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 reactiondiffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 00219606

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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 highthroughput MD with Markov state models (MSMs), it is now possible to obtain longtimescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particlebased reactiondiffusion (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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