@article{NoeSmithSchuette2007, author = {No{\´e}, Frank and Smith, J. and Sch{\"u}tte, Christof}, title = {A network-based approach to biomolecular dynamics}, series = {From Computational Biophysics to Systems Biology (CBSB07). Editors}, volume = {NIC Series 36}, journal = {From Computational Biophysics to Systems Biology (CBSB07). Editors}, publisher = {John von Neumann Institute for Computing, J{\"u}lich}, year = {2007}, language = {en} } @article{SchuetteNoeMeerbachetal.2009, author = {Sch{\"u}tte, Christof and No{\´e}, Frank and Meerbach, E. and Metzner, Ph. and Hartmann, Carsten}, title = {Conformation Dynamics}, series = {Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.),}, journal = {Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.),}, publisher = {EMS publishing house}, doi = {10.4171/056-1/15}, pages = {297 -- 335}, year = {2009}, language = {en} } @article{NoeSchuetteVandenEijndenetal.2009, author = {No{\´e}, Frank and Sch{\"u}tte, Christof and Vanden-Eijnden, E. and Reich, L. and Weikl, T.}, title = {Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations}, series = {Proc. Natl. Acad. Sci. USA}, volume = {106}, journal = {Proc. Natl. Acad. Sci. USA}, number = {45}, doi = {10.1073/pnas.0905466106}, pages = {19011 -- 19016}, year = {2009}, language = {en} } @article{KostreSchuetteNoeetal.2021, author = {Kostre, Margarita and Sch{\"u}tte, Christof and No{\´e}, Frank and del Razo Sarmina, Mauricio}, title = {Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs}, series = {Multiscale Modeling \& Simulation}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {4}, publisher = {Society for Industrial and Applied Mathematics}, doi = {10.1137/20M1352739}, pages = {1659 -- 1683}, year = {2021}, abstract = {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.}, language = {en} } @article{HorenkoHartmannSchuetteetal.2007, author = {Horenko, Illia and Hartmann, Carsten and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes}, series = {Phys. Rev. E}, volume = {76}, journal = {Phys. Rev. E}, number = {01}, doi = {10.1103/PhysRevE.76.016706}, pages = {016706}, year = {2007}, language = {en} } @article{KlusNueskeKoltaietal., author = {Klus, Stefan and N{\"u}ske, Feliks and Koltai, Peter and Wu, Hao and Kevrekidis, Ioannis and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Data-driven model reduction and transfer operator approximation}, series = {Journal of Nonlinear Science}, volume = {28}, journal = {Journal of Nonlinear Science}, number = {3}, doi = {10.1007/s00332-017-9437-7}, pages = {985 -- 1010}, language = {en} } @misc{SchuetteDeuflhardNoeetal., author = {Sch{\"u}tte, Christof and Deuflhard, Peter and No{\´e}, Frank and Weber, Marcus}, title = {Design of functional molecules}, series = {MATHEON-Mathematics for Key Technologies}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Sch{\"u}tte, Christof and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, pages = {49 -- 65}, language = {en} } @article{SenneTrendelkampSchroerMeyetal.2012, author = {Senne, M. and Trendelkamp-Schroer, B. and Mey, A. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {EMMA - A software package for Markov model building and analysis}, series = {Journal of Chemical Theory and Computation}, volume = {8}, journal = {Journal of Chemical Theory and Computation}, doi = {10.1021/ct300274u}, pages = {2223 -- 2238}, year = {2012}, language = {en} } @article{MetznerNoeSchuette2009, author = {Metzner, Ph. and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {Estimating the Sampling Error}, series = {Phys. Rev. E}, volume = {80}, journal = {Phys. Rev. E}, number = {2}, publisher = {American Physical Society}, doi = {10.1103/PhysRevE.80.021106}, pages = {021106}, year = {2009}, language = {en} } @article{NoeHorenkoSchuetteetal.2007, author = {No{\´e}, Frank and Horenko, Illia and Sch{\"u}tte, Christof and Smith, J.}, title = {Hierarchical Analysis of Conformational Dynamics in Biomolecules}, series = {J. Chem. Phys.}, volume = {126}, journal = {J. Chem. Phys.}, number = {15}, doi = {10.1063/1.2714539}, pages = {155102}, year = {2007}, language = {en} }