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

Source: [MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations](<https://www.sota2.com/research/paper/68fa37d11e209131ce8b52b8>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-27T03:51:39.248Z

Authors: Manuel Dibak, Mauricio J. del Razo, David De Sancho, Christof Sch\\"utte, Frank No\\'e

Published: 2017-12-21T18:40:20.000Z

## 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.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1712.08149>)

[PDF](<https://arxiv.org/pdf/1712.08149.pdf>)