# Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics

Source: [Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics](<https://www.sota2.com/research/paper/68fa40ab1e209131ce8f52fd>)

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

Data updated: 2025-10-25T02:54:45.351Z

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

Published: 2021-03-11T19:00:00.000Z

## Abstract

A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD lacks a mathematical framework to derive coupling schemes; is limited to isotropic ligands in a single conformational state, and is lacking a multi-particle extensions. In this work, we address these needs by developing a general MSM/RD framework by coarse-graining molecular dynamics into hybrid switching diffusion processes. Given enough data to parametrize the model, it is capable of modeling protein-protein interactions over large time- and length-scales, and it can be extended to handle multiple molecules. We derive the MSM/RD framework, and we implement and verify it for two protein-protein benchmark systems and one multiparticle implementation to model the formation of pentameric ring molecules. To enable reproducibility, we have published our code in the MSM/RD software package.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2103.06889>)

[PDF](<https://arxiv.org/pdf/2103.06889.pdf>)