Repository: Freie Universität Berlin, Math Department

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Number of items: 22.

2019

Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 0021-9606, ESSN: 1089-7690

Pinamonti, G. and Paul, F. and Noé, F. and Rodriguez, A. and Bussi, G. (2019) The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 0021-9606, ESSN: 1089-7690

Wang, J. and Olsson, S. and Wehmeyer, C. and Perez, A. and Charron, N.E. and de Fabritiis, G. and Noé, F. and Clementi, C. (2019) Machine Learning of coarse-grained Molecular Dynamics Force Fields. ACS Cent. Sci., 5 (5). pp. 755-767. ISSN 2374-7943, ESSN: 2374-7951

Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 1553-7358

Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 0021-9606, ESSN: 1089-7690

2018

Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished)

Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524

Fröhner, Chr. and Noé, F. (2018) Reversible interacting-particle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 11240-11250.

del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). 044102. ISSN 0021-9606, ESSN: 1089-7690

Dibak, M. and del Razo, M.J. and De Sancho, D. and Schütte, Ch. and Noé, F. (2018) MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 0021-9606

Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901.

2017

Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690

Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095).

Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18.

Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270.

Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934.

Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873.

2016

Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107.

Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46.

Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424

2015

Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101.

Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542.

This list was generated on Sat Jul 20 14:41:09 2019 CEST.