@article{SchnauberThomaHeineetal.2016, author = {Schnauber, Peter and Thoma, Alexander and Heine, Christoph V. and Schlehahn, Alexander and Gantz, Liron and Gschrey, Manuel and Schmidt, Ronny and Hopfmann, Caspar and Wohlfeil, Benjamin and Schulze, Jan-Hindrick and Strittmatter, Andre and Heindel, Tobias and Rodt, Sven and Woggon, Ulrike and Gershoni, David and Reitzenstein, Stephan}, title = {Bright Single-Photon Sources Based on Anti-Reflection Coated Deterministic Quantum Dot Microlenses}, volume = {4}, journal = {Technologies}, number = {1}, doi = {10.3390/technologies4010001}, pages = {1}, year = {2016}, language = {en} } @article{WolffGutscheSteeletal.2015, author = {Wolff, Christian and Gutsche, Philipp and Steel, Michael J. and Eggleton, Benjamin J. and Poulton, Christopher G.}, title = {Power limits and a figure of merit for stimulated Brillouin scattering in the presence of third and fifth order loss}, volume = {23}, journal = {Opt. Express}, number = {20}, arxiv = {http://arxiv.org/abs/1508.02458}, doi = {10.1364/OE.23.026628}, pages = {26628 -- 26638}, year = {2015}, abstract = {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.}, language = {en} } @article{KryvenRoeblitzSchuette2015, author = {Kryven, Ivan and R{\"o}blitz, Susanna and Sch{\"u}tte, Christof}, title = {Solution of the chemical master equation by radial basis functions approximation with interface tracking}, volume = {9}, journal = {BMC Systems Biology}, number = {67}, doi = {10.1186/s12918-015-0210-y}, pages = {1 -- 12}, year = {2015}, abstract = {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}, language = {en} } @inproceedings{BoethDudaHinzmannetal.2015, author = {Boeth, Heide and Duda, Georg and Hinzmann, Daniel and Taylor, William R. and Ehrig, Rainald and Witaschek, Tom and Buttgereit, Frank}, title = {Objektive Quantifizierung der Morgensteifigkeit als Parameter f{\"u}r rheumatoide Arthritis im Metacarpophalangealgelenk}, booktitle = {9. Jahrestagung der Deutschen Gesellschaft f{\"u}r Biomechanik (DGfB), Bonn}, year = {2015}, language = {de} } @inproceedings{BurgerHammerschmidtHerrmannetal.2015, author = {Burger, Sven and Hammerschmidt, Martin and Herrmann, Sven and Pomplun, Jan and Schmidt, Frank}, title = {Reduced basis methods for optimization of nano-photonic devices}, booktitle = {Proc. Int. Conf. Numerical Simulation of Optoelectronic Devices (NUSOD)}, doi = {10.1109/NUSOD.2015.7292871}, pages = {159}, year = {2015}, language = {en} } @article{EncisoSchuetteDelleSite2015, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {Influence of pH and sequence in peptide aggregation via molecular simulation}, volume = {143}, journal = {Journal of Chemical Physics}, number = {24}, doi = {https://doi.org/10.1063/1.4935707}, year = {2015}, language = {en} } @misc{WeberQuer2015, author = {Weber, Marcus and Quer, Jannes}, title = {Estimating exit rates in rare event dynamical systems via extrapolation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56622}, year = {2015}, abstract = {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.}, language = {en} } @misc{EhrigDierkesSchaeferetal.2016, author = {Ehrig, Rainald and Dierkes, Thomas and Sch{\"a}fer, Stefan and R{\"o}blitz, Susanna and Tronci, Enrico and Mancini, Toni and Salvo, Ivano and Alimguzhin, Vadim and Mari, Federico and Melatti, Igor and Massini, Annalisa and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian and Leeners, Brigitte}, title = {An Integrative Approach for Model Driven Computation of Treatments in Reproductive Medicine}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57103}, year = {2016}, abstract = {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.}, language = {en} } @misc{DeuflhardHege2015, author = {Deuflhard, Peter and Hege, Hans-Christian}, title = {Raumtiefe in Malerei und Computergrafik}, journal = {R{\"a}ume - Bilder - Kulturen}, editor = {Lepper, Verena and Deuflhard, Peter and Markschies, Christoph}, publisher = {Walter De Gruyter}, isbn = {978-3-11-035993-0}, pages = {33 -- 46}, year = {2015}, abstract = {Einf{\"u}hrung: Die Tiefenwirkung dreidimensionaler R{\"a}ume 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 europ{\"a}ischen Malerei. Hieraus abgeleitete Prinzipien, soweit sie im Rechner realisierbar scheinen, stellen wir in Kap. 3 am Beispiel moderner Methoden der mathematischen Visualisierung vor.}, language = {de} } @book{OPUS4-5717, title = {R{\"a}ume - Bilder - Kulturen}, editor = {Lepper, Verena and Deuflhard, Peter and Markschies, Christoph}, publisher = {De Gruyter}, isbn = {978-3-11-035993-0}, year = {2015}, language = {de} } @misc{WillenbockelSchuette2016, author = {Willenbockel, Christian Tobias and Sch{\"u}tte, Christof}, title = {Variational Bayesian Inference and Model Selection for the Stochastic Block Model with Irrelevant Vertices}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57003}, year = {2016}, abstract = {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.}, language = {en} } @misc{StoetzelEhrigBoeretal.2016, author = {St{\"o}tzel, Claudia and Ehrig, Rainald and Boer, H. Marike T. and Pl{\"o}ntzke, Julia and R{\"o}blitz, Susanna}, title = {Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57039}, year = {2016}, abstract = {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.}, language = {en} } @article{LedentsovJrShchukinLedentsovJretal.2016, author = {Ledentsov, Jr., Nikolay and Shchukin, Vitaly and Ledentsov, Jr., Nikolay and Kropp, J{\"o}rg-R. and Burger, Sven and Schmidt, Frank}, title = {Direct Evidence of the Leaky Emission in Oxide-Confined Vertical Cavity Lasers}, volume = {52}, journal = {IEEE J. Quant. Electron.}, number = {3}, doi = {10.1109/JQE.2016.2518081}, pages = {2400207}, year = {2016}, language = {en} } @article{SchuetteSarich2015, author = {Sch{\"u}tte, Christof and Sarich, Marco}, title = {A Critical Appraisal of Markov State Models}, volume = {224}, journal = {The European Physical Journal Special Topics}, number = {12}, doi = {10.1140/epjst/e2015-02421-0}, pages = {2445 -- 2462}, year = {2015}, abstract = {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.}, language = {en} } @misc{PloentzkeBergStoetzeletal.2015, author = {Pl{\"o}ntzke, Julia and Berg, Mascha and St{\"o}tzel, Claudia and R{\"o}blitz, Susanna}, title = {A systems biology approach to bovine fertility and metabolism: Development of a glucose insulin model.}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56453}, year = {2015}, abstract = {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.}, language = {en} } @article{StoetzelRoeblitzSiebert2015, author = {St{\"o}tzel, Claudia and R{\"o}blitz, Susanna and Siebert, Heike}, title = {Complementing ODE-based System Analysis Using Boolean Networks Derived from an Euler-like Transformation}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0140954}, year = {2015}, language = {en} } @inproceedings{JaegerBarthHammerschmidtetal.2015, author = {J{\"a}ger, Klaus and Barth, Carlo and Hammerschmidt, Martin and Herrmann, Sven and Burger, Sven and Schmidt, Frank and Becker, Christiane}, title = {Sinusoidal Nanotextures for Coupling Light into c-Si Thin-Film Solar Cells}, booktitle = {Light, Energy and the Environement 2015}, doi = {10.1364/PV.2015.PTu4B.3}, pages = {PTu4B.3}, year = {2015}, language = {en} } @inproceedings{BarthJaegerBurgeretal.2015, author = {Barth, Carlo and J{\"a}ger, Klaus and Burger, Sven and Hammerschmidt, Martin and Schmidt, Frank and Becker, Christiane}, title = {Design of Photonic Crystals with Near-Surface Field Enhancement}, booktitle = {Light, Energy and the Environement 2015}, doi = {10.1364/PV.2015.JTu5A.9}, pages = {JTu5A.9}, year = {2015}, language = {en} } @inproceedings{ThomaSchnauberGschreyetal.2015, author = {Thoma, Alexander and Schnauber, Peter and Gschrey, Manuel and Schmidt, Ronny and Wohlfeil, Benjamin and Seifried, Marc and Schulze, Jan-Hindrick and Burger, Sven and Schmidt, Frank and Strittmatter, Andre and Rodt, Sven and Heindel, Tobias and Reitzenstein, Stephan}, title = {Indistinguishable Photons from Deterministic Quantum Dot Microlenses}, booktitle = {European Conference on Lasers and Electro-Optics - European Quantum Electronics Conference}, doi = {10.1364/IPRSN.2015.IS4A.6}, pages = {EA_8_5}, year = {2015}, language = {en} } @misc{KrauseFackeldeyKrause2013, author = {Krause, Dorian and Fackeldey, Konstantin and Krause, Rolf}, title = {A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements}, issn = {1438-0064}, doi = {10.1007/978-3-319-00786-1_14}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42354}, year = {2013}, abstract = {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.}, language = {en} } @misc{HartmannBanischSarichetal.2013, author = {Hartmann, Carsten and Banisch, Ralf and Sarich, Marco and Badowski, Thomas and Sch{\"u}tte, Christof}, title = {Characterization of Rare Events in Molecular Dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42410}, year = {2013}, abstract = {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.}, language = {en} } @misc{SarichBanischHartmannetal.2013, author = {Sarich, Marco and Banisch, Ralf and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Markov State Models for Rare Events in Molecular Dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42420}, year = {2013}, abstract = {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.}, language = {en} } @misc{GoetschelWeiserMaierhoferetal.2012, author = {G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane and Richter, Regina}, title = {Data Enhancement for Active Thermography}, journal = {E-book Proceedings, 11th International Conference on Quantitative Infrared Thermography, Naples}, editor = {Cardone, Gennaro}, year = {2012}, abstract = {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.}, language = {en} } @article{BujotzekSchuettNielsenetal.2014, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling}, volume = {52}, journal = {Journal of Mathematical Chemistry}, number = {3}, doi = {10.1007/s10910-013-0265-1}, pages = {781 -- 804}, year = {2014}, language = {de} } @article{WeberFackeldey2014, author = {Weber, Marcus and Fackeldey, Konstantin}, title = {Local Refinements in Classical Molecular Dynamics Simulations}, volume = {490}, journal = {J. Phys. Conf. Ser.}, pages = {012016}, year = {2014}, language = {en} } @article{Weiser2013, author = {Weiser, Martin}, title = {On goal-oriented adaptivity for elliptic optimal control problems}, volume = {28}, journal = {Opt. Meth. Softw.}, number = {13}, pages = {969 -- 992}, year = {2013}, abstract = {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.}, language = {en} } @article{DeuflhardSchielaWeiser2012, author = {Deuflhard, Peter and Schiela, Anton and Weiser, Martin}, title = {Mathematical Cancer Therapy Planning in Deep Regional Hyperthermia}, volume = {21}, journal = {Acta Numerica}, pages = {307 -- 378}, year = {2012}, abstract = {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.}, language = {en} } @misc{GoetschelWeiserSchiela2012, author = {G{\"o}tschel, Sebastian and Weiser, Martin and Schiela, Anton}, title = {Solving Optimal Control Problems with the Kaskade 7 Finite Element Toolbox}, journal = {Advances in DUNE}, editor = {Dedner, A. and Flemisch, B. and Kl{\"o}fkorn, R.}, publisher = {Springer}, pages = {101 -- 112}, year = {2012}, abstract = {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.}, language = {en} } @book{DieterGoetzKuemmereretal.2010, author = {Dieter, H. H. and G{\"o}tz, K. and K{\"u}mmerer, K. and Rechenberg, B. and Keil, F.}, title = {Handlungsm{\"o}glichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren R{\"u}ckst{\"a}nden in das Roh- und Trinkwasser.}, editor = {Dieter, H.H. and G{\"o}tz, K. and K{\"u}mmerer, K. and Rechenberg, B. and Keil, F.}, publisher = {Umweltbundesamt}, year = {2010}, language = {de} } @misc{SchuetteNielsenWeber2014, author = {Sch{\"u}tte, Christof and Nielsen, Adam and Weber, Marcus}, title = {Markov State Models and Molecular Alchemy}, issn = {1438-0064}, doi = {10.1080/00268976.2014.944597}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-46718}, year = {2014}, abstract = {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.}, language = {en} } @article{Weiser2015, author = {Weiser, Martin}, title = {Faster SDC convergence on non-equidistant grids by DIRK sweeps}, volume = {55}, journal = {BIT Numerical Mathematics}, number = {4}, doi = {10.1007/s10543-014-0540-y}, pages = {1219 -- 1241}, year = {2015}, abstract = {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.}, language = {en} } @article{WeiserGoetschel2012, author = {Weiser, Martin and G{\"o}tschel, Sebastian}, title = {State Trajectory Compression for Optimal Control with Parabolic PDEs}, volume = {34}, journal = {SIAM J. Sci. Comput.}, number = {1}, doi = {10.1137/11082172X}, pages = {A161 -- A184}, year = {2012}, abstract = {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.}, language = {en} } @misc{NadobnyWeihrauchWeiseretal.2007, author = {Nadobny, Johanna and Weihrauch, Mirko and Weiser, Martin and Gellermann, Johanna and Wlodarczyk, Waldemar and Budach, Volker and Wust, Peter}, title = {Advances in the Planning and Control of the MR-guided Regional Hyperthermia Applications}, journal = {Proc. Int. Conf. Electromagnetics in Advanced Applications, ICEAA 2007, Torino, Italy}, pages = {1010 -- 1013}, year = {2007}, language = {en} } @article{GoetschelWeiser2010, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {State Trajectory Compression in Optimal Control}, volume = {10}, journal = {PAMM}, number = {1}, doi = {10.1002/pamm.201010282}, pages = {579 -- 580}, year = {2010}, abstract = {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.}, language = {en} } @misc{Weiser2010, author = {Weiser, Martin}, title = {Delayed Residual Compensation for Bidomain Equations}, volume = {1281}, journal = {AIP Conference Proceedings}, doi = {10.1063/1.3498495}, pages = {419 -- 422}, year = {2010}, abstract = {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.}, language = {en} } @misc{WeiserErdmannDeuflhard2010, author = {Weiser, Martin and Erdmann, Bodo and Deuflhard, Peter}, title = {On Efficiency and Accuracy in Cardioelectric Simulation}, journal = {Progress in Industrial Mathematics at ECMI 2008}, editor = {Wilson, E. and Fitt, A. and Ockendon, H. and Norbury, J.}, publisher = {Springer}, pages = {371 -- 376}, year = {2010}, abstract = {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.}, language = {en} } @article{WilhelmsSeemannWeiseretal.2010, author = {Wilhelms, Mathias and Seemann, Gunnar and Weiser, Martin and D{\"o}ssel, Olaf}, title = {Benchmarking Solvers of the Monodomain Equation in Cardiac Electrophysiological Modeling}, volume = {55}, journal = {Biomed. Engineer.}, doi = {10.1515/BMT.2010.712}, pages = {99 -- 102}, year = {2010}, language = {en} } @misc{WustWeihrauchWeiseretal.2010, author = {Wust, Peter and Weihrauch, Mirko and Weiser, Martin and Gellermann, Johanna and Eisenhardt, Steffen and Chobrok, Thorsten and Budach, Volker}, title = {Optimization of clinical radiofrequency hyperthermia by use of MR-thermography in a hybrid system}, journal = {World Congress on Medical Physics and Biomedical Engineering, September 2009, Munich, Germany}, editor = {D{\"o}ssel, O. and Schlegel, W. and Magjarevic, R.}, publisher = {Springer}, pages = {174 -- 175}, year = {2010}, language = {en} } @article{AndraeDurmazFackeldeyetal.2013, author = {Andrae, Karsten and Durmaz, Vedat and Fackeldey, Konstantin and Scharkoi, Olga and Weber, Marcus}, title = {Medizin aus dem Computer}, volume = {62}, journal = {Der Anaesthesist}, number = {7}, publisher = {Springer}, doi = {10.1007/s00101-013-2202-x}, pages = {561 -- 557}, year = {2013}, language = {de} } @article{LubkollSchielaWeiser2014, author = {Lubkoll, Lars and Schiela, Anton and Weiser, Martin}, title = {An optimal control problem in polyconvex hyperelasticity}, volume = {52}, journal = {SIAM J. Control Opt.}, number = {3}, doi = {10.1137/120876629}, pages = {1403 -- 1422}, year = {2014}, abstract = {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.}, language = {en} } @article{ScharkoiEsslingerBeckeretal.2011, author = {Scharkoi, O. and Esslinger, Susanne and Becker, Roland and Weber, Marcus and Nehls, Irene}, title = {Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites}, volume = {73}, journal = {Organohalogen Compounds}, pages = {730 -- 733}, year = {2011}, language = {de} } @article{DurmazSchmidtSabrietal.2013, author = {Durmaz, Vedat and Schmidt, Sebastian and Sabri, Peggy and Piechotta, Christian and Weber, Marcus}, title = {A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens}, volume = {53}, journal = {Journal of Chemical Information and Modeling}, number = {10}, pages = {2681 -- 2688}, year = {2013}, language = {en} } @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} }