2023
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Enric Ribera Borrell, Jannes Quer, Lorenz Richter, Christof Schütte |
Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics
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SIAM Journal on Scientific Computing (SISC), pp. S298-S323, 2023 (epub ahead of print) |
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Christof Schütte, Stefan Klus, Carsten Hartmann |
Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning
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Acta Numerica, Vol.32, pp. 517-673, 2023 (preprint available as ZIB-Report 22-25) |
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Alexander Sikorski
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VoronoiGraph.jl
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2023 |
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2022
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Jannes Quer, Enric Ribera Borrell |
Connecting Stochastic Optimal Control and Reinforcement Learning
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Journal of Mathematical Physics, 2022 (under review) |
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arXiv
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Martin Heida, Alexander Sikorski, Marcus Weber |
Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension
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SIAM Journal on Numerical Analysis, 2022 (under review) |
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DOI
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Alexander Sikorski, Enric Ribera Borrell, Marcus Weber |
Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN
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Journal of Mathematical Physics, 2022 (under review) |
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arXiv
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Anna-Simone Frank, Alexander Sikorski, Susanna Röblitz |
Spectral clustering of Markov chain transition matrices with complex eigenvalues
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Journal of Computational and Applied Mathematics, 2022 (under review) |
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arXiv
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2021
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Renata Sechi, Alexander Sikorski, Marcus Weber |
Estimation of the Koopman Generator by Newton's Extrapolation
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Multiscale Modeling and Simulation, 19(2), pp. 758-774, 2021 |
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Enric Ribera Borrell, Jannes Quer, Lorenz Richter, Christof Schütte |
Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics
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ZIB-Report 21-40 |
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Renata Sechi, Marcus Weber, Karsten Heyne |
MSM building and projection for the analysis of time-resolved spectra
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Proceedings in Applied Mathematics and Mechanics, p. e202100102, 2021 |
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URN
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Luca Donati, Marcus Weber, Bettina G. Keller |
Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux
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Journal of Physics: Condensed Matter, 33(11), p. 115902, 2021 |
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Alexander Sikorski, Marcus Weber, Christof Schütte |
The Augmented Jump Chain
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Advanced Theory and Simulations, 4(4), 2021 |
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arXiv
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2019
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Wei Zhang
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Ergodic SDEs on submanifolds and related numerical sampling schemes
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ESAIM: Mathematical Modelling and Numerical Analysis, 2019 |
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arXiv
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Konstantin Fackeldey, Peter Koltai, Peter Nevir, Henning Rust, Axel Schild, Marcus Weber |
From metastable to coherent sets - Time-discretization schemes
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Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol.29, pp. 012101-012101, 2019 (preprint available as ZIB-Report 17-74) |
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Carsten Hartmann, Christof Schütte, Wei Zhang |
Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms
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Journal of Statistical Physics, 175(6), pp. 1214-1261, 2019 |
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arXiv
DOI
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Tony Lelièvre, Wei Zhang |
Pathwise estimates for effective dynamics: the case of nonlinear vectorial reaction coordinates
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Multiscale Modeling and Simulation, pp. 1019-1051, 2019 |
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arXiv
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2018
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Jannes Quer, Luca Donati, Bettina Keller, Marcus Weber |
An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates
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SIAM Journal on Scientific Computing, 40(2), pp. A653-A670, 2018 (preprint available as ZIB-Report 17-09) |
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Stefan Klus, Feliks Nüske, Peter Koltai, Hao Wu, Ioannis Kevrekidis, Christof Schütte, Frank Noé |
Data-driven model reduction and transfer operator approximation
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Journal of Nonlinear Science, 28(3), pp. 985-1010, 2018 |
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DOI
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Luca Donati, Martin Heida, Bettina G. Keller, Marcus Weber |
Estimation of the infinitesimal generator by square-root approximation
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J. Phys.: Condens. Matter, 30(42), pp. 425201-425201, 2018 |
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DOI
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Marcus Weber
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Implications of PCCA+ in Molecular Simulation
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Computation, 6(1), p. 20, 2018 |
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Jannes Quer |
Importance Sampling for metastable dynamical systems in molecular dynamics
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Doctoral thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2018 |
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Wei Zhang, Carsten Hartmann, Max von Kleist |
Optimal control of Markov jump processes: Asymptotic analysis, algorithms and applications to the modeling of chemical reaction systems
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Communications in Mathematical Sciences, pp. 293-331, 2018 |
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Peter Koltai, Hao Wu, Frank Noé, Christof Schütte |
Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics
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Computation, 6(1), 2018 |
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Konstantin Fackeldey, Alexander Sikorski, Marcus Weber |
Spectral Clustering for Non-Reversible Markov Chains
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Computational and Applied Mathematics, 37(5), pp. 6376-6391, 2018 (preprint available as ) |
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DOI
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Marcus Weber
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Supplementary: Implications of PCCA+ in Molecular Simulation
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2018 |
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2017
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Philipp Lorenz, Frederik Wolf, Jonas Braun, Natasa Djurdjevac Conrad, Philipp Hövel |
Capturing the Dynamics of Hashtag-Communities
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International Workshop on Complex Networks and their Applications, pp. 401-413, 2017 |
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Marcus Weber
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Eigenvalues of non-reversible Markov chains – A case study
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ZIB-Report 17-13 |
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Konstantin Fackeldey, Amir Niknejad, Marcus Weber |
Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation
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Special Matrices, pp. 73-81, 2017 |
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Konstantin Fackeldey, Marcus Weber |
GenPCCA -- Markov State Models for Non-Equilibrium Steady States
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Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29, pp. 70-80, 2017 |
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Carsten Hartmann, Christof Schütte, Marcus Weber, Wei Zhang |
Importance sampling in path space for diffusion processes with slow-fast variables
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Probability Theory and Related Fields, pp. 1-52, 2017 |
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Marcus Weber, Konstantin Fackeldey, Christof Schütte |
Set-Free Markov State Model Building
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Journal of Chemical Physics, 146(12), 2017 (preprint available as ZIB-Report 17-10) |
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DOI
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Jannes Quer, Han Cheng Lie |
Some connections between importance sampling and enhanced sampling methods in molecular dynamics
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Journal of Chemical Physics, 2017 (accepted for publication on 2017-10-31, preprint available as ZIB-Report 17-30) |
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S. Rüdrich, Marco Sarich, Christof Schütte |
Utilizing hitting times for finding metastable sets in non-reversible Markov chains
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Journal of Comp. Dynamics, 2017 (under review, preprint available as ) |
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Carsten Hartmann, Lorenz Richter, Christof Schütte, Wei Zhang |
Variational characterization of free energy: theory and algorithms
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Entropy, 19(11), 2017 (preprint available as ) |
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2016
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Carsten Hartmann, Christof Schütte, Wei Zhang |
Model reduction algorithms for optimal control and importance sampling of diffusions
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Nonlinearity, 29(8), pp. 2298-2326, 2016 |
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DOI
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Stefan Klus, Peter Koltai, Christof Schütte |
On the numerical approximation of the Perron-Frobenius and Koopman operator
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Journal of Computational Dynamics, 3(1), pp. 51-77, 2016 |
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Adam Nielsen |
The Monte Carlo Computation Error of Transition Probabilities
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Statistics & Probability Letters, Vol.118, pp. 163-170, 2016 (preprint available as ZIB-Report 16-37) |
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2015
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Christoph Lange |
Approximating and Clustering Markov Chains via Kullback-Leibler-Divergence
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Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2015 |
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Adam Nielsen, Marcus Weber |
Computing the nearest reversible Markov chain
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Numerical Linear Algebra with Applications, 22(3), pp. 483-499, 2015 (preprint available as ) |
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Oliver Zwingel |
Die Cross-Entropy-Methode für stochastische Optimierungsprobleme
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Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2015 |
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Marcus Weber, Jannes Quer |
Estimating exit rates in rare event dynamical systems via extrapolation
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ZIB-Report 15-54 |
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URN
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Christof Schütte, Adam Nielsen, Marcus Weber |
Markov State Models and Molecular Alchemy
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Molecular Physics, 113(1), pp. 69-78, 2015 (preprint available as ) |
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2014
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Wei Zhang, Han Wang, Carsten Hartmann, Marcus Weber, Christof Schütte |
Applications of the cross-entropy method to importance sampling and optimal control of diffusions
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Siam Journal on Scientific Computing, 36(6), pp. A2654-A2672, 2014 (preprint available as ZIB-Report 14-10) |
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DOI
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Han Wang, Christof Schütte |
Building Markov State Models for Periodically Driven Non-Equilibrium Systems
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ZIB-Report 14-46 |
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URN
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Marco Sarich, Christof Schütte |
Markov Model Theory
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An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Vol.797, pp. 23-44, Gregory R. Bowman, Vijay S. Pande, Frank Noé (Eds.), Springer, 2014 |
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Marco Sarich, Natasa Djurdjevac Conrad, Sharon Bruckner, Tim Conrad, Christof Schütte |
Modularity revisited: A novel dynamics-based concept for decomposing complex networks
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Journal of Computational Dynamics, 1(1), pp. 191-212, 2014 |
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Molecular Dynamics Simulation
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Giovanni Ciccotti, Mauro Ferrario, Christof Schütte (Eds.), Multidisciplinary Digital Publishing Institute (MDPI), 2014 |
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Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber |
ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling
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Journal of Mathematical Chemistry, 52(3), pp. 781-804, 2014 (preprint available as ZIB-Report 13-58) |
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2013
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Marco Sarich, Ralf Banisch, Carsten Hartmann, Christof Schütte |
Markov State Models for Rare Events in Molecular Dynamics
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Entropy (Special Issue), 16(1), pp. 258-286, 2013 (preprint available as ) |
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2012
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Han Cheng Lie |
A Meshless Method for Conformational Analysis
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Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2012 |
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