Repository: Freie Universität Berlin, Math Department

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

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

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Official URL: https://dx.doi.org/10.1063/1.5020294

Abstract

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B <--> C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

Item Type:Article
Additional Information:SFB1114 Preprint in arXiv:1712.08149 (https://arxiv.org/abs/1712.08149)
Subjects:Mathematical and Computer Sciences
Mathematical and Computer Sciences > Mathematics
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science
Department of Mathematics and Computer Science > Institute of Mathematics
Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:2304
Deposited By: BioComp Admin
Deposited On:12 Mar 2019 14:36
Last Modified:25 Jun 2019 14:24

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