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 - 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 - 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 - 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 - 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 - 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 - 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 - Wulkow, Michael T1 - Modellierung von Einleitungen in kleine Fließgewässer JF - gwf Wasser Abwasser Y1 - 1996 VL - 137 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 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 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 -