TY - GEN A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On metastability and Markov state models for non-stationary molecular dynamics BT - 2016 Editor's Choice of The Journal of Chemical Physics T2 - The Journal of Chemical Physics N2 - We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples. T3 - ZIB-Report - 16-11 KW - coherent set, KW - Markov state model KW - non-equilibrium molecular dynamics KW - metastability Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57869 SN - 1438-0064 VL - 174103 ET - 145 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Poulikakos, Lisa A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Time-harmonic optical chirality in inhomogeneous space JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2209551 VL - 9756 SP - 97560X ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Weber, Marcus A1 - Schütte, Christof T1 - Finding dominant structures of nonreversible Markov processes JF - Multiscale Modeling and Simulation Y1 - 2016 U6 - https://doi.org/10.1137/15M1032272 VL - 14 IS - 4 SP - 1319 EP - 1340 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Pomplun, Jan A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs JF - Proc. SPIE N2 - Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58187 VL - 9756 SP - 97561R ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures JF - Proc. SPIE N2 - Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell's equation. Highly accurate geometrical modelling and numerical accuracy at low computational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scattering at optical wavelengths of periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range. Y1 - 2016 U6 - https://doi.org/10.1117/12.2212367 VL - 9742 SP - 97420M ER - TY - GEN A1 - Gutsche, Philipp A1 - Läuter, Matthias A1 - Schmidt, Frank T1 - Parameter-dependent Parallel Block Sparse Arnoldi and Döhler Algorithms on Distributed Systems N2 - We summarize the basics and first results of the analyses within our ZIB Bridge Project and give an outlook on further studies broadening the usage of hardware acceleration within the Finite Element Method (FEM) based solution of Maxwell’s equations. T3 - ZIB-Report - 16-15 KW - Generalized Eigenvalue Problem KW - Many Integrated Core Coprocessor (MIC) KW - Finite Element Method Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58202 SN - 1438-0064 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for electromagnetic scattering problem: a case study for FinFETs JF - Optical and Quantum Electronics N2 - Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occurring e. g. in optical metrology. The reduced basis method pre- sented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources. Y1 - 2016 U6 - https://doi.org/10.1007/s11082-016-0530-1 VL - 48 SP - 250 ER - TY - THES A1 - Nielsen, Adam T1 - Computation Schemes for Transfer Operators Y1 - 2016 ER - TY - THES A1 - Sikorski, Alexander T1 - PCCA+ and Its Application to Spatial Time Series Clustering Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58769 ER - TY - GEN A1 - Bojarovski, Stefan A1 - Hege, Hans-Christian A1 - Lie, Han Cheng A1 - Weber, Marcus T1 - Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales T2 - Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany N2 - Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models. Y1 - 2015 ER - TY - BOOK A1 - Weiser, Martin T1 - Inside Finite Elements N2 - All relevant implementation aspects of finite element methods are discussed in this book. The focus is on algorithms and data structures as well as on their concrete implementation. Theory is covered as far as it gives insight into the construction of algorithms.Throughout the exercises a complete FE-solver for scalar 2D problems will be implemented in Matlab/Octave. Y1 - 2016 PB - De Gruyter ER - TY - JOUR A1 - Krebek, von, Larissa K. S. A1 - Achazi, Andreas J. A1 - Solleder, Marthe A1 - Weber, Marcus A1 - Paulus, Beate A1 - Schalley, Christoph A. T1 - Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements JF - Chem. Eur. J. Y1 - 2016 U6 - https://doi.org/10.1002/chem.201603098 N1 - Has been announced under the title: Cooperativity in Multivalent Binding: A Detailed Experimental and Theoretical Thermochemical Study of Divalent Crown Ether-Ammonium Complexes VL - 22 IS - 43 SP - 15475 EP - 15484 ER -