teil der Arbeit wird das Konzept der ganzzahligen Programmierung vorgestellt und die Lösungsmöglichkeiten für Wegeprobleme, die sich darüber ergeben. Schließlich wurden die vorgestellten Algorithmen am Beispiel des S- und U-Bahnnetzes von Berlin implementiert und mit Programmen, die die gleichen Fragen über ganzzahlige Programmierung lösen, verglichen. T3 - ZIB-Report - 08-26 KW - Graphen KW - Wegeprobleme KW - Zählen KW - Graphs KW - path problems KW - counting Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10782 SN - 1438-0064 ER - TY - GEN A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin N2 - Der Artikel gibt einen Einblick in das reiche Feld der Zusammenarbeit zwischen Mathematik und Medizin. Beispielhaft werden drei Erfolgsmodelle dargestellt: Medizinische Bildgebung, mathematische Modellierung und Biosignalverarbeitung im Bereich der Dynamik des Herzens sowie mathematische Modellierung und Simulation in der Krebstherapie Hyperthermie und der Mund-Kiefer-Gesichts-Chirurgie. In allen Fällen existiert ein Gleichklang der Interessen von Medizin und Mathematik: Beide Disziplinen wollen die Resultate schnell und zuverlässig. Für die Klinik heißt das, dass notwendige Rechnungen in möglichst kurzer Zeit, und zwar auf dem PC, ablaufen müssen und dass die Resultate so genau und belastbar sein müssen, dass medizinische Entscheidungen darauf aufbauen können. Für die Mathematik folgt daraus, dass höchste Anforderungen an die Effizienz der verwendeten Algorithmen und die darauf aufbauende Software in Numerik und Visualisierung zu stellen sind. Jedes Kapitel endet mit einer Darstellung der Perspektive des jeweiligen Gebietes. Abschließend werden mögliche Handlungsoptionen für Politik und Wirtschaft diskutiert. T3 - ZIB-Report - 08-25 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10776 SN - 1438-0064 ER - TY - THES A1 - Böhner, Dörte T1 - Chancen und Risiken Digitaler Rechtebeschreibung für wissenschaftliche Bibliotheken in Deutschland - Möglichkeiten und Perspektiven von Digital Rights Management T1 - Chances and risks of Digital Rights Description for academic libraries in Germany - Possibilities and perspectives of Digital Rights Management N2 - Wissenschaftliche Bibliotheken sind Vermittler von digitalen Medieninhalten. Sie müssen ihren Nutzern einen Zugang zu ihnen ermöglichen. Digitales Rechte Management (DRM), eingesetzt von den Verlagen, soll Nutzung und Zugang kontrollieren. Bibliotheken stehen DRM daher misstrauisch gegenüber, da dieses als Gefahr für die Wissenschaft und ihre (digitalen) Bibliotheken gesehen wird. Nur eine effektive Auseinandersetzung der wissenschaftlichen Bibliotheken mit der jeweiligen Politik der Verlage und den Verfahrensweisen bei DRM ermöglicht es ihnen, ihre Rolle als Vermittler und 'Gedächtnis der Menschheit' auch weiterhin erfolgreich wahrnehmen zu können. Unbestritten ist, dass DRM in seiner restriktiven Form die tägliche Arbeit der Bibliotheken erschwert. Deshalb müssen sie sich aktiv an der Standardisierung, der Entwicklung von Nutzungskonzepten und der Gestaltung der Rahmenbedingungen beteiligen. N2 - Academic libraries are mediators of digital content. They have to ensure access for their patrons. Digital Rights Management (DRM), used by publishers, should control access and usage. Libraries mistrust DRM, because it is seen as a danger to scholarship, sciences and their (digital) libraries. Libraries only can persist as the 'archive of all human knowledge' if they start an effective controversy about the publishers' policies and if they know how DRM works. It is uncontentious that the restrictive form of DRM will complicate the everyday work of libraries. Therefore they have to engage in the prozess of standardization, in the development of concepts of usage and in the definition of general conditions of DRM. KW - Digital Rights Management KW - Urheberrecht KW - Lizenzvertrag KW - Rechtebeschreibung KW - Rechtebeschreibungssprache KW - Digital Rights Management KW - Licence Agreement KW - German Copyright Law KW - Rights Description KW - Rights Description Language Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9271 ER - TY - THES A1 - Zilske, Michael T1 - Adaptives Remeshing von nicht-mannigfaltigen Dreiecksnetzen T1 - Adaptive remeshing of non-manifold triangle meshes N2 - In dieser Arbeit wird eine Serie von Remeshing-Verfahren um die Berücksichtigung von nicht-mannigfaltigen Dreiecksvernetzungen und Merkmalskantenzügen erweitert. Die betrachteten Verfahren arbeiten im Wesentlichen lokal. Daher können die im Rahmen dieser Arbeit entwickelten Erweiterungen, die nicht-mannigfaltige Kantenzüge und Merkmalskantenzüge betreffen, separat beschrieben werden. Dabei wird ein Ansatz verfolgt, beide Arten von besonderen Kantenzügen aufgrund ihrer Gemeinsamkeiten einheitlich zu behandeln. Dieser besteht zum einen darin, eine Korrespondenz zwischen Kantenzügen auf der Eingabe- und der Ausgabefläche zu erhalten, indem die Remeshing-Operationen auf den Kantenzügen in entsprechend eingeschränkter Weise verwendet werden. Zum anderen wird beschrieben, wie die Abtastdichte der Kantenzüge dynamisch an die Abtastdichte der Umgebung angepasst werden kann, um für weitgehende Isotropie in der Nähe von Merkmalskantenzügen zu sorgen. N2 - A unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines is presented. The method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature lines as well as the input mesh. KW - Vernetzung KW - Merkmalslinien KW - Knotendichte KW - Topologie KW - Dreiecksqualität KW - meshing KW - feature lines KW - node density KW - topology KW - triangle quality Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-474 ER - TY - GEN A1 - Schiela, Anton T1 - State constrained optimal control problems with states of low regularity N2 - We consider first order optimality conditions for state constrained optimal control problems. In particular we study the case where the state equation has not enough regularity to admit existence of a Slater point in function space. We overcome this difficulty by a special transformation. Under a density condition we show existence of Lagrange multipliers, which have a representation via measures and additional regularity properties. T3 - ZIB-Report - 08-24 KW - optimal control KW - state constraints KW - optimality conditions Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-509 SN - 1438-0064 ER - TY - GEN T1 - Jahresbericht 2007 T1 - Annual 2007 T3 - Jahresbericht - 2007 KW - Annual Report Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-498 SN - 0934-5892 ER - TY - GEN A1 - Grötschel, Martin T1 - Tiefensuche: Bemerkungen zur Algorithmengeschichte T1 - Depth-first search: Remarks on the history of algorithms N2 - Dieser kurze Aufsatz zur Algorithmengeschichte ist Eberhard Knobloch, meinem Lieblings-Mathematikhistoriker, zum 65. Geburtstag gewidmet. Eberhard Knobloch hat immer, wenn ich ihm eine historische Frage zur Mathematik stellte, eine Antwort gewusst – fast immer auch sofort. Erst als ich mich selbst ein wenig und dazu amateurhaft mit Mathematikgeschichte beschäftigte, wurde mir bewusst, wie schwierig dieses „Geschäft“ ist. Man muss nicht nur mehrere (alte) Sprachen beherrschen, sondern auch die wissenschaftliche Bedeutung von Begriffen und Symbolen in früheren Zeiten kennen. Man muss zusätzlich herausfinden, was zur Zeit der Entstehung der Texte „allgemeines Wissen“ war, insbesondere, was seinerzeit gültige Beweisideen und -schritte waren, und daher damals keiner präzisen Definition oder Einführung bedurfte. Es gibt aber noch eine Steigerung des historischen Schwierigkeitsgrades: Algorithmengeschichte. Dies möchte ich in diesem Artikel kurz darlegen in der Hoffnung, dass sich Wissenschaftshistoriker dieses Themas noch intensiver annehmen, als sie das bisher tun. Der Grund ist, dass heute Algorithmen viele Bereiche unserer Alltagswelt steuern und unser tägliches Leben oft von funktionierenden Algorithmen abhängt. Daher wäre eine bessere Kenntnis der Algorithmengeschichte von großem Interesse. T3 - ZIB-Report - 08-23 KW - Algorithmengeschichte KW - Algorithmus Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9628 SN - 1438-0064 ER - TY - GEN A1 - Schlechte, Thomas A1 - Borndörfer, Ralf T1 - Balancing Efficiency and Robustness – A Bi-criteria Optimization Approach to Railway Track Allocation N2 - Technical restrictions and challenging details let railway traffic become one of the most complex transportation systems. Routing trains in a conflict-free way through a track network is one of the basic scheduling problems for any railway company. This article focuses on a robust extension of this problem, also known as train timetabling problem (TTP), which consists in finding a schedule, a conflict free set of train routes, of maximum value for a given railway network. However, timetables are not only required to be profitable. Railway companies are also interested in reliable and robust solutions. Intuitively, we expect a more robust track allocation to be one where disruptions arising from delays are less likely to be propagated causing delays of subsequent trains. This trade-off between an efficient use of railway infrastructure and the prospects of recovery leads us to a bi-criteria optimization approach. On the one hand we want to maximize the profit of a schedule, that is more or less to maximize the number of feasible routed trains. On the other hand if two trains are scheduled as tight as possible after each other it is clear that a delay of the first one always affects the subsequent train. We present extensions of the integer programming formulation in [BorndoerferSchlechte2007] for solving (TTP). These models can incorporate both aspects, because of the additional track configuration variables. We discuss how these variables can directly be used to measure a certain type of robustness of a timetable. For these models which can be solved by column generation techniques, we propose so-called scalarization techniques, see [Ehrgott2005], to determine efficient solutions. Here, an efficient solution is one which does not allow any improvement in profit and robustness at the same time. We prove that the LP-relaxation of the (TTP) including an additional $\epsilon$-constraint remains solvable in polynomial time. Finally, we present some preliminary results on macroscopic real-world data of a part of the German long distance railway network. T3 - ZIB-Report - 08-22 KW - Train Timetabling Problem KW - Bicriteria Optimization KW - Column Generation Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10763 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Lutz-Westphal, Brigitte T1 - Diskrete Mathematik und ihre Anwendungen: Auf dem Weg zu authentischem Mathematikunterricht N2 - Das heutige Leben ist durchdrungen von komplexen Technologien. Ohne Kommunikationsnetze, Internet, Mobilfunk, Logistik, Verkehrstechnik, medizinische Apparate, etc. könnte die moderne Gesellschaft nicht funktionieren. Fast alle dieser Technologien haben einen hohen Mathematikanteil. Der "normale Bürger"' weiss davon nichts, der Schulunterricht könnte dem ein wenig abhelfen. Einige mathematische Aspekte dieser Technologien sind einfach und sogar spielerisch intuitiv zugänglich. Solche Anwendungen, die zusätzlich noch der Lebensumwelt der Schüler zugehören, können dazu genutzt werden, die mathematische Modellierung, also die mathematische Herangehensweise an die Lösung praktischer Fragen, anschaulich zu erläutern. Gerade in der diskreten Mathematik können hier, quasi "nebenbei" mathematische Theorien erarbeitet und Teilaspekte (Definitionen, Fragestellungen, einfache Sachverhalte) durch eigenständiges Entdecken der Schüler entwickelt werden. Wir beginnen mit einigen Beispielen. T3 - ZIB-Report - 08-21 KW - Diskrete Mathematik KW - Mathematikunterricht in Schulen KW - authentischer Mathematikunterricht Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10758 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Jaeger, Ulrich T1 - Planung von öffentlichem Personenverkehr N2 - Millionen von Menschen werden allein in Deutschland täglich von Bussen, Bahnen und Flugzeugen transportiert. Der öffentliche Personenverkehr (ÖV) ist von großer Bedeutung für die Lebensqualität einzelner aber auch für die Leistungsfähigkeit ganzer Regionen. Qualität und Effizienz von ÖV-Systemen hängen ab von politischen Rahmenbedingungen (staatlich geplant, wettbewerblich organisiert) und der Eignung der Infrastruktur (Schienensysteme, Flughafenstandorte), vom vorhandenen Verkehrsangebot (Fahr- und Flugplan), von der Verwendung angemessener Technologien (Informations-, Kontroll- und Buchungssysteme) und dem bestmöglichen Einsatz der Betriebsmittel (Energie, Fahrzeuge und Personal). Die hierbei auftretenden Entscheidungs-, Planungs- und Optimierungsprobleme sind z.T. gigantisch und "schreien" aufgrund ihrer hohen Komplexität nach Unterstützung durch Mathematik. Dieser Artikel skizziert den Stand und die Bedeutung des Einsatzes von Mathematik bei der Planung und Durchführung von öffentlichem Personenverkehr, beschreibt die bestehenden Herausforderungen und regt zukunftsweisende Maßnahmen an. T3 - ZIB-Report - 08-20 KW - Produktionsfaktor Mathematik KW - Öffentlicher Personenverkehr KW - Diskrete Optimierung KW - Operations Research Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10744 SN - 1438-0064 ER - TY - GEN A1 - Erol, Berkan A1 - Klemenz, Marc A1 - Schlechte, Thomas A1 - Schultz, Sören A1 - Tanner, Andreas T1 - TTPLIB 2008 - A Library for Train Timetabling Problems N2 - We introduce (TTPlib), a data library for train timetabling problems that can be accessed at http://ttplib.zib.de. In version 1.0, the library contains data related to 50 scenarios. Most instances result from the combination of macroscopic railway networks and several train request sets for the German long distance area containing Hannover, Kassel and Fulda, short denoted by Ha-Ka-Fu. In this paper, we introduce the data concepts of TTPlib, describe the scenarios included in the library and provide a free visualization tool TraVis. T3 - ZIB-Report - 08-19 KW - Fahrplanung KW - Problembibliothek KW - Optimierung KW - Train Timetabling Problem KW - Data Library KW - Optimization Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10732 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Probabilistic analysis of Online Bin Coloring algorithms via Stochastic Comparison N2 - This paper proposes a new method for probabilistic analysis of online algorithms that is based on the notion of stochastic dominance. We develop the method for the Online Bin Coloring problem introduced by Krumke et al. Using methods for the stochastic comparison of Markov chains we establish the strong result that the performance of the online algorithm GreedyFit is stochastically dominated by the performance of the algorithm OneBin for any number of items processed. This result gives a more realistic picture than competitive analysis and explains the behavior observed in simulations. T3 - ZIB-Report - 08-18 KW - Stochastische Dominanz KW - Online-Algorithmen KW - Markov-Ketten KW - Probabilistische Analyse KW - stochastic dominance KW - online algorithms KW - Markov chains KW - probabilistic analysis Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10726 SN - 1438-0064 ER - TY - GEN A1 - Prüfert, Uwe A1 - Schiela, Anton T1 - The minimization of an L^{\infty}-functional subject to an elliptic PDE and state constraints N2 - We study the optimal control of a maximum-norm objective functional subject to an elliptic-type PDE and pointwise state constraints. The problem is transformed into a problem where the non-differentiable L^{\infty}-norm in the functional will be replaced by a scalar variable and additional state constraints. This problem is solved by barrier methods. We will show the existence and convergence of the central path for a class of barrier functions. Numerical experiments complete the presentation. T3 - ZIB-Report - 08-17 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10714 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - Models for Fare Planning in Public Transport N2 - The optimization of fare systems in public transit allows to pursue objectives such as the maximization of demand, revenue, profit, or social welfare. We propose a non-linear optimization approach to fare planning that is based on a detailed discrete choice model of user behavior. The approach allows to analyze different fare structures, optimization objectives, and operational scenarios involving, e.g., subsidies. We use the resulting models to compute optimized fare systems for the city of Potsdam, Germany. T3 - ZIB-Report - 08-16 KW - Preisplanung KW - Nachfragefunktion KW - Optimierung KW - Nahverkehr Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10708 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - The Parametric Solution of Underdetermined linear ODEs N2 - The purpose of this paper is twofold. An immediate practical use of the presented algorithm is its applicability to the parametric solution of underdetermined linear ordinary differential equations (ODEs) with coefficients that are arbitrary analytic functions in the independent variable. A second conceptual aim is to present an algorithm that is in some sense dual to the fundamental Euclids algorithm, and thus an alternative to the special case of a Gr\"{o}bner basis algorithm as it is used for solving linear ODE-systems. In the paper Euclids algorithm and the new dual version' are compared and their complementary strengths are analysed on the task of solving underdetermined ODEs. An implementation of the described algorithm is interactively accessible at http://lie.math.brocku.ca/crack/uode. T3 - ZIB-Report - 08-15 KW - linear ODEs KW - underdetermined systems KW - Euclid's algorithm KW - computer algebra KW - Reduce KW - Crack Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10693 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas A1 - Neun, Winfried T1 - About a Computer Algebra based online Mathtest N2 - The article describes the online mathematics test {\tt http://lie.math.brocku.ca/mathtest}, its typical applications and experiences gathered. T3 - ZIB-Report - 08-14 KW - accessment of mathematical skills KW - computer algebra KW - online Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10688 SN - 1438-0064 ER - TY - GEN A1 - Tsarev, Sergey A1 - Wolf, Thomas T1 - Classification of 3-dimensional integrable scalar discrete equations N2 - We classify all integrable 3-dimensional scalar discrete affine linear equations $Q_3=0$ on an elementary cubic cell of the lattice ${\mathbb Z}^3$. An equation $Q_3=0$ %of such form is called integrable if it may be consistently imposed on all $3$-dimensional elementary faces of the lattice ${\mathbb Z}^4$. Under the natural requirement of invariance of the equation under the action of the complete group of symmetries of the cube we prove that the only ontrivial(non-linearizable) integrable equation from this class is the well-known dBKP-system. T3 - ZIB-Report - 08-13 KW - integrable systems KW - discrete equations KW - large polynomial systems KW - computer algebra KW - REDUCE KW - FORM KW - Crack Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10667 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Pfetsch, Marc T1 - Solving Pseudo-Boolean Problems with SCIP N2 - Pseudo-Boolean problems generalize SAT problems by allowing linear constraints and a linear objective function. Different solvers, mainly having their roots in the SAT domain, have been proposed and compared,for instance, in Pseudo-Boolean evaluations. One can also formulate Pseudo-Boolean models as integer programming models. That is,Pseudo-Boolean problems lie on the border between the SAT domain and the integer programming field. In this paper, we approach Pseudo-Boolean problems from the integer programming side. We introduce the framework SCIP that implements constraint integer programming techniques. It integrates methods from constraint programming, integer programming, and SAT-solving: the solution of linear programming relaxations, propagation of linear as well as nonlinear constraints, and conflict analysis. We argue that this approach is suitable for Pseudo-Boolean instances containing general linear constraints, while it is less efficient for pure SAT problems. We present extensive computational experiments on the test set used for the Pseudo-Boolean evaluation 2007. We show that our approach is very efficient for optimization instances and competitive for feasibility problems. For the nonlinear parts, we also investigate the influence of linear programming relaxations and propagation methods on the performance. It turns out that both techniques are helpful for obtaining an efficient solution method. T3 - ZIB-Report - 08-12 KW - Pseudo-Boolean KW - Constraint Programming KW - Ganzzahlige Programmierung KW - Branch-And-Cut KW - Optimierungssoftware KW - Pseudo-Boolean KW - constraint integer programming KW - integer programming KW - branch-and-cut KW - optimization software Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10671 SN - 1438-0064 ER - TY - GEN A1 - Anco, Stephen A1 - Bluman, George A1 - Wolf, Thomas T1 - Invertible Mappings of Nonlinear PDEs to Linear PDEs Through Admitted Conservation Laws N2 - An algorithmic method using conservation law multipliers is introduced that yields necessary and sufficient conditions to find invertible mappings of a given nonlinear PDE to some linear PDE and to construct such a mapping when it exists. Previous methods yielded such conditions from admitted point or contact symmetries of the nonlinear PDE. Through examples, these two linearization approaches are contrasted. T3 - ZIB-Report - 08-11 KW - conservation laws KW - linearization KW - symmetries Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10652 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - On solving large systems of polynomial equations appearing in Discrete Differential Geometry N2 - The paper describes a method for solution of very large overdetermined algebraic polynomial systems on an example that appears from a classification of all integrable 3-dimensional scalar discrete quasilinear equations $Q_3=0$ on an elementary cubic cell of the lattice ${\mathbb Z}^3$. The overdetermined polynomial algebraic system that has to be solved is far too large to be formulated. A probing' technique which replaces independent variables by random integers or zero allows to formulate subsets of this system. An automatic alteration of equation formulating steps and equation solving steps leads to an iteration process that solves the computational problem. T3 - ZIB-Report - 08-10 KW - integrable systems KW - discrete equations KW - large polynomial systems KW - computer algebra KW - REDUCE Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10646 SN - 1438-0064 ER - TY - GEN A1 - Achterberg, Tobias A1 - Heinz, Stefan A1 - Koch, Thorsten T1 - Counting solutions of integer programs using unrestricted subtree detection N2 - In the recent years there has been tremendous progress in the development of algorithms to find optimal solutions for integer programs. In many applications it is, however, desirable (or even necessary) to generate all feasible solutions. Examples arise in the areas of hardware and software verification and discrete geometry. In this paper, we investigate how to extend branch-and-cut integer programming frameworks to support the generation of all solutions. We propose a method to detect so-called unrestricted subtrees, which allows us to prune the integer program search tree and to collect several solutions simultaneously. We present computational results of this branch-and-count paradigm which show the potential of the unrestricted subtree detection. T3 - ZIB-Report - 08-09 KW - Zählen KW - ganzzahlige Programme KW - IP KW - counting KW - integer programming KW - IP Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10632 SN - 1438-0064 ER - TY - GEN A1 - Streuer, Thomas A1 - Stüben, Hinnerk T1 - Simulations of QCD in the Era of Sustained Tflop/s Computing N2 - The latest machine generation installed at supercomputer centres in Germany offers a peak performance in the tens of Tflop/s range. We study performance and scaling of our quantum chromodynamics simulation programme BQCD that we obtained on two of these machines, an IBM Blue Gene/L and an SGI Altix 4700. We compare the performance of Fortran/MPI code with assembler code. The latter allows to exploit concurrency at more levels, in particular in overlapping communication and computation as well as prefetching data from main memory. T3 - ZIB-Report - 07-48 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10623 SN - 1438-0064 ER - TY - GEN A1 - Stephan, Rüdiger T1 - On the cardinality constrained matroid polytope N2 - Edmonds showed that the so-called rank inequalities and the nonnegativity constraints provide a complete linear description of the matroid polytope. By essentially adding Grötschel's cardinality forcing inequalities, we obtain a complete linear description of the cardinality constrained matroid polytope which is the convex hull of the incidence vectors of those independent sets that have a feasible cardinality. Moreover, we show how the separation problem for the cardinality forcing inequalities can be reduced to that for the rank inequalities. We also give necessary and sufficient conditions for a cardinality forcing inequality to be facet defining. T3 - ZIB-Report - 08-08 KW - Matroid-Polytop KW - Kardinalitätsbeschränkung KW - Separationsalgorithmus KW - Matroid Polytope KW - Cardinality constraints KW - Separation algorithm Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10614 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - An Extended Mathematical Framework for Barrier Methods in Function Space N2 - An extended mathematical framework for barrier methods for state constrained optimal control compared to [Schiela, ZIB-Report 07-07] is considered. This allows to apply the results derived there to more general classes of optimal control problems, in particular to boundary control and finite dimensional control. T3 - ZIB-Report - 08-07 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10593 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Roggenbuck, Robert A1 - Sperber, Wolfram A1 - Dalitz, Wolfgang T1 - Weiterentwicklung und Ausbau des Internet-Informationsdienstes "Math&Industry" T1 - Math&Industry (II) N2 - Mit dem Informationsdienst Math&Industry soll ein Prototyp eines dezentralen Informationssystems für Förderprogramme und Forschungsprojekte geschaffen werden, das sich auf andere Programme (bezüglich angewandter Mathematik, aber auch darüber hinaus) übertragen lässt. Das betrifft sowohl die Konzeption (Strukturierung der Informationen) als auch die Werkzeuge, die anderen BMBF-Förderprogrammen zur Verfügung gestellt werden können. Damit sollen diese in die Lage versetzt werden, die in Math&Industry entwickelten Konzepte und Werkzeuge an ihre spezifischen Bedürfnisse anzupassen. T3 - ZIB-Report - 08-06 KW - Internet services KW - distributed systems KW - XML KW - RDF KW - Internet services KW - distributed systems KW - XML KW - RDF Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10584 SN - 1438-0064 ER - TY - GEN A1 - Oevermann, Michael A1 - Schmidt, Heiko A1 - Kerstein, Alan R. T1 - Linear-Eddy Modeling of Autoignition under Thermal Stratification N2 - The influence of thermal stratification on autoignition at constant volume and high pressure is investigated under turbulent conditions using the one-dimensional Linear-Eddy Model (LEM) and detailed hydrogen/air chemistry. Results are presented for the influence of initial temperature inhomogeneities on the heat release rate and the relative importance of diffusion and chemical reactions. The predicted heat release rates are compared with heat release rates of Chen et al. and Hawkes et al. obtained by two-dimensional Direct Numerical Simulations (DNS). Using the definition of Chen et al. for the displacement speed of the H2 mass fraction tracked at the location of maximum heat release, and a comparison of budget terms, different combustion modes including ignition front propagation and deflagration waves are identified and the results are compared to the DNS data. The LEM approach shows qualitatively and quantitatively reasonable agreement with the DNS data over the whole range of investigated temperature fluctuations. The results presented in this work suggest that LEM is a potential candidate as a sub-model for CFD calculations of HCCI engines. T3 - ZIB-Report - 08-05 KW - HCCI KW - Selbstzündung KW - Turbulenz KW - Linear-Eddy Modell KW - HCCI KW - autoignition KW - thermal explosion KW - turbulence KW - Linear-Eddy Model Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10562 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - Angebotsplanung im öffentlichen Nahverkehr T1 - Service Design in Public Transport N2 - Die Angebotsplanung im öffentlichen Nahverkehr umfasst die Aufgaben der Netz-, Linien-,Fahr- und Preisplanung. Wir stellen zwei mathematische Optimierungsmodelle zur Linien- und Preisplanung vor. Wir zeigen anhand von Berechnungen für die Verkehrsbetriebe in Potsdam(ViP), dass sich damit komplexe Zusammenhänge quantitativ analysieren lassen. Auf diese Weise untersuchen wir die Auswirkungen von Freiheitsgraden auf die Konstruktion von Linien und die Wahl von Reisewegen der Passagiere, Abhängigkeiten zwischen Kosten und Reisezeiten sowie den Einfluss verschiedener Preissysteme auf Nachfrage und Kostendeckung. T3 - ZIB-Report - 08-04 KW - Preisplanung KW - Linienplanung KW - Optimierung Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10555 SN - 1438-0064 ER - TY - GEN A1 - Carqué, Gunter A1 - Owinoh, Antony Z. A1 - Klein, Rupert A1 - Majda, Andrew J. T1 - Asymptotic Scale Analysis of Precipitating Clouds N2 - Asymptotic analyses of the three dimensional compressible flow equations coupled with transport equations for the mixing ratios of water vapour, cloud water and rain water are described. We obtain reduced systems of equations for two particular regimes of length and time scales: Models for the long time evolution of deep convective columns and for the short time evolution of shallow convective layers. The asymptotic deep convective column model is anelastic, yet the vertical motion is pressure free, i.e., it evolves freely in interaction with buoyancy while the horizontal divergence adjusts to fullfil the anelastic constraint. The perturbation pressure guaranteeing compliance with the horizontal divergence constraint obeys a Poisson-type equation. Surprisingly, the vertical velocity plays an important role in the horizontal dynamics through the Coriolis term. The vertical acceleration in a saturated column is directly determined by the buoyancy induced by potential temperature differences relative to the background stratification. This potential temperature deviation is a conserved quantity. Evaporation is the only important microphysical process in the undersaturated regime. The evaporation rate depends on the saturation deficit and the amount of rain water present and determines the (downward) vertical velocity and the distribution of water vapour. To connect the deep convective column solutions to top and bottom boundary conditions, a different flow regime needs to be accounted for. Within shallow layers whose depth is comparable to the column diameters, adjustment to physical boundary conditions can take place. This is the second regime considered in this report. The shallow convective layer regime is shown to be asymptotically described by Boussinesq-type equations. These equations are closed by evolution equations which show that, in the saturated regime, the distributions of potential temperature and cloud water are determined by a condensation rate that is directly proportional to the vertical velocity. In the undersaturated regime, the potential temperature distribution is determined by the amount of rain present, since the water vapour in this case is shown to be a conserved quantity. In both regimes the distribution of rain water depends on the rain water flux. T3 - ZIB-Report - 08-03 KW - atmospheric moist convection KW - deep convection KW - shallow convection KW - precipitating clouds KW - asymptotic analysis Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10548 SN - 1438-0064 ER - TY - GEN A1 - Schmidt, Heiko A1 - Oevermann, Michael A1 - Bastiaans, Rob J.M. A1 - Kerstein, Alan R. T1 - A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds N2 - In this paper we propose a technique for a priori turbulent flame speed tabulation (TFST) for a given parameter space in standard combustion-regime diagrams. It can be used as a subgrid-scale (SGS) model in Large Eddy Simulation (LES). In a first step, stationary laminar flamelets are computed and stored over the progress variable following the ideas of flamelet generated manifolds (FGM). In a second step, the incompressible one-dimensional Navier-Stokes equations supplemented by the equation for the progress variable are solved on a grid that resolves all turbulent scales. Additionally, turbulent transport is implemented via the linear eddy model (LEM). The turbulent flame structures are solved until a statistically stationary mean value of the turbulent flame speed has been reached. The results are stored in a table that could be used by large scale premixed combustion models, e.g. front tracking schemes. Results are compared to an algebraic model and to direct numerical simulations (DNS). T3 - ZIB-Report - 08-02 KW - Verbrennung KW - Flammenstrukturen KW - stochastisches Turbulenzmodell KW - FGM KW - turbulente Brenngeschwindigkeiten KW - turbulent premixed combustion KW - flame structures KW - linear eddy model KW - flamelet generated manifolds KW - turbulent flame speeds Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10532 SN - 1438-0064 ER - TY - GEN A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Koch, Thorsten A1 - Wolter, Kati T1 - Constraint Integer Programming: a New Approach to Integrate CP and MIP N2 - This article introduces constraint integer programming (CIP), which is a novel way to combine constraint programming (CP) and mixed integer programming (MIP) methodologies. CIP is a generalization of MIP that supports the notion of general constraints as in CP. This approach is supported by the CIP framework SCIP, which also integrates techniques from SAT solving. SCIP is available in source code and free for non-commercial use. We demonstrate the usefulness of CIP on two tasks. First, we apply the constraint integer programming approach to pure mixed integer programs. Computational experiments show that SCIP is almost competitive to current state-of-the-art commercial MIP solvers. Second, we employ the CIP framework to solve chip design verification problems, which involve some highly non-linear constraint types that are very hard to handle by pure MIP solvers. The CIP approach is very effective here: it can apply the full sophisticated MIP machinery to the linear part of the problem, while dealing with the non-linear constraints by employing constraint programming techniques. T3 - ZIB-Report - 08-01 KW - Constraint Programming KW - Ganzzahlige Programmierung KW - Branch-And-Cut KW - Optimierungssoftware KW - Chipverifikation KW - constraint programming KW - mixed integer programming KW - branch-and-cut KW - optimization software KW - chip verification Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10520 SN - 1438-0064 ER - TY - GEN A1 - Kuberek, Monika T1 - Open Access – Aufbau, Pflege und Betrieb lokaler Publikationsserver in der KOBV-Zentrale N2 - Zur Unterstützung der Bibliotheken bei ihren Open-Access-Aktivitäten betreibt die KOBV-Zentrale seit Anfang 2005 den Service "Opus- und Archivierungsdienste". Die KOBV-Zentrale agiert als Application Service Provider (ASP) für sämtliche technischen Komponenten des Publikationsprozesses, indem sie die gesamte technische Infrastruktur bereitstellt und betreibt – angefangen bei den lokalen Publikationsservern bis hin zu lokalen Repositories zur Archivierung der elektronischen Dokumente. Der vorliegende Text ist die schriftliche Fassung eines gleichnamigen Vortrages auf der 31. ASpB-Tagung "Kooperation versus Eigenprofil?" der Arbeitsgemeinschaft der Spezialbibliotheken, die vom 25.-28. September 2007 in der Technischen Universität Berlin stattfand. T3 - ZIB-Report - 07-47 KW - DINI-Zertifikat KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) KW - Open Access KW - Open Archive Initiative KW - Opus-Publikationssoftware Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10514 SN - 1438-0064 ER - TY - GEN A1 - Kuberek, Monika T1 - Volltextserver der Verbünde – Integrierter Zugriff auf lizenzierte Zeitschriftenartikel und freie elektronische Dokumente unter Einsatz von Suchmaschinentechnologie N2 - Die Intention ist der kooperative Aufbau einer Infrastruktur durch die Bibliotheksverbünde, um den Nutzern Volltext-Angebote dauerhaft und komfortabel zur Verfügung zu stellen: Zeitschriftenartikel und elektronische Dokumente werden mittels Suchmaschinentechnologie indexiert und unter Berücksichtigung von Zugriffsrechten zugänglich gemacht. Realisiert ist dies bereits im KOBV-Volltextserver, der seit Ende 2005 im Routinebetrieb läuft. Vorstellbar ist ein überregionales Netz von Volltextservern der Verbünde, die mittels Suchmaschinentechnologie indiziert und nahtlos in das regionale und lokale Literaturangebot integriert werden. Bei den lizenzierten Materialien sind insbesondere auch die Rechte der Verlage zu wahren und entsprechende Rechtemanagement-Verfahren einzusetzen. Es gilt, transparente Verfahren zu konzipieren und umzusetzen, um für die Verlage die notwendige Vertrauensbasis zu schaffen und gleichzeitig den Einrichtungen ihren berechtigten Zugriff auf die Volltexte zu sichern. Der vorliegende Text ist die schriftliche Fassung eines Vortrages auf dem 3. Leipziger Kongress für Information und Bibliothek "Information und Ethik", der vom 19.-22. März 2007 im Congress Center Leipzig stattfand. T3 - ZIB-Report - 07-46 KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Suchmaschinentechnologie KW - Volltextrecherche KW - Volltextserver Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10508 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin T1 - Pointwise Nonlinear Scaling for Reaction-Diffusion-Equations N2 - Parabolic reaction-diffusion systems may develop sharp moving reaction fronts which pose a challenge even for adaptive finite element methods. We propose a method to transform the equation into an equivalent form that usually exhibits solutions which are easier to discretize, giving higher accuracy for a given number of degrees of freedom. The transformation is realized as an efficiently computable pointwise nonlinear scaling that is optimized for prototypical planar travelling wave solutions of the underlying reaction-diffusion equation. The gain in either performance or accuracy is demonstrated on different numerical examples. T3 - ZIB-Report - 07-45 KW - reaction-diffusion equations KW - travelling waves KW - nonlinear scaling KW - discretization error Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10493 SN - 1438-0064 ER - TY - THES A1 - Baum, Daniel T1 - A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules N2 - One crucial step in virtual drug design is the identification of new lead structures with respect to a pharmacological target molecule. The search for new lead structures is often done with the help of a pharmacophore, which carries the essential structural as well as physico-chemical properties that a molecule needs to have in order to bind to the target molecule. In the absence of the target molecule, such a pharmacophore can be established by comparison of a set of active compounds. In order to identify their common features,a multiple alignment of all or most of the active compounds is necessary. Moreover, since the “outer shape” of the molecules plays a major role in the interaction between drug and target, an alignment algorithm aiming at the identification of common binding properties needs to consider the molecule’s “outer shape”, which can be approximated by the solvent excluded surface. In this thesis, we present a new approach to molecular surface alignment based on a discrete representation of shape as well as physico-chemical properties by points distributed on the solvent excluded surface. We propose a new method to distribute points regularly on a surface w.r.t. a smoothly varying point density given on that surface. Since the point distribution algorithm is not restricted to molecular surfaces, it might also be of interest for other applications. For the computation of pairwise surface alignments, we extend an existing point matching scheme to surface points, and we develop an efficient data structure speeding up the computation by a factor of three. Moreover, we present an approach to compute multiple alignments from pairwise alignments, which is able to handle a large number of surface points. All algorithms are evaluated on two sets of molecules: eight thermolysin inhibitors and seven HIV-1 protease inhibitors. Finally, we compare the results obtained from surface alignment with the results obtained by applying an atom alignment approach. N2 - Die Identifizierung neuer Leitstrukturen (lead structures) zur Entwicklung optimierter Wirkstoffe ist ein äußerst wichtiger Schritt in der virtuellen Wirkstoffentwicklung (virtual drug design). Die Suche nach neuen Leitstrukturen wird oft mit Hilfe eines Pharmakophor-Modells durchgeführt, welches die wichtigsten strukturellen wie auch physiko-chemischen Eigenschaften eines bindenden Moleküls in sich vereint. Ist das Zielmolekül (target) nicht bekannt, kann das Pharmakophor-Modell mit Hilfe des Vergleiches aktiver Moleküle erstellt werden. Hier ist insbesondere die gleichzeitige Überlagerung (multiple alignment) aller oder nahezu aller Moleküle notwendig. Da bei der Interaktion zweier Moleküle die "äußere Form" der Moleküle eine besondere Rolle spielt, sollte diese von jedem Überlagerungsalgorithmus, der sich mit der Identifizierung von Bindungseigenschaften befasst, berücksichtigt werden. Dabei kann die "äußere Form" durch eine bestimmte Art von molekularer Oberfläche approximiert werden, die man als solvent excluded surface bezeichnet. In dieser Arbeit stellen wir einen neuen Ansatz zur Überlagerung molekularer Oberflächen dar, der auf einer diskreten Repräsentation sowohl der Form als auch der molekularen Eigenschaften mittels Punkten beruht. Um die Punkte auf der molekularen Oberfläche möglichst regulär entsprechend einer gegebenen Punktdichte zu verteilen, entwickeln wir eine neue Methode. Diese Methode ist nicht auf Moleküloberflächen beschränkt und könnte daher auch für andere Anwendungen von Interesse sein. Basierend auf einem bekannten Point-Matching Verfahren entwickeln wir einen Point-Matching Algorithmus für Oberflächenpunkte. Dazu erarbeiten wir u.a. eine effiziente Datenstruktur, die den Algorithmus um einen Faktor von drei beschleunigt. Darüberhinaus stellen wir einen Ansatz vor, der Mehrfachüberlagerungen (multiple alignments) aus paarweisen Überlagerungen berechnet. Die Herausforderung besteht hierbei vor allem in der großen Anzahl von Punkten, die berücksichtigt werden muss. Die vorgestellten Algorithmen werden an zwei Gruppen von Molekülen evaluiert, wobei die erste Gruppe aus acht Thermolysin Inhibitoren besteht, die zweite aus sieben HIV-1 Protease Inhibitoren. Darüberhinaus vergleichen wir die Ergebnisse der Oberflächenüberlagerung mit denen einer Atommittelpunktüberlagerung. KW - molecular surface alignment KW - point-based approximation KW - multiple alignment Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000002759-2 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000002759 ER - TY - GEN A1 - Schiela, Anton T1 - An Interior Point Method in Function Space for the Efficient Solution of State Constrained Optimal Control Problems N2 - We propose and analyse an interior point path-following method in function space for state constrained optimal control. Our emphasis is on proving convergence in function space and on constructing a practical path-following algorithm. In particular, the introduction of a pointwise damping step leads to a very efficient method, as verified by numerical experiments. T3 - ZIB-Report - 07-44 KW - interior point methods in function space KW - optimal control KW - state constraints Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10471 SN - 1438-0064 ER - TY - GEN A1 - Plantikow, Stefan T1 - Transaktionen für verteilte Wikis auf strukturierten Overlay-Netzwerken T1 - Transactions for Distributed Wikis on Structured Overlay Networks N2 - Die Arbeit präsentiert ein Transaktionsverfahren für strukturierte Overlay-Netzwerke, das an die Erfordernisse verteilter Informationssysteme mit relationalem Datenmodell angepasst ist. Insbesondere wird der Einsatz von Transaktionen für verteilte Wikis betrachtet, die moderne Funktionalitäten, wie Metadaten und zusätzliche Indexe für die Navigation, unterstützen. Konsistenz und Dauerhaftigkeit der gespeicherten Daten erfordert die Behandlung von Knotenausfällen. Die Arbeit schlägt dafür das Zellenmodell vor: Das Overlay wird aus replizierten Zustandsmaschinen gebildet, um Verfügbarkeit zu gewährleisten. Das Transaktionsverfahren baut darauf auf und verwendet Two-Phase-Commit mit Fehlererkennung und Widerherstellung von ausgefallenen Transaktionsmanagern. Anwendungen wird eine Auswahl an pessimistischen und hybrid-optimistischen Nebenläufigkeitskontrollverfahren geboten, die die Minimierung von Latenzeffekten und die schnelle Ausführung von Nur-Lese-Transaktionen ermöglichen. Für die Beispielanwendung Wiki wird der erforderliche Pseudocode angegeben und die verschiedenen Nebenläufigkeitskontrollverfahren hinsichtlich ihrer Nachrichtenkomplexität verglichen. N2 - The report presents a transaction processing scheme for structured overlay networks and uses it to develop a distributed Wiki application based on a relational data model. The Wiki supports rich metadata and additional indexes for navigation purposes. Ensuring consistency and durability requires handling of node failures. Such failures are masked by providing high availability of nodes. This in turn is achieved by constructing the overlay from replicated state machines (cell model). Atomicity is realized using two phase commit with additional support for failure detection and restoration of the transaction manager. The developed transaction processing scheme provides the application with a mixture of pessimistic, hybrid optimistic and multiversioning concurrency control techniques to minimize the impact of replication on latency and optimize for read operations. The pseudocode of the relevant Wiki functions is presented and the different concurrency control techniques are evaluated in terms of message complexit T3 - ZIB-Report - 07-43 KW - Verteilte Transaktionen KW - Strukturierte Overlay-Netzwerke KW - Peer-to-Peer KW - Wikis KW - Nebenläufigkeitskontrolle KW - distributed transactions KW - structured overlay networks KW - peer-to-peer KW - wikis KW - concurrency control Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10466 SN - 1438-0064 ER - TY - GEN A1 - Busch, Hubert A1 - Droebes, Ursula A1 - Fröhlich, Marek A1 - Schimmel, Christian T1 - Das Berliner Wissenschaftsnetz BRAIN 2007 T1 - Berlin Research Area Information Network BRAIN 2007 N2 - Berlin als Stadtstaat ist Kommune und Land der Bundesrepublik zugleich und Standort vieler renommier-ter Wissenschafts- und Kultureinrichtungen. In enger Zusammenarbeit der Wissenschaftseinrichtungen mit dem IT-Dienstleistungszentrum Berlin (ITDZ, ehemals Landesbetrieb für Informationstechnik), der für die Behörden Berlins zuständigen Einrichtung, wurde seit 1993 ein landeseigenes Glasfasernetz mit einer derzeitigen Länge von 856 km Glasfaserkabel (je Kabel bis zu 144 Einzelfasern) zur gemeinsamen Nutzung von Wissenschaft und Verwaltung errichtet und weiter ausgebaut. 1994 erfolgte der offizielle Start des Berliner Wissenschaftsnetzes BRAIN (Berlin Research Area Information Network), als durch einen Beschluss des Senats von Berlin die Nutzung des landeseigenen Glasfasernetzes durch die Wissen-schaftseinrichtungen festgeschrieben wurde. Bereits 1995 wurden durch die Wissenschaftseinrichtungen auf diesem Glasfasernetz die ersten sieben Anschlüsse in ATM-Technik (Classical BRAIN-ATM) in Betrieb genommen, 1999 wurden anschließend auch erste Strecken in Ethernet-Technik (Classical BRAIN-GE) betrieben. Diese heterogenen Netze mit unterschiedlichen Netzgeräten wurden dezentral von den Netzadministratoren der beteiligten Einrichtungen nach globalen Absprachen betreut. Die dezentrale Administration erschwerte das Management und die Erweiterungen der Gesamtnetze. Basierend auf den vorliegenden Erfahrungen vereinbarten die Berliner Wissenschaftseinrichtungen, ein technisch neues Verbundnetz in Gigabit-Ethernet-Technik mit einheitlichen Geräten und einem zentralen Netzwerkmana-gement aufzubauen und zu betreiben. Seit November 2003 betreibt BRAIN auf dem landeseignen Glasfasernetz ein auf MPLS-Technik basie-rendes Gigabit-Ethernet-Netz, das „BRAIN-Verbundnetz“, mit den Diensten LAN-to-LAN-Kopplung der Einrichtungen, regionaler IP-Verkehr, Übergang zum Verwaltungsnetz und WiN-Backup. Das BRAIN-Verbundnetz löste die dezentral betreuten Vorläufernetze komplett ab. Von den derzeit 27 BRAIN-Teilnehmern nutzen 24 Einrichtungen an 53 in der Stadt verteilten Standorten die Dienste des BRAIN-Verbundnetzes, 18 Standorte sind mit 1000 Mbit/s und 35 Standorte mit 100 Mbit/s angeschlossen. Für verteilte Standorte einer Einrichtung besteht zudem die Möglichkeit, diese über dedizierte Fasern oder Bandbreiten miteinander zu vernetzen. Seit dem 2. Quartal 2007 wird im Rahmen eines Pilotprojekts der Nutzen eines zentral gemanagten Fibre Channel-Netzwerks "BRAIN-SAN" ermittelt, um Möglichkeiten einer verteilten Datenhaltung der Berliner Hochschulen und wissenschaftlichen Einrichtungen zu schaf-fen. Zusätzlich zu den vorgenannten Diensten nutzt der DFN-Verein die BRAIN-Struktur für die Verbindun-gen der X-WiN-Kernnetzknoten in Berlin und Potsdam untereinander und für Zugangsleitungen zu den Anwendern. Mit Stand 2007 nutzt das Berliner Wissenschaftsnetz BRAIN vom landeigenen Glasfasernetz 2100 km Einzelfasern und verbindet insgesamt 43 Einrichtungen (BRAIN-Teilnehmer und DFN-Anwender) aus Wissenschaft, Bildung und Kultur mit 129 Standorten. Der Betrieb von BRAIN wird im wesentlichen durch seine Nutzer finanziert. Das Land Berlin trägt aller-dings pauschal die überwiegenden Kosten für die Wartung des Glasfasernetzes, soweit es vom ITDZ be-reit gestellt wird. Zentrales Planungs- und Steuerungsorgan für BRAIN ist die von der Senatsverwaltung für Bildung, Wis-senschaft und Forschung eingerichtete BRAIN-Planungsgruppe. Sie besteht aus Mitarbeitern der Rechen-zentren der drei Berliner Universitäten und des ZIB. Nach außen wird BRAIN in rechtlicher und wirtschaftlicher Hinsicht treuhänderisch vom ZIB vertreten, die BRAIN-Geschäftsstelle befindet sich ebenfalls im ZIB. N2 - Berlin as a city state is both local authority and federal state of the Federal Republic, as well as a location of many renowned institutions of research and culture. In close cooperation of the institutions of research with the IT service centre Berlin (ITDZ, the former Landesbetrieb für Informationstechnik) - which is the appropriate facility for the authorities of Berlin - a glass fibre network of a total extension of 856 kilome-tres of fibre optics (144 fibres each cable optic) for the common use of research and administration has been established and advanced since 1993. In 1994, when a resolution of the Senate of Berlin laid down the use of the appropriate fibre networks by the research facilities, this was the official beginning of the Berlin Research Area Information Network (BRAIN). The first seven interfaces in this fibre network in ATM technology (Classical BRAIN-ATM) were already established by the research facilities in 1995. In 1999, first systems run in Ethernet technology (Classical BRAIN-GE). These heterogeneous networks with different interfaces have been supported locally by the network administrators of the research facili-ties following global agreements. Management and advancement of the overall networks were encum-bered by these local administrations. Based on the existing experience, Berlin's research facilities agreed on the building and advancement of a technically new integrated network in gigabit Ethernet technology with standardised facilities and a centrally managed network. Since November 2003 the Berlin Research Area Information Network established a Gigabit Ethernet - called “BRAIN Integrated Network” - based on MPLS technology, including LAN to LAN linking of the facilities, local IP traffic, interface to the administration's network and WIN back-up. This BRAIN Inte-grated Network has completely replaced the locally administered predecessor networks. 24 of 27 BRAIN participants use the services of the BRAIN Integrated Network on 53 locations spread all over the city. 18 locations are connected with 1000 Mbit/s and 35 locations with 100 Mbit/s. Moreover, spread locations of a single facility have the possibililty to communicate by dedicated fibres or bandwidths. From the 2nd quarter 2007 within the scope of a pilot scheme, the advantage of a centrally administered fibre channel network "BRAIN-SAN" will be determined in order to accomplish possibilities of a spread data manage-ment of Berlin's universities and research facilities. In addition to the aforementioned services the DFN association makes use of BRAIN's structure for the connection of the X-WiN-core network nodes in Berlin and Potsdam und for access pathways to the us-ers. As from 2007, Berlin's research network BRAIN uses 2100 kilometres of single fibres from the country's fibre glass network and connects a total of 43 facilities (BRAIN participants and DFN users) from re-search, education and culture with 129 locations. The operations of BRAIN are funded basically by its users. However, the country of Berlin bears most of the costs for the maintenance of the glass fibre network, as far as it is provided by ITDZ. Central planning and steering body for BRAIN is the BRAIN planning group, which has been arranged by the administration of the Senatsverwaltung für Bildung, Wissenschaft und Forschung. It consists of staff from the computing centres of Berlin's three universities and of ZIB. BRAIN is represented legally and economically on a trust basis by the ZIB, where the BRAIN office is located also. T3 - ZIB-Report - 07-42 KW - Wissenschaftsnetz KW - Glasfasernetz KW - LAN-to-LAN-Kopplung KW - IP-Verkehr KW - Research Netzwork KW - Fibre Network KW - LAN to LAN linking KW - IP traffic Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10458 SN - 1438-0064 ER - TY - GEN A1 - Zachow, Stefan A1 - Zilske, Michael A1 - Hege, Hans-Christian T1 - 3D reconstruction of individual anatomy from medical image data: Segmentation and geometry processing N2 - For medical diagnosis, visualization, and model-based therapy planning three-dimensional geometric reconstructions of individual anatomical structures are often indispensable. Computer-assisted, model-based planning procedures typically cover specific modifications of “virtual anatomy” as well as numeric simulations of associated phenomena, like e.g. mechanical loads, fluid dynamics, or diffusion processes, in order to evaluate a potential therapeutic outcome. Since internal anatomical structures cannot be measured optically or mechanically in vivo, three-dimensional reconstruction of tomographic image data remains the method of choice. In this work the process chain of individual anatomy reconstruction is described which consists of segmentation of medical image data, geometrical reconstruction of all relevant tissue interfaces, up to the generation of geometric approximations (boundary surfaces and volumetric meshes) of three-dimensional anatomy being suited for finite element analysis. All results presented herein are generated with amira ® – a highly interactive software system for 3D data analysis, visualization and geometry reconstruction. T3 - ZIB-Report - 07-41 KW - Medical image segmentation KW - computational geometry KW - virtual anatomy KW - finite element meshes Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10440 SN - 1438-0064 ER - TY - THES A1 - Harks, Tobias T1 - Multicommodity Routing Problems-Selfish Behavior and Online Aspects- N2 - In this thesis, we study multicommodity routing problems in networks, in which commodities have to be routed from source to destination nodes. Such problems model for instance the traffic flows in street networks, data flows in the Internet, or production flows in factories. In most of these applications, the quality of a flow depends on load dependent cost functions on the edges of the given network. The total cost of a flow is usually defined as the sum of the arc cost of the network. An optimal flow minimizes this cost. A main focus of this thesis is to investigate online multicommodity routing problems in networks, in which commodities have to be routed sequentially. Arcs are equipped with load dependent price functions defining routing costs, which have to be minimized. We discuss a greedy online algorithm that routes (fractionally) each commodity by minimizing a convex cost function that depends on the previously routed flow. We present a competitive analysis of this algorithm and prove upper bounds of (d+1)^(d+1) for polynomial price functions with nonnegative coefficients and maximum degree d. For networks with two nodes and parallel arcs, we show that this algorithm returns an optimal solution. Without restrictions on the price functions and network, no algorithm is competitive. We also investigate a variant in which the demands have to be routed unsplittably. In this case, it is NP-hard to compute the offline optimum. Furthermore, we study selfish routing problems (network games). In a network game, players route demand in a network with minimum cost. In this setting, we study the quality of Nash equilibria compared to the the system optimum (price of anarchy) in network games with nonatomic and atomic players and spittable flow. As a main result, we prove upper bounds on the price of anarchy for polynomial latency functions with nonnegative coefficients and maximum degree d, which improve upon the previous best ones. N2 - Diese Arbeit befasst sich mit Mehrgüterflussproblemen, in denen Güter mit einer bestimmten Rate durch ein gegebenes Netzwerk geleitet werden müssen. Mithilfe von Mehrgüterflussproblemen können zum Beispiel Verkehrsflüsse in Strassenverkehrsnetzen oder im Internet modelliert werden. In diesen Anwendungen wird die Effizienz von Routenzuweisungen für Güter durch lastabhängige Kostenfunktionen auf den Kanten eines gegebenen Netzwerks definiert. Die Gesamtkosten eines Mehrgüterflüsses sind durch die Summe der Kosten auf den Kanten definiert. Ein optimaler Mehrgüterfluss minimiert diese Gesamtkosten. Ein wesentlicher Bestandteil dieser Arbeit ist die Untersuchung sogenannter Online Algorithmen, die Routen für bekannte Güternachfragen berechnen, ohne vollständiges Wissen über zukünftige Güternachfragen zu haben. Es konnte ein Online Algorithmus gefunden werden, dessen Gesamtkosten für polynomielle Kostenfunktionen mit endlichem Grad nicht beliebig von denen einer optimalen Lösung abweichen. Für die Berechung einer optimalen Lösung müssen alle Güternachfragen a priori vorliegen. Dieses Gütekriterium gilt unabhängig von der gewählten Netzwerktopologie oder der Eingabesequenz von Gütern. Desweiteren befasst sich diese Arbeit mit der Effizienz egoistischer Routenwahl einzelner Nutzer verglichen zu einer optimalen Routenwahl. Egoistisches Verhalten von Nutzern kann mithilfe von nichtkooperativer Spieltheorie untersucht werden. Nutzer werden als strategisch agierende Spieler betrachtet, die ihren Profit maximieren. Als Standardwerkzeug zur Analyse solcher Spiele hat sich das Konzept des Nash Gleichgewichts bewährt. Das Nash Gleichweicht beschreibt eine stabile Strategieverteilung der Spieler, in der kein Spieler einen höheren Profit erzielen kann, wenn er einseitig seine Strategie ändert. Als Hauptergebnis dieser Arbeit konnte für polynomielle Kostenfunktionen mit endlichem Grad gezeigt werden, dass die Gesamtkosten eines Nash Gleichgewichts für sogennante atomare Spieler, die einen diskreten Anteil der gesamten Güternachfrage kontrollieren, nicht beliebig von den Gesamtkosten einer optimalen Lösung abweichen. In this thesis, we study multicommodity routing problems in networks, in which commodities have to be routed from source to destination nodes. Such problems model for instance the traffic flows in street networks, data flows in the Internet, or production flows in factories. In most of these applications, the quality of a flow depends on load dependent cost functions on the edges of the given network. The total cost of a flow is usually defined as the sum of the arc cost of the network. An optimal flow minimizes this cost. A main focus of this thesis is to investigate online multicommodity routing problems in networks, in which commodities have to be routed sequentially. Arcs are equipped with load dependent price functions defining routing costs, which have to be minimized. We discuss a greedy online algorithm that routes (fractionally) each commodity by minimizing a convex cost function that depends on the previously routed flow. We present a competitive analysis of this algorithm and prove upper bounds of (d+1)^(d+1) for polynomial price functions with nonnegative coefficients and maximum degree d. For networks with two nodes and parallel arcs, we show that this algorithm returns an optimal solution. Without restrictions on the price functions and network, no algorithm is competitive. We also investigate a variant in which the demands have to be routed unsplittably. In this case, it is NP-hard to compute the offline optimum. Furthermore, we study selfish routing problems (network games). In a network game, players route demand in a network with minimum cost. In this setting, we study the quality of Nash equilibria compared to the the system optimum (price of anarchy) in network games with nonatomic and atomic players and spittable flow. As a main result, we prove upper bounds on the price of anarchy for polynomial latency functions with nonnegative coefficients and maximum degree d, which improve upon the previous best ones. KW - Mehrgueterflussprobleme KW - Online Optimierung KW - Algorithmische Spieltheorie. KW - Multicommodity Flow KW - Online Optimization KW - Algorithmic Game Theory Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10426 SN - 3867273596 ER - TY - GEN A1 - Hinze, Michael A1 - Schiela, Anton T1 - Discretization of Interior Point Methods for State Constrained Elliptic Optimal Control Problems: Optimal Error Estimates and Parameter Adjustment N2 - An adjustment scheme for the relaxation parameter of interior point approaches to the numerical solution of pointwise state constrained elliptic optimal control problems is introduced. The method is based on error estimates of an associated finite element discretization of the relaxed problems and optimally selects the relaxation parameter in dependence on the mesh size of discretization. The finite element analysis for the relaxed problems is carried out and a numerical example is presented which confirms our analytical findings. T3 - ZIB-Report - 07-40 KW - Elliptic optimal control problem KW - error estimates KW - interior point method KW - pointwise state constraints Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10414 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Nemhauser, George T1 - George Dantzig's contributions to integer programming N2 - This paper reviews George Dantzig's contribution to integer programming, especially his seminal work with Fulkerson and Johnson on the traveling salesman problem T3 - ZIB-Report - 07-39 KW - George Dantzig KW - integer programming KW - traveling salesman problem KW - TSP KW - mixed-integer programs Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10393 SN - 1438-0064 ER - TY - GEN A1 - Franck, Hildegard A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Radu, Raluca T1 - Automatisierte Fernleihe im KOBV - Handbuch für Bibliotheken - 2. Auflage N2 - Im Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) wird für die Online-Fernleihe der Zentrale-Fernleihserver (ZFL-Server) der Firma Sisis eingesetzt. Die Software ist in der KOBV-Zentrale installiert. Der ZFL-Server dient im KOBV sowohl für die Bestellung von Monographien als auch für die Bestellung von Aufsatzkopien aus Zeitschriften. Prinzipiell gibt es zwei Verfahren, mit denen sich Bibliotheken an der Online-Fernleihe beteiligen können: das E-Mail-Verfahren und das SLNP-Verfahren. Auf beide wird im Handbuch eingegangen. Die Online-Fernleihe wurde im KOBV eingeführt, um die Fernleihe für die Benutzer zu beschleunigen, das Verfahren für die Bibliotheksmitarbeiter zu vereinfachen und den Arbeitsaufwand zu reduzieren. Sie basiert darauf, dass eine Bestellung anhand eines gefundenen Treffers ausgelöst wird – d.h. die bibliographischen Daten sind bereits verifiziert und in einem Katalog nachgewiesen. Anschließend werden die Fernleihbestellungen über den ZFL-Server automatisch ausgeführt und verwaltet – sowohl in der regionalen KOBV-Fernleihe als auch in der verbundübergreifenden Fernleihe mit den deutschen Bibliotheksverbünden. Der ZFL-Server besteht aus verschiedenen technischen Komponenten. Eine dieser Komponenten ist das Bibliothekskonto, eine Internetanwendung, in der die Bestellverwaltung des ZFL-Servers für die Bibliotheksbediensteten transparent gemacht wird. Sowohl für die aktive als auch für die passive Fernleihe ist im Bibliothekskonto der Status der Bearbeitung zu jedem Zeitpunkt ersichtlich, z.B. in welcher Bibliothek sich die Bestellung gerade befindet, wann sie dort eingegangen ist und wann sie weggeschickt wurde, ob mit positivem oder negativem Ergebnis. Das Bibliothekskonto ist damit für die Bibliothek ein komfortables Instrument zum Überwachen der Fernleihbestellungen, in dem sie zudem – falls notwendig – in den Bestellvorgang eingreifen kann. Dazu hat jede Bibliothek im Bibliothekskonto eine eigene, Passwort-geschützte Dienstoberfläche. Das vorliegende Handbuch beschreibt die Vorgänge der Bestellverwaltung im Bibliothekskonto. Es richtet sich an Bibliotheksmitarbeiter, die sich mit den einzelnen Arbeitsschritten der Online-Fernleihe vertraut machen wollen. Darüber hinaus ist es zum Nachschlagen gedacht, wenn sich in der täglichen Arbeit Unklarheiten ergeben. T3 - ZIB-Report - 07-38 KW - Bibliotheksverbund KW - KOBV KW - KOBV-Fernleihe KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Online-Fernleihe KW - Verbundübergreifende Fernleihe KW - ZF Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10385 SN - 1438-0064 ER - TY - THES A1 - Weider, Steffen T1 - Integration of Vehicle and Duty Scheduling in Public Transport N2 - This thesis describes the algorithm IS-OPT that integrates scheduling of vehicles and duties in public bus transit. IS-OPT is the first algorithm which solves integrated vehicle and duty scheduling problems arising in medium sized carriers such that its solutions can be used in daily operations without further adaptions. This thesis is structured as follows: The first chapter highlights mathematical models of the planning process of public transit companies and examines their potential for integrating them with other planning steps. It also introduces descriptions of the vehicle and the duty scheduling problem. Chapter 2 motivates why it can be useful to integrate vehicle and duty scheduling, explains approaches of the literature, and gives an outline of our algorithm IS-OPT. The following chapters go into the details of the most important techniques and methods of IS-OPT: In Chapter 3 we describe how we use Lagrangean relaxation in a column generation framework. Next, in Chapter 4, we describe a variant of the proximal bundle method (PBM) that is used to approximate linear programs occurring in the solution process. We introduce here a new variant of the PBM which is able to utilize inexact function evaluation and the use of epsilon-subgradients. We also show the convergence of this method under certain assumptions. Chapter 5 treats the generation of duties for the duty scheduling problem. This problem is modeled as a resourceconstraint- shortest-path-problem with non-linear side constraints and nearly linear objective function. It is solved in a two-stage approach. At first we calculate lower bounds on the reduced costs of duties using certain nodes by a new inexact label-setting algorithm. Then we use these bounds to speed up a depth-first-search algorithm that finds feasible duties. In Chapter 6 we present the primal heuristic of IS-OPT that solves the integrated problem to integrality. We introduce a new branch-and-bound based heuristic which we call rapid branching. Rapid branching uses the proximal bundle method to compute lower bounds, it introduces a heuristic node selection scheme, and it utilizes a new branching rule that fixes sets of many variables at once. The common approach to solve the problems occurring in IS-OPT is to trade inexactness of the solutions for speed of the algorithms. This enables, as we show in Chapter 7, to solve large real world integrated problems by IS-OPT. The scheduled produced by IS-OPT save up to 5% of the vehicle and duty cost of existing schedules of regional and urban public transport companies. N2 - Diese Arbeit beschreibt den Algorithmus IS-OPT, welcher der erste Algorithmus ist, der integrierte Umlauf- und Dienstplanungsprobleme für mittelgroße Verkehrsunternehmen löst und dabei alle betrieblichen Einzelheiten berücksichtigt. Seine Lösungen können daher direkt in den täglichen Betrieb übernommen werden. Im ersten Kapitel werden mathematische Modelle für verschiedenen Probleme aus dem Planungsprozess von Nahverkehrsunternehmen beschrieben. Es werden Ansätze zur Integration der einzelnen Probleme untersucht. In diesem Kapitel werden außerdem das Umlauf- und das Dienstplanungsproblem eingeführt. Kapitel 2 motiviert, warum Integration von Umlauf- und Dienstplanung hilfreich ist oder in welchen Fällen sie sogar unabdingbar ist; es gibt einen Überblick über die vorhanden Literatur zur integrierten Umlauf- und Dienstplanung und umreißt unseren Algorithmus IS-OPT. Die weiteren Kapitel behandeln die in IS-OPT verwendeten Methoden: In Kapitel 3 beschreiben wir, wie Spaltenerzeugung für lineare Programme mit Lagrange-Relaxierung und Subgradienten-Verfahren kombiniert werden kann. In Kapitel 4 wird unsere Variante der proximalen Bündelmethode beschrieben. Diese wird benutzt um näherungsweise primale und duale Lösungen von lineare Programmen zu berechnen. Unsere Variante ist angepasst, um auch mit ungenauer Funktionsauswertung und Epsilon-Subgradienten arbeiten zu können. Wir zeigen die Konvergenz dieser Variante unter bestimmten Annahmen. Kapitel 5 behandelt das Erzeugen von Diensten für das Dienstplanungsproblem. Dieses Problem ist als ein Kürzeste-Wege-Problem mit nichtlinearen Nebenbedingungen und fast linearer Zielfunktion modelliert. Wir lösen es, indem zuerst Schranken für die reduzierten Kosten von Diensten, die bestimmte Knoten benutzen, berechnet werden. Diese Schranken werden benutzt, um in einem Tiefensuchalgorithmus den Suchbaum klein zu halten. Im Kapitel 6 präsentieren wir die neu entwickelte Heuristik "Rapid Branching", die eine ganzzahlige Lösung des integrierten Problems berechnet. Rapid Branching kann als eine spezielle Branch-and-Bound-Heuristik gesehen werden, welche die Bündelmethode benutzt. In den Knoten des Suchbaums können mehrere Variablen auf einmal fixiert werden, die mit Hilfe einer Perturbationsheuristik ausgewählt werden. In Kapitel 7 schließlich zeigen wir, daß wir mit IS-OPT auch große Probleminstanzen aus der Praxis lösen können und dabei bis zu 5% der Fahrzeug- und Dienstkosten sparen können. KW - Öffentlicher Personennahverkehr KW - lineare Optimierung KW - Umlaufplanung KW - Dienstplanung KW - Integration KW - Public Transport KW - linear Optimization KW - vehicle scheduling KW - duty scheduling KW - integration Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-16240 ER - TY - GEN A1 - Achterberg, Tobias A1 - Brinkmann, Raik A1 - Wedler, Markus T1 - Property Checking with Constraint Integer Programming N2 - We address the property checking problem for SoC design verification at the register transfer level (RTL) by integrating techniques from integer programming, constraint programming, and SAT solving. Specialized domain propagation and preprocessing algorithms for individual RTL operations extend a general constraint integer programming framework. Conflict clauses are learned by analyzing infeasible LPs and deductions, and by employing reverse propagation. Experimental results show that our approach outperforms SAT techniques for proving the validity of properties on circuits containing arithmetics. T3 - ZIB-Report - 07-37 KW - formale Chip Verifikation KW - constraint integer programming KW - scip KW - Eigenschaftsprüfer KW - formal chip verification KW - constraint integer programming KW - scip KW - property checking KW - micro chip Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10376 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Hiller, Benjamin A1 - Tuchscherer, Andreas T1 - Combinatorial Online Optimization: Elevators & Yellow Angels N2 - In \emph{classical optimization} it is assumed that full information about the problem to be solved is given. This, in particular, includes that all data are at hand. The real world may not be so nice'' to optimizers. Some problem constraints may not be known, the data may be corrupted, or some data may not be available at the moments when decisions have to be made. The last issue is the subject of \emph{online optimization} which will be addressed here. We explain some theory that has been developed to cope with such situations and provide examples from practice where unavailable information is not the result of bad data handling but an inevitable phenomenon. T3 - ZIB-Report - 07-36 KW - Online-Optimierung KW - Aufzugssteuerung KW - Dispatching von Fahrzeugen KW - online optimization KW - elevator control KW - vehicle dispatching Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10360 SN - 1438-0064 ER - TY - GEN A1 - Schiela, Anton T1 - Optimality Conditions for Convex State Constrained Optimal Control Problems with Discontinuous States N2 - We discuss first order optimality conditions for state constrained optimal control problems. Our concern is the treatment of problems, where the solution of the state equation is not known to be continuous, as in the case of boundary control in three space dimensions or optimal control with parabolic partial differential equations. We show existence of measure valued Lagrangian multipliers, which have just enough additional regularity to be applicable to all possibly discontinuous solutions of the state equation. T3 - ZIB-Report - 07-35 KW - optimal control KW - state constraints KW - optimality conditions Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10342 SN - 1438-0064 ER - TY - GEN A1 - Antoine, Xavier A1 - Arnold, Anton A1 - Besse, Christophe A1 - Ehrhardt, Matthias A1 - Schädle, Achim T1 - A Review of Transparent and Artificial Boundary Conditions Techniques for Linear and Nonlinear Schrödinger Equations N2 - In this review article we discuss different techniques to solve numerically the time-dependent Schrödinger equation on unbounded domains. We present in detail the most recent approaches and describe briefly alternative ideas pointing out the relations between these works. We conclude with several numerical examples from different application areas to compare the presented techniques. We mainly focus on the one-dimensional problem but also touch upon the situation in two space dimensions and the cubic nonlinear case. T3 - ZIB-Report - 07-34 KW - Schrödinger equation KW - transparent boundary condition KW - discrete convolution KW - unbounded domain Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10332 SN - 1438-0064 ER - TY - GEN A1 - Bley, Andreas T1 - Routing and Capacity Optimization for IP networks N2 - This article describes the main concepts and techniques that have been developed during the last year at ZIB to solve dimensioning and routing optimization problems for IP networks. We discuss the problem of deciding if a given path set corresponds to an unsplittable shortest path routing, the fundamental properties of such path sets, and the computational complexity of some basic network planning problems for this routing type. Then we describe an integer-linear programming approach to solve such problems in practice. This approach has been used successfully in the planning of the German national education and research network for several years. T3 - ZIB-Report - 07-33 KW - kombinatorische Optimierung KW - gemischt-ganzzahlige Programmierung KW - kürzeste-Wege Routing KW - Approximationsalgorithmen KW - combinatorial optimization KW - mixed-integer programming KW - shortest path routing KW - approximation algorithms Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10323 SN - 1438-0064 ER - TY - GEN A1 - Schenk, Olaf A1 - Wächter, Andreas A1 - Weiser, Martin T1 - Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization N2 - Fast nonlinear programming methods following the all-at-once approach usually employ Newton's method for solving linearized Karush-Kuhn-Tucker (KKT) systems. In nonconvex problems, the Newton direction is only guaranteed to be a descent direction if the Hessian of the Lagrange function is positive definite on the nullspace of the active constraints, otherwise some modifications to Newton's method are necessary. This condition can be verified using the signs of the KKT's eigenvalues (inertia), which are usually available from direct solvers for the arising linear saddle point problems. Iterative solvers are mandatory for very large-scale problems, but in general do not provide the inertia. Here we present a preconditioner based on a multilevel incomplete $LBL^T$ factorization, from which an approximation of the inertia can be obtained. The suitability of the heuristics for application in optimization methods is verified on an interior point method applied to the CUTE and COPS test problems, on large-scale 3D PDE-constrained optimal control problems, as well as 3D PDE-constrained optimization in biomedical cancer hyperthermia treatment planning. The efficiency of the preconditioner is demonstrated on convex and nonconvex problems with $150^3$ state variables and $150^2$ control variables, both subject to bound constraints. T3 - ZIB-Report - 07-32 KW - nonconvex constrained optimization KW - interior-point method KW - inertia KW - multilevel incomplete factorization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10314 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus A1 - Becker, Roland A1 - Köppen, Robert A1 - Durmaz, Vedat T1 - Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane N2 - In this paper, we investigate the interconversion processes of the major flame retardant -- 1,2,5,6,9,10-hexabromocyclododecane (HBCD) -- by the means of statistical thermodynamics based on classical force-fields. Three ideas will be presented. First, the application of classical hybrid Monte-Carlo simulations for quantum mechanical processes will be justified. Second, the problem of insufficient convergence properties of hybrid Monte-Carlo methods for the generation of low temperature canonical ensembles will be solved by an interpolation approach. Furthermore, it will be shown how free energy differences can be used for a rate matrix computation. The results of our numerical simulations will be compared to experimental results. T3 - ZIB-Report - 07-31 KW - Markov process KW - molecular dynamics KW - rate matrix Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10308 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo T1 - Heuristics of the Branch-Cut-and-Price-Framework SCIP N2 - In this paper we give an overview of the heuristics which are integrated into the open source branch-cut-and-price-framework SCIP. We briefly describe the fundamental ideas of different categories of heuristics and present some computational results which demonstrate the impact of heuristics on the overall solving process of SCIP. T3 - ZIB-Report - 07-30 KW - Primalheuristiken KW - Gemischt-Ganzzahlige Programmierung KW - Branch and Cut KW - SCIP KW - mixed integer programming KW - primal heuristics KW - branch and cut KW - SCIP Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10280 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Liebchen, Christian T1 - When Periodic Timetables are Suboptimal N2 - The timetable is the essence of the service offered by any provider of public transport'' (Jonathan Tyler, CASPT 2006). Indeed, the timetable has a major impact on both operating costs and on passenger comfort. Most European agglomerations and railways use periodic timetables in which operation repeats in regular intervals. In contrast, many North and South American municipalities use trip timetables in which the vehicle trips are scheduled individually subject to frequency constraints. We compare these two strategies with respect to vehicle operation costs. It turns out that for short time horizons, periodic timetabling can be suboptimal; for sufficiently long time horizons, however, periodic timetabling can always be done in an optimal way'. T3 - ZIB-Report - 07-29 KW - Taktfahrplan KW - Fahrplan KW - Nahverkehr KW - periodic timetable KW - trip timetable KW - public transport Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9151 SN - 1438-0064 ER - TY - GEN A1 - Berthold, Timo T1 - RENS - Relaxation Enforced Neighborhood Search N2 - In the recent years, a couple of quite successful large neighborhood search heuristics for mixed integer programs has been published. Up to our knowledge, all of them are improvement heuristics. We present a new start heuristic for general MIPs working in the spirit of large neighborhood search. It constructs a sub-MIP which represents the space of all feasible roundings of some fractional point - normally the optimum of the LP-relaxation of the original MIP. Thereby, one is able to determine whether a point can be rounded to a feasible solution and which is the best possible rounding. Furthermore, a slightly modified version of RENS proves to be a well-performing heuristic inside the branch-cut-and-price-framework SCIP. T3 - ZIB-Report - 07-28 KW - Primalheuristiken KW - Gemischt-Ganzzahlige Programmierung KW - Nachbarschaftssuche KW - mixed integer programming KW - primal heuristics KW - large neighborhood search Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4264 SN - 1438-0064 ER - TY - THES A1 - Bley, Andreas T1 - Routing and Capacity Optimization for IP Networks N2 - This thesis is concerned with dimensioning and routing optimization problems for communication networks that employ a shortest path routing protocol such as OSPF, IS-IS, or RIP. These protocols are widely used in the Internet. With these routing protocols, all end-to-end data streams are routed along shortest paths with respect to a metric of link lengths. The network administrator can configure the routing only by modifying this metric. In this thesis we consider the unsplittable shortest path routing variant, where each communication demand must be sent unsplit through the network. This requires that all shortest paths are uniquely determined. The major difficulties in planning such networks are that the routing can be controlled only indirectly via the routing metric and that all routing paths depend on the same routing metric. This leads to rather complicated and subtle interdependencies among the paths that comprise a valid routing. In contrast to most other routing schemes, the paths for different communication demands cannot be configured independent of each other. Part I of the thesis is dedicated to the relation between path sets and routing metrics and to the combinatorial properties of those path sets that comprise a valid unsplittable shortest path routing. Besides reviewing known approaches to find a compatible metric for a given path set (or to prove that none exists) and discussing some properties of valid path sets, we show that the problem of finding a compatible metric with integer lengths as small as possible and the problem of finding a smallest possible conflict in the given path set are both NP-hard to approximate within a constant factor. In Part II of the thesis we discuss the relation between unsplittable shortest path routing and several other routing schemes and we analyze the computational complexity of three basic unsplittable shortest path routing problems. We show that the lowest congestion that can be obtained with unsplittable shortest path routing may significantly exceed that achievable with other routing paradigms and we prove several non-approximability results for unsplittable shortest path routing problems that are stronger than those for the corresponding unsplittable flow problems. In addition, we derive various polynomial time approximation algorithms for general and special cases of these problems. In Part III of the thesis we finally develop an integer linear programming approach to solve these and more realistic unsplittable shortest path routing problems to optimality. We present alternative formulations for these problems, discuss their strength and computational complexity, and show how to derive strong valid inequalities. Eventually, we describe our implementation of this solution approach and report on the numerical results obtained for real-world problems that came up in the planning the German National Research and Education Networks G-WiN and X-WiN and for several benchmark instances. N2 - Die Arbeit befasst sich mit der Kapazitäts- und Routenplanung für Kommunikationsnetze, die ein kürzeste-Wege Routingprotokoll verwenden. Diese Art von Protokollen ist im Internet weit verbreitet. Bei diesen Routingverfahren wird für jede Verbindung im Netz ein Längenwert festgelegt, diese Längen formen die sogenannte Routingmetrik. Die Routingwege der Kommunikationsbedarfe sind dann die jeweiligen kürzesten Wege bezüglich dieser Metrik. Bei der in der Arbeit untersuchten Variante dieser Routingprotokolle wird zusätzlich verlangt, dass es je Kommunikationsbedarf genau einen eindeutigen kürzesten Weg gibt. Die Schwierigkeit bei der Planung solcher Netze besteht darin, dass sich die Routingwege einerseits nur indirekt über die Routingmetrik beeinflussen lassen, andererseits aber alle Routingwege von der gleichen Metrik abhängen. Dadurch können die Wege verschiedener Kommunikationsanforderungen nicht wie bei anderen Routingverfahren unabhängig voneinander gewählt werden. Im erstem Teil der Arbeit werden der Zusammenhang zwischen gegebenen Wegesystemen und kompatiblen Routingmetriken sowie die Beziehungen der Wege eines zulässigen eindeutige-kürzeste-Wege-Routings untereinander untersucht. Dabei wird unter Anderem gezeigt, dass es NP-schwer ist, eine kompatible Metrik mit kleinstmöglichen Routinglängen zu einem gegebenen Wegesystem zu finden. Es wird auch bewiesen, dass das Finden eines kleinstmöglichen Konfliktes in einem gegebenen Wegesystem, zu dem keine kompatible Metrik existiert, NP-schwer ist. Im zweiten Teil der Arbeit wird die Approximierbarkeit von drei grundlegenden Netz- und Routenplanungsproblemen mit eindeutige-kürzeste-Wege-Routing untersucht. Für diese Probleme werden stärkere Nichtapproximierbarkeitsresultate als für die entsprechenden Einwege-Routing Probleme bewiesen und es werden verschiedene polynomiale Approximationsverfahren für allgemeine und Spezialfälle entworfen. Ausserdem wird die Beziehung zwischen eindeutige-kürzeste-Wege-Routing und anderen Routingverfahren diskutiert. Im dritten und letzten Teil der Arbeit wird ein (gemischt-) ganzzahliger Lösungsansatz für Planungsprobleme mit eindeutige-kürzeste-Wege-Routing vorgestellt. Für die im zweiten Teil diskutierten grundlegenden Netz- und Routenplanungsprobleme werden verschiedene (gemischt-) ganzzahlige lineare Modelle vorgestellt und es wird deren Lösbarkeit und die Stärke ihrer LP Relaxierungen untersucht. Es wird auch gezeigt, wie sich starke gültig Ungleichungen aus den in diesen Modellen enthalten Substrukturen ableiten lassen. Schlielich werden am Ende der Arbeit die Software-Implementierung dieses Lösungsverfahrens für eine praxisrelevante Verallgemeinerung der Planungsprobleme sowie die damit erzielten numerischen Ergebnisse vorgestellt und diskutiert. KW - kombinatorische Optimierung KW - gemischt-ganzzahlige Programmierung KW - kürzeste-Wege Routing KW - Approximationsalgorithmen KW - combinatorial optimization KW - mixed-integer programming KW - shortest path routing KW - approximation algorithms Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-15530 SN - 978-3-86727-281-0 ER - TY - GEN A1 - Rusch, Beate A1 - Block, Barbara A1 - Labner, Josef T1 - Katalogisierung kooperativ gemacht N2 - Bereits seit den siebziger Jahren katalogisieren Bibliotheken arbeitsteilig in Verbünden. Allerdings macht die Kooperation bislang oftmals an den Grenzen traditionell gewachsener Verbundstrukturen halt. Das ist ein Grund dafür, dass in Deutschland und Österreich das gleiche Buch im schlimmsten Fall an zahlreichen Stellen gleichzeitig katalogisiert wird, ohne dass der eine von der Arbeit des anderen profitiert. In dem folgenden Report werden erstmals konkrete Schritte beschrieben, die eine verteilte Katalogisierung über Verbundgrenzen hinweg verbessern. Dazu gehören Vereinbarungen für die Indexierung und die Suche über Z39.50, Regeln für gegenseitige Datenlieferungen und nicht zuletzt die Einführung einer eindeutigen Identifikationsnummer, die die erstkatalogisierende Institution vergibt. Der vorliegende Artikel ist ein vorläufiger Zwischenbericht der von der Arbeitsgemeinschaft der Verbundsysteme eingesetzten Arbeitsgruppe „Kooperative Neukatalogisierung“. T3 - ZIB-Report - 07-27 KW - Verbünde KW - Katalogisierung KW - Datenanreicherung KW - Z39.50 KW - Library KW - Catalog Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10264 SN - 1438-0064 ER - TY - THES A1 - Achterberg, Tobias T1 - Constraint Integer Programming N2 - This thesis introduces the novel paradigm of constraint integer programming (CIP), which integrates constraint programming (CP) and mixed integer programming (MIP) modeling and solving techniques. It is supplemented by the software SCIP, which is a solver and framework for constraint integer programming that also features SAT solving techniques. SCIP is freely available in source code for academic and non-commercial purposes. Our constraint integer programming approach is a generalization of MIP that allows for the inclusion of arbitrary constraints, as long as they turn into linear constraints on the continuous variables after all integer variables have been fixed. The constraints, may they be linear or more complex, are treated by any combination of CP and MIP techniques: the propagation of the domains by constraint specific algorithms, the generation of a linear relaxation and its solving by LP methods, and the strengthening of the LP by cutting plane separation. The current version of SCIP comes with all of the necessary components to solve mixed integer programs. In the thesis, we cover most of these ingredients and present extensive computational results to compare different variants for the individual building blocks of a MIP solver. We focus on the algorithms and their impact on the overall performance of the solver. In addition to mixed integer programming, the thesis deals with chip design verification, which is an important topic of electronic design automation. Chip manufacturers have to make sure that the logic design of a circuit conforms to the specification of the chip. Otherwise, the chip would show an erroneous behavior that may cause failures in the device where it is employed. An important subproblem of chip design verification is the property checking problem, which is to verify whether a circuit satisfies a specified property. We show how this problem can be modeled as constraint integer program and provide a number of problem-specific algorithms that exploit the structure of the individual constraints and the circuit as a whole. Another set of extensive computational benchmarks compares our CIP approach to the current state-of-the-art SAT methodology and documents the success of our method. N2 - Diese Arbeit stellt einen integrierten Ansatz aus Constraint Programming (CP) und Gemischt-Ganzzahliger Programmierung (Mixed Integer Programming, MIP) vor, den wir Constraint Integer Programming (CIP) nennen. Sowohl Modellierungs- als auch Lösungstechniken beider Felder fließen in den neuen integrierten Ansatz ein, um die unterschiedlichen Stärken der beiden Gebiete zu kombinieren. Als weiteren Beitrag stellen wir der wissenschaftlichen Gemeinschaft die Software SCIP zur Verfügung, die ein Framework für Constraint Integer Programming darstellt und zusätzlich Techniken des SAT-Lösens beinhaltet. SCIP ist im Source Code für akademische und nicht-kommerzielle Zwecke frei erhältlich. Unser Ansatz des Constraint Integer Programming ist eine Verallgemeinerung von MIP, die zusätzlich die Verwendung beliebiger Constraints erlaubt, solange sich diese durch lineare Bedingungen ausdrücken lassen falls alle ganzzahligen Variablen auf feste Werte eingestellt sind. Die Constraints werden von einer beliebigen Kombination aus CP- und MIP-Techniken behandelt. Dies beinhaltet insbesondere die Domain Propagation, die Relaxierung der Constraints durch lineare Ungleichungen, sowie die Verstärkung der Relaxierung durch dynamisch generierte Schnittebenen. Die derzeitige Version von SCIP enthält alle Komponenten, die für das effiziente Lösen von Gemischt-Ganzzahligen Programmen benötigt werden. Die vorliegende Arbeit liefert eine ausführliche Beschreibung dieser Komponenten und bewertet verschiedene Varianten in Hinblick auf ihren Einfluß auf das Gesamt-Lösungsverhalten anhand von aufwendigen praktischen Experimenten. Dabei wird besonders auf die algorithmischen Aspekte eingegangen. Der zweite Hauptteil der Arbeit befasst sich mit der Chip-Design-Verifikation, die ein wichtiges Thema innerhalb des Fachgebiets der Electronic Design Automation darstellt. Chip-Hersteller müssen sicherstellen, dass der logische Entwurf einer Schaltung der gegebenen Spezifikation entspricht. Andernfalls würde der Chip fehlerhaftes Verhalten aufweisen, dass zu Fehlfunktionen innerhalb des Gerätes führen kann, in dem der Chip verwendet wird. Ein wichtiges Teilproblem in diesem Feld ist das Eigenschafts-Verifikations-Problem, bei dem geprüft wird, ob der gegebene Schaltkreisentwurf eine gewünschte Eigenschaft aufweist. Wir zeigen, wie dieses Problem als Constraint Integer Program modelliert werden kann und geben eine Reihe von problemspezifischen Algorithmen an, die die Struktur der einzelnen Constraints und der Gesamtschaltung ausnutzen. Testrechnungen auf Industrie-Beispielen vergleichen unseren Ansatz mit den bisher verwendeten SAT-Techniken und belegen den Erfolg unserer Methode. KW - Ganzzahlige Programmierung KW - Constraint Programmierung KW - SAT KW - Chip-Verifikation KW - integer programming KW - constraint programming KW - SAT KW - chip verification Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-16117 ER - TY - THES A1 - Plantikow, Stefan T1 - Transaktionen für verteilte Wikis auf strukturierten Overlay Netzwerken T1 - Transactions for Distributed Wikis on Structured Overlay Networks N2 - Die Diplomarbeit präsentiert ein Transaktionsverfahren für strukturierte Overlay-Netzwerke, das an die Erfordernisse verteilter Informationssysteme mit relationalem Datenmodell angepasst ist. Insbesondere wird der Einsatz von Transaktionen für verteilte Wikis betrachtet, die moderne Funktionalitäten, wie Metadaten und zusätzliche Indexe für die Navigation, unterstützen. Konsistenz und Dauerhaftigkeit der gespeicherten Daten erfordert die Behandlung von Knotenausfällen. Die Arbeit schlägt dafür das Zellenmodell vor: Das Overlay wird aus replizierten Zustandsmaschinen gebildet, um Verfügbarkeit zu gewährleisten. Das Transaktionsverfahren baut darauf auf und verwendet Two-Phase-Commit mit Fehlererkennung und Widerherstellung von ausgefallenen Transaktionsmanagern. Anwendungen wird eine Auswahl an pessimistischen und hybrid-optimistischen Nebenläufigkeitskontrollverfahren geboten, die die Minimierung von Latenzeffekten und die schnelle Ausführung von Nur-Lese-Transaktionen ermöglichen. Für die Beispielanwendung Wiki wird der erforderliche Pseudocode angegeben und die verschiedenen Nebenläufigkeitskontrollverfahren hinsichtlich ihrer Nachrichtenkomplexität verglichen. N2 - The diploma thesis presents a transaction processing scheme for structured overlay networks and uses it to develop a distributed Wiki application based on a relational data model. The Wiki supports rich metadata and additional indexes for navigation purposes. Ensuring consistency and durability requires handling of node failures. Such failures are masked by providing high availability of nodes. This in turn is achieved by constructing the overlay from replicated state machines (cell model). Atomicity is realized using two phase commit with additional support for failure detection and restoration of the transaction manager. The developed transaction processing scheme provides the application with a mixture of pessimistic, hybrid optimistic and multiversioning concurrency control techniques to minimize the impact of replication on latency and optimize for read operations. The pseudocode of the relevant Wiki functions is presented and the different concurrency control techniques are evaluated in terms of message complexity. KW - Verteilte Transaktionen KW - Content Management Systeme KW - Strukturierte Overlay-Netzwerke KW - Konsistenz KW - Nebenläufigkeitskontrolle KW - distributed transactions KW - content management systems KW - structured overlay networks KW - consistency KW - concurrency control Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10176 ER - TY - GEN A1 - Hiller, Benjamin A1 - Tuchscherer, Andreas T1 - Real-Time Destination-Call Elevator Group Control on Embedded Microcontrollers N2 - Algorithmic control of elevator systems has been studied for a long time. More recently, a new paradigm for elevator control has emerged. In destination call systems, the passenger specifies not only the direction of his ride, but the destination floor. Such a destination call system is very interesting from an optimization point of view, since more information is available earlier, which should allow improved planning. However, the real-world destination call system envisioned by our industry partner requires that each destination call (i.e. passenger) is assigned to a serving elevator immediately. This early assignment restricts the potential gained from the destination information. Another aspect is that there is no way to specify the destination floor in the cabin. Therefore, the elevator has to stop on every destination floor of an assigned call, although the passenger may not have boarded the cabin, e.g. due to insufficient capacity. In this paper we introduce a new destination call control algorithm suited to this setting. Since the control algorithm for an entire elevator group has to run on embedded microprocessors, computing resources are very scarce. Since exact optimization is not feasible on such hardware, the algorithm is an insertion heuristic using a non-trivial data structure to maintain a set of tours. To assess the performance of our algorithm, we compare it to similar and more powerful algorithms by simulation. We also compare to algorithms for a conventional system and with a more idealized destination call system. This gives an indication of the relative potentials of these systems. In particular, we assess how the above real-world restrictions influence performance. The algorithm introduced has been implemented by our industry partner for real-world use. T3 - ZIB-Report - 07-26 KW - Aufzugsgruppensteuerung KW - Zielrufsteuerung KW - Echzeitoptimierung KW - Online-Optimierung KW - elevator group control KW - destination call system KW - real time optimation KW - online optimization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10108 SN - 1438-0064 ER - TY - GEN A1 - Kaibel, Volker A1 - Stephan, Rüdiger T1 - On cardinality constrained cycle and path polytopes N2 - We consider polytopes associated with cardinality constrained path and cycle problems defined on a directed or undirected graph. We present integer characterizations of these polytopes by facet defining linear inequalities for which the separation problem can be solved in polynomial time. Moreover, we give further facet defining inequalities, in particular those that are specific to odd/even paths and cycles. T3 - ZIB-Report - 07-25 KW - path KW - cycles KW - integer characterizations KW - facets Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10093 SN - 1438-0064 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Die Wissenschaftsgalaxis: Wie soll die zukünftige wissenschaftliche Informationsversorgung aussehen? N2 - Wissenschaftler sind an qualitativ hochwertiger Information interessiert, selten an Informationsversorgung selbst. Es ist ihnen in Fragen der Organisation meistens egal, von welchem Versorger sie das Material, das sie benötigen, bekommen. Sie wollen einfach nur alles, was sie brauchen, jederzeit, überall, sofort und möglichst kostengünstig oder gar kostenlos haben. Im Prinzip ist das möglich. Seit mindestens zehn Jahren werden so gut wie alle wissenschaftlichen Dokumente (Artikel, Messdaten,…) elektronisch erstellt. Eigentlich bräuchte man diese nur ins Internet zu stellen, und damit wäre alles verfügbar. Irgendwie funktioniert diese einfache Idee nicht so richtig, obwohl viele Anstrengungen von den verschiedensten Einrichtungen und Individuen unternommen werden, z. B. durch Open-Access-Bemühungen. Was sind die Gründe dafür? Die Fortschritte beim schnellen Zugriff auf Information im Internet sind atemberaubend (siehe Google), dennoch ist der zielgerichtete Zugriff auf wissenschaftlich relevante Information weiterhin nur oberflächlich vorhanden. Die Hindernisse sind vielfältiger Natur: Bequemlichkeit und Unwissen der Autoren, Gewohnheiten der Nutzer und Informationsvermittler, Barrieren durch Copyrights und Verlagsstrategien, Eitelkeiten. In diesem Artikel werden einige der Probleme erläutert, die dem Traum des Aufbaus der wissenschaftlichen Universalbibliothek entgegenstehen. Gleichzeitig wird skizziert, wie man auf dem Weg zur Verwirklichung des Traums ein Stück vorankommen und wie die zukünftige wissenschaftliche Informationsversorgung gestaltet werden kann. T3 - ZIB-Report - 07-24 KW - wissenschaftliche Informationsversorgung KW - Open Access KW - digitale Bibliothek KW - Bibliothek der Zukunft KW - World Digital Mathematics Library KW - Open Access Catalog KW - Online Public Access Catalog Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10032 ER - TY - THES A1 - Gerber, Susanne T1 - Perfusionsmodellierung in menschlichen Tumoren N2 - Im Rahmen dieser Arbeit wurde ein individuell anpassungsfähiges Modell entwickelt und implementiert, das die Perfusion in menschlichen soliden Tumoren beschreibt und für verschiedene Zeitpunkte w¨ahrend regionaler Hyperthermie ein lokal abhängiges Temperaturprofil berechnet. Da vor jeder Simulation alle wichtigen Parameter anhand von Ultraschall-, MRT- oder Angiogrammbildern individuell bestimmt werden können, wird eine patientenspezifische Aussage ¨uber das intratumorale Antwortverhalten bereits vor der eigentlichen Behandlung möglich. In Abh¨angigkeit von der Qualität der zur Verfügung stehenden anatomischen Daten über das zu simulierende Gebiet kann das Modell beliebig verfeinert oder bei Mangel an detaillierten Informationen auch mit Minimaldaten und reduzierter räumlicher Genauigkeit benutzt werden. Die für eine Simulation benötigten 2- oder 3- dimensionalen Geometrien können leicht mit der am ZIB entwickelten Software Amira erstellt und zur Berechnung in KARDOS, einem ebenfalls am ZIB implementierten Löser für nichtlineare partielle Differentialgleichungen, eingelesen werden. Mit Hilfe dieses Modells wird eine einfache, aber realistische und aussagekräftige Simulation für die Therapieplanung einer klinischen Hyperthermieanwendung ermöglicht, die innerhalb kurzer Zeit vorbereitet und durchgeführt werden kann. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9923 ER - TY - THES A1 - Maiwald, Gunar T1 - Entity Resolution für Zitationen mit Probabilistischen Relationalen Modellen N2 - In dieser Diplomarbeit wird untersucht, wie auf der Basis von Literaturreferenzen ein Zitationsgraph durch ein automatisches Verfahren aufgebaut werden kann. Zur Lösung des Problems werden Probabilistische Relationale Modelle herangezogen. Eine problemspezifische Erweiterung des Modells ermöglicht es, dass bestehende Unsicherheiten im Zitationsgraphen mit Hilfe eines Inferenzverfahrens aufgelöst werden können. Zur Evaluierung des Verfahren werden Experimente auf dem Cora-Datensatz durchgeführt. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9899 ER - TY - GEN A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - P2P Routing of Range Queries in Skewed Multidimensional Data Sets N2 - We present a middleware to store multidimensional data sets on Internet-scale distributed systems and to efficiently perform range queries on them. Our structured overlay network \emph{SONAR (Structured Overlay Network with Arbitrary Range queries)} puts keys which are adjacent in the key space on logically adjacent nodes in the overlay and is thereby able to process multidimensional range queries with a single logarithmic data lookup and local forwarding. The specified ranges may have arbitrary shapes like rectangles, circles, spheres or polygons. Empirical results demonstrate the routing performance of SONAR on several data sets, ranging from real-world data to artificially constructed worst case distributions. We study the quality of SONAR's routing information which is based on local knowledge only and measure the indegree of the overlay nodes to find potential hot spots in the routing process. We show that SONAR's routing table is self-adjusting, even under extreme situations, keeping always a maximum of $\lceil \log N \rceil$ routing entries. T3 - ZIB-Report - 07-23 KW - structured overlays KW - range queries KW - routing KW - multidimensional data sets Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9671 SN - 1438-0064 ER - TY - GEN A1 - Harks, Tobias A1 - Heinz, Stefan A1 - Pfetsch, Marc A1 - Vredeveld, Tjark T1 - Online Multicommodity Routing with Time Windows N2 - We consider a multicommodity routing problem, where demands are released \emph{online} and have to be routed in a network during specified time windows. The objective is to minimize a time and load dependent convex cost function of the aggregate arc flow. First, we study the fractional routing variant. We present two online algorithms, called Seq and Seq$^2$. Our first main result states that, for cost functions defined by polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of Seq and Seq$^2$ is at most $(d+1)^{d+1}$, which is tight. We also present lower bounds of $(0.265\,(d+1))^{d+1}$ for any online algorithm. In the case of a network with two nodes and parallel arcs, we prove a lower bound of $(2-\frac{1}{2} \sqrt{3})$ on the competitive ratio for Seq and Seq$^2$, even for affine linear price functions. Furthermore, we study resource augmentation, where the online algorithm has to route less demand than the offline adversary. Second, we consider unsplittable routings. For this setting, we present two online algorithms, called U-Seq and U-Seq$^2$. We prove that for polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of U-Seq and U-Seq$^2$ is bounded by $O{1.77^d\,d^{d+1}}$. We present lower bounds of $(0.5307\,(d+1))^{d+1}$ for any online algorithm and $(d+1)^{d+1}$ for our algorithms. Third, we consider a special case of our framework: online load balancing in the $\ell_p$-norm. For the fractional and unsplittable variant of this problem, we show that our online algorithms are $p$ and $O{p}$ competitive, respectively. Such results where previously known only for scheduling jobs on restricted (un)related parallel machines. T3 - ZIB-Report - 07-22 KW - Online Optimization KW - Routing KW - Telecommunications Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9654 SN - 1438-0064 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Bayer, Georg A1 - Engel, Thomas T1 - Single-layer Cuts for Multi-layer Network Design Problems N2 - We study a planning problem arising in SDH/WDM multi-layer telecommunication network design. The goal is to find a minimum cost installation of link and node hardware of both network layers such that traffic demands can be realized via grooming and a survivable routing. We present a mixed-integer programming formulation that takes many practical side constraints into account, including node hardware, several bitrates, and survivability against single physical node or link failures. This model is solved using a branch-and-cut approach with problem-specific preprocessing and cutting planes based on either of the two layers. On several realistic two-layer planning scenarios, we show that these cutting planes are still useful in the multi-layer context, helping to increase the dual bound and to reduce the optimality gaps. T3 - ZIB-Report - 07-21 KW - telecommunication network KW - multi-layer network design KW - mixed-integer programming KW - cutting planes Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9641 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Solving Railway Track Allocation Problems N2 - The \emph{optimal track allocation problem} (\textsc{OPTRA}), also known as the train routing problem or the train timetabling problem, is to find, in a given railway network, a conflict-free set of train routes of maximum value. We propose a novel integer programming formulation for this problem that is based on additional configuration' variables. Its LP-relaxation can be solved in polynomial time. These results are the theoretical basis for a column generation algorithm to solve large-scale track allocation problems. Computational results for the Hanover-Kassel-Fulda area of the German long distance railway network involving up to 570 trains are reported. T3 - ZIB-Report - 07-20 KW - railway track allocation KW - timetabling KW - column generation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9631 SN - 1438-0064 ER - TY - GEN A1 - Kube, Susanna A1 - Lasser, Caroline A1 - Weber, Marcus T1 - Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics N2 - Wigner transformation provides a one-to-one correspondence between functions on position space (wave functions) and functions on phase space (Wigner functions). Weighted integrals of Wigner functions yield quadratic quantities of wave functions like position and momentum densities or expectation values. For molecular quantum systems, suitably modified classical transport of Wigner functions provides an asymptotic approximation of the dynamics in the high energy regime. The article addresses the computation of Wigner functions by Monte Carlo quadrature. An ad aption of the Metropolis algorithm for the approximation of signed measures with disconnected support is systematically tested in combination with a surface hopping algorithm for non-adiabatic quantum dynamics. The numerical experiments give expectation values and level populations with an error of two to three percent, which agrees with the theoretically expected accuracy. T3 - ZIB-Report - 07-17 KW - Metropolis Monte Carlo KW - approximation KW - quadrature KW - oscillating functions Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9604 ER - TY - GEN A1 - Weber, Marcus T1 - Conformation-based transition state theory N2 - For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator ${\cal P}^\tau$ does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of the operator and can be interpreted as a decomposition of the state space into (fuzzy) sets. The conformation-based transition state theory presented here can be seen as a first step in conformation dynamics towards the computation of essential dynamical properties of molecular systems without time-consuming molecular dynamics simulations. T3 - ZIB-Report - 07-18 KW - dynamical systems KW - transition state theory KW - rare events Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9612 ER - TY - THES A1 - Zymolka, Adrian T1 - Design of Survivable Optical Networks by Mathematical Optimization N2 - Abstract The cost-efficient design of survivable optical telecommunication networks is the topic of this thesis. In cooperation with network operators, we have developed suitable concepts and mathematical optimization methods to solve this comprehensive planning task in practice. Optical technology is more and more employed in modern telecommunication networks. Digital information is thereby transmitted as short light pulses through glass fibers. Moreover, the optical medium allows for simultaneous transmissions on a single fiber by use of different wavelengths. Recent optical switches enable a direct forwarding of optical channels in the network nodes without the previously required signal retransformation to electronics. Their integration creates ongoing optical connections,which are called lightpaths. We study the problem of finding cost-efficient configurations of optical networks which meet specified communication requirements. A configuration comprises the determination of all lightpaths to establish as well as the detailed allocation of all required devices and systems. We use a flexible modeling framework for a realistic representation of the networks and their composition. For different network architectures, we formulate integer linear programs which model the design task in detail. Moreover, network survivability is an important issue due to the immense bandwidths offered by optical technology. Operators therefore request for designs which perpetuate protected connections and guarantee for a defined minimum throughput in case of malfunctions. In order to achieve an effective realization of scalable protection, we present a novel survivability concept tailored to optical networks and integrate several variants into the models. Our solution approach is based on a suitable model decomposition into two subtasks which separates two individually hard subproblems and enables this way to compute cost-efficient designs with approved quality guarantee. The first subtask consists of routing the connections with corresponding dimensioning of capacities and constitutes a common core task in the area of network planning. Sophisticated methods for such problems have already been developed and are deployed by appropriate integration. The second subtask is characteristic for optical networks and seeks for a conflict-free assignment of available wavelengths to the lightpaths using a minimum number of involved wavelength converters. For this coloring-like task, we derive particular models and study methods to estimate the number of unavoidable conversions. As constructive approach, we develop heuristics and an exact branch-and-price algorithm. Finally, we carry out an extensive computational study on realistic data, provided by our industrial partners. As twofold purpose, we demonstrate the potential of our approach for computing good solutions with quality guarantee, and we exemplify its flexibility for application to network design and analysis. KW - network design KW - optical networks KW - integer programming KW - mathematical optimization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10408 ER - TY - GEN A1 - Harks, Tobias A1 - Heinz, Stefan A1 - Pfetsch, Marc T1 - Competitive Online Multicommodity Routing N2 - In this paper we study online multicommodity routing problems in networks, in which commodities have to be routed sequentially. The flow of each commodity can be split on several paths. Arcs are equipped with load dependent price functions defining routing costs, which have to be minimized. We discuss a greedy online algorithm that routes each commodity by minimizing a convex cost function that only depends on the demands previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is 4K2 (1+K)2 -competitive, where K is the number of commodities. For the single-source single-destination case, this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably. T3 - ZIB-Report - 07-16 KW - Online Optimization KW - Routing KW - Telecommunications Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9599 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Pioro, Michal A1 - Tomaszewski, Artur A1 - Wessäly, Roland T1 - SNDlib 1.0--Survivable Network Design Library N2 - We provide information on the Survivable Network Design Library (SNDlib), a data library for fixed telecommunication network design that can be accessed at http://sndlib.zib.de. In version 1.0, the library contains data related to 22 networks which, combined with a set of selected planning parameters, leads to 830 network planning problem instances. In this paper, we provide a mathematical model for each planning problem considered in the library and describe the data concepts of the SNDlib. Furthermore, we provide statistical information and details about the origin of the data sets. T3 - ZIB-Report - 07-15 KW - telecommunication network design KW - data library KW - optimization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9582 ER - TY - GEN A1 - Raack, Christian A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - Capacitated network design using general flow-cutset inequalities N2 - This paper deals with directed, bidirected, and undirected capacitated network design problems. Using mixed integer rounding (MIR), we generalize flow-cutset inequalities to these three link types and to an arbitrary modular link capacity structure, and propose a generic separation algorithm. In an extensive computational study on 54 instances from the Survivable Network Design Library (SNDlib), we show that the performance of cplex can significantly be enhanced by this class of cutting planes. The computations reveal the particular importance of the subclass of cutset-inequalities. T3 - ZIB-Report - 07-14 KW - general flow-cutset inequalities KW - capacitated network design KW - mixed integer rounding KW - SNDlib Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9576 ER - TY - GEN A1 - Vater, Stefan A1 - Klein, Rupert T1 - Stability of a Cartesian Grid Projection Method for Zero Froude Number Shallow Water Flows N2 - In this paper a Godunov-type projection method for computing approximate solutions of the zero Froude number (incompressible) shallow water equations is presented. It is second-order accurate and locally conserves height (mass) and momentum. To enforce the underlying divergence constraint on the velocity field, the predicted numerical fluxes, computed with a standard second order method for hyperbolic conservation laws, are corrected in two steps. First, a MAC-type projection adjusts the advective velocity divergence. In a second projection step, additional momentum flux corrections are computed to obtain new time level cell-centered velocities, which satisfy another discrete version of the divergence constraint. The scheme features an exact and stable second projection. It is obtained by a Petrov-Galerkin finite element ansatz with piecewise bilinear trial functions for the unknown incompressible height and piecewise constant test functions. The stability of the projection is proved using the theory of generalized mixed finite elements, which goes back to Nicola{\"i}des (1982). In order to do so, the validity of three different inf-sup conditions has to be shown. Since the zero Froude number shallow water equations have the same mathematical structure as the incompressible Euler equations of isentropic gas dynamics, the method can be easily transfered to the computation of incompressible variable density flow problems. T3 - ZIB-Report - 07-13 KW - incompressible flows KW - shallow water equations KW - projection method KW - stability KW - mixed finite elements KW - inf-sup-condition Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9562 ER - TY - GEN A1 - Geerdes, Hans-Florian A1 - Eisenblätter, Andreas T1 - Reconciling Theory and Practice: A Revised Pole Equation for W-CDMA Cell Powers N2 - The performance evaluation of W-CDMA networks is intricate as cells are strongly coupled through interference. Pole equations have been developed as a simple tool to analyze cell capacity. Numerous scientific contributions have been made on their basis. In the established forms, the pole equations rely on strong assumptions such as homogeneous traffic, uniform users, and constant downlink orthogonality factor. These assumptions are not met in realistic scenarios. Hence, the pole equations are typically used during initial network dimensioning only. Actual network (fine-) planning requires a more faithful analysis of each individual cell's capacity. Complex analytical analysis or Monte-Carlo simulations are used for this purposes. In this paper, we generalize the pole equations to include inhomogeneous data. We show how the equations can be parametrized in a cell-specific way provided the transmit powers are known. This allows to carry over prior results to realistic settings. This is illustrated with an example: Based on the pole equation, we investigate the accuracy of average snapshot'' approximations for downlink transmit powers used in state-of-the-art network optimization schemes. We confirm that the analytical insights apply to practice-relevant settings on the basis of results from detailed Monte-Carlo simulation on realistic datasets. T3 - ZIB-Report - 07-11 Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9543 ER - TY - GEN A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Transparent boundary conditons for time-dependent problems N2 - A new approach to derive transparent boundary conditions (TBCs) for wave, Schrödinger, heat and drift-diffusion equations is presented. It relies on the pole condition and distinguishes between physical reasonable and unreasonable solutions by the location of the singularities of the spatial Laplace transform of the exterior solution. To obtain a numerical algorithm, a Möbius transform is applied to map the Laplace transform onto the unit disc. In the transformed coordinate the solution is expanded into a power series. Finally, equations for the coefficients of the power series are derived. These are coupled to the equation in the interior, and yield transparent boundary conditions. Numerical results are presented in the last section, showing that the error introduced by the new approximate TBCs decays exponentially in the number of coefficients. T3 - ZIB-Report - 07-12 KW - transparent boundary condition KW - non-reflecting boundary condition KW - pole condition KW - wave equation KW - Schrödinger equation KW - drift diffusion equation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9558 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian A1 - Kutschka, Manuel T1 - Algorithms to Separate {0,1/2}-Chvatal-Gomory Cuts N2 - Chvatal-Gomory cuts are among the most well-known classes of cutting planes for general integer linear programs (ILPs). In case the constraint multipliers are either 0 or $\frac{1}{2}$, such cuts are known as $\{0,\frac{1}{2}\}$-cuts. It has been proven by Caprara and Fischetti (1996) that separation of $\{0,\frac{1}{2}\}$-cuts is NP-hard. In this paper, we study ways to separate $\{0,\frac{1}{2}\}$-cuts effectively in practice. We propose a range of preprocessing rules to reduce the size of the separation problem. The core of the preprocessing builds a Gaussian elimination-like procedure. To separate the most violated $\{0,\frac{1}{2}\}$-cut, we formulate the (reduced) problem as integer linear program. Some simple heuristic separation routines complete the algorithmic framework. Computational experiments on benchmark instances show that the combination of preprocessing with exact and/or heuristic separation is a very vital idea to generate strong generic cutting planes for integer linear programs and to reduce the overall computation times of state-of-the-art ILP-solvers. T3 - ZIB-Report - 07-10 KW - {0 KW - 1/2}-Chvatal-Gomory cuts KW - separation algorithms KW - integer programming Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9531 ER - TY - GEN T1 - Jahresbericht 2006 T3 - Jahresbericht - 2006 KW - Annual Report Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9812 SN - 0934-5892 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Lutz-Westphal, Brigitte T1 - Bessel'scher Irrgarten N2 - Dieser Artikel berichtet über eine erfolgreiche Schüleraktivität, die seit Jahren am Zuse-Institut Berlin (ZIB) bei Besuchen von Schülergruppen erprobt und verfeinert worden ist. Das hier zusammengestellte Material ist gedacht als Basis für eine Unterrichtseinheit in Leistungskursen Mathematik an Gymnasien. Inhaltlich wird von einem zwar für Schüler (wie auch Lehrer) neuen, aber leicht fasslichen Gegenstand ausgegangen: der Drei-Term-Rekursion für Besselfunktionen. Die Struktur wird erklärt und in ein kleines Programm umgesetzt. Dazu teilen sich die Schüler selbstorganisierend in Gruppen ein, die mit unterschiedlichen Taschenrechnern "um die Wette" rechnen. Die Schüler und Schülerinnen erfahren unmittelbar die katastrophale Wirkung von an sich kleinen'' Rundungsfehlern, sie landen -- ebenso wie der Supercomputer des ZIB -- im Bessel'schen Irrgarten''. Die auftretenden Phänomene werden mathematisch elementar erklärt, wobei lediglich auf das Konzept der linearen Unabhängigkeit zurückgegriffen wird. Das dabei gewonnene vertiefte Verständnis fließt ein in die Konstruktion eines klassischen Algorithmus sowie eines wesentlich verbesserten Horner-artigen Algorithmus. T3 - ZIB-Report - 07-09 KW - Rundungsfehler KW - Drei-Term-Rekursionen KW - Bessel-Rekursion Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9525 ER - TY - GEN A1 - Raack, Christian A1 - Koster, Arie M.C.A. A1 - Wessäly, Roland T1 - On the strength of cut-based inequalities for capacitated network design polyhedra N2 - In this paper we study capacitated network design problems, differentiating directed, bidirected and undirected link capacity models. We complement existing polyhedral results for the three variants by new classes of facet-defining valid inequalities and unified lifting results. For this, we study the restriction of the problems to a cut of the network. First, we show that facets of the resulting cutset polyhedra translate into facets of the original network design polyhedra if the two subgraphs defined by the network cut are (strongly) connected. Second, we provide an analysis of the facial structure of cutset polyhedra, elaborating the differences caused by the three different types of capacity constraints. We present flow-cutset inequalities for all three models and show under which conditions these are facet-defining. We also state a new class of facets for the bidirected and undirected case and it is shown how to handle multiple capacity modules by Mixed Integer Rounding (MIR). T3 - ZIB-Report - 07-08 KW - cutset-polyhedra KW - flow-cutset inequalities KW - network design KW - mixed integer programming Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9512 ER - TY - GEN A1 - Imhof, Andres T1 - Zweieinhalb Jahre Open-Linking im KOBV-Portal: Ein Erfahrungsbericht N2 - Die Zentrale des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV) betreibt seit Januar 2004 das KOBV-Portal, in dem u.a. vielfältige Open-Linking-Dienste eingebunden sind. Dieser Beitrag erläutert Open-Linking allgemein und stellt die KOBV spezifischen Dienste im Detail vor. Dabei wird auch die Zugriffsentwicklung auf die KOBV-Open-Linking-Dienste evaluiert. Ein Ergebnis ist, dass signifikante Steigerungen der Nutzung erst dann bewirkt werden, wenn Maßnahmen durchgeführt werden, die erstens die Open-Linking-Dienste stärker ins Bewusstsein der NutzerInnen rücken und zweitens den Weg dorthin im KOBV-Portal verkürzen. Vor allem muss ein schneller Weg zu den Open-Linking-Diensten gewährleistet sein, um die Nutzung deutlich zu steigern. Um zusätzlich den Bekanntheitsgrad der Open-Linking-Dienste bundesweit zu erhöhen, regt die KOBV-Zentrale andere Bibliotheken und Verbünde dazu an, analoge Open-Linking-Dienste einzurichten. Auf diese Weise wird die Handhabung von Open-Linking selbstverständlicher. T3 - ZIB-Report - 07-06 KW - Open-Linking KW - Reference-Linking KW - kontextsensitives Linking KW - KOBV-Portal KW - KOBV-Dienste Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9499 ER - TY - GEN A1 - Schiela, Anton T1 - Barrier Methods for Optimal Control Problems with State Constraints N2 - We study barrier methods for state constrained optimal control problems with PDEs. In the focus of our analysis is the path of minimizers of the barrier subproblems with the aim to provide a solid theoretical basis for function space oriented path-following algorithms. We establish results on existence, continuity and convergence of this path. Moreover, we consider the structure of barrier subdifferentials, which play the role of dual variables. T3 - ZIB-Report - 07-07 KW - interior point methods in function space KW - optimal control KW - state constraints Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9504 ER - TY - GEN A1 - Jokar, Sadegh A1 - Pfetsch, Marc T1 - Exact and Approximate Sparse Solutions of Underdetermined Linear Equations N2 - In this paper, we empirically investigate the NP-hard problem of finding sparse solutions to linear equation systems, i.e., solutions with as few nonzeros as possible. This problem has received considerable interest in the sparse approximation and signal processing literature, recently. We use a branch-and-cut approach via the maximum feasible subsystem problem to compute optimal solutions for small instances and investigate the uniqueness of the optimal solutions. We furthermore discuss five (modifications of) heuristics for this problem that appear in different parts of the literature. For small instances, the exact optimal solutions allow us to evaluate the quality of the heuristics, while for larger instances we compare their relative performance. One outcome is that the basis pursuit heuristic performs worse, compared to the other methods. Among the best heuristics are a method due to Mangasarian and a bilinear approach. T3 - ZIB-Report - 07-05 KW - sparse representations KW - basis pursuit KW - orthogonal matching pursuit KW - maximum feasible subsystem problem Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9488 ER - TY - GEN A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Jahnke, Tobias A1 - Wulkow, Michael T1 - Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation N2 - \begin{abstract} In systems biology, the stochastic description of biochemical reaction kinetics is increasingly being employed to model gene regulatory networks and signalling pathways. Mathematically speaking, such models require the numerical solution of the underlying evolution equat ion, also known as the chemical master equation (CME). Up to now, the CME has almost exclusively been treated by Monte-Carlo techniques, the most prominent of which is the simulation algorithm suggest ed by Gillespie in 1976. Since this algorithm requires an update for each single reaction event, realizations can be computationally very costly. As an alternative, we here propose a novel approach, which focuses on the discrete partial differential equation (PDE) structure of the CME and thus allows to adopt ideas from adaptive discrete Galerkin methods (as designed by two of the present authors in 1989), which have proven to be highly efficient in the mathematical modelling of polyreaction kinetics. Among the two different options of discretizing the CME as a discrete PDE, the method of lines approach (first space, then time) and the Rothe method (first time, then space), we select the latter one for clear theoretical and algorithmic reasons. First numeric al experiments at a challenging model problem illustrate the promising features of the proposed method and, at the same time, indicate lines of necessary further research. \end{abstract} T3 - ZIB-Report - 07-04 KW - adaptive discrete Galerkin methods KW - adaptive Rothe method KW - discrete Chebyshev polynomials KW - stochastic reactions kinetics KW - chemical master equation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9471 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Models for Railway Track Allocation N2 - This article is about the optimal track allocation problem (OPTRA) to find, in a given railway network, a conflict free set of train routes of maximum value. We study two types of integer programming formulations: a standard formulation that models block conflicts in terms of packing constraints, and a new extended formulation that is based on additional configuration' variables. We show that the packing constraints in the standard formulation stem from an interval graph, and that they can be separated in polynomial time. It follows that the LP relaxation of a strong version of this model, including all clique inequalities from block conflicts, can be solved in polynomial time. We prove that the extended formulation produces the same LP bound, and that it can also be computed with this model in polynomial time. Albeit the two formulations are in this sense equivalent, the extended formulation has advantages from a computational point of view, because it features a constant number of rows and is therefore amenable to standard column generation techniques. Results of an empirical model comparison on mesoscopic data for the Hannover-Fulda-Kassel region of the German long distance railway network are reported. T3 - ZIB-Report - 07-02 KW - Railway Slot Allocation KW - Train Timetabling KW - Combinatorial Optimization KW - Linear and Integer Programming Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9451 ER - TY - GEN A1 - Zilske, Michael A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Adaptive Remeshing of Non-Manifold Surfaces N2 - We present a unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines, which together form a feature skeleton. Our method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature skeleton and the input mesh. T3 - ZIB-Report - 07-01 KW - remeshing KW - non-manifold KW - mesh quality optimization Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9445 ER - TY - THES A1 - Weber, Marcus T1 - Meshless Methods in Confirmation Dynamics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10232 ER - TY - THES A1 - Berthold, Timo T1 - Primal Heuristics for Mixed Integer Programs N2 - A lot of problems arising in Combinatorial Optimization and Operations Research can be formulated as Mixed Integer Programs (MIP). Although MIP-solving is an NP-hard optimization problem, many practically relevant instances can be solved in reasonable time. In modern MIP-solvers like the branch-cut-and-price-framework SCIP, primal heuristics play a major role in finding and improving feasible solutions at the early steps of the solution process. This helps to reduce the overall computational effort, guides the remaining search process, and proves the feasibility of the MIP model. Furthermore, a heuristic solution with a small gap to optimality often is sufficient in practice. We investigate 16 different heuristics, all of which are available in SCIP. Four of them arise from the literature of the last decade, nine are specific implementations of general heuristic ideas, three have been newly developed. We present an improved version of the feasibility pump heuristic by Fischetti et al., which in experiments produced solutions with only a third of the optimality gap compared to the original version. Furthermore, we introduce two new Large Neighborhood Search (LNS) heuristics. Crossover is an LNS improvement heuristic making use of similarities of diverse MIP solutions to generate new incumbent solutions. RENS is an LNS rounding heuristic which evaluates the space of all possible roundings of a fractional LP-solution. This heuristic makes it possible to determine whether a point can be rounded to an integer solution and which is the best possible rounding. We conclude with a computational comparison of all described heuristics. It points out that a single heuristic on its own has only a slight impact on the overall performance of SCIP, but the combination of all of them reduces the running time by a factor of two compared to a version without any heuristics. Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10293 ER - TY - THES A1 - Lichtenstein, Tom T1 - Implementation eines Resourcebrokers im Kontext eines Grid-Datenmanagement-Systems Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9968 ER - TY - THES A1 - Meltzer, Jörg T1 - Vergleich von Co-Reservierungs-Algorithmen in Grid-Umgebungen N2 - In dieser Arbeit werden effiziente Co-Reservierungs-Algorithmen vorgestellt, mit denen Rechenressourcen mehrerer Cluster im Grid reserviert werden können. Es werden fünf Algorithmen vorgestellt, die flexible Co-Reservierungsanfragen ermöglichen. In einer Co-Reservierungsanfrage müssen die angeforderten CPUs der Teilreservierungen exakt festgelegt werden. Die Cluster und die Startzeiten, bei denen die Teilreservierungen durchgeführt werden, ermittelt ein Co-Reservierungs-Algorithmus erst bei der Anfragebearbeitung. Die Benutzer können die Startzeit in der Anfrage eingrenzen, in dem sie eine früheste Startzeit und eine Deadline angeben. In den bisher entwickelten Reservierungsverfahren können Benutzer nur starre Co-Reservierungsanfragen stellen, in denen sie für alle Attribute der Teilreservierungen exakte Werte angeben müssen. Eine flexible Co-Reservierungsanfrage erlaubt einem Grid-Reservierungsdienst optimierte Reservierungsvarianten durchzuführen, da er aus vielen Reservierungsvarianten auswählen kann. Die Anwendungen von lokalen Benutzern können durch die Grid-Reservierungen verzögert werden. Bei der Auswahl der Reservierungsvarianten kann ein Grid-Reservierungsdienst dies berücksichtigen und den negativen Einfluß der Grid-Reservierungen verringern. Bei zwei Co-Reservierungs-Algorithmen werden auch zusätzliche Sortiervorgaben des Klienten bei der Auswahl der Reservierungsvarianten beachtet. Die Algorithmen wurden durch Simulationen mit dem Workload eines realen großen Supercomputers ausgewertet. Die Untersuchungen zeigen, daß sowohl die lokalen als auch die Grid-Benutzer von den flexiblen Anfragen profitieren können. Den lokalen Benutzern wurden die Ressourcen weniger oft durch zu früh gestellte Reservierungsanfragen entzogen. Die Grid- Benutzer können ihrerseits komfortabel eine optimierte Reservierungsvariante durchführen lassen. Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9972 ER - TY - THES A1 - Moser, Monika T1 - Platzierung von Replikaten in Verteilten Systemen Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9995 ER - TY - THES A1 - Riemer, Alexander T1 - Accuracy, Stability, Convergence of Rigorous Thermodynamic Sampling Methods Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10052 ER - TY - GEN A1 - Weber, Marcus A1 - Kube, Susanna A1 - Riemer, Alexander A1 - Bujotzek, Alexander T1 - Efficient Sampling of the Stationary Distribution of Metastable Dynamical Systems N2 - In this article we aim at an efficient sampling of the stationary distribution of dynamical systems in the presence of metastabilities. In the past decade many sophisticated algorithms have been inven ted in this field. We do not want to simply add a further one. We address the problem that one has applied a sampling algorithm for a dynamical system many times. This leads to different samplings which more or less represent the stationary distribution partially very well, but which are still far away from ergodicity or from the global stationary distribution. We will show how these samplings can be joined together in order to get one global sampling of the stationary distribution. T3 - ZIB-Report - 07-03 KW - dynamical systems KW - stationary distribution KW - rare events KW - metastability KW - cluster analysis Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9467 ER - TY - GEN A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Roitzsch, Rainer A1 - Lines, Glenn Terje T1 - Adaptive Finite Element Simulation of Ventricular Fibrillation Dynamics N2 - The dynamics of ventricular fibrillation caused by irregular excitation is simulated in the frame of the monodomain model with an action potential model due to Aliev-Panfilov for a human 3D geometry. The numerical solution of this multiscale reaction-diffusion problem is attacked by algorithms which are fully adaptive in both space and time (code library {\sc Kardos}). The obtained results clearly demonstrate an accurate resolution of the cardiac potential during the excitation and the plateau phases (in the regular cycle) as well as after a reentrant excitation (in the irregular cycle). T3 - ZIB-Report - 06-49 KW - reaction-diffusion equations KW - Aliev-Panfilov model KW - electrocardiology KW - adaptive finite elements KW - adaptive time integration KW - adaptive Rothe method Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9431 ER - TY - GEN A1 - Kaibel, Volker A1 - Peinhardt, Matthias A1 - Pfetsch, Marc T1 - Orbitopal Fixing N2 - The topic of this paper are integer programming models in which a subset of 0/1-variables encode a partitioning of a set of objects into disjoint subsets. Such models can be surprisingly hard to solve by branch-and-cut algorithms if the permutation of the subsets of the partition is irrelevant. This kind of symmetry unnecessarily blows up the branch-and-cut tree. We present a general tool, called orbitopal fixing, for enhancing the capabilities of branch-and-cut algorithms in solving this kind of symmetric integer programming models. We devise a linear time algorithm that, applied at each node of the branch-and-cut tree, removes redundant parts of the tree produced by the above mentioned permutations. The method relies on certain polyhedra, called orbitopes, which have been investigated in (Kaibel and Pfetsch (2006)). However, it does not add inequalities to the model, and thus, it does not increase the difficulty of solving the linear programming relaxations. We demonstrate the computational power of orbitopal fixing at the example of a graph partitioning problem motivated from frequency planning in mobile telecommunication networks. T3 - ZIB-Report - 06-48 KW - symmetry breaking KW - variable fixing KW - orbitopes Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9422 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Koster, Arie M.C.A. A1 - Raack, Christian A1 - Wessäly, Roland T1 - Two-layer Network Design by Branch-and-Cut featuring MIP-based Heuristics N2 - This paper deals with MIP-based primal heuristics to be used within a branch-and-cut approach for solving multi-layer telecommunication network design problems. Based on a mixed-integer programming formulation for two network layers, we present three heuristics for solving important subproblems, two of which solve a sub-MIP. On multi-layer planning instances with many parallel logical links, we show the effectiveness of our heuristics in finding good solutions early in the branch-and-cut search tree. T3 - ZIB-Report - 06-47 KW - multi-layer network design KW - integer programming KW - branch-and-cut KW - heuristics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9412 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Waiting times for M/M systems under generalized processor sharing N2 - We consider a system where the arrivals form a Poisson process and the required service times of the requests are exponentially distributed. According to the generalized processor sharing discipline, each request in the system receives a fraction of the capacity of one processor which depends on the actual number of requests in the system. We derive systems of ordinary differential equations for the LST and for the moments of the conditional waiting time of a request with given required service time as well as a stable and fast recursive algorithm for the LST of the second moment of the conditional waiting time, which in particular yields the second moment of the unconditional waiting time. Moreover, asymptotically tight upper bounds for the moments of the conditional waiting time are given. The presented numerical results for the first two moments of the sojourn times in the $M/M/m-PS$ system show that the proposed algorithms work well. T3 - ZIB-Report - 06-46 KW - Poisson arrivals KW - exponential service times KW - generalized processor sharing KW - many-server KW - permanent customers KW - M/M/m-PS KW - waiting time KW - sojourn t Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9404 ER - TY - GEN A1 - Lopez-Fernandez, Maria A1 - Lubich, Christian A1 - Schädle, Achim T1 - Adaptive, Fast and Oblivious Convolution in Evolution Equations with Memory N2 - To approximate convolutions which occur in evolution equations with memory terms, a variable-stepsize algorithm is presented for which advancing $N$ steps requires only $O(N\log N)$ operations and $O(\log N)$ active memory, in place of $O(N^2)$ operations and $O(N)$ memory for a direct implementation. A basic feature of the fast algorithm is the reduction, via contour integral representations, to differential equations which are solved numerically with adaptive step sizes. Rather than the kernel itself, its Laplace transform is used in the algorithm. The algorithm is illustrated on three examples: a blow-up example originating from a Schrödinger equation with concentrated nonlinearity, chemical reactions with inhibited diffusion, and viscoelasticity with a fractional order constitutive law. T3 - ZIB-Report - 06-45 KW - convolution quadrature KW - adaptivity KW - Volterra integral equations KW - numerical inverse Laplace transform KW - anomalous diffusion KW - fractional order visco Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9399 ER - TY - GEN A1 - May, Patrick A1 - Bauer, Markus A1 - Köberle, Christian A1 - Klau, Gunnar T1 - A computational approach to microRNA detection N2 - During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures. T3 - ZIB-Report - 06-44 KW - microRNA Smith-Waterman RNA folding Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9383 ER - TY - GEN A1 - Harks, Tobias T1 - Nash Equilibria in Online Sequential Routing Games N2 - In this paper, we study the efficiency of Nash equilibria for a sequence of nonatomic routing games. We assume that the games are played consecutively in time in an online fashion: by the time of playing game $i$, future games $i+1,\dots,n$ are not known, and, once players of game $i$ are in equilibrium, their corresponding strategies and costs remain fixed. Given a sequence of games, the cost for the sequence of Nash equilibria is defined as the sum of the cost of each game. We analyze the efficiency of a sequence of Nash equilibria in terms of competitive analysis arising in the online optimization field. Our main result states that the online algorithm $\sl {SeqNash}$ consisting of the sequence of Nash equilibria is $\frac{4n}{2+n}$-competitive for affine linear latency functions. For $n=1$, this result contains the bound on the price of anarchy of $\frac{4}{3}$ for affine linear latency functions of Roughgarden and Tardos [2002] as a special case. Furthermore, we analyze a problem variant with a modified cost function that reflects the total congestion cost, when all games have been played. In this case, we prove an upper bound of $\frac{4n}{2+n}$ on the competitive ratio of $\sl {SeqNash}$. We further prove a lower bound of $\frac{3n-2}{n}$ of $\sl {SeqNash}$ showing that for $n=2$ our upper bound is tight. T3 - ZIB-Report - 06-43 KW - Congestion Game KW - Online Optimization KW - Nash equilibria Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9376 ER - TY - GEN A1 - Deuflhard, Peter A1 - Krause, Rolf A1 - Ertel, Susanne T1 - A Contact-Stabilized Newmark Method for Dynamical Contact Problems N2 - The numerical integration of dynamical contact problems often leads to instabilities at contact boundaries caused by the non-penetration condition between bodies in contact. Even a recent energy dissipative modification due to Kane et al. (1999), which discretizes the non-penetration constraints implicitly, is not able to circumvent artificial oscillations. For this reason, the present paper suggests a contact stabilization which avoids artificial oscillations at contact interfaces and is also energy dissipative. The key idea of this contact stabilization is an additional $L^2$-projection at contact interfaces, which can easily be added to any existing time integration scheme. In case of a lumped mass matrix, this projection can be carried out completely locally, thus creating only negligible additional numerical cost. For the new scheme, an elementary analysis is given, which is confirmed by numerical findings in an illustrative test example (Hertzian two body contact). T3 - ZIB-Report - 06-42 KW - Numerical problems in dynamical systems KW - nonlinear stabilities Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9361 ER - TY - GEN A1 - Schiela, Anton T1 - A continuity result for Nemyckii Operators and some applications in PDE constrained optimal control N2 - This work explores two applications of a classical result on the continuity of Nemyckii operators to optimal control with PDEs. First, we present an alternative approach to the analysis of Newton's method for function space problems involving semi-smooth Nemyckii operators. A concise proof for superlinear convergence is presented, and sharpened bounds on the rate of convergence are derived. Second, we derive second order sufficient conditions for problems, where the underlying PDE has poor regularity properties. We point out that the analytical structure in both topics is essentially the same. T3 - ZIB-Report - 06-41 KW - continuity of Nemyckii Operators KW - Newton methods in function space KW - optimal control KW - second order sufficient conditions Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9354 ER - TY - THES A1 - Lutz-Westphal, Brigitte T1 - Kombinatorische Optimierung –Inhalte und Methoden für einen authentischen Mathematikunterricht N2 - wird nachgereicht Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10608 ER - TY - GEN A1 - Lügger, Joachim T1 - Neustart für Bibliotheken ins Informationszeitalter N2 - Wir erleben zu Beginn des aufkommenden Informationszeitalters mit dem Siegeszug von Google und anderen Internet-Technologien einen Wandel im Verhalten von Wissenschaftlern und Studenten, der mit dem Einsatz von {\sl Google Scholar} und {\sl Google Book Search} einen Paradigmenwechsel für Bibliotheken und Informationsversorger gleichkommt. Der Artikel untersucht die technischen Hintergründe für den Erfolg dieser besonderen Art des Information Retrievals: Fulltext Indexing und Citation Ranking als besondere Form des Information Minig. Er diskutiert Stärken und auch Schwächen des Google-Ansatzes. Der Autor stellt sich auch der Frage, unter welchen Bedingungen es möglich ist, ein zu {\sl Google Scholar} und der {\sl Google Book Search} konkurrenzfähiges Retrieval in der Landschaft der Bibliotheken und Bibliotheksverbünde zu entrichten. Die These ist, dass dieses unter Einsatz des {\sl Open Source} Indexierers {\sl Lucene} und des Web-Robots {\sl Nutch} möglich ist. Bibliotheken können durch gezielten Einsatz solcher Internet-Technologien dem Nutzer die Leistungen, welche Google uns mit seinen Tools im {\sl Visible Web} und mit Referenzen auf {\sl Citations} in der Welt der Literatur zur Verfügung stellt, in vergleichbarer Art auch für ihre eigenen durch Lizenzen geschützten digitalen Journale und ihre speziellen lokal verfügbaren Ressourcen, auf die Internet-Suchmaschinen keine Zugriff haben, anbieten. Es besteht die Hoffnung, dass Nutzer dann nicht - wie in einer kürzlichen Studie des OCLC konstatiert - überwiegend im Internet verbleiben, sondern bei ihrer Suche auch den Weg zu den Angeboten der örtlichen Bibliothek attraktiv finden. T3 - ZIB-Report - 06-40 KW - Information Retrieval KW - Volltextindizierung KW - Citation-Ranking KW - Suchmaschinen Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9347 ER - TY - GEN A1 - Weber, Marcus A1 - Walter, Lionel A1 - Kube, Susanna A1 - Deuflhard, Peter T1 - Stable computation of probability densities for metastable dynamical systems N2 - Whenever the invariant stationary density of metastable dynamical systems decomposes into almost invariant partial densities, its computation as eigenvector of some transition probability matrix is an ill-conditioned problem. In order to avoid this computational difficulty, we suggest to apply an aggregation/disaggregation method which only addresses wellconditioned sub-problems and thus results in a stable algorithm. In contrast to existing methods, the aggregation step is done via a sampling algorithm which covers only small patches of the sampling space. Finally, the theoretical analysis is illustrated by two biomolecular examples. T3 - ZIB-Report - 06-39 KW - dynamical systems KW - metastability KW - molecular conformations KW - cluster analysis KW - sampling KW - aggregation/disaggregation KW - domain decomposition Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9331 ER - TY - GEN A1 - Stephan, Rüdiger T1 - Facets of the (s,t)-p-path polytope N2 - \noindent We give a partial description of the $(s,t)-p$-path polytope of a directed graph $D$ which is the convex hull of the incidence vectors of simple directed $(s,t)$-paths in $D$ of length $p$. First, we point out how the $(s,t)-p$-path polytope is located in the family of path and cycle polyhedra. Next, we give some classes of valid inequalities which are very similar to inequalities which are valid for the $p$-cycle polytope, that is, the convex hull of the incidence vectors of simple cycles of length $p$ in $D$. We give necessary and sufficient conditions for these inequalities to be facet defining. Furthermore, we consider a class of inequalities that has been identifie d to be valid for $(s,t)$-paths of cardinality at most $p$. Finally, we transfer the results to related polytopes, in particular, the undirected counterpart of the $(s,t)-p$-path polytope. T3 - ZIB-Report - 06-38 Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9328 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Matera, Sebastian A1 - Wilmanski, Krzysztof T1 - Adaptive Linearly Implicit Methods for Linear Poroelastic Equations N2 - Adaptive numerical methods in time and space are introduced and studied for linear poroelastic models in two and three space dimensions. We present equivalent models for linear poroelasticity and choose both the {\em displacement--pressure} and the {\em stress--pressure} formulation for our computations. Their discretizations are provided by means of linearly implicit schemes in time and linear finite elements in space. Our concept of adaptivity opens a way to a fast and reliable simulation of different loading cases defined by corresponding boundary conditions. We present some examples using our code {\sf Kardos} and show that the method works efficiently. In particular, it could be used in the simulation of some bone healing models. T3 - ZIB-Report - 06-37 KW - Poroelasticity KW - Biot's model KW - bone healing KW - adaptive finite elements KW - adaptive time integration KW - Rosenbrock methods Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9312 ER - TY - GEN A1 - Kube, Susanna A1 - Weber, Marcus T1 - Coarse Grained Molecular Kinetics N2 - The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by clustering methods like the Robust Perron Cluster Analysis (PCCA+). Up to now it is an open question how this coarse graining in space can be transformed to a coarse graining of the Markov chain while preserving the essential dynamic information. In the following article we aim at a consistent coarse graining of transition probabilities or rates on the basis of metastable conformations such that important physical and mathematical relations are preserved. This approach is new because PCCA+ computes molecular conformations as linear combinations of the dominant eigenvectors of the transition matrix which does not hold for other clustering methods. T3 - ZIB-Report - 06-35 Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9299 ER - TY - GEN A1 - Daubechies, Ingrid A1 - Teschke, Gerd A1 - Vese, Luminita T1 - Iteratively Solving Linear Inverse Problems under General Convex Contraints N2 - We consider linear inverse problems where the solution is assumed to fulfill some general homogeneous convex constraint. We develop an algorithm that amounts to a projected Landweber iteration and that provides and iterative approach to the solution of this inverse problem. For relatively moderate assumptions on the constraint we can always prove weak convergence of the iterative scheme. In certain cases, i.e. for special families of convex constraints, weak convergence implies norm convergence. The presented approach covers a wide range of problems, e.g. Besov- or BV-restoration for which we present also numerical experiments in the context of image processing. T3 - ZIB-Report - 06-36 KW - Linear Inverse Problems KW - Landweber Iteration KW - Besov- and BV Image Restoration Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9304 ER - TY - GEN A1 - Imhof, Andres T1 - RSWK/SWD und Faceted Browsing: neue Möglichkeiten einer inhaltlich-intuitiven Navigation N2 - Das deutschsprachige Bibliothekswesen verfügt mit den \glqq Regeln für den Schlagwortkatalog \grqq (RSWK) unter Verwendung der \glqq Schlagwortnormdatei \grqq (SWD) über ein Instrumentarium, welches zusammen mit einem \glqq Faceted Browsing \grqq das bisher bestehende Angebot für ein Information Retrieval optimal ergänzen kann. Die Verbindung zwischen Standardvokabular (SWD) und Kettenbildung (RSWK) einerseits und eine nach Facetten-Eigenschaften gegliederte Navigation andererseits unterstützt bestmöglich eine inhaltlich bezogene Recherche. Die Stärken und Schwächen der RSWK/SWD werden erörtert und auch Klassifikationen (DDC und RVK) als mögliche Facetten diskutiert. T3 - ZIB-Report - 06-34 KW - RSWK KW - SWD KW - Faceted Browsing KW - Facetten KW - facettierte Navigation KW - Information Retrieval Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9289 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Fomin, Fedor V. A1 - Koster, Arie M.C.A. A1 - Kratsch, Dieter A1 - Thilikos, Dimitrios M. T1 - On exact algorithms for treewidth N2 - We give experimental and theoretical results on the problem of computing the treewidth of a graph by exact exponential time algorithms using exponential space or using only polynomial space. We first report on an implementation of a dynamic programming algorithm for computing the treewidth of a graph with running time $O^\ast(2^n)$. This algorithm is based on the old dynamic programming method introduced by Held and Karp for the {\sc Tra veling Salesman} problem. We use some optimizations that do not affect the worst case running time but improve on the running time on actual instances and can be seen to be practical for small instances. However, our experiments show that the space use d by the algorithm is an important factor to what input sizes the algorithm is effective. For this purpose, we settle the problem of computing treewidth under the restriction that the space used is only polynomial. In this direction we give a simple $O^\ast(4^n)$ al gorithm that requires {\em polynomial} space. We also show that with a more complicated algorithm, using balanced separators, {\sc Treewidth} can be computed in $O^\ast(2.9512^n)$ time and polynomial space. T3 - ZIB-Report - 06-32 KW - treewidth KW - exponential algorithms Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9265 ER - TY - GEN A1 - Meyer, Holger A1 - Moll, Sebastian A1 - Cordes, Frank A1 - Weber, Marcus T1 - ConFlow? A new space-based Application for complete Conformational Analysis of Molecules N2 - Biochemical interactions are determined by the 3D-structure of the involved components - thus the identification of conformations is a key for many applications in rational drug design. {\sf ConFlow} is a new multilevel approach to conformational analysis with main focus on completeness in investigation of conformational space. In contrast to known conformational analysis, the starting point for design is a space-based description of conformational areas. A tight integration of sampling and analysis leads to an identification of conformational areas simultaneously during sampling. An incremental decomposition of high-dimensional conformational space is used to guide the analysis. A new concept for the description of conformations and their path connected components based on convex hulls and {\em Hypercubes}is developed. The first results of the {\sf ConFlow} application constitute a 'proof of concept' and are further more highly encouraging. In comparison to conventional industrial applications, {\sf ConFlow} achieves higher accuracy and a specified degree of completeness with comparable effort. T3 - ZIB-Report - 06-31 KW - conformational-analysis in-silico-screening drug-design Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9258 ER - TY - GEN A1 - Kaibel, Volker A1 - Koch, Thorsten T1 - Mathematik für den Volkssport N2 - "`Volkssport Sudoku"' titelt der Stern in seiner Ausgabe vom 24. Mai2006. In der Tat traut sich derzeit kaum noch eine Zeitung, ohne Sudoku zu erscheinen. Die Begeisterung am Lösen dieser Zahlenrätsel offenbart eine unvermutete Freude am algorithmischen Arbeiten. Mathematisch kann man Sudokus als lineare diophantische Gleichungssysteme mit Nichtnegativitätsbedingungen formulieren. Solche ganzzahligen linearen Programme sind die wichtigsten Modellierungswerkzeuge in zahlreichen Anwendungsgebieten wie z.B. der Optimierung von Telekommunikations- und Verkehrsnetzen. Moderne Verfahren zur Lösung dieser Optimierungsprobleme sind durch Sudokus allerdings deutlich weniger zu beeindrucken als Zeitungsleser. T3 - ZIB-Report - 06-28 KW - Sudoku KW - Integer Programming KW - General Public Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9225 ER - TY - GEN A1 - Abboud, Nadine A1 - Grötschel, Martin A1 - Koch, Thorsten T1 - Mathematical Methods for Physical Layout of Printed Circuit Boards: An Overview N2 - This article surveys mathematical models and methods used for physical PCB layout, i.e., component placement and wire routing. The main concepts are briefly described together with relevant references. T3 - ZIB-Report - 06-29 KW - PCB Design KW - placement KW - routing Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9231 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Wagler, Annegret T1 - The extreme points of QSTAB(G) and its implications N2 - Perfect graphs constitute a well-studied graph class with a rich structure, reflected by many characterizations w.r.t different concepts. Perfect graphs are, e.g., characterized as precisely those graphs $G$ where the stable set polytope STAB$(G)$ coincides with the clique constraint stable set polytope QSTAB$(G)$. For all imperfect graphs STAB$(G) \subset$ QSTAB$(G)$ holds and, therefore, it is natural to measure imperfection in terms of the difference between STAB$(G)$ and QSTAB$(G)$. Several concepts have been developed in this direction, for instance the dilation ratio of STAB$(G)$ and QSTAB$(G)$ which is equivalent to the imperfection ratio imp$(G)$ of $G$. To determine imp$(G)$, both knowledge on the facets of STAB$(G)$ and the extreme points of QSTAB$(G)$ is required. The anti-blocking theory of polyhedra yields all {\em dominating} extreme points of QSTAB$(G)$, provided a complete description of the facets of STAB$(\overline G)$ is known. As this is typically not the case, we extend the result on anti-blocking polyhedra to a {\em complete} characterization of the extreme points of QSTAB$(G)$ by establishing a 1-1 correspondence to the facet-defining subgraphs of $\overline G$. We discuss several consequences, in particular, we give alternative proofs of several famous results. T3 - ZIB-Report - 06-30 KW - perfect graphs KW - imperfection ratio KW - stable set polytope Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9249 ER - TY - GEN A1 - Harks, Tobias A1 - Heinz, Stefan A1 - Pfetsch, Marc T1 - Competitive Online Multicommodity Routing N2 - We study online multicommodity minimum cost routing problems in networks, where commodities have to be routed sequentially. Arcs are equipped with load dependent price functions defining the routing weights. We discuss an online algorithm that routes each commodity by minimizing a convex cost function that depends on the demands that are previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is $4K/2+K$-competitive, where $K$ is the number of commodities. For the parallel arc case this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably. T3 - ZIB-Report - 06-27 KW - Online Optimization KW - Routing KW - Telecommunications Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9212 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the stability of the multi-queue multi-server processor sharing with limited service N2 - We consider a multi-queue multi-server system with $n$ servers (processors) and $m$ queues. At the system there arrives a stationary and ergodic stream of $m$ different types of requests with service requirements which are served according to the following $k$-limited head of the line processor sharing discipline: The first $k$ requests at the head of the $m$ queues are served in processor sharing by the $n$ processors, where each request may receive at most the capacity of one processor. By means of sample path analysis and Loynes' monotonicity method, a stationary and ergodic state process is constructed, and a necessary as well as a sufficient condition for the stability of the $m$ separate queues are given, which are tight within the class of all stationary ergodic inputs. These conditions lead to tight necessary and sufficient conditions for the whole system, also in case of permanent customers, generalizing an earlier result by the authors for the case of $n$=$k$=1. T3 - ZIB-Report - 06-25 KW - head of the line processor sharing KW - thread pools KW - many queues KW - many servers KW - general input KW - batch arrivals KW - permanent customers KW - marked point p Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9199 ER - TY - GEN A1 - May, Patrick A1 - Steinke, Thomas T1 - THESEUS - Protein Structure Prediction at ZIB N2 - THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004. T3 - ZIB-Report - 06-24 KW - Protein Structure Prediction KW - Bioinformatics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9184 ER - TY - GEN T1 - Jahresbericht 2005 T3 - Jahresbericht - 2005 KW - Annual Report Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9804 SN - 0934-5892 ER - TY - GEN A1 - Walter, Lionel A1 - Weber, Marcus T1 - ConfJump : a fast biomolecular sampling method which drills tunnels through high mountains N2 - In order to compute the thermodynamic weights of the different metastable conformations of a molecule, we want to approximate the molecule's Boltzmann distribution in a reasonable time. This is an essential issue in computational drug design. The energy landscape of active biomolecules is generally very rough with a lot of high barriers and low regions. Many of the algorithms that perform such samplings (e.g. the hybrid Monte Carlo method) have difficulties with such landscapes. They are trapped in low-energy regions for a very long time and cannot overcome high barriers. Moving from one low-energy region to another is a very rare event. For these reasons, the distribution of the generated sampling points converges very slowly against the thermodynamically correct distribution of the molecule. The idea of ConfJump is to use $a~priori$ knowledge of the localization of low-energy regions to enhance the sampling with artificial jumps between these low-energy regions. The artificial jumps are combined with the hybrid Monte Carlo method. This allows the computation of some dynamical properties of the molecule. In ConfJump, the detailed balance condition is satisfied and the mathematically correct molecular distribution is sampled. T3 - ZIB-Report - 06-26 KW - Monte Carlo simulation KW - rare events KW - rough potential energy function KW - molecular dynamics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9204 ER - TY - GEN A1 - Achterberg, Tobias A1 - Grötschel, Martin A1 - Koch, Thorsten T1 - Software for Teaching Modeling of Integer Programming Problems N2 - Modern applications of mathematical programming must take into account a multitude of technical details, business demands, and legal requirements. Teaching the mathematical modeling of such issues and their interrelations requires real-world examples that are well beyond the toy sizes that can be tackled with the student editions of most commercial software packages. We present a new tool, which is freely available for academic use including complete source code. It consists of an algebraic modeling language and a linear mixed integer programming solver. The performance and features of the tool are in the range of current state-of-the-art commercial tools, though not in all aspects as good as the best ones. Our tool does allow the execution and analysis of large real-world instances in the classroom and can therefore enhance the teaching of problem solving issues. Teaching experience has been gathered and practical usability was tested in classes at several universities and a two week intensive block course at TU Berlin. The feedback from students and teachers has been very positive. T3 - ZIB-Report - 06-23 KW - Integer Programming KW - Modelling KW - MIP-Solver KW - Algebraic Modelling Languages KW - Teaching Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9176 ER - TY - GEN A1 - Kaibel, Volker A1 - Peinhardt, Matthias T1 - On the Bottleneck Shortest Path Problem N2 - The Bottleneck Shortest Path Problem is a basic problem in network optimization. The goal is to determine the limiting capacity of any path between two specified vertices of the network. This is equivalent to determining the unsplittable maximum flow between the two vertices. In this note we analyze the complexity of the problem, its relation to the Shortest Path Problem, and the impact of the underlying machine/computation model. T3 - ZIB-Report - 06-22 KW - unsplittable flow KW - linear time algorithm KW - shortest path Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9160 ER - TY - GEN A1 - Grötschel, Martin A1 - Hinrichs, Hinrich A1 - Schröer, Klaus A1 - Tuchscherer, Andreas T1 - Ein gemischt-ganzzahliges lineares Optimierungsmodell für ein Laserschweißproblem im Karosseriebau N2 - Wir beschäftigen uns mit dem Problem der Betriebsplanung von Laserschweißrobotern im Karosseriebau. Gegeben ist eine Menge von Schweißnähten, die innerhalb einer Fertigungszelle an einem Karosserieteil gefertigt werden müssen. Die Schweißnähte werden durch mehrere parallel betriebene Roboter bearbeitet. Die Aufgabe besteht darin, für jeden Roboter eine Reihenfolge und eine zeitliche Koordinierung seiner Bewegungen zu finden, so dass alle Schweißnähte innerhalb der Taktzeit der Fertigungszelle bearbeitet werden und so wenig Laserquellen wie möglich eingesetzt werden. Dabei müssen einige Nebenbedingungen berücksichtigt werden. Für dieses spezielle Schweißproblem haben wir eine Formulierung als gemischt-ganzzahliges lineares Programm entwickelt, welches sich für die untersuchten praktischen Fälle sehr schnell lösen lässt. T3 - ZIB-Report - 06-21 KW - Laserschweißen KW - Gemischt-ganzzahlige Optimierung Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9141 ER - TY - GEN A1 - Heinz, Stefan A1 - Kaibel, Volker A1 - Peinhardt, Matthias A1 - Rambau, Jörg A1 - Tuchscherer, Andreas T1 - LP-Based Local Approximation for Markov Decision Problems N2 - The standard computational methods for computing the optimal value functions of Markov Decision Problems (MDP) require the exploration of the entire state space. This is practically infeasible for applications with huge numbers of states as they arise, e.\,g., from modeling the decisions in online optimization problems by MDPs. Exploiting column generation techniques, we propose and apply an LP-based method to determine an $\varepsilon$-approximation of the optimal value function at a given state by inspecting only states in a small neighborhood. In the context of online optimization problems, we use these methods in order to evaluate the quality of concrete policies with respect to given initial states. Moreover, the tools can also be used to obtain evidence of the impact of single decisions. This way, they can be utilized in the design of policies. T3 - ZIB-Report - 06-20 KW - Markov decision problem KW - linear programming KW - column generation Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9131 ER - TY - GEN A1 - Shioura, Akiyoshi A1 - Tanaka, Ken'ichiro T1 - Polynomial-Time Algorithms for Linear and Convex Optimization on Jump Systems N2 - The concept of jump system, introduced by Buchet and Cunningham (1995), is a set of integer points with a certain exchange property. In this paper, we discuss several linear and convex optimization problems on jump systems and show that these problems can be solved in polynomial time under the assumption that a membership oracle for a jump system is available. We firstly present a polynomial-time implementation of the greedy algorithm for the minimization of a linear function. We then consider the minimization of a separable-convex function on a jump system, and propose the first polynomial-time algorithm for this problem. The algorithm is based on the domain reduction approach developed in Shioura (1998). We finally consider the concept of M-convex functions on constant-parity jump systems which has been recently proposed by Murota (2006). It is shown that the minimization of an M-convex function can be solved in polynomial time by the domain reduction approach. T3 - ZIB-Report - 06-19 KW - jump system KW - discrete convex function KW - bisubmodular function KW - bisubmodular polyhedron KW - polynomial-time algorithm Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9122 ER - TY - GEN A1 - Reinecke, Isabel A1 - Deuflhard, Peter T1 - A Complex Mathematical Model of the Human Menstrual Cycle N2 - This paper aims at presenting the complex coupled network of the human menstrual cycle to the interested community. Beyond the presently popular smaller models, where important network components arise only as extremely simplified source terms, we add: the GnRH pulse generator in the hypothalamus, receptor binding, and the biosynthesis in the ovaries. Simulation and parameter identification are left to a forthcoming paper. T3 - ZIB-Report - 06-18 Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9112 ER - TY - GEN A1 - Kaibel, Volker A1 - Pfetsch, Marc T1 - Packing and Partitioning Orbitopes N2 - We introduce orbitopes as the convex hulls of 0/1-matrices that are lexicographically maximal subject to a group acting on the columns. Special cases are packing and partitioning orbitopes, which arise from restrictions to matrices with at most or exactly one 1-entry in each row, respectively. The goal of investigating these polytopes is to gain insight into ways of breaking certain symmetries in integer programs by adding constraints, e.g., for a well-known formulation of the graph coloring problem. We provide a thorough polyhedral investigation of packing and partitioning orbitopes for the cases in which the group acting on the columns is the cyclic group or the symmetric group. Our main results are complete linear inequality descriptions of these polytopes by facet-defining inequalities. For the cyclic group case, the descriptions turn out to be totally unimodular, while for the symmetric group case, both the description and the proof are more involved. The associated separation problems can be solved in linear time. T3 - ZIB-Report - 06-17 KW - integer programming KW - symmetry breaking KW - lexicographic representatives Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9104 ER - TY - GEN A1 - Schiela, Anton T1 - Convergence of the Control Reduced Interior Point Method for PDE Constrained Optimal Control with State Constraints N2 - We propose a variant of the control reduced interior point method for the solution of state constrained problems. We show convergence of the corresponding interior point pathfollowing algorithm in function space. Morever, we provide error bounds for the iterates. T3 - ZIB-Report - 06-16 KW - interior point methods in function space KW - optimal control KW - state constraints Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9099 ER - TY - GEN A1 - Hülsermann, Ralf A1 - Jäger, Monika A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland A1 - Zymolka, Adrian T1 - Availability and Cost Based Evaluation of Demand-wise Shared Protection N2 - In this paper, we investigate the connection availabilities for the new protection scheme Demand-wise Shared Protection (DSP) and describe an appropriate approach for their computation. The exemplary case study on two realistic network scenarios shows that in most cases the availabilities for DSP are comparable with that for 1+1 path protection and better than in case of shared path protection. T3 - ZIB-Report - 06-15 KW - demand-wise shared protection KW - network availability KW - network optimization Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9080 ER - TY - GEN A1 - Csorba, Peter A1 - Lutz, Frank H. T1 - Graph Coloring Manifolds N2 - We introduce a new and rich class of graph coloring manifolds via the Hom complex construction of Lov\´{a}sz. The class comprises examples of Stiefel manifolds, series of spheres and products of spheres, cubical surfaces, as well as examples of Seifert manifolds. Asymptotically, graph coloring manifolds provide examples of highly connected, highly symmetric manifolds. T3 - ZIB-Report - 06-11 KW - graph coloring complexes KW - Hom complexes KW - flag complexes KW - graph coloring manifolds Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9043 ER - TY - GEN A1 - Hougardy, Stefan A1 - Lutz, Frank H. A1 - Zelke, Mariano T1 - Polyhedra of Genus 2 with 10 Vertices and Minimal Coordinates N2 - We give coordinate-minimal geometric realizations in general position of all 865 vertex-minimal triangulations of the orientable surface of genus 2 in the 4x4x4-cube. T3 - ZIB-Report - 06-12 KW - triangulated surfaces KW - minimal triangulations KW - polyhedral realizations Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9054 ER - TY - GEN A1 - Hougardy, Stefan A1 - Lutz, Frank H. A1 - Zelke, Mariano T1 - Polyhedra of Genus 3 with 10 Vertices and Minimal Coordinates N2 - We give coordinate-minimal geometric realizations in general position for 17 of the 20 vertex-minimal triangulations of the orientable surface of genus 3 in the 5x5x5-cube. T3 - ZIB-Report - 06-13 KW - triangulated surfaces KW - minimal triangulations KW - polyhedral realizations Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9064 ER - TY - GEN A1 - Lutz, Frank H. T1 - Combinatorial 3-Manifolds with 10 Vertices N2 - We give a complete enumeration of combinatorial 3-manifolds with 10 vertices: There are precisely 247882 triangulated 3-spheres with 10 vertices as well as 518 vertex-minimal triangulations of the sphere product $S^2 x S^1$ and 615 triangulations of the twisted sphere product $S^2 \underline{x} S^1$. An analysis of the 3-spheres with up to 10 vertices shows that all these spheres are shellable, but that there are 29 vertex-minimal non-shellable 3-balls with 9 vertices. T3 - ZIB-Report - 06-14 KW - triangulated manifolds KW - enumeration KW - minimal triangulations KW - shellability Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9071 ER - TY - GEN A1 - Lutz, Frank H. T1 - Enumeration and Random Realization of Triangulated Surfaces N2 - We discuss different approaches for the enumeration of triangulated surfaces. In particular, we enumerate all triangulated surfaces with 9 and 10 vertices. We also show how geometric realizations of orientable surfaces with few vertices can be obtained by choosing coordinates randomly. T3 - ZIB-Report - 06-07 KW - triangulated surfaces KW - polyhedral manifolds Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9012 ER - TY - GEN A1 - Lutz, Frank H. T1 - Triangulated Manifolds with Few Vertices: Combinatorial Manifolds N2 - In this survey on combinatorial properties of triangulated manifolds we discuss various lower bounds on the number of vertices of simplicial and combinatorial manifolds. Moreover, we give a list of all known examples of vertex-minimal triangulations. T3 - ZIB-Report - 06-08 KW - triangulated manifolds KW - combinatorial properties KW - minimal triangulations Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9028 ER - TY - GEN A1 - Köhler, Ekkehard G. A1 - Lutz, Frank H. T1 - Triangulated Manifolds with Few Vertices: Vertex-Transitive Triangulations I N2 - We describe an algorithm for the enumeration of (candidates of) vertex-transitive combinatorial $d$-manifolds. With an implementation of our algorithm, we determine, up to combinatorial equivalence, all combinatorial manifolds with a vertex-transitive automorphism group on $n\leq 13$ vertices. With the exception of actions of groups of small order, the enumeration is extended to 14 and 15 vertices. T3 - ZIB-Report - 06-09 KW - triangulated manifolds KW - vertex-transitive triangulations Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9031 ER - TY - GEN A1 - Froyland, Gary A1 - Koch, Thorsten A1 - Megow, Nicole A1 - Duane, Emily A1 - Wren, Howard T1 - Optimizing the Landside Operation of a Container Terminal N2 - This paper concerns the problem of operating a landside container exchange area that is serviced by multiple semi-automated rail mounted gantry cranes (RMGs) that are moving on a single bi-directional traveling lane. Such a facility is being built by Patrick Corporation at the Port Botany terminal in Sydney. The gantry cranes are a scarce resource and handle the bulk of container movements. Thus, they require a sophisticated analysis to achieve near optimal utilization. We present a three stage algorithm to manage the container exchange facility, including the scheduling of cranes, the control of associated short-term container stacking, and the allocation of delivery locations for trucks and other container transporters. The key components of our approach are a time scale decomposition, whereby an integer program controls decisions across a long time horizon to produce a balanced plan that is fed to a series of short time scale online subproblems, and a highly efficient space-time divisioning of short term storage areas. A computational evaluation shows that our heuristic can find effective solutions for the planning problem; on real-world data it yields a solution at most~8\% above a lower bound on optimal RMG utilization. T3 - ZIB-Report - 06-06 KW - Integer Programming KW - Container Terminal KW - Intermediate Storage Area KW - Landside operation KW - Yard crane scheduling KW - Storage space allocation Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9004 ER - TY - GEN A1 - Oevermann, Michael A1 - Klein, Rupert T1 - A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces N2 - We present a finite volume method for the solution of the two-dimensional Poisson equation $ \nabla\cdot( \beta( {\mbox{\boldmath $x$}}) \nabla u({\mbox{\boldmath $x$}})) = f(\mbox{\boldmath $x$}) $ with variable, discontinuous coefficients and solution discontinuities on irregular domains. The method uses bilinear ansatz functions on Cartesian grids for the solution $u({\mbox{\boldmath $x$})$ resulting in a compact nine-point stencil. The resulting linear problem has been solved with a standard multigrid solver. Singularities associated with vanishing partial volumes of intersected grid cells or the dual bilinear ansatz itself are removed by a two-step asymptotic approach. The method achieves second order of accuracy in the $L^\infty$ and $L^2$ norm. T3 - ZIB-Report - 06-05 KW - Poisson equation KW - finite volume methods KW - embedded interface KW - ariable and discontinuous coefficients KW - discontinuous solution Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8996 ER - TY - GEN A1 - Schädle, Achim A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Klose, Roland A1 - Schmidt, Frank T1 - Domain Decomposition Method for Maxwell's Equations: Scattering off Periodic Structures N2 - We present a domain decomposition approach for the computation of the electromagnetic field within periodic structures. We use a Schwarz method with transparent boundary conditions at the interfaces of the domains. Transparent boundary conditions are approximated by the perfectly matched layer method (PML). To cope with Wood anomalies appearing in periodic structures an adaptive strategy to determine optimal PML parameters is developed. We focus on the application to typical EUV lithography line masks. Light propagation within the multi-layer stack of the EUV mask is treated analytically. This results in a drastic reduction of the computational costs and allows for the simulation of next generation lithography masks on a standard personal computer. T3 - ZIB-Report - 06-04 KW - domain decomposition KW - conical diffraction KW - electro-magnetic scattering KW - Maxwell's equations KW - Lithography KW - finite elements Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8984 ER - TY - GEN A1 - Shioura, Akiyoshi T1 - Note on L#-convex Function Minimization Algorithms: Comparison of Murota's and Kolmogorov's Algorithms N2 - The concept of L##-convexity is introduced by Fujishige--Murota (2000) as a discrete convexity for functions defined over the integer lattice. The main aim of this note is to understand the difference of the two algorithms for L##-convex function minimization: Murota's steepest descent algorithm (2003) and Kolmogorov's primal algorithm (2005). T3 - ZIB-Report - 06-03 Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8979 ER - TY - GEN A1 - Bley, Andreas T1 - Approximability of Unsplittable Shortest Path Routing Problems N2 - In this paper, we discuss the relation of unsplittable shortest path routing (USPR) to other routing schemes and study the approximability of three USPR network planning problems. Given a digraph $D=(V,A)$ and a set $K$ of directed commodities, an USPR is a set of flow paths $\Phi_{(s,t)}$, $(s,t)\in K$, such that there exists a metric $\lambda=(\lambda_a)\in \mathbb{Z}^A_+$ with respect to which each $\Phi_{(s,t)}$ is the unique shortest $(s,t)$-path. In the \textsc{Min-Con-USPR} problem, we seek for an USPR that minimizes the maximum congestion over all arcs. We show that this problem is hard to approximate within a factor of $\mathcal{O}(|V|^{1-\epsilon})$, but easily approximable within min$(|A|,|K|)$ in general and within $\mathcal{O}(1)$ if the underlying graph is an undirected cycle or a bidirected ring. We also construct examples where the minimum congestion that can be obtained by USPR is a factor of $\Omega(|V|^2)$ larger than that achievable by unsplittable flow routing or by shortest multi-path routing, and a factor of $\Omega(|V|)$ larger than by unsplittable source-invariant routing. In the CAP-USPR problem, we seek for a minimum cost installation of integer arc capacities that admit an USPR of the given commodities. We prove that this problem is $\mathcal{NP}$-hard to approximate within $2-\epsilon$ (even in the undirected case), and we devise approximation algorithms for various special cases. The fixed charge network design problem \textsc{Cap-USPR}, where the task is to find a minimum cost subgraph of $D$ whose fixed arc capacities admit an USPR of the commodities, is shown to be $\mathcal{NPO}$-complete. All three problems are of great practical interest in the planning of telecommunication networks that are based on shortest path routing protocols. Our results indicate that they are harder than the corresponding unsplittable flow or shortest multi-path routing problems. T3 - ZIB-Report - 06-02 KW - Shortest path routing KW - unsplittable flow KW - computational complexity KW - approximation Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8968 ER - TY - THES A1 - Clasen, Malte T1 - Beleuchtung von Landschaften in interaktiver Darstellung N2 - Inhalt dieser Diplomarbeit ist ein Beleuchtungs- und Visualisierungsmodell für Pflanzen im interaktiven Landschaftsrendering. Ziel ist die qualitativ hochwertige Darstellung von einzelnen Individuen nahe des Betrachters, der seine Position in einer ansonsten statischen Szene frei wählen kann. Um dies zu erreichen wird zunächst vorgestellt, wie ausgehend von einfachen 3D-Modellen und Materialien ein physikalisch basiertes Reflexionsmodell parametrisiert werden kann. Grund hierfür ist der oftmals vorhandene umfangreiche Datenbestand, der auf die OpenGL-Materialien oder ähnliche Shader optimiert ist. Anschließend wird gezeigt, wie die Echtzeit-Renderingtechniken Shadow Mapping und Precomputed Radiance Transfer kombiniert werden können, um sowohl exakte hochfrequente direkte Beleuchtung als auch niederfrequentes indirektes Streulicht zu berücksichtigen. Diese Kombination wird an Hand der Pfad-Notation des Monte-Carlo-Path-Tracing eingeführt und begründet. Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9906 ER - TY - THES A1 - Heinz, Stefan T1 - Policies for Online Target Date Assignment Problems: Competitive Analysis versus Expected Performance Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9933 ER - TY - THES A1 - Zachow, Stefan T1 - Computergestützte 3D Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung T1 - Computer assisted 3D osteotomy planning in cranio-maxillofacial surgery under consideration of facial soft tissue arrangement N2 - In der Arbeit wird die computergestützte Planung von chirurgisch gesetzten Knochenfrakturen bzw. Knochenschnitten (sogenannten Osteotomien) an dreidimensionalen, computergrafischen Schädelmodellen, sowie die Umpositionierung separierter knöcherner Segmente im Kontext der rekonstruktiven MKG-Chirurgie behandelt. Durch die 3D Modellierung und Visualisierung anatomischer Strukturen, sowie der 3D Osteotomie- und Umstellungsplanung unter Einbeziehung der resultierenden Weichgewebedeformation wird den Chirurgen ein Werkzeug an die Hand gegeben, mit dem eine Therapieplanung am Computer durchgeführt und diese in Hinblick auf Funktion und Ästhetik bewertet werden kann. Unterschiedliche Strategien können dabei erprobt und in ihrer Auswirkung erfasst werden. Dazu wird ein methodischer Ansatz vorgestellt, der zum einen die chirurgische Planung im Vergleich zu existierenden Ansätzen deutlich verbessert und zum anderen eine robuste Weichgewebeprognose, durch den Einsatz geeigneter Planungsmodelle und eines physikalisch basierten Weichgewebemodells unter Nutzung numerischer Lösungsverfahren in die Planung integriert. Die Visualisierung der Planungsergebnisse erlaubt sowohl eine anschauliche und überzeugende, präoperative Patientenaufklärung, als auch die Demonstration möglicher Vorgehensweisen und deren Auswirkungen für die chirurgische Ausbildung. Ferner ergänzen die Planungsdaten die Falldokumentation und liefern einen Beitrag zur Qualitätssicherung. Die Arbeit ist in sieben Kapitel gegliedert und wie folgt strukturiert: Zuerst wird die medizinische Aufgabenstellung bei der chirurgischen Rekonstruktion von Knochenfehlbildungen und -fehlstellungen in der kraniofazialen Chirurgie sowie die daraus resultierenden Anforderungen an die Therapieplanung beschrieben. Anschließend folgt ein umfassender Überblick über entsprechende Vorarbeiten zur computergestützten Planung knochenverlagernder Operationen und eine kritische Bestandsaufnahme der noch vorhandenen Defizite. Nach der Vorstellung des eigenen Planungsansatzes wird die Generierung individueller, qualitativ hochwertiger 3D Planungsmodelle aus tomografischen Bilddaten beschrieben, die den Anforderungen an eine intuitive, 3D Planung von Umstellungsosteotomien entsprechen und eine Simulation der daraus resultierenden Weichgewebedeformation mittels der Finite-Elemente Methode (FEM) ermöglichen. Die Methoden der 3D Schnittplanung an computergrafischen Modellen werden analysiert und eine 3D Osteotomieplanung an polygonalen Schädelmodellen entwickelt, die es ermöglicht, intuitiv durch Definition von Schnittlinien am 3D Knochenmodell, eine den chirurgischen Anforderungen entsprechende Schnittplanung unter Berücksichtigung von Risikostrukturen durchzuführen. Separierte Knochensegmente lassen sich im Anschluss interaktiv umpositionieren und die resultierende Gesamtanordnung hinsichtlich einer funktionellen Rehabilitation bewerten. Aufgrund des in dieser Arbeit gewählten, physikalisch basierten Modellierungsansatzes kann unter Berücksichtigung des gesamten Weichgewebevolumens aus der Knochenverlagerung direkt die resultierende Gesichtsform berechnet werden. Dies wird anhand von 13 exemplarischen Fallstudien anschaulich demonstriert, wobei die Prognosequalität mittels postoperativer Fotografien und postoperativer CT-Daten überprüft und belegt wird. Die Arbeit wird mit einem Ausblick auf erweiterte Modellierungsansätze und einem Konzept für eine integrierte, klinisch einsetzbare Planungsumgebung abgeschlossen. N2 - In cranio-maxillofacial surgery, physicians are often faced with skeletal malformations that require complex bone relocations. Especially in severe cases of congenital dysgnathia (misalignment of upper and lower jaw) or hemifacial microsomia (asymmetric bone and tissue development), where multiple bone segments are to be mobilized and relocated simultaneously and in relation to each other, careful preoperative planning is mandatory. At present in clinical routine not all possible strategies can be planned and assessed with regard to functional rehabilitation. Moreover, the aesthetic outcome, i.e. the postoperative facial appearance, can only be estimated by a surgeon's experience and hardly communicated to the patient. On this account, a preoperative planning of complex osteotomies with bone relocations on a computerized model of a patient's head, including a reliable three-dimensional prediction and visualization of the post-surgical facial appearance is a highly appreciated possibility cranio-maxillofacial surgeons are longing for. This work, being performed at Zuse Institute Berlin (ZIB), addresses such a computer based 3D~surgery planning. A processing pipeline has been established and a simulation environment has been developed on basis of the software Amira, enabling a surgeon to perform bone cuts and bone rearrangements in an intuitive manner on virtual patient models. In addition, a prediction of the patients' postoperative appearance according to the relocated bone can be simulated and visualized realistically. For a meaningful planning of surgical procedures, anatomically correct patient models providing all relevant details are reconstructed from tomographic data with high fidelity. These patient models reliably represent bony structures as well as the facial soft tissue. Unstructured volumetric grids of the soft tissue are generated for a fast and efficient numerical solution of partial differential equations, describing tissue deformation on the foundation of 3D elastomechanics. The planning of osteotomies (bone cuts) for the mobilization and relocation of bone segments is performed in accordance to the planning on basis of life size replicas of a patient's skull, i.e. stereolitographic models. Osteotomy lines can be drawn on top of the polygonal planning models using suitable input devices. After evaluation of the consequence of a planned cut with regard to vulnerable inner structures (nerves, teeth etc.) the model is separated accordingly. A relocation of bone segments can be performed unrestrictedly in 3D or restricted to a translation or rotation within arbitrarily chosen planes under consideration of cephalometric guidelines. Bone and tooth collisions can be evaluated for functional analysis or orthodontic treatment planning with possible integration of digitized dental plaster casts. As a result of the preoperative planning, a single transformation matrix, encoding translation and rotation, or a sequence of such matrices are provided for each bone segment. Both the osteotomy paths and the transformation parameters can finally be used for intra-operative navigation. In the course of the planning, the relocated positions of bone segments serve as an input for the simulation of the resulting soft tissue deformation. Since bone and surrounding soft tissue share common boundaries that are either fixed or translocated, the resulting configuration of the entire tissue volume can be computed from the given boundary displacements by numerical minimization of the internal strain energy on basis of a biomechanical model, using a finite-element approach. In collaboration with different surgeons and hospitals more than 25 treatments have been accompanied by preoperative planning so far ranging from mandibular and midfacial hypoplasia to complex hemifacial microsomia. 13 of these cases are presented within this work. Simulation results were validated on the basis of photographs as well as of postoperative CT data, showing a good correlation between simulation and postoperative outcome. Further aspects of improving the modeling approach are discussed. It has been demonstrated that 3D~osteotomy planning on virtual patient models can be performed intuitively, and that 3D~tissue deformation for cranio-maxillofacial osteotomy planning can be predicted numerically without using heuristic ratios. It can be stated that by using 3D~planning software, a surgeon gains a better spatial understanding of complex dysplasia, and the 3D~soft tissue prediction gives an additional criterion for the assessment of the planned strategy. It turned out that, especially in complex cases such as hemifacial microsomia or for decisions bet­ween mono- and bimaxillary advancements, a 3D~planning aid is extremely helpful. The conclusion is, that images and animations created within the planning phase provide a valuable planning criterion for maxillofacial surgeons as well as a demonstrative information for patients and their relatives, thus greatly enhancing patient information, as well as surgical education. All data that result from the planning are also important for documentation and quality assurance. 3D osteotomy planning, including soft tissue prediction, likely will become a new paradigm of plastic and reconstructive surgery planning in the future. An assortment of results can be found under: http://www.zib.de/visual/medical/projects KW - MKG-Chirurgie KW - Mund-Kiefer-Gesichtschirurgie KW - Therapieplanung KW - Osteotomie KW - Weichgewebeprädiktion KW - computer assisted surgery KW - therapy planning KW - osteotomy KW - soft tissue prediction KW - CAS Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10432 SN - 3899631986 ER - TY - THES A1 - Raack, Christian T1 - Employing Mixed-Integer Rounding in Telecommunication Network Design N2 - In dieser Diplomarbeit werden grundlegende Probleme der kostenoptimalen Dimensionierung von Telekommunikationsnetzwerken untersucht. Diese werden als lineare gemischt ganzzahlige Programme formuliert, wobei sich in der Modellierung auf die Konzepte Routing und Kapazitätszuweisung beschränkt wird. Es werden parallel drei übliche, aus der Praxis motivierte Möglichkeiten behandelt, die auf gerichteten oder ungerichteten Kanten eines Netzwerkes installierte Kapazität zu nutzen. Diese unterscheiden wir als DIrected, BIdirected und UNdirected. Die studierten Probleme treten als Relaxierungen vieler realistischer Fragestellungen der Netzwerkoptimierung auf. Sie enthalten elementare Strukturen, deren Studium ausschlaggebend ist für das Verständnis komplexerer Modelle. Letztere können zusätzliche Erfordernisse berücksichtigen, wie zum Beispiel die Ausfallsicherheit von Netzwerken. Zur Lösung solcher NP-schweren Optimierungsprobleme werden erfolgreich Branch & Bound und Schnittebenenverfahren kombiniert (Branch & Cut). Für die Wirksamkeit dieser Algorithmen ist es sehr nützlich, möglichst genaue Kenntnisse der Struktur der Seitenflächen der zugrundeliegenden Polyeder zu haben, welche die konvexe Hülle der Lösungsmenge beschreiben. Es sind starke gültige Ungleichungen zu finden, welche hochdimensionale Seitenflächen oder sogar Facetten definieren. Diese sollten zudem schnell separiert werden können und die numerische Stabilität der Algorithmen möglichst nicht beeinflussen. Diese Arbeit beschäftigt sich im Wesentlichen mit der sehr allgemeinen Rundungstechnik Mixed- Integer Rounding (MIR) zur Verstärkung gültiger Ungleichungen unter Verwendung der Ganzzahligkeitsnebenbedingungen. Es wird eine MIR-Prozedur motiviert, bestehend aus den Schritten Aggregieren, Substituieren, Komplementieren und Skalieren, welche durch Ausnutzung der Struktur der gegebenen Parameter zu einer gültigen Basisungleichung führt, die dann durch MIR eine starke und oft facetten-induzierende Ungleichung gibt. Es werden verschieden Klassen solcher Ungleichungen untersucht und auf ihre Praxistauglichkeit beim Einsatz in Branch & Cut-Verfahren getestet. Nach einer kurzen Einführung werden in Kapitel 2 die für uns in dieser Diplomarbeit relevanten Probleme definiert. Kapitel 3 gibt eine ausführliche Übersicht über die Technik MIR.Wir beschäftigen uns vor allen Dingen mit den Begriffen Superadditivität und Lifting und behandeln Aspekte wie Numerik und beschränkte Variablen. Kapitel 4 und Kapitel 5 umfassen Untersuchungen zu so genannten cut sets. Diese Polyeder werden durch Schnitte in Netzwerken definiert und relaxieren die von uns behandelten Probleme. Hauptsächlich durch MIR entwickeln wir sowohl neue als auch bekannte Klassen von facetten-definierenden Ungleichungen für cut sets, wobei strukturelle Unterschiede herausgearbeitet werden, die durch die drei verschiedenen Typen der Kapzitätsbereitstellung und durch beschränkte Variablen entstehen. Als ein zentrales Resultat wird bewiesen unter welchen Bedingungen facetten-induzierende Ungleichungen für cut sets auch Facetten der zugehörigen relaxierten Polyeder sind. Im Kapitel 6 geben wir weitere Typen von MIR-Ungleichungen an, die auf anderen Netzwerkstrukturen basieren und weisen ferner auf offene Fragen sowie interessante Ideen hin. Das Kapitel 7 widmet sich schließlich der Entwicklung und Implementation von Separationsalgorithmen. Wir testen einige der entwickelten Ungleichungsklassen mit Hinblick auf Ihre Wirksamkeit zur Lösung von realistischen Problemen der Netzwerkdimensionierung aus der Telekommunikation und diskutieren die Ergebnisse. Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10023 ER - TY - THES A1 - Witte, Jochen T1 - Implementierung einer NFS Schnittstelle im Kontext eines Grid-Datenmanagement-Systems N2 - Diese Arbeit dokumentiert den Entwurf und die Implementierung einer NFS-Schnittstelle zum ZIBDMS. Das ZIBDMS, welches derzeit am Zuse-Institut Berlin entwickelt wird, ist ein Managementsystem für verteilte Daten in heterogenen Umgebungen [10]. Es soll die einfache Benutzung von Mechanismen zur Replikation sowie neue Möglichkeiten des Zugriffs und der Verwaltung von Metadaten und Datenobjekten ermöglichen. Dem Nutzer bietet das System verschiedene Sichten: Neben der klassischen, hierarchischen Sicht mit Verzeichnissen und Dateien wird auch eine attributbasierte Zugriffsmethode angeboten, in der Datenobjekte ausschließlich über Attribut/Wert-Paare referenziert werden. Für den Benutzer transparent, soll sich das System im Hinblick auf die Verfügbarkeit von Daten und Metadaten selbsttätig optimieren. Um Skalierbarkeit gew¨ahrleisten zu können, werden intern Peer-to-Peer- Techniken entwickelt und benutzt. Die NFS-Schnittstelle erhöht die Nutzbarkeit des Systems, da Client- Implementierungen für nahezu alle Betriebssysteme zur Verfügung stehen. Der Benutzer kann so über das gewohnte Dateisystem Daten und Metadaten pflegen, ohne spezifisches Vorwissen zu benötigen. In dieser Arbeit wird untersucht, inwiefern sich die Semantik des ZIBDMS auf jene des NFS-Protokolls übertragen läßt. Weiterhin wird das Konzept von Pseudodateien beschrieben und diskutiert, inwiefern es eine brauchbare Lösung darstellt, den im Vergleich zur NFS-Semantik wesentlich größeren Funktionsumfang des ZIBDMS für den Anwender nutzbar zu machen. Pseudodateien sind nicht-persistente Objekte, welche für den Benutzer als reguläre Datei sichtbar werden und die erweiterte Funktionalitäten wie die Bearbeitung von Metadaten oder die Platzierung von Replikaten über die Dateisystem-Sicht des NFS zur Verfügung stellen sollen. Schließlich werden Leistungsmessungen an den benutzten Komponenten des ZIBDMS vorgenommen und vergleichbaren Systemen gegen übergestellt. Die Aufmerksamkeit liegt hier auf der zugrundeliegenden Katalog-Technologie sowie dem durch das NFS-Protokoll verursachten Overhead. Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10081 ER - TY - THES A1 - Pham, The Anh T1 - Einbettung neuer Verwaltungsmethoden in die hierarchische Dateisystemsicht N2 - Die hierarchische Organisation von Dateien beherrscht Computersysteme seit vielen Jahren und wird sich vermutlich auch in Zukunft weiterhin durchsetzen. Dennoch stößt diese Verwaltungsmethode in einem klassischen hierarchischen Dateisystem bei dem jährlichen rasanten Zuwachs an neuen Daten an ihre Grenzen, auch wenn Nutzer eine ausgefeilte Verzeichnisstruktur mit einer disziplinierten Namensgebung konsequent auf- und ausbauen. Um den Überblick über die Dateien zu behalten, werden in dieser Arbeit neue Verwaltungsmethoden vorgestellt und in die hierarchische Dateisystemsicht eingebettet. Auf der Basis des hierarchischen Dateisystems bietet ein metadatenbasiertes Dateisystem neben dem hierarchischen Zugriff noch einen flexiblen, assoziativen Zugriff auf Dateien über virtuelle Objekte, indem Suchmethoden in Form einer Anfrage auf in einer Datenbank gespeicherte Index- und Metadaten angewendet werden. Das Ergebnis dieser Abfrage wird mit Hilfe von virtuellen Verzeichnissen und virtuellen Dateien in einer übersichtlichen Form dargestellt, so dass eine Nutzung der hierarchischen Sicht weiterhin intuitiv fortgesetzt wird. Das Datenmanagementsystem ZIBDMS, welches einen verteilten Metadatenkatalog und einen Dateireplikationskatalog beinhaltet, ermöglicht es, die oben genannten Verwaltungsmethoden für die NFS-Schnittstelle, CORBA-Middleware und Web Services transparent zu implementieren. Zudem stellt ZIBDMS weitere neue Dateiverwaltungsmethoden zur Verfügung, die sich in die hierarchische Dateisystemsicht integrieren lassen. Metadaten in Form von Attribut-Wert-Paaren lassen sich als virtuelle Datei darstellen und editieren. Eine Collection bietet die Möglichkeit, Dateien in einem logischen virtuellen Ordner zu organisieren. Mit einem Dependency-Graph lassen sich Dateien zueinander in Relation stellen, so dass eine Linkstruktur zwischen Dateien ausgedrückt werden kann. Das Verweiskonzept eines klassischen hierarchischen Dateisystems wird im ZIBDMS um eine neue Verweisart Weak-Link erweitert, um einen aktualisierbaren, konsistenten und zyklenfreien symbolischen Link anzubieten. In einer hierarchischen Sicht lässt sich durch Verweise ein Baum bilden, in dem eine Navigation und Verweisauflistung möglich sind, was außer ZIBDMS noch kein anderes System bietet. N2 - The hierarchical organization of files has dominated computer systems for many years and this will probably not change in the near future. However, with the rapid annual growth of new data this classical hierarchical file system management method reaches its limitations, even when the user consistently sets up and continually expands an elaborated directory structure with well-disciplined naming. This paper introduces new management methods to maintain an overview of all files which can be embedded in the hierarchical file system. A metadata-based file system, which is based on the hierarchical file system, offers, in addition to hierarchical access, a more flexible and associative access to files via virtual objects by providing query capabilities of index- and metadata which are stored in a database. The query results are presented in a clearly-arranged form of virtual directories and virtual files so that the intuitive hierarchical view continues to be maintained. The data management system ZIBDMS, which contains a distributed metadata catalog and a file replication catalog, permits a transparent implementation of these management methods for the NFS interface, CORBA-middleware or web services. Furthermore, ZIBDMS provides other new file management methods that can be integrated into the hierarchical file system view. Metadata in form of attribute-value-pairs can be presented and edited with a virtual file. A Collection makes it possible to organize files in logical virtual folders. Using a Dependency graph, files can be related to each other and expressed through a link structure between these files. In the ZIBDMS the reference concept of a classical hierarchal file system is extended with a new kind of reference called Weak Link in order to provide up-to-date, consistent and cycle-free symbolic links. With the references a tree can be established in a hierarchical view in which navigation and listing of references are possible; this capability is only possible in the ZIBDMS system. Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10014 ER - TY - GEN A1 - Kube, Susanna A1 - Weber, Marcus T1 - Identification of Metastabilities in Monomolecular Conformation Kinetics N2 - The identification of metastable conformations of molecules plays an important role in computational drug design. One main difficulty is the fact that the underlying dynamic processes take place in high dimensional spaces. Although the restriction of degrees of freedom to a few dihedral angles significantly reduces the complexity of the problem, the existing algorithms are time-consuming. They are based on the approximation of transition probabilities by an extensive sampling of states according to the Boltzmann distribution. We present a method which can identify metastable conformations without sampling the complete distribution. Our algorithm is based on local transition rates and uses only pointwise information about the potential energy surface. In order to apply the cluster algorithm PCCA+, we compute a few eigenvectors of the rate matrix by the Jacobi-Davidson method. Interpolation techniques are applied to approximate the thermodynamical weights of the clusters. The concluding example illustrates our approach for epigallocatechine, a molecule which can be described by seven dihedral angles. T3 - ZIB-Report - 06-01 KW - metastable conformations KW - potential energy surface KW - transition rates KW - eigenvectors KW - clustering Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8956 ER - TY - GEN A1 - Kuberek, Monika T1 - KOBV-Volltextserver - Langfristiger Zugriff auf Kluwer-, Springer- und Elsevier-Zeitschriften N2 - Seit einigen Jahren lizenzieren Bibliotheken mit erheblichem finanziellen Aufwand elektronische Zeitschriften. Anders als bei einer Papierausgabe ist der dauerhafte Zugriff auf die bezahlten Dokumente allerdings nicht garantiert: Die e-Zeitschriften liegen auf dem Verlagsserver, und der Verlag schaltet den Zugriff (meist IP-Range des Campus) auf seinem Server frei. Wird der Zugriff von Verlagsseite abgeschaltet, erlöschen sämtliche Zugriffsrechte, auch auf die in der Vergangenheit lizenzierten und bezahlten Zeitschriften. Auf die neuen Abonnementbedingungen hat das Friedrich-Althoff-Konsortium (FAK) reagiert und in seinen Vertr"agen den Erwerb der Archivdaten beim Auslaufen eines Vertrages festgeschrieben. Im Rahmen eines Projektes baut die KOBV-Zentrale einen Zeitschriftenserver auf, um den Zugriff auf die lizenzierten elektronischen Zeitschriften auch nach Ablauf der Lizenzverträge zu gewährleisten. Den Grundstock bilden die vom FAK in den Jahren 1997-2003 lizenzierten elektronischen Zeitschriften der Verlage Kluwer Academic Press, Springer und Elsevier - ein Volumen von rund 1.600 Zeitschriftentiteln mit knapp 1.400.000 Artikeln. Beim Aufbau des Zeitschriftenservers kommt der vertraglich-organisatorischen Komponente eine ebenso wichtige Rolle zu wie der technischen Realisierung. Hier hat die KOBV-Zentrale ein transparentes Verfahren konzipiert und umgesetzt, um für die Verlage die notwendige Vertrauensbasis zu schaffen und gleichzeitig den Einrichtungen ihren berechtigten Zugriff auf die Zeitschriften-Volltexte zu sichern. Die Zeitschriftenartikel werden sowohl im Rahmen des KOBV-Volltextservers, einem neuen Internet-Dienst der KOBV-Zentrale, zugänglich gemacht - volltext-indiziert mit der Suchmaschine Swish-e - als auch integriert in die Metadatensuche und den Open-Linking-Dienst des KOBV-Portals. Während die Metadatenrecherche und die Sicht auf die Abstracts für alle offen sind, ist der Zugriff auf die Artikel-Volltexte auf die an den Verträgen beteiligten Einrichtungen beschränkt. Dazu wurde ein Authentifizierungsverfahren auf der Basis von IP-Ranges eingerichtet. Der vorliegende Text ist die schriftliche Fassung eines gleichnamigen Vortrages auf der ASpB-Tagung 2005 \glqq Spezialbibliotheken zwischen Auftrag und Ressourcen{\grqq} der Arbeitsgemeinschaft der Spezialbibliotheken, die vom 06.-09. September 2005 in der Technischen Universität München stattfand. T3 - ZIB-Report - 05-59 KW - Archivierung KW - Authentifizierung KW - Autorisierung KW - Bibliotheksverbund KW - Dokumentenserver KW - elektronische Dokumente KW - elektronische Zeitschriften KW - KOB Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8921 ER - TY - GEN A1 - Heinz, Stefan A1 - Krumke, Sven A1 - Megow, Nicole A1 - Rambau, Jörg A1 - Tuchscherer, Andreas A1 - Vredeveld, Tjark T1 - The Online Target Date Assignment Problem N2 - Many online problems encountered in real-life involve a two-stage decision process: upon arrival of a new request, an irrevocable first-stage decision (the assignment of a specific resource to the request) must be made immediately, while in a second stage process, certain ``subinstances'' (that is, the instances of all requests assigned to a particular resource) can be solved to optimality (offline) later. We introduce the novel concept of an \emph{Online Target Date Assignment Problem} (\textsc{OnlineTDAP}) as a general framework for online problems with this nature. Requests for the \textsc{OnlineTDAP} become known at certain dates. An online algorithm has to assign a target date to each request, specifying on which date the request should be processed (e.\,g., an appointment with a customer for a washing machine repair). The cost at a target date is given by the \emph{downstream cost}, the optimal cost of processing all requests at that date w.\,r.\,t.\ some fixed downstream offline optimization problem (e.\,g., the cost of an optimal dispatch for service technicians). We provide general competitive algorithms for the \textsc{OnlineTDAP} independently of the particular downstream problem, when the overall objective is to minimize either the sum or the maximum of all downstream costs. As the first basic examples, we analyze the competitive ratios of our algorithms for the par ticular academic downstream problems of bin-packing, nonpreemptive scheduling on identical parallel machines, and routing a traveling salesman. T3 - ZIB-Report - 05-61 KW - Online Algorithms KW - Online Target Date Assignment Problem Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8945 ER - TY - GEN A1 - Block, Barbara A1 - Hengel, Christel A1 - Heuvelmann, Reinhold A1 - Katz, Cornelia A1 - Rusch, Beate A1 - Schmidgall, Karin A1 - Sigrist, Barbara T1 - Maschinelles Austauschformat für Bibliotheken und die Functional Requirements for Bibliographic Records. Oder: Wieviel FRBR verträgt MAB? N2 - Die Functional Requirements for Bibliographic Records, kurz FRBR, sind eine Empfehlung der International Federation of Library Associations and Institutions (IFLA) von 1998 zur Neustrukturierung von Bibliothekskatalogen. Mit den FRBR wird ein logisches Denkmodell für bibliografische Beschreibungen vorgelegt. Die Diskussion über dieses Modell befindet sich im deutschsprachigen Raum - anders als im angloamerikanischen - noch in den Anfängen. Dem möchte dieser Aufsatz entgegen wirken, indem die Frage gestellt wird, inwieweit sich die logisch gedachten FRBR-Einheiten in den existierenden Daten wieder finden lassen. Dazu werden die Entitäten mit den dazugehörigen Attributen dem in der Bibliothekswelt Deutschlands und Österreichs üblichen MAB-Format (Maschinelles Austauschformat für Bibliotheken) gegenübergestellt und auf ihre Kompatibilität hin untersucht. Die Autoren sind Mitglieder der überregionalen {\glqq}Expertengruppe Datenformate{\grqq}, in der Formatfragen, die das Bibliothekswesen betreffen, diskutiert werden, insbesondere aber das MAB-Format gepflegt wird. T3 - ZIB-Report - 05-60 KW - Bibliotheken KW - Bibliographisches Datenformat KW - MAB KW - FRBR KW - Functional Requierements for Bibliographic Records Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8938 ER - TY - GEN A1 - Grötschel, Martin T1 - Das Problem mit der Komplexität: P = NP? N2 - Was Komplexität ist, weiß niemand so richtig. In vielen Wissenschaftsgebieten wird der Begriff Komplexität verwendet, überall mit etwas anderer Bedeutung. Mathematik und Informatik hab en eine eigene Theorie hierzu entwickelt: die Komplexitätstheorie. Sie stellt zwar grundlegende Begriffe bereit, aber leider sind die meisten wichtigen Fragestellungen noch ungelöst. Diese kurze Einführung konzentriert sich auf einen speziellen, aber bedeutenden Aspekt der Theorie: Lösbarkeit von Problemen in deterministischer und nichtdeterministischer polynomialer Zeit. Hinter der für Uneingeweihte etwas kryptischen Frage "P = NP?" verbirgt sich das derzeit wichtigste Problem der Komplexitätstheorie. Anhand dieser Fragestellung werden einige Aspekte der Theorie erläutert und formell erklärt, was "P = NP?" bedeutet. Es geht nicht nur um komplizierte algorithmische Mathematik und Informatik, sondern um grundsätzliche Fragen unserer Lebensumwelt. Kann man vielleicht beweisen, dass es für viele Probleme unseres Alltags keine effizienten Lösungsmethoden gibt? T3 - ZIB-Report - 05-58 KW - Komplexität KW - Komplexitätstheorie Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8916 ER - TY - GEN A1 - Gruber, Claus G. A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland A1 - Zymolka, Adrian T1 - A new model and a computational study for Demand-wise Shared Protection N2 - This report combines the contributions to INOC 2005 (Wessälly et al., 2005) and DRCN 2005 (Gruber et al., 2005). A new integer linear programming model for the end-to-end survivability concept deman d-wise shared protection (DSP) is presented. DSP is based on the idea that backup capacity is dedicated to a particular demand, but shared within a demand. It combines advantages of dedicated and shared protection: It is more cost-efficient than dedicated protection and operationally easier than shared protection. In a previous model for DSP, the number of working and backup paths to be configured for a particular demand has been an input parameter; in the more general model for DSP investigated in this paper, this value is part of the decisions to take. To use the new DSP model algorithmically, we suggest a branch-and-cut approach which employs a column generation procedure to deal with the exponential number of routing variables. A computational study to compare the new resilience mechanism DSP with dedicated and shared path protection is performed. The results for five realistic network planning scenarios reveal that the best solutions for DSP are on average 15\% percent better than the corresponding 1+1 dedicated path protection solutions, and only 15\% percent worse than shared path protection. T3 - ZIB-Report - 05-55 KW - demand-wise shared protection KW - resilience KW - network design KW - integer linear programming Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8880 ER - TY - GEN A1 - Grötschel, Martin T1 - Schnelle Rundreisen: Das Travelling Salesman-Problem N2 - Das Travelling-Salesman-Problem (TSP) ist das am intensivsten untersuchte kombinatorische Optimierungsproblem. In diesem Abschnitt wird eine Einführung in das TSP gegeben. Es werden Problemstellungen erläutert, Anwendungen skizziert und einige Schwierigkeiten bei der korrekten Modellierung der Zielfunktion dargelegt. Es ist gar nicht so klar, was in einem konkreten Problem die wirkliche Entfernung ist. Exakte und approximative Lösungsverfahren werden an Beispielen skizziert, und es wird angedeutet, dass man, obwohl TSPs zu den theoretisch schweren Problemen zählen, in der Praxis TSPs von atemberaubender Größe lösen kann. T3 - ZIB-Report - 05-57 KW - Travelling-Salesman-Problem KW - TSP KW - Rundreisen KW - optimale Tour Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8901 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Grigoriev, Alexander A1 - Koster, Arie M.C.A. T1 - Treewidth Lower Bounds with Brambles N2 - In this paper we present a new technique for computing lower bounds for graph treewidth. Our technique is based on the fact that the treewidth of a graph $G$ is the maximum order of a bramble of $G$ minus one. We give two algorithms: one for general graphs, and one for planar graphs. The algorithm for planar graphs is shown to give a lower bound for both the treewidth and branchwidth that is at most a constant factor away from the optimum. For both algorithms, we report on extensive computational experiments that show that the algorithms give often excellent lower bounds, in particular when applied to (close to) planar graphs. T3 - ZIB-Report - 05-54 KW - treewidth KW - lower bounds KW - branchwidth KW - brambles Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8878 ER - TY - GEN A1 - Hiller, Benjamin T1 - Probabilistic Competitive Analysis of a Dial-a-Ride Problem on Trees Under High Load N2 - In this paper we consider a simple variant of the Online Dial-a-Ride Problem from a probabilistic point of view. To this end, we look at a probabilistic version of this online Dial-a-Ride problem and introduce a probabilistic notion of the competitive ratio which states that an algorithm performs well on the vast majority of the instances. Our main result is that under the assumption of high load a certain online algorithm is probabilistically $(1+o(1))$-competitive if the underlying graph is a tree. This result can be extended to general graphs by using well-known approximation techniques at the expense of a distortion factor~$O(\log\|V\|)$. T3 - ZIB-Report - 05-56 KW - probabilistic competitive analysis KW - Dial-a-Ride problem KW - online algorithms KW - IGNORE strategy Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8896 ER - TY - GEN A1 - Kiselev, Arthemy V. A1 - Wolf, Thomas T1 - On weakly non-local, nilpotent, and super-recursion operators for N=1 super-equations N2 - We consider nonlinear, scaling-invariant $N=1$ boson$+$fermion supersymmetric systems whose right-hand sides are homogeneous differential polynomials and satisfy some natural assumptions. We select the super-systems that admit infinitely many higher symmetries generated by recursion operators; we further restrict ourselves to the case when the dilaton dimensions of the bosonic and fermionic super-fields coincide and the weight of the time is half the weight of the spatial variable. We discover five systems that satisfy these assumptions; one system is transformed to the purely bosonic Burgers equation. We construct local, nilpotent, triangular, weakly non-local, and super-recursion operators for their symmetry algebras. T3 - ZIB-Report - 05-52 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8850 ER - TY - GEN A1 - Kiselev, Arthemy V. A1 - Wolf, Thomas T1 - Supersymmetric representations and integrable super-extensions of the Burgers and Boussinesq equations N2 - New evolutionary supersymmetric systems whose right-hand sides are homogeneous differential polynomials and which possess infinitely many higher symmetries are constructed. Their intrinsic geometry (symmetries, conservation laws, recursion operators, Hamiltonian structures, and exact solutions) is analyzed by using algebraic methods. A supersymmetric $N=1$ representation of the Burgers equation is obtained. An $N=2$ KdV-component system that reduces to the Burgers equation in the diagonal $N=1$ case $\theta^1=\theta^2$ is found; the $N=2$ Burgers equation admits and $N=2$ modified KdV symmetry. A one\/-\/parametric family of $N=0$ super\/-\/systems that exte nd the Burgers equation is described; we relate the systems within this family with the Burgers equation on associative algebras. A supersymmetric boson$+$fermion representation of the dispersionless Boussinesq equation is investigated. We solve this equation explicitly and construct its integrable deformation that generates two infinite sequences of the Hamiltonians. The Boussinesq equation with dispersion is embedded in a one-parametric family of two-component systems with dissipation. We finally construct a three-parametric supersymmetric system that incorporates the Boussinesq equation with dispersion and dissipation but never retracts to it for any values of the parameters. T3 - ZIB-Report - 05-53 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8869 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Wagler, Annegret T1 - Comparing Imperfection Ratio and Imperfection Index for Graph Classes N2 - Perfect graphs constitute a well-studied graph class with a rich structure, reflected by many characterizations with respect to different concepts. Perfect graphs are, for instance, precisely those graphs $G$ where the stable set polytope $STAB(G)$ coincides with the fractional stable set polytope $QSTAB(G)$. For all imperfect graphs $G$ it holds that $STAB(G) \subset QSTAB(G)$. It is, therefore, natural to use the difference between the two polytopes in order to decide how far an imperfect graph is away from being perfect; we discuss three different concepts, involving the facet set of $STAB( G)$, the disjunctive index of $QSTAB(G)$, and the dilation ratio of the two polytopes. Including only certain types of facets for $STAB(G)$, we obtain graphs that are in some sense close to perfect graphs, for example minimally immperfect graphs, and certain other classes of so-called rank-perfect graphs. The imperfection ratio has been introduced by (Gerke and McDiarmid, 2001) as the dilation ratio of $STAB(G)$ and $QSTAB(G)$, whereas (Aguilera et al., 2003) suggest to take the disjunctive index of $Q STAB(G)$ as the imperfection index of $G$. For both invariants there exist no general upper bounds, but there are bounds known for the imperfection ratio of several graph classes (Coulonges et al. 2005, Gerke and McDiarmid, 2001). Outgoing from a graph-theoretical interpretation of the imperfection index, we conclude that the imperfection index is NP-hard to compute and we prove that there exists no upper bound on the imperfect ion index for those graph classes with a known bounded imperfection ratio. Comparing the two invariants on those classes, it seems that the imperfection index measures imperfection much more roughly than the imperfection ratio; therefoe, discuss possible directions for refinements. T3 - ZIB-Report - 05-50 KW - perfect graphs KW - imperfection ratio KW - imperfection index Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8836 ER - TY - GEN A1 - Koch, Thorsten T1 - Rapid Mathematical Programming or How to Solve Sudoku Puzzles in a few Seconds N2 - Using the popular puzzle game of Sudoku, this article highlights some of the ideas and topics covered in ZR-04-58. T3 - ZIB-Report - 05-51 KW - Integer Programming KW - Sudoku KW - IP KW - MIP KW - Zimpl KW - Modelling language Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8845 ER - TY - GEN A1 - Steinbach, Marc T1 - Topological Index Criteria in DAE for Water Networks N2 - The dynamics of pressurized water distribution networks are naturally modeled by differential algebraic equations (DAE). This paper investigates fundamental structural properties of such a DAE model under weak regularity assumptions. The usual partial derivative-based index-1 condition is shown to be necessary and sufficient for several index concepts, as well as sufficient for solvability in a strong sense. Using the physical properties of nonlinear network elements and the inherent saddle point structure of network hydraulics, we then derive purely topological index criteria based on the network graph and the choice of control variables. Several examples illustrate the theoretical results and explore different non-index-1 situations. A brief discussion of the implications for operative planning by discrete time DAE boundary value problems concludes the paper. T3 - ZIB-Report - 05-49 KW - Water network KW - differential-algebraic equation KW - solvability KW - topological index criteria Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8821 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Sternbeck, Andre A1 - Stüben, Hinnerk T1 - Probing the Aoki phase with N_f=2 Wilson fermions at finite temperature N2 - In this letter we report on a numerical investigation of the Aoki phase in the case of finite temperature which continues our former study at zero temperature. We have performed simulations with Wilson fermions at $\beta=4.6$ using lattices with temporal extension $N_{\tau}=4$. In contrast to the zero temperature case, the existence of an Aoki phase can be confirmed for a small range in $\kappa$ at $\beta=4.6$, however, shifted slightly to lower $\kappa$. Despite fine-tuning $\kappa$ we could not separate the thermal transition line from the Aoki phase. T3 - ZIB-Report - 05-48 KW - Wilson fermions KW - phase diagram KW - parity-flavor symmetry KW - Aoki phase KW - finite temperature Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8812 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Die Vision einer individuellen quantitativen Medizin N2 - Die Autoren schreiben dieses Papier aus der eingeschränkten Sicht der Mathematik und der Informationstechnik. Um den speziellen Beitrag dieser Disziplinen überhaupt diskutieren zu können, sehen wir uns jedoch gezwungen, einen Rahmen abzustecken, den wir für das Jahr 2020 vorhersehen -- nach Wahrscheinlichkeit und aus unserem engeren fachlichen Blickwinkel. Vorab bitten wir schon einmal bei den medizinischen Fachleuten um Nachsicht, wenn wir uns in ihrem Revier allzu dillettantisch bewegen. Vielleicht fördert aber auch unser eingeschränkter Blickwinkel ansonsten unbedachte Aspekte zutage -- das hoffen wir zumindest. T3 - ZIB-Report - 05-47 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8805 ER - TY - GEN A1 - Pfetsch, Marc T1 - A Branch-And-Cut for the Maximum Feasible Subsystem Problem N2 - We present a branch-and-cut algorithm for the NP-hard maximum feasible subsystem problem: For a given infeasible linear inequality system, determine a feasible subsystem containing as many inequalities as possible. The complementary problem, where one has to remove as few inequalities as possible in order to render the system feasible, can be formulated as a set covering problem. The rows of this formulation correspond to irreducible infeasible subsystems, which can be exponentially many. The main issue of a branch-and-cut algorithm for MaxFS is to efficiently find such infeasible subsystems. We present three heuristics for the corresponding NP-hard separation problem and discuss further cutting planes. This paper contains an extensive computational study of our implementation on a variety of instances arising in a number of applications. T3 - ZIB-Report - 05-46 KW - infeasible linear inequality system KW - irreducible infeasible subsystem KW - (IIS) maximum feasible subsystem problem KW - minimum IIS-cover KW - branch-and-cut Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8797 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Lukac, Sascha A1 - Mitusch, Kay A1 - Schlechte, Thomas A1 - Schultz, Sören A1 - Tanner, Andreas T1 - An Auctioning Approach to Railway Slot Allocation N2 - We present an approach to implement an auction of railway slots. Railway network, train driving characteristics, and safety requirements are described by a simplified, but still complex macroscopic model. In this environment, slots are modelled as combinations of scheduled track segments. The auction design builds on the iterative combinatorial auction. However, combinatorial bids are restricted to some types of slot bundles that realize positive synergies between slots. We present a bidding language that allows bidding for these slot bundles. An integer programming approach is proposed to solve the winner determination problem of our auction. Computational results for auction simulations in the Hannover-Fulda-Kassel area of the German railway network give evidence that auction approaches can induce a more efficient use of railway capacity. T3 - ZIB-Report - 05-45 KW - Railway Slot Allocation KW - Train Dispatching KW - Combinatorial Auctions Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8786 ER - TY - GEN A1 - Griesse, Roland A1 - Weiser, Martin T1 - On the Interplay Between Interior Point Approximation and Parametric Sensitivities in Optimal Control N2 - This paper is concerned with the sensitivities of function space oriented interior point approximations in parameter dependent problems. For an abstract setting that covers control constrained optimal control problems, the convergence of interior point sensitivities to the sensitivities of the optimal solution is shown. Error bounds for $L_q$ norms are derived and illustrated with numerical examples. T3 - ZIB-Report - 05-44 KW - interior point methods KW - parametric sensitivity KW - optimal control Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8773 ER - TY - GEN A1 - Kube, Susanna A1 - Weber, Marcus T1 - Conformation Kinetics as a Reduced Model for Transition Pathways N2 - The complexity of molecular kinetics can be reduced significantly by a restriction to metastable conformations which are almost invariant sets of molecular dynamical systems. With the Robust Perron Cl uster Analysis PCCA+, developed by Weber and Deuflhard, we have a tool available which can be used to identify these conformations from a transition probability matrix. This method can also be applied to the corresponding transition rate matrix which provides important information concerning transition pathways of single molecules. In the present paper, we explain the relationship between these tw o concepts and the extraction of conformation kinetics from transition rates. Moreover, we show how transition rates can be approximated and conclude with numerical examples. T3 - ZIB-Report - 05-43 KW - conformation kinetics KW - transition rates KW - Robust Perron Cluster Analysis Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8763 ER - TY - THES A1 - Kähler, Ralf T1 - Accelerated Volume Rendering on Structured Adaptive Meshes N2 - Multi-scale phenomena are abundant in many application fields. Representing and numerically simulating such processes is a challenging task since quite different scales have to be resolved, which often requires enormous amounts of storage and computational power. An important strategy in this context is adaptivity, i.e. local adjustment of the spatio-temporal resolution to the details to be resolved. A standard representation therefore are hierarchical, locally refined grids. A specific adaptive approach for solving partial differential equations, usually called AMR (Adaptive Mesh Refinement), was introduced in 1984. The basic idea is to combine the simplicity of structured grids and the advantages of local refinement. In this numerical scheme the computations are started on a set of coarse, potentially overlapping structured grids, that cover the computational domain. Local error criteria are applied to detect regions that require higher resolution. These are covered by subgrids with decreasing mesh spacing, which do not replace, but rather overlap the refined regions of the coarser patches. The equations are advanced on the finer subgrids and the refinement procedure recursively continues until all cells fulfill the considered error criteria, giving rise to a hierarchy of nested levels of refinement. In 1989 a variant of this scheme, called Structured Adaptive Mesh Refinement (SAMR), which reduces some of the complexity of the original approach, was proposed. While the separate subgrids in the AMR scheme could be rotated against each other, in SAMR they are aligned with the major axes of the coordinate system, which for example simplifies the computation of fluxes of (conserved) quantities through the cell faces. SAMR has become more and more popular in the last decade, and nowadays it is applied in many domains like hydrodynamics, meteorology and in particular in cosmology and relativistic astrophysics. Due to this growing popularity, an increasing number of scientists is in need of appropriate interactive visualization techniques to interpret and analyze AMR simulation data. Tools for both, 2D analysis to quantitatively convey the information within single slices and 3D representations to apprehend the overall structure are required. In this thesis we develop direct and indirect volume visualization algorithms for scalar fields that are defined on structured Adaptive Mesh Refinement (SAMR) grids. In particular algorithms for planar slicing and the display of height fields, C0-continuous isosurface extraction, software-, and hardware-based direct volume rendering and temporal interpolation for cell-, and vertex-centered data on unrestricted SAMR grids are proposed. Additionally we investigate the applicability of SAMR data structures for accelerated software-, and hardware-based volume rendering of large 3D scalar data. KW - Visualization KW - Volume Rendering KW - Adaptive Mesh Refinement Data Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-2005002769 ER - TY - GEN A1 - Achterberg, Tobias A1 - Berthold, Timo T1 - Improving the Feasibility Pump N2 - The Feasibility Pump of Fischetti, Glover, Lodi, and Bertacco has proved to be a very successful heuristic for finding feasible solutions of mixed integer programs. The quality of the solutions in terms of the objective value, however, tends to be poor. This paper proposes a slight modification of the algorithm in order to find better solutions. Extensive computational results show the success of this variant: in 89 out of 121 MIP instances the modified version produces improved solutions in comparison to the original Feasibility Pump. T3 - ZIB-Report - 05-42 KW - mixed integer programming KW - primal heuristics KW - feasibility pump Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8754 ER - TY - GEN A1 - Pham, The Anh T1 - Einbettung neuer Verwaltungsmethoden in die hierarchische Dateisystemsicht N2 - Die hierarchische Organisation von Dateien beherrscht Computersysteme seit vielen Jahren und wird sich vermutlich auch in Zukunft weiterhin durchsetzen. Dennoch stößt diese Verwaltungsmethode in einem klassischen hierarchischen Dateisystem bei dem jährlichen rasanten Zuwachs an neuen Daten an ihre Grenzen, auch wenn Nutzer eine ausgefeilte Verzeichnisstruktur mit einer disziplinierten Namensgebung konsequent auf- und ausbauen. Um den Überblick über die Dateien zu behalten, werden in dieser Arbeit neue Verwaltungsmethoden vorgestellt und in die hierarchische Dateisystemsicht eingebettet. Auf der Basis des hierarchischen Dateisystems bietet ein metadatenbasiertes Dateisystem neben dem hierarchischen Zugriff noch einen flexiblen, assoziativen Zugriff auf Dateien über virtuelle Objekte, indem Suchmethoden in Form einer Anfrage auf in einer Datenbank gespeicherte Index- und Metadaten angewendet werden. Das Ergebnis dieser Abfrage wird mit Hilfe von virtuellen Verzeichnissen und virtuellen Dateien in einer übersichtlichen Form dargestellt, so dass eine Nutzung der hierarchischen Sicht weiterhin intuitiv fortgesetzt wird. Das Datenmanagementsystem ZIBDMS, welches einen verteilten Metadatenkatalog und einen Dateireplikationskatalog beinhaltet, ermöglicht es, die oben genannten Verwaltungsmethoden für die NFS-Schnittstelle, CORBA-Middleware und Web Services transparent zu implementieren. Zudem stellt ZIBDMS weitere neue Dateiverwaltungsmethoden zur Verfügung, die sich in die hierarchische Dateisystemsicht integrieren lassen. Metadaten in Form von Attribut-Wert-Paaren lassen sich als virtuelle Datei darstellen und editieren. Eine Collection bietet die Möglichkeit, Dateien in einem logischen virtuellen Ordner zu organisieren. Mit einem Dependency-Graph lassen sich Dateien zueinander in Relation stellen, so dass eine Linkstruktur zwischen Dateien ausgedrückt werden kann. Das Verweiskonzept eines klassischen hierarchischen Dateisystems wird im ZIBDMS um eine neue Verweisart Weak-Link erweitert, um einen aktualisierbaren, konsistenten und zyklenfreien symbolischen Link anzubieten. In einer hierarchischen Sicht lässt sich durch Verweise ein Baum bilden, in dem eine Navigation und Verweisauflistung möglich sind, was außer ZIBDMS noch kein anderes System bietet. N2 - The hierarchical organization of files has dominated computer systems for many years and this will probably not change in the near future. However, with the rapid annual growth of new data this classical hierarchical file system management method reaches its limitations, even when the user consistently sets up and continually expands an elaborated directory structure with well-disciplined naming. This paper introduces new management methods to maintain an overview of all files which can be embedded in the hierarchical file system. A metadata-based file system, which is based on the hierarchical file system, offers, in addition to hierarchical access, a more flexible and associative access to files via virtual objects by providing query capabilities of index- and metadata which are stored in a database. The query results are presented in a clearly-arranged form of virtual directories and virtual files so that the intuitive hierarchical view continues to be maintained. The data management system ZIBDMS, which contains a distributed metadata catalog and a file replication catalog, permits a transparent implementation of these management methods for the NFS interface, CORBA-middleware or web services. Furthermore, ZIBDMS provides other new file management methods that can be integrated into the hierarchical file system view. Metadata in form of attribute-value-pairs can be presented and edited with a virtual file. A Collection makes it possible to organize files in logical virtual folders. Using a Dependency graph, files can be related to each other and expressed through a link structure between these files. In the ZIBDMS the reference concept of a classical hierarchal file system is extended with a new kind of reference called Weak Link in order to provide up-to-date, consistent and cycle-free symbolic links. With the references a tree can be established in a hierarchical view in which navigation and listing of references are possible; this capability is only possible in the ZIBDMS system. T3 - ZIB-Report - 05-41 KW - ZIBDMS KW - Datenmanagementsystem KW - semantisch KW - Indizierung KW - metadatenbasiert KW - hierarchisch KW - Dateisystem KW - semantic file system KW - XMLFS KW - Context Fil Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8747 ER - TY - GEN A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Chord#: Structured Overlay Network for Non-Uniform Load-Distribution N2 - \newcommand{\chordsharp}{Chord$^\##$} Data lookup is a fundamental problem in peer-to-peer systems: Given a key, find the node that stores the associated object. Chord and other P2P algorithms use distributed hash tables (DHTs) to distribute the keys and nodes evenly across a logical ring. Using an efficient routing strategy, DHTs provide a routing performance of $O (\log N)$ in networks of $N$ nodes. While the routing performance has been shown to be optimal, the uniform key distribution makes it impossible for DHTs to support range queries. For range queries, consecutive keys must be stored on lo gically neighboring nodes. In this paper, we present an enhancement of Chord that eliminates the hash function while keeping the same routing performance. The resulting algorithm, named \chordsharp{}, provides a richer function ality while maintaining the same complexity. In addition to Chord, \chordsharp{} adapts to load imbalance. T3 - ZIB-Report - 05-40 KW - DHT KW - P2P KW - Range Queries Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8736 ER - TY - GEN A1 - Novikov, Yakov A1 - Brinkmann, Raik T1 - Foundations of Hierarchical SAT-Solving N2 - The theory of hierarchical Boolean satisfiability (SAT) solving proposed in this paper is based on a strict axiomatic system and introduces a new important notion of implicativity. The theory makes evident that increasing implicativity is the core of SAT-solving. We provide a theoretical basis for increasing the implicativity of a given SAT instance and for organizing SAT-solving in a hierarchical way. The theory opens a new domain of research: SAT-model construction. Now quite different mathematical models can be used within practical SAT-solvers. The theory covers many advanced techniques such as circuit-oriented SAT-solving, mixed BDD/CNF SAT-solving, merging gates, using pseudo-Boolean constraints, using state machines for representation of Boolean functions, arithmetic reasoning, and managing don t cares. We believe that hierarchical SAT-solving is a cardinal direction of research in practical SAT-solving. T3 - ZIB-Report - 05-38 KW - SAT KW - implicativity KW - verification KW - Boolean vector function KW - satisfiability KW - Bounded-Model-Checking KW - BMC KW - model KW - block KW - hierarchy Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8728 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Schelten, Uwe A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - A Column Generation Approach to Airline Crew Scheduling N2 - The airline crew scheduling problem deals with the construction of crew rotations in order to cover the flights of a given schedule at minimum cost. The problem involves complex rules for the legality and costs of individual pairings and base constraints for the availability of crews at home bases. A typical instance considers a planning horizon of one month and several thousand flights. We propose a column generation approach for solving airline crew scheduling problems that is based on a set partitioning model. We discuss algorithmic aspects such as the use of bundle techniques for the fast, approximate solution of linear programs, a pairing generator that combines Lagrangean shortest path and callback techniques, and a novel rapid branching'' IP heuristic. Computational results for a number of industrial instances are reported. Our approach has been implemented within the commercial crew scheduling system NetLine/Crew of Lufthansa Systems Berlin GmbH. T3 - ZIB-Report - 05-37 KW - Integer Programming KW - Airline Crew Scheduling KW - Branch and Generate Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8713 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - Optimal Fares for Public Transport N2 - The \emph{fare planning problem} for public transport is to design a system of fares that maximize the revenue. We introduce a nonlinear optimization model to approach this problem. It is based on a d iscrete choice logit model that expresses demand as a function of the fares. We illustrate our approach by computing and comparing two different fare systems for the intercity network of the Netherlands. T3 - ZIB-Report - 05-35 KW - fare planning KW - demand function KW - discrete choice model Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8698 ER - TY - GEN A1 - Pfetsch, Marc A1 - Borndörfer, Ralf T1 - Routing in Line Planning for Public Transportation N2 - The line planning problem is one of the fundamental problems in strategic planning of public and rail transport. It consists in finding lines and corresponding frequencies in a network such that a giv en demand can be satisfied. There are two objectives. Passengers want to minimize travel times, the transport company wishes to minimize operating costs. We investigate three variants of a multi-commo dity flow model for line planning that differ with respect to passenger routings. The first model allows arbitrary routings, the second only unsplittable routings, and the third only shortest path rou tings with respect to the network. We compare these models theoretically and computationally on data for the city of Potsdam. T3 - ZIB-Report - 05-36 KW - line planning KW - column generation KW - passenger routing Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8706 ER - TY - GEN A1 - Kuberek, Monika A1 - Radu, Raluca T1 - Online-Fernleihe im KOBV - Handbuch für Bibliotheken N2 - \documentclass[12pt]{article} \usepackage{german} \parindent=0pt \begin{document} Im KOBV wird für die Online-Fernleihe der Zentrale-Fernleihserver (ZFL-Server) der Firma Sisis eingesetzt. Die Software ist in der KOBV-Zentrale installiert. Der ZFL-Server dient im KOBV sowohl für die Bestellung von Monographien als auch für die Bestellung von Aufsatzkopien aus Zeitschriften. Prinzipiell gibt es zwei Verfahren, mit denen sich Bibliotheken an der Online-Fernleihe beteiligen können: das E-Mail-Verfahren und das SLNP-Verfahren. Auf beide wird im Handbuch eingegangen. Die Online-Fernleihe wurde im KOBV eingeführt, um die Fernleihe für die Benutzer zu beschleunigen, das Verfahren für die Bibliotheksmitarbeiter zu vereinfachen und den Arbeitsaufwand zu reduzieren. Sie basiert darauf, dass eine Bestellung anhand eines gefundenen Treffers ausgelöst wird - d.h. die bibliographischen Daten sind bereits verifiziert und in einem Katalog nachgewiesen. Anschlie\"send werden die Fernleihbestellungen über den ZFL-Server automatisch ausgeführt und verwaltet - sowohl in der regionalen KOBV-Fernleihe als auch in der verbundübergreifenden Fernleihe mit den deutschen Bibliotheksverbünden. Der ZFL-Server besteht aus verschiedenen technischen Komponenten. Eine dieser Komponenten ist das Bibliothekskonto, eine Internetanwendung, in der die Bestellverwaltung des ZFL-Servers im Internet für die Bibliotheksbediensteten transparent gemacht wird. Sowohl für die aktive als auch für die passive Fernleihe ist im Bibliothekskonto der Status der Bearbeitung zu jedem Zeitpunkt ersichtlich, z.B. in welcher Bibliothek sich die Bestellung gerade befindet, wann sie dort eingegangen ist und wann sie weggeschickt wurde, ob mit positivem oder negativem Ergebnis. Das Bibliothekskonto ist damit für die Bibliothek ein komfortables Instrument zum Überwachen der Fernleihbestellungen, in dem sie zudem - falls notwendig - in den Bestellvorgang eingreifen kann. Dazu hat jede Bibliothek im Bibliothekskonto eine eigene, Passwort-geschützte Dienstoberfläche. Das vorliegende Handbuch beschreibt die Vorgänge der Bestellverwaltung im Bibliothekskonto. Es richtet sich an Bibliotheksmitarbeiter, die sich mit den einzelnen Arbeitsschritten der Online-Fernleihe vertraut machen wollen. Darüber hinaus ist es zum Nachschlagen gedacht, wenn sich in der täglichen Arbeit Unklarheiten ergeben. \end{document} T3 - ZIB-Report - 05-34 KW - Bibliotheksverbund KW - KOBV KW - KOBV-Fernleihe KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Online-Fernleihe KW - Verbundübergreifende Fernleihe Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8681 ER - TY - GEN A1 - Hildebrandt, Klaus A1 - Polthier, Konrad A1 - Preuß, Eike T1 - Evolution of 3d Curves under Strict Spatial Constraints N2 - We present a new algorithm for fairing of space curves with respect spatial constraints based on a vector valued curvature function. Smoothing with the vector valued curvature function is superior to standard Frenet techniques since the individual scalar components can be modeled similar to curvature-based curve smoothing techniques in 2d. This paper describes a curve smoothing flow that satisfies strict spatial constraints and allows simultaneous control of both curvature functions. T3 - ZIB-Report - 05-33 KW - curve fairing KW - curve smoothing KW - curvature smoothing flow Y1 - 2005 N1 - kein Volltext, Artikel ist in Verlagspublikation erschienen, der Preprint wurde offensichtlich vor längerer Zeit zurückgezogen (keine urn). Kossick 20. 11. 13 ER - TY - GEN A1 - Burgschweiger, Jens A1 - Gnädig, Bernd A1 - Steinbach, Marc T1 - Nonlinear Programming Techniques for Operative Planning in Large Drinking Water Networks N2 - Mathematical decision support for operative planning in water supply systems is highly desirable but leads to very difficult optimization problems. We propose a nonlinear programming approach that yields practically satisfactory operating schedules in acceptable computing time even for large networks. Based on a carefully designed model supporting gradient-based optimization algorithms, this approach employs a special initialization strategy for convergence acceleration, special minimum up and down time constraints together with pump aggregation to handle switching decisions, and several network reduction techniques for further speed-up. Results for selected application scenarios at Berliner Wasserbetriebe demonstrate the success of the approach. T3 - ZIB-Report - 05-31 KW - Water supply KW - large-scale nonlinear programming KW - convergence enhancement KW - discrete decisions KW - network reduction Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8657 ER - TY - GEN A1 - Burgschweiger, Jens A1 - Gnädig, Bernd A1 - Steinbach, Marc T1 - Optimierte Tagesplanung im Berliner Trinkwassernetz N2 - Der Artikel beschreibt ein mathematisches Optimierungssystem zur Betriebsplanung in großen Wassernetzen, das bei den Berliner Wasserbetrieben eingesetzt wird. Für das Berliner Versorgungsnetz werden Optimierungsergebnisse vorgestellt. T3 - ZIB-Report - 05-32 KW - Trinkwasserversorgung KW - kostenminimale Betriebsplanung KW - nichtlineare Optimierung KW - diskrete Entscheidungen Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8668 ER - TY - GEN A1 - Franzone, Piero Colli A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Pavarino, Luca Franco T1 - Adaptivity in Space and Time for Reaction-Diffusion Systems in Electrocardiology N2 - Adaptive numerical methods in space and time are introduced and studied for multiscale cardiac reaction-diffusion models in three dimensions. The evolution of a complete heartbeat, from the excitation to the recovery phase, is simulated with both the anisotropic Bidomain and Monodomain models, coupled with either a variant of the simple FitzHugh-Nagumo model or the more complex phase-I Luo-Rudy ionic model. The simulations are performed with the {\sc kardos} library, that employs adaptive finite elements in space and adaptive linearly implicit methods in time. The numerical results show that this adaptive method successfully solves these complex cardiac reaction-diffusion models on three-dimensional domains of moderate sizes. By automatically adapting the spatial meshes and time steps to the proper scales in each phase of the heartbeat, the method accurately resolves the evolution of the intra- and extra-cellular potentials, gating variables and ion concentrations during the excitation, plateau and recovery phases. T3 - ZIB-Report - 05-30 KW - reaction-diffusion equations KW - cardiac Bidomain and Monodomain models KW - adaptive finite elements KW - adaptive time integration Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8649 ER - TY - GEN T1 - Jahresbericht 2004 T3 - Jahresbericht - 2004 KW - Annual Report Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9799 SN - 0934-5892 ER - TY - GEN A1 - Boev, Ivan A1 - Hodoroaba, Lavinia A1 - Imhof, Andres T1 - Der KOBV-Metadaten-Austausch-Parser (KMA-Parser): Ein Werkzeug für Metadata-Sharing N2 - \\ Zusammenfassung: Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) betreibt für das KOBV-Portal einen Austausch von Beschreibungen zu elektronischen Ressourcen (Metadaten), der zwisc zwischen verschiedenen Informationsportalen in der Region durchgeführt wird. Die unterschiedlichen Informationsportale verwenden verschiedene Metadaten-Schemata und Austausch-Formate für ihre Ressourcebeschreibungen. Um die Heterogenität der Metadaten zu überwinden, wurde der KOBV-Metadaten-Austausch-Parser (KMA-Parser) entwickelt. Andere Metadaten-Schemata werden auf das KOBV-Metadaten-Schema abgebildet. Der KMA-Parser führt gegebenenfalls eine Format-Transformation durch, konvertiert die Inhalte einzelner Elemente über Konkordanzen und erzeugt neue Metadaten-Elemente aus vorhandenen Feldern. Er validiert den Inhalt auf Vollständigkeit und steuert den Austausch der Metadaten zwischen den Portalen. Der Umwandlungsprozess funktioniert jedoch nicht nur in die Richtung des KOBV-Portals, sondern auch in die entgegengesetzte Richtung. Der Artikel beschreibt die einzelnen Vorgänge im KMA-Parser und schildert die Erfahrungen im Umgang mit der Heterogenität von Metadaten. Die gewonnenen Erfahrungen verweisen auf grundlegende Perspektiven in der universellen Zusammenarbeit von Informationsanbietern und -providern.The Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) has built a framework for a bi-directional exchange workflow of electronic resourcesÆ descriptions (metadata) between the KOBV Portal and other Information Portals in the region. The Information Portals use different exchange formats, metadata schemata and controlled vocabularies for their descriptions of resources. In order to overcome this metadata heterogeneity, an application, the KOBV Metadata Exchange Parser (KMA-Parser), has been developed. The KMA-Parser maps the local portalsÆ metadata schemata into the metadata schema of the KOBV Portal. If necessary, it transforms the exchange format, converts contents of individual elements by means roduces new metadata elements on the basis of existent elements. It checks elementsÆ contents on completeness and controls the metadata exchange between the portals. However, the transformation process takes place not only towards the KOBV Portal, but al so vice versa. The article describes the individual processes in the KMA Parser and depicts the experiences in handling the metadataÆs heterogeneity. The experiences gathered give an idea of the prospects for a universal cooperation between information suppliers and providers. T3 - ZIB-Report - 05-29 KW - KOBV-Portal KW - Metadata-Sharing KW - Metadaten-Austausch KW - Vernetzung von Portalen Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8636 ER - TY - GEN A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Martin, Alexander T1 - MIPLIB 2003 N2 - This paper reports on the fourth version of the Mixed Integer Programming Library. Since ({\sc miplib}) is to provide a concise set of challenging problems, it became necessary to purge instances that became too easy. We present an overview of the 27 new problems and statistical data for all 60 instances. T3 - ZIB-Report - 05-28 KW - Mathematical Programming KW - Mixed Integer Programming KW - IP KW - MIP KW - Optimization KW - Instances Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8625 ER - TY - GEN A1 - Lopez-Fernandez, Maria A1 - Palencia, Cesar A1 - Schädle, Achim T1 - A spectral order method for inverting sectorial Laplace transforms N2 - Laplace transforms which admit a holomorphic extension to some sector strictly containing the right half plane and exhibiting a potential behavior are considered. A spectral order, parallelizable method for their numerical inversion is proposed. The method takes into account the available information about the errors arising in the evaluations. Several numerical illustrations are provided. T3 - ZIB-Report - 05-26 KW - Laplace transform KW - numerical inversion KW - parabolic KW - spectral order KW - parallelizable Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8607 ER - TY - GEN A1 - Schädle, Achim A1 - Zschiedrich, Lin T1 - Additive Schwarz method for scattering problems using the PML method at interfaces N2 - Scattering problems in integrated optics can be modeled in simple cases by the Helmholtz equation. The computational domain is truncated by a non-reflecting boundary condition. We investigate Schwarz algorithms with a sort of DtN operator, realized by the PML-method, at the interfaces of the sub-domains as an iterative solver. T3 - ZIB-Report - 05-27 KW - perfectly matched layer KW - Helmholtz equation KW - scattering KW - domain decomposition Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8613 ER - TY - GEN A1 - Imhof, Andres A1 - Malo, Markus T1 - Aufbau einer verteilten Fachredaktion für freie Internet-Ressourcen im KOBV-Portal N2 - Die KOBV-Zentrale betreibt mit dem KOBV-Portal neben der Metasuche in freien Online-Katalogen und Datenbanken ein Nachweisinstrument für elektronische Ressourcen, die von den Bibliotheken Berlin-Brandenburgs lizenziert sind und darüber hinaus diejenigen, die frei zugänglich sowie wissenschaftlich relevant sind. Die Erschließung der freien Ressourcen übernimmt eine kooperative Fachredaktion, die sich aus FachreferentInnen und -lektorInnen aus der Region rekrutiert. Dabei übernimmt jede beteiligte Person die Betreuung einer oder mehrerer Fachgruppen der Dewey Decimal-Classification (DDC) eigenverantwortlich. Die Aufgabe aller FachredakteurInnen besteht in der inhaltlichen Beschreibung, der Klassifizierung, der Vergabe von Schlagworten und der regelmäßigen Reevaluation der einzelnen Ressourcen. Die KOBV-Zentrale hat hierfür einen Kriterienkatalog entwickelt, der als Grundlage für die Beurteilung von elektronischen Ressourcen dient. Erschlossen werden die Ressourcen schließlich über ein webbasierte Eingabe-Tool, dem Metadata-Tool der KOBV-Zentrale. Über eine Mailingliste wird der Abstimmungsbedarf untereinander gedeckt und Diskussionen geführt, die das Projekt weiterführen sollen. Der Artikel beschreibt das Konzept der kooperativen Fachredaktion für freie Ressourcen, die Vorgänge und die Arbeiten, die für die Initiierung notwendig waren. T3 - ZIB-Report - 05-25 KW - Redaktion KW - freie Ressourcen KW - Informationsportal KW - Digibib KW - Digitale Bibliothek KW - Bestandsnachweis KW - elektronische Ressourcen KW - MetaLib Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8599 ER - TY - GEN A1 - Hildebrandt, Klaus A1 - Polthier, Konrad A1 - Wardetzky, Max T1 - On the Convergence of Metric and Geometric Properties of Polyhedral Surfaces N2 - We provide conditions for convergence of polyhedral surfaces and their discrete geometric properties to smooth surfaces embedded in Euclidian $3$-space. The notion of totally normal convergence is shown to be equivalent to the convergence of either one of the following: surface area, intrinsic metric, and Laplace-Beltrami operators. We further s how that totally normal convergence implies convergence results for shortest geodesics, mean curvature, and solutions to the Dirichlet problem. This work provides the justification for a discrete theory of differential geometric operators defined on polyhedral surfaces based on a variational formulation. T3 - ZIB-Report - 05-24 KW - Discrete Geometry KW - Differential Geometry KW - Numerical Analysis Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8587 ER - TY - GEN A1 - Grötschel, Martin A1 - Roggenbuck, Robert A1 - Sperber, Wolfram T1 - Entwicklung und Aufbau des Internet-Dienstes "Math&Industry" N2 - Die Anwendung mathematischer Methoden und Verfahren wird immer mehr zur Voraussetzung innovativer Produkte und Dienstleistungen. Um neue Produkte und Dienstleistungen zu entwickeln, müssen die Produktions- und technologischen Prozesse mathematisch modelliert, beschrieben und optimiert werden. Diesen Umstand Rechnung tragend, hat das Bundesministerium für Bildung und Forschung (BMBF) 1993 begonnen, den Einsatz mathematischer Verfahren und Methoden in der Mathematik über ein spezielles Mathematikprogramm zu fördern. Inzwischen hat die vierte Förderperiode des Mathematikprogramms begonnen. \par Das Medium Internet und insbesondere das WWW sind für die Sichtbarkeit und Transparenz wissenschaftlicher Resultate in den letzten zehn Jahren immer wichtiger geworden. Wer nicht im Web "'sichtbar"' ist, läuft Gefahr, nicht wahrgenommen zu werden. Intention und Ziel des durchgeführten Projekts war es, ein Konzept für eine qualitativ hochwertige und umfassende Darstellung des BMBF Mathematikprogramms, insbesondere der in den Projekten erzielten Ergebnisse, zu entwickeln und zu realisieren und damit den Stellenwert und die Akzeptanz mathematischer Forschung in der Gesellschaft zu festigen und den Wissenstransfer zwischen mathematischer Forschung sowie Forschung und Entwicklung in der Wirtschaft und dem Dienstleistungsbereich zu fördern. T3 - ZIB-Report - 05-23 KW - Internet services KW - distributed systems KW - XML KW - RDF Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8573 ER - TY - GEN A1 - Bley, Andreas A1 - Pattloch, Marcus T1 - Modellierung und Optimierung der X-WiN Plattform N2 - In diesem Artikel werden die Optimierungsmodelle und -verfahren beschrieben, die bei der Planung des Kernnetzes und der Zugangsinfrastruktur des X-WiN verwendet wurden. T3 - ZIB-Report - 05-21 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8551 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Neumann, Marika A1 - Pfetsch, Marc T1 - Fare Planning for Public Transport N2 - In this paper we introduce the fare planning problem for public transport which consists in designing a system of fares maximizing revenue. We propose a new simple general model for this problem. It i s based on a demand function and constraints for the different fares. The constraints define the structure of the fare system, e.g., distance dependent fares or zone fares. We discuss a simple example with a quadratic demand function and distance dependent fares. Then we introduce a more realistic discrete choice model in which passengers choose between different alternatives depending on the numb er of trips per month. We demonstrate the examples by computational experiments. T3 - ZIB-Report - 05-20 KW - fare planning KW - demand function KW - discrete choice model Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8541 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - Public Transport to the fORe! N2 - Can OR methods help the public transport industry to break even? The article gives evidence that there exist significant potentials in this direction, which can be harnessed by a combination of modern mathematical methods and local planning knowledge. Many of the planning steps in public transport are classical combinatorial problems, which can be solved in unprecedented size and quality due the rapid progress in large-scale optimization. Three examples on vehicle scheduling, duty scheduling, and integrated vehicle and duty scheduling illustrate the level that has been reached and the improvements that can be achieved today. Extensions of such methods to further questions of strategic, online, and market-oriented planning are currently investigated. In this way, OR can make a significant contribution to answer the basic but extremely difficult question ``What is a good public transport network?. T3 - ZIB-Report - 05-22 KW - Public transport KW - vehicle scheduling KW - duty scheduling Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8562 UR - http://www.lionhrtpub.com/orms/orms-4-06/frtransport.html ER - TY - GEN A1 - Achterberg, Tobias T1 - Conflict Analysis in Mixed Integer Programming N2 - Conflict analysis for infeasible subproblems is one of the key ingredients in modern SAT solvers to cope with large real-world instances. In contrast, it is common practice for today's mixed integer programming solvers to just discard infeasible subproblems and the information they reveal. In this paper we try to remedy this situation by generalizing the SAT infeasibility analysis to mixed integer programming. We present heuristics for branch-and-cut solvers to generate valid inequalities from the current infeasible subproblem and the associated branching information. SAT techniques can then be used to strengthen the resulting cuts. We performed computational experiments which show the potential of our method: On feasible MIP instances, the number of required branching nodes was reduced by 50\% in the geometric mean. However, the total solving time increased by 15\%. on infeasible MIPs arising in the context of chip verification, the number of nodes was reduced by 90\%, thereby reducing the solving time by 60\%. T3 - ZIB-Report - 05-19 KW - mixed integer programming KW - branch and cut KW - conflict analysis KW - SAT Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8537 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - A Column-Generation Approach to Line Planning in Public Transport N2 - The line planning problem is one of the fundamental problems in strategic planning of public and rail transport. It consists in finding lines and corresponding frequencies in a transport network such that a given travel demand can be satisfied. There are (at least) two objectives. The transport company wishes to minimize operating costs, the passengers want to minimize travel times. We propose a n ew multi-commodity flow model for line planning. Its main features, in comparison to existing models, are that the passenger paths can be freely routed and that the lines are generated dynamically. We discuss properties of this model and investigate its complexity. Results with data for the city of Potsdam, Germany, are reported. T3 - ZIB-Report - 05-18 KW - line planning KW - column generation Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8522 ER - TY - GEN A1 - Weber, Marcus A1 - Meyer, Holger T1 - ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights N2 - This paper introduces a new algorithm of conformational analysis based on mesh-free methods as described in [M. Weber. Mehless methods in Conformation Dynamics.(2005)]. The adaptive decomposition of the conformational space by softly limiting functions avoids trapping effects and allows adaptive refinement strategies. These properties of the algorithm makes ZIBgridfree particularly suitable for the complete exploration of high-dimensional conformational space. The adaptive control of the algorithm benefits from the tight integration of molecular simulation and conformational analysis. An emphasized part of the analysis is the Robust Perron Cluster Analysis (PCCA+) based on the work of Peter Deuflhard and Marcus Weber. PCCA+ supports an almost-characteristic cluster definition with an outstanding mapping of transition states. The outcome is expressed by the metastable sets of conformations, their thermodynamic weights and flexibility. T3 - ZIB-Report - 05-17 KW - Molecular Dynamics KW - Meshfree Methods KW - Conformation Analysis KW - Quality Functions Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8514 ER - TY - GEN A1 - Lange, Carsten A1 - Polthier, Konrad T1 - Anisotropic Smoothing of Point Sets N2 - The use of point sets instead of meshes became more popular during the last years. We present a new method for anisotropic fairing of a point sampled surface using an anisotropic geometric mean curvature flow. The main advantage of our approach is that the evolution removes noise from a point set while it detects and enhances geometric features of the surface such as edges and corners. We derive a shape operator, principal curvature properties of a point set, and an anisotropic Laplacian of the surface. This anisotropic Laplacian reflects curvature properties which can be understood as the point set analogue of Taubin's curvature-tensor for polyhedral surfaces. We combine these discrete tools with techniques from geometric diffusion and image processing. Several applications demonstrate the efficiency and accuracy of our method. T3 - ZIB-Report - 05-16 KW - point sets KW - anisotropic mean curvature KW - anisotropic sampling KW - shape operator KW - principal curvatures KW - anisotropic Laplace KW - mean curvature flow KW - f Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8508 ER - TY - THES A1 - Koch, Thorsten T1 - Rapid Mathematical Programming N2 - The thesis deals with the implementation and application of out-of-the-box tools in linear and mixed integer programming. It documents the lessons learned and conclusions drawn from five years of implementing, maintaining, extending, and using several computer codes to solve real-life industrial problems. By means of several examples it is demonstrated how to apply algebraic modeling languages to rapidly devise mathematical models of real-world problems. It is shown that today's MIP solvers are capable of solving the resulting mixed integer programs, leading to an approach that delivers results very quickly. Even though, problems are tackled that not long ago required the implementation of specialized branch-and-cut algorithms. In the first part of the thesis the modeling language Zimpl is introduced. Chapter 2 contains a complete description of the language. In the subsequent chapter details of the implementation are described. Both theoretical and practical considerations are discussed. Aspects of software engineering, error prevention, and detection are addressed. In the second part several real-world projects are examined that employed the methodology and the tools developed in the first part. Chapter 4 presents three projects from the telecommunication industry dealing with facility location problems. Chapter 5 characterizes questions that arise in UMTS planning. Problems, models, and solutions are discussed. Special emphasis is put on the dependency of the precision of the input data and the results. Possible reasons for unexpected and undesirable solutions are explained. Finally, the Steiner tree packing problem in graphs, a well-known hard combinatorial problem, is revisited. A formerly known, but not yet used model is applied to combine switchbox wire routing and via minimization. All instances known from the literature are solved by this approach, as are some newly generated bigger problem instances. T3 - ZIB-Report - 04-58 KW - Modelling Languages KW - Mixed Integer Programming KW - Steiner Tree Packing in Graphs KW - Location Planning in Telecommunications KW - UMTS Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8346 ER - TY - GEN A1 - Schiela, Anton A1 - Weiser, Martin T1 - Superlinear Convergence of the Control Reduced Interior Point Method for PDE Constrained Optimization N2 - A thorough convergence analysis of the Control Reduced Interior Point Method in function space is performed. This recently proposed method is a primal interior point pathfollowing scheme with the special feature, that the control variable is eliminated from the optimality system. Apart from global linear convergence we show, that this method converges locally almost quadratically, if the optimal solution satisfies a function space analogue to a non-degeneracy condition. In numerical experiments we observe, that a prototype implementation of our method behaves in compliance with our theoretical results. T3 - ZIB-Report - 05-15 KW - interior point methods in function space KW - optimal control KW - superlinear convergence Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8490 ER - TY - GEN A1 - Gärtner, Bernd A1 - Kaibel, Volker T1 - Two New Bounds for the Random-Edge Simplex Algorithm N2 - We prove that the Random-Edge simplex algorithm requires an expected number of at most $13n/sqrt(d)$ pivot steps on any simple d-polytope with n vertices. This is the first nontrivial upper bound for general polytopes. We also describe a refined analysis that potentially yields much better bounds for specific classes of polytopes. As one application, we show that for combinatorial d-cubes, the trivial upper bound of $2^d$ on the performance of Random-Edge can asymptotically be improved by any desired polynomial factor in d. T3 - ZIB-Report - 05-14 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8483 ER - TY - GEN A1 - Koster, Arie M.C.A. T1 - Wavelength Assignment in Multi-Fiber WDM Networks by Generalized Edge Coloring N2 - In this paper, we study wavelength assignment problems in multi-fiber WDM networks. We focus on the special case that all lightpaths have at most two links. This in particular holds in case the network topology is a star. As the links incident to a specific node in a meshed topology form a star subnetwork, results for stars are also of interest for general meshed topologies. We show that wavelength assignment with at most two links per lightpath can be modeled as a generalized edge coloring problem. By this relation, we show that for a network with an even number of fibers at all links and at most two links per lightpath, all lightpaths can be assigned a wavelength without conversion. Moreover, we derive a lower bound on the number of lightpaths to be converted for networks with arbitrary numbers of fibers at the links. A comparison with linear programming lower bounds reveals that the bounds coincide for problems with at most two links per lightpath. For meshed topologies, the cumulative lower bound over all star subnetworks equals the best known solution value for all realistic wavelength assignment instances available, by this proving optimality. T3 - ZIB-Report - 05-13 KW - wavelength assignment KW - optical networks KW - graph theory KW - combinatorial optimization KW - integer programming Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8478 ER - TY - GEN A1 - Andrzejak, Artur A1 - Hermann, Ulf A1 - Sahai, Akhil T1 - FeedbackFlow - An Adaptive Workflow Generator for System Management N2 - We describe a prototypical framework that further automates system management by composing complex management tasks from elementary actions, and executing composite tasks with feedback-awareness. {\sl FEEDBACKFLOW} implements a general closed control loop of \emph{planning - execution - result validation - replanning}, and generates workflows of system management actions in an adaptive manner. System-dependent behaviour of the loop is specified by declarative description of the domain (essentially descriptions of available actions), and statement of the goal. We evaluate the design of this framework on examples taken from resource construction in Utility Computing environments, and discuss the challenges we have encountered. Our implementation utilizes external components such as \emph{MBP}, a \emph{PDDL}-conform planner, and \emph{Triana}, a workflow specification and execution framework. An alternative approach involving \emph{BPEL4WS} is discussed. T3 - ZIB-Report - 05-12 KW - workflow generation KW - system management KW - planning Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8467 ER - TY - GEN A1 - Helmberg, Christoph A1 - Röhl, Stefan T1 - A Case Study of Joint Online Truck Scheduling and Inventory Management for Multiple Warehouses N2 - For a real world problem --- transporting pallets between warehouses in order to guarantee sufficient supply for known and additional stochastic demand --- we propose a solution approach via convex relaxation of an integer programming formulation, suitable for online optimization. The essential new element linking routing and inventory management is a convex piecewise linear cost function that is based on minimizing the expected number of pallets that still need transportation. For speed, the convex relaxation is solved approximately by a bundle approach yielding an online schedule in 5 to 12 minutes for up to 3 warehouses and 40000 articles; in contrast, computation times of state of the art LP-solvers are prohibitive for online application. In extensive numerical experiments on a real world data stream, the approximate solutions exhibit negligible loss in quality; in long term simulations the proposed method reduces the average number of pallets needing transportation due to short term demand to less than half the number observed in the data stream. T3 - ZIB-Report - 05-11 KW - convex relaxation KW - integer programming KW - stochastic demand KW - network models KW - large scale problems KW - bundle method KW - logistics KW - vehicle routing Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8454 ER - TY - GEN A1 - Schädle, Achim A1 - Lopez-Fernandez, Maria A1 - Lubich, Christian T1 - Fast and oblivious convolution quadrature N2 - We give an algorithm to compute $N$ steps of a convolution quadrature approximation to a continuous temporal convolution using only $O(N\, \log N)$ multiplications and $O(\log N)$ active memory. The method does not require evaluations of the convolution kernel, but instead $O(\log N)$ evaluations of its Laplace transform, which is assumed sectorial. The algorithm can be used for the stable numerical solution with quasi-optimal complexity of linear and nonlinear integral and integro-differential equations of convolution type. In a numerical example we apply it to solve a subdiffusion equation with transparent boundary conditions. T3 - ZIB-Report - 05-09 KW - convolution KW - numerical integration KW - Runge-Kutta methods KW - Volterra integral equation KW - anomalous diffusion Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8437 ER - TY - GEN A1 - Lopez-Fernandez, Maria A1 - Lubich, Christian A1 - Palencia, Cesar A1 - Schädle, Achim T1 - Fast Runge-Kutta approximation of inhomogeneous parabolic equations N2 - The result after $N$ steps of an implicit Runge-Kutta time discretization of an inhomogeneous linear parabolic differential equation is computed, up to accuracy $\varepsilon$, by solving only $$O\Big(\log N\, \log \frac1\varepsilon \Big) $$ linear systems of equations. We derive, analyse, and numerically illustrate this fast algorithm. T3 - ZIB-Report - 05-10 KW - parabolic equation KW - Runge-Kutta methods Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8443 ER - TY - GEN A1 - Busch, Hubert T1 - Abschlußbericht des DFN-Projekts "Virtueller Supercomputer Berlin - Hannover" N2 - Mit der Installation des neuen Hochleistungsrechners für die norddeutschen Länder (HLRN) steht den Wissenschaftlern ein außergewöhnlich leistungsfähiges System zur Verfügung. Durch die Verteilung der Rechenelemente auf zwei verschiedene Standorte in Berlin (ZIB) und Hannover (RRZN) entstehen jedoch auch neue Herausforderungen für den Betrieb und die effiziente Nutzung des Rechners. Inhalt dieses Projektes ist die Erforschung und Lösung der durch die Verteilung des Systems hervorgerufenen Probleme (z.B. Scheduling, Kommunikation, I/O). Es werden effiziente Lösungen zur Bereitstellung eines virtuellen, hoch-performanten und transparenten Systems entwickelt, die auf vergleichbare Installationen übertragbar sind. T3 - ZIB-Report - 04-57 KW - Verteilte Systeme KW - Virtuelle Supercomputer Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8337 ER - TY - GEN A1 - Wolf, Thomas T1 - Partial and complete linearization of PDEs based on conservation laws N2 - A method based on infinite parameter conservation laws is described to factor linear differential operators out of nonlinear partial differential equations (PDEs) or out of differential consequences of nonlinear PDEs. This includes a complete linearization to an equivalent linear PDE (-system) if that is possible. Infinite parameter conservation laws can be computed, for example, with the computer algebra package {\sc ConLaw}. T3 - ZIB-Report - 05-06 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8409 ER - TY - GEN A1 - Wolf, Thomas T1 - Integrable quadratic Hamiltonians with a linear Lie-Poisson bracket N2 - Quadratic Hamiltonians with a linear Lie-Poisson bracket have a number of applications in mechanics. For example, the Lie-Poisson bracket $e(3)$ includes the Euler-Poinsot model describing motion of a rigid body around a fixed point under gravity and the Kirchhoff model describes the motion of a rigid body in ideal fluid. Advances in computer algebra algorithms, in implementations and hardware, together allow the computation of Hamiltonians with higher degree first integrals providing new results in the search for integrable models. A computer algebra module enabling related computations in a 3-dimensional vector formalism is described. T3 - ZIB-Report - 05-07 KW - Hamilton systems KW - Integrability KW - Computer algebra Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8414 ER - TY - GEN A1 - Anco, Stephen A1 - Wolf, Thomas T1 - Some classifications of hyperbolic vector evolution equations N2 - Motivated by recent work on integrable flows of curves and 1+1 dimensional sigma models, several $O(N)$-invariant classes of hyperbolic equations $Utx=f(U,Ut,Ux)$ for an $N$-component vector $U(t,x)$ are considered. In each class we find all scaling-homogeneous equations admitting a higher symmetry of least possible scaling weight. Sigma model interpretations of these equations are presented. T3 - ZIB-Report - 05-08 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8429 ER - TY - GEN A1 - Tsuchida, Takayuki A1 - Wolf, Thomas T1 - Classification of polynomial integrable systems of mixed scalar and vector evolution equations. I N2 - We perform a classification of integrable systems of mixed scalar and vector evolution equations with respect to higher symmetries. We consider polynomial systems that are homogeneous under a suitable weighting of variables. This paper deals with the KdV weighting, the Burgers (or potential KdV or modified KdV) weighting, the Ibragimov--Shabat weighting and two unfamiliar weightings. The case of other weightings will be studied in a subsequent paper. Making an ansatz for undetermined coefficients and using a computer package for solving bilinear algebraic systems, we give the complete lists of $2^{\mbox{\scriptsize nd }}$order systems with a $3^{\mbox{\scriptsize rd }}$order or a $4^{\mbox{\scriptsize th }}$order symmetry and $3^{\mbox{\scriptsize rd }}$order systems with a $5^{\mbox{\scriptsize th }}$order symmetry. For all but a few systems in the lists, we show that the system (or, at least a subsystem of it) admits either a Lax representation or a linearizing transformation. A thorough comparison with recent work of Foursov and Olver is made. T3 - ZIB-Report - 05-05 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8391 ER - TY - GEN A1 - Bley, Andreas T1 - Inapproximability Results for the Inverse Shortest Paths Problem with Integer Length and Unique Shortest Paths N2 - We study the complexity of two Inverse Shortest Paths (ISP) problems with integer arc lengths and the requirement for uniquely determined shortest paths. Given a collection of paths in a directed graph, the task is to find positive integer arc lengths such that the given paths are uniquely determined shortest paths between their respective terminals. The first problem seeks for arc lengths that minimize the length of the longest of the prescribed paths. In the second problem, the length of the longest arc is to be minimized. We show that it is $np-hard$ to approximate the minimal longest path length within a factor less than $8/7$ or the minimal longest arc length within a factor less than $9/8$. This answers the (previously) open question whether these problems are $np-hard$ or not. We also present a simple algorithm that achieves an $\mathcal{O}(|V|)$-approximation guarantee for both variants. Both ISP problems arise in the planning of telecommunication networks with shortest path routing protocols. Our results imply that it is $\mathcal{NP}$-hard to decide whether a given path set can be realized with a real shortest path routing protocol such as OSPF, IS-IS, or RIP. T3 - ZIB-Report - 05-04 KW - Inverse Shortest Paths KW - Computational Complexity KW - Approximation KW - Shortest Path Routing Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8388 ER - TY - GEN A1 - Kanaeva, Zara T1 - Ranking: Google und CiteSeer N2 - Im Rahmen des klassischen Information Retrieval wurden verschiedene Verfahren für das Ranking sowie die Suche in einer homogenen strukturlosen Dokumentenmenge entwickelt. Die Erfolge der Suchmas chine Google haben gezeigt, dass die Suche in einer zwar inhomogenen aber zusammenhängenden Dokumentenmenge wie dem Internet unter Berücksichtigung der Dokumentenverbindungen (Links) sehr ef fektiv sein kann. Unter den von der Suchmaschine Google realisierten Konzepten ist ein Verfahren zum Ranking von Suchergebnissen (PageRank), das in diesem Artikel kurz erklärt wird. % Darüber hinaus wird auf die Konzepte eines Systems namens CiteSeer eingegangen, welches automatisch bibliographische Angaben indexiert (engl. \glqq Autonomous Citation Indexing\grqq, ACI). Letzteres erzeugt aus einer Menge von nicht-vernetzten wissenschaftlichen Dokumenten eine zusammenhängende Dokumentenmenge und ermöglicht den Einsatz von Ranking-Verfahren, die auf den von Google genutzten Verfahren basieren. T3 - ZIB-Report - 04-55 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8315 ER - TY - GEN A1 - Kanaeva, Zara T1 - Verteilter Dokumenten Speicher: Erfahrungen mit der Suchmaschine Fast N2 - In diesem Bericht wurden Erfahrungen mit der Suchmaschine FAST im Rahmen des Projektes Verteilter Contentspeicher sowie die Suchmaschine FAST beschrieben. Das Ziel des Projektes Verteilter Contentspeicher war die Speicherung, Erschließung und das Angebot der digitalen Bestände der Journale und Dokumente der KOBV-Bibliotheken zu ermöglichen. Die Eignung der Suchmaschine FAST für das Projektvorhaben wurde systematisch und gründlich getestet, indem verschiedene Dokumentmengen mit FAST indexiert wurden. T3 - ZIB-Report - 04-56 Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8326 ER - TY - GEN A1 - Hodoroaba, Lavinia A1 - Imhof, Andres A1 - Malo, Markus T1 - Das Profil des KOBV-Portals N2 - Zahlreiche lokale, nationale und internationale Informationsportale existieren mit zum Teil gleichen Angeboten und Dienstleistungen nebeneinander. Da der Aufbau und Betrieb von Portalen kostspielig ist, sollten die einzelnen Dienstleistungen abgestimmt und sinnvoll untereinander vernetzt werden. Für eine solch anzustrebende Kooperation unter Portalen ist es notwendig, ein jeweils eigenes Portalprofil zu definieren, um bei einer Gegenüberstellung der Profile die Abgrenzungen und Verknüpfungspunkte deutlich werden zu lassen. Die KOBV-Zentrale möchte mit der Profilbeschreibung des KOBV-Portals beginnen und so die eigenen Angebote des regionalen Portals mit denen anderer auf sinnvolle Weise verknüpfen. Für diese Positionsbestimmung werden die Dienstleistungen, die Zielgruppe, die Kriterien für die Ressourcenauswahl sowie die Abgrenzung zu anderen Portalen dargelegt. T3 - ZIB-Report - 04-54 KW - Informationsportal KW - Portal KW - Verbundportal KW - Digibib KW - Profilbeschreibung KW - Sammelprofil KW - KOBV-Suchmaschine KW - Digitale Bibliothek Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8292 ER - TY - GEN A1 - Friese, Philipp A1 - Rambau, Jörg T1 - Online-Optimization of Multi-Elevator Transport Systems with Reoptimization Algorithms based on Set-Partitioning Models N2 - We develop and experimentally compare policies for the control of a system of $k$ elevators with capacity one in a transport environment with $\ell$ floors, an idealized version of a pallet elevator system in a large distribution center of the Herlitz PBS AG in Falkensee. Each elevator in the idealized system has an individual waiting queue of infinite capacity. On each floor, requests arrive over time in global waiting queues of infinite capacity. The goal is to find a policy that, without any knowledge about future requests, assigns an elevator to each req uest and a schedule to each elevator so that certain expected cost functions (e.g., the average or the maximal flow times) are minimized. We show that a reoptimization policy for minimizing average sq uared waiting times can be implemented to run in real-time ($1\,s$) using dynamic column generation. Moreover, in discrete event simulations with Poisson input it outperforms other commonly used polic ies like multi-server variants of greedy and nearest neighbor. T3 - ZIB-Report - 05-03 KW - elevator group control KW - policy KW - reoptimization KW - online KW - real-time KW - simulation Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8373 ER - TY - THES A1 - Hiller, Benjamin T1 - Bad Guys are Rare: Probabilistic Analysis of an Elementary Dial-a-Ride Problem N2 - This thesis deals with a Dial-a-Ride problem on trees and considers both offline and online versions of this problem. We study the behavior of certain algorithms on random instances, i.e. we do probabilistic analysis. The focus is on results describing the typical behavior of the algorithms, i.e. results holding with (asymptotically) high probability. For the offline version, we present a simplified proof of a result of Coja-Oghlan, Krumke und Nierhoff. The results states that some heuristic using a minimum spanning tree to approximate a Steiner tree gives optimal results with high probability. This explains why this heuristic produces optimal solutions quite often. In the second part, probabilistic online versions of the problem are introduced. We study the online strategies REPLAN and IGNORE. Regarding the IGNORE strategy we can show that it works almost optimal under high load with high probability. KW - Dial-a-Ride problem on trees KW - probabilistic analysis KW - online algorithms Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10114 ER - TY - GEN A1 - Bosse, Hartwig A1 - Grötschel, Martin A1 - Henk, Martin T1 - Polynomial Inequalities Representing Polyhedra N2 - Our main result is that every $n$-dimensional polytope can be described by at most $2n-1$ polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an $n$-dimensional pointed polyhedral cone we prove the bound $2n-2$ and for arbitrary polyhedra we get a constructible representation by $2n$ polynomial inequalities. T3 - ZIB-Report - 04-53 KW - polyhedra and polytopes KW - semi-algebraic sets KW - polyhedral combinatorics KW - polynomial inequalities KW - stability index Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8284 ER - TY - GEN A1 - Baum, Daniel T1 - Multiple Semi-flexible 3D Superposition of Drug-sized Molecules N2 - In this paper we describe a new algorithm for multiple semi-flexible superpositioning of drug-sized molecules. The algorithm identifies structural similarities of two or more molecules. When comparing a set of molecules on the basis of their three-dimensional structures, one is faced with two main problems. (1) Molecular structures are not fixed but flexible, i.e., a molecule adopts different forms. To address this problem, we consider a set of conformers per molecule. As conformers we use representatives of conformational ensembles, generated by the program ZIBMol. (2) The degree of similarity may vary considerably among the molecules. This problem is addressed by searching for similar substructures present in arbitrary subsets of the given set of molecules. The algorithm requires to preselect a reference molecule. All molecules are compared to this reference molecule. For this pairwise comparison we use a two-step approach. Clique detection on the correspondence graph of the molecular structures is used to generate start transformations, which are then iteratively improved to compute large common substructures. The results of the pairwise comparisons are efficiently merged using binary matching trees. All common substructures that were found, whether they are common to all or only a few molecules, are ranked according to different criteria, such as number of molecules containing the substructure, size of substructure, and geometric fit. For evaluating the geometric fit, we extend a known scoring function by introducing weights which allow to favor potential pharmacophore points. Despite considering the full atomic information for identifying multiple structural similarities, our algorithm is quite fast. Thus it is well suited as an interactive tool for the exploration of structural similarities of drug-sized molecules. T3 - ZIB-Report - 04-52 KW - pharmaceutical drug design KW - multiple superposition KW - semi-flexible alignment KW - clique detection KW - iterative closest point KW - matching tree Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8278 ER - TY - GEN A1 - Schmidt-Ehrenberg, Johannes A1 - Hege, Hans-Christian T1 - Visual Analysis of Molecular Conformations by Means of a Dynamic Density Mixture Model N2 - We propose an approach for transforming the sampling of a molecular conformation distribution into an analytical model based on Hidden Markov Models. The model describes the sampled shape density as a mixture of multivariate unimodal densities. Thus, it delivers an interpretation of the sampled density as a set of typical shapes that appear with different probabilities and are characterized by their geometry, their variability and transition probabilities between the shapes. The gained model is used to identify atom groups of constant shape that are connected by metastable torsion angles. Based on this description an alignment for the original sampling is computed. As it takes into account the different shapes contained in the sampled set, this alignment allows to compute reasonable average shapes and meaningful shape density plots. Furthermore, it enables us to visualize typical conformations. T3 - ZIB-Report - 05-02 KW - multimodal circular distribution KW - mixture estimation KW - molecular conformations Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8361 ER - TY - GEN A1 - Steidinger, Alexander T1 - Data Management for Processing Molecules N2 - Molecular dynamics simulations of possible ligands for proteins yield large amounts of data in the form of trajectories which are further processed in order to find metastable conformations. These conformations can then be used for docking between ligand and protein. Around this core computation procedure lots of other data have to be managed. It should also be possible for external users not involved in program development to perform computations. As a paradigm for other fields where a similar constitution of program usage and data processing is found we present a software architecture for data generation, access and management. Requirements for this system include: Ease of use, graphical user interface, persistent storage of data concerning molecules, users, programs, program parameters, metadata, and results. A mere storage in the file system would render a quick overview of data more or less impossible. On the other hand, storing large amounts of binary data in a database doesn't yield any advantage concerning speed of access. Therefore, a hybrid approach combining file system and database is appropriate. The system should be easily extensible by inserting new applications which can be controlled and whose results can be collected and stored. The software system described here consists of different components, the presentation layer (graphical user interface), the business logic, the persistence layer (relational database plus file system), and an interface to the compute cluster (batch system for parallel processing). We will discuss the alternatives and take a closer look at the components. T3 - ZIB-Report - 05-01 KW - molecular structure KW - molecular comparison KW - fingerprints KW - software architecture KW - thin client KW - web interface KW - web server KW - relational database KW - b Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8358 ER - TY - GEN A1 - Hochmuth, Reinhard T1 - Homogenization for a Nonlocal Coupling Model N2 - In [7,8,12] homogenization techniques are applied to derive an anisotropic variant of the bio-heat transfer equation as asymptotic result of boundary value problems providing a microscopic description for microvascular tissue. In view of a future application on treatment planning in hyperthermia, we investigate here the homogenization limit for a coupling model, which takes additionally into account the influence of convective heat transfer in medium size blood vessels. This leads to second order elliptic boundary value problems with nonlocal boundary conditions on parts of the boundary. Moreover, we present asymptotic estimates for first order correctors. T3 - ZIB-Report - 04-50 KW - Homogenization KW - nonlocal boundary conditions KW - Robin boundary conditions KW - correctos KW - heat transfer KW - bio-heat equation KW - hyperthermia Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8251 ER - TY - GEN A1 - Baumeister, Timm A1 - Cordes, Frank T1 - A new Model for the Free Energy of Solvation and its Application in Protein Ligand Scoring N2 - A new and time efficient model to evaluate the free energy of solvation has been developed. The solvation free energy is separated into an electrostatic term, a hydrogen bond term, and a rest-term, combining both entropic and van der Waals effects. The electrostatic contribution is evaluated with a simplified boundary element method using the partial charges of the MMFF94 force field. The number of hydrogen bonds and the solvent excluded surface area over the surface atoms are used in a linear model to estimate the non-electrostatic contribution. This model is applied to a set of 213 small and mostly organic molecules, yielding an rmsd of 0.87kcal/mol and a correlation with experimental data of r=0.951. The model is applied as a supplementary component of the free energy of binding to estimate binding constants of protein ligand complexes. The intermolecular interaction energy is evaluated by using the MMFF94 force field. T3 - ZIB-Report - 04-51 KW - scoring KW - solvation KW - free energy Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8265 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - An Integer Programming Model for Multi-Layer Network Design N2 - We present an integer linear programming model for the design of multi-layer telecommunication networks. The formulation integrates hardware, capacity, routing, and grooming decisions in \emph{any} n umber of network layers. Practical hardware restrictions and cost can accurately be taken into account for technologies based on connection-oriented routing protocols. T3 - ZIB-Report - 04-49 KW - multi-layer networks KW - integer programming KW - network design KW - routing KW - grooming Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8248 ER - TY - GEN A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi A1 - Weiser, Martin T1 - The convergence of an interior point method for an elliptic control problem with mixed control-state constraints N2 - The paper addresses primal interior point method for state constrained PDE optimal control problems. By a Lavrentiev regularization, the state constraint is transformed to a mixed control-state constraint with bounded Lagrange multiplier. Existence and convergence of the central path are established, and linear convergence of a short-step pathfollowing method is shown. The behaviour of the regularizations are demonstrated by numerical examples. T3 - ZIB-Report - 04-47 KW - interior point methods in function space KW - optimal control KW - mixed control-state constraints KW - Lavrentiev regularization Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8223 ER - TY - GEN A1 - Burgschweiger, Jens A1 - Gnädig, Bernd A1 - Steinbach, Marc T1 - Optimization Models for Operative Planning in Drinking Water Networks N2 - The topic of this paper is minimum cost operative planning of pressurized water supply networks over a finite horizon and under reliable demand forecast. Since this is a very hard problem, it is desirable to employ sophisticated mathematical algorithms, which in turn calls for carefully designed models with suitable properties. The paper develops a nonlinear mixed integer model and a nonlinear programming model with favorable properties for gradient-based optimization methods, based on smooth component models for the network elements. In combination with further nonlinear programming techniques (to be reported elsewhere), practically satisfactory near-optimum solutions even for large networks can be generated in acceptable time using standard optimization software on a PC workstation. Such an optimization system is in operation at Berliner Wasserbetriebe. T3 - ZIB-Report - 04-48 KW - Drinking water supply KW - distribution network KW - minimum cost operative planning KW - continuous time model KW - mixed integer model KW - nonlinear programming m Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8237 ER - TY - GEN A1 - Steinbach, Marc T1 - On PDE Solution in Transient Optimization of Gas Networks N2 - Operative planning in gas distribution networks leads to large-scale mixed-integer optimization problems involving a hyperbolic PDE defined on a graph. We consider the NLP obtained under prescribed combinatorial decisions---or as relaxation in a branch and bound framework, addressing in particular the KKT systems arising in primal-dual interior methods. We propose a custom solution algorithm using sparse local projections, based on the KKT systems' structual properties induced by the discretized gas flow equations in combination with the underlying network topology. The numerical efficiency and accuracy of the algorithm are investigated, and detailed computational comparisons with a control space method and with the multifrontal solver MA27 are provided. T3 - ZIB-Report - 04-46 KW - Gas network KW - operative planning KW - PDE constrained optimization KW - KKT system factorization KW - sparse projection method Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8215 ER - TY - GEN A1 - Wolle, Thomas A1 - Koster, Arie M.C.A. A1 - Bodlaender, Hans L. T1 - A Note on Contraction Degeneracy N2 - The parameter contraction degeneracy -- the maximum minimum degree over all minors of a graph -- is a treewidth lower bound and was first defined in (Bodlaender, Koster, Wolle, 2004). In experiments it was shown that this lower bound improves upon other treewidth lower bounds. In this note, we examine some relationships between the contraction degeneracy and connected components of a graph, block s of a graph and the genus of a graph. We also look at chordal graphs, and we study an upper bound on the contraction degeneracy and another lower bound for treewidth. A data structure that can be used for algorithms computing the degeneracy and similar parameters, is also described. T3 - ZIB-Report - 04-43 KW - contraction degeneracy KW - genus of a graph KW - treewidth lower bounds Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8180 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Wolle, Thomas A1 - Bodlaender, Hans L. T1 - Degree-Based Treewidth Lower Bounds N2 - Every lower bound for treewidth can be extended by taking the maximum of the lower bound over all subgraphs or minors. This extension is shown to be a very vital idea for improving treewidth lower bounds. In this paper, we investigate a total of nine graph parameters, providing lower bounds for treewidth. The parameters have in common that they all are the vertex-degree of some vertex in a subgra ph or minor of the input graph. We show relations between these graph parameters and study their computational complexity. To allow a practical comparison of the bounds, we developed heuristic algorithms for those parameters that are NP-hard to compute. Computational experiments show that combining the treewidth lower bounds with minors can considerably improve the lower bounds. T3 - ZIB-Report - 04-44 KW - contraction degeneracy KW - Ramachandramurthi parameter KW - treewidth lower bounds Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8193 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Koster, Arie M.C.A. T1 - On the Maximum Cardinality Search Lower Bound for Treewidth N2 - The Maximum Cardinality Search algorithm visits the vertices of a graph in some order, such that at each step, an unvisited vertex that has the largest number of visited neighbors becomes visited. An MCS-ordering of a graph is an ordering of the vertices that can be generated by the Maximum Cardinality Search algorithm. The visited degree of a vertex $v$ in an MCS-ordering is the number of neighbors of $v$ that are before $v$ in the ordering. The visited degree of an MCS-ordering $\psi$ of $G$ is the maximum visited degree over all vertices $v$ in $\psi$. The maximum visited degree over all MCS-orderings of graph $G$ is called its {\em maximum visited degree}. Lucena (2003) showed that the treewidth of a graph $G$ is at least its maximum visited degree. We show that the maximum visited degree is of size $O(\log n)$ for planar graphs, and give examples of planar graphs $G$ with maximum visited degree $k$ with $O(k!)$ vertices, for all $k\in \Bbb{N}$. Given a graph $G$, it is NP-complete to determine if its maximum visited degree is at least $k$, for any fixed $k\geq 7$. Also, this problem does not have a polynomial time approximation algorithm with constant ratio, unless P=NP. Variants of the problem are also shown to be NP-complete. We also propose and experimentally analyses some heuristics for the problem. Several tiebreakers for the MCS algorithm are proposed and evaluated. We also give heuristics that give upper bounds on the value of the maximum visited degree of a graph, which appear to give results close to optimal on many graphs from real life applications. T3 - ZIB-Report - 04-45 KW - maximum cardinality search KW - treewidth KW - lower bounds KW - planar graphs KW - graph algorithms Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8201 ER - TY - GEN A1 - Koch, Thorsten A1 - Wessäly, Roland T1 - Hierarchical Infrastructure Planning in Networks N2 - In this article, strategical infrastructure planning problems in the design of large-scale telecommunication networks are discussed based on experiences from three projects with industrial partners: The access network planning of the German Gigabit-Wissenschaftsnetz (G-WiN) for DFN (Verein zur Förderung eines Deutschen Forschungsnetzes e.V.), the mobile network switching center location planning project for E-Plus Mobilfunk, and the fixed network switching center location planning project for TELEKOM AUSTRIA. We introduce a mathematical model for a hierarchical multi-commodity capacitated facility location problem, present adaptions of this basic model to the specific requirements within the different projects and discuss the individual peculiarities and model decisions made. Eventually, we present and discuss computational results of three associated case studies, illustrating '"how we did the job`` with mathematical methods. T3 - ZIB-Report - 04-42 KW - Facility Location KW - Telecommunication KW - Mixed Integer Programming Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8174 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian T1 - Provably Good Solutions for Wavelength Assignment in Optical Networks N2 - In this paper, we study the minimum converter wavelength assignment problem in optical networks. To benchmark the quality of solutions obtained by heuristics, we derive an integer programming formula tion by generalizing the formulation of Mehrotra and Trick (1996) for the vertex coloring problem. To handle the exponential number of variables, we propose a column generation approach. Computational experiments show that the value of the linear relaxation states a good lower bound and can often prove optimality of the best solution generated heuristically. T3 - ZIB-Report - 04-40 KW - wavelength assignment KW - integer programming KW - column generation Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8155 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian T1 - Linear Programming Lower Bounds for Minimum Converter Wavelength Assignment in Optical Networks N2 - In this paper, we study the conflict-free assignment of wavelengths to lightpaths in an optical network with the opportunity to place wavelength converters. To benchmark heuristics for the problem, we develop integer programming formulations and study their properties. Moreover, we study the computational performance of the column generation algorithm for solving the linear relaxation of the most promising formulation. In many cases, a non-zero lower bound on the number of required converters is generated this way. For several instances, we in fact prove optimality since the lower bound equals the best known solution value. T3 - ZIB-Report - 04-41 KW - optical networks KW - wavelength assignment KW - integer programming Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8160 ER - TY - GEN A1 - Weber, Marcus A1 - Rungsarityotin, Wasinee A1 - Schliep, Alexander T1 - Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data N2 - The problem of clustering data can be formulated as a graph partitioning problem. Spectral methods for obtaining optimal solutions have reveceived a lot of attention recently. We describe Perron Cluster Cluster Analysis (PCCA) and, for the first time, establish a connection to spectral graph partitioning. We show that in our approach a clustering can be efficiently computed using a simple linear map of the eigenvector data. To deal with the prevalent problem of noisy and possibly overlapping data we introduce the min Chi indicator which helps in selecting the number of clusters and confirming the existence of a partition of the data. This gives a non-probabilistic alternative to statistical mixture-models. We close with showing favorable results on the analysis of gene expressi on data for two different cancer types. T3 - ZIB-Report - 04-39 KW - Perron cluster analysis KW - spectral graph theory KW - clustering KW - gene expression Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8140 ER - TY - GEN A1 - Weiser, Martin A1 - Gänzler, Tobias A1 - Schiela, Anton T1 - A Control Reduced Primal Interior Point Method for PDE Constrained Optimization N2 - A primal interior point method for control constrained optimal control problems with PDE constraints is considered. Pointwise elimination of the control leads to a homotopy in the remaining state and dual variables, which is addressed by a short step pathfollowing method. The algorithm is applied to the continuous, infinite dimensional problem, where discretization is performed only in the innermost loop when solving linear equations. The a priori elimination of the least regular control permits to obtain the required accuracy with comparable coarse meshes. Convergence of the method and discretization errors are studied, and the method is illustrated at two numerical examples. T3 - ZIB-Report - 04-38 KW - interior point methods in function space KW - optimal control KW - finite elements KW - discretization error Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8138 ER - TY - GEN A1 - Joswig, Michael A1 - Pfetsch, Marc T1 - Computing Optimal Morse Matchings N2 - Morse matchings capture the essential structural information of discrete Morse functions. We show that computing optimal Morse matchings is NP-hard and give an integer programming formulation for the problem. Then we present polyhedral results for the corresponding polytope and report on computational results. T3 - ZIB-Report - 04-37 KW - discrete Morse function KW - Morse matching Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8120 ER - TY - GEN A1 - Lutz-Westphal, Brigitte T1 - Die Mathematik der kürzesten Wege. Inhalte und Methoden für den Unterricht N2 - Wie findet man den optimalen Weg im U-Bahnnetz? Das Problem wird als Graph modelliert und dann eine Breitensuche durchgeführt. Will man Weglängen oder Fahrzeiten mitberücksichtigen, so braucht man den Algorithmus von Dijkstra für gewichtige Graphen. Beim Nachdenken über diese Algorithmen werden auch Fragestellungen der Graphentheorie berührt. In einem zweiten Abschnitt werden methodische Hinweise für den Unterricht in der Sekundarstufe I und II gegeben, insbesondere, wie man Lernende dazu bringen kann, ihre Ideen für Algorithmen präzise zu analysieren und zu Papier zu bringen. T3 - ZIB-Report - 04-36 KW - Schule KW - Unterricht KW - Graphenalgorithmen KW - Graphen KW - Unterrichtsmethoden Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8116 ER - TY - GEN A1 - Lutz-Westphal, Brigitte T1 - Wie komme ich optimal zum Ziel? Unterricht über kürzeste-Wege-Algorithmen für Graphen N2 - Kürzeste Wege tauchen fast überall im Alltag auf. Daher eignet sich dieses Optimierungsproblem gut für den Unterricht. Modellierung und heuristische Vorgehensweisen werden geübt, um schließlich die klassischen kürzesten Wege-Algorithmen selbst zu erfinden. In diesem Artikel werden die Inhalte vorgestellt und konkrete Hinweise zum Unterricht in der Schule gegeben. T3 - ZIB-Report - 04-35 KW - Schule KW - Unterricht KW - kombinatorische Optimierung KW - Algorithmen Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8102 ER - TY - GEN A1 - Sokolov, Vladimir V. A1 - Wolf, Thomas T1 - Integrable quadratic Hamiltonians on so(4) and so(3,1) N2 - We investigate a special class of quadratic Hamiltonians on $so(4)$ and $so(3,1)$ and describe Hamiltonians that have additional polynomial integrals. One of the main results is a new integrable case with an integral of sixth degree. T3 - ZIB-Report - 04-33 KW - integrable quadratic Hamiltonians KW - polynomial integrals KW - classification Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8085 ER - TY - GEN A1 - Lutz-Westphal, Brigitte T1 - Unterrichtsideen zu Algorithmen der kombinatorischen Optimierung N2 - Im Rahmen von Problemstellungen der kombinatorischen Optimierung können Schülerinnen und Schüler lernen, Algorithmen selber zu entwickeln. Gleichzeitig lernen sie dabei moderne Mathematik in ihren Anwendungen kennen und erleben die Mathematik als lebendige Wissenschaft. T3 - ZIB-Report - 04-34 KW - Schule KW - Unterricht KW - kombinatorische Optimierung KW - Algorithmen Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8094 ER - TY - GEN A1 - Harks, Tobias T1 - Utility Proportional Fair Bandwidth Allocation - An Optimization Oriented Approach N2 - In this paper, we present a novel approach to the congestion control and resource allocation problem of elastic and real-time traffic in telecommunication networks. With the concept of utility functions, where each source uses a utility function to evaluate the benefit from achieving a transmission rate, we interpret the resource allocation problem as a global optimization problem. The solution to this problem is characterized by a new fairness criterion, \e{utility proportional fairness}. We argue that it is an application level performance measure, i.e. the utility that should be shared fairly among users. As a result of our analysis, we obtain congestion control laws at links and sources that are globally stable and provide a utility proportional fair resource allocation in equilibrium. We show that a utility proportional fair resource allocation also ensures utility max-min fairness for all users sharing a single path in the network. As a special case of our framework, we incorporate utility max-min fairness for the entire network. To implement our approach, neither per-flow state at the routers nor explicit feedback beside ECN (Explicit Congestion Notification) from the routers to the end-systems is required. T3 - ZIB-Report - 04-32 KW - Utility proportional fairness KW - resource allocation KW - congestion control KW - real-time applications Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8079 ER - TY - GEN A1 - Hodoroaba, Lavinia A1 - Imhof, Andres A1 - Kuberek, Monika T1 - Das KOBV-Portal, elektronische Ressourcen in Berlin-Brandenburg: Nachweis, parallele Suche und weiterführende Dienste N2 - \documentclass[12pt]{article} \usepackage{german} \parindent=0pt \begin{document} Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) hat in den Jahren 2001 bis 2003 im Rahmen des Entwicklungsprojektes ''KOBV-Informationsportal`` ein regionales Portal aufgebaut, in dem integrierte Informationsdienste fr die regionalen Bibliotheken zur Verfügung gestellt werden. Das ''KOBV-Portal - Digitale Bibliothek Berlin-Brandenburg`` wurde im Dezember 2003 in Betrieb genommen. Das KOBV-Portal bietet in seiner ersten Ausbaustufe den Nachweis über die in den großen Bibliotheken lizenzierten Ressourcen und elektronischen Zeitschriften, zudem die nahtlose Navigation mittels des Reference-Linking-Werkzeuges SFX zu verschiedenen Diensten wie Fernleihe, Subito und freien Volltexten im Internet sowie zu frei zugänglichen elektronischen Zeitschriften. Realisiert wurden ferner die Remote-Authentifizierung, mit der sich ein Nutzer, der online eine Fernleih-Bestellung aufgeben möchte, über das Internet in seiner Heimatbibliothek authentifizieren kann. Des weiteren ist der Zugriff auf lizenzierte Bestände im Campus einer Hochschule mittels IP-Checking möglich. Als weiteren wesentlichen Bestandteil des KOBV-Portals hat die KOBV-Zentrale mit den Bibliotheken einen Workflow für ein Metadata-Sharing abgestimmt und für die Adaption und Normalisierung lokaler Metadaten aus lokalen Bibliothekssystemen und -Portalen den KOBV-Metadaten-Austausch-Parser (KMA-Parser) entwickelt. Damit Bibliotheken, deren Metadaten bislang lediglich in unstrukturierter Form vorliegen, strukturierte Metadaten anlegen, liefern und nachnutzen können, hat die KOBV-Zentrale das mit einer Web-Katalogisierungsschnittstelle ausgestattete ''Metadata-Tool`` entwickelt. Die für das Metadata-Sharing entwickelten Komponenten und Module sollen den Bibliotheken die Mehrfacherfassung ersparen und ihnen die Möglichkeit der wechselseitigen Nachnutzung der Metadaten eröffnen. Der vorliegende Projekt-Abschlussbericht gibt einen Überblick über die während der Projektlaufzeit realisierten Dienste des KOBV-Portals. \end{document} T3 - ZIB-Report - 04-31 KW - Informationsportal KW - Portal KW - Verbundportal KW - Digibib KW - Digitale Bibliothek KW - Meta-Suche KW - parallele Suche KW - KOBV-Suchmaschine KW - KMA-Parser KW - Metadata Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8064 ER - TY - GEN A1 - Lügger, Joachim T1 - Zusammenarbeit mit vascoda im Rahmen des Verteilten Dokumentenservers (VDS) N2 - Die in der Arbeitsgemeinschaft der Verbundsysteme zusammengeschlossenen deutschen Verbundsysteme kooperieren zur Realisierung eines die Länder und Verbundregionen übergreifenden offenen Netzwerkes einer offenen digitalen Bibliothek, dem Verteilten Dokumentenserver (VDS). Wesentliche Bestandteile des VDS sind die in den lokalen Bibliotheken und Verbundsystemen verteilten Dokumentenspeicher. Beim Aufbau des VDS verfolgen die deutschen Verbundsysteme für ihre digitalen Ressourcen, Zeitschriften und Dokumente, folgende Ziele [AGV03]: \begin{itemize} \item{Erhalt und dauerhafte Sicherung einmal erworbener Rechte} \item{Bessere Erschließung und Integration in das eigene Angebot} \item{Nahtlose Navigation in lokalen Zeitschriften- und Dokumentenservern und zwischen digitalen Artikeln und Zeitschriften, Dokumenten und Servern} \item{Dauerhafte Sicherung des Zugriffs und perspektivisch Langzeitverfügbarkeit} \end{itemize} Die Verbundsysteme streben an, die Speicherung, Erschließung und das Angebot ihrer digitalen Materialien in einer nationalen Kooperation durchzuführen. Sie entwickeln und betreiben zu diesem Zweck Portal- und Querschnittstechnologien zur Integration ihrer dezentral gespeicherten digitalen Ressourcen mittels Internet-Technologien. T3 - ZIB-Report - 04-30 KW - kobv KW - vascoda KW - Verteilter Dokumentenserver KW - Verbundsysteme KW - Digitale Bibliothek KW - Portal Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8058 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Koster, Arie M.C.A. A1 - Wolle, Thomas T1 - Contraction and Treewidth Lower Bounds N2 - Edge contraction is shown to be a useful mechanism to improve lower bound heuristics for treewidth. A successful lower bound for treewidth is the degeneracy: the maximum over all subgraphs of the minimum degree. The degeneracy is polynomial time computable. We introduce the notion of contraction degeneracy: the maximum over all minors of the minimum degree. We show that the contraction degeneracy problem is NP-complete, even for bipartite graphs, but for fixed $k$, it is polynomial time decidable if a given graph $G$ has contraction degeneracy at least $k$. Heuristics for computing the contraction degeneracy are proposed and evaluated. It is shown that these can lead in practice to considerable improvements of the lower bound for treewidth, but can perform arbitrarily bad on some examples. A study is also made for the combination of contraction with Lucena's lower bound based on Maximum Cardinality Search (Lucena, 2003). Finally, heuristics for the treewidth are proposed and! evaluated that combine contraction with a treewidth lower bound technique by Clautiaux et al (2003). T3 - ZIB-Report - 04-29 KW - treewidth KW - contraction degeneracy KW - graph minors KW - lower bounds KW - maximum cardinality search Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8042 ER - TY - GEN A1 - Hodoroaba, Lavinia A1 - Imhof, Andres T1 - Das KOBV-Metadaten-Schema im KOBV-Portal N2 - Das KOBV-Metadaten-Schema ist von der KOBV-Zentrale entwickelt worden, um Ressourcen im Sinn von Informationskollektionen wie Datenbanken oder Fachportale zu beschreiben. Es ist ein wichtiger Bestandteil des KOBV-Portals, das die in der Region verf"ugbaren Ressourcen nachweist. Das KOBV-Metadaten-Schema dient den Bibliotheken zur Handreichung, um dem KOBV-Portal die Ressourcen mit den standardisierten und individuellen Angaben zu melden, so dass die Ressourcebeschreibungen einem austauschbaren Format entsprechen. Auf diese Weise k"onnen Ressourcebeschreibungen von anderen Bibliotheken mitgenutzt werden und ein Metadata-Sharing in der Region Berlin-Brandenburg praktiziert werden, um in diesem Bereich doppelte Arbeiten zu sparen. T3 - ZIB-Report - 04-28 KW - Metadaten KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Informationsportal KW - Metadaten-Austausch KW - Metadata-Sharing KW - Digitale Bibliot Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8038 ER - TY - GEN A1 - Weiser, Martin A1 - Schiela, Anton T1 - Function space interior point methods for PDE constrained optimization N2 - A primal-dual interior point method for optimal control problems with PDE constraints is considered. The algorithm is directly applied to the infinite dimensional problem. Existence and convergence of the central path are analyzed. Numerical results from an inexact continuation method applied to a model problem are shown. T3 - ZIB-Report - 04-27 KW - interior point methods in function space KW - optimal control KW - complementarity functions Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8027 ER - TY - GEN A1 - Kälberer, Felix A1 - Polthier, Konrad A1 - Reitebuch, Ulrich A1 - Wardetzky, Max T1 - Compressing Triangle Meshes using Geometric Infomation N2 - We introduce FreeLence, a lossless single-rate connectivity compression algorithm for triangle surface meshes. Based upon a geometry-driven traversal scheme we present two novel and simple concepts: free-valence connectivity encoding and entropy coding based on geometric context. Together these techniques yield significantly smaller rates for connectivity compression than current state of the art approaches - valence-based algorithms and Angle- Analyzer, with an average of $36\%$ improvement over the former and an average of $18\%$ over the latter on benchmark 3D models, combined with the ability to well adapt to the regularity of meshes. We also prove that our algorithm exhibits a smaller worst case entropy for a class of "'well-behaved"' triangle meshes than valence-driven connectivity encoding approaches. T3 - ZIB-Report - 04-26 KW - Mesh Compression KW - Connectivity Encoding KW - Polygonal Meshes KW - Context-based Entropy Coding Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8016 ER - TY - GEN A1 - Hildebrandt, Klaus A1 - Polthier, Konrad T1 - Anisotropic Filtering of Non-Linear Surface Features N2 - A new method for noise removal of arbitrary surfaces meshes is presented which focuses on the preservation and sharpening of non-linear geometric features such as curved surface regions and feature lines. Our method uses a prescribed mean curvature flow (PMC) for simplicial surfaces which is based on three new contributions: 1. the definition and efficient calculation of a discrete shape operator and principal curvature properties on simplicial surfaces that is fully consistent with the well-known discrete mean curvature formula, 2. an anisotropic discrete mean curvature vector that combines the advantages of the mean curvature normal with the special anisotropic behaviour along feature lines of a surface, and 3. an anisotropic prescribed mean curvature flow which converges to surfaces with an estimated mean curvature distribution and with preserved non-linear features. Additionally, the PMC flow prevents boundary shrinkage at constrained and free boundary segments. T3 - ZIB-Report - 04-25 KW - mesh smoothing KW - principal curvature KW - feature lines KW - anisotropic smoothing KW - prescribed mean curvature Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8003 ER - TY - GEN A1 - Braschoß, Katja A1 - Hansmann, Sabine A1 - Hesse, Thomas A1 - Joosten-Wilke, Ulrike A1 - Ristau, Ute A1 - Rusch, Beate A1 - Taylor, Viola T1 - Indexierung von Online-Katalogen: Ein gemeinsames Konzept der ALEPH-Anwender in Berlin N2 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) verzichtet auf eine einheitliche zentrale Verbunddatenbank zugunsten einer dezentralen, verteilten Struktur. In dieser Architektur erhält die Art der Indexierung der angesprochenen Online-Kataloge eine besondere Bedeutung. So werden sowohl Bibliotheksmitarbeiter als auch Bibliotheksbenutzer immer wieder mit der Recherche in fremden Katalogen konfrontiert, in denen unterschiedliche Indexierungsverfahren realisiert sein können. Ein abgestimmtes Indexierungskonzept verfolgt zwei grundsätzliche Ziele. Einerseits soll durch eine vereinheitlichte Indexierung die Qualität und Zuverlässigkeit der Rechercheergebnisse in der parallelen Suche in mehreren Katalogen über die KOBV-Suchmaschine erhöht werden. Gleichzeitig soll durch eine vereinheitlichte Indexierung die Akzeptanz von Suchen in entfernten Katalogen prinzipiell gesteigert und damit die Bedingungen für die gegenseitige Übernahme von Titeldaten erleichtert werden. Für die Indexierung muss zunächst die Art und der Umfang der im OPAC aufzubauenden Indices festgelegt werden. Aus Sicht des Nutzers entspricht diese Definition den möglichen Sucheinstiegen. Hat man dann entschieden, welche Indexterme aus welchen Feldern in die jeweiligen Indices einfließen sollen, muss bestimmt werden, nach welchen Regeln die Terme behandelt werden. Hier stellt sich insbesondere das Problem der Sonderzeichen wie Bindestriche, Apostrophe und Punkte oder Ziffern in Zeichenketten. Das vorliegende Konzept entstand in Zusammenarbeit der großen Universitätsbibliotheken in Berlin (der Freien Universität, der Humboldt-Universität, der Technischen Universität, der Universität der Künste) mit der KOBV-Verbundzentrale am ZIB. T3 - ZIB-Report - 04-24 KW - Datenbank KW - Online-Kataloge KW - Indexierung KW - Information-Retrieval KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7998 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - The Effect of Hop Limits on Optimal Cost in Survivable Network Design N2 - We investigate the impact of hop-limited routing paths on the total cost of a telecommunication network. For different survivability settings (dedicated protection, link and path restoration), the optimal network cost without restrictions on the admissible path set is compared to the results obtained with two strategies to impose hop limits on routing paths. In a thorough computational study on optimal solutions for nine real-world based problem instances, we show that hop limits should be avoided if the technology allows it and network cost is a major planning issue. In this case, column generation should be employed to deal with all routing paths. If hop-limits are required, these should be defined for each demand individually and as large as possible. T3 - ZIB-Report - 04-23 KW - survivable network design KW - hop limits KW - routing KW - restoration KW - branch-and-cut algorithm KW - mixed-integer programming Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7980 ER - TY - GEN A1 - Steinbach, Marc T1 - Robust Process Control by Dynamic Stochastic Programming N2 - Unnecessarily conservative behavior of standard process control techniques can be avoided by stochastic programming models when the distribution of random disturbances is known. In an earlier study we have investigated such an approach for tank level constraints of a distillation process. Here we address techniques that have accelerated the numerical solution of the large and expensive stochastic programs by a factor of six, and then present a refined optimization model for the same application. T3 - ZIB-Report - 04-20 KW - Process control KW - random disturbance KW - multistage stochastic program KW - relatively complete recourse KW - tree-sparse NLP Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7959 ER - TY - GEN A1 - Ehrhardt, Klaus A1 - Steinbach, Marc T1 - KKT Systems in Operative Planning for Gas Distribution Networks N2 - Operative planning in gas networks with prescribed binary decisions yields large scale nonlinear programs defined on graphs. We study the structure of the KKT systems arising in interior methods and present a customized direct solution algorithm. Computational results indicate that the algorithm is suitable for optimization in small and medium-sized gas networks. T3 - ZIB-Report - 04-21 KW - KKT system KW - sparse factorization KW - large-scale nonlinear program KW - gas network KW - operative planning Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7962 ER - TY - GEN A1 - Draheim, Dirk A1 - Neun, Winfried A1 - Suliman, Dima T1 - Searching and Classifying Differential Equations on the Web N2 - In this paper we describe the semantic analysis of differential equations given in the ubiquitous semi-structured formats MathML and OpenMath. The analysis is integrated in a deployed Web indexing framework. Starting from basic classifications for differential equations the proposed system architecture is amenable to extensions for further reconstruction of mathematical content on the Web. The syntactic analysis of mathematical formulae given in the considered formats must overcome ambiguities that stem from the fact that formula particles may have different encodings, which are in principle completely arbitrary. However, it turns out that the syntactic analysis can be done straightforward given some natural heuristic assumptions. T3 - ZIB-Report - 04-22 KW - Differential Equation KW - Classification KW - OpenMath KW - MathML KW - Harvest Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7975 ER - TY - GEN A1 - Lukac, Sascha T1 - Holes, Antiholes and Maximal Cliques in a Railway Model for a Single Track N2 - We present a graph theoretical model for scheduling trains on a single unidirectional track between two stations. The set of departures of all possible train types at all possible (discrete) points of time is turned into an undirected graph $\Gneu$ by joining two nodes if the corresponding departures are in conflict. This graph $\Gneu$ has no odd antiholes and no $k$-holes for any integer $k\geq 5$. In particular, any finite, node induced subgraph of $\Gneu$ is perfect. For any integer $r\geq 2$ we construct minimal headways for $r$ train types so that the resulting graph $\Gneu$ has $2r$-antiholes and $4$-holes at the same time. Hence, $\Gneu$ is neither a chordal graph nor the complement of a chordal graph, in general. At the end we analyse the maximal cliques in $G$. T3 - ZIB-Report - 04-18 KW - perfect graphs KW - holes KW - anti holes KW - cliques KW - railway Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7939 ER - TY - GEN A1 - Achterberg, Tobias T1 - SCIP - a framework to integrate Constraint and Mixed Integer Programming N2 - Constraint Programs and Mixed Integer Programs are closely related optimization problems originating from different scientific areas. Today's state-of-the-art algorithms of both fields have several strategies in common, in particular the branch-and-bound process to recursively divide the problem into smaller sub problems. On the other hand, the main techniques to process each sub problem are different, and it was observed that they have complementary strenghts. We propose a programming framework {\sffamily SCIP} that integrates techniques from both fields in order to exploit the strenghts of both, Constraint Programming and Mixed Integer Programming. In contrast to other proposals of recent years to combine both fields, {\sffamily SCIP} does not focus on easy implementation and rapid prototyping, but is tailored towards expert users in need of full, in-depth control and high performance. T3 - ZIB-Report - 04-19 KW - Mixed Integer Programming KW - MIP KW - Constraint Programming KW - CP KW - branch-and-bound Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7947 ER - TY - GEN A1 - Hiller, Benjamin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Reoptimization Gaps versus Model Errors in Online-Dispatching of Service Units for ADAC N2 - Under high load, the automated dispatching of service vehicles for the German Automobile Association (ADAC) must reoptimize a dispatch for 100--150 vehicles and 400 requests in about ten seconds to near optimality. In the presence of service contractors, this can be achieved by the column generation algorithm ZIBDIP. In metropolitan areas, however, service contractors cannot be dispatched automatically because they may decline. The problem: a model without contractors yields larger optimality gaps within ten seconds. One way-out are simplified reoptimization models. These compute a short-term dispatch containing only some of the requests: unknown future requests will influence future service anyway. The simpler the models the better the gaps, but also the larger the model error. What is more significant: reoptimization gap or reoptimization model error? We answer this question in simulations on real-world ADAC data: only the new model ZIBDIP{\footnotesize dummy} can keep up with ZIBDIP. T3 - ZIB-Report - 04-17 KW - vehicle dispatching KW - soft time windows KW - online KW - real-time KW - ADAC KW - optimality gap KW - high load Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7928 ER - TY - GEN T1 - Jahresbericht 2003 T3 - Jahresbericht - 2003 KW - Annual Report Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9781 SN - 0934-5892 ER - TY - GEN A1 - Kober, Cornelia A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Adaptive Finite Element Simulation of the Human Mandible Using a New Physiological Model of the Masticatory Muscles N2 - Structural mechanics simulation of bony organs is of general medical and biomechanical interest, because of the interdependence of the inner architecture of bone and its functional loading already stated by Wolff in 1892. This work is part of a detailed research project concerning the human mandible. By adaptive finite element techniques, stress/strain profiles occurring in the bony structure under biting were simulated. Estimates of the discretization errors, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. In general, our simulation requires a representation of the organ's geometry, an appropriate material description, and the load case due to teeth, muscle, or joint forces. In this paper, we want to focus on the influence of the masticatory system. Our goal is to capture the physiological situation as far as possible. By means of visualization techniques developed by the group, we are able to extract individual muscle fibres from computed tomography data. By a special algorithm, the fibres are expanded to fanlike (esp. for the musc. temporalis) coherent vector fields similar to the anatomical reality. The activity of the fibres can be adapted according to compartmentalisation of the muscles as measured by electromyological experiments. A refined sensitivity analysis proved remarkable impact of the presented approach on the simulation results. T3 - ZIB-Report - 04-16 KW - adaptive finite elements KW - error estimation KW - local grid refinement KW - isotropic linear elasticity KW - human mandible KW - masticatory muscles Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7917 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Wessäly, Roland T1 - UMTS Radio Network Evaluation and Optimization beyond Snapshots N2 - This paper is concerned with UMTS radio network design. Our task is to reconfigure antennas and the related cells as to improve network quality. In contrast to second generation GSM networks, \emph{interference} plays a paramount role when designing third generation radio networks. A known compact formulation for assessing the interference characteristics of a radio network as coupling relations between cells based on user snapshots is generalized to statistical average load. This enables us to overcome the notorious difficulties of snapshot-based network optimization approaches. We recall a mixed-integer programming model for the network design problem that is based on user snapshots and contrast it with a new network design model based on the average coupling formulation. Exemplarily focusing on the important problem of optimizing antenna tilts, we give computational results for a fast local search algorithm and the application of a MIP solver to both models. These results demonstrate that our new average-based approaches outperform state-of-the-art snapshot models for UMTS radio network optimization. T3 - ZIB-Report - 04-15 KW - UMTS KW - Network planning KW - Network design KW - Optimization Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7903 ER - TY - GEN A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Branching rules revisited N2 - Mixed integer programs are commonly solved with linear programming based branch-and-bound algorithms. The success of the algorithm strongly depends on the strategy used to select the variable to branch on. We present a new generalization called {\sl reliability branching} of today's state-of-the-art {\sl strong branching} and {\sl pseudocost branching} strategies for linear programming based branch-and-bound algorithms. After reviewing commonly used branching strategies and performing extensive computational studies we compare different parameter settings and show the superiority of our proposed newstrategy. T3 - ZIB-Report - 04-13 KW - Mixed-integer-programming KW - Branch-and-Bound KW - Variable selection KW - Pseudocost-Branching KW - Strong-Branching KW - Reliability-Branching Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7886 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Weider, Steffen T1 - A Bundle Method for Integrated Multi-Depot Vehicle and Duty Scheduling in Public Transit N2 - This article proposes a Lagrangean relaxation approach to solve integrated duty and vehicle scheduling problems arising in public transport. The approach is based on the proximal bundle method for the solution of concave decomposable functions, which is adapted for the approximate evaluation of the vehicle and duty scheduling components. The primal and dual information generated by the bundle method is used to guide a branch-and-bound type algorithm. Computational results for large-scale real-world integrated vehicle and duty scheduling problems with up to 1,500 timetabled trips are reported. Compared with the results of a classical sequential approach and with reference solutions, integrated scheduling offers remarkable potentials in savings and drivers' satisfaction. T3 - ZIB-Report - 04-14 KW - vehicle scheduling KW - crew scheduling KW - integrated scheduling KW - public transit KW - bundle method Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7898 ER - TY - GEN A1 - Kober, Cornelia A1 - Erdmann, Bodo A1 - Hellmich, Christian A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Anisotropic Simulation of the Human Mandible N2 - We focus on the role of anisotropic elasticity in the simulation of the load distribution in a human mandible due to a lateral bite on the leftmost premolar. Based on experimental evidence, we adopt ``local''" orthotropy of the elastic properties of the bone tissue. Since the trajectories of anisotropic elasticity are not accessible from Computer Tomographic (CT) data, they will be reconstructed from (i) the organ's geometry and (ii) from coherent structures which can be recognized from the spatial distribution of the CT values. A sensitivity analysis comprising various 3D FE simulations reveals the relevance of elastic anisotropy for the load carrying behavior of a human mandible: Comparison of the load distributions in isotropic and anisotropic simulations indicates that anisotropy seems to ``spare''" the mandible from loading. Moreover, a maximum degree of anisotropy leads to kind of an load minimization of the mandible, expressed by a minimum of different norms of local strain, evaluated throughout the organ. Thus, we may suggest that anisotropy is not only relevant, but also in some sense ``optimal''. T3 - ZIB-Report - 04-12 KW - anisotropy KW - elasticity KW - bony organ simulation KW - human mandible KW - visualization of tissue quality KW - finite element analysis Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7873 ER - TY - GEN A1 - Lutz, Frank H. T1 - Triangulated Manifolds with Few Vertices: Centrally Symmetric Spheres and Products of Spheres N2 - The aim of this paper is to give a survey of the known results concerning centrally symmetric polytopes, spheres, and manifolds. We further enumerate nearly neighborly centrally symmetric spheres and centrally symmetric products of spheres with dihedral or cyclic symmetry on few vertices, and we present an infinite series of vertex-transitive nearly neighborly centrally symmetric 3-spheres. T3 - ZIB-Report - 04-11 KW - centrally symmetric polytopes KW - crosspolytope KW - combinatorial manifolds KW - products of spheres Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7863 ER - TY - GEN A1 - Weiser, Martin A1 - Deuflhard, Peter A1 - Erdmann, Bodo T1 - Affine conjugate adaptive Newton methods for nonlinear elastomechanics N2 - The paper extends affine conjugate Newton methods from convex to nonconvex minimization, with particular emphasis on PDE problems originating from compressible hyperelasticity. Based on well-known schemes from finite dimensional nonlinear optimization, three different algorithmic variants are worked out in a function space setting, which permits an adaptive multilevel finite element implementation. These algorithms are tested on two well-known 3D test problems and a real-life example from surgical operation planning. T3 - ZIB-Report - 04-01 KW - affine conjugate Newton methods KW - nonconvex minimization KW - nonlinear elastomechnics KW - cranio-maxillofacial surgery KW - soft tissue simulation KW - multilev Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7768 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - Models for Line Planning in Public Transport N2 - The \emph{line planning problem} is one of the fundamental problems in strategic planning of public and rail transport. It consists of finding lines and corresponding frequencies in a public transport network such that a given travel demand can be satisfied. There are (at least) two objectives. The transport company wishes to minimize its operating cost; the passengers request short travel times. We propose two new multi-commodity flow models for line planning. Their main features, in comparison to existing models, are that the passenger paths can be freely routed and that the lines are generated dynamically. T3 - ZIB-Report - 04-10 KW - line planning KW - column generation Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7854 ER - TY - GEN A1 - Lamecker, Hans A1 - Lange, Thomas A1 - Seebass, Martin T1 - Segmentation of the Liver using a 3D Statistical Shape Model N2 - This paper presents an automatic approach for segmentation of the liver from computer tomography (CT) images based on a 3D statistical shape model. Segmentation of the liver is an important prerequisite in liver surgery planning. One of the major challenges in building a 3D shape model from a training set of segmented instances of an object is the determination of the correspondence between different surfaces. We propose to use a geometric approach that is based on minimizing the distortion of the correspondence mapping between two different surfaces. For the adaption of the shape model to the image data a profile model based on the grey value appearance of the liver and its surrounding tissues in contrast enhanced CT data was developed. The robustness of this method results from a previous nonlinear diffusion filtering of the image data. Special focus is turned to the quantitative evaluation of the segmentation process. Several different error measures are discussed and implemented in a study involving more than 30 livers. T3 - ZIB-Report - 04-09 KW - Statistical Shape Model KW - 3D Correspondence Problem KW - Model-Based Segmentation KW - Diffusion Filtering KW - Geometric Distortion KW - Surface Distance Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7847 ER - TY - GEN A1 - Joswig, Michael A1 - Lutz, Frank H. T1 - One-Point Suspensions and Wreath Products of Polytopes and Spheres N2 - It is known that the suspension of a simplicial complex can be realized with only one additional point. Suitable iterations of this construction generate highly symmetric simplicial complexes with a various interesting combinatorial and topological properties. In particular, infinitely many non-PL spheres as well as contactible simplicial complexes with a vertex-transitive group of automorphisms cab be contained in this way. T3 - ZIB-Report - 04-08 KW - dual wedge KW - suspension KW - wreath product KW - shellability KW - Z-acyclic complexes KW - non-PL spheres KW - Hirsch conjecture Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7836 ER - TY - GEN A1 - Baum, Daniel T1 - Finding All Maximal Cliques of a Family of Induced Subgraphs N2 - Many real world problems can be mapped onto graphs and solved with well-established efficient algorithms studied in graph theory. One such problem is to find large sets of points satisfying some mutual relationship. This problem can be transformed to the problem of finding all cliques of an undirected graph by mapping each point onto a vertex of the graph and connecting any two vertices by an edge whose corresponding points satisfy our desired relationship. Clique detection has been widely studied and there exist efficient algorithms. In this paper we study a related problem, where all points have a set of binary attributes, each of which is either 0 or 1. This is only a small limitation, since all discrete properties can be mapped onto binary attributes. In our case, we want to find large sets of points not only satisfying some mutual relationship; but, in addition, all points of a set also need to have at least one common attribute with value 1. The problem we described can be mapped onto a set of induced subgraphs, where each subgraph represents a single attribute. For attribute $i$, its associated subgraph contains those vertices corresponding to the points with attribute $i$ set to 1. We introduce the notion of a maximal clique of a family, $\mathcal{G}$, of induced subgraphs of an undirected graph, and show that determining all maximal cliques of $\mathcal{G}$ solves our problem. Furthermore, we present an efficient algorithm to compute all maximal cliques of $\mathcal{G}$. The algorithm we propose is an extension of the widely used Bron-Kerbosch algorithm. T3 - ZIB-Report - 03-53 KW - Bron-Kerbosch algorithm KW - maximal cliques KW - vertex properties KW - family of induced subgraphs KW - backtracking algorithm KW - branch and bound technique KW - re Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7758 ER - TY - GEN A1 - Wagler, Annegret T1 - The Normal Graph Conjecture is true for Circulants N2 - Normal graphs are defined in terms of cross-intersecting set families: a graph is normal if it admits a clique cover $\cal Q$ and a stable set cover $\cal S$ s.t.~every clique in $\cal Q$ intersects every stable set in $\cal S$. Normal graphs can be considered as closure of perfect graphs by means of co-normal products (Körner 1973) and graph entropy (Czisz\'ar et al. 1990). Perfect graphs have been recently characterized as those graphs without odd holes and odd antiholes as induced subgraphs (Strong Perfect Graph Theorem, Chudnovsky et al. 2002). Körner and de Simone observed that $C_5$, $C_7$, and $\overline C_7$ are minimal not normal and conjectured, as generalization of the Strong Perfect Graph Theorem, that every $C_5$, $C_7$, $\overline C_7$- free graph is normal (Normal Graph Conjecture, Körner and de Simone 1999). We prove this conjecture for a first class of graphs that generalize both odd holes and odd antiholes, the circulants, by characterizing all the normal circulants. T3 - ZIB-Report - 04-06 KW - perfect graphs KW - normal graphs KW - circulants Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7813 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Geerdes, Hans-Florian A1 - Koch, Thorsten A1 - Türke, Ulrich T1 - MOMENTUM Data Scenarios for Radio Network Planning and Simulation (Extended Abstract) N2 - We present publicly available data sets related to research on wireless networks. The scenarios contain a wide range of data and are detailed in all aspects. To our knowledge, this is the most realistic, comprehensive, and detailed \emph{public} data collection on mobile networking. We indicate example uses of this data collection in applications related tu UMTS. T3 - ZIB-Report - 04-07 KW - Radio Network Planning KW - Simulation KW - UMTS KW - Realistic Data KW - XML Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7829 ER - TY - GEN A1 - Helmes, Kurt A1 - Röhl, Stefan T1 - A Geometrical Characterization of the Multidimensional Hausdorff and Dale Polytopes with Applications to Exit Time Problems N2 - We present formulae for the corner points of the multidimensional Hausdorff and Dale Polytopes and show how these results can be used to improve linear programming models for computing e.\,g.\ moments of exit distribution of diffusion processes. Specifically, we compute the mean exit time of twodimensional Brownian motion from the unit square and the unit triangle, as well as higher moments of the exit time of time space Brownian motion from a triangle. T3 - ZIB-Report - 04-05 KW - linear programming KW - special polytopes KW - moment problems KW - Brownian motion on a triangle KW - numerical methods for exit time problems Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7807 ER - TY - GEN A1 - Bley, Andreas A1 - Koch, Thorsten A1 - Wessäly, Roland T1 - Large-scale hierarchical networks: How to compute an optimal architecture? N2 - In this article, we present a mathematical model and an algorithm to support one of the central strategic planning decisions of network operators: How to organize a large number of locations into a hierarchical network? We propose a solution approach that is based on mixed-integer programming and Lagrangian relaxation techniques. As major advantage, our approach provides not only solutions but also worst-case quality guarantees. Real-world scenarios with more than 750 locations have been solved within 30 minutes to less than 1\% off optimality. T3 - ZIB-Report - 04-04 KW - Hierarchical Networks KW - Mixed-Integer Programming KW - Lagrangian Relaxation Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7799 ER - TY - GEN A1 - Nowak, Ulrich A1 - Grah, Aleksander A1 - Schreier, Manfred T1 - Parameter Estimation and Accuracy Matching Strategies for 2-D Reactor Models N2 - The mathematical modeling of a special modular catalytic reactor kit leads to a system of partial differential equation in two space dimensions. As customary, this model contains unconfident physical parameters, which may be adapted to fit experimental data. To solve this nonlinear least squares problem we apply a damped Gauss-Newton method. A method of lines approach is used to evaluate the associated model equations. By an a priori spatial discretization a large DAE system is derived and integrated with an adaptive, linearly-implicit extrapolation method. For sensitivity evaluation we apply an internal numerical differentiation technique, which reuses linear algebra information from the model integration. In order not to interfere the control of the Gauss-Newton iteration these computations are done usually very accurately and, therefore, very costly. To overcome this difficulty, we discuss several accuracy adaptation strategies, e.g., a master-slave mode. Finally, we present some numerical experiments. T3 - ZIB-Report - 03-52 KW - parameter estimation KW - accuracy matching KW - method of lines KW - differential-algebraic systems KW - extrapolation methods KW - catalytic reactor models Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7749 ER - TY - GEN A1 - Lügger, Joachim T1 - Vorhaben: Offene Navigation und Suchmaschinen in Verbünden, Konsortien und den Wissenschaften; Schlussbericht zumTeilprojekt des BMBF-Vorhabens: Kompetenznetzwerk NeueDienste, Standardisierung, Metadaten. N2 - Die harmonische Integration der Navigation und Suche in lizenzierten Journalen und gleichzeitig in freien digitalen Dokumenten unter einer einheitlichen konsistenten Nutzeroberflache ist eines der ungelösten F&E-Probleme der Fachinformation. Hierfür sollen Elemente des Invisible Web und des Visible Web unter Berücksichtigung offener Standards nahtlos #I miteinander verbunden werden. Dem Projekt liegt ein Modell mit Internet-Index, Metasuche und Open Linking über verteilten heterogenen Speichern #I zu Grunde: Verschiedenste Server, digitale Referenzen in Artikeln und Dokumenten, Links in Datenbanken und auf Bestelldienste sollen unter Berücksichtigung von Standort-, Studien- und Lernbedingungen kooperativ miteinander vernetzt werden. Die Leistungsfähigkeit des Modells soll in Pilotimplementierungen getestet und für eine breite Anwendung vorbereitet werden. Auf dieser Basis soll das Vorhaben Verteilter Zeitschriftenserver der AG der Verbundsysteme in eigenen Teilprojekten kooperativ initiiert werden, das jetzt in das Vorhaben Verteilter Dokumentenserver von vascoda integriert ist. T3 - ZIB-Report - 03-51 KW - Metasuchmaschine KW - Internet-Suchmaschinen KW - kontextsensitives Linking KW - OpenURL KW - Verteilter Zeitschriftenserver KW - Verteilter Dokumentenserver KW - Virtu Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7737 ER - TY - THES A1 - Farshbaf-Shaker, Mohammad-Hassan T1 - Ein neues Verfahren zur Lösung des Streuproblems der Maxwell-Gleichungen Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9914 ER - TY - THES A1 - Kröller, Alexander T1 - Network Optimization: Integration of Hardware Configuration and Capacity Dimensioning Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9952 ER - TY - THES A1 - Menne, Ulrich T1 - LP approaches to survivable networks with single path routing Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9989 ER - TY - THES A1 - Orlowski, Sebastian T1 - Local and global restoration of node and link failures in telecommunication networks N2 - This diploma thesis deals with the restoration problem in telecommunication networks. The goal is to find a cost minimal capacity capacity assignment on the edges and nodes of a network such that given demands can be satisfied even in case of the failure of an edge or node in the network. Moreover, restrictions on the routing paths (like length restrictions) and hardware constraints have to be satisfied. A Mixed Integer Programming model is presented which takes into account restoration requirements as well as hardware constraints and which abstracts from a particular restoration protocol and failure situation. This abstraction provides new insight into the structure of the network restoration problem and shows that from a mathematical point of view, the commonly used restoration techniques Link Restoration, Path Restoration and Reservation are not as different as they seem to be from a practical point of view. In addition, our model allows (but is not limited to) optimizing working capacity, intended for normal use, and spare capacity, intended for rerouting purposes in case of a failure, in one step. Furthermore, our formulation of capacity cost allows taking into account the effects of discrete, non-linear cost structures which are common in practice. Up to our knowledge, no publication in the existing literature covers all these aspects, let alone in one model, although they are of major practical interest. The model has been implemented in a Branch and Cut framework. The theoretical background of the algorithmic procedure is presented in detail, including computational complexity investigations on the pricing problem. The abstraction from a particular restoration protocol turns out to be useful both from a theoretical and computational point of view. In fact, our investigations suggest a distinction into Local Restoration and Global Restoration rather than into Link Restoration,Path Restoration, Reservation and mixtures of these concepts. In addition to the theoretical aspects of the algorithmic procedure, some implementational details are briefly discussed. Our implementation has been tested on 14 real world instances, which is described in detail. One part of the computational results consists of a comparison of optimal network cost values using diffeent restoration mechanisms, applied to securing either all single node failures, all single edge failures or both. In addition, the effects of a discrete cost structure are investigated, which has rarely been considered yet in literature. Furthermore, the cost ifference between joint and successive working and spare capacity optimization is investigated. In the second part of the computational results, several heuristics for the network restoration problem are compared with respect to both solution quality and time. This diploma thesis deals with the restoration problem in telecommunication networks. The goal is to find a cost minimal capacity capacity assignment on the edges and nodes of a network such that given demands can be satisfied even in case of the failure of an edge or node in the network. Moreover, restrictions on the routing paths (like length restrictions) and hardware constraints have to be satisfied. A Mixed Integer Programming model is presented which takes into account restoration requirements as well as hardware constraints and which abstracts from a particular restoration protocol and failure situation. This abstraction provides new insight into the structure of the network restoration problem and shows that from a mathematical point of view, the commonly used restoration techniques Link Restoration, Path Restoration and Reservation are not as different as they seem to be from a practical point of view. In addition, our model allows (but is not limited to) optimizing working capacity, intended for normal use, and spare capacity, intended for rerouting purposes in case of a failure, in one step. Furthermore, our formulation of capacity cost allows taking into account the effects of discrete, non-linear cost structures which are common in practice. Up to our knowledge, no publication in the existing literature covers all these aspects, let alone in one model, although they are of major practical interest. The model has been implemented in a Branch and Cut framework. The theoretical background of the algorithmic procedure is presented in detail, including computational complexity investigations on the pricing problem. The abstraction from a particular restoration protocol turns out to be useful both from a theoretical and computational point of view. In fact, our investigations suggest a distinction into Local Restoration and Global Restoration rather than into Link Restoration, Path Restoration, Reservation and mixtures of these concepts. In addition to the theoretical aspects of the algorithmic procedure, some implementational details are briefly discussed. Our implementation has been tested on 14 real world instances, which is described in detail. One part of the computational results consists of a comparison of optimal network cost values using different restoration mechanisms, applied to securing either all single node failures, all single edge failures or both. In addition, the effects of a discrete cost structure are investigated, which has rarely been considered yet in literature. Furthermore, the cost difference between joint and successive working and spare capacity optimization is investigated. In the second part of the computational results, several heuristics for the network restoration problem are compared with respect to both solution quality and time. Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10008 ER - TY - THES A1 - Rieche, Simon T1 - Lastbalancierung in Peer-to-Peer Systemen N2 - Peer-to-Peer (P2P) Systeme werden u.a. zur Verwaltung von großen Datenmengen benutzt, die auf verschiedene Rechner verteilt sind. Benutzern soll damit der Zugriff auf Daten innerhalb des Systems leicht ermöglicht werden. Damit in P2P Systemen die Daten effizient verteilt und gesucht werden können, existieren Distributed Hash Tables. Distributed Hash Tables (DHT) sind eine Methode, um globale Informationen persistent speichern zu können. Der Wertebereich der Hashfunktion, welche die zu veröffentlichenden Einträge auf Werte abbildet, wird in Abschnitte aufgeteilt, die einzelnen Knoten zugeteilt werden. Die meisten DHTs haben aber ein Problem bei der Verteilung der Last. Die verschiedenen DHT Systeme beruhen meist auf einem identischen Ansatz der Lastverteilung. Die Last wird nur mit Hilfe einer Hashfunktion verteilt. Es wird davon ausgegangen, dass diese Funktion die Last gleichmäßig verteilt. Im Rahmen dieser Arbeit wurde ein Verfahren zur Last Verteilung entwickelt, simuliert und implementiert. Bei dem Verfahren wird die Last wie bei der Verteilung von Wärme an die Umgebung abgegeben. Es wird mit existierenden Lastbalancierungsalgorithmen verglichen. Mit diesem neuen Verfahren ist es möglich, Last in DHTs besser zu verteilen ohne große Änderungen an den DHTs vorzunehmen. Es wird gezeigt, wie mit dem Verfahren zusätzlich die Fehlertoleranz des P2P Systems erhöht werden kann. N2 - One of the many uses of Peer-to-Peer (P2P) systems is the administration of large data sets that are distributed across different computers, with the goal of facilitating user access to files within the system. Distributed Hash Tables (DHT) are designed to enable the efficient distribution and search of files, by allowing global information to be persistently stored. The range of values of the hash function (the possible entries in the published hash table) are assigned to individual nodes. Most DHTs, however, have a problem with load distribution. The various DHT systems usually operate by distributing load equally among nodes. Thus the load is distributed using the help of the hash function. One assumes this function distributes the load evenly. In the context of this work a method of distributing load has been developed, simulated and implemented. With this method load is transferred in a fashion analogous to the dissipation of heat into the environment. Comparisons with existing algorithms for load balancing are drawn. With the new procedure it is possible to better distribute load in DHTs without requiring major changes to the DHTs themselves. It is shown that with the procedure the fault tolerance of P2P systems may also be increased. Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10048 ER - TY - THES A1 - Tuchscherer, Andreas T1 - Dynamical Configuration of Transparent Optical Telecommunication Networks N2 - All-optical telecommunication networks allow for switching connections by lightpaths which can pass several network links without any opto-electronic conversion. Upon arrival of a connection request, it must be decided online, i.e., without knowledge of future requests, if it is accepted and in that case on which lightpaths the connection is routed. This online problem with the goal of maximizing the total profit gained by accepted requests is called Dynamic Singleclass Call Admission Problem (DSCA). We present existing and new algorithms for the DSCA as well as their theoretical and practical evaluation. KW - Online-Optimierung KW - Online Optimization Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10214 ER - TY - GEN A1 - Kröller, Alexander A1 - Wessäly, Roland T1 - Integrated Optimization of Hardware Configuration and Capacity. Dimensioning in SDH and opaque WDM networks N2 - We suggest a new model for the design of telecommunication networks which integrates decisions about the topology, configuration of the switching hardware, link dimensioning, and protected routing of communication demands. Applying the branch-and-cut-algorithm implemented in our network planning and optimization tool DISCNET, we demonstrate that real-world based network planning instances of such an enhanced model can be solved. T3 - ZIB-Report - 03-49 KW - Survivable Network Design KW - Integer Programming KW - Hardware Configuration KW - Routing KW - Network Models KW - Network Planning KW - Resource Allocation KW - Surviva Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7714 ER - TY - GEN A1 - Koch, Thorsten T1 - Verteilter Dokumenten-Speicher, Erfahrungen mit den Kluwer-Daten des Friedrich-Althoff-Konsortiums N2 - Dieser Bericht beschreibt die Erfahrungen und Schlussfolgerungen,die im Rahmen der VDS-Vorstudie bei der Speicherung der vom Friedrich-Althoff-Konsortium lizenzierten Zeitschriften des Kluwer-Verlages gewonnen wurden. T3 - ZIB-Report - 03-50 KW - Dokumentenspeicherung KW - Metadaten Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7726 ER - TY - GEN A1 - Weber, Marcus T1 - Clustering by using a simplex structure N2 - In this paper we interpret clustering as a mapping of data into a simplex. If the data itself has simplicial struture this mapping becomes linear. Spectral analysis is an often used tool for clustering data. We will show that corresponding singular vectors or eigenvectors comprise simplicial structure. Therefore they lead to a cluster algorithm, which consists of a simple linear mapping. An example for this kind of algorithms is the Perron cluster analysis (PCCA). We have applied it in practice to identify metastable sets of molecular dynamical systems. In contrast to other algorithms, this kind of approach provides an a priori criterion to determine the number of clusters. In this paper we extend the ideas to more general problems like clustering of bipartite graphs. T3 - ZIB-Report - 04-03 KW - cluster algorithms KW - Perron cluster analysis KW - stochastic matrices KW - bipartite graphs Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7782 ER - TY - GEN A1 - May, Andreas A1 - Eisenhardt, Steffen A1 - Schmidt-Ehrenberg, Johannes A1 - Cordes, Frank T1 - Rigid body docking for Virtual Screening N2 - A recently developed algorithm allows Rigid Body Docking of ligands to proteins, regardless of the accessibility and location of the binding site. The Docking procedure is divided into three subsequent optimization phases, two of which utilize rigid body dynamics. The last one is applied with the ligand already positioned inside the binding pocket and accounts for full flexibility. Initially, a combination of geometrical and force-field based methods is used as a Coarse Docking strategy, considering only Lennard-Jones interactions between the target and pharmaceutically relevant atoms or functional groups. The protein is subjected to a Hot Spot Analysis, which reveals points of high affinity in the protein environment towards these groups. The hot spots are distributed into different subsets according to their group affiliation. The ligand is described as a complementary point set, consisting of the same subsets. Both sets are matched in $\mathrm{I\!R}^{3}$, by superimposing members of the same subsets. In the first instance, steric inhibition is nearly neglected, preventing the system's trajectory from trapping in local minima and thus from finding false positive solutions. Hence the exact location of the binding site can be determined fast and reliably without any additional information. Subsequently, errors resulting from approximations are minimized via finetuning, this time considering both Lennard-Jones and Coulomb forces. Finally, the potential energy of the whole complex is minimized. In a first evaluation, results are rated by a reduced scoring function considering only noncovalent interaction energies. Exemplary Screening results will be given for specific ligands. T3 - ZIB-Report - 03-47 KW - docking KW - point matching KW - identification of active sites Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7690 ER - TY - GEN A1 - Boit, Alice A1 - Cordes, Frank T1 - RNA 3D-Modeling N2 - This article presents a new computational approach to the three-dimensional (3D) modeling of ribonucleic acid (RNA) sequences with unknown spatial structure. The main concept is a mapping of the query sequence onto the 3D structures of a suitable template RNA molecule. This technique called \textit{threading} has originally been developed for the modeling of protein 3D structures. The application to RNA systems bridges the information gap between the growing mass of RNA sequence data and the relatively limited number of available 3D structures. The new RNA threading method is demonstrated on a tRNA model system because sufficient representative 3D structures have experimentally been elucidated and deposited in the public databases. Nevertheless, the method is in principle transferable on all other RNA species. Algorithms are developed that decompose these template structures into their secondary structure elements and gather this information in a specific template database. The best template is chosen with public alignment and secondary structure prediction tools which are integrated in the RNA modeling module. The structural information gathered from the template and the best alignment is combined to establish a comprehensive 3D model of the query sequence. A range of complete tRNA structures has successfully been modeled with the RNA threading method. The prototype module visualizes the models and provides convenient access to the proposed 3D structures. Therefore, the method could give new insight into a variety of RNA systems which in the recent years have become increasingly important as potential new pharmaceutical agents. T3 - ZIB-Report - 03-48 KW - threading KW - alignment KW - secondary structure KW - loop decomposition KW - template library KW - relaxation Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7708 ER - TY - GEN A1 - Deuflhard, Peter A1 - (Chairs), Hyung Yong Ra T1 - Korean-German Bilateral Symposium on Scientific Computing N2 - Collection of abstracts of the Korean-German Bilateral Symposium on Scientific Computing, Berlin January 15/16, 2004 T3 - ZIB-Report - 04-02 KW - Abstracts Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7778 ER - TY - GEN A1 - Ehrhardt, Klaus A1 - Steinbach, Marc T1 - Nonlinear Optimization in Gas Networks N2 - The operative planning problem in natural gas distribution networks is addressed. An optimization model focusing on the governing PDE and other nonlinear aspects is presented together with a suitable discretization for transient optimization in large networks by SQP methods. Computational results for a range of related dynamic test problems demonstrate the viability of the approach. T3 - ZIB-Report - 03-46 KW - Gas networks KW - operative planning KW - large-scale optimization Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7687 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian T1 - Minimum Converter Wavelength Assignment in All-Optical Networks N2 - Finding conflict-free wavelength assignments with a minimum number of required conversions for a routing of the lightpaths is one of the important tasks within the design of all-optical networks. We consider this problem in multi-fiber networks with different types of WDM systems. We give a detailed description of the problem and derive its theoretical complexity. For practical application, we propose several sequential algorithms to compute appropriate wavelength assignments. We also perform computational experiments to evaluate their performance. For the iterative algorithms, we identify characteristic patterns of progression. Two of these algorithms qualify for application in practice. T3 - ZIB-Report - 03-45 KW - minimum converter wavelength assignment KW - optical networks KW - generalized coloring KW - complexity KW - heuristics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7673 ER - TY - GEN A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank T1 - A new Finite Element realization of the Perfectly Matched Layer Method for Helmholtz scattering problems on polygonal domains in 2D N2 - In this paper we propose a new finite element realization of the Perfectly Matched Layer method (PML-method). Our approach allows to deal with arbitrary shaped polygonal domains and with certain types of inhomogeneous exterior domains. Among the covered inhomogeneities are open waveguide structures playing an essential role in integrated optics. We give a detailed insight to implementation aspects. Numerical examples show exponential convergence behavior to the exact solution with the thickness of the PML sponge layer. T3 - ZIB-Report - 03-44 KW - transparent boundary conditions KW - perfectly matched layer KW - pole condition Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7662 ER - TY - GEN A1 - Geerdes, Hans-Florian A1 - Karl, Holger T1 - The Potential of Relaying in Cellular Networks N2 - Relaying is a protocol extension for cellular wireless computer networks; in order to utilize radio resources more efficiently, several hops are allowed within one cell. This paper investigates the principle potential of relaying by casting transmission scheduling as a mathematical optimization problem, namely, a linear program. We analyze the throughput gains showing that, irrespective of the concrete scheduling algorithm, performance gains of up to 30\% on average for concrete example networks are achievable. T3 - ZIB-Report - 03-42 KW - Wireless ad hoc networks KW - Resource Allocation KW - Integer Programming KW - Routing KW - Scheduling KW - Operation Research KW - Network Performance Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7641 ER - TY - GEN A1 - Geerdes, Hans-Florian T1 - Assessing Capacity Improvements by Relaying in Cellular Networks N2 - Relaying -- allowing multiple wireless hops -- is a protocol extension for cellular networks conceived to improve data throughput. Its benefits have only been quantified for small example networks. For assessing its general potential, we define a complex resource allocation\slash{}scheduling problem. Several mathematical models are presented for this problem; while a time-expanded MIP approach turns out intractable, a sophisticated column generation scheme leads to good computational results. We thereby show that for selected cases relaying can increase data throughput by 30\% on the average. T3 - ZIB-Report - 03-43 KW - Wireless ad hoc networks KW - Resource Allocation KW - Integer Programming KW - Routing KW - Scheduling KW - Operation Research KW - Network Performance Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7651 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Geerdes, Hans-Florian A1 - Junglas, Daniel A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Optimization Methods for UMTS Radio Network Planning N2 - The UMTS radio network planning problem poses the challenge of designing a cost-effective network that provides users with sufficient coverage and capacity. We describe an optimization model for this problem that is based on comprehensive planning data of the EU project MOMENTUM. We present heuristic mathematical methods for this realistic model, including computational results. T3 - ZIB-Report - 03-41 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7637 ER - TY - GEN A1 - Marenco, Javier A1 - Wagler, Annegret T1 - Chromatic Scheduling Polytopes coming from the Bandwidth Allocation Problem in Point-to-Multipoint Radio AccessSystems N2 - Point-to-Multipoint systems are one kind of radio systems supplying wireless access to voice/data communication networks. Such systems have to be run using a certain frequency spectrum, which typically causes capacity problems. Hence it is, on the one hand, necessary to reuse frequencies but, on the other hand, no interference must be caused thereby. This leads to the bandwidth allocation problem, a special case of so-called chromatic scheduling problems. Both problems are NP-hard, and there exist no polynomial time approximation algorithms with a guaranteed quality. One kind of algorithms which turned out to be successful for many other combinatorial optimization problems uses cutting plane methods. In order to apply such methods, knowledge on the associated polytopes is required. The present paper contributes to this issue, exploring basic properties of chromatic scheduling polytopes and several classes of facet-defining inequalities. T3 - ZIB-Report - 03-39 KW - Bandwidth allocation KW - polyhedral combinatorics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7614 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Hutanu, Andrei A1 - Kähler, Ralf A1 - Merzky, André A1 - Radke, Thomas A1 - Seidel, Edward A1 - Ullmer, Brygg T1 - Progressive Retrieval and Hierarchical Visualization of Large Remote Data N2 - \noindent The size of data sets produced on remote supercomputer facilities frequently exceeds the processing capabilities of local visualization workstations. This phenomenon increasingly limits scientists when analyzing results of large-scale scientific simulations. That problem gets even more prominent in scientific collaborations, spanning large virtual organizations, working on common shared sets of data distributed in Grid environments. In the visualization community, this problem is addressed by distributing the visualization pipeline. In particular, early stages of the pipeline are executed on resources closer to the initial (remote) locations of the data sets. \noindent This paper presents an efficient technique for placing the first two stages of the visualization pipeline (data access and data filter) onto remote resources. This is realized by exploiting the ``extended retrieve'' feature of GridFTP for flexible, high performance access to very large HDF5 files. We reduce the number of network transactions for filtering operations by utilizing a server side data processing plugin, and hence reduce latency overhead compared to GridFTP partial file access. The paper further describes the application of hierarchical rendering techniques on remote uniform data sets, which make use of the remote data filtering stage. T3 - ZIB-Report - 03-40 KW - remote data access KW - large files KW - visualization pipeline KW - hdf5 KW - grid Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7623 ER - TY - GEN A1 - Burger, Sven A1 - Klose, Roland A1 - Schädle, Achim A1 - Zschiedrich, Lin T1 - HelmPole - A finite element solver for scattering problems on unbounded domains: Implementation based on PML N2 - The solution of scattering problems described by the Helmholtz equation on unbounded domains is of importance for a wide variety of applications, for example in electromagnetics and acoustics. An implementation of a solver for scattering problems based on the programming language Matlab is introduced. The solver relies on the finite-element-method and on the perfectly-matched-layer-method, which allows for the simulation of scattering problems on complex geometries surrounded by inhomogeneous exterior domains. This report gives a number of detailed examples and can be understood as a user manual to the freely accessible code of the solver HelmPole. T3 - ZIB-Report - 03-38 KW - Helmholtz equation KW - finite element method KW - perfectly matched layer Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7609 ER - TY - GEN A1 - Bley, Andreas A1 - Zymolka, Adrian T1 - Planung kostenoptimaler Informations- und Kommunikations-Infrastrukturen N2 - Beim Entwurf und Ausbau von Informations- und Kommunikationsnetzwerken m{ü}ssen zahlreiche interdependente Entscheidungen getroffen und gleichzeitig mannigfaltige Bedingungen ber{ü}cksichtigt werden. Die verf{ü}gbaren technischen und organisatorischen Alternativm{ö}glichkeiten sind normalerweise so vielf{ä}ltig und komplex, dass eine manuelle Planung praktisch nicht m{ö}glich ist. In diesem Artikel wird das Potential und die Methodik der mathematischen Optimierung bei der kostenoptimalen Planung von Kommunikationsnetzen vorgestellt. Als Ausgangspunkt wird exemplarisch eine typische praktische Aufgabe, die Struktur- und Konfigurationsplanung mehrstufiger Telekommunikationsnetzwerke, dargestellt. Anschließend werden kurz die wesentlichen Modellierungstechniken und Verfahrensans{ä}tze der mathematischen Optimierung skizziert. Abschließend gehen wir auf die Planung einer ad{ä}quaten Informations- und Kommunikations- Infrastruktur f{ü}r ein dezentrales Energieversorgungsnetz ein. T3 - ZIB-Report - 03-37 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7591 ER - TY - GEN A1 - Lutz, Frank H. T1 - Triangulated Manifolds with Few Vertices: Geometric 3-Manifolds N2 - We explicitly construct small triangulations for a number of well-known $3$-dimensional manifolds and give a brief outline of some aspects of the underlying theory of $3$-manifolds and its historical development. T3 - ZIB-Report - 03-36 KW - triangulating manifolds KW - 3-manifolds KW - geometrization conjecture KW - 3-dimensional geometries KW - Seifert manifolds KW - torus bundles Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7583 ER - TY - GEN A1 - Weiser, Martin T1 - Interior Point Methods in Function Space N2 - A primal-dual interior point method for optimal control problems is considered. The algorithm is directly applied to the infinite dimensional problem. Existence and convergence of the central path are analyzed, and linear convergence of a short step pathfollowing method is established. T3 - ZIB-Report - 03-35 KW - interior point methods in function space KW - optimal control KW - complementarity functions Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7578 ER - TY - GEN A1 - Helling, Christiane A1 - Klein, Rupert A1 - Sedlmayr, Erwin T1 - The multi-scale dust formation in substellar atmospheres N2 - Substellar atmospheres are observed to be irregularly variable for which the formation of dust clouds is the most promising candidate explanation. The atmospheric gas is convectively unstable and, last but not least, colliding convective cells are seen as cause for a turbulent fluid field. Since dust formation depends on the local properties of the fluid, turbulence influences the dust formation process and may even allow the dust formation in an initially dust-hostile gas. A regime-wise investigation of dust forming substellar atmospheric situations reveals that the largest scales are determined by the interplay between gravitational settling and convective replenishment which results in a dust-stratified atmosphere. The regime of small scales is determined by the interaction of turbulent fluctuations. Resulting lane-like and curled dust distributions combine to larger and larger structures. We compile necessary criteria for a subgrid model in the frame of large scale simulations as result of our study on small scale turbulence in dust forming gases. T3 - ZIB-Report - 03-34 KW - dust formation KW - turbuelnce KW - multi-scale problem KW - substellar atmosphere Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7567 ER - TY - GEN A1 - Helling, Christiane A1 - Klein, Rupert A1 - Woitke, Peter A1 - Nowak, Ulrich A1 - Sedlmayr, Erwin T1 - Dust in Brown Dwarfs IV. Dust formation and driven turbulence on mesoscopic scales N2 - Dust formation {in brown dwarf atmospheres} is studied by utilizing a model for driven turbulence in the mesoscopic scale regime. We apply a pseudo-spectral method where waves are created and superimposed {within} a {limited} wavenumber interval. The turbulent kinetic energy distribution follows the Kolmogoroff spectrum which is assumed to be the most likely value. Such superimposed, stochastic waves may occur in a convectively active environment. They cause nucleation fronts and nucleation events and thereby initiate the dust formation process which { continues until} all condensible material is consumed. Small disturbances {are found to} have a large impact on the dust forming system. An initially dust-hostile region, which may originally be optically thin, becomes optically thick in a patchy way showing considerable variations in the dust properties during the formation process. The dust appears in lanes and curls as a result of the interaction with waves, i.e. turbulence, which form larger and larger structures with time. Aiming on a physical understanding of the variability of brown dwarfs, related to structure formation in substellar atmospheres, we work out first necessary criteria for small-scale closure models to be applied in macroscopic simulations of dust forming astrophysical systems. T3 - ZIB-Report - 03-33 KW - substellar atmospheres KW - dust formation KW - turbulence Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7555 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Koster, Arie M.C.A. T1 - Safe separators for treewidth N2 - A set of vertices $S\subseteq V$ is called a safe separator for treewidth, if $S$ is a separator of $G$, and the treewidth of $G$ equals the maximum of the treewidth over all connected components $W$ of $G-S$ of the graph, obtained by making $S$ a clique in the subgraph of $G$, induced by $W\cup S$. We show that such safe separators are a very powerful tool for preprocessing graphs when we want to compute their treewidth. We give several sufficient conditions for separators to be safe, allowing such separators, if existing, to be found in polynomial time. In particular, every minimal separator of size one or two is safe, every minimal separator of size three that does not split off a component with only one vertex is safe, and every minimal separator that is an almost clique is safe; an almost clique is a set of vertices $W$ such that there is a $v\in W$ with $W-\{v\}$ a clique. We report on experiments that show significant reductions of instance sizes for graphs from proba! bilistic networks and frequency assignment. T3 - ZIB-Report - 03-32 KW - treewidth KW - safe separators KW - preprocessing Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7544 ER - TY - GEN A1 - Khan, Arifa Ali A1 - Bakeyev, Timur A1 - Göckeler, Meinulf A1 - Horsley, Roger A1 - Pleiter, Dirk A1 - Rakow, Paul A1 - Schäfer, Andreas A1 - Schierholz, Gerrit A1 - Stüben, Hinnerk T1 - Accelerating Hasenbusch's Acceleration of Hybrid Monte Carlo N2 - Hasenbusch has proposed splitting the pseudo-fermionic action into two parts, in order to speed-up Hybrid Monte Carlo simulations of QCD. We have tested a different splitting, also using clover-improved Wilson fermions. An additional speed-up between 5 and 20\% over the original proposal was achieved in production runs. T3 - ZIB-Report - 03-30 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7520 ER - TY - GEN A1 - Bley, Andreas A1 - Koster, Arie M.C.A. A1 - Kröller, Alexander A1 - Wessäly, Roland A1 - Zymolka, Adrian T1 - Kosten- und Qualitätsoptimierung in Kommunikationsnetzen N2 - Der scharfe Wettbewerb innerhalb der Telekommunikationsbranche zwingt die Netzbetreiber dazu, ihre Investitionen genau zu planen und immer wieder Einsparungsmanahmen durchzuführen. Gleichzeitig ist es jedoch wichtig, die Qualität der angebotenen Dienste zu verbessern, um neue Kunden zu gewinnen und langfristig an sich zu binden. Die mathematische Optimierung bietet sich für viele solcher Aufgabenstellungen als hervorragend geeignetes Planungswerkzeug an. Ziel dieses Artikels ist es, ihre Methodik und ihre Anwendung speziell zur Kosten- und Qualitätsoptimierung in Kommunikationsnetzen vorzustellen. Anhand von vier konkreten Planungsaufgaben aus dem Bereich der Festnetzplanung wird aufgezeigt, wie sich komplexe Zusammenhänge in flexiblen mathematischen Modellen abbilden lassen und welche Verfahren zur automatisierten Bearbeitung der Probleme eingesetzt werden können. Die hier vorgestellten Methoden zeichnen sich insbesondere dadurch aus, dass sie neben hochwertigen Lösungen auch eine Qualittsgarantie liefern, mit der sich die Lsungen fundiert bewerten lassen. Die dokumentierten Ergebnisse aus verschiedenen Industrieprojekten belegen die Eignung und Güte der mathematischen Optimierung für die Praxis. T3 - ZIB-Report - 03-31 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7537 ER - TY - GEN A1 - Bley, Andreas T1 - A Lagrangian Approach for Integrated Network Design and Routing in IP Networks N2 - We consider the problem of designing a network that employs a non-bifurcated shortest path routing protocol. The network's nodes and the set of potential links are given together with a set of forecasted end-to-end traffic demands. All relevant hardware components installable at links or nodes are considered. The goal is to simultaneously choose the network's topology, to decide which hardware components to install on which links and nodes, and to find appropriate routing weights such that the overall network cost is minimized. In this paper, we present a mathematical optimization model for this problem and an algorithmic solution approach based on a Lagrangian relaxation. Computational results achieved with this approach for several real-world network planning problems are reported. T3 - ZIB-Report - 03-29 KW - Network Planning KW - Routing KW - IP Routing KW - Lagrangian relaxation Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7515 ER - TY - GEN A1 - Lutz, Frank H. T1 - Small Examples of Non-Constructible Simplicial Balls and Spheres N2 - We construct non-constructible simplicial $d$-spheres with $d+10$ vertices and non-constructible, non-realizable simplicial $d$-balls with $d+9$ vertices for $d\geq 3$. T3 - ZIB-Report - 03-28 KW - simplicial balls and spheres KW - constructibility KW - shellability KW - vertex-decomposability KW - knots in 3-balls and 3-spheres Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7500 ER - TY - GEN A1 - Fleuren, Maria A1 - Stüben, Hinnerk A1 - Zegwaard, Gideon T1 - MoDySim - A parallel dynamical UMTS simulator N2 - UMTS is a 3rd generation mobile telecommunication system which enables multi-service and multi-bit rate communication going beyond the possibilities of previous systems. The simulator MoDySim models UMTS in great detail. Characteristics of UMTS such as soft hand-over and the interdependency of load and capacity among neighbouring cells are challenges for the parallelisation of such a system. In this paper we explain how the software was parallelised and present performance results of a UMTS simulation for the city of Berlin. T3 - ZIB-Report - 03-26 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7489 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Sternbeck, André A1 - Stüben, Hinnerk T1 - A numerical reinvestigation of the Aoki phase with $N_f=2$ Wilson fermions at zero temperature N2 - We report on a numerical reinvestigation of the Aoki phase in lattice QCD with two flavors of Wilson fermions where the parity-flavor symmetry is spontaneously broken. For this purpose the Hybrid Monte Carlo algorithm was used and an explicit symmetry-breaking source term $h\bar{\psi} i \gamma_{5} \tau^{3}\psi$ was added to the Wilson fermion action. The order parameter $\langle\bar{\psi}i\gamma_{5}\tau^{3}\psi\rangle$ was studied at several values of $(\beta,\kappa,h)$ on lattices of sizes $4^4$ to $12^4$. Our largest lattices can be considered as infintely large allowing to extrapolate to $h=0$. The existence of a parity-flavor-breaking phase can be confirmed at $\beta=4.0$ and $\beta=4.3$ while we find no sign of parity-flavor-breaking at $\beta=4.6$ and $\beta=5.0$. T3 - ZIB-Report - 03-27 KW - Wilson fermions KW - phase diagram KW - parity-flavor symmetry KW - Aoki phase Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7492 ER - TY - GEN A1 - Bosse, Hartwig A1 - Grötschel, Martin A1 - Henk, Martin T1 - Polynomial Inequalities Representing Polyhedra N2 - Our main result is that every n-dimensional polytope can be described by at most (2n-1) polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an n-dimensional pointed polyhedral cone we prove the bound 2n-2 and for arbitrary polyhedra we get a constructible representation by 2n polynomial inequalities. T3 - ZIB-Report - 03-25 KW - polyhedra and polytopes KW - semi-algebraic sets KW - polyhedral combinatorics KW - polynomial inequalities KW - stability index Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7473 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian A1 - Jäger, Monika A1 - Hülsermann, Ralf A1 - Gerlach, Christoph T1 - Demand-wise Shared Protection for Meshed Optical Networks N2 - In this paper, a new shared protection mechanism for meshed optical networks is presented. Significant network design cost reductions can be achieved in comparison to the well-known 1+1 protection scheme. Demand-wise Shared Protection (DSP) bases on the diversification of demand routings and exploits the network connectivity to restrict the number of backup lightpaths needed to provide the desired level of prorection. Computational experiments approve the benefits of the concept DSP for cost efficient optical network designs. T3 - ZIB-Report - 03-24 KW - optical network design KW - shared protection KW - meshed optical networks KW - diversification Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7461 ER - TY - GEN A1 - Kober, Cornelia A1 - Erdmann, Bodo A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Simulation of the Human Mandible: Comparison of Bone Mineral Density and Stress/Strain Profiles due to Masticatory Muscles' Traction N2 - The correlation of the inner architecture of bone and its functional loading was already stated by Wolff in 1892. Our objective is to demonstrate this interdependence in the case of the human mandible. For this purpose, stress/strain profiles occuring at a human lateral bite were simulated. Additionally, by a combination of computer graphics modules, a three--dimensional volumetric visualization of bone mineral density could be given. Qualitative correspondences between the density profile of the jaw and the simulated stress/strain profiles could be pointed out. In the long run, this might enable the use of the simulation for diagnosis and prognosis. The solution of the underlying partial differential equations describing linear elastic material behaviour was provided by an adaptive finite element method. Estimates of the discretization errors, local grid refinement, and multilevel techniques guaranteed the reliability and efficiency of the method. T3 - ZIB-Report - 03-23 KW - linear elasticity KW - finite element method KW - adaptive grid refinement KW - stress/strain analysis KW - human mandible Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7458 ER - TY - GEN A1 - Wagler, Annegret T1 - Critical and Anticritical Edges with respect to Perfectness N2 - We call an edge $e$ of a perfect graph $G$ critical if $G-e$ is imperfect and call $e$ anticritical if $G+e$ is imperfect. The present paper surveys several questions in this context. We ask in which perfect graphs critical and anticritical edges occur and how to detect such edges. The main result by [{\sl Wagler, PhD thesis 2000}] shows that a graph does not admit any critical edge if and only if it is Meyniel. The goal is to order the edges resp.~non-edges of certain perfect graphs s.t. deleting resp.~adding all edges in this order yields a sequence of perfect graphs only. Results of [{\sl Hayward 1985}] and [{\sl Spinrad & Sritharan 1995}] show the existence of such edge orders for weakly triangulated graphs; the line-perfect graphs are precisely these graphs where all edge orders are perfect [{\sl Wagler 2001}]. Such edge orders cannot exist for every subclass of perfect graphs that contains critically resp.~anticritically perfect graphs where deleting resp.~adding an arbitrary edge yields an imperfect graph. We present several examples and properties of such graphs, discuss constructions and characterizations from [{\sl Wagler 1999, Wagler PhD thesis 2000}]. An application of the concept of critically and anticritically perfect graphs is a result due to [{\sl Hougardy & Wagler 2002}] showing that perfectness is an elusive graph property. T3 - ZIB-Report - 03-22 KW - Perfect graphs KW - critical edges KW - perfect edge orders KW - critically perfect graphs Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7446 ER - TY - GEN A1 - Pêcher, Arnaud A1 - Wagler, Annegret T1 - A construction for non-rank facets of stable set polytopes of webs N2 - Graphs with circular symmetry, called webs, are relevant for describing the stable set polytopes of two larger graph classes, quasi-line graphs [{\sl Giles and Trotter 1981, Oriolo 2001}] and claw-free graphs [{\sl Galluccio and Sassano 1997, Giles and Trotter 1981}]. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem [{\sl Grötschel, Lov\'asz, and Schrijver 1988}]. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only [{\sl Dahl 1999, Trotter 1975}] while there are examples with clique number $\geq 4$ having non-rank facets [{\sl e.g. Liebling et al. 2003, Oriolo 2001, P\^echer and Wagler 2003}]. In this paper, we provide a construction for non-rank facets of stable set polytopes of webs. We use this construction to prove, for several fixed values of $\omega$ including all odd values at least 5, that there are only finitely many webs with clique number $\omega$ whose stable set polytopes admit rank facets only. T3 - ZIB-Report - 03-21 KW - web KW - rank-perfect graph KW - stable set polytope KW - (non-)rank facet Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7437 ER - TY - GEN A1 - Deuflhard, Peter A1 - Schütte, Christof T1 - Molecular Conformation Dynamics and Computational Drug Design N2 - The paper surveys recent progress in the mathematical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time scales of $msec$ up to $min$ play the dominant role. Classical long-term molecular dynamics computations, however, would run into ill-conditioned initial value problems already after time spans of only $psec=10^{-12} sec$. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a {\em transfer operator} approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. Once this operator has been discretized, which is a hard problem of its own, a stochastic matrix arises. This matrix is then treated by {\em Perron cluster analysis}, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a Perron cluster of eigenvalues. In order to avoid the 'curse of dimension', the construction of appropriate boxes for the spatial discretization of the Markov operator requires careful consideration. As a biomolecular example we present a rather recent SARS protease inhibitor. T3 - ZIB-Report - 03-20 KW - conformation dynamics KW - Monte Carlo methods KW - transfer operations KW - Hamiltonian dynamics KW - Smoluchowski dynamics KW - metastable sets KW - Perron cluster an Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7427 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weber, Marcus T1 - Robust Perron Cluster Analysis in Conformation Dynamics N2 - The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included. T3 - ZIB-Report - 03-19 KW - Markov chains KW - cluster algorithms KW - Perron cluster analysis KW - conformation dynamics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7415 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - A sample path relation for the sojourn times in G/G/1-PS systems and its applications N2 - For the general G/G/1 processor sharing (PS) system a sample path result for the sojourn times in a busy period is proved, which yields a relation between the sojourn times under PS and FCFS discipline. In particular, the result provides a formula for the mean sojourn time in G/D/1-PS in terms of the mean sojourn time in the corresponding G/D/1-FCFS, generalizing known results for GI/M/1 and M/GI/1. Extensions of the formula provide the basis for a two-moment approximation of the mean sojourn time in G/GI/1-PS in terms of a related G/D/1-FCFS. T3 - ZIB-Report - 03-18 KW - G/G/1 KW - G/GI/1 KW - G/D/1 KW - G/M/1 KW - processor sharing KW - sojourn time KW - waiting time KW - busy period KW - sample path KW - first come first served KW - two-moment ap Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7401 ER - TY - GEN A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Visualization of Time-Dependent Adaptive Mesh Refinement Data N2 - Analysis of phenomena that simultaneously occur on quite different spatial and temporal scales require adaptive, hierarchical schemes to reduce computational and storage demands. For data represented as grid functions, the key are adaptive, hierarchical, time-dependent grids that resolve spatio-temporal details without too much redundancy. Here, so-called AMR grids gain increasing popularity. For visualization and feature identification/tracking, the underlying continuous function has to be faithfully reconstructed by spatial and temporal interpolation. Well designed interpolation methods yield better results and help to reduce the amount of data to be stored. We address the problem of temporal interpolation of AMR grid data, e.g.\ for creation of smooth animations or feature tracking. Intermediate grid hierarchies are generated by merging the cells on all refinement levels that are present in the key frames considered. Utilizing a clustering algorithm a structure of nested grids is induced on the resulting collection of cells. The grid functions are mapped to the intermediate hierarchy, thus allowing application of appropriate interpolation techniques. T3 - ZIB-Report - 03-16 KW - AMR KW - non-conforming hexahedral grids KW - multi-resolution techniques Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7384 ER - TY - GEN A1 - Benger, Werner A1 - Hege, Hans-Christian T1 - Tensor Splats N2 - An improved general-purpose technique for the visualization of symmetric positive definite tensor fields of rank two is described. It is based on a splatting technique that is built from tiny transparent glyph primitives which are capable to incorporate the full directional information content of a tensor. The result is an information-rich image that allows to read off the preferred directions in a tensor field at each point of a three-dimensional volume or two-dimensional surface. It is useful for analyzing slices or volumes of a three-dimensional tensor field and can be overlayed with standard volume rendering or color mapping. The application of the rendering technique is demonstrated on general relativistic data and the diffusion tensor field of a human brain. T3 - ZIB-Report - 03-17 KW - tensor field visualization KW - metric KW - splatting KW - volume rendering KW - general relativity KW - diffusion tensor images Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7393 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Neun, Winfried A1 - Sperber, Wolfram T1 - Semantic Annotation in Mathematics and Math-Net N2 - The Web of the future will provide a huge amount of information. We need better ways for dealing with and managing the information. A qualified semantic annotation of the information plays a key role for the Web of the future. This article gives an overview about the efforts of the mathematical community to build up a distributed and open information and communication system for mathematics: the Math-Net. The Math-Net Initiative has developed metadata schemas for some classes of Web resources which are relevant in mathematics. Math-Net Services process this information and enable the user to efficiently search and access the information. T3 - ZIB-Report - 03-15 KW - information and communication system for mathematics KW - Math-Net Semantic Webdata schemas Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7379 ER - TY - GEN A1 - Becchetti, Luca A1 - Leonardi, Stefano A1 - Marchetti-Spaccamela, Alberto A1 - Schäfer, Guido A1 - Vredeveld, Tjark T1 - Smoothening Helps: A Probabilistic Analysis of the Multi-Level Feedback Algorithm N2 - In this paper we introduce the notion of smoothed competitive analysis of online algorithms. Smoothed analysis has been proposed by [{\sl Spielman and Teng} STOC 2001] to explain the behaviour of algorithms that work well in practice while performing very poorly from a worst case analysis point of view. We apply this notion to analyze the Multi-Level Feedback (MLF) algorithm to minimize the total flow time on a sequence of jobs released over time when the processing time of a job is only known at time of completion. The initial processing times are integers in the range $[1,2^K]$. We use a partial bit randomization model, where the initial processing times are smoothened by changing the $k$ least significant bits under a quite general class of probability distributions. We show that MLF admits a smoothed competitive ratio of $O(max((2^k/\sigma)^3, (2^k/\sigma)^2 2^K-k))$, where $\sigma$ denotes the standard deviation of the distribution. In particular, we obtain a competitive ratio of $O(2^K-k)$ if $\sigma = \Theta(2^k)$. %The analysis holds for an oblivious as well as for a stronger adaptive %adversary. We also prove an $\Omega(2^{K-k})$ lower bound for any deterministic algorithm that is run on processing times smoothened according to the partial bit randomization model. For various other smoothening models, including the additive symmetric smoothening model used by [{\sl Spielman and Teng}], we give a higher lower bound of $\Omega(2^K)$. A direct consequence of our result is also the first average case analysis of MLF. We show a constant expected ratio of the total flow time of MLF to the optimum under several distributions including the uniform distribution. T3 - ZIB-Report - 03-14 KW - smoothed analysis KW - competitive analysis KW - scheduling Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7366 ER - TY - GEN T1 - Jahresbericht 2002 T3 - Jahresbericht - 2002 KW - Annual Report Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9776 SN - 0934-5892 ER - TY - GEN A1 - Weiser, Martin A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Asymptotic Mesh Independence of Newton's Method Revisited N2 - The paper presents a new affine invariant theory on asymptotic mesh independence of Newton's method in nonlinear PDEs. Compared to earlier attempts, the new approach is both much simpler and more natural from the algorithmic point of view. The theory is exemplified at collocation methods for ODE boundary value problems and at finite element methods for elliptic PDE problems. T3 - ZIB-Report - 03-13 KW - mesh independence KW - nonlinear partial differential equations KW - Newton method KW - finite element method KW - collocation method Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7352 ER - TY - GEN A1 - Coja-Oghlan, Amin A1 - Krumke, Sven A1 - Nierhoff, Till T1 - Average Case Analysis of a Hard Dial-a-Ride Problem N2 - In the dial-a-ride-problem (DARP) objects have to be moved between given sources and destinations in a transportation network by means of a server. The goal is to find a shortest transportation for the server. We study the DARP when the underlying transportation network forms a caterpillar. This special case is strongly NP-hard in the worst case. We prove that in a probabilistic setting there exists a polynomial time algorithm which almost surely finds an optimal solution. Moreover, with high probability the optimality of the solution found can be certified efficiently. We also examine the complexity of the DARP in a semi-random setting and in the unweighted case. T3 - ZIB-Report - 03-12 KW - dial-a-ride-problem KW - average case analysis KW - MST-heuristic KW - Steiner trees KW - NP-hardness Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7348 ER - TY - GEN A1 - Woitke, Peter A1 - Helling, Christiane T1 - Formation and structure of quasi-static cloud-layers in brown dwarf atmospheres N2 - In this paper, first solutions of the dust moment equations developed in [{\sl Woitke & Helling 2002}] for the description of dust formation and precipitation in brown dwarf and giant gas planet atmospheres are presented. We consider the special case of a static brown dwarf atmosphere, where dust particles continuously nucleate from the gas phase, grow by the accretion of molecules, settle gravitationally and re-evaporate thermally. Applying a kinetic description of the relevant microphysical and chemical processes for TiO$_2$-grains, the model makes predictions about the large-scale stratification of dust in the atmosphere, the depletion of molecules from the gas phase, the supersaturation of the gas in the atmosphere as well as the mean size and the mass fraction of dust grains as function of depth. Our results suggest that the nucleation occu in the upper atmosphere where the gas is cool, strongly depleted, but nevertheless highly supersaturated ($S\!\gg\!1$). These particles settle gravitationally and populate the warmer layers below, where the in-situ formation (nucleation) is ineffective or even not possible. During their descent, the particles grow up to radii $\approx\!0.3\,\mu{\rm m}\,...\,150\,\mu{\rm m}$, depending gas around the cloud base. The particles finally sink into layers which are sufficiently hot to cause their thermal evaporation. Hence, an effective transport mechanism for condensable elements exi considered solid/liquid material. In the stationary case studied here, this downward directed element transport by precipitating dust grains is balanced by an upward directed flux of condensable elements from the deep interior of the star via convective mixing (no dust without mixing). We find a self-regulation mechanism which leads to an approximate phase equilibrium ($S\!\approx\!1$) around the cloud base. The mass fraction of dust present in the atmosphere results be to approximately given by the mass fraction of condensable elements in the gas being mixed up. T3 - ZIB-Report - 03-11 KW - dust KW - precipitation KW - clouds KW - atmosphere Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7338 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian T1 - Polyhedral Investigations on Stable Multi-Sets N2 - Stable multi-sets are an evident generalization of the well-known stable sets. As integer programs, they constitute a general structure which allows for a wide applicability of the results. Moreover, the study of stable multi-sets provides new insights to well-known properties of stable sets. In this paper, we continue our investigations started in [{\sl Koster and Zymolka 2002}] and present results of three types: on the relation to other combinatorial problems, on the polyhedral structure of the stable multi-set polytope, and on the computational impact of the polyhedral results. First of all, we embed stable multi-sets in a framework of generalized set packing problems and point out several relations. The second part discusses properties of the stable multi-set polytope. We show that the vertices of the linear relaxation are half integer and have a special structure. Moreover, we strengthen the conditions for cycle inequalities to be facet defining, show that the separation problem for these inequalities is polynomial time solvable, and discuss the impact of chords in cycles. The last result allows to interpret cliques as cycles with many chords. The paper is completed with a computational study to the practical importance of the cycle inequalities. The computations show that the performance of state-of-the-art integer programming solvers can be improved significantly by including these inequalities. T3 - ZIB-Report - 03-10 KW - stable multi-sets KW - polyhedral combinatorics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7324 ER - TY - GEN A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - Comparing Restoration Concepts using Optimal Network Configurations with Integrated Hardware and Routing Decisions N2 - We investigate the impact of link and path restoration on the cost of telecommunication networks. The surprising result is the following: the cost of an optimal network configuration is almost independent of the restoration concept if (i) the installation of network elements (ADMs, DXCs, or routers) and interface cards, (ii) link capacities, and (iii) working and restoration routings are simultaneously optimized. We present a mixed-integer programming model which integrates all these decisions. Using a branch-and-cut algorithm (with column generation to deal with all potential routing paths), we solve structurally different real-world problem instances and show that the cost of optimal solutions is almost independent of the used restoration concept. In addition, we optimize spare capacities for given shortest working paths which are predetermined with respect to different link metrics. In comparison to simultaneous optimization of working and restoration routings, it turns out that this approach does not allow to obtain predictably good results. T3 - ZIB-Report - 03-09 KW - survivable network design KW - link and path restoration KW - hardware configuration KW - branch-and-cut algorithm KW - routing Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7316 ER - TY - GEN A1 - Hochmuth, Reinhard A1 - Deuflhard, Peter T1 - Multiscale Analysis for the Bio-Heat Transfer Equation N2 - The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. In [{\sl Deuflhard, Hochmuth 2002}] the authors applied homogenization techniques to derive the bio-heat transfer equation as asymptotic result of boundary value problems which provide a microscopic description for microvascular tissue. Here those results are generalized to a geometrical setting where the regions of blood are allowed to be connected. Moreover, asymptotic corrector results are derived. T3 - ZIB-Report - 03-08 KW - bio-heat equation KW - hyperthermia KW - homogenization KW - correctors KW - heat transfer KW - Robin boundary conditions Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7302 ER - TY - GEN A1 - Helling, Christiane A1 - Klein, Rupert A1 - Woitke, Peter A1 - Sedlmayr, Erwin T1 - Dust formation in brown dwarf atmospheres under conditions of driven turbulence N2 - Based on the knowledge gained from direct numerical simulations which are only possible in the microscale regime, a concept of driven turbulence is presented which allows to enter the mesoscopic scale regime. Here, dust formation under stochastic hydro- and thermodynamic conditions is studied: constructively superimposed stochastic waves initiate dust formation by the creation of singular nucleation events. It, hence, results a varying mean grain size and dust density in space and time. The newly formed dust changes the thermodynamic behavior from almost isotherm to adiabatic and chemically depletes the gas phase. T3 - ZIB-Report - 03-07 KW - dust formation KW - turbulence modelling KW - stochastic boundaries Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7294 ER - TY - GEN A1 - Borndörfer, Ralf T1 - Combinatorial Packing Problems N2 - This article investigates a certain class of combinatorial packing problems and some polyhedral relations between such problems and the set packing problem. T3 - ZIB-Report - 03-03 KW - Packing problems KW - polyhedral combinatorics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7255 ER - TY - GEN A1 - Weber, Marcus T1 - Improved Perron Cluster Analysis N2 - The problem of clustering data can often be transformed into the problem of finding a hidden block diagonal structure in a stochastic matrix. Deuflhard et al. have proposed an algorithm that state s the number $k$ of clusters and uses the sign structure of $k$ eigenvectors of the stochastic matrix to solve the cluster problem. Recently Weber and Galliat discovered that this system of eigenvectors can easily be transformed into a system of $k$ membership functions or soft characteristic functions describing the clusters. In this article we explain the corresponding cluster algorithm and point out the underlying theory. By means of numerical examples we explain how the grade of membership can be interpreted. T3 - ZIB-Report - 03-04 KW - cluster analysis KW - stochastic matrices KW - almost invariant sets Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7260 ER - TY - GEN A1 - Koch, Thorsten T1 - The final NETLIB-LP results N2 - The NETLIB has now served for 18 years as a repository of LP problem instances. From the beginning to the present day there was some uncertainness about the precise values of the optimal solutions. We implemented a program using exact rational arithmetic to compute proofs for the feasibility and optimality of an LP solution. This paper reports the \emph{exact} optimal objective values for all NETLIB problems. T3 - ZIB-Report - 03-05 KW - Linear Programming KW - Simplex KW - Netlib KW - rational arithmetic Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7274 ER - TY - GEN A1 - Sander, Oliver A1 - Krause, Rolf T1 - Automatic Construction of Boundary Parametrizations for Geometric Multigrid Solvers N2 - We present an algorithm that constructs parametrizations of boundary and interface surfaces automatically. Starting with high-resolution triangulated surfaces describing the computational domains, we iteratively simplify the surfaces yielding a coarse approximation of the boundaries with the same topological type. While simplifying we construct a function that is defined on the coarse surface and whose image is the original surface. This function allows access to the correct shape and surface normals of the original surface as well as to any kind of data defined on it. Such information can be used by geometric multigrid solvers doing adaptive mesh refinement. Our algorithm runs stable on all types of input surfaces, including those that describe domains consisting of several materials. We have used our method with success in different fields and we discuss examples from structural mechanics and biomechanics. T3 - ZIB-Report - 03-02 KW - boundary parametrization KW - surface simplification KW - multigrid KW - geometry Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7240 ER - TY - GEN A1 - Pecher, Arnaud A1 - Wagler, Annegret T1 - On Non-Rank Facets of Stable Set Polytopes of Webs with Clique Number Four N2 - Graphs with circular symmetry, called webs, are relevant w.r.t. describing the stable set polytopes of two larger graph classes, quasi-line graphs and claw-free graphs. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only while there are examples with clique number $>4$ having non-rank facets. T3 - ZIB-Report - 03-01 KW - web KW - rank-perfect graph KW - stable set polytope KW - (non-)rank facet Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7238 ER - TY - GEN A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Rascanu, Raluca T1 - Endnutzerbasierte Online-Fernleihe im KOBV - Kurzbeschreibung N2 - Der KOBV setzt für die endnutzerbasierte Online-Fernleihe den Sisis ZFL-Server (Zentraler Fernleih-Server) ein. Mit dem Einsatz des ZFL-Servers können in den Bibliotheken echte Rationalisierungseffekte erzielt werden: Der Server ist in der Lage, Fernleih-Bestellungen an lokale Systeme zu übergeben, so dass sie im lokalen System automatisch - ohne Eingreifen von Bibliotheksmitarbeitern - weiterverarbeitet werden können. Im KOBV können derzeit Sisis- und Aleph-Lokalsysteme diese Schnittstelle voll bedienen. Andere Bibliothekssysteme im KOBV, die diese Schnittstelle nicht bedienen können, werden mittels eines E-Mail-Verfahrens in die Online-Fernleihe integriert. Die vorliegende Kurzbeschreibung der Online-Fernleihe im KOBV soll - im Gegensatz zur Spezifikation, die möglichst vollständig sein sollte - einen leicht verständlichen Einblick in die Abläufe der Online-Fernleihe vermitteln. Nach einem Überblick über zu erwartende Rationalisierungseffekte ist der Ablauf einer Online-Fernleih-Bestellung - veranschaulicht durch eine Graphik mit dem technischen Aufbau im KOBV - kurz dargestellt. \vspace{6mm} {\it Hinweis:} Die von einer Arbeitsgruppe des KOBV erstellte Spezifikation zur Online-Fernleihe ist als ZIB Report 02-30 auf dem Preprint-Server des ZIB veröffentlicht. Siehe: Monika Kuberek (Red.) {\begin{rawhtml} Spezifikation für eine Verbund-Fernleih-Software im KOBV \end{rawhtml}} T3 - ZIB-Report - 02-55 KW - Bibliotheksverbund KW - Fernleihe KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Online-Fernleihe Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7221 ER - TY - GEN A1 - Brodersen, Maren A1 - Hodoroaba, Lavinia T1 - Navigation in the KOBV-Informationsportal Conceptual View N2 - The KOBV Informationsportal aims to be a universal gateway to the sources of information hosted by the partner libraries from the Berlin-Brandenburg area. Due to the large number of these sources, an intuitive navigation is an essential component of the portal. The navigation-component should preserve the partner libraries? independence and overcome their administrative and technical differences. This paper proposes a collection-level navigation with four dimensions: the sources? subject areas (e.g. the first two levels of DDC), the sources? type (e.g. e-journals, databases, OPACs, etc.), the sources? location (e.g. Berlin, Brandenburg) / the library that hosts that source and the sources? accessing state (e.g. free, restricted, etc.). T3 - ZIB-Report - 02-54 KW - Portale KW - KOBV KW - Navigation KW - Collection-level Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7216 ER - TY - GEN A1 - Litsche, Stefan T1 - Zur Zugriffskontrolle im KOBV N2 - Mit der Entwicklung des KOBV-Informationsportals soll den Benutzern in der Region Berlin-Brandenburg ein verbesserter Zugang zu Informationsressourcen geboten werden. Einen wesentlichen Anteil diese Auf der Grundlage der Analyse der Rahmenbedingungen werden Anforderungen an die Zugriffskontrolle im KOBV definiert und Lösungsmöglichkeiten auf der Ebene allgemeiner Modelle diskutiert. T3 - ZIB-Report - 02-53 KW - Zugriffskontrolle KW - Access Management KW - Informationssysteme KW - KOBV KW - Authentisierung KW - Autorisierung Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7203 ER - TY - THES A1 - Galliat, Tobias T1 - Adaptive Multilevel Cluster Analysis by Self-Organizing Box Maps N2 - Als Cluster Analyse bezeichnet man den Prozess der Suche und Beschreibung von Gruppen (Clustern) von Objekten, so daß die Objekte innerhalb eines Clusters bezüglich eines gegebenen Maßes maximal homogen sind. Die Homogenität der Objekte hängt dabei direkt oder indirekt von den Ausprägungen ab, die sie für eine Anzahl festgelegter Attribute besitzen. Die Suche nach Clustern läßt sich somit als Optimierungsproblem auffassen, wobei die Anzahl der Cluster vorher bekannt sein muß. Wenn die Anzahl der Objekte und der Attribute groß ist, spricht man von komplexen, hoch-dimensionalen Cluster Problemen. In diesem Fall ist eine direkte Optimierung zu aufwendig, und man benötigt entweder heuristische Optimierungsverfahren oder Methoden zur Reduktion der Komplexität. In der Vergangenheit wurden in der Forschung fast ausschließlich Verfahren für geometrisch basierte Clusterprobleme entwickelt. Bei diesen Problemen lassen sich die Objekte als Punkte in einem von den Attributen aufgespannten metrischen Raum modellieren; das verwendete Homogenitätsmaß basiert auf der geometrischen Distanz der den Objekten zugeordneten Punkte. Insbesondere zur Bestimmung sogenannter metastabiler Cluster sind solche Verfahren aber offensichtlich nicht geeignet, da metastabile Cluster, die z.B. in der Konformationsanalyse von Biomolekülen von zentraler Bedeutung sind, nicht auf einer geometrischen, sondern einer dynamischen Ähnlichkeit beruhen. In der vorliegenden Arbeit wird ein allgemeines Clustermodell vorgeschlagen, das zur Modellierung geometrischer, wie auch dynamischer Clusterprobleme geeignet ist. Es wird eine Methode zur Komplexitätsreduktion von Clusterproblemen vorgestellt, die auf einer zuvor generierten Komprimierung der Objekte innerhalb des Datenraumes basiert. Dabei wird bewiesen, daß eine solche Reduktion die Clusterstruktur nicht zerstört, wenn die Komprimierung fein genug ist. Mittels selbstorganisierter neuronaler Netze lassen sich geeignete Komprimierungen berechnen. Um eine signifikante Komplexitätsreduktion ohne Zerstörung der Clusterstruktur zu erzielen, werden die genannten Methoden in ein mehrstufiges Verfahren eingebettet. Da neben der Identifizierung der Cluster auch deren effiziente Beschreibung notwendig ist, wird ferner eine spezielle Art der Komprimierung vorgestellt, der eine Boxdiskretisierung des Datenraumes zugrunde liegt. Diese ermöglicht die einfache Generierung von regelbasierten Clusterbeschreibungen. Für einen speziellen Typ von Homogenitätsfunktionen, die eine stochastische Eigenschaft besitzen, wird das mehrstufige Clusterverfahren um eine Perroncluster Analyse erweitert. Dadurch wird die Anzahl der Cluster, im Gegensatz zu herkömmlichen Verfahren, nicht mehr als Eingabeparameter benötigt. Mit dem entwickelten Clusterverfahren kann erstmalig eine computergestützte Konformationsanalyse großer, für die Praxis relevanter Biomoleküle durchgeführt werden. Am Beispiel des HIV Protease Inhibitors VX-478 wird dies detailliert beschrieben. KW - Biochemical conformations KW - cluster analysis KW - molecular dynamics KW - Perron cluster analysis KW - Self-Organizing Maps KW - Biochemical conformations KW - cluster analysis KW - molecular dynamics KW - Perron cluster analysis KW - Self-Organizing Maps Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-2002001258 ER - TY - THES A1 - Schütt, Thorsten T1 - Synchronisation von verteilten Verzeichnisstrukturen N2 - Das Management von großen Datenmengen spielt eine immer wichtigere Rolle, wie aktuelle Entwicklungen in der Hochenergiephysik [2] zeigen. Für das DataGrid-Projekt zum Beispiel ist es notwendig, große Datenmengen auf mehrere Rechenzentren in Europa zu verteilen und die Daten untereinander zu synchronisieren. Auch innerhalb von Clustern gewinnen mit zunehmender Anzahl der Knoten Werkzeuge zur effizienten Synchronisation und Verteilung von Daten an Bedeutung. Im Rahmen dieser Arbeit wurde ein effizientes Verfahren zur Synchronisation von verteilten Verzeichnisstrukturen entwickelt und implementiert. Mit diesem Verfahren ist es möglich, unabhängige Änderungen an beliebigen Repositories gleichzeitig durchzuführen. Das Verfahren benötigt keine zentrale Instanz, wodurch eine gegenüber vielen existierenden Verfahren verbesserte Skalierbarkeit erreicht werden konnte. Dabei wurden Erkenntnisse aus der Graphentheorie eingesetzt und weiterentwickelt, um die Netzwerktopolo-gie und -handbreiten zwischen den Rechnern zu berücksichtigen. Durch die Verwendung einer Offline-Synchronisation werden Änderungen erst dann an andere Rechner propagiert, wenn der Nutzer dies anstößt. Das kann zum Beispiel nach einer abgeschlossenen Transaktion, die Änderungen an mehreren Dateien beinhaltet, angemessen sein. N2 - Current developments in high energy physics [2] show that the management of large datasets plays an important role. For the DataGrid project it is necessary to distribute large datasets over several computing centers all over Europe and to synchronize these datasets. Within clusters tools for efficient synchronization and distribution of data become more important, too. In this thesis, a method to synchronize distributed directory structures was developed and implemented which makes it possible to perform independent changes to arbitrary repositories simultaneously. This method needs no central instance and therefore the presented system achieves a better scalability than many existing systems. Knowledge from graph theory was used and improved to take the network topology and the network bandwidth between the computers into account. By using offline synchronization, changes will only be propagated when the user initiates it. This can be reasonable after a completed transaction which consists of changes on several files. Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10071 ER - TY - GEN A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - On the Cost of Reliability in Large Data Grids N2 - Global grid environments do not only provide massive aggregated computing power but also an unprecedented amount of distributed storage space. Unfortunately, dynamic changes caused by component failures, local decisions, and irregular data updates make it difficult to efficiently use this capacity. In this paper, we address the problem of improving data availability in the presence of unreliable components. We present an analytical model for determining an optimal combination of distributed replica catalogs, catalog sizes, and replica servers. Empirical simulation results confirm the accuracy of our theoretical analysis. Our model captures the characteristics of highly dynamic environments like peer-to-peer networks, but it can also be applied to more centralized, less dynamic grid environments like the European {\em DataGrid}. T3 - ZIB-Report - 02-52 KW - replication KW - availability KW - reliability KW - distributed catalog KW - data grid Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7195 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Koster, Arie M.C.A. A1 - Wallbaum, Randolf A1 - Wessäly, Roland T1 - Load Balancing in Signaling Transfer Points N2 - Signaling is crucial to the operation of modern telecommunication networks. A breakdown in the signaling infrastructure typically causes customer service failures, incurs revenue losses, and hampers the company image. Therefore, the signaling network has to be highest reliability and survivability. This in particular holds for the routers in such a network, called \textit{signaling transfer points\/} (STPs). The robustness of an STP can be improved by equally distributing the load over the internal processing units. Several constraints have to be taken into account. The load of the links connected to a processing unit changes over time introducing an imbalance of the load. In this paper, we show how integer linear programming can be applied to reduce the imbalance within an STP, while keeping the number of changes small. Two alternative models are presented. Computational experiments validate the integer programming approach in practice. The GSM network operator E-Plus saves substantial amounts of time and money by employing the proposed approach. T3 - ZIB-Report - 02-50 KW - Signaling network KW - STP KW - load-balancing KW - integer programming KW - computations Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7179 ER - TY - GEN A1 - Woitke, Peter A1 - Helling, Christiane T1 - Dust in brown dwarfs II. The coupled problem of dust formation and sedimentation N2 - In this paper, we quantify and discuss the physical and surface chemical processes leading to the formation, temporal evolution and sedimentation of dust grains in brown dwarf and giant gas planet atmospheres: nucleation, growth, evaporation and gravitational settling. Considering dust particles of arbitrary sizes in the different hydrodynamical regimes (free molecular flow, laminar flow, turbulent flow), we evaluate the equilibrium drift velocities (final fall speeds) and the growth rates of the particles due to accretion of molecules. We show that a depth-dependent maximum size of the order of $a_{\rm max}\!\approx\!1\,\mu{\rm m\,(upper\ regions)} \ldots 100\,\mu{\rm m\,(lower\ regions)}$ exists, which depends on the condensate and the stellar parameters, beyond which gravitational settling is faster than growth. Larger particles can probably not be formed and sustained in brown dwarf atmospheres. We furthermore argue that the acceleration towards equilibrium drift is always very fast and that the temperature increase of the grains due to the release of latent heat during the growth process is negligible. Based on these findings, we formulate the problem of dust formation coupled to the local element depletion/enrichment of the gas in brown dwarf atmospheres by means of a system of partial differential equations. These equations state an extension of the moment method developed by Gail\plus Sedlmayr\,(1988) with an additional advective term to account for the effect of size-dependent drift velocities of the grains. A dimensionless analysis of the new equations reveals a hierarchy of nucleation $\to$ growth $\to$ drift $\to$ evaporation, which characterises the life cycle of dust grains in brown dwarf atmospheres. The developed moment equations can be included into hydrodynamics or classical stellar atmosphere models. Applications of this description will be presented in a forthcoming paper of this series. T3 - ZIB-Report - 02-51 KW - dust formation KW - precipitation KW - brown dwarfs Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7186 ER - TY - GEN A1 - Wolf, Thomas T1 - Applications of CRACK in the Classification of Integrable Systems N2 - The talk given by the author at the CRM workshop on Superintegrability in Sep.\ 2002 and this related paper report on work in two subjects. One is the collaboration with Vladimir Sokolov and Takayuki Tsuchida in an effort to classify polynomial integrable vector evolution equations. The other is the computer algebra package {\sc Crack} which did the main computations in solving large bi-linear algebraic systems. Although originally designed to solve over-determined systems of partial differential equations a number of extensions made {\sc Crack} a powerful tool for solving systems of bi-linear algebraic equations. Such systems turn up in many different classification problems some of which were investigated by other participants of this workshop. Two additional applications are outlined. In the talk on which this article is based a method to reduce the length of equations was presented which proved to be useful in solving the bi-linear algebraic systems. Due to numerous asked questions about the computer program, a more complete overview is given in the appendix. T3 - ZIB-Report - 02-48 KW - Integrability KW - evolution equations KW - quadratic Hamiltonians KW - Computer algebra KW - Bi-linear algebraic systems KW - conservation laws Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7159 ER - TY - GEN A1 - Eijkhof, Frank van den A1 - Bodlaender, Hans L. A1 - Koster, Arie M.C.A. T1 - Safe reduction rules for weighted treewidth N2 - Several sets of reductions rules are known for preprocessing a graph when computing its treewidth. In this paper, we give reduction rules for a weighted variant of treewidth, motivated by the analysis of algorithms for probabilistic networks. We present two general reduction rules that are safe for weighted treewidth. They generalise many of the existing reduction rules for treewidth. Experimental results show that these reduction rules can significantly reduce the problem size for several instances of real-life probabilistic networks. T3 - ZIB-Report - 02-49 KW - weighted treewidth KW - preprocessing KW - probabilistic networks Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7164 ER - TY - GEN A1 - Helling, Christiane T1 - Circuit of Dust in Substellar Atmopsheres N2 - Substellar atmospheres are cool and dense enough that dust forms very efficiently. As soon as these particles are formed, they sizedependently precipitate due to the large gravity of the objects. Arriving in hot atmospheric layers, the dust evaporates and enriches the gas by those elements from which it has formed. The upper atmospheric layers are depleted by the same elements. Non-continuous and spatially inhomogeneous convective element replenishment, generating a turbulent fluid field, completes the circuit of dust. The formation of dust in substellar atmosphere is described by extending the classical theory of Gail\plus Sedlmayr for the case of different gas and dust velocities. Turbulence is modeled in different scale regimes which reveals turbulence as trigger for dust formation in hot environments. Both mechanisms cause the dust to be present in else wise dust-hostile region: precipitation transports the dust into hot regions, and turbulence allows the formation of dust in there. T3 - ZIB-Report - 02-47 KW - dust formation KW - drift KW - turbulence modelling Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7142 ER - TY - GEN A1 - Deuflhard, Peter T1 - A Comparison of Related Concepts in Computational Chemistry and Mathematics N2 - This article studies the relation of the two scientific languages Chemistry and Mathematics via three selected comparisons: (a) QSSA versus dynamic ILDM in reaction kinetics, (b) lumping versus discrete Galerkin methods in polymer chemistry, and (c) geometrical conformations versus metastable conformations in drug design. The common clear message from these comparisons is that chemical intuition may pave the way for mathematical concepts just as chemical concepts may gain from mathematical precisioning. Along this line, significant improvements in chemical research and engineering have already been possible -- and can be further expected in the future from the dialogue between the two scientific languages. T3 - ZIB-Report - 02-46 KW - dimension reduction KW - model reduction KW - QSSA KW - ILDM KW - reaction kinetics KW - polyreaction kinetics KW - Hamilton systems KW - conformations KW - metastability KW - d Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7138 ER - TY - THES A1 - Schmidt, Frank T1 - A New Approach to Coupled Interior-Exterior Helmholtz-Type Problems: Theory and Algorithms N2 - The work presents a new approach to the numerical solution of time-harmonic and time-dependent scattering problems. We replace Sommerfeld's radiation condition valid for the Helmholtz equation by a more general concept called pole condition. The pole condition is based on the Laplace transform of the exterior solution and allows a characterization of outgoing waves. Both new insight into the analysis of scattering problems as well as new numerical algorithms are obtained. T3 - ZIB-Report - 02-45 KW - Pole condition KW - Helmholtz equation KW - Wide angle one-way equation KW - Schroedinger equation KW - Transparent boundary conditions KW - Unbounded domains KW - Fini Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7128 ER - TY - GEN A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Torres, Luis Miguel T1 - Online-Dispatching of Automobile Service Units N2 - We present an online algorithm for a real-world vehicle dispatching problem at ADAC, the German Automobile Association. T3 - ZIB-Report - 02-44 KW - vehicle dispatching KW - soft time windows KW - online KW - real-time KW - ADAC Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7117 ER - TY - GEN A1 - Hansmann, Sabine A1 - Loesch, Sandra A1 - Morstein, Gabriele A1 - Müller, Werner A1 - Müntner, Kathrin A1 - Ristau, Ute A1 - Rusch, Beate A1 - Todt, Günter A1 - Wagenknecht, Petra T1 - Fremddatennutzung im KOBV: Eine Evaluation vom Mai / Juni 2002 N2 - Eine fremddatengestützte Katalogisierung bedeutet für die einzelne Bibliothek unbestritten eine Zeit- und Kostenersparnis. Dieser Report beleuchtet die unterschiedlichen Faktoren technischer und organisatorischer Natur, die die Fremddatennutzung in der dezentralen Struktur des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) beeinflussen. Die Ausführungen stützen sich im Wesentlichen auf eine Umfrage, die die Autoren im Mai / Juni 2002 unter KOBV-Mitgliedsbibliotheken zum Thema Fremddatennutzung durchgeführt haben. Dargelegt wird, wie komfortabel die in den KOBV-Bibliotheken eingesetzten Bibliotheksinformationssysteme eine fremddatengestützte Katalogisierung erlauben. Diskutiert wird zudem die Software ZACK, die sich als Alternative zu einem eigenen Z39.50-Client zur Datenübernahme anbietet. Erstmals seit Bestehen des Verbundes werden Zahlen veröffentlicht über den Anteil der Bibliotheken, die Fremddaten nutzen und denjenigen, die dieses Angebot nicht wahrnehmen. Dabei wird die Fremddatenutzung differenziert sowohl für den Bereich der Neuaufnahmen als auch für die Retrokatalogisierung. In der weiteren Analyse werden zusätzliche Aspekte betrachtet wie z.B. die verfügbaren bzw. gewünschten Datenbanken im Verhältnis zum sprachlichen Spektrum des erworbenen Katalogisierungsgutes. Eingegangen wird auch auf die von den Bibliotheken genannten Hauptproblemen und die gewünschten zusätzlichen Serviceleistungen auf Seiten der KOBV-Verbundzentrale. Als Ergebnis dieses Status-Quo-Berichts legt das Autorenteam eine Reihe von Empfehlungen vor, die darauf abzielen, auch für KOBV-Bibliotheken in Zukunft eine Fremddatennutzungsquote von 70 - 75 % zu erreichen. T3 - ZIB-Report - 02-43 KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Bibliotheken KW - Bibliotheksverbund KW - Fremddaten KW - Fremddatennutzung Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7104 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Roitzsch, Rainer T1 - KARDOS - User"s Guide N2 - The adaptive finite element code {\sc Kardos} solves nonlinear parabolic systems of partial differential equations. It is applied to a wide range of problems from physics, chemistry, and engineering in one, two, or three space dimensions. The implementation is based on the programming language C. Adaptive finite element techniques are employed to provide solvers of optimal complexity. This implies a posteriori error estimation, local mesh refinement, and preconditioning of linear systems. Linearely implicit time integrators of {\em Rosenbrock} type allow for controlling the time steps adaptively and for solving nonlinear problems without using {\em Newton's} iterations. The program has proved to be robust and reliable. The user's guide explains all details a user of {\sc Kardos} has to consider: the description of the partial differential equations with their boundary and initial conditions, the triangulation of the domain, and the setting of parameters controlling the numerical algorithm. A couple of examples makes familiar to problems which were treated with {\sc Kardos}. We are extending this guide continuously. The latest version is available by network: {\begin{rawhtml} Downloads. \end{rawhtml}} T3 - ZIB-Report - 02-42 KW - nonlinear parabolic systems KW - Rosenbrock methods KW - adaptivity in time and space Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7096 ER - TY - GEN A1 - Bley, Andreas A1 - Koch, Thorsten T1 - Integer programming approaches to access and backbone IP-network planning N2 - In this article we study the problem of designing a nation-wide communication network. Such networks usually consist of an access layer, a backbone layer, and maybe several intermediate layers. The nodes of each layer must be connected to those of the next layer in a tree-like fashion. The backbone layer has to satisfy certain survivability and routing constraints. Given the node locations, the demands between them, the possible connections and hardware configurations, and various other technical and administrational constraints, the goal is to decide, which node is assigned to which network level, how the nodes are connected, what hardware must be installed, and how traffic is routed in the backbone. Mixed integer linear programming models and solution methods are presented for both the access and the backbone network design problem. The focus is on the design of IP-over-SDH networks, but the access network design model and large parts of the backbone network design models are general and also applicable for other types of communication networks. Results obtained with these methods in the planning of the German research network are presented. T3 - ZIB-Report - 02-41 KW - Network design KW - Traffic enineering KW - Internet routing KW - Mixed-integer programming Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7081 ER - TY - GEN A1 - Cordes, Frank A1 - Weber, Marcus A1 - Schmidt-Ehrenberg, Johannes T1 - Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals N2 - Decomposition of the high dimensional conformational space of bio-molecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is identified by the Perron-cluster cluster analysis of a Markov process that generates the thermodynamic distribution. A necessary prerequisite of this analysis is the discretization of the conformational space. A combinatorial approach via discretization of each degree of freedom will end in the so called ''curse of dimension''. In the following paper we analyze Hybrid Monte Carlo simulations of small, drug-like biomolecules and focus on the dihedral degrees of freedom as indicators of conformational changes. To avoid the ''curse of dimension'', the projection of the underlying Markov operator on each dihedral is analyzed according to its metastability. In each decomposition step of a recursive procedure, those significant dihedrals, which indicate high metastability, are used for further decomposition. The procedure is introduced as part of a hierarchical protocol of simulations at different temperatures. The convergence of simulations within metastable subsets is used as an ''a posteriori'' criterion for a successful identification of metastability. All results are presented with the visualization program AmiraMol. T3 - ZIB-Report - 02-40 KW - metastability KW - Perron-Cluster Cluster Analysis KW - curse of dimension KW - Hybrid Monte Carlo KW - significant dihedrals Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7074 ER - TY - GEN A1 - Grötschel, Martin T1 - Cardinality Homogeneous Set Systems, Cycles in Matroids, and Associated Polytopes N2 - A subset ${\cal C}$ of the power set of a finite set $E$ is called cardinality homogeneous if, whenever ${\cal C}$ contains some set $F$, ${\cal C}$ contains all subsets of $E$ of cardinality $|F|$. Examples of such set systems ${\cal C}$ are the sets of circuits and the sets of cycles of uniform matroids and the sets of all even or of all odd cardinality subsets of $E$. With each cardinality homogeneous set system ${\cal C}$, we associate the polytope $P({\cal C})$, the convex hull of the incidence vectors of all sets in ${\cal C}$, and provide a complete and nonredundant linear description of $P({\cal C})$. We show that a greedy algorithm optimizes any linear function over $P({\cal C})$, give an explicit optimum solution of the dual linear program, and provide a polynomial time separation algorithm for the class of polytopes of type $P({\cal C})$. T3 - ZIB-Report - 02-19 KW - Cycles in Matroids KW - cardinality homogeneous set systems KW - polytopes KW - greedy algorithm KW - polyhedral combinatorics Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6868 ER - TY - GEN A1 - Hoffmann, Hans Falk A1 - Putzer, Alois A1 - Reinefeld, Alexander T1 - Vom World Wide Web zum World Wide Grid - Eine neue Informationsinfrastruktur für wissenschaftliche Anwendungen N2 - In Analogie zu den Elektrizitätsnetzen electricity grid), von denen die technische Revolution ausging, wurde der Begriff Computational Grid (kurz Grid) geprägt. Ein wichtiger Bestandteil des Systems liegt im benutzerfreundlichen Zugang und der koordinierten Nutzung der weltweit verteilten Speicherressourcen und Rechnerkapazitäten. Bei der Entwicklung dazu notwendiger Technologien und Software (Middleware) profitiert man von Kenntnissen und Erfahrungen bei der Entwicklung verteilter Algorithmen, dem Software-Engineering und dem Supercomputing. T3 - ZIB-Report - 02-39 KW - Grid-Computing Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7069 ER - TY - GEN A1 - Schlegel, Martin A1 - Marquardt, Wolfgang A1 - Ehrig, Rainald A1 - Nowak, Ulrich T1 - Sensitivity analysis of linearly-implicit differential-algebraic systems by one-step extrapolation N2 - In this work we present an approach for the sensitivity analysis of linearly-implicit differential-algebraic equation systems. Solutions for both, states and sensitivities are obtained by applying an extrapolated linearly implicit Euler discretization scheme. This approach is compared to the widely used sensitivity extensions of multi-step BDF methods by means of case studies. Especially, we point out the benefit of this method in the context of dynamic optimization using the sequential approach. T3 - ZIB-Report - 02-38 KW - sensitivity evaluation KW - differential-algebraic systems KW - extrapolation methods KW - dynamic optimization KW - optimal control Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7052 ER - TY - GEN A1 - Litsche, Stefan A1 - Otto, Dagmar T1 - Dynamisches Verlinken mit SFX und MetaLib N2 - Zeitschriften und andere Medien werden in wachsendem Maße elektronisch publiziert. Hier entsteht für die Bibliotheken, welche diese Online-Publikationen ihren Lesern zur Verfügung stellen, ein neuer Bereich der Informationsvermittlung. Mit dem aufkommenden Standard der OpenURL ergeben sich neue Möglichkeiten, dem Benutzer weiterführende Links und Dienste anzubieten. Das Document-Linking-System SFX der Firma Ex Libris ist die erste und bekannteste Anwendung, die ein Managementsystem fr die Auswertung der OpenURL implementiert. Im Rahmen eines Projektes hat die Zentrale des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) eine Evaluation von SFX durchgeführt. Als Ergebnis der Evaluation sollten Einsatzmöglichkeiten von SFX für die KOBV-Suchmaschine und in den lokalen Bibliothekssystemen und Informationsportalen aufgezeigt werden. Im Verlauf des Projektes hat sich das Produkt SFX als eine stabile Anwendung erwiesen, die dem Benutzer interessante zusätzliche Dienste bieten kann. T3 - ZIB-Report - 02-37 KW - Informationssysteme KW - Dynamisches Verlinken KW - OpenURL Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7045 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Weiser, Martin T1 - Affine Invariant Adaptive Newton Codes for Discretized PDEs N2 - The paper deals with three different Newton algorithms that have recently been worked out in the general frame of affine invariance. Of particular interest is their performance in the numerical solution of discretized boundary value problems (BVPs) for nonlinear partial differential equations (PDEs). Exact Newton methods, where the arising linear systems are solved by direct elimination, and inexact Newton methods, where an inner iteration is used instead, are synoptically presented, both in affine invariant convergence theory and in numerical experiments. The three types of algorithms are: (a) affine covariant (formerly just called affine invariant) Newton algorithms, oriented toward the iterative errors, (b) affine contravariant Newton algorithms, based on iterative residual norms, and (c) affine conjugate Newton algorithms for convex optimization problems and discrete nonlinear elliptic PDEs. T3 - ZIB-Report - 02-33 KW - Affine invariant Newton methods KW - global Newton methods KW - inexact Newton methods KW - adaptive trust region methods KW - nonlinear partial differential equa Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7005 ER - TY - GEN A1 - Hülsermann, Ralf A1 - Jäger, Monika A1 - Krumke, Sven A1 - Poensgen, Diana A1 - Rambau, Jörg A1 - Tuchscherer, Andreas T1 - Dynamic Routing Algorithms in Transparent Optical Networks An Experimental Study Based on Real Data N2 - Today's telecommunication networks are configured statically. Whenever a connection is established, the customer has permanent access to it. However, it is observed that usually the connection is not used continuously. At this point, dynamic provisioning could increase the utilization of network resources. WDM based Optical Transport Networks (OTNs) will shortly allow for fast dynamic network reconfiguration. This enables optical broadband leased line services on demand. Since service requests competing for network resources may lead to service blocking, it is vital to use appropriate strategies for routing and wavelength assignment in transparent optical networks. We simulate the service blocking probabilities of various dynamic algorithms for this problem using a well-founded traffic model for two realistic networks. One of the algorithms using shortest path routings performs best on all instances. Surprisingly, the tie-breaking rule between equally short paths in different wavelengths decides between success or failure. T3 - ZIB-Report - 02-35 KW - Dynamic Network Configuration KW - Routing and Wavelength Allocation KW - Transparent Optical Networks KW - Blocking Probability KW - Simulation Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7025 ER - TY - GEN A1 - Krumke, Sven A1 - Laura, Luigi A1 - Lipmann, Maarten A1 - Marchetti-Spaccamela, Alberto A1 - Paepe, Willem de A1 - Poensgen, Diana A1 - Stougie, Leen T1 - Non-Abusiveness Helps: An O(1)-Competitive Algorithm for Minimizing the Maximum Flow Time in the Online Traveling Salesman Problem N2 - In the online traveling salesman problem $OLTSP$ requests for visits to cities arrive online while the salesman is traveling. We study the $F{\_max}-OLTSP$ where the objective is to minimize the maximum flow time. This objective is particularly interesting for applications. Unfortunately, there can be no competitive algorithm, neither deterministic nor randomized. Hence, competitive analysis fails to distinguish online algorithms. Not even resource augmentation which is helpful in scheduling works as a remedy. This unsatisfactory situation motivates the search for alternative analysis methods. We introduce a natural restriction on the adversary for the $F{\_max}-OLTSP$ on the real line. A \emph{non-abusive adversary} may only move in a direction if there are yet unserved requests on this side. Our main result is an algorithm which achieves a constant competitive ratio against the non-abusive adversary. T3 - ZIB-Report - 02-36 KW - Online Algorithms KW - Competitive Analysis KW - Comparative Analysis Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7038 ER - TY - GEN A1 - Zymolka, Adrian A1 - Koster, Arie M.C.A. A1 - Wessäly, Roland T1 - Transparent optical network design with sparse wavelength conversion N2 - We consider the design of transparent optical networks from a practical perspective. Network operators aim at satisfying the communication demands at minimum cost. Such an optimization involves three interdependent planning issues: the dimensioning of the physical topology, the routing of lightpaths, and the wavelength assignment. Further topics include the reliability of the configuration and sparse wavelength conversion for efficient use of the capacities. In this paper, we investigate this extensive optical network design task. Using a flexible device-based model, we present an integer programming formulation that supports greenfield planning as well as expansion planning on top of an existing network. As solution method, we propose a suitable decomposition approach that separates the wavelength assignment from the dimensioning and routing. Our method in particular provides a lower bound on the total cost which allows to rate the solution quality. Computational experiments on realistic networks approve the solution approach to be appropriate. T3 - ZIB-Report - 02-34 KW - optical network design KW - wavelength conversion KW - integer programming Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7017 ER - TY - GEN A1 - Achterberg, Tobias A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Branching on History Information N2 - Mixed integer programs ($MIPs$) are commonly solved with branch and bound algorithms based on linear programming. The success and the speed of the algorithm strongly depends on the strategy used to select the branching variables. Today's state-of-the-art strategy is called \emph{pseudocost branching} and uses information of previous branchings to determine the current branching. We propose a modification of \emph{pseudocost branching} which we call \emph{history branching}. This strategy has been implemented in $SIP$, a state-of-the-art $MIP$ solver. We give computational results that show the superiority of the new strategy. T3 - ZIB-Report - 02-32 KW - Mixed Integer Programming KW - Branch-and-Bound KW - Branching Rules KW - Pseudocost Branching Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6990 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hochmuth, Reinhard T1 - Multiscale Analysis of Thermoregulation in the Human Microvascular System N2 - The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. So far the deduction of the Helmholtz term in the bio-heat transfer equation is not co role. In view of a future numerical application of this new mathematical model to treatment planning in hyperthermia we derive asymptotic estimates for first and second order correctors. T3 - ZIB-Report - 02-31 KW - bio-heat equation KW - hyperthermia KW - homogenization Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6985 ER - TY - GEN A1 - Kuberek, Monika T1 - Spezifikation für eine Verbund-Fernleih-Software im KOBV N2 - Nachdem mit der KOBV-Suchmaschine die Online-Recherche in den wichtigsten Berliner und Brandenburgischen Bibliotheken realisiert ist, gehört der Aufbau der Online-Fernleihe als einer neuen, nutzerfreundlichen Dienstleistung zu den drängendsten Desideraten des KOBV. Dem Nutzer soll ein komfortabler Service geboten werden, der ihm im Anschluss an eine erfolgreiche Recherche die nahtlose - per Knopfdruck ausgelöste - Fernleih-Bestellung auf das gewünschte Medium erlaubt. Gleichzeitig trägt die Ablösung des traditionellen, per Post und Bücherauto versandten Roten Fernleihscheines durch eine sekundenschnelle Online-Kommunikation zu einer erheblichen Beschleunigung des Fernleih-Verfahrens bei. Der KOBV beteiligt sich an der Initiative der deutschen Bibliotheksverbünde zur Automatisierung und Beschleunigung der Fernleihe. Die Realisierung soll im KOBV in einem zweistufigen Verfahren erfolgen: (1) verbundinterne Fernleihe im KOBV und (2) verbundübergreifende Fernleihe in der Zusammenarbeit mit den anderen Verbünden. Eine Verbund-Fernleih-Software für den KOBV muss insbesondere den KOBV-spezifischen Gegebenheiten genügen, die in dieser Form in den anderen deutschen Verbünden nicht anzutreffen sind. Im Jahre 2001 hat eine KOBV-Arbeitsgruppe Spezifikationen für eine Verbund-Fernleih-Software erarbeitet, in der die Besonderheiten des KOBV mit berücksichtigt sind. Beim Aufbau der automatisierten Fernleihe als einer regulären KOBV-Dienstleistung geht es nicht allein darum, einen schnellen, komfortablen Service für Nutzer einzurichten, sondern darüber hinaus um eine weitreichende Rationalisierung innerhalb der Bibliotheken. Das vorliegende Spezifikationspapier zielt auf beide Faktoren ab, indem es die Fernleihe als integrierten Dienst entwirft, der von der Bestellung bis zur Bereitstellung des Mediums in der gebenden Bibliothek automatisiert - ohne manuelles Eingreifen der Fernleihstelle - abläuft: die jetzige manuell durchgeführte Fernleihe wird durch die automatisierte Fernleihe abgelöst. T3 - ZIB-Report - 02-30 KW - Bibliotheksverbund KW - Fernleihe KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Software-Spezifikation KW - Verbund-Fernleihe KW - Verbund-Dien Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6970 ER - TY - GEN A1 - Horenko, Illia A1 - Weiser, Martin T1 - Adaptive Integration of Multidimensional Molecular Dynamics with Quantum Initial Conditions N2 - The paper presents a particle method framework for resolving molecular dynamics. Error estimators for both the temporal and spatial discretization are advocated and facilitate a fully adaptive propagation. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase-space packets are used as particles. Simplified variants are discussed shortly, which should prove to be easily implementable in common molecular dynamics codes. A concept is illustrated by numerical examples for one-dimensional dynamics in double well potential. T3 - ZIB-Report - 02-29 KW - particle methods KW - adaptivity KW - classical Liouville equation KW - molecular dynamics Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6967 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the Two-Class M/M/1 System under Preemptive Resume and Impatience of the Prioritized Customers N2 - The paper deals with the two-class priority M/M/1 system, where the prioritized class-1 customers are served under FCFS preemptive resume discipline and may become impatient during their waiting for service with generally distributed maximal waiting times but finite expectation. The class-2 customers have no impatience. The required mean service times may depend on the class of the customer. As the dynamics of class-1 customers are related to the well analyzed M/M/1+GI system, our aim is to derive characteristics for class-2 customers and for the whole system. The solution of the balance equations for the partial probability generating functions of the detailed system state process is given in terms of the weak solution of a family of boundary value problems for ordinary differential equations. By means of this solution formulae for the joint occupancy distribution and for the sojourn and waiting times of class-2 customers are derived generalizing results recently obtained by Choi et al. in case of deterministic maximal waiting times. For deterministic maximal waiting times partially new explicit formulae are given. T3 - ZIB-Report - 02-28 KW - two-class priority M/M/1 system KW - preemptive resume KW - impatient customers KW - occupancy distribution KW - waiting time KW - sojourn time Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6953 ER - TY - GEN A1 - Rusch, Beate T1 - Towards an Internet Based Information Portal for Berlin and Brandenburg N2 - The Cooperative Library Network Berlin-Brandenburg (KOBV) has set the development of a genuine library information portal for the two German Lander (federal states) Berlin and Brandenburg as its main task for the next years. This joined effort is driven by the vision of an user friendly Internet information portal which is accessible anytime, from anywhere in the world. The idea of a regional information portal can be understood as the logically consistent development of the basic ideas of the KOBV. Starting in 1997, the consortia has set the implementation of a virtual OPAC instead of a physical union catalogue as its goal. The result was the KOBV-Search Engine which already has some qualities of a portal itself. The paper begins with initial remarks about the German library world, which do form the background for the project and its initiator - the KOBV consortia. After this preliminary part, different types of portals are introduced. The basic features of the KOBV-Search Engine as one of the cornerstones of the future portal are discussed in the following. The information portal will be much richer in content and services for the end-user. Two aspects are focused on in more detail: the presentation of resources, which becomes a compelling requirement because of the broader range of content and the personalization of services, as one important feature to suit user's individual needs. T3 - ZIB-Report - 02-27 KW - Bibliotheksverbund KW - Digitale Bibliothek KW - KOBV KW - KOBV-Informationsportal KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Portal Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6949 ER - TY - GEN A1 - Grötschel, Martin T1 - P=NP? N2 - Hinter der für den Uneingeweihten etwas kryptischen Frage "P = NP?" verbirgt sich das derzeit wichtigste Problem der Komplexitätstheorie. Dieser Artikel erläutert einige Aspekte der Theorie und erklärt informell, was "P = NP?" bedeutet. Es geht nicht nur um komplizierte algorithmische Mathematik und Informatik, sondern um grundsätzliche Fragen unserer Lebensumwelt. Kann man vielleicht beweisen, dass es für viele Probleme unseres Alltags keine effizienten Lösungsmethoden gibt? T3 - ZIB-Report - 02-26 KW - computational complexity KW - P=NP Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6939 ER - TY - THES A1 - Krumke, Sven T1 - Online Optimization: Competitive Analysis and Beyond N2 - Traditional optimization techniques assume, in general, knowledge of all data of a problem instance. There are many cases in practice, however, where decisions have to be made before complete information about the data is available. In fact, it may be necessary to produce a part of the problem solution as soon as a new piece of information becomes known. This is called an \emph{online situation}, and an algorithm is termed \emph{online}, if it makes a decision (computes a partial solution) whenever a new piece of data requests an action. \emph{Competitive analysis} has become a standard yardstick to measure the quality of online algorithms. One compares the solution produced by an online algorithm to that of an optimal (clairvoyant) offline algorithm. An online algorithm is called $c$-competitive if on every input the solution it produces has cost'' at most $c$~times that of the optimal offline algorithm. This situation can be imagined as a game between an online player and a malicious adversary. Although competitive analysis is a worst-case analysis and henceforth pessimistic, it often allows important insights into the problem structure. One can obtain an idea about what kind of strategies are promising for real-world systems and why. On the other hand there are also cases where the offline adversary is simply too powerful and allows only trivial competitiveness results. This phenomenon is called hitting the triviality barrier''. We investigate several online problems by means of competitive analysis. We also introduce new concepts to overcome the weaknesses of the standard approach and to go beyond the triviality barrier. T3 - ZIB-Report - 02-25 KW - competitive analysis KW - online optimization KW - online algorithm KW - approximation algorithm Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6925 ER - TY - GEN T1 - Jahresbericht 2001 T3 - Jahresbericht - 2001 KW - Annual Report Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9764 SN - 0934-5892 ER - TY - GEN A1 - Krumke, Sven A1 - Poensgen, Diana T1 - Online Call Admission in Optical Networks with Larger Wavelength Demands N2 - In the problem of \emph{Online Call Admission in Optical Networks}, briefly called \textsc{oca}, we are given a graph $G=(V,E)$ together with a set of wavelengths~$W$ and a finite sequence $\sigma=r_1,r_2,\dots$ of calls which arrive in an online fashion. Each call~$r_j$ specifies a pair of nodes to be connected and an integral demand indicating the number of required lightpaths. A lightpath is a path in~$G$ together with a wavelength~$\lambda \in W$. Upon arrival of a call, an online algorithm must decide immediately and irrevocably whether to accept or to reject the call without any knowledge of calls which appear later in the sequence. If the call is accepted, the algorithm must provide the requested number of lightpaths to connect the specified nodes. The essential restriction is the wavelength conflict constraint: each wavelength is available only once per edge, which implies that two lightpaths sharing an edge must have different wavelengths. Each accepted call contributes a benefit equal to its demand to the overall profit. The objective in \textsc{oca} is to maximize the overall profit. Competitive algorithms for \textsc{oca} have been known for the special case where every call requests just a single lightpath. In this paper we present the first competitive online algorithms for the general case of larger demands. T3 - ZIB-Report - 02-22 KW - Call Admission KW - Routing and Wavelength Allocation KW - Optical Networks KW - Competitive Analysis KW - Colorability Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6890 ER - TY - GEN A1 - Krumke, Sven A1 - Lipmann, Maarten A1 - Paepe, Willem de A1 - Poensgen, Diana A1 - Rambau, Jörg A1 - Stougie, Leen A1 - Woeginger, Gerhard T1 - How to Cut a Cake Almost Fairly N2 - In the cake cutting problem, $n\ge2$ players want to cut a cake into $n$ pieces so that every player gets a ``fair'' share of the cake by his own measure. We describe a protocol with $n-1$~cuts in which each player can enforce to get a share of at least~$1/(2n-2)$. Moreover we show that no protocol with $n-1$~cuts can guarantee a better fraction. T3 - ZIB-Report - 02-23 KW - Fair division KW - cake cutting Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6905 ER - TY - GEN A1 - Krumke, Sven A1 - Marathe, Madhav A1 - Poensgen, Diana A1 - Ravi, Sekharipuram S. A1 - Wirth, Hans-Christoph T1 - Budgeted Maximal Graph Coverage N2 - An instance of the \emph{maximum coverage} problem is given by a set of weighted ground elements and a cost weighted family of subsets of the ground element set. The goal is to select a subfamily of total cost of at most that of a given budget maximizing the weight of the covered elements. We formulate the problem on graphs: In this situation the set of ground elements is specified by the nodes of a graph, while the family of covering sets is restricted to connected subgraphs. We show that on general graphs the problem is polynomial time solvable if restricted to sets of size at most~$2$, but becomes NP-hard if sets of size~$3$ are permitted. On trees, we prove polynomial time solvability if each node appears in a fixed number of sets. In contrast, if vertices are allowed to appear an unbounded number of times, the problem is NP-hard even on stars. We finally give polynomial time algorithms for special cases where the subgraphs form paths and the host graph is a line, a cycle or a star. T3 - ZIB-Report - 02-24 KW - budgeted maximum coverage KW - approximation algorithm KW - dynamic programming Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6918 ER - TY - GEN A1 - Litsche, Stefan A1 - Otto, Dagmar T1 - Evaluation ausgewählter Portalsysteme N2 - Die Bibliotheken des KOBV haben im Jahr 2001 die Entwicklung der KOBV-Suchmaschine zu einem gemeinsamen Informationsportal Berlin-Brandenburg und den Aufbau lokaler Bibliotheksportale als Hauptentwicklungsziele des KOBV definiert. Diese Informationsportale sollen mit Standardsoftware realisiert werden. Um die Auswahl eines Systems zu unterstützen, wurde in der Zentrale des KOBV ausgewählte Systeme untersucht. In der Arbeit werden zahlreiche Kriterien vorgestellt, auf Grund derer die betreffenden Systeme beurteilt werden. Die Kriterien umfassen sowohl Aspekte aus der Sicht der Benutzer als auch Kriterien aus der Sicht der Betreiber eines solchen Systems. Wesentliche Funktionen und die Realisierung von verschiedenen Merkmalen werden im Bericht ausführlich beschrieben. Daneben liefert eine Tabelle mit allen betrachteten Kriterien eine Übersicht über vorhandene Merkmale und der Art der Realisierung. T3 - ZIB-Report - 02-21 KW - Portale KW - Portalsysteme KW - KOBV KW - Informationsversorgung KW - Retrieval Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6882 ER - TY - GEN A1 - Deuflhard, Peter T1 - From Molecular Dynamics to Conformational Dynamics in Drug Design N2 - Computational drug design studies molecular recognition in the {\em virtual lab}. The arising Hamiltonian dynamics is known to be chaotic and ill-conditioned already after picoseconds, whereas times are $msec$ up to $min$. Classical molecular dynamics with long term trajectory computation gives, at best, information about time and statistical ensemble averages. The present paper surveys a recent new modeling approach called {\em conformational dynamics}, which is due to the author and Ch. Schütte. This approach achieves information about the dy time scales by telescoping a short term deterministic model with a statistical model. Examples of small biomolecules are included. T3 - ZIB-Report - 02-20 KW - molecular dynamics KW - conformational dynamics KW - drug design KW - Hamiltonian dynamics KW - almost invariant sets KW - transition operator KW - Markov chain KW - Perro Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6878 ER - TY - GEN A1 - Rambau, Jörg T1 - TOPCOM: Triangulations of Point Configurations and Oriented Matroids N2 - TOPCOM is a package for computing triangulations of point configurations and oriented matroids. For example, for a point configuration one can compute the chirotope, components of the flip graph of triangulations, enumerate all triangulations. The core algorithms implemented in TOPCOM are described, and implentation issues are discussed. T3 - ZIB-Report - 02-17 KW - triangulation KW - point configuration KW - oriented matroid KW - software KW - chirotope KW - circuit KW - cocircuit KW - symmetry KW - TOPCOM Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6849 ER - TY - GEN A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Torres, Luis Miguel T1 - Making the Yellow Angels Fly: Online Dispatching Of Service Vehicles in Real Time N2 - Combinatorial online optimization is an area with lots of applications and potential for significant progress, both in theory and practice. In this short note we sketch the ADACproblem, a typical large-scale online optimization problem, discuss some theoretical and pratical issues coming up, and explain, very briefly, how we approach this problem mathematically. Online problems are a battlefield of heuristics with many strong claims about their solution quality. We indicate that a stronger problem orientation and the use of a little more mathematics may yield. T3 - ZIB-Report - 02-18 KW - vehicle dispatching KW - soft time windows KW - real-time KW - column generation KW - pricing KW - branch and bound KW - real world data KW - ADAC Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6858 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Fügenschuh, Armin A1 - Koch, Thorsten A1 - Koster, Arie M.C.A. A1 - Martin, Alexander A1 - Pfender, Tobias A1 - Wegel, Oliver A1 - Wessäly, Roland T1 - Modelling Feasible Network Configurations for UMTS N2 - A model for the optimisation of the location and configuration of base stations in a UMTS network is described. The focus is primarily on modelling the configuration problem sufficiently accurate using mixed-integer variables and (essentially) linear constraints. These constraints reflect the limited downlink code capacity in each cell, the interference limitations for successful up- and downlink transmissions, the need for sufficiently strong (cell) pilot signals, and the potential gain for mobiles from being in soft(er) hand-over. It is also explained how to use the model as a basis for rating network configurations. T3 - ZIB-Report - 02-16 KW - UMTS KW - radio interface KW - network planning KW - configuration KW - perfect power control KW - mathematical model KW - mixed integer programming KW - MOMENTUM KW - IST-20 Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6837 ER - TY - GEN A1 - Grötschel, Martin A1 - Henk, Martin T1 - On the Representation of Polyhedra by Polynomial Inequalities N2 - A beautiful result of Bröcker and Scheiderer on the stability index of basic closed semi-algebraic sets implies, as a very special case, that every $d$-dimensional polyhedron admits a representation as the set of solutions of at most $d(d+1)/2$ polynomial inequalities. Even in this polyhedral case, however, no constructive proof is known, even if the quadratic upper bound is replaced by any bound depending only on the dimension. Here we give, for simple polytopes, an explicit construction of polynomials describing such a polytope. The number of used polynomials is exponential in the dimension, but in the 2- and 3-dimensional case we get the expected number $d(d+1)/2$. T3 - ZIB-Report - 02-15 KW - polyhedra and polytopes KW - semialgebraic sets KW - polyhedral combinatorics KW - polynomial inequalities Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6826 ER - TY - GEN A1 - Deuflhard, Peter T1 - Adaptive Pseudo-transient Continuation for Nonlinear Steady State Problems N2 - Pseudo--transient continuation methods are quite popular for the numerical solution of steady state problems, typically in PDEs. They are based on an embedding into a time dependent initial value problem. In the presence of dynamical invariants the Jacobian matrix of the nonlinear equation system is bound to be singular. The paper presents a convergence analysis which takes this property into account -- in contrast to known approaches. On the basis of the new analysis adaptive algorithms are suggested in detail. These include a variant with Jacobian approximations as well as inexact pseudo--transient continuation, both of which play an important role in discretized PDEs. Numerical experiments are left to future work. T3 - ZIB-Report - 02-14 KW - pseudo--transient continuation KW - linearly implicit KW - Euler discretization KW - stiff integration KW - contractivity of ordinary differential equations KW - lar Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6814 ER - TY - GEN A1 - Weber, Marcus A1 - Galliat, Tobias T1 - Characterization of Transition States in Conformational Dynamics using Fuzzy Sets N2 - Recently, a novel approach for the analysis of molecular dynamics on the basis of a transfer operator has been introduced. Therein conformations are considered to be disjoint metastable clusters within position space of a molecule. These clusters are defined by almost invariant characteristic functions that can be computed via {\em Perron Cluster} analysis. The present paper suggests to replace crisp clusters with {\em fuzzy} clusters, i.e. to replace characteristic functions with membership functions. This allows a more sufficient characterization of transiton states between different confor conformations and therefore leads to a better understanding of molecular dynamics. Fur thermore, an indicator for the uniqueness of metastable fuzzy clusters and a fast algorithm for the computation of these clusters are described. Numerical examples are included. T3 - ZIB-Report - 02-12 KW - biochemical conformations KW - conformational dynamics KW - molecular dynamics KW - cluster analysis KW - transition states KW - fuzzy sets Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6791 ER - TY - GEN A1 - Weiser, Martin T1 - Linear convergence of an interior point method for linear control constrained optimal control problems N2 - The paper provides a detailed analysis of a short step interior point algorithm applied to linear control constrained optimal control problems. Using an affine invariant local norm and an inexact Newton corrector, the well-known convergence results from finite dimensional linear programming can be extended to the infinite dimensional setting of optimal control. The present work complements a recent paper of Weiser and Deuflhard, where convergence rates have not been derived. The choice of free parameters, i.e. the corrector accuracy and the number of corrector steps, is discussed. T3 - ZIB-Report - 02-13 KW - linear optimal control KW - infinite dimensional KW - interior point methods KW - inexact Newton methods Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6809 ER - TY - GEN A1 - Hupfeld, Felix T1 - Hierarchical Structures in Attribute-based Namespaces and their Application to Browsing N2 - While attribute-value pairs are a popular method to name objects, information retrieval from those attribute-based namespaces is not an easy task. The user has to recall correct attribute names and values and master the syntax and semantics of query formulation. This paper describes hierarchical structures in attribute-based namespaces, shows how to extract them efficiently and evaluates the quality of these structures in an user experiment. It proposes an user interface for browsing attribute-named object sets which makes this task resemble todays file-system browsers and compares the usability of this interface to normal form-based methods in an user study. T3 - ZIB-Report - 03-06 Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7280 ER - TY - GEN A1 - Hougardy, Stefan A1 - Wagler, Annegret T1 - Perfectness is an Elusive Graph Property N2 - A graph property is called elusive (or evasive) if every algorithm for testing this property has to read in the worst case $n\choose 2$ entries of the adjacency matrix of the given graph. Several graph properties have been shown to be elusive, e.g. planarity (Best et al) or $k$-colorability (Bollobas). A famous conjecture of Karp says that every non-trivial monotone graph property is elusive. We prove that a non-monotone but hereditary graph property is elusive: perfectness. T3 - ZIB-Report - 02-11 KW - perfect graph KW - elusive graph property Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6787 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Weider, Steffen T1 - Integrierte Umlauf- und Dienstplanung im Öffentlichen Nahverkehr N2 - Wir beschreiben einen Ansatz zur integrierten Umlauf- und Dienstplanung im öffentlichen Nahverkehr. Der Ansatz zielt auf die Verbesserung des Gesamtwirkungsgrades dieser beiden Planungsschritte und auf die besondere Planungsproblematik im Regionalverkehr. Wir entwickeln dazu mathematische Optimierungstechniken für den Einsatz in den Planungssystemen MICROBUS II und DIVA. T3 - ZIB-Report - 02-10 KW - Integrierte Umlauf- und Dienstplanung KW - Umlaufplanung KW - Dienstplanung KW - Optimierung KW - Regionalverkehr Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6773 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequenzplanung im Mobilfunk N2 - Telekommunikation ist seit Jahren \glqq in\grqq. Zunächst gab es einen enormen Aufschwung; neue Technologien und Dienste haben eine überwältigende, nicht vorhersehbare Akzeptanz gefunden. Derzeit ist -- ausgelöst durch die UMTS-Lizenzversteigerungen, Rezessions- und Sättigungstendenzen -- eine Krise zu verzeichnen. Viele (auch wir) sind davon überzeugt, dass technischer Fortschritt und nützliche Dienste demnächst die Stimmung wieder ändern werden. Wenigen ist allerdings bewusst, welche Rolle Mathematik bei der Entwicklung und dem effizienten Einsatz vieler der neuen Kommunikationstechnologien spielt. In diesem Artikel soll kein Überblick über diesen umfangreichen Themenkreis gegeben werden. Wir zeigen lediglich an einem konkreten Beispiel aus dem Mobilfunk, der Frequenzplanung in GSM-Funknetzen, was man durch geeignete Modellierung der praktischen Fragestellung und den Einsatz problemadäquater Algorithmen erreichen kann. T3 - ZIB-Report - 02-09 KW - Telekommunikation KW - Frequenzplanung KW - Mobilfunk KW - GSM-Funknetze Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6762 ER - TY - GEN A1 - Wagler, Annegret T1 - Antiwebs are Rank-Perfect N2 - \We discuss a nested collection of three superclasses of perfect graphs: near-perfect, rank-perfect, and weakly rank-perfect graphs. For that, we start with the description of the stable set polytope for perfect graphs and allow stepwise more general facets for the stable set polytopes of the graphs in each superclass. Membership in those three classes indicates how far a graph is away from being perfect. We investigate for webs and antiwebs to which of the three classes they belong. We provide a complete description of the facets of the stable set polytope for antiwebs (with help of a result due to Shepherd on near-bipartite graphs). The main result is that antiwebs are rankperfect. T3 - ZIB-Report - 02-07 KW - relaxations of perfect graphs KW - antiwebs KW - stable set polytope Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6742 ER - TY - GEN A1 - Wolf, Thomas T1 - The integration of systems of linear PDEs using conservation laws of syzygies N2 - The purpose of the paper is to formulate and use syzygies for systems of linear PDEs. The computation of an equivalent of a GCD for linear partial differential operators will save us their factorization which is otherwise only possible algorithmically in special cases. After showing the computation with the new and the traditional method and comparing both in the next three sections, the algorithm is explained in general and an overview is given. T3 - ZIB-Report - 02-08 KW - PDE KW - syzygies KW - conservation laws Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6751 ER - TY - GEN A1 - Reinefeld, Alexander A1 - Stüben, Hinnerk A1 - Schintke, Florian A1 - Din, George T1 - GuiGen: A Toolset for Creating Customized Interfaces for Grid User Communities N2 - \textsf{\itshape{GuiGen}} is a comprehensive set of tools for creating customized graphical user interfaces (GUIs). It draws from the concept of computing portals, which are here seen as interfaces to application-specific computing services for user communities. While \textsf{\itshape{GuiGen}} was originally designed for the use in computational grids, it can be used in client/server environments as well. Compared to other GUI generators, \textsf{\itshape{GuiGen}} is more versatile and more portable. It can be employed in many different application domains and on different target platforms. With \textsf{\itshape{GuiGen}}, application experts (rather than computer scientists) are able to create their own individually tailored GUIs. T3 - ZIB-Report - 02-06 KW - Grid computing KW - customized user interfaces KW - grid user communities KW - web portals KW - XML Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6737 ER - TY - GEN A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Probieren geht über Studieren? Entscheidungshilfen für kombinatorische Online-Optimierungsprobleme in der innerbetrieblichen Logistik N2 - Die Automatisierung von innerbetrieblicher Logistik erfordert -- über die physikalische Steuerung von Geräten hinaus -- auch eine effiziente Organisation der Transporte: ein Aufgabenfeld der kombinatorischen Optimierung. Dieser Artikel illustriert anhand von konkreten Aufgabenstellungen die Online-Problematik (unvollständiges Wissen) sowie die Echtzeit-Problematik (beschränkte Rechenzeit), auf die man in der innerbetrieblichen Logistik trifft. Der Text gibt einen Überblick über allgemeine Konstruktionsprinzipien für Online-Algorithmen und Bewertungsmethoden, die bei der Entscheidung helfen, welche Algorithmen für eine vorliegende Problemstellung geeignet sind. T3 - ZIB-Report - 02-05 KW - Logistik KW - Hochregallagerbediengeräte KW - Kommissioniermobile KW - Aufzüge KW - Online-Optimierung KW - Echtzeit-Optimierung KW - Simulation KW - kompetitive Analyse Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6723 ER - TY - GEN A1 - Kuberek, Monika A1 - Lill, Monika A1 - Litsche, Stefan A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Otto, Dagmar A1 - Rusch, Beate T1 - Entwicklungsprojekt "KOBV-Informationsportal" : Teilprojekte der 1. Stufe N2 - Die KOBV-Suchmaschine hat seit ihrer Inbetriebnahme Ende 1999 entscheidend zur Verbesserung der Informationsinfrastruktur in Berlin und Brandenburg beigetragen. Auf der Basis der offenen Plattform KOBV-Suchmaschine wird die KOBV-Zentrale gemeinsam mit den Bibliotheken in den nächsten Jahren das Dienstleistungsangebot des KOBV und seiner Bibliotheken kontinuierlich erweitern. Dabei sollen die Prinzipien des KOBV - Offenheit, Heterogenität und Dezentralität auf technischer und organisatorischer Ebene - gewahrt bleiben. Die einzelnen KOBV-Bibliotheken werden sich mit ihren Angeboten in unterschiedlicher Weise im Web positionieren. Die Integration auf regionaler Ebene kann und soll die lokalen Angebote nicht künstlich vereinheitlichen. Das kooperative Portal, das in der Region aufgebaut wird, ist als System geplant, in dem zentrales Portal und lokale Portale nicht hierarchisch einander zugeordnet, sondern miteinander vernetzt sind. Das \glqq KOBV-Informationsportal \grqq soll in der KOBV-Zentrale im Rahmen eines wissenschaftlichen Projektes von Mitte 2001 bis Ende 2003 aufgebaut werden. Das vorliegende Papier gibt einen ersten allgemeinen Einblick, welche Funktionen das \glqq KOBV-Informationsporta \grqq umfassen soll und stellt die Teilprojekte der 1. Stufe vor. T3 - ZIB-Report - 01-41 KW - Bibliotheksverbund KW - Digitale Bibliothek KW - KOBV KW - KOBV-Informationsportal KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Portal Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6678 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank T1 - On the Numerical Solution of Nonlinear Schrödinger type equations in fiber optics N2 - The aim of this paper is to develop fast methods for the solution of nonlinear Schrödinger type equations in fiber optics. Using the method of lines we have to solve a stiff system of ordinary differential equations where the eigenvalues of the Jacobian are close to the imaginary axis. This is usually done by a Split Step method. Here we consider the extrapolation of Split Step methods with adaptive order and step size control. For more complicated nonlinearities, in particular stimulated Raman scattering, Split Step methods are less efficient since symmetry is either destroyed or requires much additional effort. In this case we use implicit Runge Kutta formulas of Gauß type. The key point for the efficient implementation of these methods is that the system of nonlinear algebraic equations can be solved without setting up the Jacobian. The proposed methods are compared to other methods, in particular exponential integrators, the method of Marcuse, and the method of Blow and Wood. T3 - ZIB-Report - 02-04 KW - nonlinear Schroedinger equation KW - split step methods KW - extrapolation KW - collocation methods Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6715 ER - TY - GEN A1 - Wagler, Annegret T1 - Relaxing Perfectness: Which Graphs are 'Almost' Perfect? N2 - For all perfect graphs, the stable set polytope STAB$(G)$ coincides with the fractional stable set polytope QSTAB$(G)$, whereas STAB$(G) \subset$ QSTAB$(G)$ holds iff $G$ is imperfect. Padberg asked in the early seventies for ``almost'' perfect graphs. He characterized those graphs for which the difference between STAB$(G)$ and QSTAB$(G)$ is smallest possible. We develop this idea further and define three polytopes between STAB$(G)$ and QSTAB$(G)$ by allowing certain sets of cutting planes only to cut off all the fractional vertices of QSTAB$(G)$. The difference between QSTAB$(G)$ and the largest of the three polytopes coinciding with STAB$(G)$ gives some information on the stage of imperfectness of the graph~$G$. We obtain a nested collection of three superclasses of perfect graphs and survey which graphs are known to belong to one of those three superclasses. This answers the question: which graphs are ``almost'' perfect? T3 - ZIB-Report - 02-03 KW - perfect graph KW - stable set polytope KW - relaxations Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6700 ER - TY - GEN A1 - Pfeifle, Julian A1 - Rambau, Jörg T1 - Computing Triangulations Using Oriented Matroids N2 - Oriented matroids are combinatorial structures that encode the combinatorics of point configurations. The set of all triangulations of a point configuration depends only on its oriented matroid. We survey the most important ingredients necessary to exploit oriented matroids as a data structure for computing all triangulations of a point configuration, and report on experience with an implementation of these concepts in the software package TOPCOM. Next, we briefly overview the construction and an application of the secondary polytope of a point configuration, and calculate some examples illustrating how our tools were integrated into the {\sc polymake} framework. T3 - ZIB-Report - 02-02 KW - triangulation KW - oriented matroid KW - software KW - chirotope KW - circuit KW - cocircuit KW - symmetry KW - regular KW - secondary polytope KW - hypergeometric function Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6692 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - A new method for the solution of scattering problems N2 - We present a new efficient algorithm for the solution of direct time-harmonic scattering problems based on the Laplace transform. This method does not rely on an explicit knowledge of a Green function or a series representation of the solution, and it can be used for the solution of problems with radially symmetric potentials and problems with waveguides. The starting point is an alternative characterization of outgoing waves called \emph{pole condition}, which is equivalent to Sommerfeld's radiation condition for problems with radially symmetric potentials. We obtain a new representation formula, which can be used for a numerical evaluation of the exterior field in a postprocessing step. Based on previous theoretical studies, we discuss the numerical realization of our algorithm and compare its performance to the PML method. T3 - ZIB-Report - 02-01 KW - transparent boundary conditions KW - inhomogeneous exterior domains KW - Laplace transform Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6683 ER - TY - THES A1 - Eisenblätter, Andreas T1 - Frequency Assignment in GSM Networks: Models, Heuristics, and Lower Bounds N2 - Mobile cellular communcication is a key technology in today's information age. Despite the continuing improvements in equipment design, interference is and will remain a limiting factor for the use of radio communication. This Ph. D. thesis investigates how to prevent interference to the largest possible extent when assigning the available frequencies to the base stations of a GSM cellular network. The topic is addressed from two directions: first, new algorithms are presented to compute "good" frequency assignments fast; second, a novel approach, based on semidef inite programming, is employed to provide lower bounds for the amount of unavoidable interference. The new methods proposed for automatic frequency planning are compared in terms of running times and effectiveness in computational experiments, where the planning instances are taken from practice. For most of the heuristics the running time behavior is adequate for inter active planning; at the same time, they provide reasonable assignments from a practical point of view (compared to the currently best known, but substantially slower planning methods). In fact, several of these methods are successfully applied by the German GSM network operator E-Plus. The currently best lower bounds on the amount of unavoidable (co-channel) interference are obtained from solving semidefinite programs These programs arise as nonpolyhedral relaxation of a minimum /c-parti tion problem on complete graphs. The success of this approach is made plausible by revealing structural relations between the feasible set of the semidefinite program and a polytope associated with an integer linear programming formulation of the minimum ^-partition problem. Comparable relations are not known to hold for any polynomial time solvable polyhedral relaxation of the minimum ^-partition problem. The appli cation described is one of the first of semidefinite programming for large industrial problems in combinatorial optimization. Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10132 ER - TY - GEN A1 - Aardal, Karen I. A1 - Hoesel, Stan P.M. van A1 - Koster, Arie M.C.A. A1 - Mannino, Carlo A1 - Sassano, Antonio T1 - Models and Solution Techniques for Frequency Assignment Problems N2 - {\begin{rawhtml} Revised Version unter http://dx.doi.org/10.1007/s10479-007-0178-0 \end{rawhtml}} Wireless communication is used in many different situations such as mobile telephony, radio and TV broadcasting, satellite communication, and military operations. In each of these situations a frequency assignment problem arises with application specific characteristics. Researchers have developed different modelling ideas for each of the features of the problem, such as the handling of interference among radio signals, the availability of frequencies, and the optimization criterion. This survey gives an overview of the models and methods that the literature provides on the topic. We present a broad description of the practical settings in which frequency assignment is applied. We also present a classification of the different models and formulations described in the literature, such that the common features of the models are emphasized. The solution methods are divided in two parts. Optimization and lower bounding techniques on the one hand, and heuristic search techniques on the other hand. The literature is classified according to the used methods. Again, we emphasize the common features, used in the different papers. The quality of the solution methods is compared, whenever possible, on publicly available benchmark instances. T3 - ZIB-Report - 01-40 KW - frequency assignment Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6667 ER - TY - GEN A1 - Bodlaender, Hans L. A1 - Koster, Arie M.C.A. A1 - Eijkhof, Frank van den A1 - Gaag, Linda C. van der T1 - Pre-processing for Triangulation of Probabilistic Networks N2 - The currently most efficient algorithm for inference with a probabilistic network builds upon a triangulation of a network's graph. In this paper, we show that pre-processing can help in finding good triangulations for probabilistic networks, that is, triangulations with a minimal maximum clique size. We provide a set of rules for stepwise reducing a graph, without losing optimality. This reduction allows us to solve the triangulation problem on a smaller graph. From the smaller graph's triangulation, a triangulation of the original graph is obtained by reversing the reduction steps. Our experimental results show that the graphs of some well-known real-life probabilistic networks can be triangulated optimally just by preprocessing; for other networks, huge reductions in their graph's size are obtained. T3 - ZIB-Report - 01-39 KW - triangulation KW - treewidth KW - probabilistic networks KW - pre-processing Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6655 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Bodlaender, Hans L. A1 - Hoesel, Stan P.M. van T1 - Treewidth: Computational Experiments N2 - Many {\cal NP}-hard graph problems can be solved in polynomial time for graphs with bounded treewidth. Equivalent results are known for pathwidth and branchwidth. In recent years, several studies have shown that this result is not only of theoretical interest but can successfully be applied to find (almost) optimal solutions or lower bounds for diverse optimization problems. To apply a tree decomposition approach, the treewidth of the graph has to be determined, independently of the application at hand. Although for fixed $k$, linear time algorithms exist to solve the decision problem ``treewidth $\leq k$'', their practical use is very limited. The computational tractability of treewidth has been rarely studied so far. In this paper, we compare four heuristics and two lower bounds for instances from applications such as the frequency assignment problem and the vertex coloring problem. Three of the heuristics are based on well-known algorithms to recognize triangulated graphs. The fourth heuristic recursively improves a tree decomposition by the computation of minimal separating vertex sets in subgraphs. Lower bounds can be computed from maximal cliques and the minimum degree of induced subgraphs. A computational analysis shows that the treewidth of several graphs can be identified by these methods. For other graphs, however, more sophisticated techniques are necessary. T3 - ZIB-Report - 01-38 KW - treewidth KW - heuristics KW - lower bounds KW - computations Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6644 ER - TY - GEN A1 - Helmberg, Christoph T1 - Numerical Evaluation of SBmethod N2 - We report numerical results for SBmethod --- a publically available implementation of the spectral bundle method --- applied to the 7$^{th}$ DIMACS challenge test sets that are semidefinite relaxations of combinatorial optimization problems. The performance of the code is heavily influenced by parameters that control bundle update and eigenvalue computation. Unfortunately, no mathematically sound guidelines for setting them are known. Based on our experience with SBmethod, we propose heuristics for dynamically updating the parameters as well as a heuristc for improving the starting point. These are now the default settings of SBmethod Version 1.1. We compare their performance on the DIMACS instances to our previous best choices for Version 1.0. SBmethod Version 1.1 is also part of the independent DIMACS benchmark by H.~Mittelmann. Based on these results we try to analyze strengths and weaknesses of our approach in comparison to other codes for large scale semidefinite programming. T3 - ZIB-Report - 01-37 KW - semidefinite programming KW - large scale methods KW - computational KW - semidefinite relaxations Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6637 ER - TY - GEN A1 - Kuberek, Monika T1 - Der KOBV - eine regionale Service-Einrichtung für Nutzer und Bibliothekare N2 - Dem vorliegenden Aufsatz liegt ein Vortrag zugrunde, den die Verfasserin auf der Ersten Gemeinsamen Fachtagung der DBV-Landesverbände Berlin und Brandenburg "Wir machen den Weg frei : Fusionen - Kooperationen in Berlin und Brandenburg" am 17. Oktober 2001 gehalten hat, in der Vortragsreihe "Möglichkeiten und Grenzen von Ausleih- und bibliographischen Verbünden - VÖB Berlin, VÖB Brandenburg, KOBV". Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) ist angetreten, um auf der Basis neuer Technologien zeitgemäße, nutzerorientierte Dienstleistungen für den Informationsbereich zu entwickeln und die Informationsinfrastruktur in der Region Berlin-Brandenburg neu zu organisieren. Dabei setzt der KOBV insbesondere auf das Internet. Die Verfasserin beschreibt die einzelnen Stufen, in denen die Dienste des KOBV aufgebaut wurden und kontinuierlich weiter ausgebaut werden. Dabei zeigt sie Vorteile auf, die Nutzern und Bibliotheken durch den Verbund entstehen, und lotet gleichzeitig die Grenzen aus, die dem Verbund gesetzt sind. T3 - ZIB-Report - 01-36 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Service-Einrichtung KW - Service-Einrichtung KOBV KW - Verbund-Dienstleistu Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6620 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Individual Overflow and Freed Carried Traffics for a Link with Trunk Reservation N2 - Two traffic streams $\Phi_1$, $\Phi_2$ are offered a link. The calls of $\Phi_i$ require exponential holding times with parameter $\mu$ and are accepted if less than $C_i$ trunks are occupied. Approximating the $\Phi_i$ by appropriate renewal processes meeting their first two moments, defined as the moments of the numbers of calls in virtual links of infinite capacity to which the traffic streams as freed traffics are virtually directed and where the calls get fresh exponential i.i.d.\ holding times with parameter $\mu$, stable recursive algorithms of complexity $O(\max(C_1,C_2))$ are derived for the first two defined as above moments of the individual overflow and freed carried traffics. The results offer a unified handling of both overflow and carried traffics in circuit switching networks with trunk reservation, providing a basis for new two-moment network dimensioning algorithms. T3 - ZIB-Report - 01-35 KW - trunk reservation KW - overflow traffic KW - freed carried traffic KW - factorial moments KW - peakedness KW - two-moment method KW - circuit switching network Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6615 ER - TY - GEN A1 - Sokolov, Vladimir V. A1 - Wolf, Thomas T1 - Classification of integrable polynomial vector evolution equations N2 - Several classes of systems of evolution equations with one or two vector unknowns are considered. We investigate also systems with one vector and one scalar unknown. For these classes all equations having the simplest higher symmetry are listed. T3 - ZIB-Report - 01-34 Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6601 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Stüben, Hinnerk T1 - Parallel tempering in full QCD with Wilson fermions N2 - We study the performance of QCD simulations with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering on $10^4$ and $12^4$ lattices. In order to compare tempered with standard simulations, covariance matrices between sub-ensembles have to be formulated and evaluated using the general properties of autocorrelations of the parallel tempering algorithm. We find that rendering the hopping parameter $\kappa$ dynamical does not lead to an essential improvement. We point out possible reasons for this observation and discuss more suitable ways of applying parallel tempering to QCD. T3 - ZIB-Report - 01-33 KW - QCD KW - parallel tempering KW - correlation analysis Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6593 ER - TY - GEN A1 - Zöckler, Malte A1 - Rein, Karlheinz A1 - Brandt, Robert A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Creating Virtual Insect Brains with Amira N2 - By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants. T3 - ZIB-Report - 01-32 KW - visualization KW - anatomical atlas Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6589 ER - TY - GEN A1 - Kober, Cornelia A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Prohaska, Steffen A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Anisotrope Materialmodellierung für den menschlichen Unterkiefer N2 - Im Rahmen der biomechanischen Simulation knöcherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungelöst. Computertomographische Datensätze liefern eine räumliche Verteilung der (Röntgen-)Dichte und ermöglichen damit eine gute Darstellung der individuellen Geometrie. Weiter können die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsabängige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz für eine anisotrope Materialbeschreibung vorgestellt, die es ermöglicht, den Einfluss der individuellen knöchernen Struktur auf das makroskopische Materialverhalten abzuschätzen. T3 - ZIB-Report - 01-31 KW - menschlicher Unterkiefer KW - Simulation mit der Methode der finiten Elemente KW - innerer Aufbau des Knochens KW - anisotrope Elastizität Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6574 ER - TY - GEN A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Interactive Volume Rendering of Adaptive Mesh Refinement Data N2 - Many phenomena in nature and engineering happen simultaneously on rather diverse spatial and temporal scales, i.e.\ exhibit a multi-scale character. Therefore various hierarchical data structures and numerical schemes have been devised to represent quantitatively such phenomena. A special numerical multilevel technique, associated with a particular hierarchical data structure, is so-called Adaptive Mesh Refinement (AMR). This scheme achieves locally very high spatial and temporal resolutions. Due to its popularity, many scientists are in need of interactive visualization tools for AMR data. In this article we present a 3D texture-based volume rendering algorithm for AMR data, that directly utilizes the hierarchical structure. Thereby interactive rendering even for large data sets is achieved. In particular the problems of interpolation artifacts, opacity corrections, and texture memory limitations are addressed. The algorithm's value in practice is demonstrated with simulation and image data. T3 - ZIB-Report - 01-30 KW - Scalar field visualization KW - multiresolution volume rendering KW - AMR hierarchies KW - 3D texture mapping Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6561 ER - TY - GEN A1 - Grötschel, Martin T1 - Telota - was soll das? N2 - Telota ist ein Kunstwort, das für alle Aktivitäten der Berlin-Brandenburgischen Akademie der Wissenschaften steht, die der Förderung von Forschung, Kommunikation und Präsentation durch elektronische Medien dienen. In diesem Artikel werden die Entstehung des Telota-Projektes geschildert und die Ziele diskutiert, die mit diesem Projekt erreicht werden sollen. Es geht darum, moderne Informationstechnik bewusst, geplant und nachhaltig für alle Belange der {\rm BBAW} einzusetzen. Informationstechnische Werkzeuge sollen für die wissenschaftliche Arbeit effizient genutzt werden; die Information nach innen und nach außen soll deutlich verbessert werden; eine bessere Kommunikationsinfrastuktur soll die Zusammenarbeit fördern. T3 - ZIB-Report - 01-27 KW - BBAW KW - Telota-Projekt KW - elektronische Publikation Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6538 ER - TY - GEN A1 - Grötschel, Martin T1 - Empfehlungen des Wissenschaftsrates zur digitalen Informationsversorgung durch Hochschulbibliotheken N2 - Der Wissenschaftsrat hat in seiner Juli-Sitzung 2001 \glqq Empfehlungen zur digitalen Informationsversorgung durch Hochschulbibliotheken \grqq verabschiedet. Einige der Vorschläge des Wissenschaftsrates können, falls sie von den angesprochenen Institutionen aufgenommen werden, zu einer nachhaltigen Veränderung der wissenschaftlichen Informationslandschaft führen. In meinem kurzen Kommentar zu diesem Papier möchte ich auf einige dieser Anregungen hinweisen. T3 - ZIB-Report - 01-28 KW - Wissenschaftsrat KW - digitale Informationsversorgung KW - Hochschulbibliotheken Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6546 ER - TY - GEN A1 - Grötschel, Martin T1 - Mein digitaler Traum N2 - Von welcher "Informationsumwelt" träumt jemand, der für seine wissenschaftliche (und sonstige) Arbeit digitale Informationstechnologie intensiv einsetzt? In diesem Artikel beschreibe ich meinen "digitalen Traum". Er ist ganz einfach zu formulieren:"Ich will alles und zwar sofort, jederzeit, "überall" und kostenlos zur Verfügung haben." Ich schildere, was davon heute schon (fast) realisiert ist und was noch fehlt. Ich skizziere einige zentrale Schwierigkeiten der vollständigen Realisierung und skizziere mögliche Lösungen. T3 - ZIB-Report - 01-29 KW - digitale Informationstechnologie KW - digitale Information KW - BBAW Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6558 ER - TY - GEN A1 - Helmberg, Christoph T1 - A Cutting Plane Algorithm for Large Scale Semidefinite Relaxations N2 - The recent spectral bundle method allows to compute, within reasonable time, approximate dual solutions of large scale semidefinite quadratic 0-1 programming relaxations. We show that it also generates a sequence of primal approximations that converge to a primal optimal solution. Separating with respect to these approximations gives rise to a cutting plane algorithm that converges to the optimal solution under reasonable assumptions on the separation oracle and the feasible set. We have implemented a practical variant of the cutting plane algorithm for improving semidefinite relaxations of constrained quadratic 0-1 programming problems by odd-cycle inequalities. We also consider separating odd-cycle inequalities with respect to a larger support than given by the cost matrix and present a heuristic for selecting this support. Our preliminary computational results for max-cut instances on toroidal grid graphs and balanced bisection instances indicate that warm start is highly efficient and that enlarging the support may sometimes improve the quality of relaxations considerably. T3 - ZIB-Report - 01-26 KW - bisection KW - equicut KW - max-cut KW - semidefinite programming KW - spectral bundle method KW - subgradient method KW - quadratic 0-1 programming Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6527 ER - TY - GEN A1 - Kähler, Ralf A1 - Simon, Mark A1 - Hege, Hans-Christian T1 - Fast Volume Rendering of Sparse High-Resolution Datasets Using Adaptive Mesh Refinement Hierarchies N2 - In this paper we present an algorithm that accelerates 3D texture-based volume rendering of large and sparse data sets. A hierarchical data structure (known as AMR tree) consisting of nested uniform grids is employed in order to efficiently encode regions of interest. The hierarchies resulting from this kind of space partitioning yield a good balance between the amount of volume to render and the number of texture bricks -- a prerequisite for fast rendering. Comparing our approach to an octree based algorithm we show that our algorithm increases rendering performance significantly for sparse data. A further advantage is that less parameter tuning is necessary. T3 - ZIB-Report - 01-25 KW - scalar field visualization KW - volume visualization KW - volume rendering KW - 3D texture mapping KW - hierarchical space partitioning KW - AMR tree KW - octree KW - spar Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6516 ER - TY - GEN A1 - Steinbach, Marc T1 - General Information Constraints in Stochastic Programs N2 - Scenario tree models of stochastic programs arise naturally under standard nonanticipativity assumptions. We demonstrate how tree-sparse programs cover the general case, with \emph{arbitrary} information constraints. Detailed examples and intuitive interpretations illuminate the basic thoughts behind the abstract but elementary construction. T3 - ZIB-Report - 01-24 KW - information constraints KW - general nonanticipativity KW - sigma-fields KW - filtrations KW - scenarios KW - stochastic programs KW - tree-sparse programs Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6502 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Solving time-harmonic scattering problems based on the pole condition: Convergence of the PML method N2 - In this paper we study the PML method for Helmholtz-type scattering problems with radially symmetric potential. The PML method consists in surrounding the computational domain by a \textbf{P}erfectly \textbf{M}atched sponge \textbf{L}ayer. We prove that the approximate solution obtained by the PML method converges exponentially fast to the true solution in the computational domain as the thickness of the sponge layer tends to infinity. This is a generalization of results by Lassas and Somersalo based on boundary integral eqaution techniques. Here we use techniques based on the pole condition instead. This makes it possible to treat problems without an explicitly known fundamental solution. T3 - ZIB-Report - 01-23 KW - transparent boundary conditions KW - PML KW - pole condition Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6494 ER - TY - GEN A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Torres, Luis Miguel T1 - Real-Time Dispatching of Guided and Unguided Automobile Service Units with Soft Time Windows N2 - Given a set of service requests (events), a set of guided servers (units), and a set of unguided service contractors (conts), the vehicle dispatching problem {\sl vdp} is the task to find an assignment of events to units and conts as well as tours for all units starting at their current positions and ending at their home positions (dispatch) such that the total cost of the dispatch is minimized. The cost of a dispatch is the sum of unit costs, cont costs, and event costs. Unit costs consist of driving costs, service costs and overtime costs; cont costs consist of a fixed cost per service; event costs consist of late costs linear in the late time, which occur whenever the service of the event starts later than its deadline. The program \textsf{ZIBDIP} based on dynamic column generation and set partitioning yields solutions on heavy-load real-world instances (215 events, 95 units) in less than a minute that are no worse than 1\% from optimum on state-of-the-art personal computers. T3 - ZIB-Report - 01-22 KW - vehicle dispatching KW - soft time windows KW - real-time KW - column generation KW - pricing KW - branch and bound KW - real world data KW - ADAC Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6484 ER - TY - GEN A1 - Otto, Dagmar T1 - Informationsportale und Digitale Bibliotheken N2 - Im ersten Teil des folgenden Aufsatzes werden allgemeine Überlegungen zur Entwicklung von Bibliotheken hin zu Informationsvermittlungsstellen für sowohl elektronische wie auch gedruckte Medien angestellt. Basierend auf den Ergebnissen der Evaluation digitaler Bibliotheken und Informationsportale in Deutschland wird ein erster Kriterienkatalog für ein Verbund-Informationsportal für den Kooperativen Bibliotheksverbund Berlin-Brandenburg entwickelt. Im Anhang befindet sich der Statusbericht über Informationsportale und digitale Bibliotheken in Deutschland. Dazu wurden sieben digitale Bibliotheken auf Verbundebene und 21 Bibliotheken nach Bundesländern evaluiert. T3 - ZIB-Report - 01-21 KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Bibliotheksverbund KW - Informationsportal KW - Portal KW - Digitale Bibliothek Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6479 ER - TY - GEN A1 - Koch, Thorsten T1 - ZIMPL User Guide N2 - {\sc Zimpl} is a little language to translate the mathematical model of a problem into a linear or (mixed-)integer mathematical program expressed in {\tt lp} or {\tt mps} file format which can be read by a LP or MIP solver. T3 - ZIB-Report - 01-20 KW - LP KW - IP KW - Modelling Language KW - Integer Programming Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6466 ER - TY - GEN A1 - Jeltsch, Rolf A1 - Strang, Gilbert A1 - Deuflhard, Peter T1 - First SIAM-EMS Conference "Applied Mathematics in our Changing World" Berlin 2001 - Collection of Abstracts N2 - Collection of abstracts of the first SIAM-EMS conference Applied Mathematics in our Changing World'' in Berlin, September 2-6, 2001. T3 - ZIB-Report - 01-19 KW - Abstracts Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6452 ER - TY - GEN A1 - Wagler, Annegret T1 - Rank-Perfect and Weakly Rank-Perfect Graphs N2 - An edge of a perfect graph $G$ is critical if $G-e$ is imperfect. We would like to decide whether $G - e$ is still {\sl almost perfect} or already {\sl very imperfect}. Via relaxations of the stable set polytope of a graph, we define two superclasses of perfect graphs: rank-perfect and weakly rank-perfect graphs. Membership in those two classes indicates how far an imperfect graph is away from being perfect. We study the cases, when a critical edge is removed from the line graph of a bipartite graph or from the complement of such a graph. T3 - ZIB-Report - 01-18 KW - perfect graphs KW - rank-perfect graphs KW - weakly rank-perfect graphs KW - stable set polytope KW - critical edges Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6448 ER - TY - GEN A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Winter, Thomas A1 - Zimmermann, Uwe T1 - Combinatorial Online Optimization in Real Time N2 - Optimization is the task of finding an optimum solution to a given problem. When the decision variables are discrete we speak of a combinatorial optimization problem. Such a problem is online when decisions have to be made before all data of the problem are known. And we speak of a real-time online problem when online decisions have to be computed within very tight time bounds. This paper surveys the are of combinatorial online and real-time optimization, it discusses, in particular, the concepts with which online and real-time algorithms can be analyzed. T3 - ZIB-Report - 01-16 KW - Online Optimization KW - Realtime Optimization KW - Competitive Analysis KW - Heuristics KW - Survey Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6424 ER - TY - GEN A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Online Optimization of Complex Transportation Systems N2 - This paper discusses online optimization of real-world transportation systems. We concentrate on transportation problems arising in production and manufacturing processes, in particular in company internal logistics. We describe basic techniques to design online optimization algorithms for such systems, but our main focus is decision support for the planner: which online algorithm is the most appropriate one in a particular setting? We show by means of several examples that traditional methods for the evaluation of online algorithms often do not suffice to judge the strengths and weaknesses of online algorithms. We present modifications of well-known evaluation techniques and some new methods, and we argue that the selection of an online algorithm to be employed in practice should be based on a sound combination of several theoretical and practical evaluation criteria, including simulation. T3 - ZIB-Report - 01-17 Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6438 ER - TY - GEN A1 - Ehrig, Rainald A1 - Ofenloch, Oliver A1 - Schaber, Karlheinz A1 - Deuflhard, Peter T1 - Modelling and Simulation of Aerosol Formation by Heterogeneous Nucleation in Gas-Liquid Contact Devices N2 - This paper describes a new simulation tool for the prediction of aerosol formation and behavior in gas--liquid contact devices such as absorbers, scrubbers, quench coolers, and condensers as well as multistage gas cleaning processes, respectively. Aerosol formation can impact severely the separation efficiency of gas cleaning processes. Aerosol or fog formation can arise by spontaneous condensation or desublimation in supersaturated gas phases. The rigorous description of the mass and energy transfer between the gas phase, the liquid phase, and the growing aerosol droplets leads to a system of partial differential and algebraic equations. For the solution of these systems we have developed the plant simulation tool AerCoDe. This program bases upon the linearly--implicit Euler discretisation, which in combination with extrapolation permits an adaptive step size and order control. Typical simulation results of a multistage industrial flue gas scrubbing process are presented. It is shown, that experimental data can be confirmed if the number concentration of condensation nuclei as an input parameter is roughly known. T3 - ZIB-Report - 01-15 KW - aerosols KW - heterogeneous nucleation KW - two-phase flow KW - balance equations KW - extrapolation methods Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6416 ER - TY - GEN A1 - Grötschel, Martin T1 - Copyright und elektronisches Publizieren: Auf dem Weg zu vernünftigen Regelungen? N2 - Das \emph{Committee on Electronic Information and Communication} (CEIC) der \emph{International Mathematical Union} (IMU) hat die Aufgabe, sich über die langfristige Informationsversorgung in der Mathematik Gedanken zu machen und Lösungsvorschläge hierfür zu erarbeiten. Das Kernthema ist natürlich "`Elektronisches Publizieren"'. Dazu gehören auch Copyright-Regelungen. % Sie sind -- % neben einer Andeutung der weiteren CEIC-Pläne -- der Fokus dieses % kurzen Artikels. Er schließt mit einem von der IMU verabschiedeten % Aufruf zu vernünftigem Verhalten bei Copyright-Vereinbarungen. Eine % nachhaltige Befolgung dieses Aufrufs -- verbunden mit weiteren % Aktivitäten -- könnte die (derzeit kaum noch bezahlbare und % dadurch gefährdete) Literaturversorgung nachhaltig zum Positiven % verändern. Mit diesem Artikel beginnt eine kleine Serie von Aufsätzen, in denen ich (in meiner Funktion als eines von elf CEIC-Mitgliedern) die Empfehlungen des CEIC erläutern werde. % Das heutige Thema sind die % CEIC-Vorschläge zum Copyright T3 - ZIB-Report - 01-13 KW - Copyright KW - elektronisches Publizieren KW - IMU KW - CEIC Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6395 ER - TY - GEN A1 - Erdmann, Bodo A1 - Kober, Cornelia A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Deuflhard, Peter T1 - Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible N2 - By computed tomography data (CT), the individual geometry of the mandible is quite well reproduced, also the separation between cortical and trabecular bone. Using anatomical knowledge about the architecture and the functional potential of the masticatory muscles, realistic situations were approximated. The solution of the underlying partial differential equations describing linear elastic material behaviour is provided by an adaptive finite element method. Estimations of the discretization error, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. T3 - ZIB-Report - 01-14 KW - mandible KW - sensitivity analysis KW - finite element method KW - adaptive grid refinement Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6403 ER - TY - GEN A1 - Weiser, Martin A1 - Deuflhard, Peter T1 - The Central Path towards the Numerical Solution of Optimal Control Problems N2 - A new approach to the numerical solution of optimal control problems including control and state constraints is presented. Like hybrid methods, the approach aims at combining the advantages of direct and indirect methods. Unlike hybrid methods, however, our method is directly based on interior-point concepts in function space --- realized via an adaptive multilevel scheme applied to the complementarity formulation and numerical continuation along the central path. Existence of the central path and its continuation towards the solution point is analyzed in some theoretical detail. An adaptive stepsize control with respect to the duality gap parameter is worked out in the framework of affine invariant inexact Newton methods. Finally, the performance of a first version of our new type of algorithm is documented by the successful treatment of the well-known intricate windshear problem. T3 - ZIB-Report - 01-12 KW - optimal control KW - interior point methods KW - affine invariance Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6380 ER - TY - GEN A1 - Reinefeld, Alexander A1 - Lindenstruth, Volker T1 - How to Build a High-Performance Compute Cluster for the Grid N2 - The success of large-scale multi-national projects like the forthcoming analysis of the LHC particle collision data at CERN relies to a great extent on the ability to efficiently utilize computing a management software (Datagrid, Globus, etc.), while the effective integration of computing nodes has been largely neglected up to now. This is the focus of our work. We present a framework for a high-performance cluster that can be used as a reliable computing node in the Grid. We outline the cluster architecture, the management of distributed data and the seamless intergration of the cluster into the Grid environment. T3 - ZIB-Report - 01-11 KW - cluster architecture KW - resource management KW - Grid computing Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6374 ER - TY - GEN A1 - Kuberek, Monika T1 - KOBV: institutionalisiert N2 - Der Aufsatz ist die ausgearbeitete Fassung eines Vortrages, gehalten am 05.04.2001 auf dem 91. Deutschen Bibliothekartag in Bielefeld. Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) ist im Rahmen eines wissenschaftlichen Projektes in den Jahren 1997 bis 2000 am Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) aufgebaut worden. Nachdem das Projekt erfolgreich abgeschlossen ist, wird der KOBV 2001 institutionalisiert. In dem Vortrag hat die Verfasserin einen Überblick über das bisher Erreichte, den derzeitigen Stand und die Perspektiven des neuen Verbundes gegeben. Der KOBV stellt eine neue Art von Bibliotheksverbund dar. Sein technisches Konzept und sein organisatorischer Aufbau basieren auf der {\sl Internetphilosophie}. Den informationstechnischen Kern bildet eine Suchmaschine, die die heterogenen lokalen Bibliothekssysteme miteinander verbindet. Die KOBV-Organisation ist dezentral. Sie wird getragen von der Kooperation der Bibliotheken in Berlin und Brandenburg. Eine kleine Verbundzentrale koordiniert dieses Geflecht vernetzter lokaler Einheiten, vertritt den KOBV nach außen und arbeitet - in Form von Projekten - an seiner Weiterentwicklung. Der Entwicklungsaspekt und die Nutzerorientierung sind zwei wesentliche Komponenten in der Verbundarbeit. Berlin und Brandenburg haben auf engem Raum zahlreiche Bibliotheken mit großen, reichhaltigen Medienbeständen. Mittel- bis langfristig sollen Bibliotheken aller Sparten und Größen in den KOBV integriert werden, seien es wissenschaftliche Universalbibliotheken, universitäre Bibliothekssysteme, Spezialbibliotheken, Behörden- und Parlamentsbibliotheken oder öffentliche Bibliotheken. Auch regionale Bibliotheksverbünde können als Subverbünde am KOBV teilnehmen. Mit der KOBV-Suchmaschine ist eine offene Plattform geschaffen worden, auf der weitere Entwicklungen aufsetzen können. Der Aufbau einer virtuellen Regionalbibliothek mit Bestell- und Lieferkomponenten ist eines der Ziele. Darüber hinaus ist es die Vision, in der Region ein virtuelles {\sl Wissensportal} aufzubauen, das dem Nutzer unter einer Adresse den umfassenden Zugang und die umfassende Bereitstellung von Informationen aller Art bietet. T3 - ZIB-Report - 01-10 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6360 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the Moments of the Overflow and Freed Carried Traffic for the GI/M/C/0 System N2 - In circuit switching networks call streams are characterized by their mean and peakedness (two-moment method). The $GI/M/C/0$ system is used to model a single link, where the $GI$-stream is determined by fitting moments appropriately. For the moments of the overflow traffic of a $GI/M/C/0$ system there are efficient numerical algorithms available. However, for the moments of the freed carried traffic, defined as the moments of a virtual link of infinite capacity to which the process of calls accepted by the link (carried arrival process) is virtually directed and where the virtual calls get fresh exponential i.i.d.\ holding times, only complex numerical algorithms are available. This is the reason why the concept of the freed carried traffic is not used rigorously. The main result of this paper is an efficient algorithm for computing the moments of the freed carried traffic, in particular an explicit formula for its peakedness. This result offers a unified handling of both overflow and carried traffics in networks. Furthermore, some refined characteristics for the overflow and freed carried streams are derived. T3 - ZIB-Report - 01-09 KW - GI/M/C/0 system KW - overflow traffic KW - freed carried traffic KW - carried arrival process KW - factorial moments KW - peakedness KW - two-moment method KW - difference Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6355 ER - TY - GEN T1 - Jahresbericht 2000 T3 - Jahresbericht - 2000 KW - Annual Report Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9751 SN - 0934-5892 ER - TY - GEN A1 - Steinbach, Marc T1 - Tree-Sparse Convex Programs N2 - Dynamic stochastic programs are prototypical for optimization problems with an inherent tree structure inducing characteristic sparsity patterns in the KKT systems of interior methods. We propose an integrated modeling and solution approach for such tree-sparse programs. Three closely related natural formulations are theoretically analyzed from a control-theoretic viewpoint and compared to each other. Associated KKT solution algorithms with linear complexity are developed and comparisons to other interior approaches and related problem formulations are discussed. T3 - ZIB-Report - 01-08 KW - Convex program KW - tree KW - discrete-time optimal control multistage stochastic program KW - recursive factorization KW - local projection Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6340 ER - TY - GEN A1 - Krumke, Sven A1 - Paepe, Willem de A1 - Rambau, Jörg A1 - Stougie, Leen T1 - Online Bin-Coloring N2 - We introduce a new problem that was motivated by a (more complicated) problem arising in a robotized assembly enviroment. The bin coloring problem is to pack unit size colored items into bins, such that the maximum number of different colors per bin is minimized. Each bin has size~$B\in\mathbb{N}$. The packing process is subject to the constraint that at any moment in time at most $q\in\mathbb{N}$ bins may be partially filled. Moreover, bins may only be closed if they are filled completely. An online algorithm must pack each item must be packed without knowledge of any future items. We investigate the existence of competitive online algorithms for the online uniform binpacking problem. We show upper bounds for the bin coloring problem. We prove an upper bound of $3q$ - 1 and a lower bound of $2q$ for the competitive ratio of a natural greedy-type algorithm, and show that surprisingly a trivial algorithm which uses only one open bin has a strictly better competitive ratio of $2q$ - 1. Morever, we show that any deterministic algorithm has a competitive ratio $\Omega (q)$ and that randomization does not improve this lower bound even when the adversary is oblivious. T3 - ZIB-Report - 01-07 KW - Online Optimization KW - randomized algorithms KW - lower bounds KW - competitive analysis Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6338 ER - TY - GEN A1 - Byun, Chul-Young T1 - Lower Bounds for Large-Scale Set Partitioning Problems N2 - In this work we concentrate on developing methods which determine good lower bounds for set partitioning problems (SPP) in an appropriate amount of time. We found out that it makes sense to use the Lagrangian relaxation method for this task. The Lagrangian relaxed problem of SPP has a simple structure, which leads to algorithms and heuristics, whose total complexity per iteration depends linearly on the number of non-zeros of the problem matrix of SPP. In contrast, other methods like simplex methods or interior point methods have a complexity of higher order. Because the problem matrices of our tested instances are sparse, the linear dependence becomes an advantage for the algorithms and heuristics mentioned above. As a reference for the state-of-the-art we have applied the dual simplex method and the barrier function method, implemented in CPLEX. The methods, which we have developed and compared with those of CPLEX, are SBM, CAM, CCBM, and CBM. SBM is a subgradient bundle method derived from the basic subgradient method, which is a global convergent method for determining the maximum of concave functions. CAM is a coordinate ascent method, where the convex coordinate bundle method CCBM and the coordinate bundle method CBM are derivatives from CAM. We observed that the basic subgradient and the coordinate ascent method are improved if bundling techniques can be used. But the motivation for bundling differs for both approaches. In the former case bundling helps to approximate a minimum norm subgradient, which provides a steepest ascent direction, in order to speed up the performance. In the latter case bundling enables proceeding along directions, which are not restricted on the coordinate directions. By this the performance is accelerated. Among all used techniques stabilization is worth mentioning. Stabilization improves the performance especially at the beginning by avoiding too big steps during the proceeding. This leads to a more stabilized progression. Stabilization was successfully applied to SBM, CAM, CCBM, and CBM. As an overall result we conclude the following: \begin{enumerate} \item CPLEX computes the optimal objective values, whereas SBM and CBM has on average a gap of under $1.5\%$. \item In comparison to CPLEX baropt, SBM, CAM, and CBM the algorithm CCBM has a slow convergence because of the convex combination of ascent coordinate directions. An alternative is to relax the convex combination to a simple sum of the corresponding directions. This idea is realized in CBM. \item If we focus on the running time rather than on optimality then CBM is on average the fastest algorithm. \end{enumerate} Note that methods like SBM or CBM are applied on static SPP instances in order to determine a good lower bound. For solving SPP we need dynamical methods. Due to the complex topic of dynamical methods we will not discuss them, but a certain technique is worth mentioning. It is called column generation. We have indicated that this technique needs good Lagrangian multipliers of the corresponding SPP instances in order to generate further columns (in our case duties), which are added to the current SPP instance. Those multipliers are by-products of methods like our six considered methods. Due to the large number of such generation steps the running time depends on the computation time of these methods. Therefore, CBM fits more to this technique than CPLEX baropt or SBM. To sum it up it can be said that applications such as a duty scheduling can be described as set partitioning problems, whose lower bound can be solved by simplex, interior points, subgradient, or coordinate ascent methods. It turns out that the interior points method CPLEX baropt and the heuristic CBM have good performances. Furthermore, good Lagrangian multipliers, which are by-products of these methods, can be used by techniques like column generation. For this particular technique it also turns out that among our tested algorithms CBM is the most efficient one. In general we can state that real-world applications, which have to solve a large number of Lagrangian relaxed SPP instances can improve their performance by using CBM. T3 - ZIB-Report - 01-06 KW - Set Partitioning KW - Lagrangean Relaxation KW - Dual Ascent Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6321 ER - TY - GEN A1 - Garrido, Izaskun A1 - Steinbach, Marc T1 - A Multistage Stochastic Programming Approach in Real-Time Process Control N2 - Standard model predictive control for real-time operation of industrial production processes may be inefficient in the presence of substantial uncertainties. To avoid overly conservative disturbance corrections while ensuring safe operation, random influences should be taken into account explicitly. We propose a multistage stochastic programming approach within the model predictive control framework and apply it to a distillation process with a feed tank buffering external sources. A preliminary comparison to a probabilistic constraints approach is given and first computational results for the distillation process are presented. T3 - ZIB-Report - 01-05 KW - Process Control KW - Real-Time Optimization KW - Multistage Stochastic Programming Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6317 ER - TY - GEN A1 - Henrion, Rene A1 - Li, Pu A1 - Möller, Andris A1 - Steinbach, Marc A1 - Wendt, Moritz A1 - Wozny, Günter T1 - Stochastic Optimization for Operating Chemical Processes Under Uncertainty N2 - Mathematical optimization techniques are on their way to becoming a standard tool in chemical process engineering. While such approaches are usually based on deterministic models, uncertainties such as external disturbances play a significant role in many real-life applications. The present article gives an introduction to practical issues of process operation and to basic mathematical concepts required for the explicit treatment of uncertainties by stochastic optimization. T3 - ZIB-Report - 01-04 KW - Uncertainty KW - Chemical Processes KW - Multistage Stochastic Programs KW - Probabilistic Constraints Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6304 ER - TY - GEN A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations N2 - Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. UCMC aims at avoiding the typical metastable or trapping behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. Therefore, the state space of the chain has to be hierarchically decomposed into its metastable conformations. This is done by means of combining the technique of conformation analysis as recently introduced by the authors, and appropriate annealing strategies. We present a detailed examination of the uncoupling-coupling procedure which uncovers its theoretical background, and illustrates the hierarchical algorithmic approach. Furthermore, application of the UCMC algorithm to the $n$-pentane molecule allows us to discuss the effect of its crucial steps in a typical molecular scenario. T3 - ZIB-Report - 01-03 KW - almost invariant sets KW - bridge sampling KW - metastability KW - hierarchical annealing KW - hybrid Monte Carlo KW - $n$-pentane molecule KW - ratio of normalizing co Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6296 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Duty Scheduling in Public Transit N2 - This article is about \emph{adaptive column generation techniques} for the solution of duty scheduling problems in public transit. The current optimization status is exploited in an adaptive approach to guide the subroutines for duty generation, LP resolution, and schedule construction toward relevant parts of a large problem. Computational results for three European scenarios are reported. T3 - ZIB-Report - 01-02 KW - Duty Scheduling KW - Constraint Shortest Paths Problem KW - Column Generation Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6286 ER - TY - GEN A1 - Grötschel, Martin A1 - Fonseca, Irene A1 - Davis, Mark T1 - Round Table: The Impact of Mathematical Research on Industry and Vice Versa N2 - This paper is a summary of the Round Table: ``The Impact of Mathematical Research on Industry and Vice Versa'' held at 3ecm in Barcelona on July 11, 2000. The round table started with contributions of the three panelists. Irene Fonseca, the panel chair, opened the discussion by stating six questions addressing the main issues of the round table topic. She presented the panel's answers to these questions, drawing on many examples from her own academic experience. In the following additional presentations, the other two panel members added further points of view based on their personal involvement with industry. The round table ended with a lively discussion with members from the audience. This written summary of the oral presentations follows the structure of the round table indicated above. T3 - ZIB-Report - 00-57 KW - industrial mathematics KW - applications in industry Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6259 ER - TY - GEN A1 - Grötschel, Martin T1 - Frequency Assignment in Mobile Phone Systems N2 - Wireless communication networks employ radio frequencies to establish communication links. The available radio spectrum is very limited. To meet today's radio communication demand, this resource has to be administered and reused carefully in order to control mutual interference. The reuse can be organized via separation in space, time, or frequency, for example. The problem, therefore, arises to distribute frequencies to links in a ``reasonable manner''. This is the basic form of the frequency assignment problem. What ``reasonable'' means, how to quantify this measure of quality, which technical side constraints to consider cannot be answered in general. The exact specification of this task and its mathematical model depend heavily on the particular application considered. In this paper we discuss this issue with respect to the GSM standard for mobile communication. T3 - ZIB-Report - 00-58 KW - frequency assignment KW - telecommunication KW - mobile phone KW - integer programming KW - coloring Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6265 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Solving time-harmonic scattering problems based on the condition: Theory N2 - The pole condition is a general concept for the theoretical analysis and the numerical solution of a variety of wave propagation problems. It says that the Laplace transform of the physical solution in radial direction has no poles in the lower complex half-plane. In the present paper we show that for the Helmholtz equation with a radially symmetric potential the pole condition is equivalent to Sommerfeld's radiation condition. Moreover, a new representation formula based on the pole condition is derived and used to prove existence, uniqueness and asymptotic properties of solutions. This lays the foundations of a promising new algorithm to solve time-harmonic scattering problems numerically and provides a new approach for analyzing existing algorithms such as the Perfectly Matched Layer (PML) method and the Bayliss-Gunzburger-Turkel (BGT) algorithm. T3 - ZIB-Report - 01-01 KW - transparent boundary conditions KW - Laplace transform KW - Sommerfeld radiation condition Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6279 ER - TY - THES A1 - Wagler, Annegret T1 - Critical Edges in Perfect Graphs Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10220 ER - TY - THES A1 - Stolle, Hermann T1 - Mathematische Modellierung und Lösung von Optimierungsproblemen bei der Planung von Telefonnetzen Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:83-opus-1419 ER - TY - THES A1 - Wessäly, Roland T1 - Dimensioning Survivable Capacitated Networks N2 - In der vorliegenden Dissertation untersuchen wir die Optimierung von ausfallsicheren Telekommunikationsnetzwerken. Wir präsentieren unterschiedliche gemischt-ganzzahlige Modelle für die diskrete Kapazitätsttruktu,, sowie für die Sicherung des Netzes gegen den Ausfall einzelner Komponenten. Die Modelle wurden in einer Kooperation mit der E-Plus Mobilfunk GmbH verwendet. Die theoretischen Resultate wurden in Algorithmen umgesetzt und in das von uns entiickllte Netzwerksoptimierungswerkzeug Discnet (Dimensioning Survivable Capaiitated NETworks) integriert, welches seit mehreren Jahren in der Planung bei E-Plus eingesetzt wird. Wir betrachten das Transportnetzllanungsproblem eines Telekommunikationsanbieters. Dieses Problem setzt auf logischen Kommunikattonsanforerrungen zwischen den Standorten (Knoten) des zu planenden Netzes und potentiell inslallirrbaren Verbindungen (Kanten) zwischen derselben Knotenmenge auf. Ein Kapazitätsmodell stellt die Information bereit, welche Kapazitäten auf den potentiellen Kanten verfügbar sind. Wir betrachten zwei Modelle. Entweder ist eine explizite Liste der verfügbaren Kapazittten gegeben oder eine Menge von sogenannten Basiskapazitäten, die auf jeder Kante indiviuelll kombiniert werden können. Die Basiskapazitäten müßen paarweise ganzzahlige Vielfache voneinander sein. Man beachte, daß diese Eigenschaft von den internationalen Standards PDH und SDH erfüllt wiid. Ein Ausfallsicherheitsmodell stellt die Information bereit, wie das zu planende Netz gegen den Ausfall einzelner Netzkomponenten geschützt werden soll. Wir betrachten sinnvolle Kombinationen der Modelle Diversification, Reservation und Path Restoration. Das erste Modell garantiert Ausfallsicherheit durch kommunikationsbedarfsabhängige Beschränkung des Prozentsatzes, der durch einzelne Netzkomponenten geroutet werden darf. Bei den beiden anderen Modelle können Kommunikationsbedarfe bei Ausfall einer Netzkomponente auf unterschiedliche Weise neu geroutet werden. Ziel der Planung ist eine ktstenminimlle Kapatitätsentscheidung, die eine Routenllanung aller Kommunikationsbedarfe gemäß den Ausfallsicherheitsanforderungen ermöglicht. Wir entwickeln ein Schnittebenenverfahren zur Lösung der betrachteten Optimiergngsrrobleme. Zu diesem Zweck untersuchen wir Polyeder, die mit den verschiedenen Problemen assoziiert sind. Wir präsentieren neue Klassen von Ungleichungen, entwickeln Separationsalgorithmen und Heuristiken. Mit dem Schnittebenenverfahren werden untere und obere Schranken für den Wert von Oitimallösungen berechnet, und daher ist es möglich, Qualitätsgarantien für die berechneten Löungen anzugeben. Parallel zur Beschreibung der implementierten Algorithmen präsentieren wir umfangreiche Tests mit praktisch relevanten Daten, die zu Problemen mit mehr als 2 Billionen Variablen führen. KW - Ausfallsichere Telekommunikationsnetzwerke KW - Schnittebenenverfahren Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10158 ER - TY - THES A1 - Schintke, Florian T1 - Ermittlung von Programmlaufzeiten anhand von Speicherzugriffen, Microbenchmarks und Simulation von Speicherhierarchien N2 - Kostenmodelle dienen der Ermittlung von Programmlaufzeiten, zum Vergleich der Effizienz von Algorithmen und zur Analyse des Verhaltens von Speicherhierarchien. Ein neuartiges Kostenmodell ist das Latency-of-Data-Access (LDA) Modell, das mehrere hierarchische Speicherebenen mit unterschiedlichen Latenzzeiten berücksichtigt. In dieser Diplomarbeit wird ein Simulator für Speicherhierarchien präsentiert, der die Berechnung von Programmausführungszeiten nach dem LDA-Modell erlaubt. Mit Hilfe des Simulators wird die These geprüft, daß mit diesem Modell die Ausführungszeit eines Programms adäquat abgeschätzt werden kann. Mit dem Simulator ist es erstmals praktikabel möglich, Programmausführungszeiten nach dem LDA-Modell zu bestimmen. Der Simulator kann für Systeme mit unterschiedlichen Speicherarchitekturen konfiguriert werden und unterstützt Mehrprozessorsysteme mit gemeinsamem Speicher (SMP-Systeme) mit verschiedenen Kohärenzprotokollen. Der Simulator kann mit den Ergebnissen von Microbenchmarks konfiguriert werden, die die Architekturparameter einer Speicherhierarchie messen. Die Ergebnisse bestätigen die These nicht nur für Einzelprozessorsysteme, sondern auch für SMP-Systeme, wo gleichzeitig interagierende Prozessoren gegenseitig ihre Zugriffsse-quenz auf Zwischenspeicher beeinflussen. Zusätzlich wurde eine neue Einsatzmöglichkeit des LDA-Modells entwickelt, um die Ausführungszeit von Programmteilen zu bestimmen. Einzelne Zugriffskosten können einem mehrerer parallel laufender Modelle zugeordnet werden. Dadurch können Kosten, die Zugriffe auf einzelne Speicherbereiche verursachen, separat bestimmt werden. Diese Profiling-Technik erlaubt Optimierungen an Datenstrukturen und Speicherzugriffsmustern durch präzise und gezielte Informationsproduktion. N2 - Cost models are used to determine the execution time of programs, to compare the efficiency of algorithms, and to analyse the behaviour of memory hierarchies. The Latency-of-Data-Access (LDA) model that takes into account multiple hierarchical memory levels with different latencies, is a newly proposed, innovative cost model. In this diploma-thesis, a simulator for memory hierarchies is presented that allows the calculation of execution times using the LDA model. The simulator is used to prove the claim that the execution time of a program can be accurately estimated with the LDA model. With the simulator, it is for the first time possible to determine the execution time of programs with this model in a practical way. The simulator can be configured for systems with various cache architectures and supports shared memory (SMP) multiprocessor systems with different cache coherence protocols. The simulator can be configured with the results from Microbenchmarks which measure the architectural properties of a memory hierarchy. The results confirm the claim not only for single processor systems, but also for SMP systems, where concurrently interacting processors influence each others cache access sequence. Additionally, a new field of usage of the LDA model was developed to determine execution times of program parts. Single access costs can be assigned to one of several parallel running models. As an example the costs of accesses to different memory areas can be split and determined separately. This profiling technique allows to optimise data structures and memory access patterns of sequential and parallel SMP programs by precise production of information. Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10063 ER - TY - GEN A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Online Optimierung N2 - Wie soll man einen Aufzug steuern, wenn man keine Informationen über zukünftige Fahraufträge besitzt? Soll man eine Bahncard kaufen, wenn die nächsten Bahnreisen noch unbekannt sind? In der klassischen kombinatorischen Optimierung geht man davon aus, daß die Daten jeder Probleminstanz vollständig gegeben sind. In vielen Fällen modelliert diese \emph{Offline-Optimierung} jedoch die Situationen aus Anwendungen nur ungenügend. Zahlreiche Problemstellungen in der Praxis sind in natürlicher Weise \emph{online}: Sie erfordern Entscheidungen, die unmittelbar und ohne Wissen zukünftiger Ereignisse getroffen werden müssen. Als ein Standardmittel zur Beurteilung von Online-Algorithmen hat sich die \emph{kompetitive Analyse} durchgesetzt. Dabei vergleicht man den Zielfunktionswert einer vom Online-Algorithmus generierten Lösung mit dem Wert einer optimalen Offline-Lösung. Mit Hilfe der kompetitiven Analyse werden im Skript Algorithmen zum Caching, Netzwerk-Routing, Scheduling und zu Transportaufgaben untersucht. Auch die Schwächen der kompetitiven Analyse werden aufgezeigt und alternative Analysekonzepte vorgestellt. Neben der theoretischen Seite werden auch die Anwendungen der Online-Optimierung in der Praxis, vor allem bei Problemen der innerbetrieblichen Logistik, beleuchtet. Bei der Steuerung automatischer Transportsysteme tritt eine Fülle von Online-Problemen auf. Hierbei werden an die Algorithmen oftmals weitere Anforderungen gestellt. So müssen Entscheidungen unter strikten Zeitbeschränkungen gefällt werden (Echtzeit-Anforderungen). Dieses Skript ist aus dem Online-Teil der Vorlesung -Ausgewählte Kapitel aus der ganzzahligen Optimierung- (Wintersemester~1999/2000) und der Vorlesung -Online Optimierung- (Sommersemester~2000) an der Technischen Universität Berlin entstanden. T3 - ZIB-Report - 00-55 KW - Kompetitive Analyse KW - Online Optimierung KW - Online Algorithmen Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6238 ER - TY - GEN A1 - Volkwein, Stefan A1 - Weiser, Martin T1 - Affine Invariant Convergence Analysis for Inexact Augmented Lagrangian-SQP Methods N2 - An affine invariant convergence analysis for inexact augmented Lagrangian-SQP methods is presented. The theory is used for the construction of an accuracy matching between iteration errors and truncation errors, which arise from the inexact linear system solves. The theoretical investigations are illustrated numerically by an optimal control problem for the Burgers equation. T3 - ZIB-Report - 00-56 KW - nonlinear programming KW - multiplier methods KW - affine invariant norms KW - Burgers' equation Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6243 ER - TY - GEN A1 - Stüben, Hinnerk T1 - Hadron masses from dynamical, non-perturbatively O(a) improved Wilson fermions N2 - We present results on light hadron masses from simulations of full QCD and report on experiences in running such simulations on a Hitachi SR8000-F1 supercomputer. T3 - ZIB-Report - 00-52 KW - QCD KW - Hadron masses Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6205 ER - TY - GEN A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Weider, Steffen T1 - An Approximation Algorithm for the Non-Preemptive Capacitated Dial-a-Ride Problem N2 - In the Capacitated Dial-a-Ride Problem (CDARP) we are given a transportation network and a finite set of transportation jobs. Each job specifies the source and target location which are both part of the network. A server which can carry at most $C$~objects at a time can move on the transportation network in order to process the transportation requests. The problem CDARP consists of finding a shortest transportation for the jobs starting and ending at a designated start location. In this paper we are concerned with the restriction of CDARP to graphs which are simple paths. This setting arises for instance when modelling applications in elevator transportation systems. It is known that even for this restricted class of graphs CDARP is NP-hard to solve. We provide a polynomial time approximation algorithm that finds a transportion of length at most thrice the length of the optimal transportation. T3 - ZIB-Report - 00-53 KW - NP-completeness KW - polynomial-time approximation algorithms KW - stacker-crane problem KW - vehicle Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6217 ER - TY - GEN A1 - Schmidt, Frank A1 - Friese, Tilmann A1 - Zschiedrich, Lin A1 - Deuflhard, Peter T1 - Adaptive Multigrid Methods for the Vectorial Maxwell Eigenvalue Problem for Optical Waveguide Design N2 - This paper has been motivated by the need for a fast robust adaptive multigrid method to solve the vectorial Maxwell eigenvalue problem arising from the design of optical chips. Our nonlinear multigrid methods are based on a previous method for the scalar Helmholtz equation, which must be modified to cope with the null space of the Maxwell operator due to the divergence condition. We present two different approaches. First, we present a multigrid algorithm based on an edge element discretization of time-harmonic Maxwell's equations, including the divergence condition. Second, an explicit elimination of longitudinal magnetic components leads to a nodal discretization known to avoid discrete \emph{spurious modes} also and a vectorial eigenvalue problem, for which we present a multigrid solver. Numerical examples show that the edge element discretization clearly outperforms the nodal element approach. T3 - ZIB-Report - 00-54 KW - Maxwell's equations KW - eigenvalue problem KW - edge elements KW - multigrid methods KW - waveguide KW - optical chip design Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6228 ER - TY - GEN A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank T1 - Automatic Identification of Metastable Conformations via Self-Organized Neural Networks N2 - As has been shown recently, the identification of metastable chemical conformations leads to a Perron cluster eigenvalue problem for a reversible Markov operator. Naive discretization of this operator would suffer from combinatorial explosion. As a first remedy, a pre-identification of essential degrees of freedom out of the set of torsion angles had been applied up to now. The present paper suggests a different approach based on neural networks: its idea is to discretize the Markov operator via self-organizing (box) maps. The thus obtained box discretization then serves as a prerequisite for the subsequent Perron cluster analysis. Moreover, this approach also permits exploitation of additional structure within embedded simulations. As it turns out, the new method is fully automatic and efficient also in the treatment of biomolecules. This is exemplified by numerical results. T3 - ZIB-Report - 00-51 KW - biochemical conformations KW - cluster analysis KW - Molecular Dynamics KW - Monte-Carlo methods KW - operator discretization KW - Perron cluster Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6197 ER - TY - GEN A1 - Sander, Oliver A1 - Runge, Daniel T1 - Fast Surface Reconstruction Using a Probe Sphere N2 - We introduce a new method for reconstructing a triangular surface from an unorganized set of points in space. It is based on placing a probe sphere on the point set and rolling it around, connecting all triples of points with a triangle that the sphere comes to rest on. Therefore, the algorithm interpolates, rather than approximates, the input points. The method needs considerably less running time than previous algorithms and yields good results on point sets that are reasonably well-behaved. T3 - ZIB-Report - 00-50 KW - Surface Reconstruction KW - Computational Geometry Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6181 ER - TY - GEN A1 - Wagler, Annegret T1 - Critical and Anticritical Edges in Perfect Graphs N2 - We call an edge $e$ of a perfect graph $G$ critical if $G-e$ is imperfect and say further that $e$ is anticritical with respect to the complementary graph $\overline G$. We ask in which perfect graphs critical and anticritical edges occur and how to find critical and anticritical edges in perfect graphs. Finally, we study whether we can order the edges of certain perfect graphs such that deleting all the edges yields a sequence of perfect graphs ending up with a stable set. T3 - ZIB-Report - 00-49 KW - perfect graphs KW - critical edges KW - anticritical edges Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6174 ER - TY - GEN A1 - Bley, Andreas A1 - Koch, Thorsten T1 - Optimierung in der Planung und beim Aufbau des G-WiN N2 - Ende Juni diesen Jahres wurde das Gigabit-Wissenschaftsnetz offiziell gestartet. In der zweijährigen Vorbereitungsphase wurden nicht nur die technischen Möglichkeiten der neuen Übertragungstechniken und Dienste getestet. Es wurden auch verschiedene Fragestellungen zum effizienten Einsatz der verfügbaren Ressourcen für den Betrieb des G-WiN untersucht. In diesem Artikel beschreiben wir, wie das G-WiN zu seiner jetzigen Struktur und Topologie gekommen ist. T3 - ZIB-Report - 00-48 Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6169 ER - TY - GEN A1 - Rambau, Jörg T1 - Triangulierungen von Punktmengen und Polyedern N2 - Dieser Report wurde im Sommersemester 2000 an der TU Berlin in einer Spezialvorlesung über Triangulierungen von Punktmengen und Polyedern als Skriptum verwendet. Nach einem motivierenden Kapitel werden grundlegende Begriffe und Konstruktionen in der Theorie der Triangulierungen von Punktmengen und Polyedern vorgestellt. Danach werden als weiterführende Themen reguläre Triangulierungen, Sekundärpolytope, bistellare Operationen, höhere Stasheff-Tamari-Halbordnungen und Triangulierungen mit wenigen bzw. gar keinen Flips behandelt. Ein Kapitel über Enumeration und Optimierung beschließt die Zusammenstellung. T3 - ZIB-Report - 00-46 KW - point configuration KW - triangulation KW - polytope KW - polyhedron KW - Gale diagram KW - secondary polytope KW - cyclic polytope KW - graph of all triangulations KW - conn Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6145 ER - TY - GEN A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequency Planning and Ramifications of Coloring N2 - This paper surveys frequency assignment problems coming up in planning wireless communication services. It particularly focuses on cellular mobile phone systems such as GSM, a technology that revolutionizes communication. Traditional vertex coloring provides a conceptual framework for the mathematical modeling of many frequency planning problems. This basic form, however, needs various extensions to cover technical and organizational side constraints. Among these ramifications are $T$-coloring and list coloring. To model all the subtleties, the techniques of integer programming have proven to be very useful. The ability to produce good frequency plans in practice is essential for the quality of mobile phone networks. The present algorithmic solution methods employ variants of some of the traditional coloring heuristics as well as more sophisticated machinery from mathematical programming. This paper will also address this issue. Finally, this paper discusses several practical frequency assignment problems in detail, states the associated mathematical models, and also points to public electronic libraries of frequency assignment problems from practice. The associated graphs have up to several thousand nodes and range from rather sparse to almost complete. T3 - ZIB-Report - 00-47 KW - frequency assignment KW - graph coloring Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6152 ER - TY - GEN A1 - Rambau, Jörg T1 - Circuit Admissible Triangulations of Oriented Matroids N2 - All triangulations of euclidean oriented matroids are of the same PL-homeomorphism type by a result of Anderson. That means all triangulations of euclidean acyclic oriented matroids are PL-homeomorphic to PL-balls and that all triangulations of totally cyclic oriented matroids are PL-homeomorphic to PL-spheres. For non-euclidean oriented matroids this question is wide open. One key point in the proof of Anderson is the following fact: for every triangulation of a euclidean oriented matroid the adjacency graph of the set of all simplices ``intersecting'' a segment $[p_-p_+]$ is a path. We call this graph the $[p_-p_+]$-adjacency graph of the triangulation. While we cannot solve the problem of the topological type of triangulations of general oriented matroids we show in this note that for every circuit admissible triangulation of an arbitrary oriented matroid the $[p_-p_+]$-adjacency graph is a path. T3 - ZIB-Report - 00-45 KW - triangulations of oriented matroids KW - topological type KW - segment adjacency graph Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6139 ER - TY - GEN A1 - Grötschel, Martin T1 - Mathematik in der Industrie: interessante Branchen und zukünftige Einsatzfelder N2 - Dieser kurze Artikel hat keine umfassende Übersicht zum Ziel. Basierend auf eigenen Erfahrungen durch Projekte mit Industriefirmen möchte ich einige Branchen erwähnen, bei denen nach meiner Einschätzung Mathematik in Zukunft zunehmend Anwendung finden wird. Ich werde das anhand konkreter Beispiele erläutern. Mathematik ersetzt in der Regel traditionelle Analyse-, Planungs- und Entwurfstechniken. Den (nicht leichten) Schritt zum Einsatz mathematischer Methoden macht ein Praktiker nur, wenn es sich für ihn ``lohnt''. Wann sich dies lohnt, ist schwer abzuschätzen. Man kann aber einige Indikatoren dafür finden, ob eine Branche für den Einsatz von Mathematik ``reif'' ist. Ob es dann dazu kommt, hängt von vielen Faktoren ab, nicht zuletzt von der Psychologie und dem sozialen Umfeld der beteiligten Personen sowie der Bereitschaft, sich auf ein so schwieriges Terrain zu begeben und Kompromisse einzugehen. Gerade letzteres fällt Mathematikern gelegentlich schwer. T3 - ZIB-Report - 00-44 KW - Mathematics in Industry KW - Telecommunication KW - Energy KW - Transportation Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6125 ER - TY - GEN A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lill, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) N2 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) wurde in den Jahren 1997-2000 im Rahmen eines wissenschaftlichen Projektes eingerichtet. Er stellt eine neuartige Form von Bibliotheksverbund dar. Sein technisches Konzept und sein organisatorischer Aufbau basieren auf der Internetphilosophie. Den informationstechnischen Kern bildet eine Suchmaschine, die die heterogenen lokalen Bibliothekssysteme miteinander verbindet. Die KOBV-Organisation ist dezentral. Sie wird getragen von der Kooperation der Bibliotheken in Berlin und Brandenburg; diese werden von einer kleinen Verbundzentrale unterstützt. Die KOBV-Suchmaschine ist zu erreichen unter: {\begin{rawhtml} http://www.kobv.de/suche/ \end{rawhtml}} T3 - ZIB-Report - 00-43 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6118 ER - TY - GEN A1 - Kuberek, Monika A1 - Lill, Monika A1 - Lohrum, Stefan A1 - Rusch, Beate T1 - Spezifikation der Schnittstelle zwischen KOBV-Suchmaschine und Lokalsystemen N2 - Die Kommunikation zwischen der KOBV-Suchmaschine und entfernten Bibliotheksinformationssystemen unterschiedlicher Hersteller wird über das Standardprotokoll Z39.50 abgewickelt. Die Suchmaschine ermöglicht Online-Recherchen in lokalen Bibliotheksinformationssystemen, die dazu ein Z39.50 Target (Server) zur Verfügung stellen müssen. Die Suchmaschine liefert ihre Daten ebenfalls über Z39.50 aus. Ein Lokalsystem benötigt hierfür einen Z39.50 Origin (Client). In dem Papier wird die Schnittstelle zwischen der KOBV-Suchmaschine und lokalen Bibliothekssystemen spezifiziert: Es werden die grundlegenden Anforderungen an Lokalsysteme definiert und die Konfigurationsparameter für die Z39.50-Kommunikation zwischen KOBV-Suchmaschine und Lokalsystemen beschrieben. T3 - ZIB-Report - 00-42 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Web-Link KW - Z39.50 KW - Z39.50-Protokoll Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6106 ER - TY - GEN A1 - Heidl, Sebastian A1 - Staudemeyer, Ralf T1 - Implementation von WAP-Diensten für die SGI/CRAY T3E des ZIB N2 - Die zunehmende Verfügbarkeit von mobilen Geräten, die mit einem Internetanschluß ausgerüstet sind, bringt auch eine steigende Nachfrage nach Informationsdiensten für diese Art von Clients mit sich. Das ZIB stellt mit seinem Höchstleistungsrechner vom Typ SGI/CRAY T3E Wissenschaftlern große Rechenkapazitäten zur Verfügung. Im Rahmen dieser Studienarbeit wurde ein WAP-Interface zur T3E entwickelt, das es den Nutzern ermöglicht, über ein mobiles, WAP-fähiges Gerät Informationen zur Betriebsbereitschaft und zur Auslastung des Höchstleistungsrechners, sowie Informationen zu den von ihnen in Auftrag gegebenen Rechenjobs abzurufen. Die Untersuchung der aktuellen Möglichkeiten in der mobilen Kommunikation brachte einige Einschränkungen für das geplante Informationsangebot mit sich. So mußte auf Grund von Sicherheitsbedenken auf eine tatsächliche Interaktionsmöglichkeit (z.B. neue Rechenjobs zu starten) verzichtet werden. Demgegenüber konnte gezeigt werden, daß die Bereitstellung der gleichen Informationen für unterschiedliche Arten von Clients (WWW-Browser $\rightarrow$ HTML, WAP-Browser $\rightarrow$ WML) durch die Verwendung von XML als internes Datenformat problemlos möglich ist. Es hat sich gezeigt, daß die Bereitstellung eines WAP-Informationsdienstes auf Grund verschiedener Inkompatibilitätsprobleme (verschiedene Gateways, verschiedene WAP-Browser) mit erheblichem Aufwand verbunden sein kann. An dieser Stelle besteht noch Handlungsbedarf seitens der Hersteller dieser Softwarepakete. T3 - ZIB-Report - 00-41 KW - WAP KW - T3E KW - wireless KW - supercomputing KW - kannel KW - XML KW - cocoon Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6098 ER - TY - GEN A1 - Kuberek, Monika T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) - Konzept, Erfahrungen, Ausblick - N2 - Der Aufsatz ist die ausgearbeitete Fassung eines Vortrages, gehalten auf dem 2. BSZ-Kolloquium des Bibliotheksservice-Zentrums Baden-Württemberg (BSZ) am 10. Oktober 2000 in Konstanz. Der Kooperative Bibliotheksverbund Berlin-Brandenburg, kurz KOBV, ist ein sehr junger Verbund - genauer gesagt, befindet er sich im Oktober 2000 immer noch in der Aufbauphase. Das KOBV-Projekt hat am 1. April 1997 begonnen und wird am 31. Dezember 2000 enden. Ab 2001 wird der KOBV in eine institutionalisierte Form überführt, die - wie bereits das Projekt - am Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) - angesiedelt wird. Mit dem KOBV wurde ein in technischer wie auch in organisatorischer Hinsicht neuartiger Bibliotheksverbund aufgebaut, der auf der \glqq Internetphilosophie\grqq basiert: Den technischen Kern bildet eine eigens entwickelte Suchmaschine; die Organisation ist dezentral ausgerichtet und gründet sich auf der Kooperation der KOBV-Partner. In dem Vortrag werden das technische und das organisatorische Verbundkonzept vorgestellt, über die Erfahrungen nach einjähriger Betriebsdauer berichtet und ein kurzer Ausblick darüber gegeben, wie es mit dem KOBV weitergeht. T3 - ZIB-Report - 00-39 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6079 ER - TY - GEN A1 - Steinbach, Marc T1 - Autos, Ziegen und Streithähne N2 - Das aus den Medien bekannte umstrittene Ziegenproblem (auch Drei-Türen-Problem genannt) wird vollständig analysiert und gelöst. In der Streitfrage spielen sprachliche Mehrdeutigkeiten der Problemformulierung eine wesentliche Rolle; zudem werden Zufallsereignisse mit willkürlicher Information über deren Ergebnisse verwechselt. Tatsächlich erweisen sich beide strittigen Lösungen als teilweise richtige Bestandteile der Gesamtlösung. Die Argumentation wird in allgemeinverständlicher Sprache geführt und anschliessend durch eine formale mathematische Betrachtung ergänzt. T3 - ZIB-Report - 00-40 KW - Ziegenproblem KW - Zufall KW - Willkür Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6087 ER - TY - GEN A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Voß, Stefan T1 - SteinLib: An Updated Library on Steiner Tree Problems in Graphs N2 - In this paper we present the {\em SteinLib}, a library of data sets for the Steiner tree problem in graphs. This library extends former libraries on Steiner tree problems by many new interesting and difficult instances, most of them arising from real-world applications. We give a survey on the difficulty of these problem instances by giving references to state-of-the-art software packages that were the first or are currently among the best to solve these instances. T3 - ZIB-Report - 00-37 KW - Steiner Trees KW - Mathematical Programming Testdata Library Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6056 ER - TY - GEN A1 - Keller, Axel A1 - Reinefeld, Alexander T1 - Anatomy of a Resource Management System for HPC-Clusters N2 - Workstation clusters are often not only used for high-throughput computing in time-sharing mode but also for running complex parallel jobs in space-sharing mode. This poses several difficulties to the resource management system, which must be able to reserve computing resources for exclusive use and also to determine an optimal process mapping for a given system topology. On the basis of our CCS software, we describe the anatomy of a modern resource management system. Like Codine, Condor, and LSF, CCS provides mechanisms for the user-friendly system access and management of clusters. But unlike them, CCS is targeted at the effective support of space-sharing parallel and even metacomputers. Among other features, CCS provides a versatile resource description facility, topology-based process mapping, pluggable schedulers, and hooks to metacomputer management. T3 - ZIB-Report - 00-38 KW - Resource Management System KW - Metacomputer Management Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6063 ER - TY - GEN A1 - Koster, Arie M.C.A. A1 - Zymolka, Adrian T1 - Stable Multi-Sets N2 - In this paper we introduce a generalization of stable sets: stable multi-sets. A stable multi-set is an assignment of integers to the vertices of a graph, such that specified bounds on vertices and edges are not exceeded. In case all vertex and edge bounds equal one, stable multi-sets are equivalent to stable sets. For the stable multi-set problem, we derive reduction rules and study the associated polytope. We state necessary and sufficient conditions for the extreme points of the linear relaxation to be integer. These conditions generalize the conditions for the stable set polytope. Moreover, the classes of odd cycle and clique inequalities for stable sets are generalized to stable multi-sets and conditions for them to be facet defining are determined. The study of stable multi-sets is initiated by optimization problems in the field of telecommunication networks. Stable multi-sets emerge as an important substructure in the design of optical networks. T3 - ZIB-Report - 00-36 KW - stable multi-sets KW - polyhedral combinatorics Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6047 ER - TY - THES A1 - Helmberg, Christoph T1 - Semidefinite Programming for Combinatorial Optimization N2 - This book offers a self-contained introduction to the field of semidefinite programming, its applications in combinatorial optimization, and its computational methods. We equip the reader with the basic results from linear algebra on positive semidefinite matrices and the cone spanned by them. Starting from linear programming, we introduce semidefinite programs and discuss the associated duality theory. We then turn to semidefinite relaxations of combinatorial optimization and illustrate their interrelation. In the second half we deal with computational methods for solving semidefinite programs. First, the interior point approach, its iteration complexity, and implementational issues are discussed. Next, we explain in great detail the spectral bundle method, which is particularly suited for large scale semidefinite programming. One of the most successful techniques in integer linear programming is the cutting plane approach which improves an initial relaxation by adding violated inequalities. We explore possibilities to combine the two solution methods with the cutting plane approach in order to strengthen semidefinite relaxations of combinatorial optimization problems. T3 - ZIB-Report - 00-34 KW - positive semidefinite matrices KW - semidefinite cone KW - semidefinite Programming KW - semidefinite duality KW - combinatorial optimization KW - max-cut KW - quadrati Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6022 ER - TY - GEN A1 - Helmberg, Christoph T1 - SBmethod --- A C++ Implementation of the Spectral Bundle Method. Manual to Version 1.1 N2 - \texttt{SBmethod}, Version 1.1, is an implementation of the spectral bundle method for eigenvalue optimization problems of the form \begin{displaymath} \min_{y\in \mathbf{R}^m}\;\; a\;\lambda_{\max}(C-\sum_{i=1}^{m} A_i y_i)+b^Ty. \end{displaymath} The design variables $y_i$ may be sign constrained, $C$ and and $A_i$ are given real symmetric matrices, $b\in\mathbf{R}^m$ allows to specify a linear cost term, and $a>0$ is a constant multiplier for the maximum eigenvalue function $\lambda_{\max}(\cdot)$. The code is intended for large scale problems and allows to exploit structural properties of the matrices such as sparsity and low rank structure. The manual contains instructions for installation and use of the program. It describes in detail input format, options, and output. The meaning of the variables and parameters is made precise by relating them to a mathematical description of the algorithm in pseudocode. T3 - ZIB-Report - 00-35 KW - semidefinite programming KW - semidefinite relaxations KW - spectral bundle method KW - eigenvalue optimization KW - large-scale problems Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6039 ER - TY - GEN A1 - Schintke, Florian T1 - Ermittlung von Programmlaufzeiten anhand von Speicherzugriffen, Microbenchmarks und Simulation vonSpeicherhierarchien N2 - \\{\bf Zusammenfassung:} Kostenmodelle dienen der Ermittlung von Programmlaufzeiten, zum Vergleich der Effizienz von Algorithmen und zur Analyse des Verhaltens von Speicherhierarchien. Ein neuartiges Kostenmodell ist das Latency-of-Data-Access (LDA) Modell, das mehrere hierarchische Speicherebenen mit unterschiedlichen Latenzzeiten berü{}cksichtigt. In dieser Diplomarbeit wird ein Simulator fü{}r Speicherhierarchien prä{}sentiert, der die Berechnung von Programmausfü{}hrungszeiten nach dem LDA-Modell erlaubt. Mit Hilfe des Simulators wird die These geprü{}ft, da\ss{} mit diesem Modell die Ausfü{}hrungszeit eines Programms adä{}quat abgeschä{}tzt werden kann. Mit dem Simulator ist es erstmals praktikabel mö{}glich, Programmausfü{}hrungszeiten nach dem LDA-Modell zu bestimmen. Der Simulator kann fü{}r Systeme mit unterschiedlichen Speicherarchitekturen konfiguriert werden und unterstü{}tzt Mehrprozessorsysteme mit gemeinsamem Speicher (SMP-Systeme) mit verschiedenen Kohä{}renzprotokollen. Der Simulator kann mit den Ergebnissen von Microbenchmarks konfiguriert werden, die die Architekturparameter einer Speicherhierarchie messen. Die Ergebnisse bestä{}tigen die These nicht nur fü{}r Einzelprozessorsysteme, sondern auch fü{}r SMP-Systeme, wo gleichzeitig interagierende Prozessoren gegenseitig ihre Zugriffssequenz auf Zwischenspeicher beeinflussen. Zusä{}tzlich wurde eine neue Einsatzmö{}glichkeit des LDA-Modells entwickelt, um die Ausfü{}hrungszeit von Programmteilen zu bestimmen. Einzelne Zugriffskosten kö{}nnen einem mehrerer parallel laufender Modelle zugeordnet werden. Dadurch kö{}nnen Kosten, die Zugriffe auf einzelne Speicherbereiche verursachen, separat bestimmt werden. Diese Profiling-Technik erlaubt Optimierungen an Datenstrukturen und Speicherzugriffsmustern durch prä{}zise und gezielte Informationsproduktion.Cost models are used to determine the execution time of programs, to compare the efficiency of algorithms, and to analyse the behaviour of memory hierarchies. The Latency-of-Data-Access (LDA) model that takes into account multiple hierarchical memory levels with different latencies, is a newly proposed, innovative cost model. In this diploma-thesis, a simulator for memory hierarchies is presented that allows the calculation of execution times using the LDA-model. The simulator is used to prove the claim that the execution time of a program can be accurately estimated with the LDA-model. With the simulator, it is for the first time possible to determine the execution time of programs with this model in a practical way. The simulator can be configured for systems with various cache architectures and supports shared memory (SMP) multiprocessor systems with different cache coherence protocols. The simulator can be configured with the results from microbenchmarks which measure the architectural properties of a memory hierarchy. The results confirm the claim not only for single processor systems, but also for SMP systems, where concurrently interacting processors influence each others cache access sequence. Additionally, a new field of usage of the LDA-model was developed to determine execution times of program parts. Single access costs can be assigned to one of several parallel running models. As an example the costs of accesses to different memory areas can be split and determined separately. This profiling technique allows to optimise data structures and memory access patterns of sequential and parallel SMP programs by precise production of information. T3 - ZIB-Report - 00-33 KW - Cache-Simulator KW - Microbenchmarks KW - SMP-System KW - Kostenmodell KW - Speicherhierarchie Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6018 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Merzky, Andre A1 - Zachow, Stefan T1 - Distributed Visualization with OpenGL Vizserver: Practical Experiences N2 - The increasing demand for distributed solutions in computing technology does not stop when it comes to visualization techniques. However, the capabilities of todays applications to perform remote rendering are limited by historical design legacys. Especially the popular X11 protokoll, which has been proven to be extremely flexible and usefull for remote 2D graphics applications, breaks down for the case of remote 3D rendering. In this white paper, we give a short overview of generic remote rendering technologies available today, and compare their performance to the recently released vizserver by SGI: a network extension to the SGI OpenGL rendering engines. T3 - ZIB-Report - 00-31 KW - remote visualization KW - high performance computing Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5992 ER - TY - GEN A1 - Gatermann, Karin T1 - Counting stable solutions of sparse polynomial systems in chemistry N2 - The polynomial differential system modelling the behavior of a chemical reaction is given by graphtheoretic structures. The concepts from toric geometry are applied to study the steady states and stable steady states. Deformed toric varieties give some insight and enable graph theoretic interpretations. The importance of the circuits in the directed graph are emphazised. The counting of positive solutions of a sparse polynomial system by B.\ Sturmfels is generalized to the counting of stable positive solutions in case of a polynomial differential equation. The generalization is based on a method by sparse resultants to detect whether a system may have a Hopf bifurcation. Special examples from chemistry are used to illustrate the theoretical results. T3 - ZIB-Report - 00-32 KW - mass action kinetics KW - toric variety KW - stability KW - circuit Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6007 ER - TY - GEN A1 - Potra, Florian T1 - A path-following method for linear complementarity problems based on the affine invariant Kantorovich Theorem N2 - A path following algorithm for linear complementarity problems is presented. Given a point $z$ that approximates a point $z(\tau)$ on the central path with complementarity gap $\tau$, one determines a parameter $\theta\in (0,1)$ so that this point satisfies the hypothesis of the affine invariant Kantorovich Theorem for the equation defining $z((1-\theta)\tau)$. It is shown that $\theta$ is bounded below by a multiple of $n^{-1/2}$, where $n$ is the dimension of the problem. Since the hypothesis of of the Kantorovich Theorem is satisfied the sequence generated by Newton's method, or by the simplified Newton method, will converge to $z((1-\theta)\tau)$. We show that the number of steps required to obtain an acceptable approximation of $z((1-\theta)\tau)$ is bounded above by a number independent of $n$. Therefore the algorithm has $O(\sqrt{n}L)$-iteration complexity. The parameters of the algorithm can be determined in such a way that only one Newton step is needed each time the complementarity gap is decreased. T3 - ZIB-Report - 00-30 KW - Linear complementarity problem KW - interior-point algorithm KW - path-following KW - Kantorovich Theorem Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5981 ER - TY - GEN A1 - Wagler, Annegret T1 - The Classes of Critically and Anticritically Perfect Graphs N2 - We focus on two new types of extremal graphs with respect to perfectness: critically and anticritically perfect graphs that lose their perfectness by simply deleting and adding an arbitrary edge, respectively. We present examples and study properties in order to compare critically and anticritically perfect graphs with minimally imperfect graphs, another type of extremal graphs with respect to perfectness. We discuss two attempts to characterize the classes of all critically and anticritically perfect graphs and give a brief overview on classes of perfect graphs which contain critically or anticritically perfect graphs. T3 - ZIB-Report - 00-29 KW - perfect graphs KW - critically perfect graphs KW - anticritically perfect graphs Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5975 ER - TY - GEN A1 - Seebass, Martin A1 - Beck, Rudolf A1 - Gellermann, Johanna A1 - Nadobny, Jacek A1 - Wust, Peter T1 - Electromagnetic phased arrays for regional hyperthermia -- optimal frequency and antenna arrangement N2 - In this paper we investigate the effects of the three-dimensional arrangement of antennas and frequency on temperature distributions that can be achieved in regional hyperthermia using an electromagnetic phased array. We compare the results of power-based and temperature-based optimization. Thus we are able to explain the discrepancies between previous studies favouring more antenna rings on the one hand and more antennas per ring on the other hand. We analyze the sensitivity of the results with respect to changes in amplitudes and phases as well as patient position. This analysis can be used for different purposes. First, it provides additional criteria for selecting the optimal frequency. Second, it can be used for specifying the required phase and amplitude accuracy for a real phased array system. Furthermore, it may serve as a basis for technological developments in order to reduce both types of sensitivities described above. T3 - ZIB-Report - 00-28 KW - Pelvic heating KW - phased array optimization Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5961 ER - TY - GEN A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Zöckler, Malte A1 - Hege, Hans-Christian T1 - Hyperthermia Treatment Planning with HyperPlan - User's Manual N2 - HyperPlan is a software system for performing 3D-simulations and treatment planning in regional hyperthermia. It allows the user to understand the complex effects of electromagnetic wave propagation and heat transport inside a patient's body. Optimized power amplitudes and phase settings can be calculated for the BSD radiowave applicators Sigma 60 and Sigma 2000 (eye-applicator). HyperPlan is built on top of the modular, object-oriented visualization system Amira. This system already contains powerful algorithms for image processing, geometric modelling and 3D graphics display. HyperPlan provides a number of hyperthermia-specific modules, allowing the user to create 3D tetrahedral patient models suitable for treatment planning. In addition, all numerical simulation modules required for hyperthermia simulation are part of HyperPlan. This guide provides a step-by-step introduction to hyperthermia planning using HyperPlan. It also describes the usage of the underlying visualization system Amira. T3 - ZIB-Report - 00-27 KW - image segmentation KW - grid generation KW - visualization KW - therapy planning Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5957 ER - TY - GEN A1 - Huisinga, Wilhelm T1 - The Essential Spectral Radius and Asymptotic Properties of Transfer Operators N2 - The statistical behavior of deterministic and stochastic dynamical systems may be described using transfer operators, which generalize the notion of Frobenius Perron and Koopman operators. Since numerical techniques to analyze dynamical systems based on eigenvalues problems for the corresponding transfer operator have emerged, bounds on its essential spectral radius became of interest. This article shows that they are also of great theoretical interest. We give an analytical representation of the essential spectral radius in $L^{1}\!(\mu)$, which then is exploited to analyze the asymptotical properties of transfer operators by combining results from functional analysis, Markov operators and Markov chain theory. In particular, it is shown, that an essential spectral radius less than $1$, constrictiveness and some weak form'' of the so--called Doeblin condition are equivalent. Finally, we apply the results to study three main problem classes: deterministic systems, stochastically perturbed deterministic systems and stochastic systems. T3 - ZIB-Report - 00-26 KW - constrictive KW - asymptotically stable KW - exact KW - asymptotically periodic KW - ergodic KW - aperiodic KW - Frobenius Perron operator KW - Koopman operator KW - Markov o Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5942 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Stüben, Hinnerk T1 - Parallel tempering and decorrelation of topological charge in full QCD N2 - The improvement of simulations of QCD with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering is studied on $10^4$ and $12^4$ lattices. As an indicator for decorrelation the topological charge is used. T3 - ZIB-Report - 00-25 KW - QCD KW - parallel tempering KW - topological charge Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5930 ER - TY - GEN A1 - Sperber, Wolfram A1 - Dalitz, Wolfgang T1 - Portale, Search Engines und Math-Net N2 - Wie sucht ein Wissenschaftler im Internet die ben"otigten Informationen für seine Arbeit? Welche relevanten Informationen gibt es überhaupt im Web? Sind dafür solche Suchmaschinen wie AltaVista, Google oder HotBot die richtigen Werkzeuge? Die Antwort der Mathematiker heisst Math-Net, ein Informations- und Kommunikationssystem für die Mathematik. Math-Net besteht zunächst aus den Informationen von Personen und Institutionen, die ihre für die Mathematik relevanten Informationen dort bereitstellen wollen. Das soll i.a. auf den Web-Servern der Personen oder Institutionen geschehen. Hierin unterscheidet sich die Situation im Math-Net nicht von der im WWW insgesamt. Im Math-Net sollen aber die Informationen in einheitlicher Weise erschlossen werden. Dazu gibt es sowohl für Server als auch für die Dokumente Empfehlungen für deren Strukturierung. Die lokalen Informationen werden dann im Math-Net durch automatische Verfahren gesammelt, ausgewertet und indexiert. Diese Indexe sind die Basis für die Math-Net Dienste. Das sind Search Engines und Portale, die einen qualifizierten und effizienten Zugang zu den Informationen im Math-Net bieten. Die Math-Net Dienste sind auf die Mathematik spezialisiert. Im Gegensatz zu den oben erwähnten universellen Suchmaschinen decken sie nur einen winzigen Bruchteil des Web ab, aber dafür den für die Mathematik relevanten Teil. Math-Net ist mehr als nur Search Engine oder Portal zu Informationen in der Mathematik. Es ist auch ein Informations- und Kommunikationssystem sowie ein Publikationsmedium für die Mathematik. Die mathematische Community hat sich in der Math-Net Initiative organisiert. Diese Initiative wird von der International Mathematical Union (IMU), der weltweiten Dachorganisation der mathematischen Gesellschaften, koordiniert. Die Entwicklung des Math-Net wird von dem breiten Konsens der Mathematiker getragen, den Zugang zu der für die Mathematik relevanten Information zu erleichtern und zu verbessern. T3 - ZIB-Report - 00-24 KW - Math-Net KW - Portals KW - search engines KW - information retrieval Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5923 ER - TY - GEN A1 - Lügger, Joachim T1 - Über Suchmaschinen, Verbünde und die Integration von Informationsangeboten N2 - Die Entwicklung einer bibliothekarischen Suchmaschine ist das technisch-organisatorische Herztück des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV). Auf dem Wege über diese Innovation verfolgen die Länder Berlin und Brandenburg und ihre Bibliotheken das Ziel, ihr Bibliothekswesen zu erneuern und zu reorganisieren. Die Entwicklung der Suchmaschine ist für die Partner im KOBV-Projekt kein Selbstzweck, sondern nur Mittel zum Zweck - insbesondere, um die heterogene Welt der in Berlin und in Brandenburg eingesetzten integrierten Bibliotheksinformationssysteme harmonisch miteinender zu verbinden. Mit der KOBV-Suchmaschine sind informationstechnische Sichtweisen und Methoden entstanden, die sich potentiell auch auf die überregionale Arbeit des KOBV auswirken können und in Kooperation mit den Bibliotheksverbänden auf die Zusammenarbeit der Verbünde insgesamt. Der Artikel konzentriert sich am Beispiel der KOBV-Such¡ma¡schine auch auf diesen Aspekt. Auf die Bibliotheken kommen mit dem Internet und dem World Wide Web für sie neuartige Medien, Mittel und Aufgaben zu, in erster Linie aus dem Bereich der Wissenschaften und der wissenschaftlichen Fachgesellschaften. Die Herausforderung besteht darin, die neuen elektronischen Informationen und Angebote zu integrieren. Das Stichwort hierzu lautet digitale Bibliothek bzw. virtuelle Fachbibliothek. Auch zu der Diskussion um diese aktuelle Entwicklung will der Artikel einen Beitrag leisten. T3 - ZIB-Report - 00-23 KW - Suchmaschinen KW - Integration Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5919 ER - TY - GEN A1 - Hoesel, Stan P.M. van A1 - Koster, Arie M.C.A. A1 - Leensel, Robert L.M.J. van de A1 - Savelsbergh, Martin W.P. T1 - Polyhedral Results for the Edge Capacity Polytope N2 - Network loading problems occur in the design of telecommunication networks, in many different settings. The polyhedral structure of this problem is important in developing solution methods for the problem. In this paper we investigate the polytope of the problem restricted to one edge of the network (the edge capacity problem). We describe classes of strong valid inequalities for the edge capacity polytope, and we derive conditions under which these constraints define facets. As the edge capacity problem is a relaxation of the network loading problem, their polytopes are intimately related. We, therefore, also give conditions under which the inequalities of the edge capacity polytope define facets of the network loading polytope. Furthermore, some structural properties are derived, such as the relation of the edge capacity polytope to the knapsack polytope. We conclude the theoretical part of this paper with some lifting theorems, where we show that this problem is polynomially solvable for most of our classes of valid inequalities. In a computational study the quality of the constraints is investigated. Here, we show that the valid inequalities of the edge capacity polytope are not only important for solving the edge capacity problem, but also for the network loading problem, showing that the edge capacity problem is an important subproblem. T3 - ZIB-Report - 00-22 KW - network design KW - mixed integer programming KW - cutting planes KW - knapsack with integer capacity Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5907 ER - TY - GEN A1 - Lang, Jens A1 - Erdmann, Bodo T1 - Adaptive Linearly Implicit Methods for Heat and Mass Transfer Problems N2 - Dynamical process simulation of complex real-life problems often requires the use of modern algorithms, which automatically adapt both the time and space discretization in order to get error-controlled approximations of the solution. In this paper, a combination of linearly implicit time integrators of Rosenbrock type and adaptive multilevel finite elements based on a posteriori error estimates is presented. This approach has proven to work quite satisfactorily for a wide range of challenging practical problems. We show the performance of our adaptive method for two applications that arise in the study of flame balls and brine transport in porous media. T3 - ZIB-Report - 00-21 KW - Nonlinear time-dependent PDEs KW - Rosenbrock methods KW - multilevel finite elements KW - local refinement KW - a posteriori error estimates Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5892 ER - TY - GEN A1 - Meyer, Michael A1 - Schnurre, Rüdiger A1 - Reissbrodt, Rolf A1 - Trowitzsch-Kienast, Wolfram T1 - Computer-aided design of novel siderophores: Pyridinochelin N2 - Pyridinochelin, a novel catecholate type siderophore, has been designed on the basis of the active analog enterobactin. Growth promotion tests indicate that this synthetic siderophore feeds various pathogenic bacteria effectively with iron even though it lacks one catecholate group compared to enterobactin. The superposition of the siderophore structures suggests that the structure of the skeleton connecting the catecholate groups might be an important factor for the iron transport. T3 - ZIB-Report - 00-20 KW - bioorganic chemistry KW - drug design KW - molecular modeling KW - iron transport KW - siderophore Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5887 ER - TY - GEN A1 - Krumke, Sven A1 - Noltemeier, Hartmut A1 - Wirth, Hans-Christoph T1 - Graphentheoretische Konzepte und Algorithmen N2 - Das vorliegende Skript bietet eine Einf{ü}hrung in die Graphentheorie und graphentheoretische Algorithmen. Im zweiten Kapitel werden Grundbegriffe der Graphentheorie vorgestellt. Das dritte Kapitel besch{ä}ftigt sich mit der Existenz von Wegen in Graphen. Hier wird auch die L{ö}suung des ber{ü}hmten K{ö}nigsberger Br{ü}ckenproblems aufgezeigt und der Satz von Euler bewiesen. Im vierten Kapitel wird gezeigt, wie man auf einfache Weise die Zusammenhangskomponenten eines Graphen bestimmen kann. Im Kapitel sechs wird dann sp{ä}ter mit der Tiefensuche ein Verfahren vorgestellt, das schneller arbeitet und mit dessen Hilfe man noch mehr Informationen {ü}ber die Struktur eines Graphen gewinnen kann. In den folgenden Kapiteln werden Algorithmen vorgestellt, um minimale aufspannenden B{ä}ume, k{ü}rzeste Wege und maximale Fl{ü}sse in Graphen zu bestimmen. Am Ende des Skripts wird ein kurzer Einblick in die planaren Graphen und Graphhomomorphismen geboten. T3 - ZIB-Report - 00-19 KW - Graphen KW - Algorithmen KW - Komplexit{ä}t KW - kombinatorische Optimierung Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5873 ER - TY - GEN A1 - Koster, Arie M.C.A. T1 - Re-Optimization of Signaling Transfer Points N2 - In this paper we describe the results of a computational study towards the (re)optimization of signaling transfer points (STPs) in telecommunication networks. The best performance of an STP is achieved whenever the traffic load is evenly distributed among the internal components. Due to the continuously changing traffic pattern, the load of the components has to be re-optimized on a regular basis. Besides the balancing objective also the number of rearrangements have to be taken into account. In this paper we present two alternative formulations to deal with both requirements. Computational results show that for both formulations (near) optimal solutions can be obtained within reasonable time limits. T3 - ZIB-Report - 00-18 KW - Telecommunications KW - Modeling KW - Integer Programming Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5863 ER - TY - GEN T1 - Jahresbericht 1999 T3 - Jahresbericht - 1999 KW - Annual Report Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9749 SN - 0934-5892 ER - TY - GEN A1 - Steinbach, Marc T1 - Hierarchical Sparsity in Multistage Convex Stochastic Programs N2 - Interior point methods for multistage stochastic programs involve KKT systems with a characteristic global block structure induced by dynamic equations on the scenario tree. We generalize the recursive solution algorithm proposed in an earlier paper so that its linear complexity extends to a refined tree-sparse KKT structure. Then we analyze how the block operations can be specialized to take advantage of problem-specific sparse substructures. Savings of memory and operations for a financial engineering application are discussed in detail. T3 - ZIB-Report - 00-15 KW - Multistage Stochastic Programs KW - Hierarchical KKT Sparsity Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5837 ER - TY - GEN A1 - Oevermann, Michael A1 - Klein, Rupert A1 - Berger, Marsha A1 - Goodman, Jonathan T1 - A Projection Method for Two-Phase Incompressible Flow with Surface Tension and Sharp Interface Resolution N2 - We present a fully second order projection method for the simulation of two-phase incompressible flow with surface tension. The Navier-Stokes equations are solved with a projection method on a fixed Cartesian grid. The free interface between the two fluids is tracked with a level set approach. The conditions at the interface for the pressure, the pressure gradient, and the velocity are explicitly incorporated into the scheme leading to a sharp representation of the pressure discontinuity and the interfacial force. The scheme in the presented form does not introduce additional points in the standard finite difference stencils. Computational results are compared with analytic solutions for a static round bubble, damped surface waves, and Rayleigh-Taylor instabilities. T3 - ZIB-Report - 00-17 KW - Two-phase flow KW - immersed interface method KW - incompressible flow KW - projection method KW - level set KW - multi grid Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5851 ER - TY - GEN A1 - Meyer, Michael A1 - Steinke, Thomas A1 - Brandl, Maria A1 - Sühnel, Jürgen T1 - Density functional study of guanine and uracil quartets and of guanine quartet metal/ion complexes N2 - The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density functional calculations. The total interaction energy $\Delta$E$^{T}$ of the $\it{C}$$_{4h}$-symmetric guanine quartet consisting of Hoogsteen type base pairs with two hydrogen bonds between two neighbour bases is -66.07 kcal/mol at the highest level. The uracil quartet with C6-H6...O4 interactions between the individual bases has only a small interaction energy of -20.92 kcal/mol and the interaction energy of -24.63 kcal/mol for the alternative structure with N3-H3...O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25 \% to all interaction energies. Complexes of metal ions with G-quartets can be classified into different structure types. The one with Ca$^{2+}$ in the central cavity adopts a $\it{C}$$_{4h}$-symmetric structure with coplanar bases, whereas the energies of the planar and non-planar Na$^{+}$ complexes are almost identical. The small ions Li$^{+}$, Be$^{2+}$, Cu$^{+}$ and Zn$^{2+}$ prefer a non-planar $\it{S}$$_{4}$-symmetric structure. The lack of co-planarity prevents probably a stacking of these base quartets. The central cavity is too small for K$^{+}$ ions and therefore this ion favours in contrast to all other investigated ions a $\it{C}$$_{4}$-symmetric complex, which is 4.73 kcal/mol more stable than the $\it{C}$$_{4h}$-symmetric one. The distance 1.665 {\AA} between K$^{+}$ and the root mean squares plane of the guanine bases is approximately half of the distance between two stacked G-quartets. The total interaction energy of alkaline earth ion complexes exceeds the ones with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen-bonded biological systems. Compared with the before mentioned methods the HCTH functional leads to longer hydrogen bonds and different relative energies for two U-quartets. Finally we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C-H...O contacts in the uracil quartet. In the G-quartet the MMFF94 hydrogen bond distances N2-H22...N7 are shorter than the DFT distances, whereas the N1-H1...O6 distances are longer. T3 - ZIB-Report - 00-16 KW - density functional theory KW - effective core potential KW - hydrogen bond KW - guanine KW - uracil KW - metal ion KW - C-H...O interaction Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5842 ER - TY - GEN A1 - Bienstock, Daniel A1 - Bley, Andreas T1 - Capacitated Network Design with Multicast Commodities N2 - This paper addresses the problem of designing a minimum cost network whose capacities are sufficiently large to allow a feasible routing of a given set of multicast commodities. A multicast commodity consists of a set of two or mo re terminals that need to be connected by a so called broadcast tree, which consumes on all of its edges a capacity as large as the demand value associated with that commodity. We model the network design problem with multicast commodities as the problem of packing capacitated Steiner trees in a graph. In the first part of the paper we present three mixed-integer programming formulations for this problem. The first natural formulation uses only one integer capacity variable for each edge and and one binary tree variable for each commodity-edge pair. Applying well-known techniques from the Steiner tree problem, we then develop a stronger directed and a multicommodity flow based mixed-integer programming formulation. In the second part of the paper we study the associated polyhedra and derive valid and even facet defining inequalities for the natural formulation. Finally, we describe separation algorithms for these inequalities and present computational results that demonstrate the strength of our extended formulations. T3 - ZIB-Report - 00-14 KW - multicast network design KW - Steiner tree packing Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5823 ER - TY - GEN A1 - Galliat, Tobias A1 - Deuflhard, Peter T1 - Adaptive hierarchical cluster analysis by Self-Organizing Box Maps N2 - The present paper aims at an extension of {\sc Kohonen's} Self-Organizing Map (SOM) algorithm to be called Self-Organizing Box Map (SOBM) algorithm; it generates box codebooks in lieu of point codebooks. Box codebooks just like point codebooks indirectly define a Voronoi tessellation of the input space, so that each codebook vector represents a unique set of points. Each box codebook vector comprises a multi-dimensional interval that approximates the related partition of the Voronoi tessellation. Upon using the automated cluster identification method that has recently been developed by the authors, the codebook vectors can be grouped in such a way that each group represents a point cluster in the input space. Since the clustering usually depends on the size of the SOM, one cannot be sure, whether the clustering comes out to be optimal. Refinement of part of the identified clusters would often improve the results. This paper presents the concept of an adaptive multilevel cluster algorithm that performs such refinements automatically. Moreover the paper introduces a concept of essential dimensions and suggests a method for their identification based on our herein suggested box codebooks. Applications of the algorithm to molecular dynamics will be described in a forthcoming paper. T3 - ZIB-Report - 00-13 KW - Self-Organizing Maps KW - cluster analysis KW - Voronoi tessellation KW - feature extraction KW - essential dimensions KW - multilevel methods Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5815 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Asymptotic Results and a Markovian Approximation for the M(n)/M(n)/s+GI System N2 - In this paper for the $M(n)/M(n)/s+GI$ system, i.e.\ for a $s$-server queueing system where the calls in the queue may leave the system due to impatience, we present new asymptotic results for the intensities of calls leaving the system due to impatience and a Markovian system approximation where these results are applied. Furthermore, we present a new proof for the formulae of the conditional density of the virtual waiting time distributions, recently given by Movaghar for the less general $M(n)/M/s+GI$ system. Also we obtain new explicit expressions for refined virtual waiting time characteristics as a byproduct. T3 - ZIB-Report - 00-12 KW - M(n)/M(n)/s+GI system KW - limited waiting times KW - finite buffer KW - virtual waiting times KW - blocking- KW - abandon probability KW - impatience rates KW - asymptotic Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5801 ER - TY - GEN A1 - Rusch, Beate T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg: Erste Erfahrungen im Produkionsbetrieb N2 - In diesem Artikel wird der Status des Projekts Kooperativer Bibliotheksverbund Berlin-Brandenburg beschrieben, der im November 1999 mit der KOBV-Suchmaschine seinen produktiven Betrieb aufgenommen hat. Die Recherchemöglichkeiten im WWW werden erläutert, Zugriffszahlen genannt und Entwicklungsperspektiven skizziert. Dieser Bericht entspricht der schriftlichen Fassung eines gleichnamigen Vortrages, der auf dem 1. Gemeinsamen Kongreß der Bundesvereinigung Deutscher Bibliotheksverbände e.V. und der Deutschen Gesellschaft für Informationswissenschaft und Informationspraxis e.V. Information und Öffentlichkeit gehalten wurde, der vom 20. bis 23. März 2000 in Leipzig stattfand. T3 - ZIB-Report - 00-11 KW - Bibliotheksverbund KW - KOBV KW - KOBV-Projekt KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - KOBV-Suchmaschine Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5793 ER - TY - GEN A1 - Konjevod, Goran A1 - Krumke, Sven A1 - Marathe, Madhav T1 - Budget Constrained Minimum Cost Connected Medians N2 - Several practical instances of network design problems require the network to satisfy multiple constraints. In this paper, we address the \emph{Budget Constrained Connected Median Problem}: We are given an undirected graph $G = (V,E)$ with two different edge-weight functions $c$ (modeling the construction or communication cost) and $d$ (modeling the service distance), and a bound~$B$ on the total service distance. The goal is to find a subtree~$T$ of $G$ with minimum $c$-cost $c(T)$ subject to the constraint that the sum of the service distances of all the remaining nodes $v \in V\setminus T$ to their closest neighbor in~$T$ does not exceed the specified budget~$B$. This problem has applications in optical network design and the efficient maintenance of distributed databases. We formulate this problem as bicriteria network design problem, and present bicriteria approximation algorithms. We also prove lower bounds on the approximability of the problem that demonstrate that our performance ratios are close to best possible T3 - ZIB-Report - 00-10 KW - NP-hardness KW - Approximation Algorithms KW - Network Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5783 ER - TY - GEN A1 - Blom, Michiel A1 - Krumke, Sven A1 - Paepe, Willem de A1 - Stougie, Leen T1 - The Online-TSP Against Fair Adversaries N2 - In the online traveling salesman problem requests for visits to cities (points in a metric space) arrive online while the salesman is traveling. The salesman moves at no more than unit speed and starts and ends his work at a designated origin. The objective is to find a routing for the salesman which finishes as early as possible. Performance of algorithms is measured through their competitive ratio, comparing the outcome of the algorithms with that of an adversary who provides the problem instance and therefore is able to achieve the optimal offline solution. Objections against such omnipotent adversaries have lead us to devise an adversary that is in a natural way, in the context of routing problems, more restricted in power. For the exposition we consider the online traveling salesman problem on the metric space given by the non-negative part of the real line. We show that a very natural strategy is~$3/2$-competitive against the conventional adversary, which matches the lower bound on competitive ratios achievable for algorithms for this problem. Against the more ``\emph{fair adversary}'', that we propose, we show that there exists an algorithm with competitive ratio $\frac{1+\sqrt{17}}{4}\approx 1.28$ and provide a matching lower bound. We also show competitiveness results for a special class of algorithms (called zealous algorithms) that do not allow waiting time for the server as long as there are requests unserved. T3 - ZIB-Report - 00-09 KW - Vehicle Routing KW - Online-Algorithms KW - Competitive Analysis Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5779 ER - TY - GEN A1 - Krumke, Sven T1 - News from the Online Traveling Repairman N2 - The traveling repairman problem (TRP) is a variant of the famous traveling salesman problem (TSP). The objective for the TRP is to minimize the latency, that is the the weighted sum of completion times of the cities, where the completion time of a city is defined to be the time in the tour before the city is reached. In the online traveling repairman problem (OLTRP) requests for visits to cities (points in a metric space) arrive online while the repairman is traveling. We analyze the performance of algorithms using competitive analysis, where the cost of an online algorithm is compared to that of an optimal offline algorithm. An optimal offline algorithm knows the entire request sequence in advance and can serve it with minimum cost. Recently, Feuerstein and Stougie presented a $9$-competitive algorithm for the OLTRP on the real line. In this paper we show how to use techniques from online-scheduling to obtain an $8$-competitive deterministic algorithm which works for any metric space. We also present a randomized algorithm which has a competitive ratio of $\frac{4}{\ln 2}\approx 5.7708$ against an oblivious adversary. All of our results also hold for the ``dial-a-ride'' generalization of the OLTRP, where objects have to be picked up and delivered by a server. T3 - ZIB-Report - 00-08 KW - Traveling Repairman KW - Latency KW - Dial-a-Ride-Problem KW - Competitive Analysis Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5767 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin T1 - Progress Towards a Combined MRI/Hyperthermia System N2 - Regional hyperthermia, a clinical cancer therapy, is the main topic of the Sonderforschungsbereich Hyperthermia: Scientific Methods and Clinical Applications'' at Berlin. In recent years, technological improvements towards a better concentration of heat to the desired target region have been achieved. These include a rather sophisticated integrated software environment for therapy planning and a new hyperthermia applicator. In a next step, a detailed closed loop monitoring of the actual treatment is to be developed. For this purpose the hyperthermia applicator is combined with an MRI system, which will allow to check the positioning of the patients and to measure individual blood perfusion as well as the 3D temperature distribution. The measurements will then be employed for an on-line control of the whole treatment. In this intended setting, new fast feedback control algorithms will come into play. T3 - ZIB-Report - 00-07 KW - hyperthermia KW - medical therapy planning KW - applicator design KW - interventional MRI Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5755 ER - TY - GEN A1 - Yevick, David A1 - Friese, Tilmann A1 - Schmidt, Frank T1 - A Comparison of Transparent Boundary Conditions for the Fresnel Equation N2 - We establish the relationship between the transparent boundary condition (BPP) of Baskakov and Popov [Wave Motion 14 (1991) 121-128] and Pakpadakis et. al. [J. Acoust. Soc. Am. 92 (1992) 2030-2038] and a second boundary condition (SDY) introduced by Schmidt and Deuflhard [Comp. Math. Appl. 29 (1995) 53-76] and Schmidt and Yevick [J. Compu. Phys. 134 (1997) 96-107], that is explicitly tailored to the form of the underlying numerical propagation scheme. Our analysis demonstrates that if the domain is first discretized in the propagation direction, the SDY expression can be obtained by applying the exact sequence of steps used to derive the BPP procedure. The BPP method is thus an approximate realization of the computationally far simpler and unconditionally stable SDY boundary condition. T3 - ZIB-Report - 00-05 KW - Fresnel equation KW - transparent boundary condition Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5738 ER - TY - GEN A1 - Schmidt, Frank T1 - Discrete Nonreflecting Boundary Conditions for the Helmholtz Equation N2 - We derive exact discrete nonreflecting boundary conditions for time-harmonic scattering problems modeled by the Helmholtz equation. The main idea is to consider the exterior problem as an initial value problem with initial data given on the boundary of the computational domain. The solution of the exterior problem is obtained via Laplace transformation techniques which supply the boundary conditions in terms of discrete Dirichlet-to-Neumann operators. T3 - ZIB-Report - 00-06 KW - Helmholtz equation KW - transparent boundary consitions KW - finite element method Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5744 ER - TY - GEN A1 - Fischer, Alexander T1 - An Uncoupling-Coupling Technique for Markov Chain Monte Carlo Methods N2 - Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. By determining almost invariant sets of the associated Markov operator, the Monte Carlo sampling splits by a hierarchical annealing process into the essential regions of the state space; therefore UCMC aims at avoiding the typical metastable behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. The correct weighting factors for the various Markov chains are obtained via a coupling matrix, that connects the samplings from the different almost invariant sets. The underlying mathematical structure of this approach is given by a general examination of the uncoupling-coupling procedure. Furthermore, the overall algorithmic scheme of UCMC is applied to the $n$-pentane molecule, a well-known example from molecular dynamics. T3 - ZIB-Report - 00-04 KW - almost invariant sets KW - bridge sampling KW - cluster analysis KW - hierarchical annealing KW - Markov chains KW - Monte Carlo KW - $n$-pentane molecule KW - ratio of no Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5720 ER - TY - GEN A1 - Grötschel, Martin T1 - Verkehrsplanung: Bessere Lösungen mit Mathematik N2 - Anwendungen der Mathematik in der Verkehrs- und Transporttechnologie haben eine große und bedeutende Tradition. Natürlich wurden die ersten Fahrzeuge mit der ingenieurmäßigen Methode von Versuch, Irrtum und Verbesserung entworfen. Aber schon sehr bald kamen mathematische Berechnungen hinzu, mit denen mechanische Eigenschaften von Fahrzeugteilen ermittelt und zum Teil optimiert wurden. Die hierzu erforderliche Mathematik wurde in diesem Jahrhundert zu einem mächtigen Werkzeugkasten ausgebaut. Mit diesem kann man heute z.B. hocheffiziente Motoren mit geringem Schadstoffausstoß entwerfen, aerodynamisch günstige Fahrzeugprofile ermitteln und Flugzeugflügel berechnen, die die gewünschte Last sicher und mit geringem Treibstoffaufwand tragen. Die Mathematik unterstützt die Technologie des Verkehrs beginnend bei globalen Designfragen bis hin zur Spezifizierung von Materialeigenschaften kleinster Bauteile; sie berechnet mit hoher Präzision energieoptimale Bahnen von Raumflugkörpern oder zeitoptimale Trajektorien für Flugzeuge, steuert automatische Roboteranlagen oder innerbetriebliche Transportsysteme. T3 - ZIB-Report - SC-99-54 KW - transportation planning KW - applications of integer programming KW - public transportation Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4439 ER - TY - GEN A1 - Lang, Jens A1 - Merz, Wilhelm T1 - Two-Dimensional Adaptive Simulation of Dopant Diffusion in Silicon N2 - One important step in the fabrication of silicon-based integrated circuits is the creation of semiconducting areas by diffusion of dopant impurities into silicon. Complex models have been developed to investigate the redistribution of dopants and point defects. In general, numerical analysis of the resulting PDEs is the central tool to assess the modelling process. We present an adaptive approach which is able to judge the quality of the numerical approximation and which provides an automatic mesh improvement. Using linearly implicit methods in time and multilevel finite elements in space, we are able to integrate efficiently the arising reaction-drift-diffusion equations with high accuracy. Two different diffusion processes of practical interest are simulated. T3 - ZIB-Report - 00-03 KW - Semiconductor devices KW - nonlinear reaction-drift-diffusion equations KW - mesh control KW - multilevel finite elements KW - Rosenbrock methods Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5716 ER - TY - GEN A1 - Wolf, Thomas T1 - The Symbolic Integration of Exact PDEs N2 - An algorithm is described to decide if a given polynomial differential expression $\Delta$ of multivariate functions is exact, i.e. whether there exists a first integral $P$ such that $D_xP = \Delta$ for any one of a set of variables $x$ and to provide the integral $P$. A generalization is given to allow integration in the case that the exactness is prohibited by terms which contain only functions of not all the independent variables. T3 - ZIB-Report - 00-02 KW - symbolic integration KW - partial differential equations Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5702 ER - TY - GEN A1 - Ehrig, Rainald A1 - Nowak, Ulrich T1 - Algorithmen- und Softwareoptimierung für die Satellitenbahn- und Schwerefeldmodellierung N2 - Dieser Report enthält die Ergebnisse der Untersuchungen, die gemäss dem Forschungs-- und Entwicklungsvertrag Gravity zwischen dem GeoForschungsZentrum Potsdam und dem Konrad--Zuse--Zentrum Berlin vorgenommen wurden. Die damit vereinbarte wissenschaftliche Kooperation hat die folgenden Ziele: \item{die am GFZ vorhandenen Algorithmen und Softwaremodule auf ihre Effizienz hisichtlich Nutzung der Rechnerresourcen zu untersuchen und Lösungen für einen schnelleren Datendurchsatz zu entwickeln und zu implementieren,} \item{Methoden zur Regularisierung und Lösung schlecht konditionierter Normalgleichungssysteme (für Schwerefeldkoeffizienten) kritisch zu untersuchen und eine mathematisch objektive Strategie der Regularisierung zu entwickeln, und} \item{insbesondere im Hinblick auf die Anforderungen bei GRACE, verschiedene Bahnintegrationsverfahren hinsichtlich ihrer numerischen Genauigkeit und Einsatzmöglichkeiten zu untersuchen.} T3 - ZIB-Report - 00-01 KW - geodesy KW - gravity field models KW - regularization KW - ill-posed systems KW - orbit integration Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5694 ER - TY - GEN A1 - Benger, Werner A1 - Hege, Hans-Christian A1 - Heusler, Stefan T1 - Visions of Numerical Relativity 1999 N2 - We present visualizations of recent supercomputer simulations from numerical relativity, exploiting the progress in visualization techniques and numerical methods also from an artistic point of view. The sequences have been compiled into a video tape, showing colliding black holes, orbiting and merging neutron stars as well as collapsing gravitational waves. In this paper we give some background information and provide a glance at the presented sequences. T3 - ZIB-Report - SC-99-53 KW - General Relativity KW - Data Visualization KW - Numerical Simulations Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4429 ER - TY - GEN A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg N2 - Im Herbst 1999 ging der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) in Routinebetrieb. In technischer Hinsicht setzt der KOBV auf ein neuartiges, zukunftsweisendes Verbundkonzept, in dem die zentrale Datenbank mit dem Verbundkatalog ersetzt wird durch verteilte Datenbanken und lokale Kataloge, die durch das Netz (Internet) miteinander verbunden sind. Die zentrale Recherchefunktion wird ersetzt durch die KOBV-Suchmaschine. Beschrieben werden die Hintergründe, die zu diesem Konzept geführt haben, die Kriterien, die die Architekturentscheidungen der Software bestimmt haben, sowie die einzelnen realisierten Komponenten. T3 - ZIB-Report - SC-99-52 KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - KOBV-Suchmaschine KW - Architektur der Suchmaschine KW - Verteilte Suche KW - Gemeinsamer Index Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4418 ER - TY - GEN A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Die KOBV-Suchmaschine geht in Routinebetrieb N2 - Im Herbst 1999 nimmt die KOBV-Suchmaschine, das technische "Herzstück" des KOBV, den Routinebetrieb auf. Nach einer kurzen Einführung in die politischen und rechtlichen Grundlagen des KOBV-Projektes werden in diesem Aufsatz die Funktionalitäten der KOBV-Suchmaschine, ihre Leistungen für Bibliotheksbenutzer und Bibliothekare, vorgestellt. Der Aufsatz schließt mit einem Überblick über den bisherigen Projektverlauf und der Erläuterung der wichtigsten Prinzipien des KOBV - Offenheit, Dezentralität und Heterogenität. T3 - ZIB-Report - SC-99-51 KW - Bibliotheksverbund KW - KOBV KW - KOBV-Projekt KW - KOBV-Suchmaschine KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Suchmaschine Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4407 ER - TY - GEN A1 - Kuberek, Monika T1 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) - Ein innovatives Verbundkonzept für die Region N2 - Auf dem 89. Deutschen Bibliothekartag, der vom 25. bis 29. Mai 1999 in Freiburg (Breisgau) stattgefunden hat, wurde der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) zum ersten Mal der großen bibliothekarischen Öffentlichkeit vorgestellt. Am KOBV-Stand, der im Rahmen des gemeinsamen Standes der Arbeitsgemeinschaft der Verbundsysteme organisiert wurde, führte die KOBV-Projektgruppe Funktionalitäten der KOBV-Suchmaschine vor. In der Vortragsreihe zum Themenkreis XI "Neue Entwicklungen in den Verbund- und Lokalsystemen", die unter Mitwirkung der Arbeitsgemeinschaft der Verbundsysteme veranstaltet wurde, war der KOBV mit einem eigenen Vortrag vertreten: "Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) - Ein innovatives Verbundkonzept für die Region". In dem Vortrag hat die Verfasserin einen umfassenden Überblick über das KOBV-Projekt und den bisherigen Projektverlauf gegeben, die Projektziele und den politischen Rahmen erörtert sowie die KOBV-Suchmaschine, das technische Kernstück des neuen Verbundes, vorgestellt. Der hier vorliegende Text ist die schriftlich ausgearbeitete Fassung dieses Vortrages. T3 - ZIB-Report - SC-99-50 KW - Bibliotheksverbund KW - KOBV KW - KOBV-Projekt KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4399 ER - TY - GEN A1 - Helmberg, Christoph T1 - The m-Cost ATSP N2 - Although the m-ATSP (or multi traveling salesman problem) is well known for its importance in scheduling and vehicle routing, it has, to the best of our knowledge, never been studied polyhedraly, i.e., it has always been transformed to the standard ATSP. This transformation is valid only if the cost of an arc from node $i$ to node $j$ is the same for all machines. In many practical applications this is not the case, machines produce with different speeds and require different (usually sequence dependent) setup times. We present first results of a polyhedral analysis of the m-ATSP in full generality. For this we exploit the tight relation between the subproblem for one machine and the prize collecting traveling salesman problem. We show that, for $m\ge 3$ machines, all facets of the one machine subproblem also define facets of the m-ATSP polytope. In particular the inequalities corresponding to the subtour elimination constraints in the one machine subproblems are facet defining for m-ATSP for $m\ge 2$ and can be separated in polynomial time. Furthermore, they imply the subtour elimination constraints for the ATSP-problem obtained via the standard transformation for identical machines. In addition, we identify a new class of facet defining inequalities of the one machine subproblem, that are also facet defining for m-ATSP for $m\ge 2$. To illustrate the efficacy of the approach we present numerical results for a scheduling problem with non-identical machines, arising in the production of gift wrap at Herlitz PBS AG. T3 - ZIB-Report - SC-99-48 KW - ATSP KW - polyhedral relaxations KW - scheduling KW - nonidentical machines Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4374 ER - TY - GEN A1 - Helmberg, Christoph T1 - Semidefinite Programming N2 - Due to its many applications in control theory, robust optimization, combinatorial optimization and eigenvalue optimization, semidefinite programming had been in wide spread use even before the development of efficient algorithms brought it into the realm of tractability. Today it is one of the basic modeling and optimization tools along with linear and quadratic programming. Our survey is an introduction to semidefinite programming, its duality and complexity theory, its applications and algorithms. T3 - ZIB-Report - SC-99-49 KW - semidefinite programming Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4382 ER - TY - GEN A1 - Stüben, Hinnerk T1 - Decorrelation of the Topological Charge in Tempered Simulations of Full QCD N2 - The improvement of simulations of QCD with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering is studied. As an indicator for decorrelation the topological charge is used. T3 - ZIB-Report - SC-99-47 KW - QCD KW - parallel tempering KW - topological charge Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4369 ER - TY - GEN A1 - Marchand, Hugues A1 - Martin, Alexander A1 - Weismantel, Robert A1 - Wolsey, Laurence T1 - Cutting Planes in Integer and Mixed Integer Programming N2 - This survey presents cutting planes that are useful or potentially useful in solving mixed integer programs. Valid inequalities for i) general integer programs, ii) problems with local structure such as knapsack constraints, and iii) problems with 0-1 coefficient matrices, such as set packing, are examined in turn. Finally the use of valid inequalities for classes of problems with structure, such as network design, is explored. T3 - ZIB-Report - SC-99-44 KW - Mixed Integer Programming KW - Cutting Planes Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4339 ER - TY - GEN A1 - Friese, Tilman A1 - Schmidt, Frank A1 - Yevick, David T1 - Transparent Boundary Conditions for a Wide-Angle Approximation of the One-Way Helmholtz Equation N2 - We present nonlocal discrete transparent boundary conditions for a fourth-order wide-angle approximation of the two-dimensional Helmholtz equation. The boundary conditions are exact in the sense that they supply the same discrete solution on a bounded interior domain as would be obtained by considering the problem on the entire unbounded domain with zero boundary conditions at infinity. The proposed algorithm results in an unconditionally stable propagation method. Numerical examples from optics illustrate the efficiency of our approach. T3 - ZIB-Report - SC-99-45 KW - Helmholtz equation KW - Wide-angle approximation KW - Transparent boundary conditions KW - Finite-element method Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4345 ER - TY - GEN A1 - Schmidt, Frank A1 - Friese, Tilmann A1 - Yevick, David T1 - Transparent Boundary Conditions for Split-Step Pade Approximations of the One-Way Helmholtz Equation N2 - In this paper, we generalize the nonlocal discrete transparent boundary condition introduced by Schmidt and Deuflhard {[}Comp. Math. Appl. 29 (1995) 53-76{]} and Schmidt and Yevick {[}J. Comput. Phys. 134 (1997) 96-107{]} to propagation methods based on arbitrary Pad\'e approximations to the two-dimensional one-way Helmholtz equation. Our approach leads to a recursive formula for the coefficients appearing in the nonlocal condition which then yields an unconditionally stable propagation method. T3 - ZIB-Report - SC-99-46 KW - Helmholtz equation KW - Wide-angle approximation KW - Pad/'e split step approximation KW - Transparent boundary conditions KW - Finite-element method Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4353 ER - TY - GEN A1 - Benger, Werner A1 - Hege, Hans-Christian A1 - Merzky, Andre A1 - Radke, Thomas A1 - Seidel, Edward T1 - Efficient Distributed File I/O for Visualization in Grid Environments N2 - Large scale simulations running in metacomputing environments face the problem of efficient file I/O. For efficiency it is desirable to write data locally, distributed across the computing environment, and then to minimize data transfer, i.e.\ reduce remote file access. Both aspects require I/O approaches which differ from existing paradigms. For the data output of distributed simulations, one wants to use fast local parallel I/O for all participating nodes, producing a single distributed logical file, while keeping changes to the simulation code as small as possible. For reading the data file as in postprocessing and file based visualization, one wants to have efficient partial access to remote and distributed files, using a global naming scheme and efficient data caching, and again keeping the changes to the postprocessing code small. However, all available software solutions require the entire data to be staged locally (involving possible data recombination and conversion), or suffer from the performance problems of remote or distributed file systems. In this paper we show how to interface the HDF5 I/O library via its flexible Virtual File Driver layer to the Globus Data Grid. We show, that combining these two toolkits in a suitable way provides us with a new I/O framework, which allows efficient, secure, distributed and parallel file I/O in a metacomputing environment. T3 - ZIB-Report - SC-99-43 KW - Grid KW - Data Grid KW - Globus KW - HDF5 KW - Cactus KW - CCTK KW - Amira KW - VFD KW - Storage Systems Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4326 ER - TY - GEN A1 - Galliat, Tobias T1 - Clustering Data of Different Information Levels N2 - For using Data Mining, especially cluster analysis, one needs measures to determine the similarity or distance between data objects. In many application fields the data objects can have different information levels. In this case the widely used euclidean distance is an inappropriate measure. The present paper describes a concept how to use data of different information levels in cluster analysis and suggests an appropriate similarity measure. An example from practice is included, that shows the usefulness of the concept and the measure in combination with {\sc Kohonens} Self-Organizing Map algorithm, a well-known and powerful tool for cluster analysis. T3 - ZIB-Report - SC-99-42 KW - cluster analysis KW - Data Mining KW - data preprocessing KW - information theory KW - missing values KW - Self-Organizing Maps KW - similarity measures Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4319 ER - TY - GEN A1 - Powell, Gary A1 - Weiser, Martin T1 - Container Adaptors N2 - The C++ standard template library has many useful containers for data. The standard library includes two adpators, queue, and stack. The authors have extended this model along the lines of relational database semantics. Sometimes the analogy is striking, and we will point it out occasionally. An adaptor allows the standard algorithms to be used on a subset or modification of the data without having to copy the data elements into a new container. The authors provide many useful adaptors which can be used together to produce interesting views of data in a container. T3 - ZIB-Report - SC-99-41 KW - C++ KW - STL KW - views Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4308 ER - TY - GEN A1 - Beck, Rudolf T1 - Algebraic Multigrid by Component Splitting for Edge Elements on Simplicial Triangulations N2 - Our focus is on Maxwell's equations in the low frequency range; two specific applications we aim at are time-stepping schemes for eddy current computations and the stationary double-curl equation for time-harmonic fields. We assume that the computational domain is discretized by triangles or tetrahedrons; for the finite element approximation we choose N\'{e}d\'{e}lec's $H(curl)$-conforming edge elements of the lowest order. For the solution of the arising linear equation systems we devise an algebraic multigrid preconditioner based on a spatial component splitting of the field. Mesh coarsening takes place in an auxiliary subspace, which is constructed with the aid of a nodal vector basis. Within this subspace coarse grids are created by exploiting the matrix graphs. Additionally, we have to cope with the kernel of the $curl$-operator, which comprises a considerable part of the spectral modes on the grid. Fortunately, the kernel modes are accessible via a discrete Helmholtz decomposition of the fields; they are smoothed by additional algebraic multigrid cycles. Numerical experiments are included in order to assess the efficacy of the proposed algorithms. T3 - ZIB-Report - SC-99-40 KW - Algebraic multigrid KW - mesh coarsening KW - edge elements KW - N\'{e}d\'{e}lec spaces KW - Maxwell's equations Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4290 ER - TY - GEN A1 - Schmidt-Ehrenberg, Johannes A1 - Hege, Hans-Christian T1 - Visualizing Quantum Mechanical Phenomena N2 - In this paper we discuss several ways to visualize stationary and non-stationary quantum mechanical systems. We demonstrate an approach for the quantitative interpretation of probability density isovalues which yields a reasonable correlation between isosurfaces for different timesteps. As an intuitive quantity for visualizing the momentum of a quantum system we propose the probability flow density which can be treated by vector field visualization techniques. Finally, we discuss the visualization of non-stationary systems by a sequence of single timestep images. T3 - ZIB-Report - SC-99-39 KW - quantum dynamics KW - isosurfaces KW - probability flow KW - animation Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4287 ER - TY - GEN A1 - Galliat, Tobias A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification N2 - One of the important tasks in Data Mining is automated cluster analysis. Self-Organizing Maps (SOMs) introduced by {\sc Kohonen} are, in principle, a powerful tool for this task. Up to now, however, its cluster identification part is still open to personal bias. The present paper suggests a new approach towards automated cluster identification based on a combination of SOMs with an eigenmode analysis that has recently been developed by {\sc Deuflhard et al.} in the context of molecular conformational dynamics. Details of the algorithm are worked out. Numerical examples from Data Mining and Molecular Dynamics are included. T3 - ZIB-Report - SC-99-38 KW - Self-Organizing Maps KW - cluster analysis Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4279 ER - TY - GEN A1 - Helmberg, Christoph A1 - Kiwiel, K.C. T1 - A Spectral Bundle Method with Bounds N2 - Semidefinite relaxations of quadratic 0-1 programming or graph partitioning problems are well known to be of high quality. However, solving them by primal-dual interior point methods can take much time even for problems of moderate size. The recent spectral bundle method of Helmberg and Rendl can solve quite efficiently large structured equality-constrained semidefinite programs if the trace of the primal matrix variable is fixed, as happens in many applications. We extend the method so that it can handle inequality constraints without seriously increasing computation time. Encouraging preliminary computational results are reported. T3 - ZIB-Report - SC-99-37 KW - Eigenvalue optimization KW - convex optimization Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4256 ER - TY - GEN A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems N2 - The article surveys the development of novel mathematical concepts and algorithmic approaches based thereon in view of their possible applicability to biomolecular design. Both a first deterministic approach, based on the Frobenius-Perron operator corresponding to the flow of the Hamiltonian dynamics, and later stochastic approaches, based on a spatial Markov operator or on Langevin dynamics, can be subsumed under the unified mathematical roof of the transfer operator approach to effective dynamics of molecular systems. The key idea of constructing specific transfer operators especially taylored for the purpose of conformational dynamics appears as the red line throughout the paper. Different steps of the algorithm are exemplified by a trinucleotide molecular system as a small representative of possible RNA drug molecules. T3 - ZIB-Report - SC-99-36 KW - Transfer operator KW - Markov process KW - Markov chain KW - molecular dynamics KW - biomolecular conformations KW - canonical ensemble KW - transition prohability KW - Ha Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4247 ER - TY - GEN A1 - Linke, Matthias A1 - Krebs, Carsten A1 - Schünemann, Marion T1 - Metacomputing zwischen Berlin und Rostock N2 - Das Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) und das Rechenzentrum der Universität Rostock, beide Einrichtungen betreiben massiv-parallele Rechner vom Typ CRAY T3E, haben sich an Hand einer Anwendung aus dem Bereich der Botanik mit den Möglichkeiten der Verteilung auf zwei Parallelrechner, gekoppelt nur über das Breitband-Wissenschaftsnetz des Deutschen Forschungsnetzes, vertraut gemacht. Das Projekt besteht aus zwei Teilen. Im ersten Teil wird ausführlich das zwischen den Rechnern liegende Netz und die Ergebnisse einer Performanceanalyse dieses Netzes dokumentiert. Der zweite Teil beschreibt die Anwendung "Simulation des Wachstums von Pflanzen"' sowie die Ergebnisse der Verteilung dieser Anwendung auf beide Rechner. \begin{center} \bf{Abstract} \end{center} The "'Konrad-Zuse-Zentrum für Informationstechnik Berlin"' (ZIB) and the Computing Centre of the University of Rostock operate high-performance computers of type CRAY T3E. In this project an application from the area of the botany is distributed on two parallel computers, only coupled through the Broadband Science Network of the German Research Network (DFN). This project consists of two parts. In the first part the network which is situated between the computers and the results of a performance analysis is documented in detail. The second part describes the application "'Simulation of the growth of plants"' as well as the results of the distribution of this application to both computers. T3 - ZIB-Report - SC-99-35 KW - Metacomputing KW - Performanceanalyse KW - verteilte Anwendung KW - Latenzzeiten KW - Bandbreite Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4239 ER - TY - GEN A1 - Deuflhard, Peter T1 - Differential Equations in Technology and Medicine. Computational Concepts, Adaptive Algorithms, and Virtual Labs N2 - This series of lectures has been given to a class of mathematics postdocs at a European summer school on Computational Mathematics Driven by Industrial Applications in Martina Franca, Italy (organized by CIME). It deals with a variety of challenging real life problems selected from clinical cancer therapy, communication technology, polymer production, and pharmaceutical drug design. All of these problems from rather diverse application areas share two common features: (a) they have been modelled by various differential equations -- elliptic, parabolic, or Schrödinger--type partial differential equations, countable ordinary diffential equations, or Hamiltonian systems, (b) their numerical solution has turned out to be real challenge to computational mathematics. T3 - ZIB-Report - SC-99-34 KW - differential equations: KW - ordinary KW - partial KW - countable KW - hamiltonian KW - finite element methods: KW - adaptive KW - multilevel KW - grid generation KW - medical t Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4223 ER - TY - GEN A1 - Zöckler, Malte A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast and Intuitive Generation of Geometric Shape Transitions N2 - We describe a novel method for continuously transforming two triangulated models of arbitrary topology into each other. Equal global topology for both objects is assumed, extensions for genus changes during metamorphosis are provided. The proposed method addresses the major challenge in 3D metamorphosis, namely specifying the morphing process intuitively, with minimal user interaction and sufficient detail. Corresponding regions and point features are interactively identified. These regions are parametrized automatically and consistently, providing a basis for smooth interpolation. Utilizing suitable 3D interaction techniques a simple and intuitive control over the whole morphing process is offered. T3 - ZIB-Report - SC-99-33 KW - morphing KW - surface parametrization KW - shape transition Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4219 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Der Schnellste Weg zum Ziel N2 - Wir geben eine Einführung in die Mathematik von und mit Wegen. Nicht auf dem kürzesten, aber auf einem hoffentlich kurzweiligen Weg! T3 - ZIB-Report - SC-99-32 KW - Kürzeste Wege KW - Kombinatorische Optimierung KW - Operations Research Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4209 ER - TY - GEN A1 - Steinbach, Marc T1 - Markowitz Revisited: Single-Period and Multi-Period Mean-Variance Models N2 - Mean-variance portfolio analysis provided the first quantitative treatment of the tradeoff between profit and risk. We investigate in detail the interplay between objective and constraints in a number of single-period variants, including semi-variance models. Particular emphasis is laid on avoiding the penalization of overperformance. The results are then used as building blocks in the development and theoretical analysis of multi-period models based on scenario trees. A key property is the possibility to remove surplus money in future decisions, yielding approximate downside risk minimization. T3 - ZIB-Report - SC-99-30 KW - mean-variance analysis KW - downside risk KW - multi-period model Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4183 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - Solving the Asymmetric Travelling Salesman Problem with Time Windows by Branch-and-Cut N2 - Many optimization problems have several equivalent mathematical models. It is often not apparent which of these models is most suitable for practical computation, in particular, when a certain application with a specific range of instance sizes is in focus. Our paper addresses the Asymmetric Travelling Salesman Problem with time windows (ATSP-TW) from such a point of view. The real--world application we aim at is the control of a stacker crane in a warehouse. We have implemented codes based on three alternative integer programming formulations of the ATSP-TW and more than ten heuristics. Computational results for real-world instances with up to 233 nodes are reported, showing that a new model presented in a companion paper outperforms the other two models we considered --- at least for our special application --- and that the heuristics provide acceptable solutions. T3 - ZIB-Report - SC-99-31 KW - Asymmetric Travelling Salesman Problem KW - Time Windows KW - Integer Programs KW - Branch&Cut-Algorithm KW - Heuristics KW - Control of Stacker Cranes Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4191 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Stüben, Hinnerk T1 - Decorrelation of the topological charge in tempered Hybrid Monte Carlo simulations of QCD N2 - We study the improvement of simulations of QCD with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering. As an indicator for decorrelation we use the topological charge. T3 - ZIB-Report - SC-99-28 KW - QCD KW - parallel tempering KW - topological charge Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4168 ER - TY - GEN A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Wo bleibt der Aufzug? N2 - Dieser Artikel gibt eine allgemeinverständliche Einführung in die spezielle Problematik kombinatorischer Online-Problem am Beispiel der Fahrstuhlsteuerung. T3 - ZIB-Report - SC-99-29 KW - Aufzugsteuerung KW - Online-Optimierung KW - Echtzeit-Optimierung KW - kompetitive Analyse Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4175 ER - TY - GEN A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - On Conformational Dynamics induced by Langevin Processes N2 - The function of many important biomolecules is related to their dynamic properties and their ability to switch between different {\em conformations}, which are understood as {\em almost invariant} or {\em metastable} subsets of the positional state space of the system. Recently, the present authors and their coworkers presented a novel algorithmic scheme for the direct numerical determination of such metastable subsets and the transition probability between them. Although being different in most aspects, this method exploits the same basic idea as {\sc Dellnitz} and {\sc Junge} in their approach to almost invariance in discrete dynamical systems: the almost invariant sets are computed via certain eigenvectors of the Markov operators associated with the dynamical behavior. In the present article we analyze the application of this approach to (high--friction) Langevin models describing the dynamical behavior of molecular systems coupled to a heat bath. We will see that this can be related to theoretical results for (symmetric) semigroups of Markov operators going back to {\sc Davies}. We concentrate on a comparison of our approach in respect to random perturbations of dynamical systems. T3 - ZIB-Report - SC-99-25 KW - Smoluchowski equation KW - Fokker--Planck equation KW - semigroup of Markov operators KW - canonical ensemble KW - small noise KW - first exit time KW - half time perio Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4130 ER - TY - THES A1 - Gatermann, Karin T1 - Computer Algebra Methods for Equivariant Dynamical Systems N2 - An introductory chapter on Groebner bases is given which also includes new results on the detection of Groebner bases for sparse polynomial systems. Algorithms for the computation of invariants and equivariants for finite groups, compact Lie groups and algebraic groups are presented and efficient implementation and time comparision are discussed. This chapter also inlcudes improvements of the computation of Noether normalisation and Stanley decomposition. These results are applied in symmetric bifurcation theory and equivariant dynamics. As preparation of the investigation of the orbit space reduction three methods are compared for solving symmetric polynomial systems exactly. The method of orbit space reduction is improved by using the Cohen-Macaulayness of the invariant ring and nested Noether normalization. Finally this is applied for a case of mode interaction in the Taylor-Couette problem. T3 - ZIB-Report - SC-99-26 KW - Groebner bases KW - algorithmic invariant theory KW - equivariant dynamics KW - orbit space reduction Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4140 ER - TY - GEN A1 - Gatermann, Karin A1 - Huber, Birkett T1 - A family of sparse polynomial systems arising in chemical reaction systems N2 - A class of sparse polynomial systems is investigated which is defined by a weighted directed graph and a weighted bipartite graph. They arise in the model of mass action kinetics for chemical reaction systems. In this application the number of real positive solutions within a certain affine subspace is of particular interest. We show that the simplest cases are equivalent to binomial systems while in general the solution structure is highly determined by the properties of the two graphs. First we recall results by Feinberg and give rigorous proofs. Secondly, we explain how the graphs determine the Newton polytopes of the system of sparse polynomials and thus determine the solution structure. The results on positive solutions from real algebraic geometry are applied to this particular situation. Examples illustrate the theoretical results. T3 - ZIB-Report - SC-99-27 KW - mass action kinetics KW - sparse polynomial systems KW - positive solutions Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4150 ER - TY - GEN A1 - Grötschel, Martin A1 - Dalitz, Wolfgang T1 - Math-Net Abschlussbericht N2 - Das Math-Net ist ein verteiltes Informationssystem f"ur die Mathematik. Es basiert auf den lokalen Informationsangeboten der Fachbereiche, die im Math-Net integriert, nutzerfreundlich aufbereitet und zug"anglich gemacht werden sollen. Das Math-Net ist durch die freiwillige Mitarbeit weiterer Institutionen in Deutschland zu einem flächendeckenden Dienst ausgebaut worden. Die am Projekt beteiligten Institutionen haben die mathematischen Institutionen in ihrer Region beim Aufbau eines qualitativ hochwertigen lokalen Informationsangebotes unterstützt und die Integration der lokalen Informationsangebote in das Math-Net koordiniert. T3 - ZIB-Report - SC-99-24 KW - Information System KW - Math-Net KW - Math-Net-Links KW - Dublin Core KW - Harvest Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4120 ER - TY - GEN A1 - Meyer, Michael T1 - Ab Initio Study of Flavonoids N2 - Flavone and the flavylium ion have been studied at Hartree-Fock, M{\o}ller-Plesset and B3LYP hybrid density functional level to determine the structures and barriers to internal rotation. Both molecules have a high perpendicular barrier about the single bond connecting the phenyl ring with the benzopyrone and benzopyrylium ring, respectively. In contrast to biphenyl both molecules have low coplanar barriers. B3LYP overestimates the perpendicular barrier heights compared to other methods. The dependence of the population and orbital energies on the torsion has been investigated and the structures of both flavonoids have been estimated by means of a reaction field model. T3 - ZIB-Report - SC-99-23 KW - flavonol KW - conformation KW - reaction field KW - structure Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4110 ER - TY - GEN A1 - Beck, Rudolf T1 - Graph-Based Algebraic Multigrid for Lagrange-Type Finite Elements on Simplicial Meshes N2 - We present an algebraic multigrid preconditioner which uses only the graphs of system matrices. Some elementary coarsening rules are stated, from which an advancing front algorithm for the selection of coarse grid nodes is derived. This technique can be applied to linear Lagrange-type finite element discretizations; for higher-order elements an extension of the multigrid algorithm is provided. Both two- and three-dimensional second order elliptic problems can be handled. Numerical experiments show that the resulting convergence acceleration is comparable to classical geometric multigrid. T3 - ZIB-Report - SC-99-22 KW - Algebraic multigrid KW - mesh coarsening KW - preconditioning Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4100 ER - TY - GEN A1 - Schneider, Wolfram T1 - Ein verteiltes Bibliotheks-Informationssystem auf Basis des Z39.50 Protokolls N2 - \\{\bf Zusammenfassung: }Diese Diplomarbeit beschreibt ein verteiltes Bibliotheks-Informationssystem für bibliographische Datenbanken im Internet. Der Name des Systems ist ZACK. Der Benutzer kann mit ZACK in einer oder mehreren bibliographischen Datenbanken nach einem Dokument suchen und die Treffer in die eigene lokale Datenbank übernehmen. Mit der Übernahme der Datensätze aus einer fremden Datenbank wird die Erfassung neuer Dokumente wesentlich erleichtert, da die Eigenkatalogisierung auf ein Minimum beschränkt werden kann. Es wird doppelte Arbeit vermieden, und die Datensätze haben eine gleichbleibend hohe Qualität. Bei der verteilten Suche mit ZACK wird parallel in mehreren Datenbanken gesucht. Dubletten werden als solche erkannt. Dem Benutzer wird eine übersichtliche Kurztrefferliste ohne doppelte Einträge angeboten. Er kann dann selbst entscheiden, aus welcher Datenbank er die Datensätze übernimmt. Die verteilte Suche hat in der Praxis eine deutlich bessere Trefferquote gebracht als die Suche in nur einer Datenbank. Dabei bleibt die Antwortzeit in einem für den Benutzer akzeptablen Rahmen. Die Kurztrefferliste wird durch die Dublettenkontrolle kürzer und übersichtlicher. English Title: A Distributed Library Information System on the Basis of the Z39.50 Protocol This diploma thesis desribes a distributed library information system for bibliographic databases in the Internet. The name of the system is ZACK. With ZACK the user is able to search for a particular document in several databases and to include the matches in his/her own local database. The inclusion of data records from an external database makes the capture of new documents much easier, as internal cataloging is reduced to a minimum. Double work is eliminated and a continuously high quality of data record is ensured. The distributed search by means of ZACK is carried out in several databases in parallel. Duplicates are recognized; and a short list of matches without double entries is offered. The user can then decide for himself from which database to include data records. In practice, a distributed search has produced far better results than the search in one particular database. Response times are within an acceptable limit for the user. The short list of hits is made clearer and more concise by the duplicate check. The diploma thesis is also available in PDF, HTML, and ASCII format: http://wolfram.schneider.org/lv/diplom/ . T3 - ZIB-Report - SC-99-21 KW - Z39.50 KW - duplication KW - distributed library KW - search engine KW - Dubletten KW - parallel Suche KW - verteiltes Bibliothekssystem KW - Metasuchmaschine Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4092 ER - TY - THES A1 - Lang, Jens T1 - Adaptive Multilevel Solution of Nonlinear Parabolic PDE Systems. Theory, Algorithm, and Applications N2 - This monograph has been written to illustrate the interlocking of theory, algorithm, and application in developing solution techniques for complex PDE systems. A deep theoretical understanding is necessary to produce a powerful idea leading to a successful algorithm. Efficient and robust implementation is the key to make the algorithm perform satisfactorily. The extra insight obtained by solving real--life problems brings out the structure of the method more clearly and suggests often ways to improve the numerical algorithm. It is my intention to impart the beauty and complexity found in both the theoretical investigation of the adaptive algorithm proposed here, i.e., the coupling of Rosenbrock methods in time and multilevel finite elements in space, and its realization. I hope that this method will find many more interesting applications. T3 - ZIB-Report - SC-99-20 KW - Adaptive multilevel finite elements KW - Rosenbrock methods KW - a posteriori error estimates KW - Rothe method Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4089 ER - TY - GEN A1 - Deuflhard, Peter A1 - Klein, Rupert A1 - Reinefeld, Alexander A1 - Stüben, Hinnerk T1 - Power-User und Supercomputer N2 - Abstract-Sammlung zum gleichnamigen Workshop am ZIB vom 19.--20. Mai 1999 T3 - ZIB-Report - SC-99-19 KW - Benutzertreffen KW - Höchstleistungsrechner Nord KW - HLRN Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4070 ER - TY - THES A1 - Schütte, Christof T1 - Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules N2 - The function of many important biomolecules comes from their dynamic properties and their ability to switch between different {\em conformations}. In a conformation, the large scale geometric structure of the molecule is understood to be conserved, whereas on smaller scales the system may well rotate, oscillate or fluctuate. In a recent article [J. Comp. Phys., 151,1 (1999)], the present author and coworkers demonstrated that (a) conformations can be understood as almost invariant sets of some Markov chain being defined via the Hamiltonian system governing the molecular dynamics and that (b) these sets can efficiently be computed via eigenvectors of the corresponding Markov operator. The persent manuscript reviews the mathematical modelling steps behind the novel concept, includes a rigorous analytical justification of this approach and especially of the numerical details of the algorithm, and illustrates its performance when applied to realistic molecular systems. T3 - ZIB-Report - SC-99-18 KW - biochemical conformation KW - almost invariant set KW - Markov chain KW - Hamiltonian system KW - Markov operator KW - quasi-compact operator KW - Perron root KW - Perron- Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4063 ER - TY - GEN A1 - Grötschel, Martin T1 - My Favorite Theorem: Characterizations of Perfect Graphs N2 - This paper summarizes and discusses various characterizations of perfect graphs and mentions some open problems in this area. T3 - ZIB-Report - SC-99-17 KW - graph theory KW - perfect graphs KW - integer programming Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4053 ER - TY - GEN A1 - Kuberek, Monika T1 - Gemeinsamer KOBV-Standard N2 - Der neue ''verteilte'' Bibliotheksverbund KOBV erfordert neue Arbeitsweisen und neue Formen der Zusammenarbeit der Bibliotheken untereinander. Im KOBV wird es keine zentrale Erschließung geben, sondern die Erschließung wird lokal, in den Bibliotheken durchgeführt. Entsprechend ihren Nutzerbedürfnissen bestimmen die Bibliotheken die Erschließungsart, den Erschließungsumfang und die Erschließungstiefe selbst. Als gemeinsamer regionaler Standard wird lediglich ein ''Mindeststandard'' auf der Basis von RAK-WB definiert. Dieser Gemeinsame KOBV-Standard berücksichtigt vor allem suchrelevante Elemente, um den Nutzern im KOBV möglichst einheitliche Sucheinstiege zu bieten. Der Gemeinsame KOBV-Standard wird in diesem Papier vorgestellt. T3 - ZIB-Report - SC-99-14 KW - Bibliotheksverbund KW - Erschließung KW - KOBV KW - KOBV-Standard KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Verbundkooperation Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4027 ER - TY - GEN A1 - Kuberek, Monika T1 - Umgang mit hierarchischen Strukturen des MAB2-Datenformates in der KOBV-Suchmaschine N2 - Die KOBV-Suchmaschine verarbeitet Daten im bibliographischen Datenformat MAB2 (Maschinelles Austauschformat für Bibliotheken, Ausgabe 2), das in deutschsprachigen Ländern angewandt wird. Im MAB2-Format sind für mehrbändige begrenzte Werke und fortlaufende Sammelwerke hierarchische Strukturen realisiert - mit bis zu drei Hierarchiestufen und unterschiedlichem Aufbau, je nachdem, ob es sich um ein begrenztes Werk oder um ein Werk ohne geplanten Abschluß handelt. Jede hierarchische Stufe entspricht einem Datensatz, die zusammengehörigen Datensätze sind miteinander verknüpft. Inhaltlich enthält eine Stufe oft nur Teilinformationen des Werkes; erst die Stufen zusammen ergeben die vollständige Information. In der KOBV-Suchmaschine werden Dokumente aus verschiedenen Bibliotheken zusammengeführt. Hierarchische Strukturen potenzieren gewissermaßen die mit der Dublettenbehandlung (Match- und Merge-Verfahren) verbundene Problematik: Es müssen nicht nur Datensätze aus verschiedenen Bibliotheken zusammengeführt werden, sondern darüber hinaus die zusammengehörigen Datensätze der unterschiedlichen Hierarchiestufen. Der Artikel enthält eine ausführliche Analyse der in MAB2 vorkommenden hierarchischen Strukturen, beschreibt die Anforderungen für die Lieferung hierarchischer Datensätze aus den lokalen Systemen und stellt das Verfahren vor, wie in der KOBV-Suchmaschine mit diesen hierarchischen Datenstrukturen bei der Dublettenbehandlung umgegangen wird. Anhand von Fallbeispielen wird die Problematik der Verknüpfung zusammengeführter h-Sätze erörtert. Die KOBV-Suchmaschine verarbeitet Daten im bibliographischen Datenformat MAB2 (Maschinelles Austauschformat für Bibliotheken, Ausgabe 2), das in deutschsprachigen Ländern angewandt wird. Im MAB2-Format sind für mehrbändige begrenzte Werke und fortlaufende Sammelwerke hierarchische Strukturen realisiert - mit bis zu drei Hierarchiestufen und unterschiedlichem Aufbau, je nachdem, ob es sich um ein begrenztes Werk oder um ein Werk ohne geplanten Abschluß handelt. Jede hierarchische Stufe entspricht einem Datensatz, die zusammengehörigen Datensätze sind miteinander verknüpft. Inhaltlich enthält eine Stufe oft nur Teilinformationen des Werkes; erst die Stufen zusammen ergeben die vollständige Information. In der KOBV-Suchmaschine werden Dokumente aus verschiedenen Bibliotheken zusammengeführt. Hierarchische Strukturen potenzieren gewissermaßen die mit der Dublettenbehandlung (Match- und Merge-Verfahren) verbundene Problematik: Es müssen nicht nur Datensätze aus verschiedenen Bibliotheken zusammengeführt werden, sondern darüber hinaus die zusammengehörigen Datensätze der unterschiedlichen Hierarchiestufen. Der Artikel enthält eine ausführliche Analyse der in MAB2 vorkommenden hierarchischen Strukturen, beschreibt die Anforderungen für die Lieferung hierarchischer Datensätze aus den lokalen Systemen und stellt das Verfahren vor, wie in der KOBV-Suchmaschine mit diesen hierarchischen Datenstrukturen bei der Dublettenbehandlung umgegangen wird. Anhand von Fallbeispielen wird die Problematik der Verknüpfung zusammengeführter h-Sätze erörtert. T3 - ZIB-Report - SC-99-15 KW - Bibliographisches Datenformat KW - Datenformat KW - Deduplication KW - Dublettenbehandlung KW - Hierarchische Struktur KW - KOBV KW - KOBV-Suchmaschine KW - Kooperativer B Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4030 ER - TY - GEN A1 - Kuberek, Monika T1 - Dublettenbehandlung (Match- und Merge-Verfahren) in der KOBV-Suchmaschine - Grundlagen - N2 - Die Recherche über die KOBV-Suchmaschine liefert Datensätze aus unterschiedlichen Bibliotheken. Damit der Nutzer nicht viele, unter Umständen lange Listen für jede Bibliothek durchblättern muss werden die Datensätze in der KOBV-Suchmaschine einer Dublettenbehandlung (Match- und Merge-Verfahren) unterzogen. Ziel dieses Verfahrens ist es, dem Nutzer möglichst nur einen einzigen Datensatz mit allen zugehörigen Bestandsnachweisen aus den Bibliotheken anzuzeigen. In dem vorliegenden Papier steht das Match-Verfahren, das von der KOBV-Projektgruppe eigens für den Einsatz in der KOBV-Suchmaschine entwickelt wurde, im Vordergrund. Das Merge-Verfahren, das auf Konzepte von Ex Libris zurückgeht, ist lediglich am Rande erwähnt. Ziel bei der Entwicklung des Match- und Merge-Verfahrens war es, in der KOBV-Suchmaschine ein Verfahren zu implementieren, das vollkommen automatisiert, ohne Zuhilfenahme manueller und intellektueller Eingriffe, abläuft. In diesem Papier sind die Grundlagen zum Match- und Merge-Verfahren in der KOBV-Suchmaschine zusammengefaßt. Zunächst wird definiert, was unter einer Dublette überhaupt zu verstehen ist. Die Begriffe Dokument und Werk werden analysiert, die wesentlich sind für die Entscheidung, welche Datensätze in der KOBV-Suchmaschine letztendlich zusammengeführt werden. Anhand umfassender Literaturrecherchen werden die zur Dublettenbehandlung herangezogenen bibliographischen Beschreibungselemente (Attribute) in verschiedenen MARC- und MAB-Datenbanken ermittelt und grundsätzliche Probleme beim Erkennen dubletter bibliographischer Datensätze aufgezeigt. Schließlich werden Verfahren vorgestellt und diskutiert, wie die Attribute in das Match- und Merge-Verfahren eingebunden werden: bei nur einer Gewichtung (positiver Wert) und bei zwei Gewichtungen (positiver und negativer Wert). Auf dieser Basis werden Tabellen mit Werten für zwei unterschiedliche Gewichtungsverfahren in der KOBV-Suchmaschine entwickelt, die als Ausgangswerte für erste Testverfahren in den Match- und Merge-Algorithmus in der KOBV-Suchmaschine implementiert werden. T3 - ZIB-Report - SC-99-16 KW - Dublettenbehandlung KW - KOBV KW - KOBV-Suchmaschine KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Match- und Merge-Verfahren Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4042 ER - TY - GEN A1 - Rusch, Beate T1 - Normierungen von Zeichenfolgen als erster Schritt des Match - Zur Dublettenbehandlung im Kooperativen BibliotheksverbundBerlin-Brandenburg - N2 - Im Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) wird die verteilte Suche in heterogenen Datenbank mit einer integrierten Dublettenerkennung und -zusammenfuehrung realisiert. Beschrieben werden die einzelnen attributspezifischen Normierungsschritte, die dem eigentlichen Vergleich (MATCH) zweier Datensätze vorangehen. T3 - ZIB-Report - SC-99-13 KW - normalization of strings KW - de-duplication method KW - distributed library system Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4010 ER - TY - GEN A1 - Backhaus, Peter A1 - Schmidt, Burkhard A1 - Dantus, Marcos T1 - Control of photoassociation yield: A quantum-dynamical study of the mercury system to explore the role of pulse duration from nanoseconds to femtoseconds N2 - The photoassociation process shows strong dependence on the temporal duration of the electromagnetic field pulses and their frequencies. This dependence is investigated using quantum mechanical simulations that include all ranges of impact parameters and contributions from bound-to-bound transitions. The photoassociation yield of mercury atoms to produce excimer dimers is enhanced for short (ps) and for ultrashort (fs) pulse durations. Ultrashort laser pulses effectively overlap the entire range of free-to-bound transition, therefore achieving a maximum probability. Short pulses show a maximum in the photoassociation yield when their carrier frequency overlaps a particular free-to-bound spectroscopic resonance. Implications of these calculations on efforts to control bimolecular reactions are discussed. T3 - ZIB-Report - SC-99-12 KW - photoassociation KW - laser pulse control Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4001 ER - TY - GEN T1 - Jahresbericht 1998 T3 - Jahresbericht - 1998 KW - Annual Report Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9731 SN - 0934-5892 ER - TY - GEN A1 - Schmidt, Burkhard A1 - Zdanska, Petra T1 - Solution of the Time-Dependent Schroedinger Equation for Highly Symmetric Potentials N2 - The method of symmetry adapted wavepackets (SAWP) to solve the time-dependent Schrödinger equation for a highly symmetric potential energy surface is introduced. The angular dependence of a quantum-mechanical wavepackets is expanded in spherical harmonics where the number of close-coupled equations for the corresponding radial functions can be efficiently reduced by symmetry adaption of the rotational basis using the SWAP approach. Various techniques to generate symmetry adapted spherical harmonics (SASHs) for the point groups of highest symmetry (octahedral, icosahedral) are discussed. The standard projection operator technique involves the use of Wigner rotation matrices. Two methods to circumvent numerical instabilities occuring for large azimuthal quantum numbers are suggested. The first is based on a numerical scheme which employs Gaussian integrations yielding exact and stable results. The second is a recursive algorithm to generate higher order SASHs accurately and efficiently from lower order ones. The paper gives a complete set of ``seed functions'' generated by projection techniques which can be used obtain SASHs for all irreducible representations of the octahedral and icosahedral point groups recursively. T3 - ZIB-Report - SC-99-11 KW - Schroedinger Equation KW - quantum mechanics KW - symmetry KW - group theory Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3996 ER - TY - GEN A1 - Schütte, Christof T1 - Partial Wigner Transforms and the Quantum--Classical Liouville Equation N2 - In molecular dynamics applications there is a growing interest in mixed quantum-classical models. The {\em quantum-classical Liouville equation} (QCL) describes most atoms of the molecular system under consideration by means of classical phase space density but an important, small portion of the system by means of quantum mechanics. The QCL is derived from the full quantum dynamical (QD) description by applying the Wigner transform to the classical part'' of the system only. We discuss the conditions under which the QCL model approximates the full QD evolution of the system. First, analysis of the asymptotic properties of the Wigner transform shows that solving the QCL yields a first order approximation of full quantum dynamics. Second, we discuss the adiabatic limit of the QCL. This discussion shows that the QCL solutions may be interpretated as classical phase space densities, at least near the adiabatic limit. Third, it is demonstrated that the QCL yields good approximations of {\em non-adiabatic quantum effects,} especially near so-called {\em avoided crossings} where most quantum-classical models fail. T3 - ZIB-Report - SC-99-10 KW - QCMD KW - quantum-classical Liouville equation KW - surface hopping KW - Wigner transform KW - asymptotic expansion KW - nonadiabatic effects Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3983 ER - TY - GEN A1 - Hauptmeier, Dietrich A1 - Krumke, Sven A1 - Rambau, Jörg T1 - The Online Dial-a-Ride Problem under Reasonable Load N2 - In this paper, we analyze algorithms for the online dial-a-ride problem with request sets that fulfill a certain worst-case restriction: roughly speaking, a set of requests for the online dial-a-ride problem is reasonable if the requests that come up in a sufficiently large time period can be served in a time period of at most the same length. This new notion is a stability criterion implying that the system is not overloaded. The new concept is used to analyze the online dial-a-ride problem for the minimization of the maximal resp.\ average flow time. Under reasonable load it is possible to distinguish the performance of two particular algorithms for this problem, which seems to be impossible by means of classical competitive analysis. T3 - ZIB-Report - SC-99-08 KW - online optimization KW - competitive analysis KW - elevator Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3961 ER - TY - GEN A1 - Grötschel, Martin A1 - Hauptmeier, Dietrich A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Simulation Studies for the Online-Dial-a-Ride Problem N2 - In a large distribution center of Herlitz AG, Berlin, we invesigated the elevator subsystem of the fully automated pallet transportation system. Each elevator may carry one pallet and has to serve eight levels. The goal is to minimize the average resp.\ the maximum flow time. The variants of this elevator control problem have been subject of recent theoretical research and are known as online-dial-a-ride problems. In this paper we investigate several online algorithms for several versions of online-dial-a-ride problems by means of a simulation program, developed on the basis of the simulation library AMSEL. We draw statistics from samples of randomly generated data providing for different load situations. Moreover, we provide preliminary studies with real production data for a system of five elevators connected by a conveyor circuit, as can be found at the Herlitz plant. We show which algorithms are best under certain load situations and which lead to break downs under particular circumstances. T3 - ZIB-Report - SC-99-09 KW - online optimization KW - competitive analysis KW - elevator KW - simulation studies Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3976 ER - TY - GEN A1 - Braess, Dietrich A1 - Deuflhard, Peter A1 - Lipnikov, Konstantin T1 - A Subspace Cascadic Multigrid Method for Mortar Elements N2 - A cascadic multigrid (CMG) method for elliptic problems with strong material jumps is proposed and analyzed. Non--matching grids at interfaces between subdomains are allowed and treated by mortar elements. The arising saddle point problems are solved by a subspace confined conjugate gradient method as smoother for the CMG. Details of algorithmic realization including adaptivity are elaborated. Numerical results illustrate the efficiency of this CMG algorithm. T3 - ZIB-Report - SC-99-07 KW - Finite Elements KW - Rayleigh-Ritz and Galerkin Methods KW - Multigrid Methods KW - Domain Decomposition Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3954 ER - TY - GEN A1 - Hauptmeier, Dietrich A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Wirth., Hans-Christoph T1 - Euler is Standing in Line N2 - In this paper we study algorithms for ``Dial-a-Ride'' transportation problems. In the basic version of the problem we are given transportation jobs between the vertices of a graph and the goal is to find a shortest transportation that serves all the jobs. This problem is known to be NP-hard even on trees. We consider the extension when precedence relations between the jobs with the same source are given. Our results include a polynomial time algorithm on paths and an approximation algorithm on general graphs with a performance of~$9/4$. For trees we improve the performance to~$5/3$. T3 - ZIB-Report - SC-99-06 KW - NP-completeness KW - polynomial-time approximation algorithms KW - stacker-crane problem KW - vehicle routing KW - elevator system KW - Eulerian Cycle Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3947 ER - TY - GEN A1 - Lohrum, Stefan A1 - Schneider, Wolfram A1 - Willenborg, Josef T1 - De-duplication in KOBV N2 - In KOBV we offer the user an efficient tool for searching regional and worldwide accessible library catalogues (KOBV search engine). Search is performed by a distributed Z39.50 retrieval and an index based quicksearch. Due to the number of catalogues, result sets may contain a significant amount of duplicate records. Therefore we integrate a de-duplication procedure into KOBV search engine. It is part of the distributed search and the KOBV quicksearch as well. Main goals are the presentation of uniform retrieval results, the preservation of retrieval quality and cutting off redundant information. At least we keep an eye on efficiency. De-duplication is fully parametrizable, so that settings can be changed easily on line. T3 - ZIB-Report - SC-99-05 KW - de-duplication method KW - distributed library system KW - clustering Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3931 ER - TY - GEN A1 - Seewald, Frank A1 - Pollei, Anja A1 - Kraume, Matthias A1 - Mittelbach, Walter A1 - Lang., Jens T1 - Numerical Calculation of the Heat Transfer in an Adsorption Energy Storage with KARDOS N2 - A new seasonal energy storage for thermal solar systems has been developed on the basis of an adsorption-desorption process. Design and optimization of this storage will be supported by numerical simulations of heat and mass transfer with KARDOS. This paper focuses on the unsteady heat transfer during the major operating step of energetic discharge of the storage, which is characterized by conductive heat transfer in the fixed bed and a strong heat source caused by the adsorption enthalpy. Results are interpreted concerning the influence of variations in the parameter set. The method of implementation of the differential equation will be shown as well as the post-processing and gridwriting programs. T3 - ZIB-Report - SC-99-04 Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3927 ER - TY - THES A1 - Martin, Alexander T1 - Integer Programs with Block Structure N2 - In this thesis we study and solve integer programs with block structure, i.\,e., problems that after the removal of certain rows (or columns) of the constraint matrix decompose into independent subproblems. The matrices associated with each subproblem are called blocks and the rows (columns) to be removed linking constraints (columns). Integer programs with block structure come up in a natural way in many real-world applications. The methods that are widely used to tackle integer programs with block structure are decomposition methods. The idea is to decouple the linking constraints (variables) from the problem and treat them at a superordinate level, often called master problem. The resulting residual subordinate problem then decomposes into independent subproblems that often can be solved more efficiently. Decomposition methods now work alternately on the master and subordinate problem and iteratively exchange information to solve the original problem to optimality. In Part I we follow a different approach. We treat the integer programming problem as a whole and keep the linking constraints in the formulation. We consider the associated polyhedra and investigate the polyhedral consequences of the involved linking constraints. The variety and complexity of the new inequalities that come into play is illustrated on three different types of real-world problems. The applications arise in the design of electronic circuits, in telecommunication and production planning. We develop a branch-and-cut algorithm for each of these problems, and our computational results show the benefits and limits of the polyhedral approach to solve these real-world models with block structure. Part II of the thesis deals with general mixed integer programming problems, that is integer programs with no apparent structure in the constraint matrix. We will discuss in Chapter 5 the main ingredients of an LP based branch-and-bound algorithm for the solution of general integer programs. Chapter 6 then asks the question whether general integer programs decompose into certain block structures and investigate whether it is possible to recognize such a structure. The remaining two chapters exploit information about the block structure of an integer program. In Chapter 7 we parallelize parts of the dual simplex algorithm, the method that is commonly used for the solution of the underlying linear programs within a branch-and-cut algorithm. In Chapter 8 we try to detect small blocks in the constraint matrix and to derive new cutting planes that strengthen the integer programming formulation. These inequalities may be associated with the intersection of several knapsack problems. We will see that they significantly improve the quality of the general integer programming solver introduced in Chapter 5. T3 - ZIB-Report - SC-99-03 KW - integer programming KW - cutting planes KW - block structure Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3911 ER - TY - GEN A1 - Huber, Birkett A1 - Rambau, Jörg A1 - Santos, Francisco T1 - The Cayley Trick, lifting subdivisions and the Bohne-Dress theorem on zonotopal tilings N2 - In 1994, Sturmfels gave a polyhedral version of the Cayley Trick of elimination theory: he established an order-preserving bijection between the posets of \emph{coherent} mixed subdivisions of a Minkowski sum $\mathcal{A}_1+\cdots+\mathcal{A}_r$ of point configurations and of \emph{coherent} polyhedral subdivisions of the associated Cayley embedding $\mathcal{C}(\mathcal{A}_1,\dots,\mathcal{A}_r)$. In this paper we extend this correspondence in a natural way to cover also \emph{non-coherent} subdivisions. As an application, we show that the Cayley Trick combined with results of Santos on subdivisions of Lawrence polytopes provides a new independent proof of the Bohne-Dress Theorem on zonotopal tilings. This application uses a combinatorial characterization of lifting subdivisions, also originally proved by Santos. T3 - ZIB-Report - SC-98-44 KW - Polyhedral subdivision KW - fiber polytope KW - mixed subdivision KW - lifting subdivision KW - Minkowski sum KW - Cayley Trick KW - Bohne-Dress Theorem Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3874 ER - TY - GEN A1 - Athanasiadis, Christos A. A1 - Rambau, Jörg A1 - Santos, Francisco T1 - The Generalized Baues Problem for Cyclic Polytopes II N2 - Given an affine surjection of polytopes $\pi: P \to Q$, the Generalized Baues Problem asks whether the poset of all proper polyhedral subdivisions of $Q$ which are induced by the map $\pi$ has the homotopy type of a sphere. We extend earlier work of the last two authors on subdivisions of cyclic polytopes to give an affirmative answer to the problem for the natural surjections between cyclic polytopes $\pi: C(n,d') \to C(n,d)$ for all $1 \leq d < d' < n$. T3 - ZIB-Report - SC-98-43 KW - Generalized Baues Problem KW - Polyhedral Subdivisions KW - Induced Subdivisions KW - Poset KW - Spherical KW - Cyclic Polytopes KW - Bistellar Operations Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3862 ER - TY - GEN A1 - Decker, Ingmar T1 - A Picture-based Document Retrieval Service for the Electronic Visualization Library N2 - This report describes the development of an experimental service for picture-based document retrieval for the Electronic Visualization Library (EVlib). The EVlib is a digital library for scientific visualization, established at the Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB). The picture-based retrieval service allows users to look for documents by describing the pictures they contain. This query method was developed based on the assumption that (1) pictures often represent relevant parts of the contents of a document, and (2) pictures are often remembered well. A picture-based approach provides a new quality of accessing and exploring scientific literature. Motivation, concepts and realization of our service are outlined. Results of a user test are presented, too. The results indicate that this service can be used for searching and browsing the document collection in principle. On the other hand, problems were detected which can give fruitful hints for future work concerning document and image retrieval. T3 - ZIB-Report - TR-98-07 KW - information retrieval KW - image retrieval KW - digital library KW - picture memory KW - visualization KW - user interface Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5689 ER - TY - GEN A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo N2 - Recently, a novel concept for the computation of essential features of the dynamics of Hamiltonian systems (such as molecular dynamics) has been proposed. The realization of this concept had been based on subdivision techniques applied to the Frobenius--Perron operator for the dynamical system. The present paper suggests an alternative but related concept that merges the conceptual advantages of the dynamical systems approach with the appropriate statistical physics framework. This approach allows to define the phrase ``conformation'' in terms of the dynamical behavior of the molecular system and to characterize the dynamical stability of conformations. In a first step, the frequency of conformational changes is characterized in statistical terms leading to the definition of some Markov operator $T$ that describes the corresponding transition probabilities within the canonical ensemble. In a second step, a discretization of $T$ via specific hybrid Monte Carlo techniques is shown to lead to a stochastic matrix $P$. With these theoretical preparations, an identification algorithm for conformations is applicable. It is demonstrated that the discretization of $T$ can be restricted to few essential degrees of freedom so that the combinatorial explosion of discretization boxes is prevented and biomolecular systems can be attacked. Numerical results for the n-pentane molecule and the triribonucleotide adenylyl\emph{(3'-5')}cytidylyl\emph{(3'-5')}cytidin are given and interpreted. T3 - ZIB-Report - SC-98-45 KW - conformation KW - conformational dynamics KW - hybrid Monte Carlo KW - reweighting KW - essential degrees of freedom KW - transition probabilities KW - Markov operator Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3889 ER - TY - GEN A1 - Wolf, Thomas T1 - A comparison of four approaches to the calculation of conservation laws N2 - The paper compares computational aspects of four approaches to compute conservation laws of single differential equations or systems of them, ODEs and PDEs. The only restriction, required by two of the four corresponding computer algebra programs, is that each DE has to be solvable for a leading derivative. Extra constraints may be given. Examples of new conservation laws include non-polynomial expressions, an explicit variable dependence and conservation laws involving arbitrary functions. Examples involve the following equations: Ito, Liouville, Burgers, Kadomtsev-Petviashvili, Karney-Sen-Chu-Verheest, Boussinesq, Tzetzeica, Benney. T3 - ZIB-Report - SC-99-01 Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3896 ER - TY - GEN A1 - Sokolov, Vladimir V. A1 - Wolf, Thomas T1 - A symmetry test for quasilinear coupled systems N2 - It is well known that the following class of systems of evolution equations \begin{eqnarray} \label{nsgen} \cases{ u_{t}=u_{xx}+F(u,v,u_x,v_x),\cr v_{t}=-v_{xx}+G(u,v,u_x,v_x),\cr} \end{eqnarray} is very rich in integrable cases. The complete classification problem is very difficult. Here we consider only the most interesting (from our opinion) subclass of systems (1). Namely, we consider equations linear in all derivatives of the form \begin{eqnarray} \label{kvazgen} \cases{ u_t = u_{xx} + A_{1}(u,v) u_x + A_{2}(u,v) v_x + A_{0}(u,v)\cr v_t = - v_{xx} + B_{1}(u,v) v_x + B_{2}(u,v) u_x + B_{0}(u,v). \cr} \end{eqnarray} without any restrictions on the functions $A_{i}(u,v), B_{i}(u,v)$. T3 - ZIB-Report - SC-99-02 Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3901 ER - TY - THES A1 - Borndörfer, Ralf T1 - Aspects of Set Packing, Partitioning, and Covering N2 - Diese Dissertation befaßt sich mit ganzzahligen Programmen mit 0/1 Systemen: SetPacking-, Partitioning- und Covering-Probleme. Die drei Teile der Dissertation behandeln polyedrische, algorithmische und angewandte Aspekte derartiger Modelle. Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10126 ER - TY - THES A1 - Friese, Tilmann T1 - Eine Mehrgitter-Methode zur Lösung des Eigenwertproblems der komplexen Helmholtzgleichung Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-1999000133 ER - TY - GEN A1 - Best, Christoph A1 - Hege, Hans-Christian T1 - Visualizing conformations in molecular dynamics N2 - The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed. T3 - ZIB-Report - SC-98-42 KW - Molecular Dynamics KW - Conformations KW - Visualization KW - Cluster Analysis Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3859 ER - TY - GEN A1 - Best, Christoph T1 - A simple C++ library for manipulating scientific data sets as structured data N2 - Representing scientific data sets efficiently on external storage usually involves converting them to a byte string representation using specialized reader/writer routines. The resulting storage files are frequently difficult to interpret without these specialized routines as they do not contain information about the logical structure of the data. Avoiding such problems usually involves heavy-weight data format libraries or data base systems. We present a simple C++ library that allows to create and access data files that store structured data. The structure of the data is described by a data type that can be built from elementary data types (integer and floating-point numbers, byte strings) and composite data types (arrays, structures, unions). An abstract data access class presents the data to the application. Different actual data file structures can be implemented under this layer. This method is particularly suited to applications that require complex data structures, e.g. molecular dynamics simulations. Extensions such as late type binding and object persistence are discussed. T3 - ZIB-Report - TR-98-06 KW - scientific file formats KW - structured data KW - object persistence Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5674 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Strubbe, Uwe A1 - Völker, Manfred T1 - Zielorientierte Dienstplanoptimierung N2 - Dieser Artikel behandelt einen Ansatz zur zielorientierten Optimierung der Dienstplanung im ÖPNV. Der Ansatz zielt auf die vollständige Ausnutzung aller planerischen Freiheitsgrade unter korrekter Berücksichtigung von gesetzlichen, tariflichen, technischen und betrieblichen Rahmenbedingungen. Er basiert auf mathematischen Optimierungstechniken, die wir gegenwärtig in einem vom Bundesministerium für Bildung und Forschung ({\tt bmb+f}) geförderten Verbundprojekt in einer Kooperation zwischen der HanseCom GmbH, der IVU GmbH und dem Konrad-Zuse-Zentrum für Informationstechnik Berlin entwickeln. Es ist geplant, das Verfahren in die Softwareprodukte HOT II, MICROBUS II und OPUS zu integrieren. Verhandlungen mit den Berliner Verkehrsbetrieben über eine Projektbeteiligung und Integration unserer Software in BERTA sind zur Zeit im Gang. Wir beschreiben die Methodik des Ansatzes, diskutieren Aspekte seiner praktischen Verwendung, und wir berichten über den Stand der Entwicklung. T3 - ZIB-Report - SC-98-41 KW - Dienstplanung KW - Optimierung KW - Zielorientierte Planung Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3847 ER - TY - GEN A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Zachow, Stefan T1 - Mehrschichtige Oberflächenmodelle zur computergestützten Planung in der Chirurgie N2 - Polygonale Schädelmodelle bilden ein wichtiges Hilfsmittel für computergestützte Planungen im Bereich der plastischen Chirurgie. Wir beschreiben, wie derartige Modelle automatisch aus hochaufgelösten CT-Datensätzen erzeugt werden können. Durch einen lokal steuerbaren Simplifizierungsalgorithmus werden die Modelle so weit vereinfacht, daß auch auf kleineren Graphikcomputern interaktives Arbeiten möglich wird. Die Verwendung eines speziellen Transparenzmodells ermöglicht den ungehinderten Blick auf die bei der Planung relevanten Knochenstrukturen und läßt den Benutzer zugleich die Kopfumrisse des Patienten erkennen. T3 - ZIB-Report - TR-98-05 KW - Isoflächen KW - Simplifizierung KW - Transparenzen Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5661 ER - TY - THES A1 - Stalling, Detlev T1 - Fast Texture-Based Algorithms for Vector Field Visualization N2 - In this thesis we develop new methods for visualizing vector fields which specifically address three design goals: accuracy, performance, and cognition. Our methods will be general-purpose and can be applied to arbitrary vector fields in two- and three-dimensional space. The methodology behind our approach is {\em texture-based visualization}. Texture-based visualization methods imitate techniques known from experimental flow visualization, namely, the observation of randomly dispersed particles or dye injection patterns. Instead of depicting individual lines or symbols, a contiguous high-resolution image or texture is generated. This texture clearly reveals the directional structure of the field. In this way intuitive insight can be obtained and even small details of the field become visible. However, it remains unclear what kind of textures are best suited for our purpose. How do we generate them? Can we apply these methods in three-dimensional space? In particular, we focus on a technique known as {\em line integral convolution} or LIC. This method turns out to be quite versatile and well-suited for visualizing many interesting vector fields. LIC images display the integral curves or field lines of a vector field at high spatial resolution. Although conceptually quite simple, line integral convolution implies a number of interesting mathematical and algorithmic questions. T3 - ZIB-Report - SC-98-40 KW - computer graphics KW - line integral convolution KW - stream surfaces Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3838 ER - TY - GEN A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Sander, Oliver A1 - Hege, Hans-Christian T1 - Weighted Labels for 3D Image Segmentation N2 - Segmentation tools in medical imaging are either based on editing geometric curves or on the assignment of region labels to image voxels. While the first approach is well suited to describe smooth contours at subvoxel accuracy, the second approach is conceptually more simple and guarantees a unique classification of image areas. However, contours extracted from labeled images typically exhibit strong staircase artifacts and are not well suited to represent smooth tissue boundaries. In this paper we describe how this drawback can be circumvented by supplementing region labels with additional weights. We integrated our approach into an interactive segmentation system providing a well-defined set of manual and semi-automatic editing tools. All tools update both region labels as well as the corresponding weights simultaneously, thus allowing one to define segmentation results at high resolution. We applied our techniques to generate 3D polygonal models of anatomical structures. T3 - ZIB-Report - SC-98-39 KW - image processing KW - segmentation Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3828 ER - TY - GEN A1 - Kedziorski, Rafal A1 - Kehl, Detlef A1 - Paetsch, Olaf T1 - Client-Server-Anwendung zur Steuerung von Ausgabegeräten N2 - \\{\bf Zusammenfassung: }\noindent Die Steuerung von grafischen Ausgabegeräten erfordert oft mehr als ein oder zwei Optionen, wie man sie vom UNIX {\em lpr}-Kommando kennt. Hier bietet sich eine grafische Benutzungsschnittstelle zur übersichtlichen Einstellung aller möglichen Parameter und Optionen an. Wenn dieses Gerät zudem nur über eine besondere Treiber-Software zu bedienen ist und in einem heterogenen Intranet zur Verfügung gestellt werden soll, ist eine Steuerung mittels eines WWW-Servers naheliegend. Im Folgenden sollen Lösungsansätze diskutiert werden, die auf HTML/CGI- bzw. Java-Basis derartige Steuerung realisieren. {\small} It is often the case that graphical output devices need more than one or two control options like the UNIX {\em lpr}-command. A driver programme with a graphical user interface (GUI) can satisfy this requirement. If such a device shall be accessible in an heterogenous network a solution using a WWW-server can be used. Possible HTML/CGI resp. Java-based solutions are discussed in the following. T3 - ZIB-Report - TR-98-04 KW - Client-Server-Anwendungen KW - Ausgabegerätesteuerung KW - CGI KW - Java Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5658 ER - TY - GEN A1 - Schütte, Christof A1 - Nettesheim, Peter T1 - Non-Adiabatic Effects in Quantum-Classical Molecular Dynamics N2 - In molecular dynamics applications there is a growing interest in mixed quantum-classical models. The article is concerned with the so-called QCMD model. This model describes most atoms of the molecular system by the means of classical mechanics but an important, small portion of the system by the means of a wavefunction. We review the conditions under which the QCMD model is known to approximate the full quantum dynamical evolution of the system. In most quantum-classical simulations the {\em Born-Oppenheimer model} (BO) is used. In this model, the wavefunction is adiabatically coupled to the classical motion which leads to serious approximation deficiencies with respect to non-adiabatic effects in the fully quantum dynamical description of the system. In contrast to the BO model, the QCMD model does include non-adiabatic processes, e.g., transitions between the energy levels of the quantum system. It is demonstrated that, in mildly non-adiabatic scenarios, so-called {\em surface hopping} extensions of QCMD simulations yield good approximations of the non-adiabatic effects in full quantum dynamics. The algorithmic strategy of such extensions of QCMD is explained and the crucial steps of its realization are discussed with special emphasis on the numerical problems caused by highly oscillatory phase effects. T3 - ZIB-Report - SC-98-38 KW - quantum-classical molecular dynamics KW - non-adiabatic processes KW - Schrödinger equation KW - highly oscillatory phase KW - adiabatic limit KW - quantum adiabati Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3817 ER - TY - GEN A1 - Nettesheim, Peter T1 - Second Order Transitions in Quantum-Classical Molecular Dynamics N2 - Mixed quantum--classical models have attracted considerable interest due to the expectation that they correctly describe non--adiabatic processes of full quantum dynamics. One of these models, the so--called QCMD model, represents most degrees of freedom of the molecular system by the means of classical mechanics but an important, small portion of the system is modeled by a wavefunction: the wavefunction is nonlinearly coupled to the classical motion via a singularly perturbed Schrödinger equation. In extension to the analysis given by F.A.~Bornemann [{\em Homogenization in Time of Singularly Perturbed Mechanical Systems}, Lecture Notes in Mathematics, no.~1687, 1998, Springer, Berlin], the article presents an asymptotic expansion up to second order in the perturbation parameter. This result allows for the construction of new models and numerical integration schemes. T3 - ZIB-Report - SC-98-37 KW - quantum-classical molecular dynamics KW - mixed quantum-classical models KW - asymptotics KW - quantum populations Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3805 ER - TY - GEN A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods N2 - Statistical methods for analyzing large data sets of molecular configurations within the chemical concept of molecular conformations are described. The strategies are based on dependencies between configurations of a molecular ensemble; the article concentrates on dependencies induces by a) correlations between the molecular degrees of freedom, b) geometrical similarities of configurations, and c) dynamical relations between subsets of configurations. The statistical technique realizing aspect a) is based on an approach suggested by {\sc Amadei et al.} (Proteins, 17 (1993)). It allows to identify essential degrees of freedom of a molecular system and is extended in order to determine single configurations as representatives for the crucial features related to these essential degrees of freedom. Aspects b) and c) are based on statistical cluster methods. They lead to a decomposition of the available simulation data into {\em conformational ensembles} or {\em subsets} with the property that all configurations in one of these subsets share a common chemical property. In contrast to the restriction to single representative conformations, conformational ensembles include information about, e.g., structural flexibility or dynamical connectivity. The conceptual similarities and differences of the three approaches are discussed in detail and are illustrated by application to simulation data originating from a hybrid Monte Carlo sampling of a triribonucleotide. T3 - ZIB-Report - SC-98-36 KW - conformational ensemble KW - cluster method KW - structural and dynamical similarity KW - representative KW - conformation KW - essential degrees of freedom KW - transi Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3797 ER - TY - GEN A1 - Kuberek, Monika T1 - Bibliothekarische Inhalte und Zielsetzungen des KOBV N2 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) wurde 1997 auf politische Initiative hin gegründet, um für die ressourcenreiche, aber elektronisch unzulänglich erschlossene Bibliotheksregion Berlin-Brandenburg eine moderne Informationsinfrastruktur zu schaffen. Auf der Basis eines Expertengutachtens wird sowohl in technischer als auch in organisatorischer Hinsicht ein neues Kooperationsmodell entwickelt, das auf den Prinzipien der Dezentralisierung, Deregulierung und Kooperation beruht. Der vorliegende Artikel ist das Ergebnis einer bibliothekarischen Arbeitsgruppe des KOBV, die von Dezember 1997 bis März 1998 das Modell des KOBV unter bibliothekarischen Gesichtspunkten diskutiert hat. Es werden erste Leitlinien festgelegt zu den Serviceleistungen des KOBV, zu den Prinzipien der Zusammenarbeit der Bibliotheken untereinander sowie zur Einbindung des Verbundes in das Bibliothekswesen der Bundesrepublik. Damit dient der Artikel zugleich der Positionsbestimmung des KOBV innerhalb des deutschen Bibliothekswesens. T3 - ZIB-Report - TR-98-03 KW - Bibliotheksverbund KW - KOBV KW - Kooperativer Bibliotheksverbund Berlin-Brandenburg KW - Verbundkooperation KW - Verbundorganisation Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5646 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Seebass, Martin T1 - A New Nonlinear Elliptic Multilevel FEM Applied to Regional Hyperthermia N2 - In the clinical cancer therapy of regional hyperthermia nonlinear perfusion effects inside and outside the tumor seem to play a not negligible role. A stationary model of such effects leads to a nonlinear Helmholtz term within an elliptic boundary value problem. The present paper reports about the application of a recently designed adaptive multilevel FEM to this problem. For several 3D virtual patients, nonlinear versus linear model is studied. Moreover, the numerical efficiency of the new algorithm is compared with a former application of an adaptive FEM to the corresponding instationary model PDE. T3 - ZIB-Report - SC-98-35 KW - hyperthermia KW - nonlinear elliptic KW - multilevel FEM Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3785 ER - TY - GEN A1 - Kühn, Wolfgang A1 - Korzen, Manfred A1 - Paetsch, Olaf T1 - Fast Data Assimilation in Fire Tests of Steel Members N2 - This report presents a fast data assimilation method to produce an interpolating time and space temperature distribution for steel members subject to fire testing. The method assimilates collected temperature data into the numerical integration of the heat equation. This physically based method also allows the computation of lateral and axial heat flux into and inside the member. T3 - ZIB-Report - SC-98-33 KW - data assimilation KW - heat equation Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3766 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Krumke, Sven A1 - Rambau, Jörg T1 - The Online Transportation Problem: Competitive Scheduling of Elevators N2 - In this paper we consider the following online transportation problem (\textsc{Oltp}): Objects are to be transported between the vertices of a given graph. Transportation requests arrive online, specifying the objects to be transported and the corresponding source and target vertex. These requests are to be handled by a server which commences its work at a designated origin vertex and which picks up and drops objects at their starts and destinations. After the end of its service the server returns to its start. The goal of \textsc{Oltp} is to come up with a transportation schedule for the server which finishes as early as possible. We first show a lower bound of~$5/3$ for the competitive ratio of any deterministic algorithm. We then analyze two simple and natural strategies which we call \textsf{REPLAN} and \textsf{IGNORE}. \textsf{REPLAN} completely discards its schedule and recomputes a new one when a new request arrives. \textsf{IGNORE} always runs a (locally optimal) schedule for a set of known requests and ignores all new requests until this schedule is completed. We show that both strategies, \textsf{REPLAN} and \textsf{IGNORE}, are $5/2$-competitive. We also present a somewhat less natural strategy \textsf{SLEEP}, which in contrast to the other two strategies may leave the server idle from time to time although unserved requests are known. We also establish a competitive ratio of~$5/2$ for the algorithm \textsf{SLEEP}. Our results are extended to the case of ``open schedules'' where the server is not required to return to its start position at the end of its service. T3 - ZIB-Report - SC-98-34 KW - online optimization KW - competitive analysis KW - elevator Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3779 ER - TY - GEN A1 - Kühn, Wolfgang T1 - iTe 1.1 User's Guide N2 - iTe is an easy to use, interactive authoring tool for LaTeX and TeX documents. With iTe, it is possible to select arbitrary display fragments such as figures, equations, labels, captions, etc. These fragments can then be freely moved, rotated and scaled. T3 - ZIB-Report - TR-98-02 KW - TeX KW - Emacs KW - interactive editing Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5638 ER - TY - GEN A1 - Schmidt, Frank T1 - An Alternative Derivation of the Exact DtN-Map on a Circle N2 - The paper supplies an alternative derivation of the exact boundary conditions needed for the solution of time-harmonic acoustic scattering problems modeled by the Helmholtz equation. The main idea is to consider the exterior domain problem as an initial value problem with initial data given on the boundary of a disc or sphere. The solution of the exterior domain problem is obtained via Laplace transformation techniques, where the asymptotic Sommerfeld radiation condition is reformulated accordingly. T3 - ZIB-Report - SC-98-32 KW - Helmholtz equation KW - Dirichlet-to-Neumann map KW - Sommerfeld radiation condition Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3752 ER - TY - GEN A1 - Schneider, Thomas A1 - Botta, Nicola A1 - Geratz, Karl Josef A1 - Klein, Rupert T1 - Extension of finite volume compressible flow solvers to multi-dimensional, variable density zero Mach number flow N2 - When attempting to compute unsteady, variable density flows at very small or zero Mach number using a standard finite volume compressible flow solver one faces at least the following difficulties: (i) Spatial pressure variations vanish as the Mach number $M \rightarrow 0$, but they do affect the velocity field at leading order; (ii) the resulting spatial homogeneity of the leading order pressure implies an elliptic divergence constraint for the energy flux; (iii) violation of this constraint would crucially affect the transport of mass, thereby disabling a code to properly advect even a constant density distribution. A previous companion paper derived the above observations from a single time - multiple length scale asymptotic analysis for $M \ll 1$, applied to the conservation form of the governing equations and assuming an ideal gas with constant specific heats. The paper then restricted to weakly compressible one-dimensional flows and introduced a semi-implicit extension of a compressible flow solver, designed to handle the interaction of long wavelength acoustics with small scale, large amplitude density fluctuations. In the present paper we concentrate on the limit of zero Mach number for multi-dimensional, variable density flows. The construction of numerical fluxes for all conserved quantities involves: An explicit upwind step (1) yielding predictions for the nonlinear convective flux components. This procedure still neglects the influence of pressure gradients on the convective fluxes during the time step. Suitable corrections are applied in step (2), which guarantees compliance of the convective fluxes with the divergence constraint. This step requires the solution of a Poisson-type equation to obtain the relevant pressure gradients. Step (3), which requires the solution of a second Poisson-type equation, yields the yet unknown (non-convective) pressure contribution to the total flux of momentum. The final, cell centered velocity field exactly satisfies a discrete divergence constraint consistent with the asymptotic limit. Notice that step (1) can be done by any standard finite volume compressible flow solver and that the input to steps (2) and (3) involves solely the fluxes from step (1), but is independent on how these were obtained. Thus, we claim that our approach allows any such solver to be extended to simulate incompressible flows. Extensions to the weakly compressible regime $0 < M \ll 1$, reactive flows and more complex equations of state will be addressed in follow-up publications. T3 - ZIB-Report - SC-98-31 KW - Incompressible variable density flows KW - conservation laws Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3749 ER - TY - GEN A1 - Deuflhard, Peter A1 - Seebass, Martin T1 - Adaptive Multilevel FEM as Decisive Tools in the Clinical Cancer Therapy Hyperthermia N2 - The paper surveys recent progress in a joint mathematical-medical project on cancer therapy planning. Within so-called regional hyperthermia the computational task is to tune a set of coupled radiofrequency antennas such that a carefully measured tumor is locally heated, but any outside hot spots are avoided. A mathematical model of the whole clinical system -- air, applicator with antennas, water bolus, individual patient body -- involves Maxwell's equations in inhomogeneous media and a parabolic bioheat transfer equation, which represents a simplified model of heat transfer in the human body (ignoring strong blood vessel heat transport). Both PDEs need to be computed fast and to medical reliability (!) on a workstation within a clinical environment. This requirement triggered a series of new algorithmic developments to be reported here, among which is an adaptive multilevel FEM for Maxwell's equations, which dominates the numerical simulation time. In total, however, the main bulk of computation time (see Table 3 in Section 4 below) still goes into segmentation -- a necessary preprocessing step in the construction a 3D virtual patient from the input of a stack of 2D computed tomograms (left out here). T3 - ZIB-Report - SC-98-30 KW - hyperthermia KW - Maxwell's equations KW - nonlinear heat transfer KW - finite elements Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3739 ER - TY - GEN A1 - Huisinga, Wilhelm A1 - Pesce, Lorenzo A1 - Kosloff, Ronnie A1 - Saalfrank, Peter T1 - Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation N2 - Two polynomial expansions of the time-evolution superoperator to directly integrate Markovian Liouville-von Neumann (LvN) equations for quantum open systems, namely the Newton interpolation and the Faber approximation, are presented and critically compared. Details on the numerical implementation including error control, and on the performance of either method are given. In a first physical application, a damped harmonic oscillator is considered. Then, the Faber approximation is applied to compute a condensed phase absorption spectrum, for which a semi--analytical expression is derived. Finally, even more general applications are discussed. In all applications considered here it is found that both the Newton and Faber integrators are fast, general, stable, and accurate. T3 - ZIB-Report - SC-98-29 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3725 ER - TY - GEN A1 - Bruns, Winfried A1 - Gubeladze, Joseph A1 - Henk, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - A counterexample to an integer analogue of Caratheodorys theorem N2 - For $n\geq 6$ we provide a counterexample to the conjecture that every integral vector of a $n$-dimensional integral polyhedral pointed cone $C$ can be written as a nonnegative integral combination of at most $n$ elements of the Hilbert basis of $C$. In fact, we show that in general at least $\lfloor 7/6 \cdot n \rfloor$ elements of the Hilbert basis are needed. T3 - ZIB-Report - SC-98-28 KW - Integral pointed cones KW - Hilbert basis KW - integral Carathéodory property Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3718 ER - TY - GEN A1 - Steinbach, Marc T1 - Recursive Direct Optimization and Successive Refinement in Multistage Stochastic Programs N2 - The paper presents a new algorithmic approach for multistage stochastic programs which are seen as discrete optimal control problems with a characteristic dynamic structure induced by the scenario tree. To exploit that structure, we propose a highly efficient dynamic programming recursion for the computationally intensive task of KKT systems solution within a primal-dual interior point method. Convergence is drastically enhanced by a successive refinement technique providing both primal and dual initial estimates. Test runs on a multistage portfolio selection problem demonstrate the performance of the method. T3 - ZIB-Report - SC-98-27 KW - Multistage stochastic programs KW - discrete dynamics KW - tree-sparse QP KW - KKT recursion KW - successive refinement Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3706 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Scientific Information Systems and Metadata N2 - This article begins with a short survey on the history of the classification of knowledge. It briefly discusses the traditional means of keeping track of scientific progress, i.e., collecting, classifying, abstracting, and reviewing all publications in a field. The focus of the article, however, is on modern electronic information and communication systems that try to provide high-quality information by automatic document retrieval or by using metadata, a new tool to guide search engines. We report, in particular, on efforts of this type made jointly by a number of German scientific societies. A full version of this paper including all hypertext references, links to online papers and references to the literature can be found under the URL: {\tt http://elib.zib.de/math.org.softinf.pub} . T3 - ZIB-Report - SC-98-26 KW - elektronisches Publizieren KW - Metadaten KW - Dublin Core KW - Klassifikation KW - Math-Net Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3698 ER - TY - GEN A1 - Grötschel, Martin A1 - Dalitz, Wolfgang A1 - Winczewski, Vincent T1 - Math-Net: Ein Informationssystem der Mathematik N2 - In diesem Artikel geben wir einen Überblick über das Math-Net-Projekt. Wir berichten über die organisatorischen und technischen Vorgehensweisen beim Aufbau eines verteilten Informationssystems für die Mathematik in Deutschland. T3 - ZIB-Report - SC-98-25 KW - Information System KW - Math-Net KW - Math-Net-Links KW - Dublin Core KW - Harvest Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3680 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Combinatorial Online Optimization N2 - In ``classical'' optimization, all data of a problem instance are considered given. The standard theory and the usual algorithmic techniques apply to such cases only. Online optimization is different. Many decisions have to be made before all data are available. In addition, decisions once made cannot be changed. How should one act ``best'' in such an environment? In this paper we survey online problems coming up in combinatorial optimization. We first outline theoretical concepts, such as competitiveness against various adversaries, to analyze online problems and algorithms. The focus, however, lies on real-world applications. We report, in particular, on theoretical investigations and our practical experience with problems arising in transportation and the automatic handling of material. T3 - ZIB-Report - SC-98-24 KW - Online Optimization KW - competitiveness KW - combinatorial optimization KW - real-world problems Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3674 ER - TY - GEN A1 - Steinbach, Marc T1 - Recursive Direct Algorithms for Multistage Stochastic Programs in Financial Engineering N2 - Multistage stochastic programs can be seen as discrete optimal control problems with a characteristic dynamic structure induced by the scenario tree. To exploit that structure, we propose a highly efficient dynamic programming recursion for the computationally intensive task of KKT systems solution within an interior point method. Test runs on a multistage portfolio selection problem demonstrate the performance of the algorithm. T3 - ZIB-Report - SC-98-23 KW - multistage stochastic programs KW - discrete dynamics KW - tree-sparse QP KW - KKT recursion KW - finance Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3661 ER - TY - GEN A1 - Lourenco, Maria José A1 - Rosa, Samuel Costa S. A1 - Castro, Carlos Alberto Nieto de A1 - Albuquerque, C. A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Roitzsch, Rainer T1 - Simulation of the Transient Heating in an Unsymmetrical Coated Hot--Strip Sensor with a Self--Adaptive Finite Element Method N2 - The transient heating in an unsymmetrical coated hot--strip sensor was simulated with a self--adaptive finite element method. The first tests of this model show that it can determine with a small error the thermal conductivity of liquids, from the transient temperature rise in the hot--strip, deposited in a substrate and coated by an alumina spray. T3 - ZIB-Report - SC-98-22 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3656 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On a Two-Queue Priority System with Impatience and its Application to a Call Center N2 - We consider a $s$-server system with two FCFS queues, where the arrival rates at the queues and the service rate may depend on the number $n$ of customers being in service or in the first queue, but the service rate is assumed to be constant for $n>s$. The customers in the first queue are impatient. If the offered waiting time exceeds a random maximal waiting time $I$, then the customer leaves the first queue after time $I$. If $I$ is less than a given deterministic time then he leaves the system else he transits to the end of the second queue. The customers in the first queue have priority. The service of a customer from the second queue will be started if the first queue is empty and more than a given number of servers become idle. For the model being a generalization of the $M(n)/M(n)/s\!+\!GI$ system balance conditions for the density of the stationary state process are derived yielding the stability conditions and the probabilities that precisely $n$ customers are in service or in the first queue. For obtaining performance measures for the second queue a system approximation basing on fitting impatience intensities is constructed. The results are applied to the performance analysis of a call center with an integrated voice-mail-server. For an important special case a stochastic decomposition is derived illuminating the connection to the dynamics of the $M(n)/M(n)/s\!+\!GI$ system. T3 - ZIB-Report - SC-98-21 KW - two queues KW - many server KW - server reservation KW - impatience KW - occupancy distribution KW - waiting time distribution KW - approximate system KW - $M(n)/M(n)/s+GI Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3641 ER - TY - GEN A1 - Bley, Andreas T1 - On the Complexity of Vertex-Disjoint Length-Restricted Path Problems N2 - Let $G=(V,E)$ be a simple graph and $s$ and $t$ be two distinct vertices of $G$. A path in $G$ is called $\ell$-bounded for some $\ell\in\mathbb{N}$, if it does not contain more than $\ell$ edges. We study the computational complexity of approximating the optimum value for two optimization problems of finding sets of vertex-disjoint $\ell$-bounded $s,t$-paths in $G$. First, we show that computing the maximum number of vertex-disjoint $\ell$-bounded $s,t$-paths is $\mathcal{AP\kern-1pt X}$--complete for any fixed length bound $\ell\geq 5$. Second, for a given number $k\in\mathbb{N}$, $1\leq k \leq |V|-1$, and non-negative weights on the edges of $G$, the problem of finding $k$ vertex-disjoint $\ell$-bounded $s,t$-paths with minimal total weight is proven to be $\mathcal{NPO}$--complete for any length bound $\ell\geq 5$. Furthermore, we show that, even if $G$ is complete, it is $\mathcal{NP}$--complete to approximate the optimal solution value of this problem within a factor of $2^{\langle\phi\rangle^\epsilon}$ for any constant $0<\epsilon<1$, where $\langle\phi\rangle$ denotes the encoding size of the given problem instance $\phi$. We prove that these results are tight in the sense that for lengths $\ell\leq 4$ both problems are polynomially solvable, assuming that the weights satisfy a generalized triangle inequality in the weighted problem. All results presented also hold for directed and non-simple graphs. For the analogous problems where the path length restriction is replaced by the condition that all paths must have length equal to $\ell$ or where vertex-disjointness is replaced by edge-disjointness we obtain similar results. T3 - ZIB-Report - SC-98-20 KW - disjoint paths KW - length bounded paths KW - approximation KW - reducibility KW - completeness Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3639 ER - TY - THES A1 - Reich, Sebastian T1 - Dynamical Systems, Numerical Integration, and Exponentially Small Estimates N2 - Dynamical systems with two well-separated time-scales are investigated using normal form theory. Exponential estimates for the normal form truncation error are derived and applied to the numerical integration of differential equations (backward error analysis) and the reduction of highly oscillatory Hamiltonian systems (constrained dynamics and correcting potentials). The theoretical results are used to formulate new algorithms for the time integration of conservative Hamiltonian systems (projected multiple time stepping, soft constraints, rigid bodies, symplectic variable step-size methods). T3 - ZIB-Report - SC-98-19 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3622 ER - TY - GEN A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Conjunctive Cuts for Integer Programs N2 - This paper deals with a family of conjunctive inequalities. Such inequalities are needed to describe the polyhedron associated with all the integer points that satisfy several knapsack constraints simultaneously. Here we demonstrate the strength and potential of conjunctive inequalities in connection with lifting from a computational point of view. T3 - ZIB-Report - SC-98-18 KW - Polyhedral Combinatorics KW - Integer Programming KW - Separation Algorithm Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3618 ER - TY - GEN A1 - Holder, Thomas A1 - Leimkuhler, Benedict A1 - Reich, Sebastian T1 - Explicit Variable Step-Size and Time-Reversible Integration N2 - A variable step-size, semi-explicit variant of the explicit Störmer-Verlet method has been proposed for the time-reversible integration of Newton's equations of motion by Huang & Leimkuhler. Here we propose a fully explicit version of this approach applicable to explicit and symmetric integration methods for general time-reversible differential equations. As applications, we discuss the variable step-size, time-reversible, and fully explicit integration of rigid body motion and reversible Nos\'e-Hoover dynamics. T3 - ZIB-Report - SC-98-17 KW - reversible differential equations KW - time integration KW - adaptive methods Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3607 ER - TY - GEN A1 - Lang, Jens T1 - Adaptive Incompressible Flow Computations with Linearly Implicit Time Discretization and Stabilized Finite Elements N2 - Fully adaptive solutions of imcompressible flow problems employing the discretization sequence first in time then in space are presented. The time discretization is done by linearly implicit one--step methods possibly of high order with automatic step size control. A posteriori error estimates for the stabilized finite element discretization in space are obtained by solving local Dirichlet problems with higher accuracy. Once those estimates have been computed, we are able to control time and space grids with respect to required tolerances and necessary computational work. The devised method is applied to two benchmark problems in 2D. T3 - ZIB-Report - SC-98-16 KW - Incompressible Flow KW - Adaptive Stabilized Finite Element KW - Linearly Implicit Time Discretization Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3599 ER - TY - GEN T1 - Jahresbericht 1997 T3 - Jahresbericht - 1997 KW - Annual Report Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9722 SN - 0934-5892 ER - TY - GEN A1 - Roitzsch, Rainer A1 - Erdmann, Bodo A1 - Lang, Jens T1 - The Benefits of Modularization: from KASKADE to KARDOS N2 - KARDOS solves nonlinear evolution problems in 1, 2, and 3D. An adaptive multilevel finite element algorithm is used to solve the spatial problems arising from linearly implicit discretization methods in time. Local refinement and derefinement techniques are used to handle the development of the mesh over time. The software engineering techniques used to implement the modules of the KASKADE toolbox are reviewed and their application to the extended problem class is described. A notification system and dynamic construction of records are discussed and their values for the implementation of a mesh transfer operation are shown. The need for low-level and high--level interface elements of a module is discussed for the assembling procedure of KARDOS. At the end we will summarize our experiences. T3 - ZIB-Report - SC-98-15 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3586 ER - TY - GEN A1 - Rambau, Jörg A1 - Santos, Francisco T1 - The Generalized Baues Problem for Cyclic Polytopes I. N2 - The Generalized Baues Problem asks whether for a given point configuration the order complex of all its proper polyhedral subdivisions, partially ordered by refinement, is homotopy equivalent to a sphere. In this paper, an affirmative answer is given for the vertex sets of cyclic polytopes in all dimensions. This yields the first non-trivial class of point configurations with neither a bound on the dimension, the codimension, nor the number of vertice for which this is known to be true. Moreover, it is shown that all triangulations of cyclic polytopes are lifting triangulations. This contrasts the fact that in general there are many non-regular triangulations of cyclic polytopes. Beyond this, we find triangulations of $C(11,5)$ with flip deficiency. This proves---among other things---that there are triangulations of cyclic polytopes that are non-regular for every choice of points on the moment curve. T3 - ZIB-Report - SC-98-14 KW - Generalized Baues Problem KW - Polyhedral Subdivisions KW - Induced Subdivisions KW - Poset KW - Spherical KW - Cyclic Polytopes KW - Bistellar Operations KW - Flip Defici Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3579 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Martin, Alexander T1 - The Orientation Model for Frequency Assignment Problems N2 - Mobile telecommunication systems establish a large number of communication links with a limited number of available frequencies; reuse of the same or adjacent frequencies on neighboring links causes interference. The task to find an assignment of frequencies to channels with minimal interference is the frequency assignment problem. The frequency assignment problem is usually treated as a graph coloring problem where the number of colors is minimized, but this approach does not model interference minimization correctly. We give in this paper a new integer programming formulation of the frequency assignment problem, the orientation model, and develop a heuristic two-stage method to solve it. The algorithm iteratively solves an outer and an inner optimization problem. The outer problem decides for each pair of communication links which link gets the higher frequency and leads to an acyclic subdigraph problem with additional longest path restrictions. The inner problem to find an optimal assignment respecting an orientation leads to a min-cost flow problem. T3 - ZIB-Report - TR-98-01 KW - Minimum-Cost Flow Problems KW - Cellular Radio Telephone Systems KW - Frequency Assignment Problem KW - Integer Programming Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5627 ER - TY - GEN A1 - Bley, Andreas A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - Design of Broadband Virtual Private Networks: Model and Heuristics for the B–WiN N2 - We investigate the problem of designing survivable broadband virtual private networks that employ the Open Shortest Path First (OSPF) routing protocol to route the packages. The capacities available for the links of the network are a minimal capacity plus multiples of a unit capacity. Given the directed communication demands between all pairs of nodes, we wish to select the capacities in a such way, that even in case of a single node or a single link failure a specified percentage of each demand can be satisfied and the costs for these capacities are minimal. We present a mixed--integer linear programming formulation of this problem and several heuristics for its solution. Furthermore, we report on computational results with real-world data. T3 - ZIB-Report - SC-98-13 KW - Telecommunication Network Design KW - Survivable Networks KW - Network Capacity Planning KW - OSPF Routing KW - Shortest Path Routing KW - Heuristics Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3565 ER - TY - GEN A1 - Caröe, Claus C. A1 - Schultz, Rüdiger T1 - A Two-Stage Stochastic Program for Unit Commitment Under Uncertainty in a Hydro-Thermal Power System N2 - We develop a two-stage stochastic programming model with integer first-stage and mixed-integer recourse for solving the unit commitment problem in power generation in the presence of uncertainty of load profiles. The solution methodology rests on a novel scenario decomposition method for stochastic integer programming. This method combines Lagrangian relaxation of non-anticipativity constraints with branch-and-bound. It can be seen as a decomposition algorithm for large-scale mixed-integer linear programs with block-angular structure. With realistic data from a German utility we validate our model and carry out test runs. Sizes of these problems go up to 20.000 integer and 150.000 continuous variables together with up to 180.000 constraints. T3 - ZIB-Report - SC-98-11 KW - Programming KW - stochastic:Scenario Decomposition if mixed-integer programs KW - Natural resourses KW - energy:Unit commitment under uncertainty Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3543 ER - TY - GEN A1 - Dais, Dimitrios I. A1 - Haus, Utz-Uwe A1 - Henk, Martin T1 - On crepant resolutions of 2-parameter series of Gorenstein cyclic quotient singularities N2 - \noindent An immediate generalization of the classical McKay correspondence for Gorenstein quotient spaces $\Bbb{C}^{r}/G$ in dimensions $r\geq 4$ would primarily demand the existence of projective, crepant, full desingularizations. Since this is not always possible, it is natural to ask about special classes of such quotient spaces which would satisfy the above property. In this paper we give explicit necessary and sufficient conditions under which 2-parameter series of Gorenstein cyclic quotient singularities have torus-equivariant resolutions of this specific sort in all dimensions. T3 - ZIB-Report - SC-98-12 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3559 ER - TY - GEN A1 - Kornhuber, Ralf T1 - Monotone Iterations for Elliptic Variational Inequalities N2 - A wide range of free boundary problems occurring in engineering andindustry can be rewritten as a minimization problem for astrictly convex, piecewise smooth but non--differentiable energy functional.The fast solution of related discretized problemsis a very delicate question, because usual Newton techniquescannot be applied. We propose a new approach based on convex minimization and constrained Newton type linearization. While convex minimization provides global convergence of the overall iteration, the subsequent constrained Newton type linearization is intended to accelerate the convergence speed. We present a general convergence theory and discuss several applications. T3 - ZIB-Report - SC-98-10 KW - finite elements KW - multigrid methods KW - variational inequalities Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3539 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Optimization of Transportation Systems N2 - The world has experienced two hundred years of unprecedented advances in vehicle technology, transport system development, and traffic network extension. Technical progress continues but seems to have reached some limits. Congestion, pollution, and increasing costs have created, in some parts of the world, a climate of hostility against transportation technology. Mobility, however, is still increasing. What can be done? There is no panacea. Interdisciplinary cooperation is necessary, and we are going to argue in this paper that {\em Mathematics\/} can contribute significantly to the solution of some of the problems. We propose to employ methods developed in the {\em Theory of Optimization\/} to make better use of resources and existing technology. One way of optimization is better planning. We will point out that {\em Discrete Mathematics\/} provides a suitable framework for planning decisions within transportation systems. The mathematical approach leads to a better understanding of problems. Precise and quantitative models, and advanced mathematical tools allow for provable and reproducible conclusions. Modern computing equipment is suited to put such methods into practice. At present, mathematical methods contribute, in particular, to the solution of various problems of {\em operational planning}. We report about encouraging {\em results\/} achieved so far. T3 - ZIB-Report - SC-98-09 KW - Transportation Systems KW - Optimization KW - Discrete Mathematics Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3529 ER - TY - GEN A1 - Abdel-Hamid, Atef Abdel-Aziz A1 - Ascheuer, Norbert A1 - Grötschel, Martin T1 - Order Picking in an Automatic Warehouse: Solving Online Asymmetric TSPs N2 - We report on a joint project with industry that had the aim to sequence transportation requests within an automatic storage system in such a way that the overall travel time is minimized. The manufacturing environment is such that scheduling decisions have to be made before all jobs are known. We have modeled this task as an \emph{online} Asymmetric Traveling Salesman Problem (ATSP). Several heuristics for the online ATSP are compared computationally within a simulation environment to judge which should be used in practice. Compared to the priority rule used so far, the optimization package reduced the unloaded travel time by about 40~\%. Because of these significant savings our procedure was implemented as part of the control software for the stacker cranes of the storage systems. T3 - ZIB-Report - SC-98-08 KW - Traveling Salesman Problem KW - Online-Algorithm KW - Automatic Storage System Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3519 ER - TY - GEN A1 - Foupouagnigni, Mama A1 - Ronveaux, Andre A1 - Koepf, Wolfram T1 - Fourth-Order q-Difference Equation for the First Associated of the q-Classical Orthogonal Polynomials N2 - We derive the fourth order $q$-difference equation satisfied by the first associated of the $q$-classical orthogonal polynomials. The coefficients of this equation are given in terms of the polynomials $\; \sigma\;$ and $\;\tau\;$ which appear in the $q$-Pearson difference equation $\;\; D_q(\sigma\,\rho)=\tau\,\rho\;$ defining the weight $\rho$ of the $q$-classical orthogonal polynomials inside the $q$-Hahn tableau. T3 - ZIB-Report - SC-98-06 KW - q-Orthogonal polynomials KW - Fourth order q-difference equation Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3490 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Kamin, Nicola A1 - Rambau, Jörg T1 - Combinatorial Online Optimization in Practice N2 - This paper gives a short introduction into combinatorial online optimization. It explains a few evaluation concepts of online algorithms, such as competitiveness, and discusses limitations in their application to real--world problems. The main focus, however, is a survey of combinatorial online problems coming up in practice, in particular, in large scale material flow and flexible manufacturing systems. T3 - ZIB-Report - SC-98-07 KW - Online optimization KW - combinatorial optimization KW - real-world problems Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3508 ER - TY - GEN A1 - Wolters, Christof T1 - GOS Thesaurus--Handbuch zum Projekt: Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern N2 - Das GOS Thesaurus--Handbuch wurde für die Teilnehmer des von der Robert Bosch Stiftung geförderten Projekts zum Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern geschrieben. Es basiert auf verschiedenen vom Institut für Museumskunde gemeinsam mit dem ZIB durchgeführten Projekten und beschreibt mit zahlreichen Beispielen Struktur und Aufbau eines Thesaurus. T3 - ZIB-Report - TR-97-19 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5616 ER - TY - GEN A1 - Saro, Carlos A1 - Schröder, Beate A1 - Volkmann, Katrin T1 - GOS Benutzer--Handbuch. Anleitung zum Projekt: Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern N2 - Das Handbuch enthält eine ausführliche Einführung in das am ZIB für den Einsatz in der Museumsdokumentation entwickelte Datenbanksystem GOS. T3 - ZIB-Report - TR-97-16 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5584 ER - TY - GEN A1 - Clemens, Hans-H. A1 - Saro, Carlos T1 - Abschlussbericht für das Projekt: Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern N2 - Von Januar 1995 bis Februar 1997 wurde am ZIB ein von der Robert Bosch Stiftung gefördertes Projekt zum Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern durchgeführt. In dem vorliegenden Abschlußbericht werden die Ziele, die Strategie, die Durchführung und die Ergebnisse des Projekts beschrieben. T3 - ZIB-Report - TR-97-17 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5595 ER - TY - GEN A1 - Clemens, Hans-H. T1 - Systemanalyse und Datenkatalog zum Projekt: Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern N2 - Von Januar 1995 bis Februar 1997 wurde am ZIB ein von der Robert Bosch Stiftung gefördertes Projekt zum Sammlungsmanagement für kulturgeschichtliche Museen in den neuen Bundesländern durchgeführt. Die vorliegende Systemanalyse beschreibt exemplarisch die Voraussetzungen und die notwendigen Arbeitsschritte für den Aufbau einer Dokumentation in einem Museum. Ein im Anhang wiedergegebener Datenfeldkatalog hilft beim "`sanften"' Übergang von einer papiergestützten zu einer computergestützten Dokumentation. T3 - ZIB-Report - TR-97-18 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5603 ER - TY - GEN A1 - Wolf, Thomas A1 - Brandt, Andreas A1 - Mohammadzadeh, Majid T1 - Computer algebra algorithms and routines for the computation of conservation laws and fixing of gauge in differential expressions N2 - Three different approaches for the determination of conservation laws of differential equations are presented. For three corresponding REDUCE computer algebra programs CONLAW1/2/3 the necessary subroutines are discribed. One of them simplifies general solutions of overdetermined PDE systems so that all remaining free functions and constants correspond to independent conservation laws. It determines redundant functions and constants in differential expressions and is equally useful for the determination of symmetries or the fixing of gauge freedom in differential expressions. T3 - ZIB-Report - SC-98-05 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3482 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - Fast LIC with Higher Order Filter Kernels N2 - Line integral convolution (LIC) has become a well-known and popular method for visualizing vector fields. The method works by convolving a random input texture along the integral curves of the vector field. In order to accelerate image synthesis significantly, an efficient algorithm has been proposed that utilizes pixel coherence in field line direction. This algorithm, called ``fast LIC'', originally was restricted to simple box-type filter kernels. Here we describe a generalization of fast LIC for piecewise polynomial filter kernels. Expanding the filter kernels in terms of truncated power functions allows us to exploit a certain convolution theorem. The convolution integral is expressed as a linear combination of repeated integrals (or repeated sums in the discrete case). Compared to the original algorithm the additional expense for using higher order filter kernels, e.g.\ of B-spline type, is very low. Such filter kernels produce smoother, less noisier results than a box filter. This is evident from visual investigation, as well as from analysis of pixel correlations. Thus, our method represents a useful extension of the fast LIC algorithm for the creation of high-quality LIC images. T3 - ZIB-Report - SC-97-74 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3439 ER - TY - GEN A1 - Lügger, Joachim T1 - Wo ist der Opac der virtuellen Bibliothek?- Strukturen des Kooperativen Bibliotheksverbundes N2 - Als neue Herausforderung für die Bibliotheken stellen sich heute die vielfältigen Publikationsmöglichkeiten, die den Wissenschaften durch das Internet zur Verfügung stehen. Die neuen Arten der wissenschaftlichen Information zu erschließen, wird für die Bibliotheken zu den neuen Aufgaben gehören. Der Artikel diskutiert zunächst die Frage, inwieweit dabei die traditionell hohen Maßstäbe bei der bibliographischen Beschreibung und sachlichen Erschließung noch aufrechterhalten werden können. Der Autor plädiert in diesem Zusammenhang für ein reduziertes Erfassungsschema im Sinne des Dublin Core, da dieses gleichzeitig eine Arbeitsteilung zwischen Wissenschaftlern, die zu ihren eigenen Arbeiten Metadaten erstellen, und Bibliotheksmitarbeitern, die solche einfachen Beschreibungen nach professionellen Maßstäben weiterentwickeln, ermöglicht. Der zweite Teil der Arbeit stellt eine technische Interpretation des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) vor, den eine Expertengruppe als neue Informationsstruktur für diese Region vorgesehen hat. Das Modell des Kooperativen Bibliotheksverbundes sieht im Prinzip eine dezentrale Datenhaltung vor, bei der die Bibliotheken in lokale Bibliothekssysteme katalogisieren. Im Gegensatz zu traditionellen Verbünden verzichtet der KOBV auf einen Zentralkatalog. Die in den lokalen Systemen vorliegende Information hingegen wird den Nutzern über eine Suchmaschine erschlossen und zur Verfügung gestellt. Dabei wird vorausgesetzt, daß die Zielsysteme über offene Schnittstellen (Z39.50 und WWW) angesprochen werden können. Zur Optimierung der bibliothekarischen Arbeit im Sinne von Copy Cataloging und Copy Acquisition steht vor allem den KOBV-Partnern ein zentrales Fremddatenangebot sowie die in Deutschland verbreiteten Normdaten zur Verfügung. Mit der Kommunikation über das standardisierte Protokoll Z39.50 sind dabei sowohl der KOBV selbst als auch das Fremddatengebot virtuell skalierbar. Im Unterschied zu einem zentralistisch organisierten Bibliotheksverbund eröffnet der auf dezentralen Strukturen aufbauende Kooperative Bibliotheksverbunds auch die Möglichkeit, virtuelle Fachverbünde zu beispielsweise einer Disziplin zu bilden. T3 - ZIB-Report - TR-97-10 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5524 ER - TY - GEN A1 - Kuberek, Monika A1 - Lohrum, Stefan T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg - Schnittstelle Lokalsysteme-Suchmaschine, Spezifikation der Anforderungen N2 - Die Kommunikation zwischen der Suchmaschine und den Lokalsystemen findet über eine offene Schnittstelle statt. Als Standardschnittstelle dient Z39.50-1995 (auch als Z39.50, Level 3 bekannt). Grundsätzlich können auch Lokalsysteme angesprochen werden, die nur über eine WWW-Schnittstelle verfügen. Dieses Papier spezifiziert die Anforderungen, die seitens der KOBV-Suchmaschine an ein Lokalsystem gestellt werden. T3 - ZIB-Report - TR-97-11 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5538 ER - TY - GEN A1 - Kuberek, Monika T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg - Normdaten im KOBV N2 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) wird sich aktiv am Aufbau der deutschen Normdateien Gemeinsame Körperschaftsdatei (GKD), Schlagwortnormdatei (SWD) und Personennamendatei (PND) beteiligen, die in Gemeinschaftsarbeit der deutschen Bibliotheksverbünde erstellt werden. Nach der Konzeption liegen die Normdateien auf dem zentralen KOBV-Server auf und stehen über die Suchmaschine allen angeschlossenen Bibliotheken zur Verfügung. Lokal befinden sich nur die Normdatensätze, die mit Titeln verknüpft sind. Das Update der Normdaten geschieht zentral. Es werden Lösungen aufgezeigt, wie die Normdaten von den KOBV-Bibliotheken mittels offener Schnittstellen (Z39.50) genutzt und erstellt werden können und auf welche Weise der KOBV mit den Redaktionen der Normdateien zusammenarbeiten kann. Neben den technischen werden auch die organisatorischen Fragen erörtert, die mit dem neuartigen KOBV-Konzept der dezentralen Nutzung der Normdaten in den lokalen Bibliothekssystemen zusammenhängen. Weitere Themen sind die regionale Zusammenarbeit der Bibliotheken und der KOBV-Zentrale mit der Zeitschriftendatenbank (ZDB) sowie die Einbindung zusätzlicher Normdaten, wie Universal- bzw. Fachklassifikationen und Thesauri. T3 - ZIB-Report - TR-97-12 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5548 ER - TY - GEN A1 - Willenborg, Josef T1 - Die Suchmaschine des KOBV - Spezifikation der Anforderungen N2 - Das vorliegende Papier spezifiziert die Anforderungen an die Suchmaschine im Kooperativen Biblotheksverbund Berlin- Brandenburg (KOBV). Die Suchmaschine realisiert einen virtuellen Union Catalog, der auch als virtueller OPAC im Netz ansprechbar ist. Die zentrale Suchmaschine fungiert als Gateway zwischen der WWW- und der Z39.50-Welt des Internet. Mit Hilfe der Suchmaschine wird der Zugriff auf die Bibliotheken des KOBV, auf Normdaten und Fremddaten sowie auf weitere Informationsanbieter außerhalb des KOBV (über Internet und andere Netze) ermöglicht. Auf die Suchmaschine greifen sowohl Bibliotheksmitarbeiter/innen als auch Endnutzer zu, d.h. sie muß unterschiedlichen Anwenderbedürfnissen gerecht werden. T3 - ZIB-Report - TR-97-13 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5552 ER - TY - GEN A1 - Lügger(Red.), Joachim T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg - Lokale Konzepte und technische Schnittstellen N2 - Dieser Artikel faßt die Ergebnisse einer Arbeitsgruppe bestehend aus Bibliothekaren und Informatikern der Universitäts- und Hochschulbibliotheken aus Berlin und Brandenburg zusammen, welche sich im Frühjahr 1997 zusammengefunden hatte, um die Anforderungen an den Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) aus Sicht der betroffenen Institutionen zu diskutieren. Dieser Verbund verzichtet zugunsten einer verteilten Datenhaltung in den jeweiligen lokalen Bibliothekssystemen auf einen Zentralkatalog und realisiert statt dessen mittels einer Suchmaschine einen virtuellen Union-Katalog, der auch als OPAC im Internet zur Verfügung steht. Zusätzlich soll zur Unterstützung der Erwerbungs- und Katalogisierungsarbeit der wissenschaftlichen Bibliotheken ein Fremd- und Normdatenserver errichtet werden. Beschrieben werden neben den erforderlichen Internet-Schnittstellen (WWW, Z39.50), das Fremd- und Normdatenangebot als auch konkrete Anforderungen an die Suchmaschine. Dabei wird die Sicht der Bibliotheksmitarbeiter ebenso wie die der Bibliotheksbenutzer berücksichtigt. T3 - ZIB-Report - TR-97-14 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5566 ER - TY - GEN A1 - Rusch, Beate T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg - Strategien zur Nutzung von Fremddaten N2 - Ausgehend von einer Analyse der Fremddatenbedarfs in der Bibliotheksregion Berlin-Brandenburg wird überlegt, welche Fremddaten im neuen Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) in Zukunft an welchem Ort vorliegen sollten. Dabei wird konzeptionell eine Balance versucht zwischen den Daten, die zentral für die Region angeboten werden, den Daten, die die Bibliotheken (langfristig) über Z39.50 aus (verbund-) fremden Bibliotheken abrufen, und denjenigen Datenbeständen, die ausschließlich zur lokalen Nutzung vorliegen. T3 - ZIB-Report - TR-97-15 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5579 ER - TY - GEN A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains N2 - The topic of the present paper bas been motivated by a recent computational approach to identify chemical conformations and conformational changes within molecular systems. After proper discretization, the conformations show up as almost invariant aggregates in reversible nearly uncoupled Markov chains. Most of the former work on this subject treated the direct problem: given the aggregates, analyze the loose coupling in connection with the computation of the stationary distribution (aggregation/disaggregation techniques). In contrast to that the present paper focuses on the inverse problem: given the system as a whole, identify the almost invariant aggregates together with the associated transition probabilites. A rather simple and robust algorithm is suggested and illustrated by its application to the n-pentane molecule. T3 - ZIB-Report - SC-98-03 KW - essential molecular dynamics KW - nearly reducible KW - nearly completely decomposable KW - nearly uncoupled Markov chain KW - almost invariant aggregates KW - trans Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3469 ER - TY - GEN A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Hybrid Monte Carlo Method for Essential Molecular Dynamics N2 - Recently, a novel concept for the computation of essential features of Hamiltonian systems (such as those arising in molecular dynamics) has been proposed. The realization of that concept was based on subdivision techniques applied to the Frobenius--Perron operator for the dynamical system. The present paper suggests an alternative but related concept based on statistical mechanics, which allows to attack realistic molecular systems. In a first step, the frequency of conformational changes is characterized in statistical terms leading to the definition of some Markov operator $T$ that describes the corresponding transition probabilities within the canonical ensemble. In a second step, a discretization of $T$ via hybrid Monte Carlo techniques (based on short term subtrajectories only) is shown to lead to a stochastic matrix $P$. With these theoretical preparations, an identification algorithm for conformations is applicable (to be presented elsewhere). Numerical results for the n-pentane molecule are given and interpreted. T3 - ZIB-Report - SC-98-04 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3474 ER - TY - GEN A1 - Wolf, Thomas T1 - A Study of Genetic Algorithms solving a combinatorial Puzzle N2 - The suitability of Genetic Algorithms (GAs) to solve a combinatorial problem with only one solution is investigated. The dependence of the performance is studied for GA-hard and GA-soft fitness functions, both with a range of different parameter values and different encodings. T3 - ZIB-Report - SC-98-01 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3445 ER - TY - GEN A1 - Böing, Harald A1 - Koepf, Wolfram T1 - Algorithms for q-hypergeometric Summation in Computer Algebra N2 - In this paper we present a short description of $q$-analogues of Gosper's, Zeilberger's, Petkov\v{s}ek's and related algorithms. Furthermore we introduce our corresponding MAPLE implementations and show how they can be applied to prove or even derive identities associated with $q$-series. T3 - ZIB-Report - SC-98-02 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3453 ER - TY - GEN A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Seebass, Martin T1 - Impact of Nonlinear Heat Transfer on Temperature Control in Regional Hyperthermia N2 - We describe an optimization process specially designed for regional hyperthermia of deep seated tumors in order to achieve desired steady--state temperature distributions. A nonlinear three--dimensional heat transfer model based on temperature--dependent blood perfusion is applied to predict the temperature. Using linearly implicit methods in time and adaptive multilevel finite elements in space, we are able to integrate efficiently the instationary nonlinear heat equation with high accuracy. Optimal heating is obtained by minimizing an integral object function which measures the distance between desired and model predicted temperatures. A sequence of minima is calculated from successively improved constant--rate perfusion models employing a damped Newton method in an inner iteration. We compare temperature distributions for two individual patients calculated on coarse and fine spatial grids and present numerical results of optimizations for a Sigma 60 Applicator of the BSD 2000 Hyperthermia System. T3 - ZIB-Report - SC-97-73 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3426 ER - TY - GEN A1 - Foupouagnigni, Mama A1 - Ronveaux, Andre A1 - Hounkonnou, Mahouton Norbert T1 - The Fourth-Order Difference Equation Satisfied by the Associated Orthogonal Polynomials of the Delta-Laguerre-HahnClass N2 - Starting from the $ D_{ \omega}$-Riccati Difference equation satisfied by the Stieltjes function of a linear functional, we work out an algorithm which enables us to write the unique fourth-order difference equation satisfied by the associated of any integer order of orthogonal polynomials of the $ \Delta$-Laguerre-Hahn class. Moreover, in classical situations (Meixner, Charlier, Kravtchouk and Hahn), we give explicitely these difference equations; and from Hahn difference equation, we recover by limit process the difference equations satisfied by the associated of classical discrete orthogonal polynomials and differential equations satisfied by the associated of classical continuous orthogonal polynomials. T3 - ZIB-Report - SC-97-71 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3409 ER - TY - GEN A1 - Foupouagnigni, Mama A1 - Koepf, Wolfram A1 - Ronveaux, Andre T1 - Fourth Order Difference Equation for the Associated Classical Discrete Orthogonal Polynomials N2 - We derive the fourth order difference equation satisfied by the associated of order $\;r\;$ of the classical orthogonal polynomials of a discrete variable.\\The coefficients of this equation are given in terms of the polynomials $\; \sigma\;$ and $\;\tau\;$ which appear in the discrete Pearson equation $\;\;\Delta(\sigma\;\rho)=\tau\;\rho\;\;$ defining the weight $\;\rho(x)\;$ of the classical discrete orthogonal polynomials. T3 - ZIB-Report - SC-97-72 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3419 ER - TY - THES A1 - Löbel, Andreas T1 - Optimal Vehicle Scheduling in Public Transit N2 - Die vorliegende Dissertation beschäftigt sich mit der Optimierung der Fahrzeugeinsatzplanung im öffentlichen Personennahverkehr. Dieses Problem ist für die meisten praxisrelevanten Fälle schwierig (Ar'P-schwer). In dieser Arbeit präsentieren wir Methoden der ganzzahligen linearen Programmierung zur Lösung dieses Planungsproblems. "Vernünftige" mathematische Formulierungen des Fahrzeugeinsatzplanungsproblems basieren auf Netzwerkfluß-Modellen und ent sprechenden ganzzahligen linearen Programmen (LP). Dies sind sogenannte bogenorientierte Mehrgüterfluß-Modelle bzw. pfadorientierte SetPartitioning-Modelle. Wir beschäftigen uns mit beiden Ansätzen, der Schwerpunkt liegt aber auf dem bogenorientierte Mehrgüterfluß-Modell Mathematisch bearbeiten wir diese Modelle mit Branch-und-Cut- bzw. Branch-und-Cutund-Price-Methoden. Reale Anwendungen führen zu riesigen LPs mit einigen Millionen ganzzahligen Variablen. Die Behandlung solcher LPs erfordert Spalten-Erzeugungs- Verfahren (auch Column-Generation-Verfahren genannt). Basierend auf Lagrange-Relaxationen entwickeln wir hierzu neue Verfahren zur Auswahl der zu erzeugenden Spalten, die wir Lagrange-Pricing nennen. Lagrange-Pricing-Techniken haben es erstmalig ermöglicht, LPs dieser Art mit rund 70 Millionen Variablen zu lösen. Für den bogenorientierten (Mehrgüter)Fluß-Zugang beschreiben wir ausführlich, wie Lagrange-Relaxationen sowie die LP-Relaxation effizient gelöst werden. Zusätzlich schlagen wir eine Heuristik vor, die schnell gute Lösungen erzeugt. Diese Heuristik beruht auf einem sog. Schedule-FirstClusterSecond-Ansatz. Eine zentrale Aufgabe bei der Lösung dieser primalen und dualen Probleme ist dabei die effiziente Behandlung von Problemen mit einem Depot. Wir zeigen, daß das bogenorientierte Mehrgüterfluß-Modell durch eine geeignete Anwendung der Dantzig-Wolfe-Dekomposition in ein pfadorientiertes SetPartitioning-Modell überführt werden kann. Der zweite Teil dieser Arbeit präsentiert die Rechenergebnisse zu den von uns entwickelten und implementierten Verfahren. Diese Untersuchungen basieren auf realen Testdaten von drei großen deutschen Nahverkehrsunternehmen. Die implementierten Codes arbeiten zuverlässig und stabil. Die mit diesen Verfahren durchgeführten Testläufe lieferten hervorragende Ergebnisse: Bis auf ein Problem können alle Beispiele optimal gelöst werden. Die Lösungen des Branch-and-Cut-Verfahrens wurden auch mit den Planungsergebnissen der in der Praxis gegenwärtig eingesetzten Verfahren verglichen: Wir konnten zusätzlich mehrere Fahrzeuge einsparen sowie eine Kostenreduktion von bis zu 10 % aufzeigen. Der mögliche Nutzen dieser Methoden ist enorm. Beispielsweise rechnet die BVG damit, den Planungsprozeß mit den von uns entwickelten Softwaretools deutlich straffen und jährlich Einsparungen in Höhe von rund 100 Millionen Mark erzielen zu können, siehe den Artikel Auf Sparkurs zum Ziel im Rheinischer Merkur, Nummer 39, von Schmidt [1997] Teile der vorgestellten Methoden wurden bereits in die Planungssysteme BERTA (der Berliner Verkehrsbetriebe (BVG)) und MICROBUS II (der IVU Gesellschaft für Informatik, Verkehrs und Umweltplanung mbH, Berlin) integriert. Darüber hinaus hat auch die Forschungsabteilung der SIEMENS AG in München dieses System erworben. Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10169 ER - TY - GEN A1 - Nowak, Ulrich A1 - Gebauer, Susanna T1 - A New Test Frame for Ordinary Differential Equation Solvers N2 - Benchmarking of ODE methods has a long tradition. Several sets of test problems have been developed and new problems are still collected. So, a whole variety of problems can be used to check the efficiency of a method under investigation. In general, efficiency is measured by the amount of work whi ch is necessary to get a reliable solution for a prescribed accura cy. In order to quantify the term ``amount of work'' usually not only the computing time is measured but also the number of calls of functional units. To quantify the term ``quality of a numerical solution'' usually the $l_2$--norm of the true error at the final point of the integration interval is used. In our contribution we first discuss some general aspects of benchmarking. Then we present a new test frame which allows to solve typical benchmark problems with some of the state of the art integrators within a unified framework. Finally we show some results of our benchmark tests. Part of the test frame can be used interactively in the World Wide Web. T3 - ZIB-Report - SC-97-68 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3370 ER - TY - GEN A1 - Nowak, Ulrich A1 - Ehrig, Rainald A1 - Oeverdieck, Lars T1 - Parallel Extrapolation Methods and Their Application in Chemical Engineering N2 - We study the parallelization of linearly--implicit extrapolation methods for the solution of large scale systems of differential algebraic equations arising in a method of lines (MOL ) treatment of partial differential equations. In our approach we combine a slightly overlapping domain decomposi tion together with a polynomial block Neumann preconditioner. Through the explicit computation of the matrix products of the pre conditioner and the system matrix a significant gain in overall efficiency is achieved for medium--sized problems. The parallel algorithm exhibits a good scalability up to 32 proces sors on a Cray T3E. Preliminary results for computations on a workstation cluster are reported. T3 - ZIB-Report - SC-97-69 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3387 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - A Branch & Cut Algorithm for the Asymmetric Traveling Salesman Problem with Precedence Constraints N2 - In this paper we consider a variant of the classical ATSP, namely the asymmetric Hamiltonian path problem (or equivalently ATSP) with precedence constraints. In this problem precedences among the nodes are present, stating that a certain node has to precede others in any feasible sequence. This problem occurs as a basic model in scheduling and routing and has a wide range of applications varying from helicopter routing[Timlin89], sequencing in flexible manufacturing [AscheuerEscuderoGroetschelStoer90,AscheuerEscuderoGroetschelStoer93], to stacker crane routing in an automatic storage system[Ascheuer95]. We give an integer programming model and summarize known classes of valid inequalities. We describe in detail the implementation of a branch&-cut algorithm and give computational results on real world instances and benchmark problems from TSPLIB. The results we achieve indicate that our implementation outperforms other implementations found in the literature. Real world instances up to 174 nodes could be solved to optimality within a few minutes of CPU-time. As a side product we obtained a branch&cut-algorithm for the ATSP. All instances in TSPLIB could be solved to optimality in a reasonable amount of computing time. T3 - ZIB-Report - SC-97-70 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3391 ER - TY - GEN A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hiptmair, Ralf A1 - Hoppe, Ronald H. W. A1 - Wohlmuth, Barbara T1 - Adaptive Multilevel Methods for Edge Element Discretizations of Maxwell's Equations N2 - The focus of this paper is on the efficient solution of boundary value problems involving the double-- curl operator. Those arise in the computation of electromagnetic fields in various settings, for instance when solving the electric or magnetic wave equation with implicit timestepping, when tackling time--harmonic problems or in the context of eddy--current computations. Their discretization is based on on N\'ed\'elec's {\bf H(curl}; $\Omega$)--conforming edge elements on unstructured grids. In order to capture local effects and to guarantee a prescribed accuracy of the approximate solution adaptive refinement of the grid controlled by a posteriori error estimators is employed. The hierarchy of meshes created through adaptive refinement forms the foundation for the fast iterative solution of the resulting linear systems by a multigrid method. The guiding principle underlying the design of both the error estimators and the multigrid method is the separate treatment of the kernel of the curl--operator and its orthogonal complement. Only on the latter we have proper ellipticity of the problem. Yet, exploiting the existence of computationally available discrete potentials for edge element spaces, we can switch to an elliptic problem in potential space to deal with nullspace of curl. Thus both cases become amenable to strategies of error estimation and multigrid solution developed for second order elliptic problems. The efficacy of the approach is confirmed by numerical experiments which cover several model problems and an application to waveguide simulation. T3 - ZIB-Report - SC-97-66 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3356 ER - TY - GEN A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in a Mixed-Canonical Ensemble: Efficient Conformational Analysis of RNA N2 - A hybrid Monte Carlo method with adaptive temperature choice is presented, which exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature, whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. \\The algorithm was tested by comparing analytical and numerical results for the small n-butane molecule before simulations were performed for a triribonucleotide. Sampling the complex multi-minima energy landscape of these small RNA segments, we observed enforced crossing of energy barriers. T3 - ZIB-Report - SC-97-67 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3364 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - Homogenization in Time II: Mechanical Systems Subject to Friction and Gyroscopic Forces N2 - In our previous work [Preprint SC 97-48] we have studied natural mechanical systems on Riemannian manifolds with a strong constraining potential. These systems establish fast nonlinear oscillations around some equilibrium manifold. Important in applications, the problem of elimination of the fast degrees of freedom, or {\em homogenization in time}, leads to determine the singular limit of infinite strength of the constraining potential. In the present paper we extend this study to systems which are subject to external forces that are non-potential, depending in a mixed way on positions {\em and}\/ velocities. We will argue that the method of weak convergence used in [1997] covers such forces if and only if they result from viscous friction and gyroscopic terms. All the results of [1997] directly extend if there is no friction transversal to the equilibrium manifold; elsewise we show that instructive modifications apply. T3 - ZIB-Report - SC-97-65 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3348 ER - TY - GEN A1 - Schmidt, Frank T1 - Computation of Discrete Transparent Boundary Conditions for the 2D Helmholtz Equation N2 - We present a family of nonlocal transparent boundary conditions for the 2D Helmholtz equation. The whole domain, on which the Helmholtz equation is defined, is decomposed into an interior and an exterior domain. The corresponding interior Helmholtz problem is formulated as a variational problem in standard manner, representing a boundary value problem, whereas the exterior problem is posed as an initial value problem in the radial variable. This problem is then solved approximately by means of the Laplace transformation. The derived boundary conditions are asymptotically correct, model inhomogeneous exterior domains and are simple to implement. T3 - ZIB-Report - SC-97-64 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3330 ER - TY - GEN A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - GMERR - an Error Minimizing Variant of GMRES N2 - The paper analyzes a recently proposed iterative error minimizing method for the solution of linear systems. Sufficient and necessary conditions for convergence are studied, which show that the method essentially requires normal matrices. An efficient implementation similar to GMRES has been worked out in detail. Numerical tests on general non--normal matrices, of course, indicate that this approach is not competitive with GMRES. Summarizing, if error minimizing is important, one should rather choose CGNE. A computational niche for GMERR might be problems, where normal but non--symmetric matrices occur, like dissipative quantum mechanics. T3 - ZIB-Report - SC-97-63 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3323 ER - TY - GEN A1 - Wolf, Thomas T1 - Structural equations for Killing tensors of arbitrary rank N2 - An algorithm is given for bringing the equations of monomial first integrals of arbitrary degree of the geodesic motion in a Riemannian space $V_n$ into the form $(F_A)_{;k} = \sum_B \Gamma_{kAB} F_B$. The $F_A$ are the components of a Killing tensor $K_{i_1\ldots i_r}$ of arbitrary rank $r$ and its symmetrized covariant derivatives. Explicit formulas are given for rank 1,2 and 3. %The maximal number of Killing tensors %(reducible + non-reducible) is found to be %$\frac{1}{r+1}\left( ^{n + r - 1}_{\;\;\;\;\,r} \right) % \left( ^{ n+r}_{\;\;\,r} \right)$. Killing tensor equations in structural form allow the formulation of algebraic integrability conditions and are supposed to be well suited for integration as it is demonstrated in the case of flat space. An alternative proof of the reducibility of these Killing tensors is given which shows the correspondence to structural equations for rank 2 Killing tensors as formulated by Hauser & Malhiot. They used tensors with different symmetry properties. T3 - ZIB-Report - SC-97-62 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3310 ER - TY - GEN A1 - Martin, Alexander A1 - Weismantel, Robert T1 - The Intersection of Knapsack Polyhedra and Extensions N2 - This paper introduces a scheme of deriving strong cutting planes for a general integer programming problem. The scheme is related to Chvatal-Gomory cutting planes and important special cases such as odd hole and clique inequalities for the stable set polyhedron or families of inequalities for the knapsack polyhedron. We analyze how relations between covering and incomparability numbers associated with the matrix can be used to bound coefficients in these inequalities. For the intersection of several knapsack polyhedra, incomparabilities between the column vectors of the associated matrix will be shown to transfer into inequalities of the associated polyhedron. Our scheme has been incorporated into the mixed integer programming code SIP. About experimental results will be reported. T3 - ZIB-Report - SC-97-61 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3300 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Seebass, Martin T1 - Optimization of Temperature Distributions for Regional Hyperthermia Based on a Nonlinear Heat Transfer Model N2 - We describe an optimization process specially designed for regional hyperthermia of deap seated tumors in order to achieve desired steady--state temperature distributions. A nonlinear three--dimensional heat--transfer model based on temperature--dependent blood perfusion is applied to predict the temperature. Optimal heating is obtained by minimizing an integral object function which measures the distance between desired and model predicted temperatures. Sequential minima are calculated from successively improved constant--rate perfusion models employing a damped Newton method in an inner iteration. Numerical results for a Sigma 60 applicator are presented. This work has been supported by Deutsche Forschungsgemeinschaft (DFG) within the Sonderforschungsbereich 273 \glqq Hyperthermie: Methodik und Klinik \grqq . T3 - ZIB-Report - SC-97-59 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3283 ER - TY - GEN A1 - Schmidt, Frank T1 - Construction of Discrete Transparent Boundary Conditions for Schrödinger-Type Equations N2 - We present a general technique for constructing nonlocal transparent boundary conditions for time-discretized one-dimensional Schrödinger type equations. The main tool of construction is the discrete counterpart to Mikusi\'nski's continuous algebraic operator approach. Existing techniques are simplified and generalized. Both adaptive time-steps and time-dependent exterior potentials are taken into account. T3 - ZIB-Report - SC-97-60 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3292 ER - TY - GEN A1 - Wolf, Thomas T1 - Killing Pairs in Flat Space N2 - In this paper the integrability conditions for Killing pairs in flat spaces are investigated and it is shown that only trivial Killing pairs exist. T3 - ZIB-Report - SC-97-58 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3275 ER - TY - GEN A1 - Friese, Tilmann T1 - On the Computation of Eigenmodes of Integrated Optical Components N2 - The paper deals with the solution of the eigenvalue problem of the complex Helmholtz equation. We concentrate on multigrid methods for solving the algebraic eigenproblems arising from discretization with finite elements by using adaptive generated meshes. An illustrative numerical example, the simulation of a waveguide structure from integrated optics, is included. T3 - ZIB-Report - SC-97-57 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3268 ER - TY - GEN A1 - Nettesheim, Peter A1 - Reich, Sebastian T1 - Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics N2 - The overall Hamiltonian structure of the Quantum-Classical Molecular Dynamics model makes - analogously to classical molecular dynamics - symplectic integration schemes the methods of choice for long-term simulations. This has already been demonstrated by the symplectic PICKABACK method. However, this method requires a relatively small step-size due to the high-frequency quantum modes. Therefore, following related ideas from classical molecular dynamics, we investigate symplectic multiple-time-stepping methods and indicate various possibilities to overcome the step-size limitation of PICKABACK. T3 - ZIB-Report - SC-97-56 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3250 ER - TY - GEN A1 - Deuflhard, Peter A1 - Friese, Tilmann A1 - Schmidt, Frank T1 - A Nonlinear Multigrid Eigenproblem Solver for the Complex Helmholtz Equation N2 - The paper is motivated by the need for a fast robust adaptive multigrid method to solve complex Helmholtz eigenvalue problems arising from the design of optical chips. A nonlinear multigrid method is developed, which can be regarded as an extension of a previous adaptive Rayleigh quotient minimization method for selfadjoint Helmholtz eigenproblems. Since the complex Helmholtz operator is just a compact nonselfadjoint perturbation of a selfadjoint operator, linear algebra techniques like Schur decomposition can be extended from the finite dimensional case. The efficiency of the derived adaptive nonlinear multigrid method is illustrated by computations for a technologically relevant integrated optics component containing Multi Quantum Well Layers. T3 - ZIB-Report - SC-97-55 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3240 ER - TY - GEN A1 - Müller, Peter A1 - Decker, Ingmar T1 - The Electronic Visualization Library N2 - Scientific visualization is a rapidly growing research field with a need for information dissemination. This report describes the Electronic Visualization Library (EVlib), a digital library for scientific visualization. Main design goals of EVlib were an attractive user interface providing various kind of access mechanisms as well as an open interface to other already established information systems. EVlib stores fulltext versions of documents where they are available. We also provide access to BibTeX entries for every stored document. All available BibTeX entries are combined in BibTeX bibliographies which are registered with the ``Collection of Computer Science Bibliographies'' at University of Karlsruhe. Additionally, we have defined a mapping from BibTeX attributes to the Dublin Core attribute set. This mapping is used to provide a gatherer interface for the Harvest information system. This way, existing Harvest installations can immediately use EVlib as an information resource. T3 - ZIB-Report - TR-97-09 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5517 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Weismantel, Robert T1 - Discrete Relaxations of Combinatorial Programs N2 - This paper investigates {\em relations\/} among combinatorial optimization problems. To establish such relations we introduce a transformation technique \mbox{---{\em aggregation}---} that allows to relax an integer program by means of another integer program. We prove that various families of prominent inequalities for the acyclic subdigraph problem, the multiple knapsack problem, the max cut, graph, and the clique partitioning problem, the set covering problem, and the set packing problem can be derived and separated in polynomial time in this way. Our technique is algorithmic. It has been implemented and used in a set partitioning code. T3 - ZIB-Report - SC-97-54 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3230 ER - TY - GEN A1 - Reich, Sebastian T1 - Modified potential energy functions for constrained molecular dynamics N2 - In molecular dynamics the highly oscillatory vibrations in the chemical bonds are often replaced by holonomic constraints that freeze the bond length/angle to its equilibrium value. In some cases this approach can be justified if the force constants of the bond vibrations are sufficiently large. However, for moderate values of the force constant, the constrained system might lead to a dynamical behavior that is too ``rigid'' compared to the flexible model. To compensate for this effect, the concept of soft constraints was introduced [Reich 1997, Reich 1995, Reich 1996]. However, its implementation is rather expensive. In this paper, we suggest an alternative approach that modifies the force field instead of the constraint functions. This leads to a more efficient method that avoids the resonance induced instabilities of multiple-time-stepping [Bishop 1996] and the above described effect of standard constrained dynamics. T3 - ZIB-Report - SC-97-49 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3189 ER - TY - GEN A1 - Ascher, Uri A1 - Reich, Sebastian T1 - On some difficulties in integrating highly oscillatory Hamiltonian systems N2 - The numerical integration of highly oscillatory Hamiltonian systems, such as those arising in molecular dynamics or Hamiltonian partial differential equations, is a challenging task. Various methods have been suggested to overcome the step-size restrictions of explicit methods such as the Verlet method. Among these are multiple-time-stepping, constrained dynamics, and implicit methods. In this paper, we investigate the suitability of time-reversible, semi-implicit methods. Here semi-implicit means that only the highly oscillatory part is integrated by an implicit method such as the midpoint method or an energy-conserving variant of it. The hope is that such methods will allow one to use a step-size $k$ which is much larger than the period $\varepsilon$ of the fast oscillations. However, our results are discouraging. Even in the absence of resonance-type instabilities, we show that in general one must require that $k^2/\varepsilon$ be small enough. Otherwise the method might become unstable and/or it might lead to a wrong approximation of the slowly varying solution components. The latter situation might, in some cases, even require that $k/\varepsilon$ be small in order to avoid this danger. While certain (semi-implicit) energy conserving methods prove to be robust for some model problems, they may also yield deceptively-looking, wrong solutions for other simple model problems, in circumstances where the corresponding constrained dynamics formulation may not be easily derived and used. T3 - ZIB-Report - SC-97-50 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3193 ER - TY - GEN A1 - Ascher, Uri A1 - Reich, Sebastian T1 - The midpoint scheme and variants for Hamiltonian systems: advantages and pitfalls N2 - The (implicit) midpoint scheme, like higher order Gauss-collocation schemes, is algebraically stable and symplectic, and it preserves quadratic integral invariants. It may appear particularly suitable for the numerical solution of highly oscillatory Hamiltonian systems, such as those arising in molecular dynamics or structural mechanics, because there is no stability restriction when it is applied to a simple harmonic oscillator. Although it is well-known that the midpoint scheme may also exhibit instabilities in various stiff situations, one might still hope for good results when resonance-type instabilities are avoided. In this paper we investigate the suitability of the midpoint scheme for highly oscillatory, frictionless mechanical systems, where the step-size $k$ is much larger than the system's small parameter $\varepsilon$, in case that the solution remains bounded as $\varepsilon \rightarrow 0$. We show that in general one must require that $k^2/\varepsilon$ be small enough, or else, even the errors in slowly varying quantities like the energy may grow undesirably (especially when fast and slow modes are tightly coupled) or, worse, the computation may yield misleading information. In some cases this may already happen when $k = O(\varepsilon )$. The same holds for higher order collocation at Gaussian points. The encountered restrictions on $k$ are still better than the corresponding ones for explicit schemes. T3 - ZIB-Report - SC-97-51 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3201 ER - TY - GEN A1 - Reich, Sebastian T1 - Preservation of Adiabatic Invariants under Symplectic Discretization N2 - Symplectic methods, like the Verlet method, are a standard tool for the long term integration of Hamiltonian systems as they arise, for example, in molecular dynamics. One of the reasons for the popularity of symplectic methods is the conservation of energy over very long periods of time up to small fluctuations that scale with the order of the method. In this paper, we discuss a qualitative feature of Hamiltonian systems with separated time scales that is also preserved under symplectic discretization. Specifically, highly oscillatory degrees of freedom often lead to almost preserved quantities (adiabatic invariants). Using recent results from backward error analysis and normal form theory, we show that a symplectic method, like the Verlet method, preserves those adiabatic invariants. We also discuss step-size restrictions necessary to maintain adiabatic invariants in practical computations. T3 - ZIB-Report - SC-97-52 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3210 ER - TY - GEN A1 - Barth, Eric A1 - Leimkuhler, Benedict A1 - Reich, Sebastian T1 - A Time-Reversible Variable-Stepsize Integrator for Constrained Dynamics N2 - This article considers the design and implementation of variable-timestep methods for simulating holonomically constrained mechanical systems. Symplectic variable stepsizes are briefly discussed, we then consider time-reparameterization techniques employing a time-reversible (symmetric) integration method to solve the equations of motion. We give several numerical examples, including a simulation of an elastic (inextensible, unshearable) rod undergoing large deformations and collisions with the sides of a bounding box. Numerical experiments indicate that adaptive stepping can significantly smooth the numerical energy and improve the overall efficiency of the simulation. T3 - ZIB-Report - SC-97-53 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3220 ER - TY - GEN A1 - Lang, Jens A1 - Merz, Wilhelm T1 - Numerical Simulation of Single Species Dopant Diffusion in Silicon under Extrinsic Conditions N2 - In this article we consider a general model for phosphorus diffusion in silicon under extrinsic doping conditions. At such high concentrations we have to include the charged species and the internal electric field of the crystal, both of which can have profound effects on diffusion. In principle, this leads to a very large number of drift--diffusion--reaction equations: one for each charge state of every species, plus one Poisson equation to describe the internal electric field (in terms of the electron/hole concentration). The number of equations can be reduced substantially by making additional assumptions on the distribution of charge states and local equilibrium assumptions concerning the reaction terms. The resulting model turns out to be very interesting for numerical investigation. We solve the problem numerically in two space dimensions with the adaptive finite element program KARDOS and describe the numerical method used here to treat the resulting drift--diffusion--reaction problem. T3 - ZIB-Report - SC-97-47 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3163 ER - TY - THES A1 - Bornemann, Folkmar A. T1 - Homogenization in Time of Singularly Perturbed Conservative Mechanical Systems N2 - We present a particular method for the explicit elimination of rapidly oscillating micro-scales in certain singularly perturbed conservative mechanical systems. Non-linear effects call for a non-trivial averaging procedure that we call {\em homogenization in time.} This method is based on energy principles and weak convergence techniques. Since non-linear functionals are in general {\em not} weakly sequentially continuous, we have to study {\em simultaneously} the weak limits of all those non-linear quantities of the rapidly oscillating components which are of importance for the underlying problem. Using the physically motivated concepts of {\em virial theorems}, {\em adiabatic invariants}, and {\em resonances}, we will be able to establish sufficiently many relations between all these weak limits, allowing to calculate them explicitly. Our approach will be {\em paradigmatical} rather than aiming at the largest possible generality. This way, we can show most clearly how concepts and notions from the physical background of the underlying mathematical problem enter and help to determine relations between weak limit quantities. In detail we will discuss natural mechanical systems with a strong constraining potential on Riemannian manifolds, the questions of realization of holonomic constraints, and singular limits of mixed quantum-classical coupling models. This latter class of problems also leads to a new proof for the adiabatic theorem of quantum mechanics. The strength of our methodology will be illustrated by applications to problems from plasma physics, molecular dynamics and quantum chemistry. T3 - ZIB-Report - SC-97-48 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3170 ER - TY - GEN A1 - Wagler, Annegret T1 - Critical Edges in Perfect Graphs and Some Polyhedral Consequences N2 - An edge $e$ of a perfect graph $G$ is called critical if $G-e$ is imperfect. For certain graphs $G-e$ of this type, we determine all minimally imperfect subgraphs. We use this knowledge to describe inequalities inducing facets of the stable set polytope associated with $G-e$.\\ T3 - ZIB-Report - SC-97-46 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3153 ER - TY - GEN A1 - Kornhuber, Ralf T1 - Globally Convergent Multigrid Methods for Porous Medium Type Problems N2 - We consider the fast solution of large, piecewise smooth minimization problems as typically arising from the finite element discretization of porous media flow. For lack of smoothness, usual Newton multigrid methods cannot be applied. We propose a new approach based on a combination of convex minization with {\em constrained} Newton linearization. No regularization is involved. We show global convergence of the resulting monotone multigrid methods and give logarithmic upper bounds for the asymptotic convergence rates. T3 - ZIB-Report - SC-97-45 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3142 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Seebass, Martin T1 - Adaptive Solutions of Nonlinear Parabolic Equations with Application to Hyperthermia Treatments N2 - We present a self-adaptive finite element method to solve nonlinear evolution problems in 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. The proposed method is applied to hyperthermia treatments to demonstrate its potential for the solving of complicated problems. T3 - ZIB-Report - SC-97-44 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3130 ER - TY - GEN A1 - Schulz, Sandra A1 - Busch, Hubert T1 - Schlussbericht des Berliner Regionalen Testbed (BRTB) Projektes N2 - Im März 1993 wurde das Projekt ,Regionales Testbed - RTB" in den DFN-Mitteilungen bundesweit mit folgenden Zielen ausgeschrieben und festgelegt: Einführung bzw. Pilotnutzung fortgeschrittener Netztechniken, Entwicklung von Anwendungsumgebungen mit Bedarf für hohe Übertragungsraten und Einsatz von Anwendungsumgebungen durch nachgewiesene Anwendergruppen. Die Ziele sollten durch die Vernetzung einer beschränkten Anzahl von Institutionen (Universitäten, Fachhochschulen und Forschungseinrichtungen) der jeweiligen Region, die sowieso schon einen hohen Kommunikationsbedarf untereinander hatten, erreicht werden. Die Berliner Universitäten, das HMI, das ISST und das LIT führten unter Federführung des ZIB für die Region Berlin ein regionales Testbed durch; dessen Projektlaufzeit lag im wesentlichen zwischen dem 1. Oktober 1994 und dem 30. September 1996. An diesem BRTB waren fünf Anwendungen beteiligt: \begin{itemize} \item Einheitliche Datenumgebung auf heterogenen Rechnersystemen \item Ein Hotline und Consulting System \item Medizinische Bildverarbeitung \item Hypermedia-Lehreinheiten in der Studentenausbildung \item Visualisierung wissenschaftlicher Daten \end{itemize} Das wesentliche Ziel, der Aufbau von finanzierbaren regionalen Breitbandnetzen als Voraussetzung für ein deutschland-weites Breitband-Wissenschaftsnetz, ist erreicht worden. Wir danken dem DFN-Verein und dem BMBF für die Förderung dieses Projektes und allen, die zu seinem Gelingen beigetragen haben. T3 - ZIB-Report - TR-97-07 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5496 ER - TY - GEN A1 - Baumann, Wolfgang A1 - Busch, Hubert A1 - Gottschewski, Jürgen A1 - Steinke, Thomas A1 - Stüben, Hinnerk T1 - Berliner Landeshöchstleistungsrechner Parallelrechner Cray T3D/T3E: Betrieb, Nutzung, Projekte, Perspektiven für den Ausbau N2 - Seit fast drei Jahren betreibt das Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) Parallelrechner der höchsten Leistungsklasse im normalen Rechenzentrumsbetrieb. Bereits im Mai 1995 hat das ZIB über seine Erfahrungen mit dem damals leistungsstärksten Parallelrechner Deutschlands berichtet. Das Gesamtkonzept des ZIB sieht weiterhin einen Höchstleistungsrechner als unabdingbaren Bestandteil des High Performance Scientific Computing (HPSC) im ZIB vor. Der vorliegende Bericht beschreibt die aktuelle Konfiguration, Betriebserfahrungen und die Rechnernutzung sowie typische Rechenleistungen, die für einzelne Anwendungsprogramme erzielt wurden. Beschreibungen der Forschungsgebiete mit den Forschungsgruppen, die den Rechner nutzen und die Anforderungen an den Rechnerausbau, die sich aus deren Arbeiten herleiten, beschließen den Bericht. T3 - ZIB-Report - TR-97-08 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5504 ER - TY - GEN A1 - Nettesheim, Peter A1 - Schütte, Christof T1 - Numerical Integrators for Quantum-Classical Molecular Dynamics N2 - It was revealed that the QCMD model is of canonical Hamiltonian form with symplectic structure, which implies the conservation of energy. An efficient and reliable integrator for transfering these properties to the discrete solution is the symplectic and explicit {\sc Pickaback} algorithm. The only drawback of this kind of integrator is the small stepsize in time induced by the splitting techniques used to discretize the quantum evolution operator. Recent investigations concerning Krylov iteration techniques result in alternative approaches which overcome this difficulty for a wide range of problems. By using iterative methods in the evaluation of the quantum time propagator, these techniques allow for the stepsize to adapt to the coupling between the classical and the quantum mechanical subsystem. This yields a drastic reduction of the numerical effort. The pros and cons of both approaches as well as the suitable applications are discussed in the last part. T3 - ZIB-Report - SC-97-42 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3111 ER - TY - GEN A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Massively Parallel Linearly-Implicit Extrapolation Algorithms as a Powerful Tool in Process Simulation. N2 - We study the parallelization of linearly--implicit extrapolation codes for the solution of large scale PDE systems and differential algebraic equations on distributed memory machines. The main advantage of these algorithms is that they enable adapativity both in time and space. Additive Krylov--Schwarz methods yield high parallel perfomance for such extrapolation methods. Our approach combines a slightly overlapping domain decomposition together with a polynomial block Neumann preconditioner and a reduced system technique. Furthermore we get important advantages through the explicit computation of the matrix--products of the preconditioner and the matrix of the linear system. The parallel algorithms exhibit scalability up to 64 processors already for medium--sized test problems. We show that the codes are really efficient in large application systems for chemical engineering problems. T3 - ZIB-Report - SC-97-43 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3127 ER - TY - GEN A1 - Schütte, Christof A1 - Bornemann, Folkmar A. T1 - Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model N2 - In molecular dynamics applications there is a growing interest in including quantum effects for simulations of larger molecules. This paper is concerned with {\em mixed quantum-classical} models which are currently discussed: the so-called QCMD model with variants and the time-dependent Born-Oppenheimer approximation. All these models are known to approximate the full quantum dynamical evolution---under different assumptions, however. We review the meaning of these assumptions and the scope of the approximation. In particular, we characterize those typical problematic situations where a mixed model might largely deviate from the full quantum evolution. One such situation of specific interest, a non-adiabatic excitation at certain energy level crossings, can promisingly be dealt with by a modification of the QCMD model that we suggest. T3 - ZIB-Report - SC-97-41 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3102 ER - TY - GEN A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - Adaptive Time-Space Discretization for Combustion Problems N2 - We present a self--adaptive finite element method to solve combustion problems in 1D, 2D, and 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. A posteriori error estimates are obtained by constructing locally higher order solutions involving all variables of the problem. Adaptive strategies such as step size control, spatial refinement and coarsening allow us to get economically an accurate solution. Various examples are presented to demonstrate practical applications of the proposed method. T3 - ZIB-Report - SC-97-40 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3094 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Polthier, Konrad T1 - Visualization and Mathematics '97 N2 - This report contains paper abstracts of the workshop "Visualization and Mathematics" held in Berlin-Dahlem in September 1997. The meeting serves as a forum for an international community of researchers and practitioners on the application of visualization techniques in mathematics and on mathematical concepts in visualization. It is the second symposium in a series of workshops bringing together mathematicians and experts from scientific visualization. The themes of the workshop include: \begin{itemize} \item - applications in differential geometry and partial differential equations \item - algorithmic aspects of adaptive and hierarchical techniques in space and time \item - time control of animated objects and corresponding algorithms \item - algorithmic representation of objects for display, storage and exchange \item - new visualization techniques for mathematical structures \item - integration of visualization with symbolic and numerical computation. \end{itemize} T3 - ZIB-Report - TR-97-06 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5480 ER - TY - GEN A1 - Dais, Dimitrios I. A1 - Henk, Martin T1 - On a series of Gorenstein cyclic quotient singularities admitting a unique projective crepant resolution. N2 - Let $G$ be a finite subgroup of SL$\left( r,% {\mathbb{C}}\right) $. In dimensions $r=2$ and $r=3$, McKay correspondence provides a natural bijection between the set of irreducible representations of $G$ and a cohomology-ring basis of the overlying space of a projective, crepant desingularization of ${\mathbb{C}}^r/G$. For $r=2$ this desingularization is unique and is known to be determined by the Hilbert scheme of the $G$% -orbits. Similar statements (including a method of distinguishing just {\it{one}} among all possible smooth minimal models of ${\mathbb{C}}^3/G$), are very probably true for all $G$'s $\subset $ SL$\left( 3,{\mathbb{C}}\right) $ too, and recent Hilbert-scheme-techniques due to Ito, Nakamura and Reid, are expected to lead to a new fascinating uniform theory. For dimensions $r\geq 4 $, however, to apply analogous techniques one needs extra modifications. In addition, minimal models of ${\mathbb{C}}^r/G$ are smooth only under special circumstances. ${\mathbb{C}}^4/\left( \hbox{\rm involution}\right) $, for instance, cannot have any smooth minimal model. On the other hand, all abelian quotient spaces which are c.i.'s can always be fully resolved by torus-equivariant, crepant, projective morphisms. Hence, from the very beginning, the question whether a given Gorenstein quotient space ${\mathbb{C}}% ^r/G$, $r\geq 4$, admits special desingularizations of this kind, seems to be absolutely crucial.\noindent In the present paper, after a brief introduction to the existence-problem of such desingularizations (for abelian $G$'s) from the point of view of toric geometry, we prove that the Gorenstein cyclic quotient singularities of type \[ \frac 1l\,\left( 1,\ldots ,1,l-\left( r-1\right) \right) \] with $l\geq r\geq 2$, have a \textit{unique }torus-equivariant projective, crepant, partial resolution, which is full'' iff either $l\equiv 0$ mod $% \left( r-1\right) $ or $l\equiv 1$ mod $\left( r-1\right) $. As it turns out, if one of these two conditions is fulfilled, then the exceptional locus of the full desingularization consists of $\lfloor\frac{l}{r-1} \rfloor $ prime divisors, $\lfloor\frac{l}{r-1} \rfloor -1$ of which are isomorphic to the total spaces of ${\mathbb{P}}_{{\mathbb{C}}}^1$-bundles over ${\mathbb{P}}_{{\mathbb{C}}% }^{r-2}$. Moreover, it is shown that intersection numbers are computable explicitly and that the resolution morphism can be viewed as a composite of successive (normalized) blow-ups. Obviously, the monoparametrized singularity-series of the above type contains (as its first member'') the well-known Gorenstein singularity defined by the origin of the affine cone which lies over the $r$-tuple Veronese embedding of ${\mathbb{P}}_{\mathbb{C}}^{r-1}$. T3 - ZIB-Report - SC-97-39 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3084 ER - TY - GEN A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Contributions to General Mixed Integer Knapsack Problems N2 - This paper deals with a general mixed integer knapsack polyhedron for which we introduce and analyze a new family of inequalities. We discuss the value of this family both from a theoretic and a computational point of view. T3 - ZIB-Report - SC-97-38 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3075 ER - TY - GEN A1 - Helmberg, Christoph A1 - Rendl, Franz T1 - A Spectral Bundle Method for Semidefinite Programming N2 - A central drawback of interior point methods for semidefinite programs is their lack of ability to exploit problem structure in cost and coefficient matrices. This restricts applicability to problems of small dimension. Typically semidefinite relaxations arising in combinatorial applications have sparse and well structured cost and coefficient matrices of huge order. We present a method that allows to compute acceptable approximations to the optimal solution of large problems within reasonable time. Semidefinite programming problems with constant trace on the primal feasible set are equivalent to eigenvalue optimization problems. These are convex nonsmooth programming problems and can be solved by bundle methods. We propose to replace the traditional polyhedral cutting plane model constructed by means of subgradient information by a semidefinite model that is tailored for eigenvalue problems. Convergence follows from the traditional approach but a proof is included for completeness. We present numerical examples demonstrating the efficacy of the approach on combinatorial examples. T3 - ZIB-Report - SC-97-37 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3067 ER - TY - GEN A1 - Deuflhard, Peter A1 - Louis, Alfred A1 - Schlegel, W. A1 - Seebass, Martin T1 - Workshop "Scientific Computing in der Medizin" SCMED '97 N2 - Die Arbeitstagung \glqq Scientific Computing in der Medizin\grqq , kurz SCMED \grq 97, findet vom 22. - 23. September 1997 im neu errichteten Gebäude des Konrad-Zuse-Zentrums auf dem Dahlemer naturwissenschaftlichen Campus der Freien Universtät Berlin statt. T3 - ZIB-Report - TR-97-05 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5474 ER - TY - GEN A1 - Lipnikov, Konstantin A1 - Deuflhard, Peter T1 - Domain Decomposition with Subdomain CCG for Material Jump Elliptic Problems. N2 - A combination of the cascadic conjugate gradient (CCG) method for homogeneous problems with a non-overlapping domain decomposition (DD) method is studied. Mortar finite elements on interfaces are applied to permit non-matching grids in neighboring subdomains. For material jump problems, the method is designed as an alternative to the cascadic methods. T3 - ZIB-Report - SC-97-36 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3057 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Martin, Alexander T1 - Frequency Assignment in Cellular Phone Networks N2 - We present a graph-theoretic model for the \emph{frequency assignment problem} in Cellular Phone Networks: Obeying several technical and legal restrictions, frequencies have to be assigned to transceivers so that interference is as small as possible. This optimization problem is NP-hard. Good approximation cannot be guaranteed, unless P = NP. We describe several assignment heuristics. These heuristics are simple and not too hard to implement. We give an assessment of the heuristics' efficiency and practical usefulness. For this purpose, typical instances of frequency assignment problems with up to 4240 transceivers and 75 frequencies of a German cellular phone network operator are used. The results are satisfying from a practitioner's point of view. The best performing heuristics were integrated into a network planning system used in practice. T3 - ZIB-Report - SC-97-35 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3044 ER - TY - GEN A1 - Schiermeyer, Ingo A1 - Tuza, Zsolt A1 - Voigt, Margit T1 - On-line rankings of graphs N2 - A (vertex) $k$-ranking of a graph $G=(V,E)$ is a mapping $ p:V\to \{1,\dots,k\}$ such that each path with endvertices of the same color $i$ contains an internal vertex of color $\ge i+1$. In the on-line coloring algorithms, the vertices $v_1,\dots,v_n$ arrive one by one in an unrestricted order, and only the edges inside the set $\{v_1,\dots,v_i\}$ are known when the color of $v_i$ has to be chosen. We characterize those graphs for which a 3-ranking can be found on-line. We also prove that the greedy (First-Fit) on-line algorithm, assigning the smallest feasible color to the next vertex at each step, generates a $(3\log_2 n)$-ranking for the path with $n \geq 2$ vertices, independently of the order in which the vertices are received. T3 - ZIB-Report - SC-97-32 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3011 ER - TY - GEN A1 - Tuza, Zsolt A1 - Voloshin, Vitaly I. T1 - Uncolorable mixed hypergraphs N2 - A mixed hypergraph ${\cal H}=(X,{\cal A},{\cal E})$ consists of the vertex set $X$ and two families of subsets: the family of edges ${\cal E}$ and the family of co-edges ${\cal A}$. In a coloring every edge $E \in {\cal E}$ has at least two vertices of different colors, while every co-edge $A \in {\cal A}$ has at least two vertices of the same color. The smallest (largest) number of colors for which there exists a coloring of a mixed hypergraph $\cal H$ using all the colors is called the lower (upper) chromatic number and is denoted $\chi ({\cal H})$ $(\bar {\chi} ({\cal H}) )$. A mixed hypergraph is called uncolorable if it admits no coloring. \par We show that there exist uncolorable mixed hypergraphs ${\cal H}=$ $(X, {\cal A}, {\cal E})$ with arbitrary difference between the upper chromatic number $\bar{\chi } ({\cal H}_{\cal A}) $ of ${\cal H}_{\cal A}=(X,{\cal A})$ and the lower chromatic number ${\chi }({\cal H}_{\cal E})$ of ${\cal H}_{\cal E}=(X,{\cal E}).$ Moreover, for any $k=\bar \chi ({\cal H}_{\cal A})- \chi ({\cal H}_{\cal E})$, the minimum number $v(k)$ of vertices of an inclusionwise minimal uncolorable mixed hypergraph is exactly $k+4.$ \par We introduce the measure of uncolorability which is called the vertex uncolorability number and propose a greedy algorithm that finds an estimate on it, and is a mixed hypergraph coloring heuristic at the same time. \par We show that the colorability problem can be expressed as an integer linear programming problem. \par Concerning particular cases, we describe those complete $(l,m)$-uniform mixed hypergraphs which are uncolorable, and observe that for given $(l,m)$ almost all complete $(l,m)$-uniform mixed hypergraphs are uncolorable, whereas generally almost all complete mixed hypergraphs are colorable. T3 - ZIB-Report - SC-97-33 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3024 ER - TY - GEN A1 - Kratochvil, Jan A1 - Tuza, Zsolt T1 - Rankings of Directed graphs N2 - A ranking of a graph is a coloring of the vertex set with positive integers such that on every path connecting two vertices of the same color, there is a vertex of larger color. We consider the directed variant of this problem, where the above condition is imposed only on those paths in which all edges are oriented in the same direction. We show that the ranking number of a directed tree is bounded by that of its longest directed path plus one, and that it can be computed in polynomial time. Unlike the undirected case, however, deciding if the ranking number of a directed (and even of an acyclic directed) graph is bounded by a constant is NP-complete. In fact, the 3-ranking of planar bipartite acyclic digraphs is already hard. T3 - ZIB-Report - SC-97-34 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3030 ER - TY - GEN A1 - Tuza, Zsolt T1 - Graph coloring with local constraints - A survey N2 - We survey the literature on those variants of the {\em chromatic number\/} problem where not only a proper coloring has to be found (i.e., adjacent vertices must not receive the same color) but some further local restrictions are imposed on the color assignment. Mostly, the {\em list colorings\/} and the {\em precoloring extensions\/} are considered. \par In one of the most general formulations, a graph $G=(V,E)$, sets $L(v)$ of admissible colors, and natural numbers $c_v$ for the vertices $v\in V$ are given, and the question is whether there can be chosen a subset $C(v)\subseteq L(v)$ of cardinality $c_v$ for each vertex in such a way that the sets $C(v),C(v')$ are disjoint for each pair $v,v'$ of adjacent vertices. The particular case of constant $|L(v)|$ with $c_v=1$ for all $v\in V$ leads to the concept of {\em choice number}, a graph parameter showing unexpectedly different behavior compared to the chromatic number, despite these two invariants have nearly the same value for almost all graphs. \par To illustrate typical techniques, some of the proofs are sketched. T3 - ZIB-Report - SC-97-31 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3003 ER - TY - GEN A1 - Tuza, Zsolt A1 - Wagler, Annegret T1 - Minimally non-preperfect graphs of small maximum degree N2 - A graph $G$ is called preperfect if each induced subgraph $G' \subseteq G$ of order at least 2 has two vertices $x,y$ such that either all maximum cliques of $G'$ containing $x$ contain $y$, or all maximum indepentent sets of $G'$ containing $y$ contain $x$, too. Giving a partial answer to a problem of Hammer and Maffray [Combinatorica 13 (1993), 199-208], we describe new classes of minimally non-preperfect graphs, and prove the following characterizations: \begin{itemize} \item[(i)] A graph of maximum degree 4 is minimally non-preperfect if and only if it is an odd cycle of length at least 5, or the complement of a cycle of length 7, or the line graph of a 3-regular 3-connected bipartite graph. \item[(ii)] If a graph $G$ is not an odd cycle and has no isolated vertices, then its line graph is minimally non-preperfect if and only if $G$ is bipartite, 3-edge-connected, regular of degree $d$ for some $d \ge 3$, and contains no 3-edge-connected $d'$-regular subgraph for any $3 \le d' \le d$. \end{itemize} T3 - ZIB-Report - SC-97-28 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2971 ER - TY - GEN A1 - Henk, Martin A1 - Weismantel, Robert T1 - Hilbert bases of cones related to simultaneous Diophantine approximations and linear Diophantine equations N2 - This paper investigates properties of the minimal integral solutions of a linear diophantine equation. We present best possible inequalities that must be satisfied by these elements which improves on former results. We also show that the elements of the minimal Hilbert basis of the dual cone of all minimal integral solutions of a linear diophantine equation yield best approximations of a rational vector ``from above''. Relations between these cones are applied to the knapsack problem. T3 - ZIB-Report - SC-97-29 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2989 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Weismantel, Robert T1 - Set Packing Relaxations of Some Integer Programs N2 - This paper is about {\em set packing relaxations\/} of combinatorial optimization problems associated with acyclic digraphs and linear orderings, cuts and multicuts, and vertex packings themselves. Families of inequalities that are valid for such a relaxation as well as the associated separation routines carry over to the problems under investigation. T3 - ZIB-Report - SC-97-30 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2998 ER - TY - GEN A1 - Eisenblätter, Andreas T1 - A Frequency Assignment Problem in Cellular Phone Networks N2 - We present a mathematical formulation of a \emph{frequency assignment problem} encountered in cellular phone networks: frequencies have to be assigned to stationary transceivers (carriers) such that as little interference as possible is induced while obeying several technical and legal restrictions. The optimization problem is NP-hard, and no good approximation can be guaranteed---unless P = NP. We sketch some starting and improvement heuristics, and report on their successful application for solving the frequency assignment problem under consideration. Computational results on real-world instances with up to 2877 carriers and 50 frequencies are presented. T3 - ZIB-Report - SC-97-27 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2965 ER - TY - GEN A1 - Deuflhard, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Beck, Rudolf A1 - Hege, Hans-Christian T1 - Hyperthermia Treatment Planning in Clinical Cancer Therapy: Modelling, Simulation and Visualization N2 - \noindent The speaker and his co-workers in Scientific Computing and Visualization have established a close cooperation with medical doctors at the Rudolf--Virchow--Klinikum of the Humboldt University in Berlin on the topic of regional hyperthermia. In order to permit a patient--specific treatment planning, a special software system ({\sf\small HyperPlan}) has been developed. \noindent A mathematical model of the clinical system ({\it radio frequency applicator with 8 antennas, water bolus, individual patient body}) involves Maxwell's equations in inhomogeneous media and a so--called bio--heat transfer PDE describing the temperature distribution in the human body. The electromagnetic field and the thermal phenomena need to be computed at a speed suitable for the clinical environment. An individual geometric patient model is generated as a quite complicated tetrahedral ``coarse'' grid (several thousands of nodes). Both Maxwell's equations and the bio--heat transfer equation are solved on that 3D--grid by means of {\em adaptive} multilevel finite element methods, which automatically refine the grid where necessary in view of the required accuracy. Finally optimal antenna parameters for the applicator are determined . \noindent All steps of the planning process are supported by powerful visualization methods. Medical images, contours, grids, simulated electromagnetic fields and temperature distributions can be displayed in combination. A number of new algorithms and techniques had to be developed and implemented. Special emphasis has been put on advanced 3D interaction methods and user interface issues. T3 - ZIB-Report - SC-97-26 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2958 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Information Services for Mathematics in the Internet (Math-Net) N2 - The present paper gives a brief description of the Math-Net project which is carried out by nine mathematical institutions in Germany, supported by Deutsches Forschungsnetz (DFN) and Deutsche Telekom. The project aims at setting up the technical and organizational infrastructure for efficient, inexpensive and user-driven information services for mathematics. With the aid of active (structured retrieval mechanisms) and passive (profile services) components, electronic mathematical information in Germany will be made available to the scientist at his workplace. The emphasis is put on information about publications, software and data collections, teaching and research activities, but also on organizational and bibliographical information. Decentral organization structures, distributed search systems as well as the use of meta-information (metadata) in accordance with the Dublin Core (hopefully) guarantee a longterm, high-quality repository of data. The well-known mathematical software and data collection netlib\/ will be used as an example to illustrate how such a collection can be adapted to Math-Net. An integration of netlib into HyperWave offers additional perspectives and functionalities. T3 - ZIB-Report - SC-97-25 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2949 ER - TY - GEN A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - Capacity and Survivability Models for Telecommunication Networks N2 - Designing low-cost networks that survive certain failure situations is one of the prime tasks in the telecommunication industry. In this paper we survey the development of models for network survivability used in practice in the last ten years. We show how algorithms integrating polyhedral combinatorics, linear programming, and various heuristic ideas can help solve real-world network dimensioning instances to optimality or within reasonable quality guarantees in acceptable running times. The most general problem type we address is the following. Let a communication demand between each pair of nodes of a telecommunication network be given. We consider the problem of choosing, among a discrete set of possible capacities, which capacity to install on each of the possible edges of the network in order to (i) satisfy all demands, (ii) minimize the building cost of the network. \noindent In addition to determining the network topology and the edge capacities we have to provide, for each demand, a routing such that (iii) no path can carry more than a given percentage of the demand, (iv) no path in the routing exceeds a given length. \noindent We also have to make sure that (v) for every single node or edge failure, a certain percentage of the demand is reroutable. \noindent Moreover, for all failure situations feasible routings must be computed. The model described above has been developed in cooperation with a German mobile phone provider. We present a mixed-integer programming formulation of this model and computational results with data from practice. T3 - ZIB-Report - SC-97-24 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2931 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Telebus Berlin: Vehicle Scheduling in a Dial-a-Ride System N2 - {\em Telebus\/} is Berlin's dial-a-ride system for handicapped people that cannot use the public transportation system. The service is provided by a fleet of about 100 mini-busses and includes aid to get in and out of the vehicle. Telebus has between 1,000 and 1,500 transportation requests per day. The problem arises to schedule these requests into the vehicles such that punctual service is provided while operation costs should be minimum. Additional constraints include pre-rented vehicles, fixed bus driver shift lengths, obligatory breaks, and different vehicle capacities. We use a {\em set partitioning\/} approach for the solution of the bus scheduling problem that consists of two steps. The first {\em clustering\/} step identifies segments of possible bus tours (``orders'') such that more than one person is transported at a time; the aim in this step is to reduce the size of the problem and to make use of larger vehicle capacities. The problem to select a set of orders such that the traveling distance of the vehicles within the orders is minimal is a set partitioning problem that we can solve to optimality. In the second step the selected orders are {\em chained\/} to yield possible bus tours respecting all side constraints. The problem to select a set of such bus tours such that each order is serviced once and the total traveling distance of the vehicles is minimum is again a set partitioning problem that we solve approximately. We have developed a computer system for the solution of the bus scheduling problem that includes a branch-and-cut algorithm for the solution of the set partitioning problems. A version of this system is in operation at Telebus since July 1995. Its use made it possible that Telebus can service today about 30\% more requests per day for the same amount of money than before. T3 - ZIB-Report - SC-97-23 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2925 ER - TY - GEN A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - Cost-Efficient Network Synthesis from Leased Lines N2 - Given a communication demand between each pair of nodes of a network we consider the problem of deciding what capacity to install on each edge of the network in order to minimize the building cost of the network and to satisfy the demand between each pair of nodes. The feasible capacities that can be leased from a network provider are of a particular kind in our case. There are a few so-called basic capacities having the property that every basic capacity is an integral multiple of every smaller basic capacity. An edge can be equipped with a capacity only if it is an integer combination of the basic capacities. We treat, in addition, several restrictions on the routings of the demands (length restriction, diversification) and failures of single nodes or single edges. We formulate the problem as a mixed integer linear programming problem and develop a cutting plane algorithm as well as several heuristics to solve it. We report on computational results for real world data. T3 - ZIB-Report - SC-97-22 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2912 ER - TY - GEN A1 - Böing, Harald A1 - Koepf, Wolfram T1 - REDUCE Package for the Indefinite and Definite Summation of q-hypergeometric Terms N2 - This package is an implementation of the $q$-analogues of Gosper's and Zeilberger's algorithm for indefinite, and definite summation of $q$-hypergeometric terms, respectively. An expression $a_k$ is called a {\sl $q$-hypergeometric term}, if $a_{k}/a_{k-1}$ is a rational function with respect to $q^k$. Most $q$-terms are based on the {\sl $q$-shifted factorial} or {\sl qpochhammer}. Other typical $q$-hypergeometric terms are ratios of products of powers, $q$-factorials, $q$-binomial coefficients, and $q$-shifted factorials that are integer-linear in their arguments. T3 - ZIB-Report - TR-97-04 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5460 ER - TY - GEN T1 - Jahresbericht 1996 T3 - Jahresbericht - 1996 KW - Annual Report Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9712 SN - 0934-5892 ER - TY - GEN A1 - Böröczky, Karoly A1 - Henk, Martin T1 - Random Projections of Regular Polytopes N2 - Based on an approach of Affentranger&Schneider we give an asymptotic formula for the expected number of $k$-faces of the orthogonal projection of a regular $n$-crosspolytope onto a randomly chosen isotopic subspace of fixed dimension, as $n$ tends to infinity. In particular, we present a precise asymptotic formula for the (spherical) volume of spherical regular simplices, which generalizes Daniel's formula. T3 - ZIB-Report - SC-97-21 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2903 ER - TY - GEN A1 - Maas, Ulrich T1 - Efficient Calculation of Intrinsic Low-Dimensional Manifolds for the Simplification of Chemical Kinetics N2 - During the last years the interest in the numerical simulation of reacting flows has grown considerably and numerical methods are available, which allow to couple chemical kinetics with flow and molecular transport. The use of detailed physical and chemical models, involving several hundred species, is restricted to very simple flow configurations like one-dimensional systems or two-dimensional systems with very simple geometries, and models are required, which simplify chemistry without sacrificing accuracy. One method to simplify the chemical kinetics is based on Intrinsic Low-Dimensional Manifolds (ILDM). They present attractors for the chemical kinetics, i.e. fast chemical processes relax towards them, and slow chemical processes represent movements within the manifolds. Thus the identification of the ILDMs allows a decoupling of the fast time scales. The concept has been verified by many different reacting flow calculations. However, one remaining problem of the method is the efficient calculation of the low-dimensional manifolds. This problem is addressed in this paper. We present an efficient, robust method, which allows to calculate intrinsic low-dimensional manifolds of chemical reaction systems. It is based on a multi-dimensional continuation process. Examples are shown for a typical combustion system. The method is not restricted to this class, but can be applied to other chemical systems, too. T3 - ZIB-Report - SC-97-20 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2898 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the M(n)/M(m)/s Queue with impatient Calls N2 - The paper is concerned with the analysis of an $s$ server queueing system in which the calls become impatient and leave the system if their waiting time exceeds their own patience. The individual patience times are assumed to be i.i.d.\ and arbitrary distributed. The arrival and service rate may depend on the number of calls in the system and in service, respectively. For this system, denoted by $M(n)/M(m)/s+GI$, where $m=\min(n,s)$ is the number of busy servers in the system, we derive a system of integral equations for the vector of the residual patience times of the waiting calls and their original maximal patience times. By solving these equations explicitly we get the stability condition and, for the steady state of the system, the occupancy distribution and various waiting time distributions. As an application of the \mbox{$M(n)/M(m)/s+GI$} system we give a performance analysis of an Automatic Call Distributor system (ACD system) of finite capacity with outbound calls and impatient inbound calls, especially in case of patience times being the minimum of constant and exponentially distributed times. T3 - ZIB-Report - SC-97-19 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2885 ER - TY - GEN A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - Three-Dimensional Fully Adaptive Solution of Thermo-Diffusive Flame Propagation Problems N2 - In this paper we present a self--adaptive finite element method to solve flame propagation problems in 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. The proposed method is applied to an unsteady thermo--diffusive combustion model to demonstrate its potential for the solution of complicated problems. T3 - ZIB-Report - SC-97-18 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2879 ER - TY - GEN A1 - Löbel, Andreas T1 - Experiments with a Dantzig-Wolfe Decomposition for Multiple-Depot Vehicle Scheduling Problems N2 - In this paper, we present a Dantzig-Wolfe decomposition for the $NP$-hard multiple-depot vehicle scheduling problem in public mass transit. It turned out that such a decomposition approach is an unsuitable method to solve such kind of multicommodity flow problems. The major obstacle to solve such problems is that the continuous master problem relaxations become too hard to be solved efficiently. Especially for problems with more than one thousand timetabled trips, the LU factorization in solving a restricted master problem takes far too much time. We will describe our computational experiments in detail and discuss the reasons why the decomposition method fails in this case. Our computational investigations are based on real-world problems from the city of Hamburg with up to 2,283 timetabled trips. Our decomposition implementation is compared with a delayed column generation to solve the linear programming (LP) relaxation directly. This LP method can solve the LP relaxations of the integer linear programming formulation exactly for truly large-scale real-world problems of the cities of Berlin and Hamburg. T3 - ZIB-Report - SC-97-16 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2852 ER - TY - GEN A1 - Löbel, Andreas T1 - Solving Large-Scale Multiple-Depot Vehicle Scheduling Problems N2 - This paper presents an integer linear programming approach with delayed column generation for the {\em NP} Multiple-Depot Vehicle Scheduling Problem (MDVSP) in public mass transit. We describe in detail all basic ingredients of our approach that are indispensable to solve truly large-scale real-world instances to optimality, and we report on computational investigations that are based on real-world instances from the city of Berlin, the city of Hamburg, and the region around Hamburg. These real-world instances have up to 25 thousand timetabled trips and 70 million dead-head trips. Computational tests using the data of the Hamburger Hochbahn AG indicate savings of several vehicles and a cost reduction of about 10\% compared with the solution provided by HOT II, the vehicle scheduling tool of the HanseCom GmbH, Hamburg. Parts of our algorithms are already integrated in the BERTA system of the Berliner Verkehrsbetriebe (BVG) and will soon be integrated in the MICROBUS system of the Gesellschaft für Informatik, Verkehrs- und Umweltplanung mbH (IVU), Berlin. T3 - ZIB-Report - SC-97-17 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2866 ER - TY - GEN A1 - Deuflhard, Peter A1 - Reich, Sebastian T1 - 2nd International Symposium Algorithms for Macromolecular Modelling N2 - The report contains the program and the collected abstracts of the 2nd International Symposium ``Algorithms for Macromolecular Modelling''. T3 - ZIB-Report - TR-97-03 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5455 ER - TY - GEN A1 - Steinbach, Marc T1 - Optimal Motion Design Using Inverse Dynamics. N2 - Increasing demands on industrial robot operation call for optimal motion planning based on dynamic models. The resulting mathematical problems can be handled efficiently by sparse direct boundary value problem methods. Within this framework we propose a new solution technique that is closely related to the conventional kinematic approach: it eliminates the need for numerical integration of differential equations. First optimization results on a real life transport maneuver demonstrate that the technique may save over 50\,\%\ computation time. T3 - ZIB-Report - SC-97-12 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2818 ER - TY - GEN A1 - Henk, Martin A1 - Weismantel, Robert T1 - Test sets of the knapsack problem and simultaneous diophantine approximation N2 - This paper deals with the study of test sets of the knapsack problem and simultaneous diophantine approximation. The Graver test set of the knapsack problem can be derived from minimal integral solutions of linear diophantine equations. We present best possible inequalities that must be satisfied by all minimal integral solutions of a linear diophantine equation and prove that for the corresponding cone the integer analogue of Caratheodory's theorem applies when the numbers are divisible. We show that the elements of the minimal Hilbert basis of the dual cone of all minimal integral solutions of a linear diophantine equation yield best approximations of a rational vector ``from above''. A recursive algorithm for computing this Hilbert basis is discussed. We also outline an algorithm for determining a Hilbert basis of a family of cones associated with the knapsack problem. T3 - ZIB-Report - SC-97-13 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2825 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Ferreira, Carlos E. A1 - Martin, Alexander T1 - Matrix Decomposition by Branch-and-Cut N2 - In this paper we investigate whether matrices arising from linear or integer programming problems can be decomposed into so-called {\em bordered block diagonal form}. More precisely, given some matrix $A$, we try to assign as many rows as possible to some number of blocks of limited size such that no two rows assigned to different blocks intersect in a common column. Bordered block diagonal form is desirable because it can guide and speed up the solution process for linear and integer programming problems. We show that various matrices from the %LP- and MIP-libraries \Netlib{} and MIPLIB can indeed be decomposed into this form by computing optimal decompositions or decompositions with proven quality. These computations are done with a branch-and-cut algorithm based on polyhedral investigations of the matrix decomposition problem. T3 - ZIB-Report - SC-97-14 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2839 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Ferreira, Carlos E. A1 - Martin, Alexander T1 - Decomposing Matrices into Blocks N2 - In this paper we investigate whether matrices arising from linear or integer programming problems can be decomposed into so-called {\em bordered block diagonal form}. More precisely, given some matrix $A$, we try to assign as many rows as possible to some number of blocks of limited size such that no two rows assigned to different blocks intersect in a common column. Bordered block diagonal form is desirable because it can guide and speed up the solution process for linear and integer programming problems. We show that various matrices from the LP- and MIP-libraries NETLIB and MITLIB can indeed be decomposed into this form by computing optimal decompositions or decompositions with proven quality. These computations are done with a branch-and-cut algorithm based on polyhedral investigations of the matrix decomposition problem. In practice, however, one would use heuristics to find a good decomposition. We present several heuristic ideas and test their performance. Finally, we investigate the usefulness of optimal matrix decompositions into bordered block diagonal form for integer programming by using such decompositions to guide the branching process in a branch-and-cut code for general mixed integer programs. T3 - ZIB-Report - SC-97-15 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2849 ER - TY - GEN A1 - Heroth, Jörg T1 - Are Sparse Grids Suitable for the Tabulation of Reduced Chemical Systems? N2 - Reduced chemical systems are used in the numerical simulation of combustion processes. An automatic approach to generate a reduced model is the so-called intrinsic-low-dimensional manifold (ILDM) by {\sc Maas and Pope}. Thereby, the system state is tabulated as a function of some parameters. The paper analyses the storage requirements for usual interpolation schemes and for sparse grids. It also estimates the response time and gives a short description of an implementation. T3 - ZIB-Report - TR-97-02 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5441 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Optimierung des Berliner Behindertenfahrdienstes N2 - In diesem Artikel geben wir einen Überblick über das Telebus-Projekt am Konrad-Zuse-Zentrum, Berlin, durch das der Behindertenfahrdienst in Berlin reorganisiert und optimiert wurde. Wir berichten kurz über die mathematischen Probleme und, etwas ausführlicher, über die nicht-mathematischen Schwierigkeiten, die bei der Durchführung dieses Projektes auftraten. T3 - ZIB-Report - SC-97-10 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2799 ER - TY - GEN A1 - Giloi, Wolfgang K. T1 - Die Ungnade der frühen Geburt N2 - Konrad Zuse ist unserem Land bekannt als der Computerpionier, der den ersten funktionstüchtigen Rechner in der Geschichte der Menschheit realisierte. Weniger bekannt ist aber immer noch die Tatsache, daß er mit seinem Plankalkül auch die erste höhere Programmiersprache der Welt entwickelte. Zuse hatte bereits 1945 nicht nur klare Vorstellungen über die Konzepte von höheren Programmiersprachen, sondern auch über die Programmierung von Anwendungen der künstlichen Intelligenz wie der relationalen Datenspeicherung oder dem Schachspiel. Dies macht ihn auch zum ersten Informatiker der Welt und darüber hinaus zum Erfinder der künstlichen Intelligenz. T3 - ZIB-Report - SC-97-09 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2780 ER - TY - GEN A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - A polyhedral study of the asymmetric travelling salesman problem with time windows N2 - The asymmetric travelling salesman problem with time windows (ATSP-TW) is a basic model for scheduling and routing applications. In this paper we present a formulation of the problem involving only 0/1-variables associated with the arcs of the underlying digraph. This has the advantage of avoiding additional variables as well as the associated (typically very ineffective) linking constraints. In the formulation, time window restrictions are modelled by means of ``infeasible path elimination'' constraints. We present the basic form of these constraints along with some possible strengthenings. Several other classes of valid inequalities derived from related asymmetric travelling salesman problems are also described, along with a lifting theorem. We also study the ATSP-TW polytope, $P_{TW}$, defined as the convex hull of the integer solutions of our model. We show that determining the dimension of $P_{TW}$ is strongly {\em NP}--complete problem, even if only one time window is present. In this latter case, we provide a minimal equation system for $P_{TW}$. Computational experiments on the new formulation are reported in a companion paper [1997] where we show that it outperforms alternative formulations on some classes of problem instances. T3 - ZIB-Report - SC-97-11 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2807 ER - TY - GEN A1 - Friese, Tilmann T1 - MATLAB-Programme zur Lösung von Eigenwertproblemen mit einem adaptiven, nichtlinearen Mehrgitter-Verfahren. N2 - Der Report beschreibt ein {\sc Matlab}--Programmpaket zur Bestimmung von Eigenlösungen der skalaren, komplexen Helmholtzgleichung auf einem zweidimensionalen Gebiet. Die Programme ermöglichen die Berechnung der $q$ Eigenwerte mit kleinstem Realteil und der korrespondierenden Eigenfunktionen über adaptiv verfeinerten Gittern sowie die grafische Darstellung der Lösungen. Die bei der Diskretisierung entstehenden algebraischen Eigenwertprobleme werden mit einem nichtlinearen Mehrgitter--Verfahren gelöst. T3 - ZIB-Report - TR-97-01 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5438 ER - TY - GEN A1 - Mars, Marc A1 - Wolf, Thomas T1 - G2 Perfect-Fluid Cosmologies with a proper conformal Killing vector N2 - We study the Einstein field equations for spacetimes admitting a maximal two-dimensional abelian group of isometries acting orthogonally transitively on spacelike surfaces and, in addition, with at least one conformal Killing vector. The three-dimensional conformal group is restricted to the case when the two-dimensional abelian isometry subalgebra is an ideal and it is also assumed to act on non-null hypersurfaces (both, spacelike and timelike cases are studied). We consider both, diagonal and non-diagonal metrics and find all the perfect-fluid solutions under these assumptions (except those already known). We find four families of solutions, each one containing arbitrary parameters for which no differential equations remain to be integrated. We write the line-elements in a simplified form and perform a detailed study for each of these solutions, giving the kinematical quantities of the fluid velocity vector, the energy-density and pressure, values of the parameters for which the energy conditions are fulfilled everywhere, the Petrov type, the singularities in the spacetimes and the Friedmann-Lema\^{\i}tre-Robertson-Walker metrics contained in each family. T3 - ZIB-Report - SC-97-08 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2774 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - On the Singular Limit of the Quantum-Classical Molecular Dynamics Model N2 - \noindent In molecular dynamics applications there is a growing interest in so-called {\em mixed quantum-classical} models. These models describe most atoms of the molecular system by the means of classical mechanics but an important, small portion of the system by the means of quantum mechanics. A particularly extensively used model, the QCMD model, consists of a {\em singularly perturbed}\/ Schrödinger equation nonlinearly coupled to a classical Newtonian equation of motion. This paper studies the singular limit of the QCMD model for finite dimensional Hilbert spaces. The main result states that this limit is given by the time-dependent Born-Oppenheimer model of quantum theory---provided the Hamiltonian under consideration has a smooth spectral decomposition. This result is strongly related to the {\em quantum adiabatic theorem}. The proof uses the method of {\em weak convergence} by directly discussing the density matrix instead of the wave functions. This technique avoids the discussion of highly oscillatory phases. On the other hand, the limit of the QCMD model is of a different nature if the spectral decomposition of the Hamiltonian happens not to be smooth. We will present a generic example for which the limit set is not a unique trajectory of a limit dynamical system but rather a {\em funnel} consisting of infinitely many trajectories. T3 - ZIB-Report - SC-97-07 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2761 ER - TY - GEN A1 - Koepf, Wolfram A1 - Schmersau, Dieter T1 - Representations of Orthogonal Polynomials N2 - {\small Zeilberger's algorithm provides a method to compute recurrence and differential equations from given hypergeometric series representations, and an adaption of Almquist and Zeilberger computes recurrence and differential equations for hyperexponential integrals. Further versions of this algorithm allow the computation of recurrence and differential equations from Rodrigues type formulas and from generating functions. In particular, these algorithms can be used to compute the differential/difference and recurrence equations for the classical continuous and discrete orthogonal polynomials from their hypergeometric representations, and from their Rodrigues representations and generating functions. In recent work, we used an explicit formula for the recurrence equation of families of classical continuous and discrete orthogonal polynomials, in terms of the coefficients of their differential/difference equations, to give an algorithm to identify the polynomial system from a given recurrence equation. In this article we extend these results be presenting a collection of algorithms with which any of the conversions between the differential/difference equation, the hypergeometric representation, and the recurrence equation is possible. The main technique is again to use explicit formulas for structural identities of the given polynomial systems.} T3 - ZIB-Report - SC-97-06 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2756 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Zöckler, Malte T1 - A Generalized Marching Cubes Algorithm Based on Non-Binary Classifications N2 - We present a new technique for generating surface meshes from a uniform set of discrete samples. Our method extends the well-known marching cubes algorithm used for computing polygonal isosurfaces. While in marching cubes each vertex of a cubic grid cell is binary classified as lying above or below an isosurface, in our approach an arbitrary number of vertex classes can be specified. Consequently the resulting surfaces consist of patches separating volumes of two different classes each. Similar to the marching cubes algorithm all grid cells are traversed and classified according to the number of different vertex classes involved and their arrangement. The solution for each configuration is computed based on a model that assigns probabilities to the vertices and interpolates them. We introduce an automatic method to find a triangulation which approximates the boundary surfaces - implicitly given by our model - in a topological correct way. Look-up tables guarantee a high performance of the algorithm. In medical applications our method can be used to extract surfaces from a 3D segmentation of tomographic images into multiple tissue types. The resulting surfaces are well suited for subsequent volumetric mesh generation, which is needed for simulation as well as visualization tasks. The proposed algorithm provides a robust and unique solution, avoiding ambiguities occuring in other methods. The method is of great significance in modeling and animation too, where it can be used for polygonalization of non-manifold implicit surfaces. T3 - ZIB-Report - SC-97-05 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2741 ER - TY - GEN A1 - Pflug, Georg Ch. A1 - Ruszczynski, Andrzej A1 - Schultz, Rüdiger T1 - On the Glivenko-Cantelli Problem in Stochastic Programming: Mixed-Integer Linear Recourse N2 - Expected recourse functions in linear two-stage stochastic programs with mixed-integer second stage are approximated by estimating the underlying probability distribution via empirical measures. Under mild conditions, almost sure uniform convergence of the empirical means to the original expected recourse function is established. T3 - ZIB-Report - SC-97-04 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2739 ER - TY - GEN A1 - Steinbach, Marc A1 - Bock, H. Georg A1 - Kostin, Georgii V. A1 - Longman, Richard W. T1 - Mathematical Optimization in Robotics: Towards Automated High Speed Motion Planning N2 - \def\KukaRob {{\sf KUKA IR\,761}} {\small Industrial robots have greatly enhanced the performance of automated manufacturing processes during the last decades. International competition, however, creates an increasing demand to further improve both the accuracy of off-line programming and the resulting cycle times on production lines. To meet these objectives, validated dynamic robot models are required. We describe in detail the development of a generic dynamic model, specialize it to an actual industrial robot \KukaRob, and discuss the problem of dynamic calibration. Efficient and robust trajectory optimization algorithms are then presented which, when integrated into a CAD system, are suitable for routine application in an industrial environment. Our computational results for the \KukaRob\ robot performing a real life transport maneuver show that considerable gains in productivity can be achieved by minimizing the cycle time.} T3 - ZIB-Report - SC-97-03 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2722 ER - TY - GEN A1 - Helmberg, Christoph A1 - Weismantel, Robert T1 - Cutting Plane Algorithms for Semidefinite Relaxations N2 - We investigate the potential and limits of interior point based cutting plane algorithms for semidefinite relaxations on basis of implementations for max-cut and quadratic 0-1 knapsack problems. Since the latter has not been described before we present the algorithm in detail and include numerical results. T3 - ZIB-Report - SC-97-02 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2719 ER - TY - GEN A1 - Dais, Dimitrios I. A1 - Henk, Martin A1 - Ziegler, Günter M. T1 - All Abelian Quotient C.I.-Singularities Admit Projective Crepant Resolutions in All Dimensions N2 - \def\Bbb{\mathbb} For Gorenstein quotient spaces $\Bbb{C}^d/G$, a direct generalization of the classical McKay correspondence in dimensions $d\geq 4$ would primarily demand the existence of projective, crepant desingularizations. Since this turned out to be not always possible, Reid asked about special classes of such quotient spaces which would satisfy the above property. We prove that the underlying spaces of all Gorenstein abelian quotient singularities, which are embeddable as complete intersections of hypersurfaces in an affine space, have torus-equivariant projective crepant resolutions in all dimensions. We use techniques from toric and discrete geometry. T3 - ZIB-Report - SC-97-01 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2708 ER - TY - GEN A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Hege, Hans-Christian T1 - Fast Display of Illuminated Field Lines N2 - A new technique for interactive vector field visualization using large numbers of properly illuminated field lines is presented. Taking into account ambient, diffuse, and specular reflection terms as well as transparency and depth cueing, we employ a realistic shading model which significantly increases quality and realism of the resulting images. While many graphics workstations offer hardware support for illuminating surface primitives, usually no means for an accurate shading of line primitives are provided. However, we show that proper illumination of lines can be implemented by exploiting the texture mapping capabilities of modern graphics hardware. In this way high rendering performance with interactive frame rates can be achieved. We apply the technique to render large numbers of integral curves of a vector field. The impression of the resulting images can be further improved by a number of visual enhancements, like transparency and depth-cueing. We also describe methods for controlling the distribution of field lines in space. These methods enable us to use illuminated field lines for interactive exploration of vector fields. T3 - ZIB-Report - SC-96-58 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2686 ER - TY - GEN A1 - Battke, Henrik A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast Line Integral Convolution for Arbitrary Surfaces in 3D N2 - We describe an extension of the line integral convolution method (LIC) for imaging of vector fields on arbitrary surfaces in 3D space. Previous approaches were limited to curvilinear surfaces, i.e.~surfaces which can be parametrized globally using 2D-coordinates. By contrast our method also handles the case of general, possibly multiply connected surfaces. The method works by tesselating a given surface with triangles. For each triangle local euclidean coordinates are defined and a local LIC texture is computed. No scaling or distortion is involved when mapping the texture onto the surface. The characteristic length of the texture remains constant. In order to exploit the texture hardware of modern graphics computers we have developed a tiling strategy for arranging a large number of triangular texture pieces within a single rectangular texture image. In this way texture memory is utilized optimally and even large textured surfaces can be explored interactively. T3 - ZIB-Report - SC-96-59 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2690 ER - TY - THES A1 - Rambau, Jörg T1 - Polyhedral Subdivisions and Projections of Polytopes N2 - The present dissertation deals with the structure of polyhedral subdivisions of point configurations. Of particular interest are the global properties of the set of all subdivisions of a given point configuration. An important open problem in this context is the following: can one always transform any triangulation of a given point configuration to any other triangulation of the same configuration by means of bistellar operations? In other words, is the set of all triangulations of a given point configuration always bistellarly connected? The results presented in this thesis contribute progress from two directions. \begin{itemize} \item The set of all subdivisions that are induced by a polytope projection is in general not bistellarly connected in a generalized sense. This result is obtained by constructing a counterexample to the so-called Generalized Baues Conjecture.'' \item The set of all triangulations of a cyclic polytope forms a bounded poset. The covering relations are given by increasing bistellar operations. Thus we get an affirmative answer to the above question in the case of cyclic polytopes. \end{itemize} In the introduction, the mathematical environment of the structures under consideration is illuminated. The "Generalized Baues Conjecture" has connections to various mathematical concepts, such as combinatorial models for loop spaces, discriminants of polynomials in several variables, etc. The triangulation posets of cyclic polytopes are natural generalizations of the well-studied Tamari lattices in order theory. Moreover, there is a connection to the higher Bruhat orders, which have similar structural properties. As a by-product, the investigations yield the shellability of all triangulations of cyclic polytopes without new vertices. This is in particular interesting because most triangulations of cyclic polytopes are non-regular. N2 - Die vorliegende Dissertation beschäftigt sich mit strukturellen Fragen in der Theorie der polyedrischen Unterteilungen von Punktkonfigurationen. Hierbei sind vor allem globale Eigenschaften der Menge aller Unterteilungen einer gegebenen Punktkonfiguration von Interesse. Eine wichtige ungelöste Frage in diesem Zusammenhang ist die folgende: Ist es immer möglich, von einer beliebigen Triangulierung einer gegebenen Punktkonfiguration zu jeder anderen Triangulierung derselben Konfiguration zu gelangen, indem man sogenannte bistellare Operationen durchführt? Mit anderen Worten, ist die Menge aller Triangulierungen einer gegebenen Punktkonfiguration stets bistellar zusammenhängend? Die Ergebnisse der vorliegenden Doktorarbeit liefern auf zwei Seiten dieser nach wie vor offenen Frage Fortschritte: \begin{itemize} \item Die Menge aller durch eine Polytopprojektion induzierten Unterteilungen ist nicht immer --- in einem verallgemeinerten Sinne --- bistellar zusammenhängend. Dieses Resultat wird durch ein Gegenbeispiel zur sogenannten "Verallgemeinerten Baues Vermutung"' erzielt. \item Die Menge aller Triangulierungen eines zyklischen Polytops bildet eine beschränkte Halbordnung. Die Ueberdeckungsrelationen sind gerichtete bistellare Operationen. Für zyklische Polytope ist die obige Frage nach bistellarem Zusammenhang also positiv beantwortet. \end{itemize} In der Einleitung wird das mathematische Umfeld der betrachteten Strukturen näher beleuchtet: Die "Verallgemeinerte Baues Vermutung" steht in Verbindung mit verschiedensten mathematischen Konzepten, angefangen von kombinatorischen Modellen von Schleifenräumen bis hin zu Diskriminanten von Polynomen in mehreren Variablen. Die Triangulierungs-Halbordnungen von zyklischen Polytopen sind zugleich natürliche Verallgemeinerungen der gut studierten Tamari-Verbände in der Ordnungstheorie. Ausserdem existiert ein Zusammenhang mit den höheren Bruhat-Ordnungen, die ähnliche Struktureigenschaften aufweisen. Ein Nebenprodukt der Untersuchungen ist die Schälbarkeit aller Triangulierungen von zyklischen Polytopen ohne neue Ecken. Das ist um so interessanter, da die meisten Triangulierungen von zyklischen Polytopen nicht-regulär sind. KW - polyedrische Unterteilung KW - Triangulierung KW - Verallgemeinertes Baues-Problem KW - Zyklisches Polytop KW - Höhere Bruhat-Ordnung KW - polyhedral subdivision KW - triangulation KW - Generalized Baues Problem KW - cyclic polytope KW - higher Bruhat order Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10271 SN - 3-8265-1955-8 ER - TY - GEN A1 - Maas, Ulrich A1 - Nowak, Ulrich T1 - An adaptive method of lines for the simulation of complex laminar combustion processes N2 - For the simulation of one-dimensional flame configurations reliabl e numerical tools are needed which have to be both highly efficient (large num ber of parametric calculations) and at the same time accurate (in order t o avoid numerical errors). This can only be accomplished using fully adapt ive discretization techniques both in space and time together with a c ontrol of the discretization error. We present a method which accomplishes this task. It is based on a n adative MOL (method of lines) treatment. Space discretization is done by means of finite difference approxi mations on non-uniform grids. Time is discretized by the linearly-implicit Euler method. In order to control the discretization errors an extrapolation pro cedure is used in space and time. Results are presented for simple laser-induced ignition processes. The method, however, can be applied to other combustion processes, too. T3 - ZIB-Report - SC-96-56 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2665 ER - TY - GEN A1 - Frauhammer, Jörg A1 - Klein, Harald A1 - Eigenberger, Gerhart A1 - Nowak, Ulrich T1 - Solving moving boundary problems with an adaptive moving grid method: Rotary heat exchangers with condensation and evaporation N2 - A numerical method for the treatment of moving discontinuities in the model equations of chemical engineering systems is presented. The derived model describing the effects of condensation and evaporation in a regenerative air to air heat exchanger yields an illustrative example for these so called moving boundary problems. The presented adaptive moving grid method is based on the algorithm {\sc Pdex} for parabolic partial differential equations. It is shown that the method is suited for problems where the arising discontinuities cause low rates of convergence if the equations are solved with a static grid. T3 - ZIB-Report - SC-96-57 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2679 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - A Note on the Stability of the Many-Queue Head-of-the Line Processor-Sharing System with Permanent Customers N2 - We consider a single server system consisting of $n$ queues with different types of customers and $k$ permanent customers. The permanent customers and those at the head of the queues are served in processor-sharing by the service facility (head-of-the-line processor-sharing). By means of Loynes' monotonicity method a stationary work load process is constructed and using sample path analysis general stability conditions are derived. They allow to decide which queues are stable and moreover to compute the fraction of processor capacity devoted to the permanent customers. In case of a stable system the constructed stationary state process is the only one and for any initial state the system converges pathwise to the steady state. T3 - ZIB-Report - SC-96-55 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2659 ER - TY - GEN A1 - Koepf, Wolfram T1 - On a Problem of Koornwinder N2 - In this note we solve a problem about the rational representability of hypergeometric terms which represent hypergeometric sums. This problem was proposed by Koornwinder in Koornwinder, T. H.: Hypergeometric series evaluation by Zeilberger's algorithm. In: Open Problems, ed. by Walter van Assche. J. of Comput. and Appl. Math.48, 1993, 225--243. T3 - ZIB-Report - SC-96-52 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2629 ER - TY - GEN A1 - Koepf, Wolfram T1 - A Package on Orthogonal Polynomials and Special Functions N2 - In many applications (hypergeometric-type) special functions like orthogonal polynomials are needed. For example in more than 50 \% of the published solutions for the (application-oriented) questions in the Problems Section'' of SIAM Review special functions occur. In this article the Mathematica package {\tt SpecialFunctions} which can be obtained from the URL {\tt http://www.zib.de/koepf} is introduced. Algorithms to convert between power series representations and their generating functions is the main topic of this package, extending the previous package {\tt PowerSeries}. Moreover the package automatically finds differential and recurrence equations for expressions and for sums (the latter using Zeilberger's algorithm. As an application the fast computation of polynomial approximations of solutions of linear differential equations with polynomial coefficients is presented. This is the asymptotically fastest known algorithm for series computations, and it is much faster than Mathematica's builtin {\tt Series} command if applicable. Many more applications are considered. Finally the package includes implementations supporting the efficient computation of classical continuous and discrete orthogonal polynomials. T3 - ZIB-Report - SC-96-53 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2639 ER - TY - GEN A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev T1 - Numerical Algorithms and Visualization in Medical Treament Planning N2 - After a short summary on therapy planning and the underlying technologies we discuss quantitative medicine by giving a short overview on medical image data, summarizing some applications of computer based treatment planning, and outlining requirements on medical planning systems. Then we continue with a description of our medical planning system {\sf HyperPlan}. It supports typical working steps in therapy planning, like data aquisition, segmentation, grid generation, numerical simulation and optimization, accompanying these with powerful visualization and interaction techniques. T3 - ZIB-Report - SC-96-54 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2643 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Neueste Entwicklungen der Informations- und Kommunikationstechnik und ihre Auswirkungen auf den Wissenschaftsbetrieb N2 - Dieser Aufsatz ist die Ausarbeitung eines Vortrags auf der 4. Jahrestagung der Gesellschaft Information Bildung (GIB) am 10. und 11. Oktober 1996 an der Humboldt-Universität Berlin. Er enthält einen Überblick über die neuesten Entwicklungen in der Informations- und Kommunikationstechnik und beleuchtet deren Auswirkungen auf den Wissenschaftsbetrieb. Er beginnt mit historischen Anmerkungen zur Entstehung der Schrift und zur Speicherung und Übertragung von Information. Er führt, nach einer knappen Diskussion der Defizite in der gegenwärtigen Informationsversorgung und einem kurzen Ausflug in die Geschichte des Internet und des World Wide Web, zu einer Darstellung ausgewählter aktueller Aktivitäten der Wissenschaften im Bereich elektronischer Information, Kommunikation, Dokumentation und Archivierung. Dabei zeigt sich, dass sich der Begriff wissenschaftlicher Information bereits zu wandeln beginnt. Zur traditionellen papiergebundenen Information treten völlig neue Informationsarten hinzu, von Software- und Datensammlungen über multimediale Information bis hin zu Fernübertagungen von wissenschaftlichen Vorträgen und Experimenten. Eine Vielzahl von Links; (URL's bzw. anklickbaren Verweisen) soll diesen Wandel nicht nur belegen, sondern auch das rasche Auffinden wichtiger Dokumente und Quellen im Internet ermöglichen. T3 - ZIB-Report - TR-96-12 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5417 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Heyer, Gernot A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Informationsdienste für die Mathematik im Internet (Math-Net) N2 - Der Informationsaustausch in den Wissenschaften befindet sich in einer Umbruchsituation. Traditionelle, papiergebundene Publikationsformen werden durch elektronische Medien ergänzt und sogar abgelöst. Moderne Client/Server basierende Systeme und Zugriffswerkzeuge erlauben heute völlig neue Distributions- und Kommunikationsformen. In einem vom DFN und der Deutschen Telekom geförderten Projekt geht es in der vorliegenden Vorhabenbeschreibung um die konkrete inhaltliche und organisatorische Planung, ein umfassendes, möglichst alle mathematisch relevanten Ressourcen berücksichtigendes, Informationssystem für die Mathematik aufzubauen. T3 - ZIB-Report - TR-96-13 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5421 ER - TY - GEN A1 - Beck, Rudolf A1 - Hiptmair, Ralf T1 - Multilevel Solution of the Time-Harmonic Maxwell's Equations Based on Edge Elements N2 - A widely used approach for the computation of time-harmonic electromagnetic fields is based on the well-known double-curl equation for either $\vec E$ or $\vec H$. An appealing choice for finite element discretizations are edge elements, the lowest order variant of a $H(curl)$-conforming basis. However, the large nullspace of the curl-operator gives rise to serious drawbacks. It comprises a considerable part of all spectral modes on the finite element grid, polluting the solution with non-physical contributions and causing the deterioration of standard iterative solvers. We tackle these problems by a nested multilevel algorithm. After every V-cycle in the $H(curl)$-conforming basis, the non-physical contributions are removed by a projection scheme. It requires the solution of Poisson's equation in the nullspace, which can be carried out efficiently by another multilevel iteration. The whole procedure yields convergence rates independent of the refinement level of the mesh. Numerical examples demonstrate the efficiency of the method. T3 - ZIB-Report - SC-96-51 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2619 ER - TY - GEN A1 - Wagler, Annegret T1 - On Critically Perfect Graphs N2 - A perfect graph is critical if the deletion of any edge results in an imperfect graph. We give examples of such graphs and prove some basic properties. We investigate the relationship of critically perfect graphs to well-known classes of perfect graphs and study operations preserving critical perfectness. T3 - ZIB-Report - SC-96-50 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2609 ER - TY - GEN A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Highly scalable parallel linearly-implicit extrapolation algorithms N2 - We present parallel formulations of the well established extrapolation algorithms EULSIM and LIMEX and its implementation on a distributed memory architecture. The discretization of partial differential equations by the method of lines yields large banded systems, which can be efficiently solved in parallel only by iterative methods. Polynomial preconditioning with a Neumann series expansion combined with an overlapping domain decomposition appears as a very efficient, robust and highly scalable preconditioner for different iterative solvers. A further advantage of this preconditioner is that all computation can be restricted to the overlap region as long as the subdomain problems are solved exactly. With this approach the iterative algorithms operate on very short vectors, the length of the vectors depends only on the number of gridpoints in the overlap region and the number of processors, but not on the size of the linear system. As the most reliable and fast iterative methods based on this preconditioning scheme appeared GMRES or FOM and BICGSTAB. To further reduce the number of iterations in GMRES or FOM we can reuse the Krylov-spaces constructed in preceeding extrapolation steps. The implementation of the method within the program LIMEX results in a highly parallel and scalable program for solving differential algebraic problems getting an almost linear speedup up to 64 processors even for medium size problems. Results are presented for a difficult application from chemical engineering simulating the formation of aerosols in industrial gas exhaust purification. T3 - ZIB-Report - TR-96-11 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5405 ER - TY - GEN A1 - Caröe, Claus C. A1 - Schultz, Rüdiger T1 - Dual Decomposition in Stochastic Integer Programming N2 - We present an algorithm for solving stochastic integer programming problems with recourse, based on a dual decomposition scheme and Lagrangian relaxation. The approach can be applied to multi-stage problems with mixed-integer variables in each time stage. %We outline a branch-and-bound algorithm for obtaining primal feasible and %possibly optimal solutions. Numerical experience is presented for some two-stage test problems. T3 - ZIB-Report - SC-96-46 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2560 ER - TY - GEN A1 - Nettesheim, Peter A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - Chebyshev-Approximation for Wavepacket-Dynamics: better than expected N2 - The aim of this work is to study the accuracy and stability of the Chebyshev--approximation method as a time--discretization for wavepacket dynamics. For this frequently used discretization we introduce estimates of the approximation and round--off error. These estimates mathematically confirm the stability of the Chebyshev--approximation with respect to round--off errors, especially for very large stepsizes. But the results also disclose threads to the stability due to large spatial dimensions. All theoretical statements are illustrated by numerical simulations of an analytically solvable example, the harmonic quantum oszillator. T3 - ZIB-Report - SC-96-47 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2575 ER - TY - GEN A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Jonas, Peter A1 - Paul, Ulrich A1 - Wessäly, Roland T1 - Survivable Mobile Phone Architectures: Models and Solution Methods N2 - In the highly competitive area of telecommunications, cost, quality, and network management are among the most important aspects to be considered when designing a network. We study the problem of dimensioning a telecommunication network that is still operating in case of a failure of a network component. Given a demand between each pair of nodes of a telecommunication network and a finite set of possible capacities for each edge of the network, we consider the problem of deciding what capacity to install on each edge of the network in order to minimize the building cost of the network and to satisfy the demand between each pair of nodes, even if a network component fails. The routing of the demands must satisfy the following additional restrictions: (a) there is a maximum number of nodes allowed in each path between any pair of nodes (path length restriction), and (b) there is a maximum percentage of the demand between each pair of nodes that can be routed through any network component (diversification restriction). Moreover, the chosen capacities must be such that, for every single node or single edge failure, a certain percentage of the demand between any pair of nodes is reroutable (i.e. it ``survives'' the particular failure). We formulate the problem as a mixed integer linear programming problem and present a cutting plane algorithm as well as several heuristics for its solution. Furthermore, we discuss several ways to implement survivability into a telecommunication network. T3 - ZIB-Report - SC-96-48 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2582 ER - TY - GEN A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - A Network Dimensioning Tool N2 - Designing low cost networks that survive certain failure situations belongs to one of the prime tasks in the telecommunications industry. In this paper we describe a mathematical model combining several aspects of survivability that are elsewhere treated in a hierarchical fashion. We present mathematical investigations of this integrated model, a cutting plane algorithm, as well as several heuristics for its solution. Moreover, we report computational results with real world data. The problem we address is the following. Suppose, between each pair of nodes in a region, a communication demand is given. We want to determine the topology of a telecommunication network connecting the given nodes and to dimension all potential physical links. For each link, the possible capacities are restricted to a given finite set. The capacities must be chosen such that the communication demands are satisfied, even if certain network components fail, and such that the network building costs are as small as possible. Moreover, for each pair of nodes and each failure situation, we want to determine the paths on which the demand between the nodes is routed. T3 - ZIB-Report - SC-96-49 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2591 ER - TY - GEN A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Roitzsch, Rainer A1 - Werk, Roland T1 - ZGUI-Handbuch N2 - In diesem Handbuch werden die Bausteine zum Aufbau einer graphischen Benutzeroberfläche mit {\tt ZGUI} beschrieben. Auf der einen Seite stehen die Tcl/Tk--Prozeduren, die die graphischen Elemente definieren. Die Beschreibung der Anwendung der Prozeduren und der Interaktionen der Elemente bildet den ersten Teil des Handbuches. Auf der anderen Seite stehen die Anforderungen an Anwendungen, die mit einer {\tt ZGUI}--Benutzeroberlfäche gesteuert werden sollen. Hier findet man im Handbuch die Beschreibung der Anwendungsprogrammierschnittstelle (application programming interface, API). T3 - ZIB-Report - TR-96-10 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5397 ER - TY - GEN A1 - Awyong, Poh Wah A1 - Henk, Martin A1 - Scott, Paul R. T1 - Note on lattice-point-free convex bodies N2 - We prove inequalities relating the inradius of a convex body with interior containing no point of the integral lattice, with the volume or surface area of the body. These inequalities are tight and generalize previous results. T3 - ZIB-Report - SC-96-44 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2546 ER - TY - GEN A1 - Deuflhard, Peter A1 - Dellnitz, Michael A1 - Junge, Oliver A1 - Schütte, Christof T1 - Computation of Essential Molecular Dynamics by Subdivision Techniques I: Basic Concept N2 - The paper presents the concept of a new type of algorithm for the numerical computation of what the authors call the {\em essential dynamics\/} of molecular systems. Mathematically speaking, such systems are described by Hamiltonian differential equations. In the bulk of applications, individual trajectories are of no specific interest. Rather, time averages of physical observables or relaxation times of conformational changes need to be actually computed. In the language of dynamical systems, such information is contained in the natural invariant measure (infinite relaxation time) or in almost invariant sets ("large" finite relaxation times). The paper suggests the direct computation of these objects via eigenmodes of the associated Frobenius-Perron operator by means of a multilevel subdivision algorithm. The advocated approach is different to both Monte-Carlo techniques on the one hand and long term trajectory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are just structurally connected via the underlying Frobenius-Perron theory. Numerical experiments with a first version of our suggested algorithm are included to illustrate certain distinguishing properties. A more advanced version of the algorithm will be presented in a second part of this paper. T3 - ZIB-Report - SC-96-45 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2553 ER - TY - GEN A1 - Koch, Thorsten A1 - Martin, Alexander T1 - Solving Steiner Tree Problems in Graphs to Optimality N2 - In this paper we present the implementation of a branch-and-cut algorithm for solving Steiner tree problems in graphs. Our algorithm is based on an integer programming formulation for directed graphs and comprises preprocessing, separation algorithms and primal heuristics. We are able to solve all problem instances discussed in literature to optimality, including one to our knowledge not yet solved problem. We also report on our computational experiences with some very large Steiner tree problems arising from the design of electronic circuits. All test problems are gathered in a newly introduced library called {\em SteinLib} that is accessible via World Wide Web. T3 - ZIB-Report - SC-96-42 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2526 ER - TY - GEN A1 - Helmberg, Christoph T1 - Fixing Variables in Semidefinite Relaxations N2 - The standard technique of reduced cost fixing from linear programming is not trivially extensible to semidefinite relaxations as the corresponding Lagrange multipliers are usually not available. We propose a general technique for computing reasonable Lagrange multipliers to constraints which are not part of the problem description. Its specialization to the semidefinite $\left\{-1,1\right\}$ relaxation of quadratic 0-1 programming yields an efficient routine for fixing variables. The routine offers the possibility to exploit problem structure. We extend the traditional bijective map between $\left\{0,1\right\}$ and $\left\{-1,1\right\}$ formulations to the constraints such that the dual variables remain the same and structural properties are preserved. In consequence the fixing routine can efficiently be applied to optimal solutions of the semidefinite $\left\{0,1\right\}$ relaxation of constrained quadratic 0-1 programming, as well. We provide numerical results showing the efficacy of the approach. T3 - ZIB-Report - SC-96-43 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2530 ER - TY - THES A1 - Wunderling, Roland T1 - Paralleler und Objektorientierter Simplex-Algorithmus N2 - In der vorliegenden Arbeit werden neue Implementierungen des dualen und primalen revidierten Simplex-Algorithmus für die Lösung linearer Programme (LPs) vorgestellt. Dazu werden die Algorithmen mithilfe einer Zeilenbasis dargestellt, aus der über einen Spezialfall die übliche Darstellung mit einer Spaltenbasis folgt. Beide Darstellungen sind über die Dualität eng miteinander verbunden. Ausserdem wird eine theoretische Untersuchung der numerischen Stabilität von Simplex-Algorithmen durchgeführt, und es werden verschiedene Möglichkeiten der Stabilisierung diskutiert. Beide Darstellungen der Basis werden in den Implementierungen algorithmisch ausgenutzt, wobei der Einsatz der Zeilenbasis für LPs mit mehr Nebenbedingungen als Variablen Geschwindigkeitsvorteile bringt. Darüberhinaus werden weitere Beschleunigung gegenüber anderen state-of-the-art Implentierungen erzielt, und zwar durch den Einsatz eines Phase-1 LPs, das eine grösstmögliche Übereinstimmung mit dem Ausgangs-LPs aufweist, durch eine dynamische Anpassung der Faktorisierungsfrequenz für die Basis-Matrix und durch die Optimierung der Lösung linearer Gleichungssysteme für besonders dünnbesetzte Matrizen und Vektoren. Es wurden drei Implementierungen vorgenommen. Die erste läuft sequentiell auf einem PC oder einer Workstation. Ihre hohe numerische Stabilität und Effizienz durch die Integration der oben genannten Konzepte machen sie zu einem zuverlässigen Hilfsmittel für den täglichen Einsatz z.B.~in Schnittebenenverfahren zur Lösung ganzzahliger Programme. Als Programmiersprache wurde C++ verwendet, und es wurde ein objektorientierter Software-Entwurf zugrundegelegt. Dieser leistet eine hohe Flexibilität und Anpassbarkeit z.B.~für die Integration benutzerdefinierter Pricing-Strategien. Bei den anderen beiden Implentierungen handelt es sich um parallele Versionen für Parallelrechner mit gemeinsamem und für solche mit verteiltem Speicher. Dabei wird der objektorientierte Entwurf so genutzt, dass lediglich die zusätzlichen Aufgaben für die Parallelisierung (Synchronisation, Kommunikation und Verteilung der Arbeit) implementiert werden, während alle Algorithmen von der sequentiellen Implementierung geerbt werden. Die Parallelisierung setzt an vier Punkten an. Der erste und einfachste ist die parallele Berechnung eines Matrix-Vektor-Produktes. Als zweites wurden beim Pricing und Quotiententest parallele Suchalgorithmen eingesetzt. Weiter werden beim steepest-edge Pricing zwei lineare Gleichungssysteme nebenläufig gelöst. Schliesslich wird ein paralleles Block-Pivoting verwendet, bei dem Gleichungssysteme mehrerer aufeinanderfolgender Iterationen gleichzeitig gelöst werden. Ob und welche der Parallelisierungs-Konzepte eine Beschleunigung bewirken, ist problemabhängig. Es gelingt z.B.~mit 32 Prozessoren eine Beschleunigung um mehr als einen Faktor 16 zu erzielen. Schliesslich wird die parallele Lösung dünnbesetzter linearer Gleichungssysteme mit unsymmetrischen Matrizen untersucht und eine Implementierung für den Cray T3D vorgenommen. Sie enthält ein neues Verfahren des Lastausgleichs, das keinen zusätzlichen Aufwand verursacht. Die Implementierung erzielt vergleichsweise günstige Laufzeiten. T3 - ZIB-Report - TR-96-09 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5386 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Herzog, Werner A1 - Klostermeier, Fridolin A1 - Konsek, Wilhelm A1 - Küttner, Christian T1 - Kürzen muß nicht Kahlschlag heißen - das Beispiel Telebus-Behindertenfahrdienst Berlin N2 - Müssen Etatkürzungen bei staatlichen Dienstleistungseinrichtungen notwendig zu Leistungseinschränkungen oder Gebührenerhöhungen führen? Wir zeigen am Beispiel des Berliner Behindertenfahrdienstes {\em Telebus}, da\ss{} Sparzwang auch als Chance zur Verbesserung der eigenen Verwaltungs- und Arbeitsabläufe genutzt werden kann. Durch stärkere Dienstleistungsorientierung, Vereinfachung der Arbeitsabläufe und durch den Einsatz von moderner EDV und von mathematischen Optimierungsmethoden zur Fahrzeugeinsatzplanung werden bei Telebus heute staatliche Leistungen trotz geringeren Etats besser erbracht als vorher. T3 - ZIB-Report - SC-96-41 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2510 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Telebus Berlin - Mobilität für Behinderte N2 - Steigendes Mobilitätsbedürfnis der Behinderten bei angespannter Haushaltslage --- diese Situation ergab vor drei Jahren beim Berliner Behindertenfahrdienst {\em Telebus\/} Handlungsbedarf. Gleichzeitig stie\ss{} die verwendete manuelle (Fahrzeug-)Tourenplanung mit damals etwa 1.000 Fahrtwünschen pro Tag an ihre Grenzen. Zur Lösung dieser Probleme war der effiziente Einsatz von Computern und von {\em mathematischen Optimierungsverfahren\/} erforderlich. Ergebnis des daraufhin gestarteten {\em Telebus-Projektes\/} ist die Entwicklung eines neuen, alle Arbeitsabläufe unterstützenden Computersystems, das seit über einem Jahr im Einsatz ist. Herzstück dieses Systems ist ein auf mathematischen Methoden der ganzzahligen Optimierung basierendes Verfahren zur Tourenplanung. Ziel dieses Artikels ist die Beschreibung dieses Verfahrens und seiner Verwendung bei der Behindertenbeförderung. Das Beispiel Telebus zeigt, da\ss{} der Einsatz mathematischer Optimierungstechniken neue Möglichkeiten für Kosteneinsparungen bei gleichzeitiger Serviceverbesserung auch in anderen Bereichen des ÖPNV eröffnet. T3 - ZIB-Report - SC-96-40 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2500 ER - TY - GEN A1 - Kornhuber, Ralf T1 - On Robust Multigrid Methods for Piecewise Smooth Variational Problems N2 - We consider the fast solution of large, piecewise smooth minimization problems as resulting from the approximation of elliptic free boundary problems. The most delicate question in constructing a multigrid method for a nonlinear, non--smooth problem is how to represent the nonlinearity on the coarse grids. This process usually involves some kind of linearization. The basic idea of monotone multigrid methods to be presented here is first to select a neighborhood of the actual smoothed iterate in which a linearization is possible and then to constrain the coarse grid correction to this neighborhood. Such a local linearization allows to control the local corrections at each coarse grid node in such a way that the energy functional is monotonically decreasing. This approach leads to globally convergent schemes which are robust with respect to local singularities of the given problem. The numerical performance is illustrated by approximating the well-known Barenblatt solution of the porous medium equation. T3 - ZIB-Report - SC-96-38 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2487 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schemann, Martin T1 - Adaptive Rothe's Method for the 2D Wave Equation N2 - The adaptive Rothe method approaches a time-dependent PDE as an ODE in function space. This ODE is solved {\em virtually} using an adaptive state-of-the-art integrator. The {\em actual} realization of each time-step requires the numerical solution of an elliptic boundary value problem, thus {\em perturbing} the virtual function space method. The admissible size of that perturbation can be computed {\em a priori} and is prescribed as a tolerance to an adaptive multilevel finite element code, which provides each time-step with an individually adapted spatial mesh. In this way, the method avoids the well-known difficulties of the method of lines in higher space dimensions. During the last few years the adaptive Rothe method has been applied successfully to various problems with infinite speed of propagation of information. The present study concerns the adaptive Rothe method for hyperbolic equations in the model situation of the wave equation. All steps of the construction are given in detail and a numerical example (diffraction at a corner) is provided for the 2D wave equation. This example clearly indicates that the adaptive Rothe method is appropriate for problems which can generally benefit from mesh adaptation. This should be even more pronounced in the 3D case because of the strong Huygens' principle. T3 - ZIB-Report - SC-96-39 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2492 ER - TY - GEN A1 - Gatermann, Karin A1 - Guyard, Frederic T1 - Gröbner bases, invariant theory and equivariant dynamics N2 - This paper is about algorithmic invariant theory as it is required within equivariant dynamical systems. The question of generic bifurcation equations requires the knowledge of fundamental invariants and equivariants. We discuss computations which are related to this for finite groups and semisimple Lie groups. We consider questions such as the completeness of invariants and equivariants. Efficient computations are gained by the Hilbert series driven Buchberger algorithm. Applications such as orbit space reduction are presented. T3 - ZIB-Report - SC-96-37 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2470 ER - TY - GEN A1 - Dellnitz, Michael A1 - Junge, Oliver T1 - On the Approximation of Complicated Dynamical Behavior N2 - We present efficient techniques for the numerical approximation of complicated dynamical behavior. In particular, we develop numerical methods which allow to approximate SBR-measures as well as (almost) cyclic behavior of a dynamical system. The methods are based on an appropriate discretization of the Frobenius-Perron operator, and two essentially different mathematical concepts are used: the idea is to combine classical convergence results for finite dimensional approximations of compact operators with results from Ergodic Theory concerning the approximation of SBR-measures by invariant measures of stochastically perturbed systems. The efficiency of the methods is illustrated by several numerical examples. T3 - ZIB-Report - SC-96-35 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2456 ER - TY - GEN A1 - Dellnitz, Michael A1 - Junge, Oliver T1 - An Adaptive Box Refinement in Subdivision Techniques for the Approximation of Dynamical Behavior N2 - Recently subdivision techniques have been introduced in the numerical investigation of complicated temporal behavior of dynamical systems. In this article we intertwine the subdivision process with the computation of invariant measures and propose an adaptive scheme for the box refinement which is based on the combination of these methods. Using this new algorithm the numerical effort for the computation of box coverings is in general significantly reduced, and we illustrate this fact by several numerical examples. T3 - ZIB-Report - SC-96-36 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2464 ER - TY - GEN A1 - Pflug, Georg Ch. A1 - Ruszczynski, Andrzej A1 - Schultz, Rüdiger T1 - On the Glivenko-Cantelli Problem in Stochastic Programming: Linear Recourse and Extensions N2 - Integrals of optimal values of random optimization problems depending on a finite dimensional parameter are approximated by using empirical distributions instead of the original measure. Under fairly broad conditions, it is proved that uniform convergence of empirical approximations of the right hand sides of the constraints implies uniform convergence of the optimal values in the linear and convex case. T3 - ZIB-Report - SC-96-34 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2448 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Global Inexact Multilevel FEM for Nonlinear Elliptic Problems N2 - The paper deals with the multilevel solution of {\em elliptic} partial differential equations (PDEs) in a {\em finite element} setting: {\em uniform ellipticity} of the PDE then goes with {\em strict monotonicity} of the derivative of a nonlinear convex functional. A {\em Newton multigrid method} is advocated, wherein {\em linear residuals} are evaluated within the multigrid method for the computation of the Newton corrections. The globalization is performed by some {\em damping} of the ordinary Newton corrections. The convergence results and the algorithm may be regarded as an extension of those for local Newton methods presented recently by the authors. An {\em affine conjugate} global convergence theory is given, which covers both the {\em exact} Newton method (neglecting the occurrence of approximation errors) and {\em inexact} Newton--Galerkin methods addressing the crucial issue of accuracy matching between discretization and iteration errors. The obtained theoretical results are directly applied for the construction of adaptive algorithms. Finally, illustrative numerical experiments with a~{\sf NEWTON--KASKADE} code are documented. T3 - ZIB-Report - SC-96-33 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2430 ER - TY - GEN A1 - Lang, Jens T1 - Adaptive FEM for Reaction-Diffusion Equations N2 - An integrated time--space adaptive finite element method for solving mixed systems of nonlinear parabolic, elliptic, and differential algebraic equations is presented. The approach is independent of the spatial dimension. For the discretization in time we use singly diagonally linearly implicit Runge--Kutta methods of Rosenbrock type. Local time errors for the step size control are defined by an embedded strategy. A multilevel finite element Galerkin method is subsequently applied for the discretization in space. A posteriori estimates of local spatial discretization errors are obtained solving local problems with higher order approximation. Superconvergence arguments allow to simplify the required computations. Two different strategies to obtain the start grid of the multilevel process are compared. The devised method is applied to a solid--solid combustion problem. T3 - ZIB-Report - SC-96-28 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2393 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Local Inexact Newton Multilevel FEM for Nonlinear Elliptic Problems N2 - The finite element setting for nonlinear elliptic PDEs directly leads to the minimization of convex functionals. Uniform ellipticity of the underlying PDE shows up as strict convexity of the arising nonlinear functional. The paper analyzes computational variants of Newton's method for convex optimization in an affine conjugate setting, which reflects the appropriate affine transformation behavior for this class of problems. First, an affine conjugate Newton--Mysovskikh type theorem on the local quadratic convergence of the exact Newton method in Hilbert spaces is given. It can be easily extended to inexact Newton methods, where the inner iteration is only approximately solved. For fixed finite dimension, a special implementation of a Newton--PCG algorithm is worked out. In this case, the suggested monitor for the inner iteration guarantees quadratic convergence of the outer iteration. In infinite dimensional problems, the PCG method may be just formally replaced by any Galerkin method such as FEM for linear elliptic problems. Instead of the algebraic inner iteration errors we now have to control the FE discretization errors, which is a standard task performed within any adaptive multilevel method. A careful study of the information gain per computational effort leads to the result that the quadratic convergence mode of the Newton--Galerkin algorithm is the best mode for the fixed dimensional case, whereas for an adaptive variable dimensional code a special linear convergence mode of the algorithm is definitely preferable. The theoretical results are then illustrated by numerical experiments with a {\sf NEWTON--KASKADE} algorithm. T3 - ZIB-Report - SC-96-29 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2401 ER - TY - GEN A1 - Schütte, Christof A1 - Bornemann, Folkmar A. T1 - Homogenization Approach to Smoothed Molecular Dynamics N2 - {\footnotesize In classical Molecular Dynamics a molecular system is modelled by classical Hamiltonian equations of motion. The potential part of the corresponding energy function of the system includes contributions of several types of atomic interaction. Among these, some interactions represent the bond structure of the molecule. Particularly these interactions lead to extremely stiff potentials which force the solution of the equations of motion to oscillate on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles) via increasing the stiffness of the strong part of the potential to infinity. However, the naive way of doing this via holonomic constraints mistakenly ignores the energy contribution of the fast oscillations. The paper presents a mathematically rigorous discussion of the limit situation of infinite stiffness. It is demonstrated that the average of the limit solution indeed obeys a constrained Hamiltonian system but with a {\em corrected soft potential}. An explicit formula for the additive potential correction is given via a careful inspection of the limit energy of the fast oscillations. Unfortunately, the theory is valid only as long as the system does not run into certain resonances of the fast motions. Behind those resonances, there is no unique limit solution but a kind of choatic scenario for which the notion ``Takens chaos'' was coined. For demonstrating the relevance of this observation for MD, the theory is applied to a realistic, but still simple system: a single butan molecule. The appearance of ``Takens chaos'' in smoothed MD is illustrated and the consequences are discussed.} T3 - ZIB-Report - SC-96-31 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2410 ER - TY - GEN A1 - Schultz, Rüdiger T1 - A Note on Preprocessing via Fourier-Motzkin Elimination in Two-Stage Stochastic Programming N2 - Preprocessing in two-stage stochastic programming is considered from the viewpoint of Fourier-Motzkin elimination. Although of exponential complexity in general, Fourier-Motzkin elimination is shown to provide valuable insights into specific topics such as solving integer recourse stochastic programs or verifying stability conditions. Test runs with the computer code PORTA [1994] are reported. T3 - ZIB-Report - SC-96-32 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2423 ER - TY - GEN A1 - Deuflhard, Peter A1 - Heroth, Jörg A1 - Maas, Ulrich T1 - Towards Dynamical Dimension Reduction in Reactive Flow Problems N2 - The paper addresses the possibilities of reducing the overall number of degrees of freedom in large scale reactive flow computations. Attention focusses on the dimension reduction technique ILDM due to {\sc Maas and Pope}, which treats certain automatically detected fast dynamic components as algebraic equations (so-called slow manifold). In earlier papers, the dimension of the reduction had been kept constant throughout each computation. Recently, a mathematically sound and nevertheless cheap dimension monitor for the chemistry part only has been suggested by {\sc Deuflhard and Heroth}. The present paper reports about first steps taken towards the implementation of that monitor into a flame code. Moreover, a sparse grid storage scheme is advocated and analyzed in view of the construction of efficient table look--ups for nested manifolds. T3 - ZIB-Report - SC-96-27 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2383 ER - TY - GEN A1 - Baumann, Wolfgang A1 - Hege, Hans-Christian A1 - Schwarz, Uwe A1 - Stüben, Hinnerk T1 - Netzverteilte Visualisierung und Simulation N2 - Dieser Bericht beschreibt die Ergebnisse eines Anwendungsprojektes, das parallel zum Aufbau des Berliner Hochgeschwindigkeitsdatennetzes (Berlin Regional Testbed) am ZIB durchgeführt wurde. Es werden allgemeine Werkzeuge und anwendungsspezifische Arbeitsumgebungen zur netzverteilten Visualisierung und Simulation vorgestellt. Die allgemeinen Werkzeuge unterstützen folgende Aufgaben: Kopplung von Simulationen auf (Hochleistungs-)Rechnern an lokale Grafikarbeitsplätze, objektorientierte und verteilte Visualisierung, Remote-Videoaufzeichnung, Bilddatenkompression und digitaler Filmschnitt. Die spezifischen Arbeitsumgebungen wurden für Aufgaben aus den Bereichen Numerische Mathematik, Astrophysik, Strukturforschung, Chemie, Polymerphysik und Strömungsmechanik entwickelt. T3 - ZIB-Report - TR–96–08 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5379 ER - TY - GEN A1 - Löbel, Andreas T1 - Vehicle Scheduling in Public Transit and Lagrangean Pricing N2 - This paper investigates the solution of the linear programming (LP) relaxation of the multicommodity flow formulation of the multiple-depot vehicle scheduling problems arising in public mass transit. We develop a column generation technique that makes it possible to solve the huge linear programs that come up there. The technique, which we call {\em Lagrangean pricing}, is based on two different Lagrangean relaxations. We describe in detail the basic ingredients of our approach and give computational results for large-scale test data (with up to 70 million variables) from three German public transportation companies. Because of these results, we propose Lagrangean pricing as one of the basic ingredients of an effective method to solve multiple-depot vehicle scheduling problems to proven optimality. T3 - ZIB-Report - SC-96-26 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2375 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Krause, Rolf T1 - Classical and Cascadic Multigrid - A Methodical Comparison N2 - Using the full multigrid method {\em without} any coarse grid correction steps but with an a posteriori control of the number of smoothing iterations was shown by Bornemann and Deuflhard [1996] to be an optimal iteration method with respect to the energy norm. They named this new kind of multigrid iteration the {\em cascadic multigrid method}. However, numerical examples with {\em linear} finite elements raised serious doubts whether the cascadic multigrid method can be made optimal with respect to the {\em $L^2$-norm}. In this paper we prove that the cascadic multigrid method cannot be optimal for linear finite elements and show that the case might be different for higher order elements. We present a careful analysis of the two grid variant of the cascadic multigrid method providing a setting where one can understand the methodical difference between the cascadic multigrid method and the classical multigrid $V$-cycle almost immediately. As a rule of thumb we get that whenever the cascadic multigrid works the classical multigrid will work too but not vice versa. T3 - ZIB-Report - SC-96-25 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2368 ER - TY - GEN A1 - Koepf, Wolfram A1 - Schmersau, Dieter T1 - Algorithms for Classical Orthogonal Polynomials N2 - \begin{enumerate} \item[] {{\small In this article explicit formulas for the recurrence equation \[ p_{n+1}(x)=(A_n\,x+B_n)\,p_n(x)-C_n\,p_{n-1}(x) \] and the derivative rules \[ \sigma(x)\,p_n'(x)=\alpha_n\,p_{n+1}(x)+\beta_n\,p_n(x)+\gamma_n\,p_{n-1}(x) \] and \[ \sigma(x)\,p_n'(x)=(\tilde\alpha_n\,x+\tilde\beta_n)\,p_n(x)+ \tilde\gamma_n\,p_{n-1}(x) \] respectively which are valid for the orthogonal polynomial solutions $p_n(x)$ of the differential equation \[ \sigma(x)\,y''(x)+\tau(x)\,y'(x)+\lambda_n\,y(x)=0 \] of hypergeometric type are developed that depend {\sl only} on the coefficients $\sigma(x)$ and $\tau(x)$ % and $\lambda_n$ which themselves are polynomials w.r.t.\ $x$ of degrees not larger than $2$ and $1$% and $0$ , respectively. Partial solutions of this problem had been previously published by Tricomi, and recently by Y\'a\~nez, Dehesa and Nikiforov. Our formulas yield an algorithm with which it can be decided whether a given holonomic recurrence equation (i.e.\ one with polynomial coefficients) generates a family of classical orthogonal polynomials, and returns the corresponding data (density function, interval) including the standardization data in the affirmative case. In a similar way, explicit formulas for the coefficients of the recurrence equation and the difference rule \[ \sigma(x)\,\nabla p_n(x)= \alpha_n\,p_{n+1}(x)+\beta_n\,p_n(x)+\gamma_n\,p_{n-1}(x) \] of the classical orthogonal polynomials of a discrete variable are given that depend only on the coefficients $\sigma(x)$ and $\tau(x)$ of their difference equation \[ \sigma(x)\,\Delta\nabla y(x)+\tau(x)\,\Delta y(x)+\lambda_n\,y(x)=0 \;. \] Here \[ \Delta y(x)=y(x+1)-y(x) \quad\quad\mbox{and}\quad\quad \nabla y(x)=y(x)-y(x-1) \] denote the forward and backward difference operators, respectively. In particular this solves the corresponding inverse problem to find the classical discrete orthogonal polynomial solutions of a given holonomic recurrence equation. \iffalse Furthermore, an algorithmic approach to deduce these and similar properties is presented which is implementable in computer algebra, and which moreover generates relations between different standardizations of the polynomial system considered. \fi }} \end{enumerate} T3 - ZIB-Report - SC-96-23 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2340 ER - TY - GEN A1 - Koepf, Wolfram T1 - Gröbner Bases and Triangles N2 - It is well-known that by polynomial elimination methods, in particular by the computation of Gröbner bases, proofs for geometric theorems can be automatically generated. %% Several monographs On the other hand, it is much less known that Gröbner bases, in combination with rational factorization, can be even used to {\sl find} new geometric theorems. In this article such a method is described, and some new theorems on plane triangles are deduced. T3 - ZIB-Report - SC-96-24 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2350 ER - TY - GEN A1 - Kokott, Andreas A1 - Löbel, Andreas T1 - Lagrangean Relaxations and Subgradient Methods for Multiple-Depot Vehicle Scheduling Problems N2 - This paper presents two Lagrangean relaxation approaches for the {\em NP}-hard multiple-depot vehicle scheduling problem in public mass transit and reports on computational investigations. Our Lagrangean relaxation approaches can be applied to generate very tight lower bounds and to compute feasible solutions efficiently. A further application is to use the Lagrangean relaxations as new pricing strategies for a delayed column generation of a branch-and-cut approach. The computational investigations are based on real-world test sets from the cities of Berlin and Hamburg having up to 25 thousand timetabled trips and 70 million dead-head trips. T3 - ZIB-Report - SC-96-22 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2330 ER - TY - GEN A1 - Reich, Sebastian T1 - Backward Error Analysis for Numerical Integrators N2 - We consider backward error analysis of numerical approximations to ordinary differential equations, i.e., the numerical solution is formally interpreted as the exact solution of a modified differential equation. A simple recursive definition of the modified equation is stated. This recursion is used to give a new proof of the exponentially closeness of the numerical solutions and the solutions to an appropriate truncation of the modified equation. We also discuss qualitative properties of the modified equation and apply these results to the symplectic variable step-size integration of Hamiltonian systems, the conservation of adiabatic invariants, and numerical chaos associated to homoclinic orbits. T3 - ZIB-Report - SC-96-21 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2320 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Adaptive Accuracy Control for Microcanonical Car-Parrinello Simulations N2 - The Car-Parrinello (CP) approach to ab initio molecular dynamics serves as an approximation to time-dependent Born-Oppenheimer (BO) calculations. It replaces the explicit minimization of the energy functional by a fictitious Newtonian dynamics and therefore introduces an artificial mass parameter $\mu$ which controls the electronic motion. A recent theoretical investigation shows that the CP-error, i.e., the deviation of the CP--solution from the BO-solution {\em decreases} like $\mu^{1/2}$ asymptotically. Since the computational effort {\em increases} like $\mu^{-1/2}$, the choice of $\mu$ has to find a compromise between efficiency and accuracy. The asymptotical result is used in this paper to construct an easily implemented algorithm which automatically controls $\mu$: the parameter $\mu$ is repeatedly adapted during the simulation by choosing $\mu$ as large as possible while pushing an error measure below a user-given tolerance. The performance and reliability of the algorithm is illustrated by a typical example. T3 - ZIB-Report - SC-96-20 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2311 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - A Mathematical Investigation of the Car-Parrinello Method N2 - The Car-Parrinello method for ab-initio molecular dynamics avoids the explicit minimization of energy functionals given by functional density theory in the context of the quantum adiabatic approximation (time-dependent Born-Oppenheimer approximation). Instead, it introduces a fictitious classical dynamics for the electronic orbitals. For many realistic systems this concept allowed first-principle computer simulations for the first time. In this paper we study the {\em quantitative} influence of the involved parameter $\mu$, the fictitious electronic mass of the method. In particular, we prove by use of a carefully chosen two-time-scale asymptotics that the deviation of the Car-Parrinello method from the adiabatic model is of order ${\rm O}(\mu^{1/2})$ --- provided one starts in the ground state of the electronic system and the electronic excitation spectrum satisfies a certain non-degeneracy condition. Analyzing a two-level model problem we prove that our result cannot be improved in general. Finally, we show how to use the gained quantitative insight for an automatic control of the unphysical ``fake'' kinetic energy of the method. T3 - ZIB-Report - SC-96-19 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2302 ER - TY - GEN A1 - Niemann, Holger A1 - Schmidt, Dietmar A1 - Maas, Ulrich T1 - An Efficient Storage Scheme for Reduced Chemical Kinetics Based on Orthogonal Polynomials N2 - Simplified chemical kinetic schemes are a crucial prerequisite for the simulation of complex three-dimensional turbulent flows, and various methods for the generation of reduced mechanisms have been developed in the past. The method of intrinsic low-dimensional manifolds (ILDM), e.g., provides a mathematical tool for the automatic simplification of chemical kinetics, but one problem of this method is the fact that the information which comes out of the mechanism reduction procedure has to be stored for subsequent use in reacting flow calculations. In most cases tabulation procedures are used which store the relevant data (such as reduced reaction rates) in terms of the reaction progress variables, followed by table look-up during the reacting flow calculations. This can result in huge amounts of storage needed for the multi-dimensional tabulation. In order to overcome this problem we present a storage scheme which is based on orthogonal polynomials. Instead of using small tabulation cells and local mesh refinement, the thermochemical state space is divided into a small number of coarse cells. Within these coarse cells polynomial approximations are used instead of frequently used multi-linear interpolation. This leads to a considerable decrease of needed storage. The hydrogen-oxygen system is considered as an example. Even for this small chemical system we obtain a decrease of the needed storage requirement by a factor of 100. T3 - ZIB-Report - SC-96-18 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2294 ER - TY - GEN A1 - Göckeler, Meinulf A1 - Horsley, Roger A1 - Linke, Volkard A1 - Rakow, Paul A1 - Schierholz, Gerrit A1 - Stüben, Hinnerk T1 - Seeking the Equation of State of Non-Compact Lattice QED N2 - We perform a high statistics calculation of the equation of state for non-compact QED on large lattices. The calculation extends to fermionic correlation lengths of $\approx 8$, and it is combined with a finite size scaling analysis of the lattice data. T3 - ZIB-Report - SC-96-15 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2263 ER - TY - GEN A1 - Fröhlich, Jochen A1 - Lang, Jens A1 - Roitzsch, Rainer T1 - Selfadaptive Finite Element Computations with Smooth Time Controller and Anisotropic Refinement N2 - We present Multilevel Finite Element computations for twodimensional reaction-diffusion systems modelling laminar flames. These systems are prototypes for extreme stiffness in time and space. The first of these two rather general features is accounted for by an improved control mechanism for the time step. The second one is reflected through very thin travelling reaction fronts for which we propose an anisotropic discretization by local directional refinement. T3 - ZIB-Report - SC-96-16 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2270 ER - TY - GEN A1 - Schmidt, Frank A1 - Yevick, David T1 - Discrete Transparent Boundary Conditions for Schrödinger-Type Equations N2 - We present a general technique for constructing nonlocal transparent boundary conditions for one-dimensional Schrödinger-type equations. Our method supplies boundary conditions for the $\theta$-family of implicit one-step discretizations of Schrödinger's equation in time. The use of Mikusi\'nski's operator approach in time avoids direct and inverse transforms between time and frequency domains and thus implements the boundary conditions in a direct manner. T3 - ZIB-Report - SC-96-17 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2289 ER - TY - GEN T1 - Jahresbericht 1995 T3 - Jahresbericht - 1995 KW - Annual Report Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9704 SN - 0934-5892 ER - TY - GEN A1 - Stephani, Hans A1 - Wolf, Thomas T1 - Spherically symmetric perfect fluids in shearfree motion - the symmetry approach N2 - In General Relativity, the motion of expanding shearfree perfect fluids is governed by the ordinary differential equation $y^{\prime \prime }=$ $% F(x)\,y^2$ , where $F$ is an arbitrary function from which the equation of state can be computed. A complete symmetry analysis of this differential equation is given; its solutions are classified according to this scheme, and in particular the relation to Wyman's Painlev\'e analysis is clarified. T3 - ZIB-Report - SC-96-14 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2253 ER - TY - GEN A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Roitzsch, Rainer T1 - Eine graphische Oberfläche für numerische Programme N2 - Der Entwurf und die Implementierung des auf Tcl/Tk basierenden Werkzeugkastens ZGUI wird beschrieben und an einigen Beispielen erläutert. ZGUI unterstützt die Entwicklung einer graphischen Benutzeroberfläche (GUI) für die am ZIB erstellte numerische Software. Es sollen folgende Ziele erreicht werden: \begin{itemize} \item einfaches Ausprobieren anhand vordefinierter Testprobleme,\vspace*{-2mm} \item Kennenlernen numerischer Steuergrö\ss en und Verfahrensvarianten,\vspace*{-2mm} \item einfache Eingabe neuer Probleme,\vspace*{-2mm} \item einfache Nutzung graphischer Ausgabemöglichkeiten und\vspace*{-2mm} \item einheitliche Darstellung gleicher oder ähnlicher Optionen. \end{itemize} T3 - ZIB-Report - SC-96-13 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2242 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Information und Kommunikation im Umbruch N2 - Steht uns das Ende des traditionellen wissenschaftlichen Publizierens bevor? Neue Technologien eröffnen neue Chancen zur Bewältigung der Informationsflut und des gleichzeitigen Informationsmangels. Doch der Einsatz von Technik allein reicht nicht aus. T3 - ZIB-Report - TR-96-07 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5365 ER - TY - GEN A1 - Fröhlich, Jochen A1 - Schneider, Kai T1 - Computation of Decaying Turbulence in an Adaptive Wavelet Basis N2 - The paper presents computations of decaying two--dimensional turbulence in an adaptive wavelet basis. At each time step the vorticity is represented by an adaptively selected set of wavelet functions which adjusts to the instantaneous distribution of vorticity. The results of this new algorithm are compared to a classical Fourier method and a Fourier method supplemented with wavelet compression in each time step. T3 - ZIB-Report - SC-96-11 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2227 ER - TY - GEN A1 - Henk, Martin A1 - Weismantel, Robert T1 - On Hilbert bases of polyhedral cones N2 - For a polyhedral cone $C=$ pos $\{a^1,\dots,a^m\}\subset R^d$, $a^i\in Z^d$, a subset of integral vectors $H(C)\subset C \cap Z^d$ is called a Hilbert basis of $C$ iff (i) each element of $C\cap Z^d$ can be written as a non-negative integer combination of elements of $H(C)$ and (ii) $H(C)$ has minimal cardinality with respect to all subsets of $C \cap Z^d$ for which (i) holds. We show that various problems related to Hilbert bases are hard in terms of computational complexity. However, if the dimension and the number of elements of the Hilbert basis are fixed, a Hilbert basis can always be computed in polynomial time. Furthermore we introduce a (practical) algorithm for computing the Hilbert basis of a polyhedral cone. The finiteness of this method is deduced from a result about the height of a Hilbert basis which, in particular, improves on former estimates. T3 - ZIB-Report - SC-96-12 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2230 ER - TY - GEN A1 - Helmberg, Christoph A1 - Rendl, Franz A1 - Weismantel, Robert T1 - A Semidefinite Programming Approach to the Quadratic Knapsack Problem N2 - We investigate dominance relations between basic semidefinite relaxations and classes of cuts. We show that simple semidefinite relaxations are tighter than corresponding linear relaxations even in case of linear cost functions. Numerical results are presented illustrating the quality of these relaxations. T3 - ZIB-Report - SC-96-10 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2211 ER - TY - GEN A1 - Rojas, Raul T1 - Sixty Years of Computation - The Machines of Konrad Zuse N2 - This paper provides the {\em first} detailed description of the architecture of the computing machines Z1 and Z3 designed by Konrad Zuse in Berlin between 1936 to 1941. The necessary information was obtained from a careful evaluation of the patent application filed by Zuse in 1941. Additional insight was gained from a software simulation of the machine's logic. The Z1 was built using purely mechanical components, the Z3 using electromechanical relays. However, both machines shared a common logical structure and the programming model was exactly the same. We argue that both the Z1 and the Z3 possessed features akin to those of modern computers: memory and processor were separate units, the processor could handle floating-point numbers and compute the four basic arithmetical operations as well as the square root of a number. The program was stored on punched tape and was read sequentially. In the last section of this paper we bring the architecture of the Z1 and Z3 into historical perspective by offering a comparison with computing machines built in other countries. T3 - ZIB-Report - SC-96-09 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2203 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Neue Produkte für die digitale Bibliothek: die Rolle der Wissenschaften N2 - Der Artikel ist die ausgearbeitete und erweiterte Fassung eines eingeladenen Vortrags der Tagung ,,Die unendliche Bibliothek - Digitale Information in Wissenschaft, Verlag und Bibliothek''. Dieses Treffen, eine Veranstaltung des Börsenvereins des Deutschen Buchhandels e.V., der Deutschen Bibliothek und der Bundesvereinigung Deutscher Bibliothkesverbände, fand im Dezember 1995 in Bonn als Beitrag zur der heute aktuellen Debatte unter Wissenschaftlern, Verlegern, Buchhändlern, Bibliothekaren und Politikern statt, wie unser Wissen und unsere Informationen digital transferiert werden können. Der Vortrag stellte das zentrale Problem des heutigen wissenschaftlichen Informationswesens dar, die gleichzeitige Existenz von Informationsflut und Informationsmangel. Nach einer knappen Bestimmung der Veränderung der Kommunikationsstrukturen in den Wissenschaften fragte er nach den essentiellen Veränderungen der Informationsarten, d.h. nach der Natur der kommenden Globalen Digitalen Bibliothek, die als ein über die ganze Welt und auf viele Institutionen verteilter globaler Speicher gesehen wird. Der Vortrag diskutierte zum Schluss die Bedürfnisse und Interessen der Wissenschaften und ihre spezifische Verantwortung beim Übergang in die elektronische Welt. Der Tagungsband ist erschienen beim Harrassowitz Verlag, Wiesbaden, 1996. T3 - ZIB-Report - TR-96-05 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5343 ER - TY - GEN A1 - Lügger, Joachim T1 - On Changing Patterns of Mathematical Communication. Breakdowns in Traditional Publication N2 - The Internet and the new electronic means of information and communication are transforming scientific communication fundamentally. In particular, mathematicians, physicists and other natural scientists intensify, accelerate and extend their communication by the use of the Internet and its tools, from electronic mail up to the World Wide Web. In doing so, they also exchange scientific results of a new kind and quality yet unknown to traditional information providers such as publishers, libraries, and database suppliers (e.g. in the form of current research software, scientific data collections, observations and experimental data, visualizations, animations etc.). They, on the other hand, perceive the new ways, which are passing their own field of activity, as breakdowns of traditional publishing, as it was termed by the Association of Computing Machinery. In addition, scientific libraries find themselves caught in a structural crisis -- not only because of budget restraints. The {\it Deutsche Mathematiker-Vereinigung} (DMV), however, sees the new electronic means as an opportunity to master a crisis of this kind rather than a threat. By discussing concrete models, which may be - in a certain technical sense -- realizable already today, the article gives an introduction into the subject of a {\it Distributed Information- and Communication System for Mathematics}, a project prepared and planned by the DMV for the years 1996 to 1998. In the context of possible realization variants it also deals with questions of costs, resulting load of network connections, and -- showing the beginnings -- the (absolutely essential) solution of problems related to quality, authenticity, archival and intellectual property rights, which arise with the employment of electronic means. Obviously (even if not discussed explicitly) also computing centers, whose tasks and position are also affected by the electronic revolution, have the chance to find a new and forward-looking role in this field - in particular by new forms of cooperation with scientific libraries. T3 - ZIB-Report - TR-96-06 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5359 ER - TY - GEN A1 - Grötschel, Martin A1 - Löbel, Andreas A1 - Völker, Manfred T1 - Optimierung des Fahrzeugumlaufs im Öffentlichen Nahverkehr N2 - This paper addresses the problem of scheduling vehicles in a public mass transportation system. We show how this problem can be modelled as a special multicommodity flow problem and outline the solution methodology we have developed. Based on polyhedral investigations, we have designed and implemented a branch&cut algorithm and various heuristics with which real vehicle scheduling problems of truely large scale can be solved to optimality. We describe some implementation issues and report computational results. T3 - ZIB-Report - SC-96-08 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2195 ER - TY - GEN A1 - Müller, Peter T1 - Handbuch der Berliner Software Distribution (BeSD) N2 - Dieser Report beschreibt ein Konzept zur einheitlichen Bereitstellung von Software in heterogenen Umgebungen. Software kann so kooperativ durch mehrere Beteiligten (z. B. auch über Institutsgrenzen hinweg) angeboten und genutzt werden. Die Konzepte stammen ursprünglich vom Rechenzentrum der Universität Stuttgart (RUS) und wurden im Rahmen eines vom Verein zur Förderung eines Deutschen Forschungsnetzes (DFN) mit Mitteln des BMBF geförderten Projekts zur Berliner Software Distribution (BeSD) weiterentwickelt. T3 - ZIB-Report - TR-96-04 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5339 ER - TY - GEN A1 - Löbel, Andreas T1 - Solving Large-Scale Real-World Minimum-Cost Flow Problems by a Network Simplex Method N2 - This paper presents a large-scale real-world application of the minimum-cost flow problem, describes some details of a new implementation of the network simplex algorithm, and reports on computational comparisions. The real-world test sets include minimum-cost flow problems that are based on single-depot vehicle scheduling problems and on a Lagrangean relaxation of multiple-depot vehicle scheduling problems. Some of the problems are extremely large with up to 42,000 nodes and 20,000,000 arcs. The standard test problems are generated with NETGEN and include parts of the DIMACS standard problems. Our network simplex code is compared with \mbox{RELAX-IV}, Cost Scaling 2 version 3.4, and CPLEX's network solver NETOPT. T3 - ZIB-Report - SC-96-07 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2184 ER - TY - GEN A1 - Koepf, Wolfram A1 - Schmersau, Dieter T1 - Weinstein's Functions and the Askey-Gasper Identity N2 - \iffalse Recently, Todorov and Wilf independently realized that de Branges' original proof of the Bieberbach and Milin conjectures and the proof that was later given by Weinstein deal with the same special function system that de Branges had introduced in his work. In this article, we present an elementary proof of this statement based on the defining differential equations system rather than the closed representation of de Branges' function system. Our proof does neither use special functions (like Wilf's) nor the residue theorem (like Todorov's) nor the closed representation (like both), but is purely algebraic. On the other hand, by a similar algebraic treatment, the closed representation of de Branges' function system is derived. Our whole contribution can be looked at as the study of properties of the Koebe function. Therefore, in a very elementary manner it is shown that the known proofs of the Bieberbach and Milin conjectures can be understood as a consequence of the Löwner differential equation, plus properties of the Koebe function. \fi In his 1984 proof of the Bieberbach and Milin conjectures de Branges used a positivity result of special functions which follows from an identity about Jacobi polynomial sums that was found by Askey and Gasper in 1973, published in 1976. In 1991 Weinstein presented another proof of the Bieberbach and Milin conjectures, also using a special function system which (by Todorov and Wilf) was realized to be the same as de Branges'. In this article, we show how a variant of the Askey-Gasper identity can be deduced by a straightforward examination of Weinstein's functions which intimately are related with a Löwner chain of the Koebe function, and therefore with univalent functions. T3 - ZIB-Report - SC-96-06 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2175 ER - TY - GEN A1 - Fröhlich, Jochen A1 - Lang, Jens T1 - Twodimensional Cascadic Finite Element Computations of Combustion Problems N2 - We present an integrated time--space adaptive finite element method for solving systems of twodimensional nonlinear parabolic systems in complex geometry. The partial differential system is first discretized in time using a singly linearly implicit Runge--Kutta method of order three. Local time errors for the step size control are defined by an embedding strategy. These errors are used to propose a new time step by a PI controller algorithm. A multilevel finite element method with piecewise linear functions on unstructured triangular meshes is subsequently applied for the discretization in space. The local error estimate of the finite element solution steering the adaptive mesh refinement is obtained solving local problems with quadratic trial functions located essentially at the edges of the triangulation. This two--fold adaptivity successfully ensures an a priori prescribed tolerance of the solution. The devised method is applied to laminar gaseous combustion and to solid--solid alloying reactions. We demonstrate that for such demanding applications the employed error estimation and adaption strategies generate an efficient and versatile algorithm. T3 - ZIB-Report - SC-96-05 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2167 ER - TY - THES A1 - Ascheuer, Norbert T1 - Hamiltonian Path Problems in the On-line Optimization of Flexible Manufacturing Systems N2 - In this thesis we describe a practical problem that we encountered in the on--line optimization of a complex Flexible Manufacturing System. In the considered system a stacker crane has to fulfill all transportation tasks (jobs) in a single aisled automatic storage system. The jobs have to be sequenced in such a way, that the time needed for the unloaded moves is minimized. The modelling of this question leads to the so--called on--line Hamiltonian path problem. We computationally compare several on--line heuristics and derive lower bounds on the value obtained by an optimal on--line strategy by analyzing two off--line Combinatorial Optimization problems: the asymmetric Hamiltonian path problem with precedence constraints, also called sequential ordering problem (SOP), and the asymmetric Hamiltonian path problem with time windows (AHPPTW). We study the SOP and AHPPTW from a polyhedral point of view and derive several new classes of valid inequalities. Based on the polyhedral investigations we develop branch&cut algorithms for both problems and can achieve encouraging results on solving problem instances from real--world examples of the practical application. T3 - ZIB-Report - TR-96-03 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5328 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - DMV-Vorhaben. "Verbesserung des benutzerorientierten Zugriffs auf fachspezifische Online-Datenbanken und CD-ROM für Mathematische Institute der Bundesrepublik Deutschland" N2 - Der Report analysiert die Ergebnisse des Projektes ,,Verbesserung des benutzerorientierten Zugriffs auf fachspezifische Online und CD-ROM Datenbanken für Mathematische Institute der Bundesrepublik Deutschland'' der Deutschen Mathematiker-Vereinigung. An dem Projekt, das vom ZIB geleitet und koordiniert worden ist, haben mehr als 50 mathematische Fachbereiche und Forschungsinstitute teilgenommen. Dieses vom damaligen BMFT (einem Teil des jetzigen Bundesministeriums für Bildung, Wissenschaft, Forschung und Technologie) geförderte Projekt hat wesentlich dazu beigetragen, dass fachspezifische Datenbanken heute in den mathematischen Fachbereichen in Deutschland zu den selbstverständlichen Arbeitsmitteln gehören. Darüber hinaus hat das Projekt die Grundlagen für eine moderne elektronische Informations- und Kommunikationsstruktur in den mathematischen Fachbereichen gelegt. T3 - ZIB-Report - TR-96-02 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5318 ER - TY - GEN A1 - Reich, Sebastian T1 - Smoothed Langevin dynamics of highly oscillatory systems N2 - In this paper we generalize a result by Rubin and Ungar on Hamiltonian systems containing a strong constraining potential to Langevin dynamics. Such highly oscillatory systems arise, for example, in the context of molecular dynamics. We derive constrained equations of motion for the slowly varying solution components. This includes in particular the derivation of a correcting force-term that stands for the coupling of the slow and fast degrees of motion. We will identify two limiting cases: (i) the correcting force becomes, over a finite interval of time, almost identical to the force term suggested by Rubin and Ungar (weak thermal coupling) and (ii) the correcting force can be approximated by the gradient of the Fixman potential as used in statistical mechanics (strong thermal coupling). The discussion will shed some light on the question which of the two correcting potentials is more appropriate under which circumstances for molecular dynamics. In Sec.~7, we also discuss smoothing in the context of constant temperature molecular dynamics. T3 - ZIB-Report - SC-96-04 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2157 ER - TY - GEN A1 - Stalling, Detlev A1 - Steinke, Thomas T1 - Visualization of Vector Fields in Quantum Chemistry N2 - \small Many interesting phenomena in molecular systems like interactions between macro-molecules, protein-substrate docking, or channeling processes in membranes are gouverned to a high degree by classical Coulomb or van-der-Waals forces. The visualization of these force fields is important for verifying numerical simulations. Moreover, by inspecting the forces visually we can gain deeper insight into the molecular processes. Up to now the visualization of vector fields is quite unusual in computational chemistry. In fact many commercial software packages do not support this topic at all. The reason is not that vector fields are considered unimportant, but mainly because of the lack of adequate visualization methods. In this paper we survey a number of methods for vector field visualization, ranging from well-known concepts like arrow or streamline plots to more advanced techniques like line integral convolution, and show how these can be applied to computational chemistry. A combination of the most meaningful methods in an interactive 3D visualization environment can provide a powerful tool box for analysing simulations in molecular dynamics. T3 - ZIB-Report - SC-96-01 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2124 ER - TY - GEN A1 - Dentcheva, Darinka A1 - Möller, Andris A1 - Reeh, Peter A1 - Römisch, Werner A1 - Schultz, Rüdiger A1 - Schwarzbach, Gert A1 - Thomas, Jörg T1 - Optimale Blockauswahl bei der Kraftwerkseinsatzplanung N2 - The paper addresses the unit commitment problem in power plant operation planning. For a real power system comprising coal and gas fired thermal as well as pumped storage hydro plants a large-scale mixed integer optimization model for unit commitment is developed. Then primal and dual approaches to solving the optimization problem are presented and results of test runs are reported. T3 - ZIB-Report - SC-96-03 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2144 ER - TY - GEN A1 - Deuflhard, Peter A1 - Friese, Tilmann A1 - Schmidt, Frank A1 - März, Reinhard A1 - Nolting, Hans-Peter T1 - Effiziente Eigenmodenberechnung für den Entwurf integriert-optischer Chips N2 - {\bf Efficient eigenmode computation for the design of integrated optical chips.}The paper deals with adaptive multigrid methods for 2D Helmholtz eigenvalue problems arising in the design of integrated optical chips. Typical features of the technological problem are its geometric complexity, its multiscale structure, the possible occurrence of eigenvalue clusters, and the necessity of quite stringent required relative error tolerances. For reasons of sheer computational complexity, multigrid methods must be used to solve the discretized eigenvalue problems and adaptive grids must be automatically constructed to avoid an undesirable blow-up of the required number of nodes for these accuracies. In view of the problem specifications, an adaptive multigrid method based on Rayleigh quotient minimization, simultaneous eigenspace iteration, and conjugate gradient method as smoother is carefully selected. Its performance in the numerical simulation of a component of a rather recent optical chip (heterodyne receiver of HHI) is documented. T3 - ZIB-Report - SC-96-02 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2131 ER - TY - GEN A1 - Bixby, Robert E. A1 - Martin, Alexander T1 - Parallelizing the Dual Simplex Method N2 - We study the parallelization of the steepest-edge version of the dual simplex algorithm. Three different parallel implementations are examined, each of which is derived from the CPLEX dual simplex implementation. One alternative uses PVM, one general-purpose System V shared-memory constructs, and one the PowerC extension of C on a Silicon Graphics multi-processor. These versions were tested on different parallel platforms, including heterogeneous workstation clusters, Sun S20-502, Silicon Graphics multi-processors, and an IBM SP2. We report on our computational experience. T3 - ZIB-Report - SC-95-45 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2112 ER - TY - GEN A1 - Plümer, Judith A1 - Schwänzl, Roland T1 - Harvesting Mathematics N2 - Nahezu flächendeckend sind die mathematischen Fachbereiche der BRD zum Jahresende '95 im WWW vertreten. Durch die relative hohe Zahl von Servern entstehen Schwierigkeiten bei der Sichtung der angebotenen Information. Wir besprechen "Harvest" als brauchbares und gebrauchsfähiges Hilfsmittel zur Dokumentation. T3 - ZIB-Report - TR-96-01 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5306 ER - TY - THES A1 - Koch, Thorsten T1 - Jack-III Ein Branch & Cut-Verfahren zur Lösung des gewichteten Steinerbaumproblems in Graphen N2 - In der vorliegenden Arbeit werden die grundlegenden Gedanken und die Implementierung eines Branch & Cut-Algorithmus zur Lösung des gewichteten Steinerbaumproblems in Graphen beschrieben. Der Algorithmus basiert auf der linearen Relaxierung einer bidirektionalen ganzzahligen Formulierung des Problems. Wir werden das Problem einführen, drei ganzzahlige Modellierungen vorstellen, auf Reduktionsverfahren und Heuristiken eingehen sowie das Verfahren und seine Implementierung darstellen. Am Ende werden wir die Implementierung an 191 bekannten Probleminstanzen testen und auch optimale Lösungen f� ur zwei nach Wissen des Autors bis zu diesem Zeitpunkt ungelöste Instanzen liefern. Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9946 ER - TY - GEN A1 - Koepf, Wolfram T1 - Efficient Computation of Orthogonal Polynomials in Computer Algebra N2 - Orthogonal polynomials %like the Chebyshev polynomials can be calculated by computation of determinants, by the use of generating functions, in terms of Rodrigues formulas, by iterating recurrence equations, calculating the polynomial solutions of differential equations, through closed form representations and by other means. In this article, we give an overview about the efficiency of the above methods in Maple, Mathematica, and REDUCE. As a noncommercial package we include the MuPAD system. T3 - ZIB-Report - SC-95-42 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2080 ER - TY - GEN A1 - Bunke, Olaf A1 - Droge, Bernd A1 - Polzehl, Jörg T1 - Model Selection, Transformations and Variance Estimation in Nonlinear Regression N2 - The results of analyzing experimental data using a parametric model may heavily depend on the chosen model. In this paper we propose procedures for the adequate selection of nonlinear regression models if the intended use of the model is among the following: 1. prediction of future values of the response variable, 2. estimation of the unknown regression function, 3. calibration or 4. estimation of some parameter with a certain meaning in the corresponding field of application. Moreover, we propose procedures for variance modelling and for selecting an appropriate nonlinear transformation of the observations which may lead to an improved accuracy. We show how to assess the accuracy of the parameter estimators by a "moment oriented bootstrap procedure". This procedure may also be used for the construction of confidence, prediction and calibration intervals. Programs written in Splus which realize our strategy for nonlinear regression modelling and parameter estimation are described as well. The performance of the selected model is discussed, and the behaviour of the procedures is illustrated by examples. T3 - ZIB-Report - SC-95-43 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2096 ER - TY - GEN A1 - Bunke, Olaf A1 - Droge, Bernd A1 - Polzehl, Jörg T1 - Splus Tools for Model Selection in Nonlinear Regression N2 - The results of analyzing experimental data using a parametric model may heavily depend on the chosen model. With this paper we describe computational tools in Splus for the adequate selection of nonlinear regression models if the intended use of the model is among the following: 1. estimation of the unknown regression function, 2. prediction of future values of the response variable, 3. calibration or 4. estimation of some parameter with a certain meaning in the corresponding field of application. Moreover, we provide programs for variance modelling and for selecting an appropriate nonlinear transformation of the observations which may lead to an improved accuracy. We describe how the accuracy of the parameter estimators is assessed by a "moment oriented bootstrap procedure". This procedure is also used for the construction of confidence, prediction and calibration intervals. The use of our tools is illustrated by an example. Help files are given in an appendix. T3 - ZIB-Report - SC-95-44 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2104 ER - TY - GEN A1 - Reich, Sebastian T1 - Enhanced long-term simultation of Hamiltonian systems containing a strong non-convex potential N2 - Many physical systems exhibit rapid motion coupled to a slowly varying motion. Often the rapid motion is associated with a stiff contribution in the potential energy function. In this context, the situation typically considered in the literature is the one with a strictly convex potential. Under some technical assumptions, one can then show that the slow motion is reproduced by a properly constrained system. In this paper we are concerned with a different situation: Often different time-scales can be found because of many local minima and barrier crossing between these minima. We suggest here to replace the detailed motion in the minima and the local barrier crossings by a statistical model which is then coupled to the slow equations of motion over long periods of time. This leads to Langevin type equations of motion subject to an appropriate time transformation. T3 - ZIB-Report - SC-95-32 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1984 ER - TY - GEN A1 - Nettesheim, Peter T1 - An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics N2 - This paper presents an explicit and symplectic integrator called PICKABACK for quantum-classical molecular dynamics. This integration scheme is time reversible and unitary in the quantum part. We use the Lie formalism in order to construct a formal evolution operator which then is split using the Strang splitting yielding the symplectic discretization PICHABACK. Finally the new method is compared with a hybrid method in application to two examples: a collinear collision with a quantum oscillator and additionally a photodissociation process of a collinear ArHCI-molecule. T3 - ZIB-Report - SC-95-40 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2062 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Homogenization of Highly Oscillatory Hamiltonian Systems N2 - The paper studies Hamiltonian systems with a strong potential forcing the solutions to oscillate on a very small time scale. In particular, we are interested in the limit situation where the size $\epsilon$ of this small time scale tends to zero but the velocity components remain oscillating with an amplitude variation of order ${\rm O}(1)$. The process of establishing an effective initial value problem for the limit positions will be called {\em homogenization} of the Hamiltonian system. This problem occurs in mechanics as the problem of realization of holonomic constraints, in plasma physics as the problem of guiding center motion, in the simulation of biomolecules as the so called smoothing problem. We suggest the systematic use of the notion of {\em weak convergence} in order to approach this problem. This methodology helps to establish unified and short proofs of the known results which throw light on the inherent structure of the problem. Moreover, we give a careful and critical review of the literature. T3 - ZIB-Report - SC-95-39 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2050 ER - TY - GEN A1 - Löbel, Andreas A1 - Strubbe, Uwe T1 - Wagenumlaufoptimierung - Methodischer Ansatz und praktische Anwendung N2 - Im Rahmen des EDV-gestützten Systems zur {\bf{}BE}t{\bf{}R}iebseinsa{\bf{}T}zplanung und -{\bf{}A}uswertung (BERTA) der Berliner Verkehrsbetriebe (BVG) wird ein Modul zur Wagenumlaufoptimierung realisiert. In diesem Aufsatz berichten wir über die betrieblichen Anforderungen und Nebenbedingungen an eine mathematische Optimierung und erläutern unsere Konzepte zur Realisierung eines exakten mathematischen Verfahrens. T3 - ZIB-Report - SC-95-38 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2047 ER - TY - GEN A1 - Thomas, Rekha R. A1 - Weismantel, Robert T1 - Test sets and inequalities for integer programs: extended abstract N2 - This paper presents some connections between test sets and valid inequalities of integer programs. The reason for establishing such relationships is the hope that information (even partial) on one of these objects can be used to get information on the other and vice versa. We approach this study from two directions: On the one hand we examine the geometric process by which the secondary polytope associated with a matrix $A$ transforms to the state polytope as we pass from linear programs that have $A$ as coefficient matrix to the associated integer programs. The second direction establishes the notion of classes of augmentation vectors parallel to the well known concept of classes of facet defining inequalities for integer programs. We show how certain inequalities for integer programs can be derived from test sets for these programs. T3 - ZIB-Report - SC-95-36 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2021 ER - TY - GEN A1 - Helmberg, Christoph A1 - Rendl, Franz A1 - Weismantel, Robert T1 - Quadratic Knapsack Relaxations Using Cutting Planes and Semidefinite Programming: extended abstract N2 - We investigate dominance relations between basic semidefinite relaxations and classes of cuts. We show that simple semidefinite relaxations are tighter than corresponding linear relaxations even in case of linear cost functions. Numerical results are presented illustrating the quality of these relaxations. T3 - ZIB-Report - SC-95-37 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2031 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Nettesheim, Peter A1 - Schütte, Christof T1 - Quantum-Classical Molecular Dynamics as an Approximation to Full Quantum Dynamics N2 - This paper presents a mathematical derivation of a model for quantum-classical molecular dynamics (QCMD) as a {\em partial} classical limit of the full Schrödinger equation. This limit is achieved in two steps: separation of the full wavefunction and short wave asymptotics for its ``classical'' part. Both steps can be rigorously justified under certain smallness assumptions. Moreover, the results imply that neither the time-dependent self-consistent field method nor mixed quantum-semi-classical models lead to better approximations than QCMD since they depend on the separation step, too. On the other hand, the theory leads to a characterization of the critical situations in which the models are in danger of largely deviating from the solution of the full Schrödinger equation. These critical situations are exemplified in an illustrative numerical simulation: the collinear collision of an Argon atom with a harmonic quantum oscillator. T3 - ZIB-Report - SC-95-26 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1922 ER - TY - GEN A1 - Brandt, Manfred T1 - Approximations for the Distribution Function of the Sum of iid Random Variables with Compact Support in R+ N2 - In this paper a unified approach to central and decentral approximations of the distribution function $F(x,n)$ of the sum of $n$ iid random variables with compact support in $I\!\!R_+$ is given. This approach yields direct Edgeworth expansion (especially the Central limit theorem) and indirect Edgeworth expansion (Theorem of Bahadur-Rao, large deviation results) within a unified framework. An approximative inversion of the LST of $F(x,n)$ (approximation of the complex inversion integral over a line by an integral over a proper bounded arc with a proper integrand) allows to get these approximations and moreover explicit error bounds. T3 - ZIB-Report - SC-95-33 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1990 ER - TY - GEN A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the Sojourn Times for Many-Queue Head-of-the-Line Processor-Sharing Systems with Permanent Customers N2 - We consider a single server system consisting of $n$ queues with different types of customers (Poisson streams) and $k$ permanent customers. The permanent customers and those at the head of the queues are served in processor-sharing by the service facility (head-of-the-line processor-sharing). The stability condition and a pseudo work conservation law will be given for arbitrary service time distributions; for exponential service times a pseudo conservation law for the mean sojourn times can be derived. In case of two queues and exponential service times, the generating function of the stationary distribution satisfies a functional equation being a Riemann-Hilbert problem which can be reduced to a Dirichlet problem for a circle. The solution yields the mean sojourn times as an elliptic integral, which can be computed numerically very efficiently. In case $n\ge 2$ a numerical algorithm for computing the performance measures is presented, which is efficient for $n=2,3$. Since for $n\ge 4$ an exact analytical or/and numerical treatment is too complex a heuristic approximation for the mean sojourn times of the different types of customers is given, which in case of a (complete) symmetric system is exact. The numerical and simulation results show that, over a wide range of parameters, the approximation works well. T3 - ZIB-Report - SC-95-34 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2005 ER - TY - GEN A1 - Helmberg, Christoph A1 - Rendl, Franz T1 - Solving Quadratic (0,1)-Problems by Semidefinite Programs and Cuttings Planes N2 - We present computational experiments for solving quadratic $(0,1)$ problems. Our approach combines a semidefinite relaxation with a cutting plane technique, and is applied in a Branch and Bound setting. Our experiments indicate that this type of approach is very robust, and allows to solve many moderately sized problems, having say, less than 100 binary variables, in a routine manner. T3 - ZIB-Report - SC-95-35 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2012 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Optimum Path Packing on Wheels: The Consecutive Case N2 - We show that, given a wheel with nonnegative edge lengths and pairs of terminals located on the wheel's outer cycle such that the terminal pairs are in consecutive order, then a path packing, i.~e., a collection of edge disjoint paths connecting the given terminal pairs, of minimum length can be found in strongly polynomial time. Moreover, we exhibit for this case a system of linear inequalities that provides a complete and nonredundant description of the path packing polytope, which is the convex hull of all incidence vectors of path packings and their supersets. T3 - ZIB-Report - SC-95-31 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1976 ER - TY - GEN A1 - Dahl, Geir A1 - Martin, Alexander A1 - Stoer, Mechthild T1 - Routing through virtual paths in layered telecommunication networks N2 - We study a network configuration problem in telecommunications where one wants to set up paths in a capacitated network to accommodate given point-to-point traffic demand. The problem is formulated as an integer linear programming model where 0-1 variables represent different paths. An associated integral polytope is studied and different classes of facets are described. These results are used in a cutting plane algorithm. Computational results for some realistic problems are reported. T3 - ZIB-Report - SC-95-41 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2070 ER - TY - GEN A1 - Beck, Rudolf A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - KASKADE 3.0 User's Guide N2 - KASKADE 3.x was developed for the solution of partial differential equations in one, two, or three space dimensions. Its object-oriented implementation concept is based on the programming language C++$\,$.~Adaptive finite element techniques are employed to provide solution procedures of optimal computational complexity. This implies a posteriori error estimation, local mesh refinement and multilevel preconditioning. The program was designed both as a platform for further developments of adaptive multilevel codes and as a tool to tackle practical problems. Up to now we have implemented scalar problem types like stationary or transient heat conduction. The latter one is solved with the Rothe method, enabling adaptivity both in space and time. Some nonlinear phenomena like obstacle problems or two-phase Stefan problems are incorporated as well. Extensions to vector-valued functions and complex arithmetic are provided. This report helps to work with KASKADE Especially we \begin{itemize} \setlength{\parskip}{0ex} \item [{\bf --}] study a set of examples, \item [{\bf --}] explain how to define a user's problem and \item [{\bf --}] introduce a graphical user interface. \end{itemize} We are extending this guide continuously. The latest version is available by network. T3 - ZIB-Report - TR-95-11 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5269 ER - TY - GEN A1 - Fröhlich, Jochen A1 - Schneider, Kai T1 - An adaptive Wavelet-Vaguelette Algorithm for the Solution of Nonlinear PDEs N2 - The paper describes a fast algorithm for the discrete periodic wavelet transform and its inverse without using the scaling function. The approach permits to compute the decomposition of a function into a lacunary wavelet basis, i.e. a basis constituted of a subset of all basis functions up to a certain scale, without modification. The construction is then extended to operator--adapted biorthogonal wavelets. This is relevant for the solution of non--linear evolutionary PDEs where a priori information about the significant coefficients is available. We pursue the approach described in FrSc94 which is based on the explicit computation of the scalewise contributions of the approximated function to the values at points of hierarchical grids. Here, we present an improved construction employing the cardinal function of the multiresolution. The new method is applied to the Helmholtz equation and illustrated by comparative numerical results. It is then extended for the solution of a nonlinear parabolic PDE with semi--implicit discretization in time and self--adaptive wavelet discretization in space. Results with full adaptivity of the spatial wavelet discretization are presented for a one--dimensional flame front as well as for a two--dimensional problem. T3 - ZIB-Report - SC-95-28 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1941 ER - TY - GEN A1 - Deuflhard, Peter A1 - Heroth, Jörg T1 - Dynamic Dimension Reduction in ODE Models N2 - The paper analyzes a splitting technique into fast and slow dynamical components of ODE systems as suggested by {\sc Maas and Pope} recently. Their technique is based on a real block -- Schur decomposition of the Jacobian of the right hand side of the ODE. As a result of the analysis, a computationally cheap monitor for the possible necessary recovering of the splitting is derived by singular perturbation theory. Numerical experiments on moderate size, but challenging reaction kinetics problems document the efficiency of the new device within a linearly-implicit stiff integrator. T3 - ZIB-Report - SC-95-29 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1951 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - A Mathematical Approach to Smoothed Molecular Dynamics: Correcting Potentials for Freezing Bond Angles N2 - The interaction potential of molecular systems which are typically used in molecular dynamics can be split into two parts of essentially different stiffness. The strong part of the potential forces the solution of the equations of motion to oscillate on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles). However, the naive way of doing this via holonomic constraints is bound to produce incorrect results. The paper presents a mathematically rigorous discussion of the limit situation in which the stiffness of the strong part of the potential is increased to infinity. It is demonstrated that the average of the limit solution indeed obeys a constrained Hamiltonian system but with a {\em corrected soft potential}. An explicit formula for the additive potential correction is given and its significant contribution is demonstrated in an illustrative example. It appears that this correcting potential is definitely not identical with the Fixman-potential as was repeatedly assumed in the literature. T3 - ZIB-Report - SC-95-30 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1960 ER - TY - THES A1 - Zumbusch, Gerhard T1 - Simultanous h-p Adaption in Multilevel Finite Elements T3 - ZIB-Report - TR-95-14 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5298 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Löbel, Andreas T1 - Alcuin's Transportation Problems and Integer Programming N2 - The need to solve {\it transportation problems\/} was and still is one of the driving forces behind the development of the mathematical disciplines of graph theory, optimization, and operations research. Transportation problems seem to occur for the first time in the literature in the form of the four ''River Crossing Problems'' in the book Propositiones ad acuendos iuvenes. The {\it Propositiones\/} ---the oldest collection of mathematical problems written in Latin--- date back to the $8$th century A.D. and are attributed to Alcuin of York, one of the leading scholars of his time, a royal advisor to Charlemagne at his Frankish court. Alcuin's river crossing problems had no impact on the development of mathematics. However, they already display all the characteristics of today's large-scale real transportation problems. From our point of view, they could have been the starting point of combinatorics, optimization, and operations research. We show the potential of Alcuin's problems in this respect by investigating his problem~18 about a wolf, a goat and a bunch of cabbages with current mathematical methods. This way, we also provide the reader with a leisurely introduction into the modern theory of integer programming. T3 - ZIB-Report - SC-95-27 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1932 ER - TY - GEN A1 - Schmidt, Frank T1 - Simultaneous Computation of the Lowest Eigenvalue and Eigenvectors of the Helmholtz Equation N2 - This report collects a number of proposals to determine the lowest eigensolutions of the scalar Helmholtz equation. The basic routine of all discussed algorithms is the standard Rayleigh quotient minimization process. The minimization is performed in a direct multilevel manner, and a subspace iteration is used to determine simultaneously a couple of eigensolutions. As smoother the nonlinear Gauß-Seidel, the nonlinear conjugate gradient method and a preconditioned version of this method are compared with respect to their efficiency. The numerical examples are based on realistic 1D and 2D models of integrated optics components. T3 - ZIB-Report - TR-95-13 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5281 ER - TY - GEN A1 - Nowak, Ulrich T1 - A Fully Adaptive MOL-Treatment of Parabolic 1D-Problems with Extrapolation Techniques N2 - A fully adaptive method is presented for the numerical solution of highly nonlinear, coupled systems of parabolic differential equations in one space dimension. Time discretization is by means of the linearly--implicit Euler discretization. Space discretization is by finite differences on non--uniform grids. Both basic discretizations are combined with extrapolation. Based on local error estimates for both the time and the space discretization error, the accuracy of the numerical approximation is controlled and the discretization stepsizes are adapted automatically and simultaneously. The algorithm is implemented in a user friendly software package, PDEX1M. To be a powerful tool for users coming from applications the package has been equipped with some additional useful devices. T3 - ZIB-Report - SC-95-25 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1913 ER - TY - GEN A1 - Zumbusch, Gerhard T1 - Adaptive h-p approximation procedures, graded meshes and anisotropic refinement for Numerical Quadrature N2 - A set of adaptive algorithms for quadrature on multi-dimensional polyhedral domains is presented. Several kinds of refinement are discussed, covering local improvement of quadrature order and splitting the domain into sub-domains, resulting in isotropic, graded or anisotropic grids. The algorithms are pure local heuristics using no a priori knowledge or tuning parameters. This approach was motivated by results from finite element theory for optimal approximation results. Numerical experiments show the optimality of pure local greedy-like algorithms for singularity-type functions typically occurring in finite element computations. T3 - ZIB-Report - SC-95-24 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1905 ER - TY - GEN A1 - Deuflhard, Peter A1 - Gottschewski, Jürgen T1 - Das Konrad-Zuse-Zentrum für Informationstechnik Berlin. Struktur, wissenschaftliches Konzept und Einbettung in die Region N2 - Die Arbeit beschreibt Konzept, Struktur und Ausstattung des ZIB. Übergeordnetes Ziel des ZIB ist die Beschleunigung des {\it Know-how Transfers} aus der mathematischen Grundlagenforschung über die Entwicklung von Algorithmen und Software bis hin zur tatsächlichen Nutzung in der Industrie. In der Tat ist Computational Mathematics inzwischen zu einer der wichtigsten {\it Schlüsseltechnologien} geworden, die nicht zuletzt im Zusammenhang mit der Standort-Diskussion eine wichtige Rolle spielt und vermehrt spielen wird. Dazu müssen Methodenentwicklung und Rechenzentrum auf höchstem Niveau sowie interdisziplinäre Forschung möglichst vereint in einer Institution mit enger Anbindung an ein universitäres Umfeld realisiert sein. Das Konrad-Zuse-Zentrum hat die wesentlichen Voraussetzungen als SC Zentrum bereits geschaffen; ein Ausbau zum HPSC Zentrum wäre eine natürliche Entwicklung - falls die Politik diese Chance rechtzeitig begreift! T3 - ZIB-Report - TR-95-12 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5274 ER - TY - GEN A1 - Schultz, Rüdiger A1 - Stougie, Leen A1 - Vlerk, Maarten H. van der T1 - Solving Stochastic Programs with Complete Integer Recourse: a framework using Gröbner Bases N2 - In this paper we present a framework for solving stochastic programs with complete integer recourse and discretely distributed right-hand side vector, using Gröbner basis methods from computational algebra to solve the numerous second-stage integer programs. Using structural properties of the integer expected recourse function, we prove that under mild conditions an optimal solution is contained in a finite set. Furthermore, we present a basic scheme to enumerate this set and suggest possible improvements to economize on the number of function evaluations needed. T3 - ZIB-Report - SC-95-23 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1890 ER - TY - GEN A1 - Schütte, Christof A1 - Dinand, Manfred A1 - Zumbusch, Gerhard A1 - Brinkmann, Ralf T1 - Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments N2 - A theoretical investigation of the dynamic properties of integrated optical Er--doped waveguide lasers is presented. It includes the construction of a physical model and of numerical techniques which allow reliable simulations of the dynamical behaviour of the laser signal depending on essential parameters of the laser device and on its external, time--dependent pump radiation. Therefore, a physical theory is developed which describes the propagation of light and its interaction with the active substrate in the laser cavity. This is realized in two steps. First, a {\em fundamental model} based on Maxwell's equations and on rate equations for the transitions in the active medium is constructed. Since this turns out to prohibit reliable simulations, it is, in a second step, reformulated via averaging in time and space which suppresses the fluctuations on the fastest time scales but represents them correctly. For this {\em reduced model} reliable and efficient simulation techniques using adaptive control schemes are designed and implemented. We apply the linear--implicit Euler discretization with extrapolation in time and a multilevel quadrature scheme in space. Finally, the model is justified in comparison with experimental observations in four cases of technological relevance. T3 - ZIB-Report - SC-95-19 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1856 ER - TY - GEN A1 - Wolf, Thomas T1 - The program CRACK for solving PDEs in General Relativity. Lecture given at the 152. WE-Heraeus-Seminar on RELATIVITY AND SCIENTIFIC CUMPUTING: Computer Algebra, Numerics, Visualization N2 - In the introduction an approach to solving differential equations is motivated in which non-linear DEs are not attacked directly but properties like infinitesimal symmetries or the existence of an equivalent variational principle are investigated. In the course of such investigations overdetermined PDE-systems are generated which are to be solved (where the term `overdetermined' just stands for `more conditions than free functions'). In section 2.\ algorithms for simplifying and solving overdetermined PDE systems are given together with examples. References for more details of the corresponding program {\tt CRACK}, written by A.\ Brand and the author, are given. In sections 3.-05.\ applications of the program {\tt CRACK} are discussed. The first application is the investigation of symmetries of space-time metrics by solving Killing equations for Killing vectors and Killing tensors and their integrability conditions. A program {\tt CLASSYM} that formulates these equations, written by G.\ Grebot, is briefly described. In section 4.\ an example of the original application of {\tt CRACK} is discussed which is the determination of symmetries of a PDE system. The problem is to find the symmetries of an unusual unified field theory of gravitational and hadronic interactions. The application of symmetries with a program {\tt APPLYSYM} is the content of section 5.\ where an ODE, resulting from an attempt to generalize Weyl's class of solutions of Einsteins field equations, is solved. The final section is devoted to future work on, first, making a general PDE-solver more flexible and effective, and secondly, on applying it to more advanced applications. This section contains so far unpublished work. An example requiring the extension of {\tt CRACK} to deal with non-polynomial non-linearities results from an investigation of interior solutions of Einstein's field equations for a spherically symmetric perfect fluid in shear-free motion by H.\ Stephani. A possible future application of {\tt CRACK} is the determination of Killing tensors of higher rank. In the last sub-section an algorithm for formulating corresponding integrability conditions has been sketched. The maximal number of Killing tensors of rank $r$ in a $n$-dimensional Riemannian space has been found to be $\frac{1}{r+1}\left( ^{n + r - 1}_{\;\;\;\;\,r} \right) \left( ^{ n+r}_{\;\;\,r} \right)$. T3 - ZIB-Report - SC-95-22 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1881 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Aufbau elektronischer Informations- und Kommunikationsstrukturen N2 - Die vorliegende Arbeit ist die (z.T.~wesentlich) erweiterte Fassung eines Vortrages auf dem Deutschen Dokumentartag im September 1995 an der Fachhochschule Potsdam. Unser Ziel ist eine Bestandsaufnahme der gegenwärtigen Entwicklungen auf dem Gebiet der elektronischen Information und Kommunikation. Wir diskutieren Chancen und Risiken, beleuchten gesellschaftliche Rahmenbedingungen - vor allem im Vergleich mit den Vereinigten Staaten von Amerika - und skizzieren Aufgaben im Bereich von Forschung, Staat und Wirtschaft, die unserer Meinung nach noch zu bewältigen sind. Wir führen insbesondere in Gebiete ein, die vermutlich in naher Zukunft die Landschaft des Dokumentierens und Archivierens wesentlich verändern werden. Wir benutzen dabei häufig Beispiele und Modellvorstellungen aus der Mathematik, unserem eigenen Fachgebiet, die u.a. zeigen, wie Elemente des Informierens, Dokumentierens und Archivierens durch die neuen Technologien der elektronischen Datenverarbeitung und Kommunikation ineinander flie\"sen. Mehr Leistung kann mit geringeren Kosten erzielt werden. Wir schliessen mit einer Auflistung von neuen Perspektiven und Möglichkeiten zum Handeln in diesem Bereich. T3 - ZIB-Report - TR-95-10 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5252 ER - TY - GEN A1 - Schultz, Rüdiger T1 - Discontinuous Optimization Problems in Stochastic Integer Programming N2 - Integer stochastic linear programming is considered from the viewpoint of discontinuous optimization. After reviewing solution approaches via mollifier subgradients and decomposition we outline how to base a solution method on efficient pointwise calculation of the objective employing computer algebra. T3 - ZIB-Report - SC-95-20 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1861 ER - TY - GEN A1 - Schultz, Rüdiger T1 - Strong Convexity in Stochastic Programs with Complete Recourse II: Partially Random Right-Hand Side N2 - We establish a verifiable sufficient condition for strong convexity of the expected recourse as a function of the tender variable in a two-stage stochastic program with linear recourse. Generalizing a former result where all components of the second-stage right-hand side vector were random we treat the case where only a subvector of the right-hand side is random. As prerequisite, a refined analysis of the polyhedral complex of lineality regions of the second-stage value function is carried out. The sufficient condition for strong convexity allows to widen the class of recourse models for which certain quantitative results on stability and asymptotic convergence of optimal solutions are valid. T3 - ZIB-Report - SC-95-21 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1874 ER - TY - GEN A1 - Zumbusch, Gerhard T1 - Symmetric Hierarchical Polynomials and the Adaptive h-p-Version N2 - The $h$-$p$-version of finite-elements delivers a sub-exponential convergence in the energy norm. A step towards a full adaptive implementation is taken in the context of unstructured meshes of simplices with variable order $p$ in space. Both assumptions lead to desirable properties of shape functions like symmetry, $p$-hierarchy and simple coupling of elements. In a first step it is demonstrated that for standard polynomial vector spaces on simplices not all of these features can be obtained simultaneously. However, this is possible if these spaces are slightly extended or reduced. Thus a new class of polynomial shape functions is derived, which are especially well suited for three dimensional tetrahedra. The construction is completed by directly minimizing the condition numbers of the arising preconditioned local finite element matrices. The preconditioner is based on two-step domain decomposition techniques using a multigrid solver for the global linear problem $p=1$ and direct solvers for local higher order problems. Some numerical results concerning an adaptive (feedback) version of $h$-$p$ finite elements are presented. T3 - ZIB-Report - SC-95-18 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1841 ER - TY - GEN A1 - Lügger, Joachim T1 - Design-Überlegungen für ein Verteiltes Informationssystem für die Mathematik in Deutschland N2 - {\begin{footnotesize} Dieser Artikel beschreibt die ersten Schritte auf dem Wege zu einem Verteilten Informationssystem für die Mathematik, das von der ``Deutschen Mathematiker-Vereinigung'' (DMV) vorbereitet wird. Die Darstellung erfolgt aus zwei unterschiedlichen Perspektiven. Der erste Teil soll vor allem Lesern, die an der Motivation des Vorhabens und den organisatorischen Rahmenbedingungen interessiert sind, einen Zugang zu den zugrundeliegenden technischen Ideen bieten. Er skizziert zunächst die wissenschaftliche Zielsetzung des geplanten Vorhabens. Dann diskutiert er das Verteilte Informationssystem als Kombination aus einem elektronischen Nachrichtensystem (auf der Basis von E-mail), einem globalen Hypertextsystem (das die Informationsangebote der Partner des Projekts miteinander vernetzt) und einer verteilten, objektorientierten Datenbank (mit Interfaces zu den bereits genannten Komponenten). Dieser Teil schliesst mit einer knappen Betrachtung der Verhältnisse (auch der Chancen, Kosten einzusparen), die beim Übergang von traditionellen zu elektronischen Publikationsformen zu erwarten sind. Er führt insbesondere neue Möglichkeiten an, das geplante System auch für Zwecke des ``Zentralblatt für Mathematik'' einzusetzen. Der zweite Teil richtet sich an den eher technisch interessierten Leser. Er diskutiert einen ersten Vorschlag zur Strukturierung der bei den Partnern verteilt vorliegenden Informationsangebote -- vorwiegend aus Nutzersicht, d.h. möglichst unabhängig von den Idiosynkrasien der heute im Internet gegebenen Informationssysteme. Er enthält die technischen Kerngedanken zur Realisierung einer homogenen Informationsinfrastruktur bei den Partnern, die ein verteiltes und gleichzeitig hierachisches Retrieval in den Informationsangeboten der Mathematik in Deutschland ermöglichen soll. Dieser Teil benennt erste Chancen zur Implementierung innerhalb der Hyper-G- und, als Fernziel, auch der WWW-Welt. Er zeigt aber, neben den neuen Möglichkeiten, auch Risiken und Grenzen der Machbarkeit mit heutigen Mitteln auf. Die gesamte Darstellung orientiert sich an den Inhalten der bereits an anderer Stelle ausführlich vorgestellten Teilaufgaben und Teilprojekte und leitet daraus sowohl die vorgeschlagene Informationsstruktur als auch die technischen Mittel ab. Die wissenschaftlichen Inhalte und organisatorischen Ziele des Verteilten Informationssystems wurden in einer breiten (auch elektronisch geführten) Diskussion im Kreise der potentiellen Partner des Projekts ermittelt, insbesondere der Fachinformationsbeauftragten der Mathematik. Eine Anlage stellt eine vergleichende Betrachtung der Kosten auf, die einem mathematischen Fachbereich oder Forschungsinstitut bei der Weitergabe seiner wissenschaftlichen Reports auf Papier bzw. auf elektronischem Wege entstehen. \end{footnotesize}} T3 - ZIB-Report - TR-95-09 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5245 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Verteiltes Informationssystem für die Mathematik N2 - ``Das System ist zerbrochen!'', so lautet das Urteil von Keith Dennis, Professor an der Cornell University und neuer Verantwortlicher für die Mathematical Reviews, über das traditionelle Publikationswesen in der Mathematik. Was sind die Ursachen? Hauptsächlich sind es das starke Wachstum der mathematischen Literatur, die langen Verzögerungen von der Erstellung bis zum Erscheinen einer Arbeit, die hohen Ablehnungsraten bei mathematischen Journalen aufgrund beschränkter Seitenzahlen (und nicht wegen mangelnder Qualität) sowie drastisch steigende Preise für Zeitschriften und Bücher bei gleichzeitiger Reduktion der Bibliotheksetats. T3 - ZIB-Report - TR-95-06 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5218 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Distributed Information System for Mathematics (Available only in german, TR 95-06) N2 - "The system is broken'' is how Keith Dennis, professor at Cornell University and the new editor-in-chief of the Mathematical Reviews characterizes the traditional ways and means of publication in mathematics. What are the reasons? The main reasons are the extreme growth in the mathematical literature, the long delays between preparation and publication of an article, the high number of rejected papers due to page limitations (not lack of quality) as well as drastic price increases for journals and books with library budgets being reduced at the same time. T3 - ZIB-Report - TR-95-07 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5225 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Zimmermann, Uwe T1 - Wissenschaftliche Information am Wendepunkt? Zwänge, Krisen und Chancen aus Sicht der Mathematik T3 - ZIB-Report - TR-95-08 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5239 ER - TY - GEN A1 - Reich, Sebastian T1 - A Free Energy Approach to the Torsion Dynamics of Macromolecules N2 - Based on the concept of free energy, we give a Hamiltonian formulation for the torsion dynamics of macromolecules. The appropriate reaction coordinates for the free energy calculations are defined in terms of soft constraints as introduced in Brooks, B.R., Zhou, J., and Reich, S., Elastic molecular dynamics with flexible constraints, in preparation and Reich, S., Smoothed Dynamics of Highly Oscillatory Hamiltonian Systems, Physica D, to appear, 1995. We consider a few simplifications that allow one to calculate the free energy analytically and to write the corresponding equations of motion as a constrained Hamiltonian system. We also discuss a possible stochastic embedding of the reduced dynamics by means of a generalized Langevin approach. T3 - ZIB-Report - SC-95-17 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1839 ER - TY - GEN A1 - Busch, Hubert A1 - Schulz, Sandra A1 - Kroß, Günther T1 - Aufbau des Berliner Breitbandnetzes für die Wissenschaft N2 - Seit 1991 verfolgt die Berliner Wissenschaft verstärkt das Ziel, ihre Einrichtungen untereinander breitbandig mit Transferraten oberhalb von 34 Mb/s in Glasfasertechnik zu vernetzen. Im ersten Halbjahr 1995 ist es gelungen, die erste Stufe des Berliner Breitbandnetzes für die Wissenschaft ({\it Berlin Research Area Information Network - BRAIN}) aufzubauen. Dieser Bericht beschreibt die verschiedenen Phasen der Vernetzung der Wissenschaftseinrichtungen Berlins von den Anfängen im Jahre 1975 über die Planungen zum Breitbandnetz ab 1991 und die Realisierungsschritte durch die erfolgreiche Zusammenarbeit mit dem Landesamt für Informationstechnik Berlin (LIT) insbesondere bei der Verwendung von Glasfaserleitungen des Landes. Weiterhin werden der Aufbau des Berlin Regional Testbed in seiner Realisierung einschliesslich seiner Anwendungsprojekte mit Stand Juni 1995 und sodann die Pläne der Berliner Wissenschaftseinrichtungen für die zukünftige breitbandige Vernetzung einer Vielzahl von Standorten als allumfassendes Berlin Research Area Information Network dargestellt. T3 - ZIB-Report - TR-95-05 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5207 ER - TY - GEN A1 - Koepf, Wolfram T1 - REDUCE Packages on Power Series, Z-Transformation, Residues and Trigonometric Simplification N2 - In this report, we present a collection of new REDUCE packages that recently have been developed. These are the packages {\tt FPS}, {\tt ZTRANS}, {\tt RESIDUE} and {\tt TRIGSIMP} on the following topics: \begin{itemize} \item[] FPS Calculation of differential equations and formal power series representations, in particular for orthogonal polynomials and special functions of the hypergeometric type. \item[] ZTRANS Calculation of the Z-Transformation and its inverse. % to be used for the solution of linear recurrence equations. \item[] RESIDUE Calculation of residues of meromorphic functions. \item[] TRIGSIMP Simplification of expressions involving trigonometric and hyperbolic functions. \end{itemize} % These packages can be obtained via anonymous {\tt ftp} from % {\tt } in the directories {\tt ..}, ) For each of these packages, a description in form of a \LaTeX\ file is distributed together with the package. These documentations are collected here. In a final chapter, we show how to solve some difficult problems with these packages, and how they usefully can be combined. T3 - ZIB-Report - TR-95-03 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5187 ER - TY - GEN A1 - Beck, Rudolf A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - KASKADE 3.0 - An Object Oriented Adaptive Finite Element Code N2 - KASKADE 3.0 was developed for the solution of partial differential equations in one, two, or three space dimensions. Its object-oriented implementation concept is based on the programming language C++$\,$.~Adaptive finite element techniques are employed to provide solution procedures of optimal computational complexity. This implies a posteriori error estimation, local mesh refinement and multilevel preconditioning. The program was designed both as a platform for further developments of adaptive multilevel codes and as a tool to tackle practical problems. Up to now we have implemented scalar problem types like stationary or transient heat conduction. The latter one is solved with the Rothe method, enabling adaptivity both in space and time. Some nonlinear phenomena like obstacle problems or two-phase Stefan problems are incorporated as well. Extensions to vector-valued functions and complex arithmetic are provided. %Such free boundary problems ... We have implemented several iterative solvers for both symmetric and unsymmetric systems together with multiplicative and additive multilevel preconditioners. Systems arising from the nonlinear problems can be solved with lately developed monotone multigrid methods. %An object-oriented concept was chosen for KASKADE~3.0, based on the programming %language C++$\,$. This should provide the desired extensibilty and clearly %reflect the structure of the code. %A direct sparse matrix solver (Harwell MA28) is included. T3 - ZIB-Report - TR-95-04 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5199 ER - TY - GEN A1 - Deuflhard, Peter A1 - Lang, Jens A1 - Nowak, Ulrich T1 - Adaptive Algorithms in Dynamical Process Simulation N2 - Dynamical simulation of industrially relevant processes strongly advises the use of algorithms, which are {\em adaptive} both in time and in space discretization. The paper presents two alternatives: (a) a fully adaptive method of lines approach, which is based on finite difference methods and essentially applicable to 1D problems; (b) a fully adaptive Rothe method, which is based on a fast multilevel finite element method and applicable to 1D up to 3D. T3 - ZIB-Report - SC-95-16 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1823 ER - TY - THES A1 - Schultz, Rüdiger T1 - Structure and Stability in Two-Stage Stochastic Programming N2 - {\begin{footnotesize} This thesis is concerned with structural properties and the stability behaviour of two-stage stochastic programs. Chapter~1 gives an introduction into stochastic programming and a summary of the main results of the thesis. In Chapter~2 we present easily verifiable sufficient conditions for the strong convexity of the expected-recourse function in a stochastic program with linear complete recourse. Different levels of randomness in the data are considered. We start with models where only the right-hand side of the constraints is random and extend these results to the situation where also the technology matrix contains random entries. The statements on strong convexity imply new stability estimates for sets of optimal solutions when perturbing the underlying probability measure. We work out Hölder estimates (in terms of the $\mbox{L}_1$-Wasserstein distance) for optimal solution sets to linear recourse models with random technology matrix. In Chapter~3 ({\it joint work with Werner Römisch, Berlin}) we are aiming at the Lipschitz stability of optimal solution sets to linear recourse models with random right-hand side. To this end , we first adapt the distance notion for the underlying probability measures to the structure of the model and derive a Lipschitz estimate for optimal solutions based on that distance. Here, the strong convexity established in Chapter~2 turns out as an essential assumption. For applications, however, a Lipschitz estimate with respect to a more accesssible probability distance is desirable. Structural properties of the expected-recourse function finally permit such an estimate in terms of the Kolmogorov-Smirnov distance of linear transforms of the underlying measures. The general analysis is specified to estimation via empirical measures. We obtain a law of iterated logarithm, a large deviation estimate and an estimate for the asymptotic distribution of optimal solution sets. Chapters~4 and~5 deal with two-stage linear stochastic programs where integrality constraints occur in the second stage. In Chapter~4 we study basic continuity properties of the expected-recourse function for models with random right-hand side and random technology matrix. The joint continuity with respect to the decision variable and the underlying probability measure leads to qualitative statements on the stability of local optimal values and local optimal solutions. In Chapter~5 we demonstrate that a variational distance of probability measures based on a suitable Vapnik-\v{C}ervonenkis class of Borel sets leads to convergence rates of the Hölder type for the expected recourse as a function of the underlying probability measure. The rates carry over to the convergence of local optimal values. As an application we again consider estimation via empirical measures. Beside qualitative asymptotic results for optimal values and optimal solutions we obtain a law of iterated logarithm for optimal values. \end{footnotesize}} T3 - ZIB-Report - SC-95-15 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1819 ER - TY - GEN A1 - Schütte, Christof T1 - Smoothed Molecular Dynamics for Thermally Embedded Systems N2 - This paper makes use of statistical mechanics in order to construct effective potentials for Molecular Dynamics for systems with nonstationary thermal embedding. The usual approach requires the computation of a statistical ensemble of trajectories. In the context of the new model the evaluation of only one single trajectory is sufficient for the determination of all interesting quantities, which leads to an enormous reduction of computational effort. This single trajectory is the solution to a corrected Hamiltonian system with a new potential $\tilde{V}$. It turns out that $\tilde{V}$ can be defined as spatial average of the original potential $V$. Therefore, the Hamiltonian dynamics defined by $\tilde{V}$ is smoother than that effected by $V$, i.e. a numerical integration of its evolution in time allows larger stepsizes. Thus, the presented approach introduces a Molecular Dynamics with smoothed trajectories originating from spatial averaging. This is deeply connected to time--averaging in Molecular Dynamics. These two types of {\em smoothed Molecular Dynamics} share advantages (gain in efficiency, reduction of error amplification, increased stability) and problems (necessity of closing relations and adaptive control schemes) which will be explained in detail. T3 - ZIB-Report - SC-95-14 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1809 ER - TY - GEN T1 - Jahresbericht 1994 T3 - Jahresbericht - 1994 KW - Annual Report Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9699 SN - 0934-5892 ER - TY - GEN A1 - Gatermann, Karin T1 - Testing for Sn-Symmetry with a Recursive Detective N2 - In the recent years symmetric chaos has been studied intensively. One knows which symmetries are admissible as the symmetry of an attractor and which transitions are possible. The numeric has been developed using equivariant functions for detection of symmetry and augmented systems for determination of transition points. In this paper we look at this from a sophisticated group theoretic point of view and from the view of scientific computing, i.e. efficient evaluation of detectives is an important point. The constructed detectives are based on Young's seminormal form for $S_n$. An application completes the paper. T3 - ZIB-Report - SC-95-12 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1786 ER - TY - GEN A1 - Koepf, Wolfram T1 - The Identification Problem for Transcendental Functions N2 - In this article algorithmic methods are presented that have essentially been introduced into computer algebra within the last decade. The main ideas are due to Stanley[1980] and Zeilberger[1990]. Some of them had already been discovered in the last century (see e.\ g.\ Beke[1894]), but because of the complexity of the underlying algorithms have fallen into oblivion. The combination of these ideas leads to a solution of the identification problem for a large class of transcendental functions. We present implementations of these algorithms in computer algebra systems. T3 - ZIB-Report - SC-95-13 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1791 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Polthier, Konrad T1 - Visualization and Mathematics. International Workshop N2 - International Workshop with support of the Deutsche Forschungsgemeinschaft (DFG) and Max-Planck-Gesellschaft (MPG) Berlin (Dahlem), Germany, May 30 - June 2, 1995 T3 - ZIB-Report - TR-95-02 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5179 ER - TY - GEN A1 - Dellnitz, Michael A1 - Hohmann, Andreas T1 - A Subdivision Algorithm for the Computation of Unstable Manifolds and Global Attractors N2 - Each invariant set of a given dynamical system is part of the global attractor. Therefore the global attractor contains all the potentially interesting dynamics, and, in particular, it contains every (global) unstable manifold. For this reason it is of interest to have an algorithm which allows to approximate the global attractor numerically. In this article we develop such an algorithm using a subdivision technique. We prove convergence of this method in a very general setting, and, moreover, we describe the qualitative convergence behavior in the presence of a hyperbolic structure. The algorithm can successfully be applied to dynamical systems of moderate dimension, and we illustrate this fact by several numerical examples. T3 - ZIB-Report - SC-95-11 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1770 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Kommunikation am Wendepunkt - Bibliotheken im Zeitalter globaler elektronischer Netze - N2 - Durch extrem steigende Preise für traditionelle wissenschaftliche Zeitschriften bei gleichzeitiger Stagnation der Bibliotheksetats an den Hochschulen und bei weltweit weiterhin anwachsenden Forschungsleistungen ist die adäquate Versorgung der Wissenschaften mit relevanter Literatur gefährdet. Dokumentenliefersysteme werden vielerorts als Lösung dieser ``Bibliothekskrise'' propagiert. Dieser Weg ist für den derzeitigen Literaturversorgungsmarkt sinnvoll, aber er bietet keine langfristig stabile Lösung. Wenn die Grundversorgung der Bibliotheken weiter schrumpft, wird Dokumentenlieferung in der zur Zeit üblichen bzw. geplanten Form die Kosten nur noch zusätzlich in die Höhe treiben. Wir plädieren in diesem Aufsatz für einen grundsätzlich neuen Ansatz. Wir sind der Meinung, da\ss{} einzig der Übergang auf elektronische Medien eine bezahlbare, umfassende und benutzerfreundliche Versorgung der Wissenschaftler mit Literatur sichern kann. Wir zeigen -- unter anderem anhand elektronischer Zeitschriften -- wie zum Beispiel durch Kooperation von Bibliotheken mit Fachbereichen und wissenschaftlichen Gesellschaften neue Wege der Informationsversorgung beschritten werden können. Dieser Vorschlag einer neuen Organisation des wissenschaftlichen Publikationswesen erfordert Umdenken in vielen Bereichen. Neue Organisationsformen sind erforderlich, Rechte müssen anders verteilt, Aufgaben auf andere Schultern geladen werden. Die Bibliotheken werden besonders betroffen sein. Aber für sie ist die konsequente Nutzung der sich rasch ausbreitenden Informationstechnik (darunter verstehen wir u. a. globale elektronische Netze, leistungsfähige Rechner, kostengünstige Speichermedien, benutzerfreundliche Such- und Retrieval-Systeme, Entwicklung weltweit akzeptierter Datenformate) eine wirkliche und möglicherweise die einzige Chance, ihrem Auftrag zur umfassenden Versorgung der Wissenschaften mit Literatur zu gesamtwirtschaftlich niedrigen Kosten weiterhin nachzukommen. Au\ss{}erdem bietet die Bereitstellung und Archivierung wissenschaftlicher Literatur auf elektronischem Wege bedeutende Vorteile gegenüber der traditionellen Dokumentation auf Papier, die im übrigen, falls erwünscht, weiterhin betrieben werden kann. T3 - ZIB-Report - TR-95-01 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5164 ER - TY - GEN A1 - Koepf, Wolfram A1 - Schmersau, Dieter T1 - On the De Branges Theorem N2 - Recently, Todorov and Wilf independently realized that de Branges' original proof of the Bieberbach and Milin conjectures and the proof that was later given by Weinstein deal with the same special function system that de Branges had introduced in his work. In this article, we present an elementary proof of this statement based on the defining differential equations system rather than the closed representation of de Branges' function system. Our proof does neither use special functions (like Wilf's) nor the residue theorem (like Todorov's) nor the closed representation (like both), but is purely algebraic. On the other hand, by a similar algebraic treatment, the closed representation of de Branges' function system is derived. Our whole contribution can be looked at as the study of properties of the Koebe function. Therefore, in a very elementary manner it is shown that the known proofs of the Bieberbach and Milin conjectures can be understood as a consequence of the Löwner differential equation, plus properties of the Koebe function. T3 - ZIB-Report - SC-95-10 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1765 ER - TY - GEN A1 - Thomas, Rekha R. A1 - Weismantel, Robert T1 - Truncated Gröbner Bases for Integer Programming N2 - {\def\N{{\mbox{{\rm I\kern-0.22emN}}}}In this paper we introduce a multivariate grading of the toric ideal associated with the integer program $min \{ cx : Ax = b, x \in \N^n \}$, and a truncated Buchberger algorithm to solve the program. In the case of $max \{ cx : Ax \leq b, x \leq u, x \in \N^n \}$ in which all data are non-negative, this algebraic method gives rise to a combinatorial algorithm presented in UWZ94}. T3 - ZIB-Report - SC-95-09 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1750 ER - TY - GEN A1 - Schulz, Andreas S. A1 - Weismantel, Robert A1 - Ziegler, Günter M. T1 - 0/1-Integer Programming: Optimization and Augmentation are Equivalent N2 - {\def\xnew{x^{\mbox{\tiny new}}}\def\Z{{{\rm Z}\!\! Z}}For every fixed set ${\cal F}\subseteq\{0,1\}^n$ the following problems are strongly polynomial time equivalent: given a feasible point $x\in\cal F$ and a linear objective function $c\in\Z^n$, \begin{itemize} \item find a feasible point $x^*\in\cal F$ that maximizes $cx$ (Optimization), \item find a feasible point $\xnew\in\cal F$ with $c\xnew>cx$ (Augmentation), and \item find a feasible point $\xnew\in\cal F$ with $c\xnew>cx$ such that $\xnew-x$ is ``irreducible''\\(Irreducible Augmentation). \end{itemize} This generalizes results and techniques that are well known for $0/1$--integer programming problems that arise from various classes of combinatorial optimization problems.} T3 - ZIB-Report - SC-95-08 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1744 ER - TY - GEN A1 - Dellnitz, Michael A1 - Golubitsky, Martin A1 - Hohmann, Andreas A1 - Stewart, Ian T1 - Spirals in Scalar Reaction-Diffusion Equations N2 - Spiral-like patterns are an often observed phenomenon in chemical experiments such as the Belousov-Zhabotinskii reaction. The talk is concerned with a new PDE model whose solutions have the form of rotating spirals. In contrast to previous approaches it is based on a {\em scalar\/} reaction diffusion equation defined on a disk. A particular choice of boundary conditions leads to a non-selfadjoint operator which permits non-trivial dynamics. We study this equation using a combination of equivariant bifurcation theory and numerical simulations. The latter involves the direct simulation of the time dependent system as well as the computation of rotating waves and their stability. T3 - ZIB-Report - SC-95-06 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1720 ER - TY - GEN A1 - Renaut, Rosemary A1 - Fröhlich, Jochen T1 - A Pseudospectral Chebychev method for the 2D Wave Equation with Domain Stretching and Absorbing Boundary Conditions N2 - In this paper we develop a method for the simulation of wave propagation on artificially bounded domains. The acoustic wave equation is solved at all points away from the boundaries by a pseudospectral Chebychev method. Absorption at the boundaries is obtained by applying one-way wave equations at the boundaries, without the use of damping layers. The theoretical reflection coefficient for the method is compared to theoretical estimates of reflection coefficients for a Fourier model of the problem. These estimates are confirmed by numerical results. Modification of the method by a transformation of the grid to allow for better resolution at the center of the grid reduces the maximum eigenvalues of the differential operator. Consequently, for stability the maximum timestep is $O(1/N)$ as compared to $O(1/N^2)$ for the standard Chebychev method. Therefore, the Chebychev method can be implemented with efficiency comparable to that of the Fourier method. Moreover, numerical results presented demonstrate the superior performance of the new method. T3 - ZIB-Report - SC-95-07 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1730 ER - TY - GEN A1 - Wolf, Thomas T1 - Programs for Applying Symmetries of PDEs N2 - In this paper the programs {\tt APPLYSYM}, {\tt QUASILINPDE} and {\tt DETRAFO} are described which aim at the utilization of infinitesimal symmetries of differential equations. The purpose of {\tt QUASILINPDE} is the general solution of quasilinear PDEs. This procedure is used by {\tt APPLYSYM} for the application of point symmetries for either \begin{itemize} \item calculating similarity variables to perform a point transformation which lowers the order of an ODE or effectively reduces the number of explicitly occuring independent variables in a PDE(-system) or for \item generalizing given special solutions of ODEs/PDEs with new constant parameters. \end{itemize} The program {\tt DETRAFO} performs arbitrary point- and contact transformations of ODEs/PDEs and is applied if similarity and symmetry variables have been found. The program {\tt APPLYSYM} is used in connection with the program {\tt LIEPDE} for formulating and solving the conditions for point- and contact symmetries which is described in LIEPDE(1992). The actual problem solving is done in all these programs through a call to the package {\tt CRACK} for solving overdetermined PDE-systems. T3 - ZIB-Report - SC-95-05 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1710 ER - TY - GEN A1 - Gatermann, Karin A1 - Lauterbach, Reiner T1 - Automatic classification of normal forms N2 - The aim of this paper is to demonstrate a specific application of Computer Algebra to bifurcation theory with symmetry. The classification of different bifurcation phenomena in case of several parameters is automated, based on a classification of Gröbner bases of possible tangent spaces. The computations are performed in new coordinates of fundamental invariants and fundamental equivariants, with the induced weighted ordering. In order to justify the approach the theory of intrinsic modules is applied. Results for the groups $D_3, Z_2,$ and $ Z_2\times Z_2$ demonstrate that the algorithm works independent of the group and that new results are obtained. T3 - ZIB-Report - SC-95-03 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1692 ER - TY - GEN A1 - Abdel-Hamid, Atef Abdel-Aziz A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Schorer, Herbert T1 - Simulation und Optimierung einer PC-Fertigung unter Echtzeitbedingungen N2 - Die Business Unit PC in Augsburg ist die zentrale Produktionsstätte der Siemens--Nixdorf Informationssysteme (SNI) AG für Personal Computer sowie für einige Periphärgeräte. Das Werk, entworfen nach modernen CIM/CAI--Konzepten (Computer Integrated Manufacturing/ Computer Aided Industry), wurde 1987 errichtet. Bald zeigte sich jedoch, daß es für ein zu geringes Produktionsvolumen ausgelegt war und einige Komponenten des Systems Engpässe im Produktionsbetrieb darstellen. Das Management suchte nach Möglichkeiten, den Produktionsfluß zu verbessern, ohne teure technische Änderungen am System vornehmen zu müssen. Eine Forschungsgruppe des Konrad--Zuse--Zentrums für Informationstechnik (die ehemals an der Universität Augsburg ansässig war) analysierte, unterstützt von einigen Studenten und Ingenieuren der SNI, den Produktionsfluß und lokalisierte Schwachstellen. Basierend auf diesen Erkenntnissen wurden mathematische Fragestellungen erarbeitet und auf mathematischen Optimierungsverfahren basierende Softwarepakete entwickelt, die jetzt teilweise bei SNI im Einsatz sind. Im folgenden werden einige dieser Fragestellungen, deren Modellierung und mathematische Behandlung beschrieben. Einige der Ansätze, die hier dargestellt werden sollen, sind teilweise schon in Grötschel [Grö92] angesprochen worden. T3 - ZIB-Report - SC-95-04 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1700 ER - TY - GEN A1 - Brand, Rüdiger A1 - Freeden, Willi A1 - Fröhlich, Jochen T1 - An Adaptive Hierarchical Approximation Method on the Sphere Using Axisymmetric Locally Supported Basis Functions N2 - The paper discusses the approximation of scattered data on the sphere which is one of the major tasks in geomathematics. Starting from the discretization of singular integrals on the sphere the authors devise a simple approximation method that employs locally supported spherical polynomials and does not require equidistributed grids. It is the basis for a hierarchical approximation algorithm using differently scaled basis functions, adaptivity and error control. The method is applied to two examples one of which is a digital terrain model of Australia. T3 - ZIB-Report - SC-95-02 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1682 ER - TY - GEN A1 - Koepf, Wolfram T1 - Identities for Families of Orthogonal Polynomials and Special Functions N2 - In this article we present new results for families of orthogonal polynomials and special functions, that are determined by algorithmical approaches. In the first section, we present new results, especially for discrete families of orthogonal polynomials, obtained by an application of the celebrated Zeilberger algorithm. Next, we present algorithms for holonomic families $f(n,x)$ of special functions which possess a derivative rule. We call those families {\sl admissible}. A family $f(n,x)$ is holonomic if it satisfies a holonomic recurrence equation with respect to $n$, and a holonomic differential equation with respect to $x$, i.\ e. linear homogeneous equations with polynomial coefficients. The rather rigid property of admissibility has many interesting consequences, that can be used to generate and verify identities for these functions by linear algebra techniques. On the other hand, many families of special functions, in particular families of orthogonal polynomials, are admissible. We moreover present a method that generates the derivative rule from the holonomic representation of a holonomic family. % whenever one exists. As examples, we find new identities for the Jacobi polynomials and for the Whittaker functions, and for families of discrete orthogonal polynomials by the given approach. Finally, we present representations for the parameter derivatives of the Gegenbauer and the generalized Laguerre polynomials. T3 - ZIB-Report - SC-95-01 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1675 ER - TY - GEN A1 - Schmidt, Frank A1 - März, Reinhard T1 - On the Reference Wave Vector pf Paraxial Helmholtz Equations N2 - The reference wave vector of the paraxial Helmholtz equation is determined using various strategies which result all in similar expressions. The effort for its evaluation is so small that the reference wave vector can be adapted for each propagation step of an arbitrary BPM-algorithm. T3 - ZIB-Report - SC-94-38 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1660 ER - TY - GEN A1 - Zuse, Konrad T1 - Discrete Mathematics and Rechnender Raum (Computing Space) -Part 1-. Cellular Structured Space (Rechnender Raum) and Physical Phenomena -Part 2-. N2 - The first part of the report contains a lecture presented at ``Scientific Computing in der Theoretischen Physik'', a workshop organized by the DMV-Fachgruppe Scientific Computing in cooperation with the GAMM-Fachauschuß Scientific Computing at Freie Universit{ä}t Berlin in March 1994. To complete this lecture, a slightly modified version of TR 93-12 is appended. T3 - ZIB-Report - TR-94-10 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5156 ER - TY - GEN A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast and Resolution Independent Line Integral Convolution N2 - Line Integral Convolution (LIC) is a powerful technique for generating striking images and animations from vector data. Introduced in 1993, the method has rapidly found many application areas, ranging from computer arts to scientific visualization. Based upon locally filtering an input texture along a curved stream line segment in a vector field, it is able to depict directional information at high spatial resolutions. We present a new method for computing LIC images, which minimizes the total number of stream lines to be computed and thereby reduces computational costs by an order of magnitude compared to the original algorithm. Our methods utilizes fast, error-controlled numerical integrators. Decoupling the characteristic lengths in vector field grid, input texture and output image, it allows to compute filtered images at arbitrary resolution. This feature is of great significance in computer animation as well as in scientific visualization, where it can be used to explore vector data by smoothly enlarging structure of details. We also present methods for improved texture animation, employing constant filter kernels only. To obtain an optimal motion effect, spatial decay of correlation between intensities of distant pixels in the output image has to be controlled. This is achieved by blending different phase shifted box filter animations and by adaptively rescaling the contrast of the output frames. T3 - ZIB-Report - SC-94-37 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1653 ER - TY - THES A1 - Fereirra, Carlos Eduardo T1 - On Combinatorial Optimization Problems Arising in Computer System Design Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10146 ER - TY - GEN A1 - Fröhlich, Jochen A1 - Deuflhard, Peter T1 - Moving Weight Galerkin Methods for Turbulent Reactive Flows N2 - Adopting a statistical approach for the computation of turbulent combustion flows an approximation for the probability density function (PDF) of the composition variables is often required to treat the highly non-linear reaction term in a satisfactory way. One class of methods currently being used are the moment methods which employ transport equations for low order statistical moments and use a parametrized shape of the PDF. A second class solves a transport equation for the joint PDF by a Monte Carlo method. In the present paper we develop an intermediate algorithm based on a Galerkin method for the PDF transport equation. The solution is developed in terms of an orthogonal or bi-orthogonal basis of a suitable Hilbert space. The unconventional use of the related weight function as a prefactor (moving weight approach) permits adaptivity and results in a generalization of the $\beta-$closure for bounded scalar quantities. We present the approximation procedure in detail and apply it to the evolution of the composition in a homogeneous well-stirred reactor. The extension to non-homogeneous flow simulations is straightforward. T3 - ZIB-Report - SC-94-36 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1646 ER - TY - GEN A1 - Schaffers, Michel T1 - Complete Linear Descriptions for Special Instances of the Single Source Fixed Charge Network Flow Design Problem N2 - The multicommodity linear formulation of the Fixed Charge Network Flow Design problem is known to have significantly sharp linear relaxation lower bounds. However the tradeoff is the introduction of a large amount of artificial variables. We exhibit a class of special instances for which the lower bound is tight. Further we completly describe the polyhedron in the space of the natural variables. T3 - ZIB-Report - SC-94-35 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1630 ER - TY - GEN A1 - Lang, Jens T1 - Two-Dimensional Fully Adaptive Solutions of Reaction-Diffusion Equations N2 - We present an adaptive Rothe method for two--dimensional problems combining an embedded Runge--Kutta scheme in time and a multilevel finite element discretization in space. The spatial discretization error is controlled by a posteriori error estimates based on interpolation techniques. A computational example for a thermodiffusive flame propagation model illustrates the high accuracy that is possible with the proposed method. T3 - ZIB-Report - SC-94-34 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1627 ER - TY - GEN A1 - Koepf, Wolfram T1 - Algorithms for the Indefinite and Definite Summation N2 - The celebrated Zeilberger algorithm which finds holonomic recurrence equations for definite sums of hypergeometric terms $F(n,k)$ is extended to certain nonhypergeometric terms. An expression $F(n,k)$ is called hypergeometric term if both $F(n+1,k)/F(n,k)$ and $F(n,k+1)/F(n,k)$ are rational functions. Typical examples are ratios of products of exponentials, factorials, $\Gamma$ function terms, binomial coefficients, and Pochhammer symbols that are integer-linear with respect to $n$ and $k$ in their arguments. We consider the more general case of ratios of products of exponentials, factorials, $\Gamma$ function terms, binomial coefficients, and Pochhammer symbols that are rational-linear with respect to $n$ and $k$ in their arguments, and present an extended version of Zeilberger's algorithm for this case, using an extended version of Gosper's algorithm for indefinite summation. In a similar way the Wilf-Zeilberger method of rational function certification of integer-linear hypergeometric identities is extended to rational-linear hypergeometric identities. The given algorithms on definite summation apply to many cases in the literature to which neither the Zeilberger approach nor the Wilf-Zeilberger method is applicable. Examples of this type are given by theorems of Watson and Whipple, and a large list of identities (``Strange evaluations of hypergeometric series'') that were studied by Gessel and Stanton. It turns out that with our extended algorithms practically all hypergeometric identities in the literature can be verified. Finally we show how the algorithms can be used to generate new identities. REDUCE and MAPLE implementations of the given algorithms can be obtained from the author, many results of which are presented in the paper. T3 - ZIB-Report - SC-94-33 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1610 ER - TY - GEN A1 - Hansmann, Ulrich H. E. A1 - Okamoto, Yuko T1 - Multicanonical Approach in Statistical Mechanics of Peptides N2 - We test the performance of the multicanonical approach for biological molecules. The simulated molecules are frustrated systems with a complicated energy landscape. The resulting slowing down in simulations is alleviated by our ansatz. We perform a multicanonical simulation of nonpolar amino acids and study their $\alpha$-helix propensities. The results are shown to be in agreement with recent experimental results. T3 - ZIB-Report - SC-94-32 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1601 ER - TY - GEN A1 - Göckeler, Meinulf A1 - Horsley, Roger A1 - Linke, Volkard A1 - Rakow, Paul A1 - Schierholz, Gerrit A1 - Stüben, Hinnerk T1 - Probing the Continuum Limit in Non-Compact QED: New Results on Large Lattices N2 - We present new Monte Carlo results in non-compact lattice QED with staggered fermions down to $m_0 = 0.005$. This extends our previous investigations on the nature of the continuum limit of QED. T3 - ZIB-Report - SC-94-31 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1593 ER - TY - GEN A1 - Koepf, Wolfram T1 - REDUCE Package for the Indefinite and Definite Summation N2 - This article describes the REDUCE package ZEILBERG implemented by Gregor Stölting and the author. The REDUCE package ZEILBERG is a careful implementation of the Gosper (The sum package contains also a partial implementation of the Gosper algorithm.) and Zeilberger algorithms for indefinite, and definite summation of hypergeometric terms, respectively. An expression $a_k$ is called a {\sl hypergeometric term} (or {\sl closed form}), if $a_{k}/a_{k-1}$ is a rational function with respect to $k$. Typical hypergeometric terms are ratios of products of powers, factorials, $\Gamma$ function terms, binomial coefficients, and shifted factorials (Pochhammer symbols) that are integer-linear in their arguments. T3 - ZIB-Report - TR-94-09 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5147 ER - TY - GEN A1 - Urbaniak, Regina A1 - Weismantel, Robert A1 - Ziegler, Günter M. T1 - A New Variant of Buchberger's Algorithm for Integer Programming N2 - In this paper we modify Buchberger's $S$-pair reduction algorithm for computing a Gröbner basis of a toric ideal so as to apply to an integer program in inequality form with fixed right hand sides and fixed upper bounds on the variables. We formulate the algorithm in the original space and interpret the reduction steps geometrically. In fact, three variants of this algorithm are presented and we give elementary proofs for their correctness. A relationship between these (exact) algorithms, iterative improvement heuristics and the Kernighan-Lin procedure is established. T3 - ZIB-Report - SC-94-29 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1570 ER - TY - GEN A1 - Pochet, Yves A1 - Weismantel, Robert T1 - The Sequential Knapsack Polytope N2 - In this paper we describe the convex hull of all solutions of the integer bounded knapsack problem in the special case when the weights of the items are divisible. The corresponding inequalities are defined via an inductive scheme that can also be used in a more general setting. T3 - ZIB-Report - SC-94-30 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1588 ER - TY - GEN A1 - Reich, Sebastian T1 - Smoothed Dynamics of Highly Oscillatory Hamiltonian Systems N2 - We consider the numerical treatment of Hamiltonian systems that contain a potential which grows large when the system deviates from the equilibrium value of the potential. Such systems arise, e.g., in molecular dynamics simulations and the spatial discretization of Hamiltonian partial differential equations. Since the presence of highly oscillatory terms in the solutions forces any explicit integrator to use very small step-size, the numerical integration of such systems provides a challenging task. It has been suggested before to replace the strong potential by a holonomic constraint that forces the solutions to stay at the equilibrium value of the potential. This approach has, e.g., been successfully applied to the bond stretching in molecular dynamics simulations. In other cases, such as the bond-angle bending, this methods fails due to the introduced rigidity. Here we give a careful analysis of the analytical problem by means of a smoothing operator. This will lead us to the notion of the smoothed dynamics of a highly oscillatory Hamiltonian system. Based on our analysis, we suggest a new constrained formulation that maintains the flexibility of the system while at the same time suppressing the high-frequency components in the solutions and thus allowing for larger time steps. The new constrained formulation is Hamiltonian and can be discretized by the well-known SHAKE method. T3 - ZIB-Report - SC-94-28 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1564 ER - TY - GEN A1 - Aston, Philip J. A1 - Dellnitz, Michael T1 - Symmetry Breaking Bifurcations of Chaotic Attractors N2 - In an array of coupled oscillators {\em synchronous chaos} may occur in the sense that all the oscillators behave identically although the corresponding motion is chaotic. When a parameter is varied this fully symmetric dynamical state can lose its stability, and the main purpose of this paper is to investigate which type of dynamical behavior is expected to be observed once the loss of stability has occurred. The essential tool is a classification of Lyapunov exponents based on the symmetry of the underlying problem. This classification is crucial in the derivation of the analytical results but it also allows an efficient computation of the dominant Lyapunov exponent associated with each symmetry type. We show how these dominant exponents determine the stability of invariant sets possessing various instantaneous symmetries and this leads to the idea of {\em symmetry breaking bifurcations of chaotic attractors}. Finally the results and ideas are illustrated for several systems of coupled oscillators. T3 - ZIB-Report - SC-94-27 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1557 ER - TY - GEN A1 - Sturmfels, Bernd A1 - Weismantel, Robert A1 - Ziegler, Günter M. T1 - Gröbner bases of lattices, corner polyhedra, and integer programming N2 - We investigate the generating sets (``Gröbner bases'') of integer lattices which correspond to the Gröbner bases of the associated binomial ideals. Extending results in Sturmfels and Thomas, preprint 1994, we obtain a geometric characterization of the universal Gröbner basis in terms of the vertices and edges of the associated corner polyhedra. We emphasize the special case where the lattice has finite index. In this case the corner polyhedra were studied by Gomory, and there is a close connection to the ``group problem in integer programming'' Schrijver, p.~363. We present exponential lower and upper bounds for the size of a reduced Gröbner basis. The initial complex of (the ideal of) a lattice is shown to be dual to the boundary of a certain simple polyhedron. T3 - ZIB-Report - SC-94-26 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1548 ER - TY - GEN A1 - Hohmann, Andreas T1 - Multilevel Newton h-p Collocation N2 - We derive a simple accuracy matching strategy for inexact Gauss Newton methods and apply it to the numerical solution of boundary value problems of ordinary differential equations by collocation. The matching strategy is based on an affine contravariant convergence theorem, i. e. , the characteristic constants are invariant under affine transformations of the domain. The inexact Gauss Newton method is applied to an integral formulation of the BVP. As discretization for the arising linear subproblems we employ adaptive collocation at Gaussian nodes with varying local orders and stepsizes. The grids are chosen via adaptive refinement and order selection. T3 - ZIB-Report - SC-94-25 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1530 ER - TY - GEN A1 - Koepf, Wolfram T1 - Algebraische Darstellung transzendenter Funktionen N2 - In this article algorithmic methods are presented that have been incorporated in computer algebra systems in the last five years. The methods can be used to identify transcendental functions. The essential idea due to Zeilberger is to represent the functions by systems of holonomic differential and recurrence equations, and the identification procedure utilizes algorithms of Stanley and Zeilberger. Also a noncommutative version of the Buchberger algorithm can be applied. T3 - ZIB-Report - SC-94-24 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1524 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Weyer, J. T1 - Prognoserechnung zur AIDS-Ausbreitung in der Bundesrepublik Deutschland N2 - Die Autoren sind sich dar{ü}ber im klaren, daß zahlreiche Imponderabilien die Ergebnisse der vorgelegten Modellrechnungen beeinflussen k{ö}nnen. Immerhin repräsentiert jedoch das vorgelegte mathematische Modell die Summe unserer derzeitigen Kenntnisse zur Fragestellung AIDS--Epidemie; neu hinzukommende Erkenntnisse lassen sich rasch einarbeiten und in ihren Konsequenzen überschauen. Die Entwicklung neuer effizienter numerischer Methoden spielte eine Schlüsselrolle bei der tatsächlichen Simulation dieses umfangreichen realitätsnahen mathematischen Modells. T3 - ZIB-Report - SC-94-23 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1511 ER - TY - GEN A1 - Deuflhard, Peter A1 - Wulkow, Michael T1 - Simulationsverfahren für die Polymerchemie N2 - Die enorme algorithmische Beschleunigung durch diskrete Galerkin-Methoden f{ü}r abz{ä}hlbare Differentialgleichungssysteme hat der Simulation von Polymerisationsprozessen neue, industriell relevante Problembereiche er{ö}ffnet, die mit den bis dahin verf{ü}gbaren Methoden nicht zug{ä}nglich waren. T3 - ZIB-Report - SC-94-22 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1502 ER - TY - GEN A1 - Hansmann, Ulrich H. E. A1 - Okamoto, Yuko T1 - Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem. N2 - We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the effectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail Met-enkephalin, one of the simplest peptides. We show that the new method not only outperforms simulated annealing in the search of the energy groundstate but also provides more statistical-mechanical information about the system. T3 - ZIB-Report - SC-94-20 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1483 ER - TY - GEN A1 - Hansmann, Ulrich H. E. T1 - Towards Ab Initio Prediction of Protein Conformations - The Multicanonical Approach. N2 - We demonstrate the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. Unlike to simulated annealing the relationship to the canonical ensemble remains exactly controlled. Hence, the new method allows not only the prediction of the lowest-energy conformation, but also the calculation of thermodynamic quantities at various temperature from one run. T3 - ZIB-Report - SC-94-21 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1494 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Neue Perspektiven eines verteilten Informationssystems für die Mathematik. N2 - Die Kombination von elektronischer Fachinformation mit den neuen Mitteln der Kommunikation eröffnet neue Perspektiven für die Mathematik in Deutschland. Aufbauend auf das laufende, BMFT-geförderte Projekt ``Fachinformation'' der Deutschen Mathematiker-Vereinigung (DMV) plant die DMV eine Querschnittsaktivität für die Mathematik. Diese soll nicht nur die mathematischen Fachbereiche und Forschungsinstitute einbeziehen, sondern auch mathematische Forschungslabors aus der Industrie und die Informationsversorger der Mathematik, insbesondere die wissenschaftlichen Verlage, die TIB Hannover, die Bibliotheken der Universitäten und \mbox{-- nicht zuletzt --} das FIZ Karlsruhe mit dem Zentralblatt für Mathematik. \noindent Auf der technischen Grundlage des Internet und seiner weltweit verbreiteten Informationsdienste (Gopher, WAIS, WorldWideWeb, Hyper-G, ftp und E-mail) soll ein verteiltes, mathematisches Informationssystem geschaffen werden, bei dem die Partner des gemeinsamen Vorhabens ihre örtlichen Ressourcen untereinander und zugleich weltweit verfügbar machen. Diese Ziele sind durch konsequenten Einsatz von Software erreichbar, die nach dem Client-Server-Modell strukturiert und die im Internet verbreitet bzw.~anerkannt ist. \noindent Die Bereitstellung von Technik reicht keineswegs aus. Ohne die Schaffung einer personellen, organisatorischen und technischen Infrastruktur ist die Durchführung eines solchen Projekts nicht möglich. Als Massnahmen sind - für alle Partner - geplant: \hspace*{2mm} * Schaffung der Funktion des Informationsbeauftragten \hspace*{2mm} * Einrichtung eines gemeinsamen ``Forums für mathematische Information'' \hspace*{2mm} * Errichtung und Betreuung von mathematischen Informationsstationen \hspace*{2mm} * Teilnahme an nationalen und internationalen Standardisierungsmassnahmen \hspace*{2mm} * Workshops und regelmässige Schulungen, Öffentlichkeitsarbeit \noindent Als Aktivitäten - mit Focus auf mathematische Fachinformation - sind folgende Teilaufgaben und Pilotvorhaben bei allen Partnern geplant: \hspace*{2mm} * Einrichtung von elektronischen Informationssystemen \hspace*{2mm} * Verteiltes elektronisches Angebot von Preprints und Skripten (Volltexte) \hspace*{2mm} * Verteiltes elektronisches Angebot von Software- und Datensammlungen \hspace*{2mm} * Zugriff auf globale Informationssysteme in der Mathematik \hspace*{2mm} * Organisation eines Lebenden Mathematischen Museums \hspace*{2mm} * Zugriff auf elektronische Kataloge von Bibliotheken, insbesondere Fachbereichsbibliotheken \hspace*{2mm} * Schaffung eines organisatorischen Rahmens für elektronische mathematische Journale \hspace*{2mm} * Elektronisches Angebot von eingescannten historischen Dokumenten und Büchern \hspace*{2mm} * Schaffung einer Organisationsform für elektronisches Reviewing \hspace*{2mm} * Erprobung von Verfahren zur elektronischen Lieferung von Dokumenten \hspace*{2mm} * Elektronische Projektorganisation \noindent Das Vorhaben zielt ab auf die Schaffung einer informationstechnischen Infrastruktur für Datenbank-Retrieval, E-mail, ``Electronic Conferencing'' und fachspezifische Informationsnetze in exemplarischer Form für Wissenschaft und Industrie - auch für andere Fachgebiete. T3 - ZIB-Report - TR-94-07 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5122 ER - TY - GEN A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - New Perspectives of a Distributed Information System for Mathematics. N2 - \begin{footnotesize} \noindent Combining electronic specialized information, such as electronic information retrieval from central databases, with the new means of communication opens up new perspectives for mathematics in Germany. Based on the current Fachinformationsprojekt (Specialized Information Project) run by the Deutsche Mathematiker-Vereinigung (DMV) and supported by the Federal Minister for Research and Technology (BMFT), the DMV is planning a new infrastructure activity for mathematics. This activity will not only include mathematical university departments and research institutes, but also partners from mathematical research laboratories in industry as well as suppliers of mathematical information, in particular, scientific publishing houses, the Technical Information Library (TIB) Hannover, university libraries and -- last but not least -- the Fachinformationszentrum (FIZ) Karlsruhe with the Zentralblatt für Mathematik. \noindent On the technical basis of the Internet and its worldwide information services (Gopher, WAIS, World Wide Web, Hyper-G, ftp and e-mail), a distributed mathematical information system is to be created, whose partners make their local resources available both to other partners and to the worldwide Internet community. These aims can be achieved by means of the consequent use of software that is structured according to the client-server model and distributed and accepted within the Internet. \noindent Providing the technical equipment, however, is by far not enough. Without the creation of a personal, technical and organizational infrastructure, realization of such a project will not be possible. For every partner the realization of the following measures is envisaged:\\[-7mm] \noindent \end{footnotesize} \begin{small} \begin{itemize} \item[*] Establishing an Information Coordinator\/ at every participating institution\\[-8mm] \item[*] Creation of a Forum for Mathematical Information\/\\[-8mm] \item[*] Installation and maintenance of Mathematical Information Stations\/\\[-8mm] \item[*] Participation in national and international Standardization Activities\/\\[-8mm] \item[*] Regular workshops and training courses, public relations\\[-7mm] \end{itemize} \noindent The following activities (carried out by all partners or within pilot projects by special groups) focusing on mathematical and mathematics-related information are planned:\\[-7mm] \noindent \begin{itemize} \item[*] Set up of Electronic Information Systems\/ by all partners \\[-8mm] \item[*] Distributed\/ electronic offer of Preprints\/ and scripts (full texts) by all partners\\[-8mm] \item[*] Distributed\/ electronic offer of Software and Data Collections\/ by all partners\\[-8mm] \item[*] Access to Global Information Systems in Mathematics\/\\[-8mm] \item[*] Organization of a Living Museum of Mathematics\/\\[-8mm] \item[*] Access to {\it Electronic Library Catalogs,}\/ esp.~to libraries of university departments\\[-8mm] \item[*] Electronic offer of Scanned Historical Books and Documents\/\\[-8mm] \item[*] Creation and management of Electronic Mathematical Journals\/\\[-8mm] \item[*] Creation of a framework for various kinds of Electronic Reviewing\/\\[-8mm] \item[*] Testing of new methods for Electronic Document Delivery\/\\[-8mm] \item[*] Electronic Project Organization\/\\[-7mm] \end{itemize} \noindent \end{small} \begin{footnotesize} The project aims, at its beginning, at the creation of an information infrastructure for database retrieval, e-mail, electronic conferencing and subject-specific information networks. Its focus is on mathematics in Germany. The general scope, however, is broader. The project is open for discussion, coordination, and cooperation with partners in other areas of science, industry or in other countries. It is also hoped that this project may form an example along which other models of electronic information and communication can be developed. Moreover, the project is also meant to enhance the offer from German mathematics to the worldwide "give and take" within the Internet community. \end{footnotesize} T3 - ZIB-Report - TR-94-08 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5139 ER - TY - GEN A1 - Melenk, Herbert T1 - The Complexity Barrier in REDUCE - a Case Study. N2 - The power of the symbolic math system {\small REDUCE} for solving large and difficult problems in science and engineering is demonstrated by a set of model problems. These include algebraic equation solving, formal variable elimination, formal power series, symbolic treatment of differential equations and applications from theoretical physics. T3 - ZIB-Report - TR-94-06 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5119 ER - TY - THES A1 - Schütte, Christof T1 - A Quasiresonant Smoothing Algorithm for Solving Large Highly Differential Equations from Quantum Chemistry. N2 - In Quantum Chemistry the field of Laser--Assisted Molecular Control'' has received a considerable amount of attention recently. One key problem in this new field is the simulation of the dynamical reaction of a molecule subjected to external radiation. This problem is described by the Schrödinger equation, which, after eigenfunction expansion, can be written in the form of a large system of ordinary differential equations, the solutions of which show a highly oscillatory behaviour. The oscillations with high frequencies and small amplitudes confine the stepsizes of any numerical integrator -- an effect, which, in turn, blows up the simulation time. Larger stepsizes can be expected by averaging these fast oscillations, thus smoothing the trajectories. Standard smoothing techniques (averaging, filtering) would kill the whole process and thus, lead to wrong numerical results. To avoid this unwanted effect and nevertheless speed up computations, this paper presents a quasiresonant smoothing algorithm (QRS). In QRS, a natural splitting parameter $\delta$ controls the smoothing properties. An adaptive QRS--version (AQRS) is presented which includes an error estimation scheme for choosing this parameter $\delta$ in order to meet a given accuracy requirement. In AQRS $\delta$ is permanently adapted to the solution properties for computing the chemically necessary information'' only. The performance of AQRS is demonstrated in several test problems from the field Laser--Assisted Selective Excitation of Molecules'' in which the external radiation is a picosecond laser pulse. In comparison with standard methods speedup factors of the order of $10^2$ are observed. T3 - ZIB-Report - TR-94-04 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5090 ER - TY - GEN A1 - Zumbusch, Gerhard T1 - Visualizing Functions of the h-p-version of finite elements. N2 - Results from finite-element-calculations are usually visualized by colored surface- and contour-line-plots or polygonal patches or simply displaced lines and grids. In computer graphics however more advanced techniques like texture-mapping and NURBS are well established and there exist efficient algorithms and implementations. We show that these techniques are not only easy to use, but form a very natural and far more efficient approach for visualization of higher order finite-element's solutions like in $p$- and $h$-$p$-version. Texture-mapping is useful for displaying vector-valued data, too. T3 - ZIB-Report - TR-94-05 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5108 ER - TY - GEN A1 - Weismantel, Robert T1 - Hilbert Bases and the Facets of Special Knapsack Polytopes. N2 - {\def\N{{\mbox{{\rm I\kern-0.22emN}}}} Let a set $N$ of items, a capacity $F \in \N$ and weights $a_i \in \N$, $i \in N$ be given. The 0/1 knapsack polytope is the convex hull of all 0/1 vectors that satisfy the inequality $$\sum_{i \in N} a_i x_i \leq F.$$ In this paper we present a linear description of the 0/1 knapsack polytope for the special case where $a_i \in \{\mu,\lambda\}$ for all items $i \in N$ and $1 \leq \mu < \lambda \leq b$ are two natural numbers. The inequalities needed for this description involve elements of the Hilbert basis of a certain cone. The principle of generating inequalities based on elements of a Hilbert basis suggests further extensions.} T3 - ZIB-Report - SC-94-19 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1475 ER - TY - GEN A1 - Ferreira, Carlos E. A1 - Martin, Alexander A1 - Souza, Cid C. de A1 - Weismantel, Robert A1 - Wolsey, Laurence T1 - Formulations and Valid Inequalities for the Node Capacitated Graph Partitioning Problem. N2 - We investigate the problem of partitioning the nodes of a graph under capacity restriction on the sum of the node weights in each subset of the partition. The objective is to minimize the sum of the costs of the edges between the subsets of the partition. This problem has a variety of applications, for instance in the design of electronic circuits and devices. We present alternative integer programming formulations for this problem and discuss the links between these formulations. Having chosen to work in the space of edges of the multicut, we investigate the convex hull of incidence vectors of feasible multicuts. In particular, several classes of inequalities are introduced, and their strength and robustness are analyzed as various problem parameters change. T3 - ZIB-Report - SC-94-16 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1450 ER - TY - GEN A1 - Ferreira, Carlos E. A1 - Martin, Alexander A1 - Souza, Cid C. de A1 - Weismantel, Robert A1 - Wolsey, Laurence T1 - The Node Capacitated Graph Partitioning Problem: A Computational Study. N2 - In this paper we consider the problem of $k$-partitioning the nodes of a graph with capacity restrictions on the sum of the node weights in each subset of the partition, and the objective of minimizing the sum of the costs of the edges between the subsets of the partition. Based on a study of valid inequalities, we present a variety of separation heuristics for so-called cycle, cycle with ears, knapsack tree and path-block-cycle inequalities. The separation heuristics, plus primal heuristics, have been implemented in a branch-and-cut routine using a formulation including the edges with nonzero costs and node variables. Results are presented for three classes of problems: equipartitioning problems arising in finite element methods and partitioning problems associated with electronic circuit layout and compiler design. T3 - ZIB-Report - SC-94-17 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1469 ER - TY - GEN A1 - Fröhlich, Jochen T1 - Parameter Derivatives of the Jacobi Polynomials and the Gaussian Hypergeometric Function. N2 - The paper's main result is a simple derivation rule for the Jacobi polynomials with respect to their parameters, i.e. for $\partial_{\alpha} P_n^{\alpha,\beta}$, and $\partial_{\beta} P_n^{\alpha,\beta}$. It is obtained via relations for the Gaussian hypergeometric function concerning parameter derivatives and integer shifts in the first two arguments. These have an interest on their own for further applications to continuous and discrete orthogonal polynomials. The study is motivated by a Galerkin method with moving weight, presents all proofs in detail, and terminates in a brief discussion of the generated polynomials. T3 - ZIB-Report - SC-94-15 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1440 ER - TY - GEN A1 - Abdel-Hamid, Atef Abdel-Aziz A1 - Borndörfer, Ralf T1 - On the Complexity of Storage Assignment Problems. N2 - {\def\NP{\hbox{$\cal N\kern-.1667em\cal P$}} The {\sl storage assignment problem} asks for the cost minimal assignment of containers with different sizes to storage locations with different capacities. Such problems arise, for instance, in the optimal control of automatic storage devices in flexible manufacturing systems. This problem is known to be $\NP$-hard in the strong sense. We show that the storage assignment problem is $\NP$-hard for {\sl bounded sizes and capacities}, even if the sizes have values $1$ and~$2$ and the capacities value~$2$ only, a case we encountered in practice. Moreover, we prove that no polynomial time $\epsilon$-approximation algorithm exists. This means that almost all storage assignment problems arising in practice are indeed hard.} T3 - ZIB-Report - SC-94-14 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1430 ER - TY - GEN A1 - Lang, Jens T1 - High-Resolution Selfadapative Computations on Chemical Reaction-Diffusion Problems with Internal Boundaries N2 - Large chemical computations show the need for full adaptivity supporting the development of robust and highly efficient programs. For solutions possessing sharp moving spatial transitions, as travelling wavefronts or emerging boundary and internal layers, an automatic adjustment of both the space and the time stepsize is generally accepted to be more successful in efficient resolving critical regions of high spatial and temporal activity. In contrast to the widespread discretization sequence first space then time the reversed sequence first time then space is employed. Full adaptivity of the proposed algorithm is realized by combining embedded time discretization and multilevel finite element space discretization. In this paper the algorithm is described for one--dimensional problems. The numerical results show the significantly new perspectives opened by this approach. T3 - ZIB-Report - SC-94-09 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1395 ER - TY - GEN A1 - Gatermann, Karin T1 - Semi-invariants, equivariants and algorithms. N2 - The results from invariant theory and the results for semi-invariants and equivariants are summarized in a way suitable for the combination with Gröbner basis computation. An algorithm for the determination of fundamental equivariants using projections and a Poincar\'{e} series is described. Secondly, an algorithm is given for the representation of an equivariant in terms of the fundamental equivariants. Several ways for the exact determination of zeros of equivariant systems are discussed T3 - ZIB-Report - SC-94-11 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1411 ER - TY - GEN A1 - Wulff, Claudia A1 - Hohmann, Andreas A1 - Deuflhard, Peter T1 - Numerical Continuation of Periodic Orbits with Symmetry. N2 - We consider periodic orbits of autonomous parameter dependent ODE's. Starting from a shooting algorithm for the numerical computation of periodic orbits via an adaptive Poincar\'e-section we develop a pathfollowing algorithm for periodic solutions based on a tangential continuation method with implicit reparametrization. For ODE's equivariant w.r.t. a finite group we show that spatial as well as spatio-temporal symmetries of periodic orbits can be exploited within the (multiple) shooting context. We describe how turning points, period doubling bifurcations and Hopf points along the branch of periodic solutions can be handled. Furthermore equivariant Hopf points and generic secondary bifurcations of periodic orbits with $ Z_m$-symmetry are treated. We tested the code with standard examples, e.g., the period doubling cascade in the Lorenz equations. To show the efficiency of the described methods we also used the program for an application from electronics, a ring oscillator with $n $ inverters. In this example the exploitation of symmetry reduces the amount of work for the continuation of periodic orbits from ${\cal O}(n^2)$ to ${\cal O}(n)$ T3 - ZIB-Report - SC-94-12 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1421 ER - TY - GEN A1 - Koepf, Wolfram T1 - On Families of Iterated Derivatives. N2 - We give an overview of an approach on special functions due to Truesdell, and show how it can be used to develop certain type of identities for special functions. Once obtained, these identities may be verified by an independent algorithmic method for which we give some examples. T3 - ZIB-Report - TR-94-03 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5083 ER - TY - GEN A1 - Ackermann, Jörg A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - A self-adaptive multilevel finite element method for the stationary Schrödinger equation in three space dimensions. N2 - An error controlled finite elemente method (FEM) for solving stationary Schrödinger equations in three space dimensions is proposed. The method is based on an adaptive space discretization into tetrahedra and local polynomial basis functions of order $p=1$--$5$ defined on these tetrahedra. According to a local error estimator the triangulation is automatically adapted to the solution. Numerical results for standard problems appearing in vibrational motion and molecular structure calculations are presented and discussed. Relative precisions better than 1e-8 are obtained. For equilateral H$_3^{++}$ the adaptive FEM turns out to be superior to global basis set expansions in the literature. Our precise FEM results exclude in a definite manner the stability or metastability of equilateral H$_3^{++}$ in its groundstate. T3 - ZIB-Report - SC-94-10 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1403 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - On the Convergence of Cascadic Iterations for Elliptic Problems. N2 - We consider nested iterations, in which the multigrid method is replaced by some simple basic iteration procedure, and call them {\em cascadic iterations}. They were introduced by Deuflhard, who used the conjugate gradient method as basic iteration (CCG method). He demonstrated by numerical experiments that the CCG method works within a few iterations if the linear systems on coarser triangulations are solved accurately enough. Shaidurov subsequently proved multigrid complexity for the CCG method in the case of $H^2$-regular two-dimensional problems with quasi-uniform triangulations. We show that his result still holds true for a large class of smoothing iterations as basic iteration procedure in the case of two- and three-dimensional $H^{1+\alpha}$-regular problems. Moreover we show how to use cascadic iterations in adaptive codes and give in particular a new termination criterion for the CCG method. T3 - ZIB-Report - SC-94-08 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1389 ER - TY - GEN A1 - Gärtner, Bernd A1 - Ziegler, Günter M. T1 - Randomized simplex algorithms on Klee-Minty cubes. N2 - We investigate the behavior of randomized simplex algorithms on special linear programs. For this, we develop combinatorial models for the Klee-Minty cubes and similar linear programs with exponential decreasing paths. The analysis of two randomized pivot rules on the Klee-Minty cubes leads to (nearly) quadratic lower bounds for the complexity of linear programming with random pivots. Thus we disprove two bounds conjectured in the literature. At the same time, we establish quadratic upper bounds for random pivots on the linear programs under investigation. This motivates the question whether some randomized pivot rules possibly have quadratic worst-case behavior on general linear programs. T3 - ZIB-Report - SC-94-07 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1370 ER - TY - GEN A1 - Linusson, Svante T1 - Partitions with Restricted Block Sizes, Möbius Functions and the k-of-each Problem. N2 - {\newcommand{\R} {{\rm {\mbox{\protect\makebox[.15em][l]{I}R}}}} Given a list of $n$ numbers in $\R $, one wants to decide wether every number in the list occurs at least $k$ times. I will show that $(1-\epsilon)n\log_3(n/k)$ is a lower bound for the depth of a linear decision tree determining this problem. This is done by using the Björner-Lov\'asz method, which turns the problem into one of estimating the Möbius function for a certain partition lattice. I will also calculate the exponential generating function for the Möbius function of a partition poset with restricted block sizes in general.} T3 - ZIB-Report - SC-94-06 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1363 ER - TY - GEN A1 - Koepf, Wolfram A1 - Schmersau, Dieter T1 - Spaces of Functions Satisfying Simple Differential Equations. N2 - {\newcommand{\N} {{\rm {\mbox{\protect\makebox[.15em][l]{I}N}}}} In several publications the first author published an algorithm for the conversion of analytic functions for which derivative rules are given into their representing power series $\sum\limits_{k=0}^{\infty}a_{k}z^{k}$ at the origin and vice versa, implementations of which exist in {\sc Mathematica}, {\sc Maple} and {\sc Reduce}. One main part of this procedure is an algorithm to derive a homogeneous linear differential equation with polynomial coefficients for the given function. We call this type of ordinary differential equations {\sl simple}. Whereas the opposite question to find functions satisfying given differential equations is studied in great detail, our question to find differential equations that are satisfied by given functions seems to be rarely posed. In this paper we consider the family $F$ of functions satisfying a simple differential equation generated by the rational, the algebraic, and certain transcendental functions. It turns out that $F$ forms a linear space of transcendental functions. % with polynomial function coefficients. Further $F$ is closed under multiplication and under the composition with rational functions and rational powers. These results had been published by Stanley who had proved them by theoretical algebraic considerations. In contrast our treatment is purely algorithmically oriented. We present algorithms that generate simple differential equation for $f+g$, $f\cdot g$, $f\circ r$ ($r$ rational), and $f\circ x^{p/q}$ ($p,q\in\N_0$), given simple differential equations for $f$, and $g$, and give a priori estimates for the order of the resulting differential equations. We show that all order estimates are sharp. After finishing this article we realized that in independent work Salvy and Zimmermann published similar algorithms. Our treatment gives a detailed description of those algorithms and their validity.} T3 - ZIB-Report - TR-94-02 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5074 ER - TY - GEN A1 - Hohmann, Andreas T1 - Object Oriented Design of Multilevel Newton and Continuation Methods. N2 - We present a set of C++ classes that realize an abstract inexact Gauss Newton method in combination with a continuation process for the solution of parameter dependent nonlinear problems. The object oriented approach allows the continuation of different types of solutions within the same framework. \\{\bf Abstract: }We present a set of C++ classes that realize an abstract inexact Gauss Newton method in combination with a continuation process for the solution of parameter dependent nonlinear problems. The object oriented approach allows the continuation of different types of solutions within the same framework. T3 - ZIB-Report - SC-94-04 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1342 ER - TY - GEN A1 - Koepf, Wolfram T1 - Algorithmic work with orthogonal polynomials and special functions. N2 - In this article we present a method to implement orthogonal polynomials and many other special functions in Computer Algebra systems enabling the user to work with those functions appropriately, and in particular to verify different types of identities for those functions. Some of these identities like differential equations, power series representations, and hypergeometric representations can even dealt with algorithmically, i.\ e.\ they can be computed by the Computer Algebra system, rather than only verified. The types of functions that can be treated by the given technique cover the generalized hypergeometric functions, and therefore most of the special functions that can be found in mathematical dictionaries. The types of identities for which we present verification algorithms cover differential equations, power series representations, identities of the Rodrigues type, hypergeometric representations, and algorithms containing symbolic sums. The current implementations of special functions in existing Computer Algebra systems do not meet these high standards as we shall show in examples. They should be modified, and we show results of our implementations. T3 - ZIB-Report - SC-94-05 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1354 ER - TY - GEN A1 - Verschelde, Jan A1 - Gatermann, Karin T1 - Symmetric Newton Polytopes for Solving Sparse Polynomial Systems. N2 - The aim of this paper is to compute all isolated solutions to symmetric polynomial systems. Recently, it has been proved that modelling the sparse structure of the system by its Newton polytopes leads to a computational breakthrough in solving the system. In this paper, it will be shown how the Lifting Algorithm, proposed by Huber and Sturmfels, can be applied to symmetric Newton polytopes. This symmetric version of the Lifting Algorithm enables the efficient construction of the symmetric subdivision, giving rise to a symmetric homotopy, so that only the generating solutions have to be computed. Efficiency is obtained by combination with the product homotopy. Applications illustrate the practical significance of the presented approach. T3 - ZIB-Report - SC-94-03 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1331 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Sedlmayr(ed.), E. T1 - Scientific Computing in der Theoretischen Physik. Collected Abstracts. N2 - Die von der DMV-Fachgruppe Scientific Computing in Kooperation mit dem gleichnamigen GAMM-Fachausschuss organisierte Tagung \glqq Scientific Computing in der Theoretischen Physik\grqq~fand vom 16. - 18. März 1994 am Fachbereich Mathematik und Informatik der Freien Universität Berlin statt. Ziel des Workshops war, die Kontakte zwischen den Fachleuten der Gebiete {\em Computational Physics} und {\em Scientific Computing} zu intensivieren. Schwerpunkte des Workshops waren numerische Simulation von Transportmodellen der Astrophysik und Halbleiterphysik, Multilevel-Methoden für partielle Differentialgleichungen sowie Monte-Carlo-Methoden und molekulardynamische Verfahren für Probleme der Statistischen Physik und Quantenfeldtheorie. Der Workshop fand ein äusserst positives Echo und führte über 70 Teilnehmer der verschiedenen Teilgebiete der Theoretischen Physik und ca. 50 Teilnehmer aus dem Bereich der Numerischen Mathematik zusammen. \originalTeX T3 - ZIB-Report - TR-94-01 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5068 ER - TY - GEN A1 - Seebass, Martin A1 - Sullivan, Dennis A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland T1 - The Berlin Extension of the Stanford Hyperthermia Treatment. N2 - In the field of deep regional hyperthermia, one of the most widely used devices is the BSD--2000 Hyperthermia System which employs the Sigma 60 applicator. The Sigma 60 consists of four independent sources, giving it the potential to control the energy pattern within the patient. The independent amplitudes and phases, as well as frequency selection and applicator position, present a large number of parameters for the operator to determine. Computer simulation has long been recognized as an attractive approach to optimizing these parameters. A treatment planning program was used in clinical practice at Stanford University Medical Center for two years. It demonstrated the feasibility of computer simulation for deep regional hyperthermia in a clinical situation. However, several parts of this system were written in a language specific to one workstation, which severely restricted the wider distribution of the program to other users of the Sigma 60. A new treatment planning system for the BSD 2000 has been developed and put into clinical practice at the Rudolf Virchow Clinic of the Free University of Berlin. The new method, which we will refer to as the Berlin system, has a simpler model construction program and a considerably better graphics capability. However, the most important feature is that all programs are written in FORTRAN, C, or the X Window graphics system. Therefore, the entire treatment planning system is completely portable to other workstations. T3 - ZIB-Report - SC-93-35 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1304 ER - TY - GEN A1 - Weismantel, Robert T1 - On the 0/1 Knapsack Polytope. N2 - {\def\N{{\mbox{{\rm I\kern-0.22emN}}}} Given a set $N$ of items and a capacity $b \in \N$, and let $N_j$ be the set of items with weight $j$, $1 \leq j \leq b$. The 0/1 knapsack polytope is the convex hull of all 0/1 vectors that satisfy the inequality $$\sum_{j=1}^b \sum_{i \in N_j} jx_i \leq b.$$ In this paper we first present a complete linear description of the 0/1 knapsack polytope for two special cases: (a) $N_j = \emptyset$ for all $1 < j \leq \lfloor {b \over 2} \rfloor$ and (b) $N_j = \emptyset$ for all $1 < j \leq \lfloor {b \over 3} \rfloor$ and $N_j = \emptyset$ for all $j \geq \lfloor {b \over 2} \rfloor + 1$. It turns out that the inequalities that are needed for the complete description of these special polytopes are derived by means of some ``reduction principle''. This principle is then generalized to yield valid and in many cases facet defining inequalities for the general 0/1 knapsack polytope. The separation problem for this class of inequalities can be solved in pseudo polynomial time via dynamic programming techniques.} T3 - ZIB-Report - SC-94-01 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1312 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - The Steiner Tree Packing Problem in VLSI-Design. N2 - In this paper we describe several versions of the routing problem arising in VLSI design and indicate how the Steiner tree packing problem can be used to model these problems mathematically. We focus on switchbox routing problems and provide integer programming formulations for routing in the knock-knee and in the Manhattan model. We give a brief sketch of cutting plane algorithms that we developed and implemented for these two models. We report on computational experiments using standard test instances. Our codes are able to determine optimum solutions in most cases, and in particular, we can show that some of the instances have no feasible solution if Manhattan routing is used instead of knock-knee routing. T3 - ZIB-Report - SC-94-02 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1328 ER - TY - GEN A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Ulysses 2000: In Search of Optimal Solutions to Hard Combinatorial Problems. N2 - Combinatorial optimization problems pervade many areas of human problem solving especially in the fields of business, economics and engineering. Intensive mathematical research and vast increases in raw computing power have advanced the state of the art in exact and heuristic problem solving at a pace that is unprecedented in human history. We survey here in layman's terms some of the fundamental concepts and principles that have led this progress. (This article will appear -- possibly in modified form -- in a popular science magazine.) T3 - ZIB-Report - SC-93-34 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1296 ER - TY - THES A1 - Nowak, Ulrich T1 - Adaptive Linienmethoden für nichtlineare parabolische Systeme in einer Raumdimension. N2 - A new method for the numerical solution of highly nonlinear, coupled systems of parabolic differential equations in one space dimension is presented. The approach is based on a classical method of lines treatment. Time discretization is done by means of the semi--implicit Euler discretization. Space discretization is done with finite differences on non--uniform grids. Both basic discretizations are coupled with extrapolation techniques. With respect to time the extrapolation is of variable order whereas just one extrapolation step is done in space. Based on local error estimates for both, the time and the space discretization error, the accuracy of the numerical approximation is controlled and the discretization stepsizes are adapted automatically and simultaneously. Besides the local adaptation of the space grids after each integration step (static regridding), the grid may even move within each integration step (dynamic regridding). Thus, the whole algorithm has a high degree of adaptivity. Due to this fact, challenging problems from applications can be solved in an efficient and robust way. T3 - ZIB-Report - TR-93-14 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5059 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - Interpolation Spaces and Optimal Multilevel Preconditioners. N2 - This paper throws light on the connection between the optimal condition number estimate for the BPX method and constructive approximation theory. We provide a machinery, which allows to understand the optimality as a consequence of an approximation property and an inverse inequality in $H^{1+\epsilon}$, $\epsilon > 0$. This machinery constructs so-called {\em approximation spaces}, which characterize a certain rate of approximation by finite elements and relates them with interpolation spaces, which characterize a certain smoothness. T3 - ZIB-Report - SC-93-33 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1285 ER - TY - THES A1 - Hohmann, Andreas T1 - Inexact Gauss Newton Methods for Parameter Dependent Nonlinear Problems. N2 - A new approach to inexact Gauss Newton methods for the solution of underdetermined nonlinear problems is presented. It is based on a convergence theorem being invariant under affine transformations of the domain and results in an easily implementable accuracy matching strategy for the arising linear subproblems which guarantees the quadratic convergence. Thanks to the weak assumptions on the given nonlinear problem, the results provide a general framework for multilevel Newton and continuation methods. As an example, a new multilevel Newton h-p collocation method for boundary value problems of ordinary differential equations is developed. It combines the inexact Newton method with a linear collocation solver using adaptive refinement and variable orders. The performance of the resulting C++ class library {\sc Cocon} is demonstrated by some numerical examples including singular perturbed problems. In addition, the new method is applied to a realistic railway bogie model in which a branch of periodic solutions emanates from a branch of fixed points at a Hopf bifurcation. T3 - ZIB-Report - TR-93-13 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5049 ER - TY - GEN A1 - Zumbusch, Gerhard T1 - Symmetric Hierarchical Polynomials for the h-p-Version of Finite Elements. N2 - Adaptive numerical methods using the $h$-$p$-version of finite elements require special kinds of shape functions. Desirable properties of them are symmetry, hierarchy and simple coupling. In a first step it is demonstrated that for standard polynomial vector spaces not all of these features can be obtained simultaneously. However, this is possible if these spaces are extended. Thus a new class of polynomial shape functions is derived, which is well-suited for the $p$- and $h$-$p$-version of finite elements on unstructured simplices. The construction is completed by minimizing the condition numbers of the arising finite element matrices. The new shape functions are compared with standard functions widely used in the literature. T3 - ZIB-Report - SC-93-32 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1275 ER - TY - GEN A1 - Zuse, Konrad T1 - Cellular Structured Space (Rechnender Raum) and Physical Phenomena. N2 - The problem of nonlocal correlation and symmetry in space is of great importance in physical phenomena like the \underline{Einstein-Poloski-Rosen-Paradox} and others. It is shown that in Cellular Automata (Rechnender Raum) the structure of the space offers solutions for such problems. T3 - ZIB-Report - TR-93-12 KW - Cellular Automata KW - Rechnender Raum KW - Digital Particle KW - Pattern KW - Grid KW - Grid Point KW - Nonlocal Correlation KW - Similarity Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5039 ER - TY - GEN A1 - Gruntz, Dominik A1 - Koepf, Wolfram T1 - Formal Power Series. N2 - {\newcommand{\C}{{\rm {\mbox{C{\llap{{\vrule height1.52ex}\kern.4em}}}}}} \newcommand{\Z} {{\rm {\mbox{\protect\makebox[.2em][l]{\sf Z}\sf Z}}}} \newcommand{\Maple}{{\sc Maple}} Formal Laurent-Puiseux series of the form \[ f(x)=\sum\limits_{k=k_0}^{\infty}a_{k}x^{k/n} \label{eq:formalLPS} \] with coefficients $a_{k}\in\C\;(k\in\Z)$ are important in many branches of mathematics. \Maple\ supports the computation of {\em truncated\/} series with its {\tt series} command, and through the {\tt powerseries} package infinite series are available. In the latter case, the series is represented as a table of coefficients that have already been determined together with a function for computing additional coefficients. This is known as {\em lazy evaluation\/}. But these tools fail, if one is interested in an explicit formula for the coefficients $a_k$. In this article we will describe the \Maple\ implementation of an algorithm presented in several papers of the second author which computes an {\em exact\/} formal power series of a given function. This procedure will enable the user to reproduce most of the results of the extensive bibliography on series. We will give an overview of the algorithm and then present some parts of it in more detail. This package is available through the \Maple-share library with the name {\tt FPS}. We flavor this procedure with the following example. %\begin{maple} \begin{verbatim}> FormalPowerSeries(sin(x), x=0);\end{verbatim} \begin{samepage} \begin{verbatim} infinity ----- k (2 k + 1) \ (-1) x ) ---------------- / (2 k + 1)! ----- k = 0 \end{verbatim} \end{samepage} } T3 - ZIB-Report - SC-93-31 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1267 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Erdmann, Bodo A1 - Kornhuber, Ralf T1 - A Posteriori Error Estimates for Elliptic Problems. N2 - {\def\enorm {\mathop{\mbox{\boldmath{$|\!|$}}}\nolimits} Let $u \in H$ be the exact solution of a given self--adjoint elliptic boundary value problem, which is approximated by some $\tilde{u} \in {\cal S}$, $\cal S$ being a suitable finite element space. Efficient and reliable a posteriori estimates of the error $\enorm u - \tilde{u}\enorm $, measuring the (local) quality of $\tilde{u}$, play a crucial role in termination criteria and in the adaptive refinement of the underlying mesh. A well--known class of error estimates can be derived systematically by localizing the discretized defect problem using domain decomposition techniques. In the present paper, we provide a guideline for the theoretical analysis of such error estimates. We further clarify the relation to other concepts. Our analysis leads to new error estimates, which are specially suited to three space dimensions. The theoretical results are illustrated by numerical computations.} T3 - ZIB-Report - SC-93-29 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1257 ER - TY - GEN A1 - Grammel, Martin A1 - Hege, Hans-Christian A1 - Wunderling, Roland T1 - On the Impact of Communication Latencies on Distributed Sparse LU Factorization. N2 - Sparse LU factorization offers some potential for parallelism, but at a level of very fine granularity. However, most current distributed memory MIMD architectures have too high communication latencies for exploiting all parallelism available. To cope with this, latencies must be avoided by coarsening the granularity and by message fusion. However, both techniques limit the concurrency, thereby reducing the scalability. In this paper, an implementation of a parallel LU decomposition algorithm for linear programming bases is presented for distributed memory parallel computers with noticable communication latencies. Several design decisions due to latencies, including data distribution and load balancing techniques, are discussed. An approximate performance model is set up for the algorithm, which allows to quantify the impact of latencies on its performance. Finally, experimental results for an Intel iPSC/860 parallel computer are reported and discussed. T3 - ZIB-Report - SC-93-28 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1245 ER - TY - GEN A1 - Koepf, Wolfram T1 - A package on formal power series. N2 - Formal Laurent-Puiseux series of the form \[ f(x)=\sum \limits_{k=k_0}^{\infty}a_{k}x^{k/n} \] are important in many branches of mathematics. Whereas {\sc Mathematica} supports the calculation of truncated series with its {\tt Series} command, and the {\sc Mathematica} package {\tt SymbolicSum} that is shipped with {\sc Mathematica} version 2 is able to convert formal series of the type mentioned above in some instances to their corresponding generating functions, in six publications of the author we developed an algorithmic procedure to do these conversions that is implemented by the author, A.\ Rennoch and G.\ Stölting in the {\sc Mathematica} package {\tt PowerSeries}. The implementation enables the user to reproduce most of the results of the extensive bibliography on series of Hansen, E.\ R.: A table of series and products. Prentice-Hall, 1975. Moreover a subalgorithm of its own significance generates differential equations satisfied by the input function. T3 - ZIB-Report - SC-93-27 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1231 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Optimum Path Packing on Wheels: The Noncrossing Case. N2 - We show that, given a wheel with nonnegative edge lengths and pairs of terminals located on the wheel's outer cycle such that no two terminal pairs cross, then a path packing, i.~e.,a collection of edge disjoint paths connecting the given terminal pairs, of minimum length can be found in strongly polynomial time. Moreover, we exhibit for this case a system of linear inequalities that provides a complete and nonredundant description of the path packing polytope, which is the convex hull of all incidence vectors of path packings and their supersets. T3 - ZIB-Report - SC-93-26 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1225 ER - TY - GEN A1 - Richter-Gebert, Jürgen A1 - Ziegler, Günter M. T1 - Zonotopal Tilings and the Bohne-Dress Theorem. N2 - We prove a natural bijection between the polytopal tilings of a zonotope $Z$ by zonotopes, and the one-element-liftings of the oriented matroid ${\cal M}(Z)$ associated with $Z$. This yields a simple proof and a strengthening of the Bohne-Dress Theorem on zonotopal tilings. T3 - ZIB-Report - SC-93-25 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1212 ER - TY - GEN A1 - Deuflhard, Peter A1 - Schmidt, Frank T1 - Discrete Transparent Boundary Conditions for the Numerical Solution of Fresnel's Equation. N2 - The paper presents a construction scheme of deriving transparent , i. e. reflection-free, boundary conditions for the numerical solution of Fresnel's equation (being formally equivalent to Schrödinger's equation). These boundary conditions appear to be of a nonlocal Cauchy type. As it turns out, each kind of linear implicit discretization induces its own discrete transparent boundary conditions. T3 - ZIB-Report - SC-93-24 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1205 ER - TY - GEN A1 - Deuflhard, Peter A1 - Bölling, Reinhard A1 - Bott, Raoul H. T1 - Materialien zur Euler-Vorlesung in Sanssouci. N2 - Aus dem Inhalt: Vorwort; Leonhard Euler - aus der Zeit seines Wirkens in Berlin; Introductory Remarks. T3 - ZIB-Report - TR-93-10 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5029 ER - TY - GEN A1 - Deuflhard, Peter T1 - Cascadic Conjugate Gradient Methods for Elliptic Partial Differential Equations I. Algorithm and Numerical Results. N2 - Cascadic conjugate gradient methods for the numerical solution of elliptic partial differential equations consists of Galerkin finite element methods as outer iteration and (possibly preconditioned) conjugate gradient methods as inner iteration. Both iterations are known to minimize the energy norm of the arising iterations errors. A simple but efficient strategy to control the discretization errors versus the PCG iteration errors in terms of energy error norms is derived and worked out in algorithmic detail. In a unified setting, the relative merits of different preconditioners versus the case of no preconditioning is compared. Surprisingly, it appears that the cascadic conjugate gradient method without any preconditioning is not only simplest but also fastest. The numerical results seem to indicate that the cascade principle in itself already realizes some kind of preconditioning. A theoretical explanation of these observations will be given in Part II of this paper. T3 - ZIB-Report - SC-93-23 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1197 ER - TY - GEN A1 - Lang, Jens T1 - KARDOS - KAskade Reaction Diffusion One-dimensional System. N2 - A software package for the adaptive solution of time--dependent reaction--diffusion systems and linear elliptic systems in one space dimension is presented. The used algorithm is based on fundamental arguments in J.~Lang, A.~Walter: {\it A Finite Element Method Adaptive in Space and Time for Nonlinear Reaction--Diffusion Systems.} IMPACT of Computing in Science and Engineering, 4, p.~269--314 (1992). Here, only brief outlines of the algorithm are given. This software package is based on the KASKADE toolbox B.~Erdmann, J.~Lang, R.~Roitzsch: {\it KASKADE -- Manual.} To appear as Technical Report TR 93--5, Konrad--Zuse--Zentrum (ZIB) (1993). T3 - ZIB-Report - TR-93-09 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5019 ER - TY - GEN A1 - Deuflhard, Peter A1 - Ackermann, Jörg T1 - Adaptive Discrete Galerkin-Methods for Macromolecular Processes. N2 - In this paper, a rather recent algorithmic approac to the numerical simulation of macromolecula processes is surveyed. It avoids the numerical stiff integration o thousands up to millions of ODE's by constructing a scale of discret Hilbert spaces, especially weighted sequence spaces, and establishing corresponding Galerkin method. Examples including polyreactions o industrial relevance and ecological waste management by biochemica recycling illustrate the importance and efficiency of the algorithm. T3 - ZIB-Report - SC-93-22 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1180 ER - TY - GEN A1 - Stoer, Mechthild A1 - Dahl, Geir T1 - A Polyhedral Approach to Multicommodity Survivable Network Design. N2 - The design of cost-efficient networks satisfying certain survivability constraints is of major concern to the telecommunications industry. In this paper we study a problem of extending the capacity of a network by discrete steps as cheaply as possible, such that the given traffic demand can be accommodated even when a single edge or node in the network fails. We derive valid and non-redundant inequalities for the polyhedron of capacity design variables, by exploiting its relationship to connectivity network design and knapsack-like subproblems. Computational work using this model and the additional inequalities is in progress. T3 - ZIB-Report - SC-93-20 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1162 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Yserentant, Harry T1 - Multilevel Methods for Elliptic Problems on Domains not Resolved by the Coarse Grid. N2 - Elliptic boundary value problems are frequently posed on complicated domains which cannot be covered by a simple coarse initial grid as it is needed for multigrid like iterative methods. In the present article, this problem is resolved for selfadjoint second order problems and Dirichlet boundary conditions. The idea is to construct appropriate subspace decompositions of the corresponding finite element spaces by way of an embedding of the domain under consideration into a simpler domain like a square or a cube. Then the general theory of subspace correction methods can be applied. T3 - ZIB-Report - SC-93-21 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1170 ER - TY - GEN A1 - Kornhuber, Ralf T1 - Monotone Multigrid Methods for Elliptic Variational Inequalities I. N2 - Extending well--known linear concepts of successive subspace correction, we arrive at extended relaxation methods for elliptic variational inequalities. Extended underrelaxations are called monotone multigrid methods, if they are quasioptimal in a certain sense. By construction, all monotone multigrid methods are globally convergent. We take a closer look at two natural variants, which are called symmetric and unsymmetric multigrid methods, respectively. While the asymptotic convergence rates of the symmetric method suffer from insufficient coarse--grid transport, it turns out in our numerical experiments that reasonable application of the unsymmetric multigrid method may lead to the same efficiency as in the linear, unconstrained case. T3 - ZIB-Report - SC-93-18 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1147 ER - TY - GEN A1 - Kornhuber, Ralf T1 - Monotone Multigrid Methods for Elliptic Variational Inequalities II. N2 - We derive fast solvers for discrete elliptic variational inequalities of the second kind as resulting from the approximation by piecewise linear finite elements. Following the first part of this paper, monotone multigrid methods are considered as extended underrelaxations. Again, the coarse grid corrections are localized by suitable constraints, which in this case are fixed by fine grid smoothing. We consider the standard monotone multigrid method induced by the multilevel nodal basis and a truncated version. Global convergence results and asymptotic estimates for the convergence rates are given. The numerical results indicate a significant improvement in efficiency compared with previous multigrid approaches. T3 - ZIB-Report - SC-93-19 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1151 ER - TY - GEN A1 - Hohmann, Andreas T1 - An Implementation of Extrapolation Codes in C++. N2 - This report describes the new object oriented implementation of extrapolation codes {\sc Eulex, Eulsim, Difex} for ordinary differential equations. The resulting C++ class library provides a simple and flexible interface to these methods and incorporates advanced features like continuous output and order-stepsize freezing. The interface of the ODE classes allows in particular a user-defined solver for the linear systems occuring in the linearly implicit discretization scheme. The library also provides some classes for numerical objects such as vectors and (full) matrices. Due to the underlying data-view concept it is possible to access substructures without copying. In addition, we included several utility classes such as a timer and a minimal command language that may be useful in other contexts, too. T3 - ZIB-Report - TR-93-08 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5009 ER - TY - GEN A1 - Diaconics, Persi A1 - Sturmfels, Bernd T1 - Algebraic Algorithms for Sampling from Conditional Distributions. N2 - We construct Markov chain algorithms for sampling from discrete exponential families conditional on a sufficient statistic. Examples include generating tables with fixed row and column sums and higher dimensional analogs. The algorithms involve finding bases for associated polynomial ideals and so an excursion into computational algebraic geometry. T3 - ZIB-Report - SC-93-17 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1131 ER - TY - GEN A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Paths and Steiner Trees: Routing of Electronic Circuits. N2 - One of the challenging problems in the design of electronic circuits is the so-called routing problem. Roughly speaking, the task is to connect so-called terminal sets via wires on a predefined area. In addition, certain design rules are to be taken into account and an objective function such as the wiring length must be minimized. The routing problem in general is too complex to be solved in one step. Depending on the user's choice of decomposing the chip design problem into a hierarchy of stages, on the underlying technology, and on the given design rules, various subproblems arise. We discuss several variants of practically relevant routing problems and give a short overview on the underlying technologies and design rules. Many of the routing problems that come up this way can be formulated as the problem of packing so-called Steiner trees in certain graphs. We consider the Steiner tree packing problem from a polyhedral point of view and present three possibilities to define an appropriate polyhedron. Weighing their pros and cons we decide for one of these polytopes and sketch some of our investigations. T3 - ZIB-Report - SC-93-15 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1113 ER - TY - GEN A1 - Grötschel, Martin A1 - Lovász, Lászlo T1 - Combinatorial Optimization. N2 - This paper will appear as Chapter 28 of the forthcoming "Handbook on Combinatorics" (editors: R. Graham, M. Grötschel, L. Lovasz) to be published in 1994, by North-Holland. T3 - ZIB-Report - SC-93-13 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1098 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Höllerer, Tobias A1 - Stalling, Detlev T1 - Volume Rendering - Mathematicals Models and Algorithmic Aspects. N2 - In this paper various algorithms for rendering gaseous phenomena are reviewed. In computer graphics such algorithms are used to model natural scenes containing clouds, fog, flames and so on. On the other hand it has become an important technique in scientific visualization to display three dimensional scalar datasets as cloudy objects. Our emphasis is on this latter subject of so-called {\em direct volume rendering}. All algorithms will be discussed within the framework of linear transport theory. The equation of transfer is derived. This equation is suitable to describe the radiation field in a participating medium where absorption, emission, and scattering of light can occur. Almost all volume rendering algorithms can be shown to solve special cases of the equation of transfer. Related problems like the mapping from data values to model parameters or possible parallelization strategies will be discussed as well. T3 - ZIB-Report - TR-93-07 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4994 ER - TY - GEN A1 - Gatermann, Karin A1 - Werner, Bodo T1 - Secondary Hopf Bifurcation Caused by Steady-State Steady-State Mode Interaction. N2 - In two-parameter systems with symmetry two steady state bifurcation points of different symmetry types coalesce generically within one point. Under certain group theoretic conditions involving the action of the symmetry group on the kernels, we show that secondary Hopf bifurcation is borne by the mode interaction. We explain this phenomenon by using linear representation theory. For motivation an example with $D_3$-symmetry is investigated where the main properties causing the Hopf bifurcation are summarized. T3 - ZIB-Report - SC-93-16 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1122 ER - TY - GEN A1 - Schütte, Christof A1 - Hohmann, Andreas A1 - Dinand, Manfred T1 - Numerical Simulation of Relaxation Oscillations of Waveguide-Lasers. N2 - An analysis of relaxation oscillations in local Er-doped optically pumped lasers is reported. It is based on a time dependent rate equation model for a quasi-two-level-system with wavelength dependent emission- and absorption cross-sections. For the first time a numerically reliable simulation of the characteristic laser behaviour was possible: the onset and decay of the oscillations, the time-dependent repetition period and the steady state signal output power. The characteristic waveguide parameters, as the erbium-concentration profile, the polarization dependent pump- and signal mode intensity profiles, the scattering losses, the cavity length and the front and rear reflectivities were all taken into account. The basic formulas are general and can also be used for Er-doped fiber lasers. Mathematically the problem can be characterized as a large boundary value problem, which can approximately be replaced by a stiff initial value problem of ordinary differential equations. The used algorithmic replacement procedure is motivated and discussed in detail. Here, pump- and signal evolution versus time are presented for an planar Er-diffused $\rm Ti$:$\rm LiNbO_{3}$ waveguide laser. The numerically obtained results show a nearly quantitative agreement with experimental investigations. Simultanously they supply knowledge about non-measureable (space-dependent population dynamic of the Er-atoms) and till today not measured data (dynamical response of the laser by a sharp peak in the external pump). T3 - ZIB-Report - SC-93-14 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1106 ER - TY - GEN A1 - Ziegler, Günter M. T1 - Lectures on Polytopes. N2 - These lecture notes have several aims: \begin{itemize} \item to give an introduction to some basic facts about convex polytopes, with an emphasis on the basic methods that yield them (Fourier-Motzkin elimination, Schlegel diagrams, shellability, Gale transforms and oriented matroids), \item to discuss some important examples and elegant constructions (cyclic and neighborly polytopes, zonotopes, Minkowski sums, permutahedra and associahedra, fiber polytopes, the Lawrence construction) \item and to illustrate why polytope theory is exciting, with highlights like Kalai's new diameter bounds, the construction of non-rational polytopes, the Bohne-Dress tiling theorem, shellability and the upper bound theorem, .... \end{itemize} For several of these topics the decisive break-through is very recent, which suggests that there is much more discovered. T3 - ZIB-Report - TR-93-06 Y1 - 1993 N1 - No preprint available; published as Ziegler, G. M. (1994) Lectures on Polytopes. ISBN 354094365X, New York: Springer ER - TY - GEN T1 - Jahresbericht 1993 T3 - Jahresbericht - 1993 KW - Annual Report Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9668 SN - 0934-5892 ER - TY - GEN T1 - Jahresbericht 1992 T3 - Jahresbericht - 1992 KW - Annual Report Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9686 SN - 0934-5892 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Wissenschaftliches Publizieren und Elektronische Fachinformation im Umbruch: ein Situationsbericht aus der Sicht der Mathematik. N2 - In diesem Aufsatz geben wir einen Bericht über den Stand der elektronischen Fachinformation in der Mathematik in Deutschland. Wir sehen diesen Bereich nicht als ein organisatorisch isoliertes Unterfangen, sondern eingebettet in weltweite Bestrebungen und Entwicklungen in der Informationstechnik, im wissenschaftlichen Publikationswesen und natürlich auch in der Mathematik selber. Unser Artikel endet mit einigen weitreichenden (und einigen Lesern möglicherweise spektakulär erscheinenden) Vorschlägen, die sowohl die Informationsanbieter (wie die Fachinformationszentren und Verlage), die öffentlichen Geldgeber als auch die mathematischen Organisationen (wie z.~B.~ die DMV und die mathematischen Fachbereiche) betreffen. Um den gegenwärtigen Zustand der elektronischen Fachinformation und unsere Gedanken zu diesem Thema adäquat beschreiben zu können, präsentieren wir eine breit angelegte Situationsanalyse. Wir stellen den gegenwärtigen Stand der technologischen Entwicklung im elektronischen Publizieren dar und skizzieren seine Auswirkungen. Wir beschreiben das Feld der Interessen und Kräfte im Bereich des mathematischen Publizierens. Wir geben einen kurzen historischen Abriss der Geschichte der Klassifikation und des Referatewesens und zeigen, wie dieses in die elektronische Fachinformation auf dem Gebiet der Mathematik mündete und dann zum DMV-Projekt Fachinformation führte, das der Anlass zur Abfassung dieses Artikels war. Wir skizzieren die gegenwärtige Rezeption elektronischer Fachinformation in der Mathematik in Deutschland. Ausgehend von einer Darstellung und Bewertung verschiedener Modelle des Referatewesens zeigen wir unter Einbeziehung der vorhandenen technischen Gegebenheiten (elektronische Netze etc.) verschiedene Möglichkeiten zur Liberalisierung und Rationalisierung des weltweiten mathematischen Informationswesens auf. Wir sehen den Austausch von Information in engem Zusammenhang mit dem Austausch von Software im Wissenschaftsbereich und regen auch in diesem Bereich an, internationale Kooperation und Offenheit anzustreben. \originalTeX T3 - ZIB-Report - TR-93-04 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4966 ER - TY - GEN A1 - Ackermann, Jörg A1 - Roitzsch, Rainer T1 - On a Two-Dimensional Multilevel Adaptive Finite Element Method for the Time-Independent Schrödinger-Equation. N2 - The subject of this study is a multilevel Finite Element Method based on an error estimator and step by step grid refinement as an universal tool for solving time--independent Schrödinger--eigenvalue problems. Numerical results for standard problems appearing in vibrational motion and molecular electronic structure calculations are given and discussed. T3 - ZIB-Report - SC-93-12 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1086 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Roitzsch, Rainer T1 - Kaskade Manual - Version 2.0. N2 - The KASKADE toolbox defines an interface to a set of C subroutines which can be used to implement adaptive multilevel Finite Element Methods solving systems of elliptic equations in two and three space dimensions. The manual contains the description of the data structures and subroutines. The main modules of the toolbox are a runtime environment, triangulation and node handling, assembling, direct and iterative solvers for the linear systems, error estimators, refinement strategies, and graphic utilities. Additionally, we included appendices on the basic command language interface, on file formats, and on the definition of the partial differential equations which can be solved. The software is available on the ZIB ftp--server {\tt elib} in the directory {\tt pub/kaskade}. TR 93--5 supersedes TR 89--4 and TR 89--05. T3 - ZIB-Report - TR-93-05 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4970 ER - TY - GEN A1 - Reiner, Victor A1 - Ziegler, Günter M. T1 - Coxeter-associahedra. N2 - \def\KPA{\hbox{\rm KPA}}\def\A{{\rm A}}\def\KPW{\hbox{\rm KPW}}\def\W{{\rm W}}\def\B{{\rm B}} \def\D{{\rm D}} Recently M.~M.~Kapranov [Kap] defined a poset $\KPA_{n-1}$, called the {\it permuto-associahedron}, which is a hybrid between the face poset of the permutahedron and the associahedron. Its faces correspond to the partially parenthesized, ordered, partitions of the set $\{1,2,\ldots,n\}$, with a natural partial order. Kapranov showed that $\KPA_{n-1}$ is the face poset of a CW-ball, and explored its connection with a category-theoretic result of MacLane, Drinfeld's work on the Knizhnik-Zamolodchikov equations, and a certain moduli space of curves. He also asked the question of whether this CW-ball can be realized as a convex polytope. We show that this permuto-associahedron corresponds to the type $\A_{n-1}$ in a family of convex polytopes $\KPW$ associated to each of the classical Coxeter groups, $\W = \A_{n-1}, \B_n, \D_n$. The embedding of these polytopes relies on the secondary polytope construction of the associahedron due to Gel'fand, Kapranov, and Zelevinsky. Our proofs yield integral coordinates, with all vertices on a sphere, and include a complete description of the facet-defining inequalities. Also we show that for each $\W$, the dual polytope $\KPW^*$ is a refinement (as a CW-complex) of the Coxeter complex associated to $\W$, and a coarsening of the barycentric subdivision of the Coxeter complex. In the case $\W=\A_{n-1}$, this gives an elementary proof of Kapranov's original sphericity result. T3 - ZIB-Report - SC-93-11 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1075 ER - TY - GEN A1 - Langendorf, Jens A1 - Paetsch, Olaf T1 - GRAZIL - Beschreibung der Version 6.0 des Plotpaketes. N2 - GRAZIL ist ein interaktives Programmpaket zur grafischen Darstellung von zwei-dimensionalen Kurvenverläufen. Dem Benutzer stehen zahlreiche Kommandos und ein grafisches User-Interface zum Gestalten des Layouts der Zeichnung zur Verfügung. Die Eingabedaten müssen dem GRAZIL-Eingabe-Format genügen. Somit wird eine hohe Flexibilität und eine gro\"se Bandbreite der Einsatzmöglichkeiten erreicht. GRAZIL wurde mit der grafischen Grundsoftware GKS entwickelt. Dadurch kann ein breites Rechner- und Ausgabegerätespektrum genutzt werden. T3 - ZIB-Report - TR-93-01 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4930 ER - TY - GEN A1 - Schütte, Christof T1 - A quasiresonant smoothing algorithm for the fast analysis of selective vibrational excitation. N2 - One key problem in modern chemistry is the simulation of the dynamical reaction of a molecule subjected to external radiation. This is described by the Schrödinger equation, which, after eigenfunction expansion, can be written in form of a system of ordinary differential equations, whose solutions show a highly oscillatory behaviour. The oscillations with high frequencies and small amplitudes confine the stepsizes of any numerical integrator -- an effect, which, in turn, blows up the simulation time. Larger stepsizes can be expected by averaging these fast oscillations, thus smoothing the trajectories. This idea leads to the construction of a quasiresonant smoothing algorithm (QRS). In QRS, a natural and computationally available splitting parameter $\delta$ controls the smoothing properties. The performance of QRS is demonstrated in two applications treating the selective excitation of vibrational states by picosecond laser pulses. In comparison with standard methods a speedup factor of 60--100 is observed. A closer look to purely physically motivated quasiresonant approximations such as WFQRA shows some additional advantages of the above smoothing idea. Among these the possibility of an adaptive formulation of QRS via the parameter $\delta$ is of particular importance. T3 - ZIB-Report - SC-93-10 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1066 ER - TY - GEN A1 - Erdmann, Bodo A1 - Hoppe, Ronald H. W. A1 - Kornhuber, Ralf T1 - Adaptive Multilevel-Methods for Obstacle Problems in Three Space Dimensions. N2 - We consider the discretization of obstacle problems for second order elliptic differential operators in three space dimensions by piecewise linear finite elements. Linearizing the discrete problems by suitable active set strategies, the resulting linear sub--problems are solved iteratively by preconditioned cg--iterations. We propose a variant of the BPX preconditioner and prove an $O(j)$ estimate for the resulting condition number. To allow for local mesh refinement we derive semi--local and local a posteriori error estimates. The theoretical results are illustrated by numerical computations. T3 - ZIB-Report - SC-93-08 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1049 ER - TY - GEN A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Design of Survivable Networks T3 - ZIB-Report - SC-93-09 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1054 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Telebus-Disposition: Ein Konzept zur Serviceverbesserung bei gleichzeitiger Kostensenkung.[nur hausintern] N2 - "`Telebus"' ist der soziale Behindertenfahrdienst im Land Berlin. Das Telebus-Forschungsprojekt des Konrad-Zuse-Zentrums für Informationstechnik (ZIB) hat das Ziel, den Fahrdienst (insbesondere die Disposition der Telebusse) zu verbessern, d.h. kundenfreundlicher zu gestalten und gleichzeitig billiger zu machen. In diesem Bericht werden die bisherigen Ergebnisse dargestellt und weitere Möglichkeiten zur Verbesserung des Service und zur Reduzierung der Kosten skizziert. \originalTeX T3 - ZIB-Report - TR-93-03 Y1 - 1993 N1 - Volltext nur Hausintern ER - TY - GEN A1 - Weismantel, Robert A1 - Ferreira, Carlos E. A1 - Martin, Alexander T1 - A Cutting Plane Based Algorithm for the Multiple Knapsack Problem. N2 - In this paper we describe a cutting plane based algorithm for the multiple knapsack problem. We use our algorithm to solve some practical problem instances arising in the layout of electronic circuits and in the design of main frame computers, and we report on our computational experience. This includes a discussion and evaluation of separation algorithms, an LP-based primal heuristic and some implementation details. The paper is based on the polyhedral theory for the multiple knapsack polytope developed in our companion paper SC 93-04 and meant to turn this theory into an algorithmic tool for the solution of practical problems. T3 - ZIB-Report - SC-93-07 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1031 ER - TY - GEN A1 - Deuflhard, Peter T1 - A Study of Lanczos-Type Iterations for Symmetric Indefinite Linear Systems N2 - The Lanczos iteration for symmetric indefinite linear systems seems to be well--known for quite a while. However, in order to modify it with the aim of improved performance, the present paper studies certain aspects in terms of an adjoint scalar three--term recurrence. Thus, at least a different view is opened. Moreover, an alternative $3n$--implementation in terms of the Euclidean orthogonal basis has been found that easily permits generalizations. The study is understood as a start--off for further numerical investigations and experiments. T3 - ZIB-Report - SC-93-06 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1029 ER - TY - GEN A1 - Richter-Gebert, Jürgen T1 - Mechanical Theorem Proving in Projective Geometry. N2 - We present an algorithm that is able to confirm projective incidence statements by carrying out calculations in the ring of all formal determinants (brackets) of a configuration. We will describe an implementation of this power and present a series of examples treated by the prover, including {\it Pappos' and Desargues' Theorems,} the {\it Sixteen Point Theorem, Saam's Theorem, }the {\it Bundle Condition,} the uniqueness of a harmonic Point and {\it Pascal's Theorem.} T3 - ZIB-Report - SC-93-05 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1013 ER - TY - GEN A1 - Ferreira, Carlos E. A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Facets for the Multiple Knapsack Problem. N2 - In this paper we consider the multiple knapsack problem which is defined as follows: given a set $N$ of items with weights $f_i$, $i \in N$, a set $M$ of knapsacks with capacities $F_k$, $k \in M$, and a profit function $c_{ik}, i \in N, k \in M$; find an assignment of a subset of the set of items to the set of knapsacks that yields maximum profit (or minimum cost). With every instance of this problem we associate a polyhedron whose vertices are in one to one correspondence to the feasible solutions of the instance. This polytope is the subject of our investigations. In particular, we present several new classes of inequalities and work out necessary and sufficient conditions under which the corresponding inequality defines a facet. Some of these conditions involve only properties of certain knapsack constraints, and hence, apply to the generalized assignment polytope as well. The results presented here serve as the theoretical basis for solving practical problems. The algorithmic side of our study, i.e., separation algorithms, implementation details and computational experience with a branch and cut algorithm are discussed in the companion paper SC 93-07. T3 - ZIB-Report - SC-93-04 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1007 ER - TY - GEN A1 - Melenk, Herbert T1 - Algebraic Solution of Nonlinear Equation Systems in REDUCE. N2 - The strategy for solving nonlinear equation systems automatically in the computer algebra system REDUCE is described. Kernel of the solver is a factoring Buchberger algorithm. Pre -- and postprocessors enable the use of the Gröbner techniques in a black box manner. In addition to polynomials equations with surds, trigonometric functions and separable transcendental functions are covered. T3 - ZIB-Report - TR-93-02 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4944 ER - TY - GEN A1 - Ferreira, Carlos E. A1 - Grötschel, Martin A1 - Kiefl, Stefan A1 - Krispenz, Ludwig A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Some Integer Programs Arising in the Design of Main Frame Computers. N2 - In this paper we describe and discuss a problem that arises in the (global) design of a main frame computer. The task is to assign certain functional units to a given number of so called multi chip modules or printed circuit boards taking into account many technical constraints and minimizing a complex objective function. We describe the real world problem. A thorough mathematical modelling of all aspects of this problem results in a rather complicated integer program that seems to be hopelessly difficult -- at least for the present state of integer programming technology. We introduce several relaxations of the general model, which are also $NP$-hard, but seem to be more easily accessible. The mathematical relations between the relaxations and the exact formulation of the problem are discussed as well. T3 - ZIB-Report - SC-92-25 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-957 ER - TY - GEN A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Polyhedral and Computational Investigations for Designing Communication Networks with High Survivability Requirements. N2 - We consider the important practical and theoretical problem of designing a low-cost communications network which can survive failures of certain network components. Our initial interest in this area was motivated by the need to design certain ``two-connected" survivable topologies for fiber optic communication networks of interest to the regional telephone companies. In this paper, we describe some polyhedral results for network design problems with higher connectivity requirements. We also report on some preliminary computational results for a cutting plane algorithm for various real-world and random problems with high connectivity requirements which shows promise for providing good solutions to these difficult problems. \def\NP{$\cal NP$} T3 - ZIB-Report - SC-92-24 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-944 ER - TY - GEN A1 - Gatermann, Karin A1 - Werner, Bodo T1 - Group Theoretical Mode Interactions with Different Symmetries. N2 - In two-parameter systems two symmetry breaking bifurcation points of different types coalesce generically within one point. This causes secondary bifurcation points to exist. The aim of this paper is to understand this phenomenon with group theory and the innerconnectivity of irreducible representations of supergroup and subgroups. Colored pictures of examples are included. T3 - ZIB-Report - SC-93-03 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-994 ER - TY - GEN T1 - Handbuch zur Visualisierung am ZIB N2 - Scientists intending to employ scientific visualization techniques are confronted with the unpleasant task of choosing visualization software that meets their specific needs. A good choice requires consideration of several aspects. Most important are functionality, i.e. the set of supported visual representations, and restrictions due to the user's production environment (i.e. available hardware and software platforms, software compatibility constraints, need of specific input and output formats, network distribution requirements). Crucial are quality demands, ranging from simple graphics for interactive control of simulations, to images of highest quality (glossy prints, slides or video movies) for presentation purposes. Further aspects of consideration are: ease of use, level on which the user is willing to program, portability, conformity to prevalent standards, availability in the world-wide user community, future dissemination, as well as emerging trends in computer graphics and scientific visualization. The aim of this manual is to give a survey on the graphics and visualization software that is currently being provided at ZIB (mainly for internal use). The whole range of computer graphics software relevant in mathematical, natural and technical sciences is covered: image synthesis (basic and higher graphics libraries, plot programs, visualization environments, combined text and drawing programs, renderers), image processing and storage (raster and vector formats, page description languages, raster toolkits for image processing and format conversion), capturing of images as well as printing on paper and recording on photographic film or video tape. This information together with a glossary and recommendations for further reading should help prospective users in getting started and assist them in making good choices of graphics and visualization software. T3 - ZIB-Report - TR-92-07 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4920 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Routing in Grid Graphs by Cutting Planes. N2 - {\def\N{{\cal N}} \def\R{\hbox{\rm I\kern-2pt R}} \def\MN{{\rm I\kern-2pt N}} In this paper we study the following problem, which we call the weighted routing problem. Let be given a graph $G=(V,E)$ with non-negative edge weights $w_e\in\R_+$ and integer edge capacities $c_e\in\MN$ and let $\N=\{T_1,\ldots,T_N\}$, $N\ge 1$, be a list of node sets. The weighted routing problem consists in finding edge sets $S_1,\ldots,S_N$ such that, for each $k\in\{1,\ldots,N\}$, the subgraph $(V(S_k),S_k)$ contains an $[s,t]$-path for all $s,t\in T_k$, at most $c_e$ of these edge sets use edge $e$ for each $e\in E$, and such that the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from the routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the weighted routing problem from a polyhedral point of view. We define an appropriate polyhedron and try to (partially) describe this polyhedron by means of inequalities. We briefly sketch our separation algorithms for some of the presented classes of inequalities. Based on these separation routines we have implemented a branch and cut algorithm. Our algorithm is applicable to an important subclass of routing problems arising in VLSI-design, namely to problems where the underlying graph is a grid graph and the list of node sets is located on the outer face of the grid. We report on our computational experience with this class of problem instances.} T3 - ZIB-Report - SC-92-26 KW - routing in VLSI-design KW - Steiner tree KW - Steiner tree packing KW - cutting plane algorithm Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-967 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Further Facets. N2 - In this paper we continue the investigations in [GMW92a] for the \def\sbppo{Steiner tree packing polyhedron} \sbppo. We present several new classes of valid inequalities and give sufficient (and necessary) conditions for these inequalities to be facet-defining. It is intended to incorporate these inequalities into an existing cutting plane algorithm that is applicable to practical problems arising in the design of electronic circuits. T3 - ZIB-Report - SC-93-01 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-975 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Separation Algorithms. N2 - In this paper we investigate separation problems for classes of inequalities valid for the polytope associated with the Steiner tree packing problem, a problem that arises, e.~g., in VLSI routing. The separation problem for Steiner partition inequalities is ${\cal N}\hskip-2pt{\cal P}$-hard in general. We show that it can be solved in polynomial time for those instances that come up in switchbox routing. Our algorithm uses dynamic programming techniques. These techniques are also applied to the much more complicated separation problem for alternating cycle inequalities. In this case we can compute in polynomial time, given some point $y$, a lower bound for the gap $\alpha-a^Ty$ over all alternating cycle inequalities $a^Tx\ge\alpha$. This gives rise to a very effective separation heuristic. A by-product of our algorithm is the solution of a combinatorial optimization problem that is interesting in its own right: Find a shortest path in a graph where the ``length'' of a path is its usual length minus the length of its longest edge. T3 - ZIB-Report - SC-93-02 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-984 ER - TY - GEN A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - A Polyhedral Approach to Network Connectivity Problems (Extended Abstract). N2 - We present a polyhedral approach for the general problem of designing a minimum-cost network with specified connectivity requir T3 - ZIB-Report - SC-92-22 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-924 ER - TY - GEN A1 - Chu, Nguyen Ngoc T1 - An Algorithm for Optimizing a Linear Function over the Integer Efficient Set. N2 - Whereas optimization of a linear function over an efficient set is a favourite topic for theoretical studies, the problem ($P^I$) of finding a maximal value of a linear function $dx$ over an integer efficient set is still open. The problem ($P^I$) is NP-hard and it is very unlikely that the maximal objective value of the integer problem ($P^I$) in many cases is greater than the maximal objective value of it's corresponding continuous problem ($P$). In this paper we pay atention to the study of the problem ($P^I$) and some related properties of the problem ($P$). In particular, we establish conditions determining whether or not an optimal solution to the problem ($P$) is an optimal solution to the it's corresponding linear program. For the problem ($P^I$) we find an upper bound for it's optimal objective value and present an algorithm which gives a global optimal solution after a finite number of steps. We also study two particular classes of problems ($P^I$) : the bicriteria case and the case when $d$ is a nonnegative linear combination of the vectors-criteria defining the efficient set. Key words: Multiple objective linear programming, integer efficient set, efficient cone, cutting plane. T3 - ZIB-Report - SC-92-23 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-930 ER - TY - GEN A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Elektronische Fachinformation im Bereich der Mathematik an Hochschulen und Statusbericht zum DMV-Projekt. "Fachinformation". N2 - Im Bereich der Mathematik entwickelte sich in Deutschland die elektronische Fachinformation in Form der Online-Datenbank MATH und der CD-ROM CompactMATH auf der Grundlage der Arbeiten des Referateorgans "Zentralblatt für Mathematik und Ihre Grenzgebiete". Das "Zentralblatt" fand weithin Anerkennung und Verbreitung. Die Rezeption elektronischer Fachinformation ging jedoch - nicht nur im Bereich der Mathematik - nur zögerlich vonstatten. Die Gründe dafür werden in einer vom Bundesminister für Forschung und Technologie (BMFT) initiierten Studie analysiert. Ein kürzlich von der Deutschen Mathematiker - Vereinigung begonnenes und vom BMFT gefördertes Vorhaben hat die "Verbesserung des benutzerorientierten Zugriffs auf fachspezifische Online-Datenbanken und CD-ROM für Mathematische Institute in der Bundesrepublik Deutschland" zum Ziel. Insgesamt 51 mathematische Fachbereiche und Institute nehmen daran teil. Elektronische Fachinformation soll zu einem festen Bestandteil des methodischen Instrumentariums der wissenschaftlichen Arbeit werden. Diese Schrift soll die Ausgangslage in den Fachbereichen darstellen und die organisatorischen und technischen Infrastrukturmaßnahmen erläutern, mit denen den spezifischen Nutzungshemmnissen begegnet werden soll. T3 - ZIB-Report - TR-92-06 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4910 ER - TY - GEN A1 - Nowak, Ulrich T1 - Dynamic Sparsing in Stiff Extrapolation Methods. N2 - Based on a simple stability analysis for the semi--implicit Euler discretization a new dynamic sparsing procedure is derived. This procedure automatically eliminates ``small'' elements of the Jacobian matrix. As a consequence, the amount of work needed to handle the linear algebra within a semi--implicit extrapolation integrator can be reduced drastically. Within the course of integration the sparsing criterion, which decides what ``small'' means, is dynamically adapted to ensure stability of the discretization scheme. Thus, stepsize restrictions due to instability can be avoided. Numerical experiments for quite different problems show robustness and efficiency of this dynamic sparsing technique. The techniques developed here in the context of stiff extrapolation integrators can, in principle, be applied to W--methods, where exact Jacobians may be replaced by ``sufficiently good'' approximations. {\bf Keywords:} Large scale integration, extrapolation methods, stiff ODEs, W--methods, sparse matrix techniques. T3 - ZIB-Report - SC-92-21 KW - large scale integration KW - extrapolation methods KW - stiff ODEs KW - W-methods KW - sparse matrix techniques Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-911 ER - TY - GEN A1 - Yang, Shuli T1 - Numerical Riemann solutions in multi-pieces for 2-D gas dynamics systems I. Contact discontinuities. N2 - The numerical solutions of Riemann problems in three, four, five and six pieces, which only contain contact discontinuities, are presented by using Taylor FVM MmB schemes on regular triangular meshes for 2-D gas dynamics systems. The 2-D Riemann initial data are as defined in [1], under the assumption that each jump in initial data outside of the origin projects exactly one planar wave of shocks, centered rarefaction waves , or contact discontinuities. The main ends of the paper are that spirals will be shown for some configurations and the relations of the solutions between different distibutions of Riemann initial data are explained by the numerical solutions of modified Riemann problems. Key words and phrases: Riemann problem, gas dynamics systems, spiral, MmB schemes. T3 - ZIB-Report - SC-92-20 KW - Riemann problem KW - gas dynamics systems KW - spiral Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-903 ER - TY - GEN A1 - Ziegler, Günter M. T1 - Shellability of Chessboard Complexes. N2 - The matchings in a complete bipartite graph form a simplicial complex, which in many cases has strong structural properties. We use an equivalent description as chessboard complexes: the complexes of all non-taking rook positions on chessboards of various shapes. In this paper we construct `certificate $k$-shapes' $\Sigma(m,n,k)$ such that if the shape $A$ contains some $\Sigma(m,n,k)$, then the $(k{-}1)$-skeleton of the chessboard complex $\Delta(A)$ is vertex decomposable in the sense of Provan & Billera. This covers, in particular, the case of rectangular chessboards $A=[m]{\times}[n]$, for which $\Delta(A)$ is vertex decomposable if $n\ge 2m{-}1$, and the $(\lfloor{m+n+1\over3}\rfloor{-}1)$-skeleton is vertex decomposable in general. The notion of vertex decomposability is a very convenient tool to prove shellability of such combinatorially defined simplicial complexes. We establish a relation between vertex decomposability and the CL-shellability technique (for posets) of Björner & Wachs. T3 - ZIB-Report - SC-92-19 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-890 ER - TY - GEN A1 - Hohmann, Andreas A1 - Wulff, Claudia T1 - Modular Design of Extrapolation Codes. N2 - In this paper we describe a modular implementation of the well-established extrapolation codes EULEX, EULSIM and DIFEX for initial value problems of ordinary differential equations. The basic module embodies an abstract extrapolation method with order and stepsize control. Based on this module the particular integration codes only have to provide the underlying discretization schemes. T3 - ZIB-Report - TR-92-05 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4909 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - Adaptive Solution of One-Dimensional Scalar Conservation Laws with Convex Flux. N2 - A new adaptive approach for one-dimensional scalar conservation laws with convex flux is proposed. The initial data are approximated on an adaptive grid by a problem dependent, monotone interpolation procedure in such a way, that the multivalued problem of characteristic transport can be easily and explicitly solved. The unique entropy solution is chosen by means of a selection criterion due to LAX. For arbitrary times, the solutions is represented by an adaptive monotone spline interpolation. The spatial approximation is controlled by local $L^1$-error estimated. As a distinctive feature of the approach, there is no discretization in time. The method is monotone on fixed grids. Numerical examples are included, to demonstrate the predicted behavior. {\bf Key words.} method of characteristics, adaptive grids, monotone interpolation, $L^1$-error estimates {\bf AMS(MOS) subject classification.} 65M15, 65M25, 65M50. T3 - ZIB-Report - SC-92-18 KW - method of characteristics KW - adaptive grids KW - monotone interpolation KW - L1-error estimates Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-880 ER - TY - GEN A1 - Yang, Shuli T1 - MmB schemes on regular triangular meshes for 2-D conservation laws. N2 - In this paper, two classes of second order accurate high resolution schemes are presented on regular triangular meshes for initial value problem of two dimensional conservation laws. The first class are called Runge-Kutta-FVM MmB (locally Maximum- minimum Bounds preserving) schemes, which are first discretized by (FVM) finite volume method in space direction and modifying numerical fluxes, and then by Runge-Kutta methods in time direction; The second class, constructed by Taylor expansion in time, and then by FVM methods and making modifications to fluxes, are called Taylor- FVM MmB schemes. MmB properties of both schemes are proved for 2-D scalar conservation law. Numerical results are given for Riemann problems of 2-D scalar conservation law and 2-D gas dynamics systems and some comparisons are made between the two classes of the schemes. Key words and phrases: MmB schemes, 2-D, conservation laws, gas dynamics systems, Runge-Kutta-FVM, Taylor-FVM. T3 - ZIB-Report - SC-92-17 KW - MmB schemes KW - 2-D KW - conservation laws KW - gas dynamics systems KW - Runge-Kutta-FVM KW - Taylor-FVM Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-873 ER - TY - THES A1 - Weismantel, Robert T1 - Plazieren von Zellen: Theorie und Lösung eines quadratischen 0/1- Optimierungsproblems. N2 - Die vorliegende Arbeit beschäftigt sich mit dem Plazierungsproblem, welches beim Entwurf elektronischer Schaltungen auftritt. Das Plazierungsproblem modellieren wir als ein quadratisches 0/1 Optimierungsproblem unter linearen Nebenbedingungen und untersuchen das Modell komplexitätstheoretisch. Der zweite Aspekt der Arbeit bezieht sich auf die Lösung praktischer Problembeispiele im sogenannten Sea of cells"-Entwurfsstil. Zur Lösung dieser Beispiele wurde ein Prototyp implementiert und mit state of the art"-Plazierungsverfahren verglichen. Schlie\ss lich werden wir uns mit dem Clusteringproblem, das eine Variante des Mehrfachschnitt-Problems darstellt, beschäftigen. Dabei steht einerseits im Vordergrund, wie diese Probleme heuristisch gelöst werden können und wie die Integration des Ansatzes in das Plazierungsprogramm erfolgt. Andererseits soll das Clusteringproblem polyedrisch untersucht werden. T3 - ZIB-Report - TR-92-03 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4883 ER - TY - THES A1 - Martin, Alexander T1 - Packen von Steinerbäumen: Polyedrische Studien und Anwendung. N2 - Gegeben sei ein Graph $G=(V,E)$ mit positiven Kantenkapazitäten $c_e$ und Knotenmengen $T_1,\ldots,T_N$. Das Steinerbaumpackungs-Problem besteht darin, Kantenmengen $S_1,\ldots,S_N$ zu finden, so da\ss\ jedes $S_k$ die Knoten aus $T_k$ verbindet und jede Kante $e$ in höchstens $c_e$ Kantenmengen aus $S_1,\ldots,S_N$ vorkommt. Eine zulässige Lösung dieses Problems nennen wir eine Steinerbaumpackung. Ist zusätzlich eine Gewichtung der Kanten gegeben und nach einer bezüglich dieser Gewichtung minimalen Steinerbaumpackung gesucht, so sprechen wir vom gewichteten Steinerbaumpackungs-Problem. Die Motivation zum Studium dieses Problems kommt aus dem Entwurf elektronischer Schaltungen. Ein dort auftretendes Teilproblem ist das sogenannte Verdrahtungsproblem, das im wesentlichen darin besteht, gegebene Punktmengen unter bestimmten Nebenbedingungen und Optimalitätskriterien auf einer Grundfläche zu verbinden. Wir studieren das Steinerbaumpackungs-Problem aus polyedrischer Sicht und definieren ein Polyeder, dessen Ecken genau den Steinerbaumpackungen entsprechen. Anschlie\ss end versuchen wir, dieses Polyeder durch gute'' beziehungsweise facetten-definierenden Ungleichungen zu beschreiben. Basierend auf diesen Ungleichungen entwickeln wir ein Schnittebenenverfahren. Die Lösung des Schnittebenenverfahrens liefert eine untere Schranke für die Optimallösung und dient als Grundlage für die Entwicklung guter Primalheuristiken. Wir haben das von uns implementierte Schnittebenenverfahren an einem Spezialfall des Verdrahtungsproblems, dem sogenannten Switchbox-Verdrahtungsproblem, getestet und vielversprechende Ergebnisse erzielt. T3 - ZIB-Report - TR-92-04 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4894 ER - TY - GEN A1 - Leimkuhler, Benedict A1 - Reich, Sebastian T1 - The Numerical Solution of Constrained Hamiltonian Systems. N2 - A Hamiltonian system subject to smooth constraints can typically be viewed as a Hamiltonian system on a manifold. Numerical computations, however, must be performed in $ R^n$. In this paper, canonical transformations from ``Hamiltonian differential--algebraic equations'' to ODEs in Euclidean space are considered. In \S2, canonical parameterizations or local charts are developed and it is shown how these can be computed in a practical framework. In \S3 we consider the construction of unconstrained Hamiltonian ODE systems in the space in which the constraint manifold is embedded which preserve the constraint manifold as an integral invariant and whose flow reduces to the flow of the constrained system along the manifold. It is shown that certain of these unconstrained Hamiltonian systems force Lyapunov stability of the constraint--invariants, while others lead to an unstable invariant. In \S4, we compare various projection techniques which might be incorporated to better insure preservation of the constraint--invariants in the context of numerical discretization. Numerical experiments illustrate the degree to which the constraint and symplectic invariants are maintained under discretization of various formulations. {\bf Keywords:} differential--algebraic equations, Hamiltonian systems, canonical discretization schemes. {\bf AMS(MOS):} subject classification 65L05. T3 - ZIB-Report - SC-92-16 KW - differential algebraic equations KW - Hamiltonian system KW - canonical discretization schemes Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-868 ER - TY - GEN A1 - Möller, H. Michael T1 - On decomposing systems of polynomial equations with finitely many solutions. N2 - This paper deals with systems of $m$ polynomial equations in $n$ unknown, which have only finitely many solutions. A method is presented which decomposes the solution set into finitely many subsets, each of them given by a system of type \begin{displaymath} f_1(x_1)=0, f_2(x_1,x_2)=0,...,f_n(x_1,...,x_n)=0. \end{displaymath} The main tools for the decomposition are from ideal theory and use symbolical manipulations. For the ideal generated by the polynomials which describe the solution set, a lexicographical Gröbner basis is required. A particular element of this basis allows the decomposition of the solution set. A recursive application of these decomposition techniques gives finally the triangular subsystems. The algorithm gives even for non-finite solution sets often also usable decompositions. {\bf Keywords:} Algebraic variety decomposition, Gröbner bases, systems of nonlinear equations. T3 - ZIB-Report - SC-92-15 KW - Algebraic variety decomposition KW - Groebner bases KW - systems of nonlinear equations Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-851 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Erdmann, Bodo A1 - Kornhuber, Ralf T1 - Adaptive Multilevel-Methods in 3-Space Dimensions. N2 - We consider the approximate solution of selfadjoint elliptic problems in three space dimensions by piecewise linear finite elements with respect to a highly non-uniform tetrahedral mesh which is generated adaptively. The arising linear systems are solved iteratively by the conjugate gradient method provided with a multilevel preconditioner. Here, the accuracy of the iterative solution is coupled with the discretization error. as the performance of hierarchical bases preconditioners deteriorate in three space dimensions, the BPX preconditioner is used, taking special care of an efficient implementation. Reliable a-posteriori estimates for the discretization error are derived from a local comparison with the approximation resulting from piecewise quadratic elements. To illustrate the theoretical results, we consider a familiar model problem involving reentrant corners and a real-life problem arising from hyperthermia, a recent clinical method for cancer therapy. T3 - ZIB-Report - SC-92-14 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-843 ER - TY - GEN A1 - Gatermann, Karin T1 - Computation of Bifurcation Graphs. N2 - The numerical treatment of Equivariant parameter-dependent onlinear equation systems, and even more its automation requires the intensive use of group theory. This paper illustrates the group theoretic computations which are done in the preparation of the numerical computations. The bifurcation graph which gives the bifurcation subgroups is determined from the interrelationship of the irreducible representations of a group and its subgroups. The Jacobian is transformed to block diagonal structure using a modification of the transformation which transforms to block diagonal structure with respect to a supergroup. The principle of conjugacy is used everywhere to make symbolic and numerical computations even more efficient. Finally, when the symmetry reduced problems and blocks of Jacobian matrices are evaluated numerically, the fact that the given representation is a quasi-permutation representation is exploited automatically. T3 - ZIB-Report - SC-92-13 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-837 ER - TY - GEN T1 - Jahresbericht 1991 T3 - Jahresbericht - 1991 KW - Annual Report Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9825 SN - 0934-5892 ER - TY - GEN A1 - Lubich, Christian A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Engstler, Ch. T1 - MEXX - Numerical Software for the Integration of Constrained Mechanical Systems. N2 - MEXX (short for MEXanical systems eXtrapolation integrator) is a Fortran code for time integration of constrained mechanical systems. MEXX is suited for direct integration of the equations of motion in descriptor form. It is based on extrapolation of a time stepping method that is explicit in the differential equations and linearly implicit in the nonlinear constraints. It only requires the solution of well--structured systems of linear equations which can be solved with a computational work growing linearly with the number of bodies, in the case of multibody systems with few closed kinematic loops. Position and velocity constraints are enforced throughout the integration interval, whereas acceleration constraints need not be formulated. MEXX has options for time--continuous solution representation (useful for graphics) and for the location of events such as impacts. The present article describes MEXX and its underlying concepts. T3 - ZIB-Report - SC-92-12 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-823 ER - TY - GEN A1 - Bixby, Robert E. T1 - Das Implementieren des Simplex- Verfahrens: Die Startbasis. N2 - Dieses Paper enthält die ersten beiden Teile einer geplanten Serie von Aufsätzen über die $CPLEX^2$-Implementierung des Simplex- Verfahrens. Der erste Teil ist eine Einführung: er liefert eine kurze Beschreibung des Verfahrens für Probleme mit beschränkten Variablen, zusammen mit einer relativ ausführlichen Diskussion der numerischen Eigenschaften der Netlib-Probleme. Diese Probleme bilden auch das Fundament der rechnerischen Untersuchungen in den folgenden Teilen. Der zweite Teil enthält die Hauptergebnisse dieses Papers, eine Beschreibung der Methode, die von CPLEX verwendet wird, um eine Startbasis zu konstruieren. T3 - ZIB-Report - SC-92-11 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-816 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Polyhedral Investigations. N2 - Let $G=(V,E)$ be a graph and $T\subseteq V$ be a node set. We call an edge set $S$ a Steiner tree with respect to $T$ if $S$ connects all pairs of nodes in $T$. In this paper we address the following problem, which we call the weighted Steiner tree packing problem. Given a graph $G=(V,E)$ with edge weights $w_e$, edge capacities $c_e, e \in E,$ and node sets $T_1,\ldots,T_N$, find edge sets $S_1,\ldots,S_N$ such that each $S_k$ is a Steiner tree with respect to $T_k$, at most $c_e$ of these edge sets use edge $e$ for each $e\in E$, and such that the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from the routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the Steiner tree packing Problem from a polyhedral point of view and define an appropriate polyhedron, called the Steiner tree packing polyhedron. The goal of this paper is to (partially) describe this polyhedron by means of inequalities. It turns out that, under mild assumptions, each inequality that defines a facet for the (single) Steiner tree polyhedron can be lifted to a facet-defining inequality for the Steiner tree packing polyhedron. The main emphasis of this paper lies on the presentation of so-called joint inequalities that are valid and facet-defining for this polyhedron. Inequalities of this kind involve at least two Steiner trees. The classes of inequalities we have found form the basis of a branch & cut algorithm. This algorithm is described in our companion paper SC 92-09. T3 - ZIB-Report - SC-92-08 KW - cutting planes KW - Facets KW - Packing KW - polyhedron KW - Steiner tree Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-786 ER - TY - GEN A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiners Trees: A Cutting Plane Algorithm and Computational Results. N2 - In this paper we describe a cutting plane algorithm for the Steiner tree packing problem. We use our algorithm to solve some switchbox routing problems of VLSI-design and report on our computational experience. This includes a brief discussion of separation algorithms, a new LP-based primal heuristic and implementation details. The paper is based on the polyhedral theory for the Steiner tree packing polyhedron developed in our companion paper SC 92-8 and meant to turn this theory into an algorithmic tool for the solution of practical problems. T3 - ZIB-Report - SC-92-09 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-792 ER - TY - GEN A1 - Jünger, Michael A1 - Martin, Alexander A1 - Reinelt, Gerhard A1 - Weismantel, Robert T1 - Quadratic 0/1 Optimization and a Decomposition Approach for the Placement of Electronic Circuits. N2 - The placement in the layout design of electronic circiuts consists of finding a non- overlapping assignment of rectangular cells to positions on the chip so what wireability is guaranteed and certain technical constraints are met.This problem can be modelled as a quadratic 0/1- program subject to linear constraints. We will present a decomposition approach to the placement problem and give results about $NP$-hardness and the existence of $\varepsilon$-approximative algorithms for the involved optimization problems. A graphtheoretic formulation of these problems will enable us to develop approximative algorithms. Finally we will present details of the implementation of our approach and compare it to industrial state of the art placement routines. {\bf Keywords:} Quadratic 0/1 optimization, Computational Complexity, VLSI-Design. T3 - ZIB-Report - SC-92-10 KW - quadratic 0/1 optimization KW - computational complexity KW - VLSI-Design Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-803 ER - TY - GEN A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of RamanSpectroscopy. N2 - Models for occupation dynamics in discrete quantum systems lead to large or even infinite systems of ordinary differential equations. Some new mathematical techniques, developed for the simulation of chemical processes, make a numerical solution of countable systems of ordinary differential equations possible. Both, a basic physical concept for the construction of such systems and the structure of the numerical tools for solving them are presented. These conceptual aspects are illustrated by a simulation of an occupation process from spectroscopy. In this example the structures of rotation spectra observed in infrared spectroscopy are explained and some possibilities for an extension of the model are shown. T3 - ZIB-Report - SC-92-07 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-778 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Wittum, Gabriel T1 - Discretization and Iterative Solution of Convection Diffusion Equations. N2 - We propose an extended box method which turns out to be a variant of standard finite element methods in the case of pure diffusion and an extension of backward differencing to irregular grids if only convective transport is present. Together with the adaptive orientation proposed in a recent paper and a streamline ordering of the unknowns, this discretization leads to a highly efficient adaptive method for the approximation of internal layers in the case of large local Peclet numbers. T3 - ZIB-Report - SC-92-06 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-762 ER - TY - GEN A1 - Lang, Jens A1 - Walter, Artur T1 - A Finite Element Method Adaptive in Space and Time for Nonlinear Reaction-Diffusion- Systems. N2 - Large scale combustion simulations show the need for adaptive methods. First, to save computation time and mainly to resolve local and instationary phenomena. In contrast to the widespread method of lines, we look at the reaction- diffusion equations as an abstract Cauchy problem in an appropriate Hilbert space. This means, we first discretize in time, assuming the space problems solved up to a prescribed tolerance. So, we are able to control the space and time error separately in an adaptive approach. The time discretization is done by several adaptive Runge-Kutta methods whereas for the space discretization a finite element method is used. The different behaviour of the proposed approaches are demonstrated on many fundamental examples from ecology, flame propagation, electrodynamics and combustion theory. {\bf Keywords:} initial boundary value problem, Rothe- method, adaptive Runge-Kutta method, finite elements, mesh refinement. {\bf AMS CLASSIFICATION:} 65J15, 65M30, 65M50. T3 - ZIB-Report - SC-92-05 KW - initial boundary value problem KW - Rothe method KW - adaptive Runge-Kutta method KW - finite elements KW - mesh refinement Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-755 ER - TY - GEN A1 - Grötschel, Martin T1 - Discrete Mathematics in Manufacturing. N2 - Manufacturing is a topic that provides rich opportunities for important mathematical contributions to real-world problems. The purpose of this paper is to show, by means of several examples, where and how mathematical problems of a discrete nature arise in manufacturing and to demonstrate the savings and improvements that can be achieved by employing the techniques of combinatorial optimization. The topics covered range from the design phase of a product (e. g.,routing, placement and via minimization in VLSI design), the control of CNC machines (e. g., drilling and plotting), to the management of assembly lines, storage systems and whole factories. We also point out difficulties in the modelling of complex situations and outline the algorithmic methods that are used for the solution of the mathematical problems arising in manufacturing. {\bf Key words:} discrete mathematics , combinatorial optimization, applications to manufacturing. T3 - ZIB-Report - SC-92-03 KW - discrete mathematics KW - combinatorial optimization KW - applications to manufacturing Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-738 ER - TY - GEN A1 - Wakabayashi, Yoshiko T1 - Medians of Binary Relations: Computational Complexity. N2 - Let $\Re$ be the set of all binary relations on a finite set $N$ and $d$ be the symmetric difference distance defined on $\Re$. For a given profile $\Pi = (R_1,...,R_m) \in R^m$, a relation $R* \in \Re $ that minimizes the function $\sum^m_{k=1} d(R_k,R) $ is called a median relation of $\Pi$. A number of problems occuring in the social sciences, in qualitative data analysis and in multicriteria decision making can be modelled as problems of finding medians of a profile of binary relations. In these contexts the profile $\Pi$ represents collected data (preferences, similarities, games) and the objective is that of finding a median relation of $\Pi$ with some special feature (representing e. g., consensus of preferences, clustering of similar objects, ranking of teams, etc.). In this paper we analyse the computational complexity of all such problems in which the median is required to satisfy one or more of the properties: reflexitivity, symmetry, antisymmetry, transitivity and completeness. We prove that whenever transitivity is required (except when symmetry and completeness are also simultaneously required) then the corresponding median problem is $NP$-hard. In some cases we prove that they remain $NP$-hard when the profile $\Pi$ has a fixed number of binary relations. T3 - ZIB-Report - SC-92-04 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-746 ER - TY - GEN A1 - Schöffel, Klaus T1 - Computational Chemistry Software at ZIB. N2 - The following report intends to provide a survey over the computational chemistry molecular structure software installed on the supercomputers CRAY X-MP/216 and CRAY Y-MP2E/164 at ZIB. It shows what kind of problems can be tackled with the existing chemistry software, which covers a wide range of ab initio, semiempirical, molecular mechanics, and dynamics applications. T3 - ZIB-Report - TR-92-02 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4879 ER - TY - GEN A1 - Ackermann, Jörg A1 - HELFRICH, K. T1 - Radius of Convergence of the 1/Z-Expansion for Diatomic Molecules: The Ground State of the Isoelectronic H2Sequence. N2 - Using the perturbational-variational Rayleigh-Ritz matrix formalism, the 1/Z-expansion for the ground state of the isoelectronic $H_2$ sequence in the range of the internuclear distance $0.2\le R \le 9.0$ is calculated. Also lower bounds of the radius of convergence, based on Kato's theory of linear operators, are given. The numerical results of the 1/Z-expansion can be compared with the exact results and do not converge in the whole R-range. This behavior is in qualitative agreement with the lower bounds for the radius of convergence and enlights some still open properties of 1/Z- expansions for this sequence in the literature. {\bf PACS:} 31.15 + q; 31.20 Di; 31.20 Tz. T3 - ZIB-Report - SC-92-02 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-721 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Yserentant, Harry T1 - A Basic Norm Equivalence for the Theory of Multilevel Methods. N2 - Subspace decompositions of finite element spaces based on $L2$-like orthogonal projections play an important role for the construction and analysis of multigrid like iterative methods. Recently several authors proved the equivalence of the associated discrete norms with the $H^1$-norm. The present report gives an elementary, self-contained derivation of this result which is based on the use of $ K$-functionals known from the theory of interpolation spaces. {\bf Keywords:} multilevel methods, nonuniform meshes, optimal convergence rates. {\bf AMS(MOS) Subject classifications:} 65N55, 65N30, 65N50. T3 - ZIB-Report - SC-92-01 KW - multilevel methods KW - nonuniform meshes KW - optimal convergence rates Y1 - 1992 U6 - https://doi.org/10.1007/BF01388699 N1 - No preprint available ER - TY - GEN A1 - Nowak, Ulrich A1 - Weimann, Lutz T1 - A Family of Newton Codes for Systems of Highly Nonlinear Equations. N2 - This report presents new codes for the numerical solution of highly nonlinear systems. They realize the most recent variants of affine invariant Newton Techniques due to Deuflhard. The standard method is implemented in the code NLEQ1, whereas the code NLEQ2 contains a rank reduction device additionally. The code NLEQ1S is the sparse version of NLEQ1, i.e. the arising linear systems are solved with sparse matrix techniques. Within the new implementations a common design of the software in view of user interface and internal modularization is realized. Numerical experiments for some rather challenging examples illustrate robustness and efficiency of algorithm and software. T3 - ZIB-Report - TR-91-10 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4855 ER - TY - GEN A1 - Schöffel, Klaus T1 - Ab initio Quantum Chemical Calculations with GAMESS-UK and GAUSSIAN90 Program Packeges - A Comparison -. N2 - Two commercially available molecular electronic structure software packages GAUSSIAN90 and GAMESS-UK are compared. Basis for this comparison is a benchmark suite which is designed to highlight the typical range of calculations commonly performed by the ab initio computational chemist. T3 - ZIB-Report - TR-92-01 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4867 ER - TY - GEN A1 - Hohmann, Andreas T1 - An Adaptive Continuation Method for Implicitly Defined Surfaces. N2 - A new method for the numerical aproximation of an implicitly defined surface is presented. It is a generalization of the Euler- Gauss-Newton method for implicitly defined (one- parameter) curves to the case of (two-parameter) surfaces. The basic task in the more general case is an efficient combination of modern CAGD techniques (such as triangular Bernstein-Bzier patches and the nine parameter Hermite interpolant) and the rank deficient Gauss-Newton method. T3 - ZIB-Report - SC-91-20 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-705 ER - TY - GEN A1 - Godsil, C. D. A1 - Grötschel, Martin A1 - Welsh, D. J. A. T1 - Combinatorics in Statistical Physics T3 - ZIB-Report - SC-91-19 Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-694 ER - TY - GEN A1 - Wulkow, Michael T1 - Adaptive Treatment of Polyreactions in Weighted Sequence Spaces. N2 - Countable systems of ordinary differential equations appear frequently in chemistry, physics, biology and statistics. They can be considered as ordinary differential equations in sequence spaces. In this work, a fully adaptive algorithm for the computational treatment of such systems is developed. The method is based on a time discretization of an abstract Cauchy problem in Hilbert space and a discrete Galerkin approach for the discretization of the arising stationary subproblems. The Galerkin method uses orthogonal functions of a discrete variable, which are generated by certain weight functions. A theory of countable systems in the associated weighted sequence spaces is developed as well as a theory of the Galerkin method. The Galerkin equations are solved adaptively either by use of analytical properties of the orthogonal functions or by an appropriate numerical summation. The resulting algorithm CODEX is applied to examples of technological interest, in particular from polymer chemistry. T3 - ZIB-Report - SC-91-17 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-673 ER - TY - GEN A1 - Ackermann, Jörg A1 - Wulkow, Michael T1 - The Treatment of Macromolecular Processes with Chain-Length-Dependent Reaction Coefficients - An Examplefrom Soot Formation. N2 - The description of chain length distributions in macromolecular reaction kinetics leads to so-called countable systems of differential equations. In particular, when the appearing reaction rate coefficients depend on the chain length of the reacting macromolecules itself, an efficient numerical treatment of these systems is very difficult. Then even the evaluation of the right-hand side of the system can become prohibitively expensive with respect to computing time. In this paper we show how the discrete Galerkin method can be applied to such problems. The existing algorithm CODEX is improved by use of a multiplicative error correction scheme for time discretization and a new type of numerical preprocessing by means of a Gauss summation. Both ideas are exemplary for a wide class of approximation types and are described very briefly here. The new numerical techniques are tested on an example from soot formation, where the coagulation of molecules is modeled in terms of reaction coefficients depending on the surface of the particles and their collision frequency. T3 - ZIB-Report - SC-91-18 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-682 ER - TY - GEN A1 - Schöpf, R. A1 - Deuflhard, Peter T1 - OCCAL: A mixed symbolic- numeric Optimal Control CALculator. N2 - The numerical solution of optimal control problems by indirect methods (such as multiple shooting or collocation) requires a considerable amount of analytic calculation to establish a numerically tractable system. These analytic calculations, though being rather tedious in realistic examples, are nowadays mostly still done by hand-and thus prone to calculation errors. The paper aims at automating this analytic processing to a reasonable extent by means of a modern symbolic manipulation language (here: REDUCE). In its present stage of development the package OCCAL (mnemotechnically for \underline{O}ptimal \underline{C}ontrol \underline{CAL}culator) permits an interactive use, covering tasks like automatic determination of control and, in case of a singular control, of its order. In simpler problems, the present version of OCCAL automatically produces the full subroutine input for a MULtiple shooting code (MULCON) with adaptive numerical CONtinuation. In more complicate problems where singular sub-arcs may occur or where the sequence of sub-arcs of the optimal trajectory is unclear OCCAL is a significant help in reducing analytic pre-processing. Numerical examples illustrate the performance of OCCAL/MULCON. T3 - ZIB-Report - SC-91-13 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-638 ER - TY - GEN A1 - Hoppe, Ronald H. W. A1 - Kornhuber, Ralf T1 - Adaptive Multilevel - Methods for Obstacle Problems. N2 - We consider the discretization of obstacle problems for the Laplacian by piecewise linear finite elements. Assuming that the discrete problems are reduced to a sequence of linear problems by suitable active set strategies, the linear problems are solved iteratively by preconditioned c-g iterations. The proposed preconditioners are treated theoretically as abstract additive Schwarz methods and are implemented as truncated hierarchical basis preconditioners. To allow for local mesh refinement we derive semi-local and local a posteriori error estimates, providing lower and upper estimates for the discretization error. The theoretical results are illustrated by numerical computations. T3 - ZIB-Report - SC-91-16 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-667 ER - TY - GEN A1 - Gatermann, Karin A1 - Hohmann, Andreas T1 - Hexagonal Lattice Dome - Illustration of a Nontrivial Bifurcation Problem. N2 - The deformation of a hexagonal lattice dome under an external load is an example of a parameter dependent system which is equivariant under the symmetry group of a regular hexagon. In this paper the mixed symbolic-numerical algorithm SYMCON is applied to analyze its steady state solutions automatically showing their different symmetry and stability properties. T3 - ZIB-Report - SC-91-08 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-587 ER - TY - GEN A1 - Ziegler, Günter M. T1 - On the Difference Between Real and Complex Arrangements. N2 - If $B$ is an arrangement of linear complex Hyperplanes in $C^d$, then the following can be constructed from knowledge of its intersection lattice: (a) the cohomology groups of the complement [Br], (b) the cohomology algebra of the complement [OS], (c) the fundamental group of the complement, if $d\le2$, (d) the singularity link up to homeomorphism, if $d\le3$, (e) the singularity link up to homotopy type [ZZ]. If $B'$ is, more generally, a 2-arrangement in $ R^{2d}$ (an arrangement of real subspaces of codimension 2 with even-dimensional intersections), then the intersection lattice still determines (a) the cohomology groups of the complement [GM] and (e) the homotopy type of the singularity link [ZZ]. We show, however, that for 2-arrangements the data (b), (c) and (d) are not determined by the intersection lattice. They require the knowledge of extra information on sign patterns, which can be computed as determinants of linear relations, or (equivalently) as linking coefficients in the sense of knot theory. T3 - ZIB-Report - SC-91-14 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-648 ER - TY - GEN A1 - Ziegler, Günter M. A1 - Zivaljevic, R. T. T1 - Homotopy Types of Subspace Arrangements via Diagrams of Spaces. N2 - We prove combinatorial formulas for the homotopy type of the union of the subspaces in an (affine, compactified affine, spherical or projective) subspace arrangement. From these formulas we derive results of Goresky & MacPherson on the homology of the arrangement and the cohomology of its complement. The union of an arrangement can be interpreted as the direct limit of a diagram of spaces over the intersection poset. A closely related space is obtained by taking the homotopy direct limit of this diagram. Our method consists in constructing a combinatorial model diagram over the same poset, whose homotopy limit can be compared to the original one by usual homotopy comparison results for diagrams of spaces. T3 - ZIB-Report - SC-91-15 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-658 ER - TY - GEN A1 - Schmidt, Frank T1 - An Adaptive Approach to the Numerical Solution of Fresnel's Wave Equation. N2 - An adaptive approach to the numerical solution of the wave propagation in integrated optics devices with 1D cross sections is described. First, Fresnel's approximation of the exact wave equation resulting from Maxwell's equations is considered. A criterion to estimate the validity of this approximation is derived. Fresnel's wave equation being formally equivalent to Schroedinger's equation uniquely defines an initial-boundary-value problem, which is solved numerically by a stepwise calculation of the propagating field. Discretization in longitudinal direction first with stepsize control leads to a stationary subproblem for the transversal field distribution, which is then handled by an adaptive finite element method. Thus full adaptivity of the algorithm is realized. The numerical examples are concentrated on taper structures playing an essential role in integrated optics devices for telecommunication systems. T3 - ZIB-Report - SC-91-12 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-628 ER - TY - GEN A1 - Sturmfels, Bernd A1 - Ziegler, Günter M. T1 - Extension Spaces of Oriented Matriods. N2 - We study the space of all extensions of a real hyperplane arrangement by a new pseudo- hyperplane, and, more generally, of an oriented matroid by a new element. The question whether this space has the homotopy type of a sphere is a special case of the "Generalized Baues Problem" of Billera, Kapranov & Sturmfels, via the Bohne-Dress Theorem on zonotopal tilings. We prove that the extension space is spherical for the class of strongly euclidean oriented matroids. This class includes the alternating matroids and all oriented matroids of rank at most 3 or of corank at most 2. In general it is not even known whether the extension space is connected. We show that the subspace of realizable extensions is always connected but not necessarily spherical. T3 - ZIB-Report - SC-91-11 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-618 ER - TY - GEN A1 - Ziegler, Günter M. T1 - Higher Bruhat Orders and Cyclic Hyperplane Arrangements. N2 - We study the higher Bruhat orders $B(n,k)$ of Manin & Schechtman [MaS] and - characterize them in terms of inversion sets, - identify them with the posets $U(C^{n+1,r},n+1)$ of uniform extensions of the alternating oriented matroids $C^{n,r}$ for $r:=n-k$ (that is, with the extensions of a cyclic hyperplane arrangement by a new oriented pseudoplane), - show that $B(n,k)$ is a lattice for $k =1$ and for $r\le 3$, but not in general, - show that $B(n,k)$ is ordered by inclusion of inversion sets for $k=1$ and for $r\le 4$. However, $B(8,3)$ is not ordered by inclusion. This implies that the partial order $B_\subseteq (n,k)$ defined by inclusion of inversion sets differs from $B(n,k)$ in general. We show that the proper part of $B_\subseteq (n,k)$ is homotopy equivalent to $S^{r-2}$. Consequently, - $B(n,k)\simeq S^{r-2}$ for $k=1$ and for $r\le 4$. In contrast to this, we find that the uniform extension poset of an affine hyperplane arrangement is in general not graded and not a lattice even for $r=3$, and that the proper part is not always homotopy equivalent to $S^{r(M)-2}$. T3 - ZIB-Report - SC-91-10 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-607 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Pöhle, Uwe A1 - Schmidt, B. Ch. A1 - Weyer, J. T1 - Die Ausbreitung von HIV/AIDS in Ballungsgebieten. N2 - The rapidly increasing number of AIDS cases requires a realistic estimation of the future development of the HIV/AIDS disease. For that purpose we develop a large system of coupled nonlinear differential equations describing simultaneously the dynamics of the development of the disease, the population size, the gender and age structure. A set of 1650 coupled equations are linked by balanced parameters. The balancing procedure is described by a set of (formally) 2,178,000 additional algebraic conditions. As the considered system is stiff, it requires new special extrapolation methods combined with techniquees of dynamical sparsing for the solution of sparsely filled systems. According to our simulations we expect 19,0,000 deaths caused by AIDS in the Federal Republic of Germany (former territories) in the year 2000. Such an epidemical spread would tie up about 4-7 percent of the actual health care workers. T3 - ZIB-Report - TR-91-09 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4844 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - A Sharpened Condition Number Estimate for the BPX Preconditioner of Elliptic Finite Element Problems on Highly Nonuniform Triangulations. N2 - In this paper it is shown that for highly nonuniformly refined triangulations the condition number of the BPX preconditioner for elliptic finite element problems grows at most linearly in the depth of refinement. This is achieved by viewing the computational available version of the BPX preconditioner as an abstract additive Schwarz method with exact solvers. {\bf AMS CLASSIFICATION:} 65F10, 65F35, 65N20, 65N30. T3 - ZIB-Report - SC-91-09 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-596 ER - TY - GEN A1 - Deuflhard, Peter A1 - Potra, Florian T1 - A Refined Gauss-Newton- Mysovskii Theorem. N2 - The present paper contains a generalization of a refinement of the Newton- Mysovskii theorem, recently obtained by the authors, to the case of Gauss-Newton procedures for solving nonlinear least-squares problems with full Jacobians. Invariant sufficient conditions are given that ensure the convergence of the Gauss-Newton iterates towards a solution of the problem, as well as the uniqueness of that solution in an explicitely defined neighborhood. It is shown by a counter- example that the results do not carry over to the rank deficient case. T3 - ZIB-Report - SC-91-04 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-541 ER - TY - GEN A1 - Hoppe, Ronald H. W. A1 - Kornhuber, Ralf T1 - Multilevel Preconditioned CG-Iterations for Variational Inequalities. N2 - We consider such variational inequalities which either describe obstacle problems or result from an implicit time discretization of moving boundary problems of two phase Stefan type. Based on a discretization in space by means of continuous, piecewise linear finite elements with respect to a nested hierarchy of triangulations, in both cases we use iterative processes consisting of inner and outer iterations. The outer iterations are either active set strategies or generalized Newton methods while the inner iterations are preconditioned cg- iterations with multilevel preconditioners. T3 - ZIB-Report - SC-91-06 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-561 ER - TY - GEN A1 - Gajewski(Ed.), Herbert A1 - Deuflhard, Peter A1 - Markowich(ed.), A. T1 - Tagung NUMSIM '91 5.-08. Mai 1991. Collected Abstracts and Papers. N2 - NUMSIM 91 fand vom 6.-08. Mai 1991 im Wissenschaftlichen Kommunikations- & Konferenz- Zentrum der Humboldt-Universität in Gosen bei Berlin statt. Im Mittelpunkt dieses Seminars standen Probleme der numerischen Simulation von Ladungstransport- und Technologieprozessen der Mikro- und Optoelektronik. Es führte Spezialisten der physikalischen Modellierung, der numerischen Mathematik und mathematischen Analysis sowie Nutzer von Simulationsprogrammen aus dem deutschsprachigen Raum zusammen. Ziel war die Vermittlung und der Austausch von Erfahrungen, die Diskussion gemeinsamer Aufgabenstellungen und Projekte und - in Anbetracht der deutschen Vereinigung nicht zuletzt - das gegenseitige Kennen- und Verstehenlernen. T3 - ZIB-Report - TR-91-08 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4838 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - An Adaptive Multilevel Approach to Parabolic Equations in Two Space Dimensions. N2 - A new adaptive multilevel approach for linear partial differential equations is presented, which is able to handle complicated space geometries, discontinuous coefficients, inconsistent initial data. Discretization in time first (Rothe's method) with order and stepsize control is perturbed by an adaptive finite element discretization of the elliptic subproblems, whose errors are controlled independently. Thus the high standards of solving adaptively ordinary differential equations and elliptic boundary value problems are combined. A theory of time discretization in Hilbert space is developed which yields to an optimal variable order method based on a multiplicative error correction. The problem of an efficient solution of the singularly perturbed elliptic subproblems and the problem of error estimation for them can be uniquely solved within the framework of preconditioning. A Multilevel nodal basis preconditioner is derived, which allows the use of highly nonuniform triangulations. Implementation issues are discussed in detail. Numerous numerical examples in one and two space dimensions clearly show the significant perspectives opened by the new algorithmic approach. Finally an application of the method is given in the area of hyperthermia, a recent clinical method for cancer therapy. T3 - ZIB-Report - TR-91-07 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4821 ER - TY - GEN A1 - Fiedler, Bernold A1 - Scheurle, J. T1 - Discretization of Homoclinic Orbits, Rapid Forcing and "Invisible" Chaos. N2 - One-step discretizations of order $p$ and step size $\varepsilon$ of ordinary differential equations can be viewed as time-$\varepsilon$ maps of \begin{displaymath} \dot{x} (t) = f(\lambda ,x(t)) + \varepsilon^p g(\varepsilon,\lambda,t/\varepsilon,x(t)), x \in R^N,\lambda \in R, \end{displaymath} where $g$ has period $\varepsilon$ in $t$. This is a rapidly forced nonautonomous system. We study the behavior of a homoclinit orbit $\Gamma$ for $\varepsilon = 0, \lambda =0$, under discretization. Under generic assumptions we show that $\Gamma$ becomes transverse for positive $\in$. The transversality effects are estimated from above to be exponentially small in $\in$. For example, the length $l(\varepsilon$) of the parameter interval of $\lambda$ for which $\Gamma$ persists can be estimated by \begin{displaymath} l(\varepsilon)\le Cexp(-2\pi\eta/\varepsilon), \end{displaymath} where $C,\eta$ are positive constants. The coefficient $\eta$ is related to the minimal distance from the real axis of the poles of $\Gamma(t)$ in the complex time domain. Likewise, the region where complicated, "chaotic" dynamics prevail is estimated to be exponentially small, provided $x \in R^2$ and the saddle quantity of the associated equilibrium is nonzero. Our results are visualized by high precision numerical experiments. The experiments show that, due to exponential smallness, homoclinic transversality becomes pratically invisible under normal circumstances, already for only moderately small step size. {\bf Keywords:} Homoclinic orbit, ordinary differential equations, discretization, transversality, averaging, exponential smallness, chaos. {\bf Subject Classifications:} (AMS): 34C15, 34C35, 58F14, 65L60 T3 - ZIB-Report - SC-91-05 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-552 ER - TY - GEN A1 - Lang, Jens A1 - Walter, Artur T1 - An Adaptive Discontinuous Finite Element Method for the Transport Equation. N2 - In this paper we introduce a discontinuous finite element method. In our approach, it is possible to combine the advantages of finite element and finite difference methods. The main ingredients are numerical flux approximation and local orthogonal basis functions. The scheme is defined on arbitrary triangulations and can be easily extended to nonlinear problems. Two different error indicators are derived. Especially the second one is closely connected to our approach and able to handle arbitrary variing flow directions. Numerical results are given for boundary value problems in two dimensions. They demonstrate the performance of the scheme, combined with the two error indicators. {\bf Key words:} neutron transport equation, discontinuous finite element, adaptive grid refinement. {\bf Subject classifications:} AMS(MOS) 65N30, 65M15. T3 - ZIB-Report - SC-91-07 KW - neutron transport equation KW - discontinuous finite element KW - adaptive grid refinement Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-579 ER - TY - GEN A1 - Schöffel, Klaus T1 - Computational Chemistry Software for CRAY X-MP/2. N2 - The following report intends to provide a survey over the computational chemistry molecular structure software installed on CRAY X-MP/24 at ZIB. It shows what kind of problems can be tackled with the existing chemistry software, which covers a wide range of ab initio, semiempirical, molecular mechanics, and dynamics applications. T3 - ZIB-Report - TR-91-06 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4816 ER - TY - GEN A1 - Griewank, Andreas T1 - Sequential Evaluation of Adjoints and Higher Derivative Vectors by Overloading and Reverse Accumulation. N2 - Most nonlinear computations require the evaluation of first and higher derivatives of vector functions defined by computer programs. It is shown here how vectors of such partial derivatives can be obtained automatically and efficiently if the computer language allows overloading (as is or will be the case for C++, PASCAL-XSC, FORTRAN90, and other modern languages). Here, overloading facilitates the extension of arithmetic operations and univariate functions from real or complex arguments to truncated Taylor-series (or other user- defined types), and it generates instructions for the subsequent evaluation of adjoints. Similar effects can be achieved by precompilation of FORTRAN77 programs. The proposed differentiation algorithm yields gradients and higher derivatives at a small multiple of the run-time and RAM requirement of the original function evaluation program. {\bf Keywords:} Automatic Differentiation, Chain Rule, Overloading, Taylor Coefficients, Gradients, Hessians, Reverse Accumulation, Adjoint Equations. {\bf Abbreviated title:} Automatic Differentiation by Overloading. T3 - ZIB-Report - SC-91-03 KW - Automatic Differentiation KW - Chain Rule KW - Overloading KW - Taylor Coefficients KW - Gradients KW - Hessians KW - Reverse Accumulation KW - Adjoint Equations Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-539 ER - TY - GEN T1 - Jahresbericht 1990 T3 - Jahresbericht - 1990 KW - Annual Report Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9831 SN - 0934-5892 ER - TY - GEN A1 - Gottschewski, Jürgen T1 - Supercomputing During the German Reunification. N2 - The success of the German Reunification requires a unique migration from the traditional Eastern Block system to a modern free society. The successful migration must include a shift from a low state of the art in technology to the high level of science and technology present in the Western Community. The role of supercomputing in this transition will include leading the process of organizational change in research and development. The paper contains a short overview on the current state of this evolution, on the currently used political and administrative tools to keep this evolution on track, and on the influence on the Konrad-Zuse-Zentrum, which is, as a Berlin institution, in the geographical and cultural center of this transformation. T3 - ZIB-Report - TR-91-05 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4803 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Roitzsch, Rainer T1 - Self Adaptive Computation of the Breakdown Voltage of Planar pn-Junctions with Multistep Field Plates. N2 - The breakdown voltage highly depends on the electric field in the depletion area whose computation is the most time consuming part of the simulation. We present a self adaptive Finite Element Method which reduces dramatically the required computation time compared to usual Finite Difference Methods. A numerical example illustrates the efficiency and reliability of the algorithm. T3 - ZIB-Report - SC-91-02 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-525 ER - TY - GEN A1 - Lang, Jens T1 - An Adaptive Finite Element Method for Convection-Diffusion Problems by Interpolation Techniques. N2 - For adaptive solution of convection- difussion problems with the streamline-diffusion finite element method, an error estimator based on interpolation techniques is developed. It can be shown that for correctness of this error estimator a restriction of the maximum angle is to be sufficient. Compared to usual methods, the adaptive process leads to more accurate solutions at much less computational cost. Numerical tests are enclosed. {\bf Keywords: } Adaptive finite elements, convection- diffusion equation, internal and boundary layers, streamline-diffusion. {\bf Subject Classifications:} AMS(MOS): 65N15, 65N30 T3 - ZIB-Report - TR-91-04 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4795 ER - TY - GEN A1 - Noelle, Sebastian W. C. T1 - On the Limits of Operator Splitting: Numerical Experiments for the Complex Burgers Equation. N2 - A high resolution Godunov-type method is developed and applied to a two-dimensional version of the Burgers equation. On one-dimensional testproblems the scheme is second order accurate for smooth flow and resolves discontinuities sharply. On two-dimensional problems, however, large numerical oscillations are introduced when discontinuities traveling obliquely to the grid directions are present. These oscillations are caused by a Strang- type operator splitting, and cannot be eliminated using flux limiters or small timesteps. {\bf Keywords:} High resolution methods, Godunovs method, operator splitting, complex Burgers equation. {\bf AMS:} 35: A40, L45, L60, L65, L, 67. 65: M05, M10. T3 - ZIB-Report - TR-91-03 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4789 ER - TY - GEN A1 - Lügger, Joachim A1 - Dalitz, Wolfgang T1 - Verteilung mathematischer Software mittels elektronischer Netze: Die elektronische Softwarebibliothek eLib. N2 - Mit zunehmender Dezentralisierung im Bereich des Wissenschaftlichen Rechnens steigt auch der Bedarf an Softwarequellen qualitativ hochwertiger mathematischer Algorithmen. Für den Software- und Informationsaustausch wird die Einrichtung öffentlicher, elektronischer Softwarebibliotheken vorgeschlagen. Am Beispiel der eLib des ZIB werden die notwendigen technischen Konzepte, die u.a. auch in den heutigen Gegebenheiten der technischen Kommunikation begründet sind, diskutiert. Die eLib ist fenster- und menüorientiert aufgebaut und folglich im Dialog sehr einfach zu benutzen. Sie kann aber auch mit ihrer Kommandosprache allein auf dem Wege über elektronische Post abgefragt werden. Über die eLib sind, nach dem Verbund mit den Netzbibliotheken NetLib und Reduce-NetLib jetzt etwa 6000 mathematische Programme und allgemeine Dokumente verfügbar. Das Dienstleistungsangebot der eLib setzt Beiträge aus einer aktiven Benutzergemeinschaft voraus. Es besteht die Hoffnung, daß durch den öffentlichen Softwareaustausch sich Entwickler und Anwender wechselseitig in ihrer Arbeit befruchten. T3 - ZIB-Report - TR-91-02 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4774 ER - TY - GEN A1 - Bornemann, Folkmar A. A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - KASKADE - Numerical Experiments. N2 - The C-implementation of KASKADE, an adaptive solver for linear elliptic differential equations in 2D, is object of a set of numerical experiments to analyze the use of resources (time and memory) with respect to numerical accuracy. We study the dependency of the reliability, robustness, and efficiency of the program from the parameters controlling the algorithm. T3 - ZIB-Report - TR-91-01 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4762 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - An Adaptive Multilevel Approach to Parabolic Equations III. N2 - Part III of the paper is devoted to the construction of an adaptive FEM solver in two spatial dimensions, which is able to handle the singularly perturbed elliptic problems arising from discretization in time. The problems of error estimation and multilevel iterative solution of the linear systems - both uniformly well behaved with respect to the time step - can be solved simultaneously within the framework of preconditioning. A multilevel nodal basis preconditioner able to handle highly nonuniform meshes is derived. As a numerical example an application of the method to the bioheat-transfer equation is included. {\bf AMS CLASSIFICATION:} 65F10, 65F35, 65M50, 65M60, 65N30. T3 - ZIB-Report - SC-91-01 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-519 ER - TY - GEN A1 - Walter, Artur T1 - Sparse Secant Methods for the Iterative Solution of Large Nonsymmetric Linear Systems. N2 - A variety of secant methods has been revisited in view of the construction of iterative solvers for large nonsymmetric linear systems $ Ax = b $ stemming from the discretization of convection diffusion equations. In the first section, we tried to approximate $ A ^{-1} $ directly. Since the sparsity structure of A- is not known, additional storage vectors are needed during the iteration. In the next section, an incomplete factorization $ LU $ of $ A $ is the starting point and we tried to improve this easy invertible approximation of $ A $. The update is constructed in such a way that the sparsity structure of $ L $ and $ U $ is maintained. Two different sparsity preserving updates are investigated from theoretical and practical point of view. Numerical experiments on discretized PDEs of convection diffusion type in 2- D with internal layers and on "arbitrary" matrices with symmetric sparsity structure are given. {\bf Key words:} nonsymmetric linear system, sparse secant method, Broyden's method, incomplete factorization. T3 - ZIB-Report - SC-90-20 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-483 ER - TY - GEN A1 - Wulkow, Michael A1 - Deuflhard, Peter T1 - Towards an Efficient Computational Treatment of Heterogeneous Polymer Reactions. N2 - The discrete Galerkin method developed by the authors has turned out to be an efficient tool for the computational treatment of very large scale ODE systems arising in polyreaction kinetics. Up to now, this approach has been worked out in detail for homogeneous polymer reactions. The present paper deals with one line of possible extensions of the method to the case of so-called heterogeneous processes, which may appear e. g. in smog reactions. The associated mathematical models involve reaction coefficients depending on the chain length of the reacting polymer. The herein suggested extension is worked out in some detail on the basis of the earlier paper. In addition, a numerical example describing polymer degradation is included. T3 - ZIB-Report - SC-90-01 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-292 ER - TY - GEN A1 - Giloi, Wolfgang K. T1 - Konrad Zuses Plankalkül als Vorläufer moderner Programmier-modelle. (Vortrag) T3 - ZIB-Report - TR-90-13 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4759 ER - TY - GEN A1 - Nowak, Ulrich A1 - Weimann, Lutz T1 - GIANT - A Software Package for the Numerical Solution of Very Large Systems of Highly Nonlinear Equations. N2 - This report presents the final realization and implementation of a global inexact Newton method proposed by Deuflhard. In order to create a complete piece of software, a recently developed iterative solver (program GBIT) due to Deuflhard, Freund, Walter is adapted and serves as the standard iterative linear solver. Alternative linear iterative solvers may be adapted as well, e.g. the widely distributed code GMRES. The new software package GIANT (Global Inexact Affine Invariant Newton Techniques) allows an efficient and robust numerical solution of very large scale highly nonlinear systems. Due to the user friendly interface and its modular design, the software package is open for an easy adaptation to specific problems. Numerical experiments for some selected problems illustrate performance and usage of the package. T3 - ZIB-Report - TR-90-11 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4746 ER - TY - GEN A1 - Caprasse, H. A1 - Demaret, J. A1 - Gatermann, Karin A1 - Melenk, Herbert T1 - Power-Law Type Solutions of Fourth-Order Gravity N2 - We study the power-law type solutions of the fourth order field equations derived from a generic quadratic Lagrangian density in the case of multidimensional Bianchi I cosmological models. All the solutions of the system of algebraic equations have been found, using computer algebra, from a search of the Groebner bases associated to it. While, in space dimension $ d = 3 $ , the Einsteinian Kasner metric is still the most general power-law type solution, for $ d > 3 $ , no solution, other than the Minkowski space-time, is common to the three systems of equations associated with the three contributions to the Lagrangian density. In the case of a pure Riemann-squared contribution (suggested by a recent calculation of the effective action for the heterotic string), the possibility exists to realize a splitting of the $ d $-dimensional space into a ( $ d - 3 $)-dimensional internal space and a physical 3- dimensional space, the latter expanding in time as a power bigger than 2 (about 4.5 when $ d = 9 $). T3 - ZIB-Report - SC-90-18 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-466 ER - TY - GEN A1 - Wang, Daoliu T1 - Symplectic Difference Schemes for Perturbed Hamiltonian Systems. N2 - In this paper we consider symplectic difference schemes for perturbed Hamiltonian systems of integrable ones, which can cover many important problems. Symplectic difference schemes for general Hamiltonian systems can also be used to these problems. But the perturbation property has not been paid proper attention to, which is important in the method proposed here. Numerical simulation shows that, for this method the time step size can be taken quite large and the qualitative property , such as preserving invariant tori, is also better than usual symplectic difference schemes. T3 - ZIB-Report - SC-90-17 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-456 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Stüben, Hinnerk T1 - Vectorization and Parallelization of Irregular Problems via Graph coloring. N2 - Efficient implementations of irregular problems on vector and parallel architectures are generally hard to realize. An important class of problems are Gauß-Seidel iteration schemes applied to irregular data sets. The unstructured data dependences arising there prevent restructuring compilers from generating efficient code for vector or parallel machines. It is shown, how to structure the data dependences by decomposing the underlying data set using graph coloring techniques and by specifying a particular execution order already on the algorithm level. Methods to master the irregularities originating from different types of tasks are proposed. An application is given and some open issues and future developments are discussed. T3 - ZIB-Report - SC-90-16 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-443 ER - TY - GEN A1 - Roitzsch, Rainer A1 - Kornhuber, Ralf T1 - BOXES - a Program to Generate Triangulations from a Rectangular Domain Description. N2 - BOXES computes a triangulation from a 2D domain description which consists of an arbitrary set of rectangles. Each rectangle may have attributes to control the triangulating process, define subdomain classes, or specify boundary conditions. The output of the program can be used as a coarse grid for KASKADE or one of its variants. Additional features are extensive checking of the user input, graphical display, and simple editing. T3 - ZIB-Report - TR-90-09 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4738 ER - TY - GEN A1 - Ackermann, Jörg A1 - Wulkow, Michael T1 - MACRON - A Program Package for Macromalecular Reaction Kinetics. N2 - This paper presents the new program package MACRON for the simulation of macromolecular kinetics including standard chemical reactions. Such problems lead to countable (possibly) infinite systems of ordinary differential equations (CODE's), which are numerically treated by the so-called discrete Galerkin method here. By a chemical compiler the required analytical preprocessing is performed, such that the complete reaction system, standard kinetics as well as macromolecular reactions, can be entered in the chemical formalism. Typical macromolecular reaction steps are chain addition, termination, chain transfer and degradation (cracking). In order to ensure efficiency and reliability, high sophisticated numerical routines are built within the package. MACRON can be used without a detailed knowledge of the used numerical methods. As an illustration the application of MACRON to some realistic problems is presented. T3 - ZIB-Report - SC-90-14 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-423 ER - TY - GEN A1 - Wulkow, Michael A1 - Ackermann, Jörg T1 - Numerical Treatment of Polyreactions - Recent Developments. N2 - The mathematical modeling of macromolecular reactions leads to countable (possibly infinite) systems of ordinary differential equations (CODE's). This paper reviews two recent developments of the so-called discrete Galerkin method, which has been developed for the numerical treatment of countable systems, which arise e.g. in polymer chemistry. The first approach can be considered as a method of lines with moving basis functions and has been implemented recently in the program package MACRON. The second type of the Galerkin method is characterized by a so-called outer time discretization of the complete problem and an appropriate and efficient solution of the arising subproblems. This method is realized in the research code CODEX. T3 - ZIB-Report - SC-90-15 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-439 ER - TY - GEN A1 - Wulkow, Michael T1 - Numerical Treatment of Countable Systems of Ordinary Differential Equations. N2 - Countable systems of ordinary differential equations appear frequently in chemistry, physics, biology and medicine. They can be considered as ordinary differential equations in sequence spaces. In this work, a full adaptive algorithm for the computational treatment of such systems is developed. The method combines time discretization with extrapolation in Hilbert spaces with a discrete Galerkin approach as discretization of the stationary subproblems. The Galerkin method is based on orthogonal functions of a discrete variable , which are generated by certain weight functions. A theory of countable systems in the associated weighted sequence spaces is developed as well as a theory of the Galerkin method. The Galerkin equations can be assembled either by use of analytical properties of the orthogonal functions or numerically by a multilevel summation algorithm. The resulting algorithm CODEX is applied to many examples of technological interest, in particular from polymer chemistry. T3 - ZIB-Report - TR-90-08 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4728 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - An Adaptive Multilevel Approach to Parabolic Equations II. N2 - In continuation of part I this paper develops a variable-order time discretization in Hilbert space based on a multiplicative error correction. Matching of time and space errors as explained in part I allows to construct an adaptive multilevel discretization of the parabolic problem. In contrast to the extrapolation method in time, which has been used in part I, the new time discretization allows to separate space and time errors and further to solve fewer elliptic subproblems with less effort, which is essential in view of the application to space dimension greater than one. Numerical examples for space dimension one are included which clearly indicate the improvement. T3 - ZIB-Report - SC-90-13 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-410 ER - TY - GEN A1 - Walter, Artur T1 - Improvement of Incomplete Factorizations by a Sparse Secant Method. N2 - In the present paper, the improvement of an incomplete factorization of a non-symmetric matrix A is discussed. Starting from the ideas of sparsity preserving quasi-Newton methods, an algorithm is developed which improves the approximation of A by the incomplete factorization maintaining the sparsity structure of the matrices. No renumbering of the unknowns or the admittance of additional fill-in is necessary. The linear convergence of the algorithm is proved under the assumption, that $ L $ and $ U $* have the same sparsity structure and an incomplete factorization with some reasonable approximation property exits. In combination with this algorithm, the method of incomplete factorization and its several modifications are applicable to a wider class of problems with improved convergence qualities. This is shown by a numerical example. {\bf Key Words:} non-symmetric linear system, sparse secant method, incomplete factorization. AMS(MOS) {\bf Subject Classifications:} 65F10, 65N20, 65N30. T3 - ZIB-Report - SC-90-12 KW - non-symmetric linear systems KW - sparse secant method KW - incomplete factorization Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-401 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Roitzsch, Rainer T1 - Self Adaptive FEM Simulation of Reverse Biased pn-Junctions. N2 - The potential distribution of reverse biased pn-junctions can be described by a double obstacle problem for the Laplacian. This problem is solved by a self adaptive Finite Element Method involving automatic termination criteria for the iterative solver, local error estimation and local mesh refinement. Special attention is paid to the efficient resolution of the geometries typically arising in semiconductor device simulation. The algorithm is applied to a reverse biased pn- junction with multi-step field plate and stop- electrode to illustrate its efficiency and reliability. T3 - ZIB-Report - SC-90-10 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-389 ER - TY - GEN A1 - Deuflhard, Peter T1 - Zuses Werk weiterdenken. (Vortrag) T3 - ZIB-Report - TR-90-07 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4717 ER - TY - GEN A1 - Gatermann, Karin A1 - Hohmann, Andreas T1 - Symbolic Exploitation of Symmetry in Numerical Path-following. N2 - Parameter-dependent systems of nonlinear equations with symmetry are treated by a combination of symbolic and numerical computations. In the symbolic part of the algorithm the complete analysis of the symmetry occurs, and it is here where symmetrical normal forms, symmetry reduced systems, and block diagonal Jacobians are computed. Given a particular problem, the symbolic algorithm can create and compute through the list of possible bifurcations thereby forming a so-called tree of decisions correlated to the different types of symmetry breaking bifurcation points. The remaining part of the algorithm deals with the numerical pathfollowing based on the implicit reparametrisation as suggested and worked out by Deuflhard/Fiedler/Kunkel. The symmetry preserving bifurcation points are computed using recently developed augmented systems incorporating the use of symmetry. {\bf Keywords:} pathfollowing, mixed symbolic-numeric algorithm, parameter-dependent, nonlinear systems, linear representations. T3 - ZIB-Report - SC-90-11 KW - pathfollowing KW - mixed symbolic-numeric algorithm KW - parameter dependent KW - nonlinear systems KW - linear representations Y1 - 1990 N1 - No preprint available; the article appeared in: IMPACT Comput. Sci. Eng. 3 (1991) pp. 330-365 ER - TY - GEN A1 - Deuflhard, Peter A1 - Potra, Florian T1 - Asymptotic Mesh Independence of Newton-Galerkin Methods via a Refined Mysovskii Theorem. N2 - The paper presents a theoretical characterization of the often observed asymptotic mesh independence of Newton's method, which means that Newton's method applied to discretized operator equations behaves essentially the same for all sufficiently fine discretizations. The theory does not need any uniform Lipschitz assumptions that were necessary in comparable earlier treatments. The refined Newton-Mysovskii theorem, which will be of interest in a wider context, gives both existence and uniqueness of the solution and quadratic convergence for sufficiently good starting points. Attention is restricted to Galerkin approximations even though similar results should hold for finite difference methods - but corresponding proofs would certainly be more technical. As an illustrative example, adaptive 1-D collocation methods are discussed. T3 - ZIB-Report - SC-90-09 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-379 ER - TY - GEN A1 - Chevalier, C. A1 - Melenk, Herbert A1 - Warnatz, J. T1 - Automatic Generation of Reaction Mechanisms for Description of Oxidation of Higher Hydrocarbons. N2 - Oxidation mechanisms even for rather simple hydrocarbons like heptane consist due to the occurrence of many isomeric structures of thousands of reactions of hundreds of species. The automatic generation of these reaction mechanisms using artificial intelligence means is described. Results are presented for n-heptane-air mixtures, where a hand-written reaction mechanism tested against experimental data is available. T3 - ZIB-Report - SC-90-08 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-361 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Einführung in die Numerische Mathematik. N2 - Diese Vorlesung ist eine Einführung in die Numerische Mathematik als einem der drei Bereiche (neben den Naturwissenschaften und der Informatik) des am besten mit dem Begriff Scientific Computing charakterisierten Forschungsgebietes. Aufgabe dieser relativ jungen Wissenschaft ist die Entwicklung von Rechenverfahren für Probleme aus den Naturwissenschaften mit Hilfe mathematischer Methoden. T3 - ZIB-Report - TR-90-06 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4704 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Wulkow, Michael T1 - Recent Developments in Chemical Computing. N2 - The paper surveys three aspects of chemical computing, which seem to play a role in recent developments. First, extrapolation methods for the numerical treatment of differential- algebraic equations are introduced. The associated extrapolation code LIMEX has reached a certain level of sophistication, which makes it a real competitor to the elsewhere widely used multi-step code DASSL of Petzold. Second, adaptive methods of lines for partial differential equations such as those arising in combustion problems are treated. Both static and dynamic regridding techniques are discussed in some detail. Finally, some new ideas about the treatment of the kinetic equations arising from polymer reactions are presented. The new feature of the suggested approach is the application of a Galerkin procedure using sets of orthogonal polynomials over a discrete variable (which, of course, in the case of polymer reactions is the polymer degree). The new approach may open the door to a new reliable low dimensional treatment of complex polymer reactions. T3 - ZIB-Report - SC-90-07 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-359 ER - TY - GEN A1 - Deuflhard, Peter A1 - Freund, R. A1 - Walter, Artur T1 - Fast Secant Methods for the Iterative Solution of Large Nonsymmetric Linear Systems. N2 - A family of secant methods based on general rank-1 updates has been revisited in view of the construction of iterative solvers for large non- Hermitian linear systems. As it turns out, both Broydens "good" and "bad" update techniques play a special role - but should be associated with two different line search principles. For Broydens "bad" update technique, a minimum residual principle is natural - thus making it theorectically comparable with a series of well-known algorithms like GMRES. Broydens "good" update technique, however, is shown to be naturally linked with a minimum "next correction" principle - which asymptotically mimics a minimum error principle. The two minimization principles differ significantly for sufficiently large system dimension. Numerical experiments on discretized PDE's of convection diffusion type in 2-D with internal layers give a first impression of the possible power of the derived "good" Broyden variant. {\bf Key Words:} nonsymmetric linear system, secant method, rank-1 update, Broydens method, line search, GMRES. AMS(MOS) {\bf Subject Classifications:} 65F10, 65N20. T3 - ZIB-Report - SC-90-05 KW - nonsymmetric linear systems KW - secant method KW - rank-1 update KW - Broyden's method KW - line search KW - GMRES Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-330 ER - TY - GEN A1 - Wang, Daoliu T1 - On Symplectic Difference Schemes for Hamiltonian Systems. N2 - Symplectic difference schemes have been shown to be a right formalism for numerical computation of Hamiltonian systems. They are suitable to long time computation and of good qualitative properties. These properties are ensured by the fact that a symplectic difference scheme approximating to a time-independent Hamiltonian system can be regarded as a perturbed time-dependent Hamiltonian system of the original one. That is, a solution of a symplectic difference scheme is a solution of a certain perturbed time dependent Hamiltonian system evaluated at discrete (time) points. This is the main result of the paper. Moreover, linear symplectic difference schemes approximating to a linear time-independent Hamiltonian system can be regarded as a perturbed time-independent Hamiltonian system. So it has all properties that a linear Hamiltonian system has. Based on these results, stochastic webs and chaos in symplectic difference schemes are also discussed. They will appear in numerical simulation for Hamiltonian systems, even with one degree of freedom. T3 - ZIB-Report - SC-90-06 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-345 ER - TY - GEN T1 - Jahresbericht 1989 T3 - Jahresbericht - 1989 KW - Annual Report Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9847 SN - 0934-5892 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - An Adaptive Multilevel Approach to Parabolic Equations I. General Theory & 1D-Implementation. N2 - A new adaptive multilevel approach for parabolic PDE's is presented. Full adaptivity of the algorithm is realized by combining multilevel time discretization, better known as extrapolation methods, and multilevel finite element space discretization. In the theoretical part of the paper the existence of asymptotic expansions in terms of time-steps for single-step methods in Hilbert space is established. Finite element approximation then leads to perturbed expansions, whose perturbations, however, can be pushed below a necessary level by means of an adaptive grid control. The theoretical presentation is independent of space dimension. In this part I of the paper details of the algorithm and numerical examples are given for the 1D case only. The numerical results clearly show the significant perspectives opened by the new algorithmic approach. T3 - ZIB-Report - SC-90-04 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-320 ER - TY - GEN A1 - Hege, Hans-Christian T1 - Datenabhängigkeitsanalyse und Programmtransformationen auf CRAY-Rechnern mit dem Fortran-Präprozessor fpp N2 - The FORTRAN preprocessor fpp in the newly introduced Autotasking System of CRAY Research allows automatic vectorization and parallelization on basis of a data dependence analysis. An introduction into data dependence analysis is given, showing how data dependence graphs unveil opportunities for program transformations like vectorization and concurrentization. The report contains a complete description of the preprocessors functionality, its options and directives for increasing the effectiveness of the dependence analyzer and steering the code transformations. Finally, some advice is given for the practical use of fpp on CRAY computers. T3 - ZIB-Report - TR-90-04 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4685 ER - TY - GEN T1 - CRAY-Handbuch. Einführung in die Benutzung der CRAY X-MP unter UNICOS 5.1 N2 - Das CRAY-Handbuch des ZIB beschreibt nach einer grundlegenden bersicht detailliert die Handhabung von UNICOS-Dateien, die Verwendung von UNICOS-Kommandos und schließlich die (für Benutzer allein zugelassene) Ausführung von Batchjobs auf der CRAY. Neben der Erreichbarkeit der CRAY über das TCP/IP-Netz werden die Compiler FORTRAN, PASCAL und C beschrieben und schließlich auf die Optimierung der Rechenzeit ebenso wie auf die Fehlersuche eingegangen. Ein umfangreicher Anhang führt bereitgestellte Programmpakete, weiterführende Literatur, Zahlenbereiche und Zeichendarstellung an der CRAY auf. T3 - ZIB-Report - TR-90-03 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4679 ER - TY - GEN A1 - Gatermann, Karin T1 - Symbolic solution of polynomial equation systems with symmetry. N2 - Systems of polynomial equations often have symmetry. The Buchberger algorithm which may be used for the solution ignores this symmetry. It is restricted to moderate problems unless factorizing polynomials are found leading to several smaller systems. Therefore two methods are presented which use the symmetry to find factorizing polynomials, decompose the ideal and thus decrease the complexitiy of the system a lot. In a first approach projections determine factorizing polynomials as input for the solution process, if the group contains reflections with respect to a hyperplane. Two different ways are described for the symmetric group Sm and the dihedral group Dm. While for Sm subsystems are ignored if they have the same zeros modulo G as another subsystem, for the dihedral group Dm polynomials with more than two factors are generated with the help of the theory of linear representations and restrictions are used as well. These decomposition algorithms are independent of the finally used solution technique. We used the REDUCE package Groebner to solve examples from CAPRASSE, DEMARET and NOONBURG which illustrate the efficiency of our REDUCE program. A short introduction to the theory of linear representations is given. In a second approach problems of another class are transformed such that more factors are found during the computation; these transformations are based on the theory of linear representations. Examples illustrate these approaches. The range of solvable problems is enlarged significantly. T3 - ZIB-Report - SC-90-03 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-311 ER - TY - GEN A1 - Deuflhard, Peter T1 - Global Inexact Newton Methods for Very Large Scale Nonlinear Problems. N2 - Newton methods for nonlinear problems are known to require the solution of a sequence of linear problems of the same type. For very large scale problems, as understood herein, the arising linear systems can only be solved by iterative methods. Then Newtons iteration appears as outer iteration. The question of interest will be to control the accuracy of the inner iteration such that the convergence speed of Newtons method is preserved. The purpose of the paper is to combine the concept of inexact Newton methods with the concept of the affine invariant exact Newton methods - which is important for problems with ill- conditioned Jacobian matrices (such as typical 2-D or 3-D discretized partial differential equations). T3 - ZIB-Report - SC-90-02 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-303 ER - TY - GEN A1 - Maierhöfer, Gerhard A1 - Skorobohatyj, Georg T1 - Implementierung von parallelen Versionen der Gleichungslöser EULEX und EULSIM auf Transputern. N2 - Im vorliegenden Bericht wird die Parallelisierung zweier numerischer Algorithmen zur Lösung gewöhnlicher Differentialgleichungssysteme 1.Ordnung (explizite und semi-implizite Euler- Diskretisierung und $h$-Extrapolation) beschrieben. Implementiert wurden die Algorithmen mit OCCAM2 unter TDS (Transputer Development System) mit bis zu 4 Transputern T800. Meßwerte für die erreichten Beschleunigungen werden anhand mehrer Beispiele von Differentialgleichungs-systemen angegeben. {\bf Schlüsselwörter:} Adaptive, parallele Systeme; OCCAM2; Transputer; numerische Gleichungslöser; Euler-Diskretisierung; $h$-Extrapolation. T3 - ZIB-Report - TR-90-02 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4666 ER - TY - GEN A1 - Gatermann, Karin T1 - Gruppentheoretische Konstruktion von symmetrischen Kubaturformeln. N2 - $G$-invariant cubature formulas for numerical integration over n-dimensional, $G$- invariant integration regions are computed symbolically. The nodes are the common zeros of some $d$-orthogonal polynomials which build an $H$-basis of an ideal. Approaches for these polynomials depending on parameters are made with the help of the theory of linear representations of a group $G$. This theory is also used for the effective computation of necessary conditions which determines the parameters. Another approach uses invariant theory and gröbner bases. T3 - ZIB-Report - TR-90-01 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4652 ER - TY - GEN A1 - Yserentant, Harry T1 - Two Preconditioners Based on the Multi-Level Splitting of Finite Element Spaces. N2 - The hierarchical basis preconditioner and the recent preconditioner of BRAMBLE, PASCIAK and XU are derived and analyzed within a joint framework. This discussion elucidates the close relationship between both methods. Special care is devoted to highly nonuniform meshes; our theory is based exclusively on local properties like the shape regularity of the finite elements. T3 - ZIB-Report - SC-89-09 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-274 ER - TY - GEN A1 - Hoppe, Ronald H. W. T1 - Numerical Solution of Multicomponent Alloy Solidification by Multi-Grid Techniques. N2 - The solidification of an $ N $-component alloy is described by an initial boundary value problem for a system of degenerate parabolic equations modelling heat conduction and mass diffusion. Discretizing implicitly in time and by piecewise linear finite elements in the space variables, at each time step the solution of a system of quasivariational inequalities is required. For the numerical solution of that system, a multi-grid algorithm is developed by making use of game theoretic concepts and duality arguments from convex analysis. Finally, the efficiency of the algorithm is demonstrated by displaying numerical results for a ternary alloy. T3 - ZIB-Report - SC-89-10 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-285 ER - TY - GEN A1 - Maierhöfer, Gerhard A1 - Skorobohatyj, Georg T1 - Implementierung des parallelen TRAPEX auf Transputern. N2 - Der folgende Bericht ist eine Ergänzung des ZIB Technical Report TR 88-05. Entsprechend wird hier nicht auf die grundsätzlichen Fragen der Parallelisierbarkeit des sequentiellen TRAPEX eingegangen. Diese sind im TR 88-5 erörtert, die dort beschriebenen Algorithmen (vertikale und horizontale Parallelisierung) werden auch für die Transputerarchitektur verwendet. Meßergebnisse sind im letzten Teil angefügt. T3 - ZIB-Report - TR-89-08 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4649 ER - TY - GEN A1 - Grammel, Martin A1 - Maierhöfer, Gerhard A1 - Skorobohatyj, Georg T1 - Trapex in POOL-Implementierung eines numerischen Algorithmus in einer parallelen objektorientierten Sprache. N2 - Die Parallelisierung eines vorhandenen sequentiellen Programmes erfolgt im allgemeinen in der Weise, daß es auf Grund einer Analyse der Datenabhängigkeiten in mehrere parallel ausführbare Teile zerlegt wird, die ihrerseits sequentiell ablaufen und untereinander Daten austauschen. Eine parallele Programmiersprache sollte diese Vorgehensweise unterstützen, indem sie Sprachmittel zur Verfügung stellt, mittels derer sich die Modularisierung und Kommunikation bequem formulieren läßt. Nun läßt sich prinzipiell jede vorhandene sequentielle Programmiersprache um solche Konstrukte erweitern; günstiger in Hinblick auf die Strukturierung eines parallelen Programmes erscheint es aber möglicherweise, eine solche Programmiersprache zu verwenden, die die genannten Konzepte als elementare zur Verfügung stellt. Dies ist offensichtlich bei objektorientierten Programmiersprachen der Fall. Im vorliegenden Bericht wird an Hand eines Beispiels - TRAPEX -, das in POOL-T implementiert wurde, untersucht, inwieweit eine objektorientierte Sprache zur effektiven Programmierung eines numerischen Algorithmus geeignet ist. {\bf Key Words:} parallele objektorientierte Programmiersprache, Message Passing, Abstract Data Typing, Klassenhierarchi, Modul-Import-Mechanismus, Client/Server-Prinzip, Load Balancing, adaptive numerische Algorithmen, Ordnungs- und Schrittweitensteuerung, Romberg-Quadratur. T3 - ZIB-Report - TR-90-05 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4696 ER - TY - GEN A1 - Maierhöfer, Gerhard T1 - Ein paralleler adaptiver Algorithmus für die numerische Integration. N2 - Der Bericht ist die Ausarbeitung eines Vortrages, der auf dem Transputer Anwender Treffen (TAT'89) im September 1989 gehalten wurde. Es wird die Parallelisierung und Implementierung eines adaptiven Algorithmus zur numerischen Integration (Romberg Quadratur) beschrieben. Ausgewählte Meßergebnisse sind enthalten. {\bf Keywords:} Numerischer Algorithmus, Romberg Quadratur, paralleler adaptiver Algorithmus, dynamische Lastverteilung und Prozessorzahl, lokaler Speicher, Nearest-Neighbour-Architektur, Transputer, TDS, OCCAM2. T3 - ZIB-Report - SC-89-08 KW - numerischer Algorithmus KW - Romberg Quadratur KW - paralleler adaptiver Algorithmus KW - dynamische Lastverteilung und Prozessorzahl KW - lokaler Speicher KW - Near Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-265 ER - TY - GEN A1 - Bornemann, Folkmar A. T1 - Adaptive multilevel discretization in time and space for parabolic partial differential equations. N2 - The present paper developes an adaptive multilevel approach for parabolic PDE's - as a first step, for one linear scalar equation. Full adaptivity of the algorithm is conceptually realized by simultaneous multilevel discretization in both time and space. Thus the approach combines multilevel time discretization, better known as extrapolation methods, and multilevel finite element space discretization such as the hierarchical basis method. The algorithmic approach is theoretically backed by careful application of fundamental results from semigroup theory. These results help to establish the existence of asymptotic expansions (in terms of time-steps) in Hilbert space. Finite element approximation then leads to perturbed expansions, whose perturbations, however, can be pushed below a necessary level by means of an adaptive grid control. The arising space grids are not required to satisfy any quasi- uniformity assumption. Even though the theoretical presentation is independent of space dimension details of the algorithm and numerical examples are given for the 1-D case only. For the 1-D elliptic solver, which is used, an error estimator is established, which works uniformly well for a family of elliptic problems. The numerical results clearly show the significant perspectives opened by the new algorithmic approach. T3 - ZIB-Report - TR-89-07 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4638 ER - TY - GEN A1 - Huamo, Wu A1 - Shuli, Yang T1 - MmB-A New Class of Accurate High Resolution Schemes for Conservation Laws in Two Dimensions. N2 - In this paper we present the MmB schemes, which preserve the local maximum and minimum bounds of the initial data in the smallest union of mesh elements of previous time step containing the domain of dependence of the solution on the mesh element with center at point $ P $\ under consideration. In 1-D, the MmB schemes are almost identical with TVD schemes. As well-known, there is no second-order TVD scheme in 2-D, nevertheless, we present here two classes of 2-D second-order accurate MmB-schemes. It is proved that 1-D discrete MmB (or TVD) and 1-D semi-discrete TVD schemes may have second-order accuracy at (nonsonic) critical points, but cannot be of uniformly second-order accurate in the whole neighborhood of the critical points. New accurate high resolution flux limiters are suggested. Numerical results for 1-D and 2-D test problems are given. {\bf Keywords:} Difference scheme, TVD, MmB, flux limiter. T3 - ZIB-Report - SC-89-06 KW - difference scheme KW - TVD KW - MmB KW - flux limiter Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-248 ER - TY - GEN A1 - Budde, Uwe A1 - Wulkow, Michael T1 - Computation of Molecular Weight Distributions for Free Radical Polymerization Systems. N2 - Modeling of free radical polymerization leads to very large and usually stiff systems of ordinary differential equations which cannot be solved directly in an efficient way. This paper presents the application of a new approach called discrete Galerkin method to a realistic example - the polymerization of methyl methacrylate(MMA). The method is characterized by a Galerkin approximation on the basis of orthogonal polynomials of a discrete variable which represents the polymer degree. It allows the efficient computation of solutions of complete kinetic schemes with time- or moment-dependent reaction coefficients by reducing the complexity to a few differential equations. The approximation error can be controlled by an error estimation. In the case of MMA polymerization a reduction of computational effort by a factor of about 25 compared to a standard method can be obtained for the quasi-steady-state approximation of the model. In addition solutions of the instationary kinetic scheme can be easily computed. T3 - ZIB-Report - SC-89-07 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-253 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - Implementation of Portable Standard LISP for the SPARC Processor. N2 - The SPARC processor is a RISC (Reduced Instruction Set Computer) microcomputer, built into the SUN4 workstations. Since RISC processors are very well-suited for LISP processing, the implementation of a dialect of LISP (Portable Standard LISP, PSL) boded well for a great speed-up in comparison with other types of microcomputers. A first approach was done at The RAND Corporation in Santa Monica, which was derived from classical processor types like MC68000 or VAX. At the Konrad- Zuse-Zentrum für Informationstechnik Berlin (ZIB) that initial implementation was redesigned in order to adapt PSL to the specific features of the SPARC processor. The present implementation, in some parts, is very close to Cray PSL version also done in ZIB. Some timing informations are given in the appendix. T3 - ZIB-Report - TR-89-06 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4625 ER - TY - GEN A1 - Huamo, Wu T1 - On the Possible Accuracy of TVD Schemes. N2 - The paper presents a detailed analysis of the possible accuracy available for TVD schemes in one dimension with emphasis to the semi-discrete 1-D TVD schemes. The analysis shows that the widely accepted statement [1] of degeneration of accuracy at critical points for TVD schemes should be corrected. We have theorem: TVD schemes using flux limiters $ \varphi $ of the form [1], [2] may be second-order accurate at critical points if $ \varphi $ (3) + $ \varphi $(-1) = 2, but cannot be uniformly second-order accurate in the whole neighborhood of critical point. If $ \varphi $(1) = 1, then the TVD schemes are second-order accurate in the region of smooth solutions sufficiently far from the critical points. Two ways are suggested to improve the accuracy. Numerical example is given. {\bf Keywords:} Semi-discrete schemes, TVD, flux limiter, degeneration of accuracy. T3 - ZIB-Report - SC-89-03 KW - semi-discrete schemes KW - TVD KW - flux limiter KW - degeneration of accuracy Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-212 ER - TY - GEN A1 - Möller, H. Michael T1 - Multivariate Rational Interpolation: Reconstruction of Rational Functions. N2 - In this paper we consider the problem of reconstructing a multivariate rational function, when only its values at sufficiently many points are known. We use for the reconstruction of bivariate rational functions a bivariate rational interpolation operator investigated by Siemaszko [7] and a new one, compare both by examples in a Computer Algebra system, and present their multivariate generalizations. {\bf Keywords:} Multivariate rational interpolation, reconstruction, symbolic computation. T3 - ZIB-Report - SC-89-04 KW - Multivariante rational interpolation KW - reconstruction KW - symbolic computation Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-227 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Roitzsch, Rainer T1 - On Adaptive Grid Refinement in the Presence of Internal or Boundary Layers. N2 - We propose an anisotropic refinement strategy which is specially designed for the efficient numerical resolution of internal and boundary layers. This strategy is based on the directed refinement of single triangles together with adaptive multilevel grid orientation. It is demonstrated by several numerical examples that compared to usual methods, the new anisotropic refinement ends up in more stable and more accurate solutions at much less computational cost. {\bf Keywords:} Adaptive finite elements, directed refinement, adaptive grid orientation, convection diffusion equation, internal and boundary layers. T3 - ZIB-Report - SC-89-05 KW - adaptive finite elements KW - directed refinement KW - adaptive grid orientation KW - convection diffusion equation KW - internal and boundary layers Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-230 ER - TY - GEN A1 - Roitzsch, Rainer T1 - KASKADE Programmer's Manual. N2 - The Programmers Manual contains the documentation of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The interfaces of all modules are described. T3 - ZIB-Report - TR-89-05 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4617 ER - TY - GEN A1 - Roitzsch, Rainer T1 - KASKADE User's Manual. N2 - The Users Manual contains an introduction to the usage of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The manual includes a description of all commands, a simple recipe to define a new problem by changing the KASKADE source and a complete example. T3 - ZIB-Report - TR-89-04 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4605 ER - TY - GEN T1 - Jahresbericht 1988 T3 - Jahresbericht - 1988 KW - Annual Report Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9858 SN - 0934-5892 ER - TY - GEN A1 - Zha, Hongyuan T1 - Restricted Singular Value Decomposition of Matrix Triplets. N2 - In this paper we introduce the concept of restricted singular values (RSV's) of matrix triplets. A theorem concerning the RSV's of a general matrix triplet $ (A,B,C) $, where $ A \in C^{m\times n} $, $B\in C^{m\times p} $ and $ C\in C^{q\times n} $, which is called restricted singular value decomposition (RSVD) of matrix triplets, is derived. This result generalizes the wellknown SVD, GSVD and the recently proposed product induced SVD (PSVD). Connection of RSV's with the problem of determination of matrix rank under restricted perturbation is also discussed. {\bf Keywords:} Matrix rank, singular values, generalized singular values, product induced singular values, restricted singular values, matrix decompositions. T3 - ZIB-Report - SC-89-02 KW - Matrix rank KW - singular values KW - generalized singular values KW - product induced singular values KW - restricted singular values KW - matrix decompositions Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-205 ER - TY - GEN A1 - Deuflhard, Peter T1 - Numerik von Anfangswertmethoden für gewöhnliche Differentialgleichungen. N2 - Das voliegende Skriptum entstand aus einer Vorlesung, die ich im WS 87/88 an der Freien Universität Berlin im Fachbereich Mathematik gehalten habe. Mein ursprüngliches Vorlesungsmanuskript wurde von Herrn F. Bornemann in weiten Teilen überarbeitet, reorganisiert und substantiell ergänzt. Der Inhalt stammt größtenteils aus Originalarbeiten jüngeren Datums. Darüberhinaus finden sich zahlreiche Teile, die aus meiner jahrelangen Beschäftigung mit dem Thema entstanden aber unpubliziert geblieben sind. Das Skriptum erhebt nicht den Anspruch, ein Lehrbuch zu sein. Es war zunächst als Ausarbeitung für meinen studentischen Hörerkreis sowie als internes Arbeitspapier für das ZIB bestimmt. Die Kunde von der bloßen Existenz eines solchen Skriptums hat jedoch zu einer derart regen Nachfrage geführt, daß es hiermit als Technischer Report des ZIB einer breiteren ffentlichkeit zugänglich gemacht werden soll. In der vorliegenden Form richtet es sich in erster Linie an Mathematiker; es soll sich jedoch auch für Naturwissenschaftler und Ingenieure eignen, die sich einen Einblick in den theoretischen und algorithmischen Hintergrund der von ihnen verwendeten wissenschaftlichen Software verschaffen wollen. T3 - ZIB-Report - TR-89-02 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4580 ER - TY - GEN A1 - Walter, Artur T1 - Ein Finite-Element-Verfahren zur numerischen Lösung von Erhaltungsgleichungen. N2 - A new approach for the discretisation of hyperbolic conservation laws via a finite element method is developed and analysed. Appropriate forms of the Eulers equation of gas dynamic are considered to employ the algorithm in a reasonable way for this system of nonlinear equations. Both mathematical and physical stability results are obtained. A main part of the paper is devoted to the convergence proof with energy methods under strong regularity of the solution of a scalar nonlinear conservation law. Some hints on the implementation and numerical results for the calculation of transonic gasflow through a Laval nozzle are given. The necessary amount of numerical work is compared to an established finite difference method and the efficiency of the algorithm is shown. A survey on recent literature about finite element methods for hyperbolic problem is included. T3 - ZIB-Report - TR-89-03 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4597 ER - TY - GEN A1 - Zha, Hongyuan T1 - A Numerical Algorithm for Computing the Restricted Singular Value Decomposition of Matrix Triplets. N2 - This paper presents a numerical algorithm for computing the restricted singular value decomposition of matrix triplets (RSVD). It is shown that one can use unitary transformations to separate the regular part from a general matrix triplet. After preprocessing on the regular part, one obtains a matrix triplet consisting of three upper triangular matrices of the same dimensions. The RSVD of this special matrix triplet is computed using the implicit Kogbetliantz technique. The algorithm is well suited for parallel computation. {\bf Keywords:} Restricted singular values, matrix triplets, unitary transformations, implicit Kogbetliantz technique. T3 - ZIB-Report - SC-89-01 KW - restricted singular values KW - matrix triplets KW - unitary transformations KW - implicit Kogbetliantz technique Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-194 ER - TY - GEN A1 - Chow, Shui-Nee A1 - Deng, Bo A1 - Fiedler, Bernold T1 - Homoclinic Bifurcation at Resonant Eigen-values. T3 - ZIB-Report - SC-88-10 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-181 ER - TY - GEN T1 - CRAY-HANDBUCH. Einführung in die Benutzung der CRAY X-MP unter UNICOS. (veraltet) T3 - ZIB-Report - TR-89-01 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4574 ER - TY - GEN A1 - Kornhuber, Ralf A1 - Roitzsch, Rainer T1 - Adaptive Finite-Elemet- Methoden für konvektionsdominierte Randwertprobleme bei partiellen Differentialgleichungen. N2 - Ausgangspunkt bei der Behandlung konvektiv dominierter, elliptischer Probleme sind die bekannten hierarchischen Finite-Element-Methoden für den rein elliptischen Fall. Als stabile Erweiterung des Standard-Galerkin-Verfahrens wird das Stromlinien-Diffusions-Verfahren durch physikalische Überlegungen motiviert und kurz diskutiert. Anschließend zeigen wir, daß diese Methode erst in Verbindung mit einer hier erstmals vorgestellten lokalen Ausrichtung der Kanten wirksam eingesetzt werden kann. Zusammen mit einer ebenfalls neu entwickelten richtungsorientierten Verfeinerungsstrategie erhält man eine erheblich stabilere, genauere und schnellere Auflösung von Grenzschichten als mit herkömmlichen Methoden. T3 - ZIB-Report - SC-88-09 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-170 ER - TY - GEN A1 - Maierhöfer, Gerhard A1 - Skorobohatyj, Georg T1 - Parallel-TRAPEX (Ein paralleler adaptiver Algorithmus zur numerischen Integration; seine Implementierung für SUPRENUM-artige Architekturen mit SUSI). N2 - This paper describes some ways of transforming a sequential adaptive algorithm for numerical evaluation of an integral (Romberg- Quadrature with polynomial Extrapolation method) to a parallel one, such as have been implementad by the authors. We developed an algorithm which preserves the sequential adaptivity and is capable of running on various architectures, dynamically controlling the number of avtive processors depending on the problem. To study the time behaviour, we used the simulator SUSI(SUprenum SImulatur) which is able to simulate SUPRENUM-like architectures. Results are given in part 3. {\bf Keywords:} Romberg quadrature; numerical integration; parallel adaptive algorithm; SUSI; simulation; SUPRENUM; MIMD-Fortran; computer architecture; granularity; load balacing; master-slave-principle. T3 - ZIB-Report - TR-88-05 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4560 ER - TY - GEN A1 - Hoppe, Ronald H. W. A1 - Kornhuber, Ralf T1 - Multi-Grid Solution of Two Coupled Stefan Equations Arising in Induction Heating of Large Steel Slabs. N2 - Induction heating of large steel slabs can be described by a coupled system of nonlinear evolution equations of Stefan type representing the temporal and spatial distribution of the induced magnetic field and the generated temperature within the slab. Discretizing these equations implicitly in time and by finite differences in space, at each time step the solution of a system of difference inclusions is required. For the solution of that system two multi-grid algorithms are given which combined with a nested iteration type continuation strategy to proceed in time result in computationally highly efficient schemes for the numerical simulation of the induction heating process. {\bf Keywords:} induction heating, system of two coupled Stefan equations, multi-grid algorithms. {\bf Subject Classification:} AMS(MOS): 35K60, 35R35, 65H10, 65N05, 65N20, 78A25, 78A55. T3 - ZIB-Report - SC-88-08 KW - induction heating KW - system of two coupled Stefan equations KW - multi-grid algorithms Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-160 ER - TY - GEN A1 - Melenk, Herbert A1 - Möller, H. Michael A1 - Neun, Winfried T1 - Symbolic Solution of Large Stationary Chemical Kinetics Problems. N2 - The paper presents a new application of computer algebra to the treatment of steady states of reaction systems. The method is based on the Buchberger algorithm. This algorithm was modified such that it can exploit the special structure of the equations derived from reaction systems, so even large systems can be handled. In contrast to numerical approximation techniques, the algebraic solution gives a complete and definite overview of the solution space and it is even applicable when parameter values are unknown or undetermined. The algorithm, its adaptation to the problem class and its application to selected examples are presented. T3 - ZIB-Report - SC-88-07 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-157 ER - TY - GEN A1 - Deuflhard, Peter A1 - Wulkow, Michael T1 - Computational Treatment of Polyreaction Kinetics by Orthogonal Polynomials of a Discrete Variable. N2 - The paper presents a new approach to the computational treatment of polyreaction kinetics. This approach is characterized by a Galerkin method based on orthogonal polynomials of a discrete variable, the polymer degree (or chain length). In comparison with the known competing approaches (statistical moment treatment, Galerkin methods for continuous polymer models), the suggested method is shown to avoid the disadvantages and preserve the adventages of either of them. The basic idea of the method is the construction of a discrete inner product associated with a reasonably chosen probability density function. For the so-called Schulz-Flory distribution one thus obtains the discrete Laguerre polynomials, whereas the Poisson distribution leads to the Charlier polynomials. Numerical experiments for selected polyreaction mechanisms illustrate the efficiency of the proposed method. T3 - ZIB-Report - SC-88-06 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-140 ER - TY - GEN A1 - Deuflhard, Peter A1 - Leinen, P. A1 - Yserentant, Harry T1 - Concepts of an Adaptive Hierarchical Finite Element Code. N2 - The paper presents the mathematical concepts underlying the new adaptive finite element code KASKADE, which, in its present form, applies to linear scalar second-order 2-D elliptic problems on general domains. Starting point for the new development is the recent work on hierarchical finite element bases due to Yserentant (1986). It is shown that this approach permits a flexible balance between iterative solver, local error estimator, and local mesh refinement device - which are the main components of an adaptive PDE code. Without use of standard multigrid techniques, the same kind of computational complexity is achieved - independent of any uniformity restrictions on the applied meshes. In addition, the method is extremely simple and all computations are purely local - making the method particularly attractive in view of parallel computing. The algorithmic approach is illustrated by a well-known critical test problem. {\bf Keywords:} finite elements, hierarchical basis, adaptive mesh refinement, preconditioned conjugate gradient methods. T3 - ZIB-Report - SC-88-05 KW - finite elements KW - hierarchical basis KW - adaptive mesh refinement KW - preconditioned conjugate gradient methods Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-131 ER - TY - GEN A1 - Buhtz, Danuta Anna A1 - Langendorf, Jens A1 - Paetsch, Olaf T1 - GRAZIL - 3D. Ein graphisches Anwendungsprogramm zur Darstellung von Kurven- und Funktionsverläufen im räumlichen Koordinatensystem. N2 - GRAZIL - 3D ist ein interaktives Programmpaket zur graphischen Darstellung von dreidimensionalen Kurvenverläufen. Das Aussehen der räumlichen Ausgabe des Bildes wird durch Angabe des Blickwinkels und der Perspektive festgelegt. T3 - ZIB-Report - TR-88-04 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4556 ER - TY - GEN T1 - Jahresbericht 1987 T3 - Jahresbericht - 1987 KW - Annual Report Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9860 SN - 0933-7903 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - Parallel Polynomial Operations in the Buchberger Algorithm. N2 - The Buchberger algorithm is a basic tool for the solution of systems of polynomial equations in an environment of computer algebra applications. A model for overlapped processing of different steps of the algorithm is presented, which uses the data structure of the polynomials (distributive representation) for synchronization. The model can be applied for multi processors with fast access to shared data. It is tested with Cray X-MP multi processors based on a parallel version of Portable Standard Lisp (PSL 3.4). T3 - ZIB-Report - SC-88-04 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-125 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - REDUCE User s Guide for the CRAY 1 / CRAY X-MP Series Running UNICOS. Version 3.3. N2 - This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the Operating System UNICOS. The document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, (CP85). T3 - ZIB-Report - TR-88-02 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4539 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - REDUCE Installation Guide for CRAY 1 / X-MP Systems Running UNICOS. Version 3.3. N2 - This guide describes the CRAY/UNICOS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running UNICOS. This document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, publication CP84. T3 - ZIB-Report - TR-88-03 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4541 ER - TY - GEN A1 - Buhtz, Rainer A1 - Buhtz, Danuta Anna T1 - TDLG 3.1 - Ein interaktives Programm zur Darstellung dreidimensionaler Modelle auf Rastergraphikgeräten. N2 - TDLG 3.1 dient zur Darstellung von dreidimensionalen Objekten, die sich aus offenen Linienzügen, Dreieck- und Viereckelementen zusammensetzen. Dabei können verschiedene Visualisierungstechniken benutzt werden: Drahtmodell, Schattierung mit und ohne Lichtquelle, Hidden Surface Removal. Durch Verwendung von Konvertierungsprogrammen können auch IGES- und VDAFS- Dateien dargestellt werden. T3 - ZIB-Report - TR-88-01 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4522 ER - TY - GEN A1 - Melenk, Herbert A1 - Möller, H. Michael A1 - Neun, Winfried T1 - On Gröbner Bases Computation on a Supercomputer Using REDUCE. N2 - Gröbner bases are the main tool for solving systems of algebraic equations and some other problems in connection with polynomial ideals using Computer Algebra Systems. The procedure for the computation of Gröbner bases in REDUCE 3.3 has been modified in order to solve more complicated algebraic systems of equations by some general improvements and by some tools based on the specific resources of the CRAY X-MP. We present this modification and illustrate it by examples. T3 - ZIB-Report - SC-88-02 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-107 ER - TY - GEN A1 - Alexander, J. C. A1 - Fiedler, Bernold T1 - Global Decoupling of Coupled Symmetric Oscillators. N2 - We model a symmetric system of coupled oscillators as a graph with symmetry group $\gamma$. Each vertex of the graph represents an "oscillator" or a "cell" of reactants. The magnitude (concentration) of the reactants in the $ i $ th cell is represented by a vector $ x^i $. The edges represent the coupling of the cells. The cells are assumed to evolve by identical reaction-diffusion equation which depends on the sum of the reactants in the nearest neighbors. Thus the dynamics of the system is described by a nonlinear differential system \begin{flushleft} \[ \mbox {(*) \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ } \dot{x}^i = f (x^i,\sum_{j \in N_i} x^j), \mbox { \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ } \] \end{flushleft} where the sum ranges over the set $ N_i $ of neighbors of cell $ i $ . If $ f $ also has a symmetry (e.g., oddness), there are geometric conditions on the graph such that the nonlinear system $ (*) $ decouples globally into a product flow on certain sums of isotropy subspaces. Thus we may detect higher-dimensional tori of solutions of $ (*) $ which are not amenable to other types of analysis. We present a number of examples, such as bipartite graphs, complete graphs, the square, the octahedron, and a 6-dimensional cube. T3 - ZIB-Report - SC-88-03 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-113 ER - TY - GEN A1 - Neun, Winfried A1 - Melenk, Herbert T1 - Implementation of the LISP-Arbitrary Precision Arithmetic for a Vector Processor. N2 - Portable Standard LISP (PSL, Version 3.4) and REDUCE 3 were implemented for CRAY1 and Cray X- MP computers at the Konrad-Zuse-Zentrum Berlin in 1986. As an special aspect of the implementation of PSL, an interface to the vector hardware of CRAY processors was defined. With that interface and mostly driven by the needs of REDUCE applications (e.g. extensive calculations of Gröbner bases), the arbitrary precision integer arithmetic of PSL was rebuild using full power of the vector hardware. A modular arithmetic using vector hardware was also constructed. T3 - ZIB-Report - SC-88-01 Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93 ER - TY - GEN A1 - Langendorf, Jens A1 - Paetsch, Olaf T1 - GRAZIL (Graphical ZIB Language). N2 - GRAZIL ist ein interaktives Programmpaket zur graphischen Darstellung von zwei-dimensionalen Kurvenverläufen. Dem Benutzer stehen zahlreiche Kommandos zum Gestalten des Layouts der Zeichnung zur Verfügung. Die Eingabedaten müssen dem ZUGRIFF- Konzept genügen, wodurch die genaue Struktur der Daten erst zur Laufzeit bekannt sein muß und somit eine hohe Flexibilität und eine große Bandbreite der Einsatzmöglichkeiten erreicht wird. GRAZIL wurde mit der graphischen Grundsoftware BIZEPS2 und GKS entwickelt. Dadurch kann ein breites Rechner- und Ausgabegerätespektrum genutzt werden. T3 - ZIB-Report - TR-87-07 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4518 ER - TY - GEN A1 - Yserentant, Harry T1 - Preconditioning Indefinite Discretization Matrices. N2 - The finite element discretization of many elliptic boundary value problems leads to linear systems with positive definite and symmetric coefficient matrices. Many efficient preconditioners are known for these systems. We show that these preconditioning matrices can be used also for the linear systems arising from boundary value problems which are potentially indefinite due to lower order terms in the partial differential equation. Our main tool is a careful algebraic analysis of the condition numbers and the spectra of perturbed matrices which are preconditioned by the same matrices as in the unperturbed case. {\bf Keywords: }Preconditioned conjugate gradient methods, finite elements. {\bf Subject Classification: } AMS(MOS):65F10, 65N20, 65N30. T3 - ZIB-Report - SC-87-06 KW - preconditioned conjugate gradient methods KW - finite elements Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - Portable Standard LISP Implementation for CRAY X+MP Computers. Release of PSL 3.4 for COS. N2 - Portable Standard LISP (PSL) is a portable implementation of the programming language LISP constructed at the University of Utah. The version 3.4 of PSL was implemented for CRAY X-MP computers by Konrad Zuse-Zentrum Berlin; this implementation is based to an important part on the earlier implementation of PSL 3.2 at Salt Lake City, Los Alamos and Mendota Heights. T3 - ZIB-Report - TR-87-02 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4465 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - Portable Common LISP Subset Implementation for CRAY X+MP Computers. N2 - This document describes the installation procedure and maintenance for the Portable Common LISP Subset (PCLS) developed at the University of Utah. T3 - ZIB-Report - TR-87-03 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4479 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - REDUCE Installation Guide for CRAY 1 / X-MP Systems Running COS. Version 3.3. N2 - This guide describes the CRAY/COS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running COS. This document was derived from the corresponding document for Vax/Unix prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, publication CP84. T3 - ZIB-Report - TR-87-04 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4486 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - REDUCE Users Guide for the CRAY 1 / X-MP Series Running COS. Version 3.3. N2 - This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the CRAY Operating System (COS). The document was derived from the corresponding document for Vax/UNIX prepared by A.C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, (CP85). T3 - ZIB-Report - TR-87-05 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4498 ER - TY - GEN A1 - Deuflhard, Peter T1 - A Note on Extrapolation Methods for Second Order ODE Systems. N2 - A slight modification of the extended Stoermer discretization for non self-adjoint second order ODE systems is derived on the basis of a simple stability analysis. This discretization easily extends to implicit ODE systems, which are known to arise e.g. in mechanical engineering. In addition, a special variant of semi-implicit Euler discretization is proposed, which essentially treats the state variables explicitly, but their derivatives implicitly. Numerical tests over critical parameter values of the van der Pol oscillator illustrate the domain of efficiency of the suggested discretizations. T3 - ZIB-Report - SC-87-05 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79 ER - TY - GEN A1 - Buhtz, Rainer A1 - Langendorf, Jens A1 - Paetsch, Olaf A1 - Buhtz, Danuta Anna T1 - ZUGRIFF - Eine vereinheitlichte Datenspezifikation für graphische Darstellungen und ihre graphische Aufbereitung. N2 - ZUGRIFF ist eine Dateischnittstelle für Graphikausgabe speziell numerischer Anwenderprogramme. Dieser Report beschreibt den Leistungsumfang der Spezifikation sowie die interaktive graphische Verarbeitung von ZUGRIFF- Dateien. T3 - ZIB-Report - TR-87-06 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4506 ER - TY - GEN A1 - Buhtz, Rainer T1 - CGM-Concepts and their Realizations. N2 - Requirements and Design Concepts. Common Graphics Manager (CGM) is the name given to the implementation of GKS, Level 2b, developed at the Free University of Berlin (1,6). This paper is a survey over the "early GKS implementation phase" 1982. Work commenced in February 1980. At the outset some basic design decisions were necessary on account of the special scientific computer environment in Berlin, because the "Berlin GKS" was intended to be a common graphical software package for all the machines. T3 - ZIB-Report - SC-87-04 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68 ER - TY - GEN A1 - Deuflhard, Peter T1 - Uniqueness Theorems for Stiff ODE Initial Value Problems. N2 - The paper presents a new uniqueness theory for ODE initial value problems, derived in view of numerical stiff integration. The theory supplies stepsize bounds for stiff integrators that can easily be estimated in extrapolation methods. The additional devices lead to a significant speed-up of computations - in particular in combustion PDE problems. T3 - ZIB-Report - SC-87-03 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53 ER - TY - GEN T1 - Tätigkeitsbericht 1986 T3 - Jahresbericht - 1986 KW - Annual Report KW - Jahresbericht Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9871 ER - TY - GEN A1 - Bank, Randolph A1 - Dupont, Todd F. A1 - Yserentant, Harry T1 - The Hierarchical Basis Multigrid Method. N2 - We derive and analyze the hierarchical basis-multigrid method for solving discretizations of self-adjoint, elliptic boundary value problems using piecewise linear triangular finite elements. The method is analyzed as a block symmetric Gauß- Seidel iteration with inner iterations, but it is strongly related to 2-level methods, to the standard multigrid V-cycle, and to earlier Jacobi-like hierarchical basis methods. The method is very robust, and has a nearly optimal convergence rate and work estimate. It is especially well suited to difficult problems with rough solutions, discretized using highly nonuniform, adaptively refined meshes. T3 - ZIB-Report - SC-87-02 KW - hierarchical basis KW - multigrid KW - finite elements KW - adaptive mesh refinement KW - preconditioned conjugate gradient methods KW - symmetric Gauss-Seidel Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-44 ER - TY - GEN A1 - Busch, Hubert A1 - Pöhle, Uwe A1 - Stech, Wolfgang T1 - CRAY-Handbuch. - Einführung in die Benutzung der CRAY. N2 - Das vorliegende Handbuch wendet sich an alle Benutzer des für den Norddeutschen Vektorrechnerverbund im ZIB installierten Rechners CRAY X-MP/24. Ein großer Teil der Darstellung ist der Optimierung von Programmen gewidmet, die in FORTRAN geschrieben sind. Gerade weil die CRAY einer der schnellsten Rechner der Welt ist, wird jeder Benutzer früher oder später selbst auf dieses Thema stoßen, denn die Maschine ist vornehmlich für Probleme bestimmt, die für die meisten anderen Rechner zu komplex sind. Maschinen der CRAY-Leistungsklasse beziehen einen erheblichen Teil ihrer Geschwindigkeit aus der parallelen Arbeit vieler Komponenten. Programme, die die jeweilige Architektur der Maschine berücksichtigen, können um Größenordnungen schneller (also wirtschaftlicher) sein als Programme, deren Autor beim Schreiben einen sogenannten "klassischen" Rechner vor seinem geistigen Auge hatte. Daher wird auch der technische Aufbau der CRAY X-MP im Handbuch erläutert. Weitere Teile des Handbuches beschäftigen sich mit den Vorrechnern und dem Rechnernetz. T3 - ZIB-Report - TR-87-01 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4459 ER - TY - GEN A1 - Anderson, J. A1 - Galway, W. A1 - Kessler, R. A1 - Melenk, Herbert A1 - Neun, Winfried T1 - The Implementation and Optimization of Portable Standard LISP for the CRAY. N2 - Portable Standard LISP (PSL), a dialect of LISP developed at the University of Utah, has been implemented and optimized for the CRAY 1 and CRAY X-MP supercomputers. This version uses a new implementation technique that permits a step-by-step development of the PSL kernel. The initial CRAY version was acceptable, although the execution speed of the PSL was not as fast as had been anticipated. CRAY-specific optimizations were undertaken that in some cases provided a ten-fold speed improvement, resulting in a fast LISP implementation. T3 - ZIB-Report - SC-87-01 Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-31 ER - TY - GEN A1 - Melenk, Herbert A1 - Neun, Winfried T1 - Portable Standard LISP for CRAY X-MP Computers. N2 - Portable Standard LISP (PSL) is a portable implementation of the programming language LISP constructed at the University of Utah. The version 3.4 of PSL was implemented for CRAY X-MP computers by Konrad-Zuse-Zentrum Berlin; this implementation is based to an important part on the earlier implementation of PSL 3.2 at the University of Utah, Los Alamos National Laboratories and CRAY Research Inc. at Mendota Heights. During the work on implementing PSL the language LISP was investigated for areas which can be supported by vector hardware. One area was found in the COMMON LISP sequence functions and some typical application areas of LISP programming can be improved by vector processing too. A model for the implementation of vector instructions in LISP was developed. For arithmetic an experimental vectorizing extent of the PSL compiler was constructed. With this means full vector hardware capacity can become available for LISP applications. T3 - ZIB-Report - SC-86-02 Y1 - 1986 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-28 ER - TY - GEN A1 - Schuster, H. J. T1 - Tätigkeitsbericht-1985. T3 - ZIB-Report - TR-86-01 Y1 - 1986 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4443 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich T1 - Efficient Numerical Simulation and Identification of Large Chemical Reaction Systems. N2 - New, highly efficient techniques for the numerical simulation and parameter identification of large chemical reaction systems are surveyed. The survey particularly addresses to chemists, which are understood to be potential users of the distributed software packages. These packages are written in the form of interactive dialogue systems - thus enabling chemists to concentrate on the chemistry of their problem. Large scale examples from chemical research environments are included. T3 - ZIB-Report - SC-86-01 Y1 - 1986 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14 ER - TY - GEN T1 - Tätigkeitsbericht 1985 T3 - Jahresbericht - 1985 KW - Annual Report KW - Jahresbericht Y1 - 1986 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9885 ER -