@article{TyagiMalhotraThuenemannetal.2013, author = {Tyagi, Rahul and Malhotra, Shashwat and Th{\"u}nemann, Andreas F. and Sedighi, Amir and Weber, Marcus and Sch{\"a}fer, Andreas and Haag, Rainer}, title = {Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles}, volume = {117}, journal = {J. Phys. Chem. C}, number = {23}, pages = {12307 -- 12317}, year = {2013}, language = {de} } @article{ShanCarlsonBujotzeketal.2013, author = {Shan, Min and Carlson, Kathryn E. and Bujotzek, Alexander and Wellner, Anja and Gust, Ronald and Weber, Marcus and Katzenellenbogen, John A. and Haag, Rainer}, title = {Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor}, volume = {8}, journal = {ACS Chem. Biol.}, number = {4}, pages = {707 -- 715}, year = {2013}, language = {en} } @article{Weber2013, author = {Weber, Marcus}, title = {Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization}, journal = {XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series}, pages = {147 -- 157}, year = {2013}, language = {de} } @article{FackeldeyRoeblitzScharkoietal.2011, author = {Fackeldey, Konstantin and R{\"o}blitz, Susanna and Scharkoi, O. and Weber, Marcus}, title = {Soft Versus Hard Metastable Conformations in Molecular Simulations}, journal = {Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.)}, pages = {899 -- 909}, year = {2011}, language = {de} } @article{ShanBujotzekAbendrothetal.2011, author = {Shan, Min and Bujotzek, Alexander and Abendroth, Frank and Seitz, Oliver and Weber, Marcus and Haag, Rainer}, title = {Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding}, journal = {ChemBioChem, 12(17)}, doi = {10.1002/cbic.201100529}, pages = {2587 -- 2598}, year = {2011}, language = {en} } @article{GuentherLameckerWeiser2013, author = {G{\"u}nther, Andreas and Lamecker, Hans and Weiser, Martin}, title = {Flexible Shape Matching with Finite Element Based LDDMM}, volume = {105}, journal = {International Journal of Computer Vision}, number = {2}, doi = {10.1007/s11263-012-0599-3}, pages = {128 -- 143}, year = {2013}, abstract = {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.}, language = {en} } @misc{GuentherLameckerWeiser2011, author = {G{\"u}nther, Andreas and Lamecker, Hans and Weiser, Martin}, title = {Direct LDDMM of Discrete Currents with Adaptive Finite Elements}, journal = {Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability}, editor = {Pennec, X. and Joshi, S. and Nielsen, M.}, pages = {1 -- 14}, year = {2011}, abstract = {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.}, language = {en} } @misc{SchielaWeiser2010, author = {Schiela, Anton and Weiser, Martin}, title = {Barrier methods for a control problem from hyperthermia treatment planning}, journal = {Recent Advances in Optimization and its Applications in Engineering (Proceedings of 14th Belgian-French-German Conference on Optimization 2009)}, editor = {Diehl, M. and Glineur, F. and Jarlebring, E. and Michiels, W.}, publisher = {Springer}, pages = {419 -- 428}, year = {2010}, abstract = {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.}, language = {en} } @article{WeiserRoelligArndtetal.2010, author = {Weiser, Martin and R{\"o}llig, Mathias and Arndt, Ralf and Erdmann, Bodo}, title = {Development and test of a numerical model for pulse thermography in civil engineering}, volume = {46}, journal = {Heat and Mass Transfer}, number = {11-12}, pages = {1419 -- 1428}, year = {2010}, abstract = {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.}, language = {en} } @article{BlomeMaurerGreenhalgh2011, author = {Blome, Mark and Maurer, HR and Greenhalgh, S.}, title = {Geoelectric experimental design — Efficient acquisition and exploitation of complete pole-bipole data sets}, volume = {76}, journal = {GEOPHYSICS}, number = {1}, doi = {10.1190/1.3511350}, pages = {F15 -- F26}, year = {2011}, language = {en} } @article{PlattnerMaurerVorloeperetal.2012, author = {Plattner, A. and Maurer, H. and Vorloeper, J. and Blome, Mark}, title = {3-D electrical resistivity tomography using adaptive wavelet parameter grids}, volume = {189}, journal = {Geophysical Journal International}, pages = {317 -- 330}, year = {2012}, language = {en} } @article{RannebergWeiserWeihrauchetal.2010, author = {Ranneberg, Maximilian and Weiser, Martin and Weihrauch, Mirko and Budach, Volker and Gellermann, Johanna and Wust, Peter}, title = {Regularized Antenna Profile Adaptation in Online Hyperthermia Treatment}, volume = {37}, journal = {Medical Physics}, doi = {10.1118/1.3488896}, pages = {5382 -- 5394}, year = {2010}, language = {en} } @article{JaegerBarthHammerschmidtetal.2016, author = {J{\"a}ger, Klaus and Barth, Carlo and Hammerschmidt, Martin and Herrmann, Sven and Burger, Sven and Schmidt, Frank and Becker, Christiane}, title = {Simulations of sinusoidal nanotextures for coupling light into c-Si thin-film solar cells}, volume = {24}, journal = {Opt. Express}, doi = {10.1364/OE.24.00A569}, pages = {A569}, year = {2016}, language = {en} } @article{LedentsovJrShchukinKroppetal.2016, author = {Ledentsov, Jr., Nikolay and Shchukin, Vitaly and Kropp, J{\"o}rg-R. and Burger, Sven and Schmidt, Frank and Ledentsov, Jr., Nikolay}, title = {Direct visualization of the in-plane leakage of high-order transverse modes in vertical-cavity surface-emitting lasers mediated by oxide-aperture engineering}, volume = {9766}, journal = {Proc. SPIE}, doi = {10.1117/12.2208909}, pages = {976608}, year = {2016}, language = {en} } @misc{Fackeldey2010, author = {Fackeldey, Konstantin}, title = {Challenges in Atomistic-to-Continuum Coupling}, volume = {2010}, journal = {ZIB Report}, edition = {10-12}, doi = {10.1155/2015/834517}, year = {2010}, abstract = {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.}, language = {en} } @article{Durmaz2015, author = {Durmaz, Vedat}, title = {Markov model-based polymer assembly from force field-parameterized building blocks}, volume = {29}, journal = {Journal of Computer-Aided Molecular Design}, doi = {10.1007/s10822-014-9817-0}, pages = {225 -- 232}, year = {2015}, abstract = {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.}, language = {en} } @article{HeyeBeckerLuetkeEverslohetal.2016, author = {Heye, Katharina and Becker, Dennis and L{\"u}tke-Eversloh, Christian and Durmaz, Vedat and Ternes, Thomas and Oetken, Matthias and Oehlmann, J{\"o}rg}, title = {Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test}, volume = {98}, journal = {Water Research}, pages = {19 -- 27}, year = {2016}, abstract = {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.}, language = {en} } @article{LubkollSchielaWeiser2017, author = {Lubkoll, Lars and Schiela, Anton and Weiser, Martin}, title = {An affine covariant composite step method for optimization with PDEs as equality constraints}, volume = {32}, journal = {Optimization Methods and Software}, number = {5}, doi = {10.1080/10556788.2016.1241783}, pages = {1132 -- 1161}, year = {2017}, abstract = {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.}, language = {en} } @article{BienefeldZautkeGupta2016, author = {Bienefeld, Kaspar and Zautke, Fred and Gupta, Pooja}, title = {A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour - illustrated by the hygienic behaviour towards Varroa infestation}, volume = {54(5)}, journal = {Journal of Apicultural Research}, pages = {541 -- 547}, year = {2016}, language = {en} } @article{SpoetterGuptaMayeretal.2016, author = {Sp{\"o}tter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)}, volume = {107}, journal = {Journal of Heredity}, number = {3}, pages = {220 -- 227}, year = {2016}, language = {en} } @misc{GoetschelMaierhoferMuelleretal.2016, author = {G{\"o}tschel, Sebastian and Maierhofer, Christiane and M{\"u}ller, Jan P. and Rothbart, Nick and Weiser, Martin}, title = {Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58374}, year = {2016}, abstract = {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.}, language = {en} } @misc{GoetschelHoehneKolkoorietal.2016, author = {G{\"o}tschel, Sebastian and H{\"o}hne, Christian and Kolkoori, Sanjeevareddy and Mitzscherling, Steffen and Prager, Jens and Weiser, Martin}, title = {Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58386}, year = {2016}, abstract = {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.}, language = {en} } @article{PomplunBurgerZschiedrichetal.2016, author = {Pomplun, Jan and Burger, Sven and Zschiedrich, Lin and Gutsche, Philipp and Schmidt, Frank}, title = {Method for fast computation of angular light scattering spectra from 2D periodic arrays}, volume = {9778}, journal = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/1603.04169}, doi = {10.1117/12.2219666}, pages = {977839}, year = {2016}, language = {en} } @misc{KoltaiCiccottiSchuette2016, author = {Koltai, Peter and Ciccotti, Giovanni and Sch{\"u}tte, Christof}, title = {On metastability and Markov state models for non-stationary molecular dynamics}, volume = {174103}, journal = {The Journal of Chemical Physics}, edition = {145}, issn = {1438-0064}, doi = {10.1063/1.4966157}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57869}, year = {2016}, abstract = {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.}, language = {en} } @article{GutschePoulikakosHammerschmidtetal.2016, author = {Gutsche, Philipp and Poulikakos, Lisa and Hammerschmidt, Martin and Burger, Sven and Schmidt, Frank}, title = {Time-harmonic optical chirality in inhomogeneous space}, volume = {9756}, journal = {Proc. SPIE}, arxiv = {http://arxiv.org/abs/1603.05011}, doi = {10.1117/12.2209551}, pages = {97560X}, year = {2016}, language = {en} } @article{DjurdjevacConradWeberSchuette2016, author = {Djurdjevac Conrad, Natasa and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Finding dominant structures of nonreversible Markov processes}, volume = {14}, journal = {Multiscale Modeling and Simulation}, number = {4}, doi = {10.1137/15M1032272}, pages = {1319 -- 1340}, year = {2016}, language = {en} } @article{HammerschmidtBarthPomplunetal.2016, author = {Hammerschmidt, Martin and Barth, Carlo and Pomplun, Jan and Burger, Sven and Becker, Christiane and Schmidt, Frank}, title = {Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs}, volume = {9756}, journal = {Proc. SPIE}, doi = {10.1117/12.2212482}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58187}, pages = {97561R}, year = {2016}, abstract = {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.}, language = {en} } @article{HammerschmidtHerrmannPomplunetal.2016, author = {Hammerschmidt, Martin and Herrmann, Sven and Pomplun, Jan and Burger, Sven and Schmidt, Frank}, title = {Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures}, volume = {9742}, journal = {Proc. SPIE}, doi = {10.1117/12.2212367}, pages = {97420M}, year = {2016}, abstract = {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.}, language = {en} } @misc{GutscheLaeuterSchmidt2016, author = {Gutsche, Philipp and L{\"a}uter, Matthias and Schmidt, Frank}, title = {Parameter-dependent Parallel Block Sparse Arnoldi and D{\"o}hler Algorithms on Distributed Systems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58202}, year = {2016}, abstract = {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.}, language = {en} } @article{HammerschmidtHerrmannPomplunetal.2016, author = {Hammerschmidt, Martin and Herrmann, Sven and Pomplun, Jan and Burger, Sven and Schmidt, Frank}, title = {Reduced basis method for electromagnetic scattering problem: a case study for FinFETs}, volume = {48}, journal = {Optical and Quantum Electronics}, doi = {10.1007/s11082-016-0530-1}, pages = {250}, year = {2016}, abstract = {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.}, language = {en} } @phdthesis{Nielsen2016, author = {Nielsen, Adam}, title = {Computation Schemes for Transfer Operators}, year = {2016}, language = {en} } @masterthesis{Sikorski2015, type = {Bachelor Thesis}, author = {Sikorski, Alexander}, title = {PCCA+ and Its Application to Spatial Time Series Clustering}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58769}, year = {2015}, language = {en} } @misc{BojarovskiHegeLieetal.2015, author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, year = {2015}, abstract = {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.}, language = {en} } @book{Weiser2016, author = {Weiser, Martin}, title = {Inside Finite Elements}, publisher = {De Gruyter}, year = {2016}, abstract = {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.}, language = {en} } @article{KrebekvonAchaziSollederetal.2016, author = {Krebek, von, Larissa K. S. and Achazi, Andreas J. and Solleder, Marthe and Weber, Marcus and Paulus, Beate and Schalley, Christoph A.}, title = {Allosteric and Chelate Cooperativity in Divalent Crown Ether-Ammonium Complexes with Strong Binding Enhancements}, volume = {22}, journal = {Chem. Eur. J.}, number = {43}, doi = {10.1002/chem.201603098}, pages = {15475 -- 15484}, year = {2016}, language = {en} } @phdthesis{Fackeldey2015, author = {Fackeldey, Konstantin}, title = {Crossing the Scales in Structural Mechanics and Molecular Research}, year = {2015}, language = {en} } @article{OwhadiScovelSullivan2015, author = {Owhadi, Houman and Scovel, Clint and Sullivan, T. J.}, title = {On the Brittleness of Bayesian Inference}, volume = {57}, journal = {SIAM Review}, number = {4}, doi = {10.1137/130938633}, pages = {566 -- 582}, year = {2015}, abstract = {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.}, language = {en} } @book{Sullivan2015, author = {Sullivan, T. J.}, title = {Introduction to Uncertainty Quantification}, volume = {63}, publisher = {Springer}, isbn = {978-3-319-23394-9}, doi = {10.1007/978-3-319-23395-6}, year = {2015}, language = {en} } @inproceedings{BienefeldSpoetterReinschetal.2015, author = {Bienefeld, Kaspar and Sp{\"o}tter, Andreas and Reinsch, Norbert and Mayer, Manfred and Gupta, Pooja}, title = {A new approach for honeybee breeding - genomic selection}, booktitle = {44th Apimondia International Apicultural congress, 2015. Daejeon, South Korea}, year = {2015}, language = {en} } @phdthesis{Gupta2013, author = {Gupta, Pooja}, title = {Integrating high-density marker information into the genetic evaluation of the honey bee}, year = {2013}, language = {en} } @misc{GuptaRoeblitzKrauseetal.2013, author = {Gupta, Pooja and R{\"o}blitz, Susanna and Krause, Carola and Knaus, Petra and Sch{\"u}tte, Christof}, title = {Mathematical modeling of the Smad and Non-Smad BMP signaling pathways in context of cell density}, journal = {Computational Models in biology and medicine, 2013, Dresden, Germany}, year = {2013}, language = {en} } @inproceedings{GuptaKrauseRikeitetal.2014, author = {Gupta, Pooja and Krause, Carola and Rikeit, Paul and R{\"o}blitz, Susanna and Knaus, Petra and Sch{\"u}tte, Christof}, title = {Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density}, booktitle = {10th International BMP conference, 2014, Berlin, Germany}, year = {2014}, language = {en} } @misc{Brust2017, type = {Master Thesis}, author = {Brust, Lisa}, title = {Molek{\"u}ldynamik-Simulation via eines Faltungsansatzes im Potential}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65198}, year = {2017}, language = {de} } @misc{Roehl2017, type = {Master Thesis}, author = {R{\"o}hl, Susanne}, title = {Computing the minimal rebinding effect for nonreversible processes}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65203}, year = {2017}, language = {en} } @misc{Roehm2017, type = {Master Thesis}, author = {R{\"o}hm, Jonas}, title = {Non-Negative Matrix Factorization for Raman Data Spectral Analysis}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65217}, year = {2017}, language = {en} } @misc{Grever2016, type = {Master Thesis}, author = {Grever, Andreas}, title = {Estimating Missing Entries of a Partial Mean First Passage Time Matrix}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65228}, year = {2016}, language = {en} } @misc{Solleder2016, type = {Master Thesis}, author = {Solleder, Marthe}, title = {Molecular Dynamics Simulations : What is the Effect of a Spin Probe on the Drug Loading of a Nanocarrier}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65239}, year = {2016}, language = {en} } @misc{Schoepke2015, type = {Master Thesis}, author = {Sch{\"o}pke, Jessica}, title = {Korrelation f{\"u}r lineare und nichtlineare Zusammenh{\"a}nge}, year = {2015}, language = {de} } @misc{Tumescheit2014, type = {Master Thesis}, author = {Tumescheit, Charlotte}, title = {Using Birkhoff-von Neumann und Sinkhorn Algorithm to Find Dominating Cycles}, year = {2014}, language = {en} } @misc{Frech2014, type = {Master Thesis}, author = {Frech, Ralf}, title = {Das Konzept der Flussdichte und sein Bezug zur Bohmschen Mechanik}, year = {2014}, language = {de} } @misc{Makarenko2017, type = {Master Thesis}, author = {Makarenko, Oleksandra}, title = {Square Root Approximation und statistische Umgewichtungstechnik f{\"u}r das Faltungsverhalten von Polymerb{\"u}rsten}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65283}, year = {2017}, language = {de} }