TY - JOUR A1 - Noé, Frank A1 - Smith, J. A1 - Schütte, Christof T1 - A network-based approach to biomolecular dynamics JF - From Computational Biophysics to Systems Biology (CBSB07). Editors Y1 - 2007 UR - http://publications.imp.fu-berlin.de/319/ VL - NIC Series 36 PB - John von Neumann Institute for Computing, Jülich ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Meerbach, E. A1 - Metzner, Ph. A1 - Hartmann, Carsten T1 - Conformation Dynamics JF - Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), Y1 - 2009 UR - http://publications.imp.fu-berlin.de/110/ U6 - https://doi.org/10.4171/056-1/15 SP - 297 EP - 335 PB - EMS publishing house ER - TY - JOUR A1 - Noé, Frank A1 - Schütte, Christof A1 - Vanden-Eijnden, E. A1 - Reich, L. A1 - Weikl, T. T1 - Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations JF - Proc. Natl. Acad. Sci. USA Y1 - 2009 UR - http://publications.imp.fu-berlin.de/826/ U6 - https://doi.org/10.1073/pnas.0905466106 VL - 106 IS - 45 SP - 19011 EP - 19016 ER - TY - JOUR A1 - Kostre, Margarita A1 - Schütte, Christof A1 - Noé, Frank A1 - del Razo Sarmina, Mauricio T1 - Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs JF - Multiscale Modeling & Simulation N2 - Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications. Y1 - 2021 U6 - https://doi.org/10.1137/20M1352739 VL - 19 IS - 4 SP - 1659 EP - 1683 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Horenko, Illia A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/31/ U6 - https://doi.org/10.1103/PhysRevE.76.016706 VL - 76 IS - 01 SP - 016706 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Koltai, Peter A1 - Wu, Hao A1 - Kevrekidis, Ioannis A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-driven model reduction and transfer operator approximation JF - Journal of Nonlinear Science Y1 - 2018 UR - https://link.springer.com/article/10.1007/s00332-017-9437-7 U6 - https://doi.org/10.1007/s00332-017-9437-7 VL - 28 IS - 3 SP - 985 EP - 1010 ER - TY - GEN A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Noé, Frank A1 - Weber, Marcus ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Design of functional molecules T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 49 EP - 65 PB - European Mathematical Society ER - TY - JOUR A1 - Senne, M. A1 - Trendelkamp-Schroer, B. A1 - Mey, A. A1 - Schütte, Christof A1 - Noé, Frank T1 - EMMA - A software package for Markov model building and analysis JF - Journal of Chemical Theory and Computation Y1 - 2012 U6 - https://doi.org/10.1021/ct300274u VL - 8 SP - 2223 EP - 2238 ER - TY - JOUR A1 - Metzner, Ph. A1 - Noé, Frank A1 - Schütte, Christof T1 - Estimating the Sampling Error JF - Phys. Rev. E Y1 - 2009 UR - http://publications.imp.fu-berlin.de/17/ U6 - https://doi.org/10.1103/PhysRevE.80.021106 VL - 80 IS - 2 SP - 021106 PB - American Physical Society ER - TY - JOUR A1 - Noé, Frank A1 - Horenko, Illia A1 - Schütte, Christof A1 - Smith, J. T1 - Hierarchical Analysis of Conformational Dynamics in Biomolecules JF - J. Chem. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/37/ U6 - https://doi.org/10.1063/1.2714539 VL - 126 IS - 15 SP - 155102 ER -