Non-Equilibrium Markov State Modeling of the Globule-Stretch Transition

TL;DR

This paper introduces a systematic method to build coarse-grained Markov state models from molecular dynamics data for non-equilibrium steady states, applied to polymer globule-stretch transitions in shear flow.

Contribution

The paper presents a novel approach for constructing Markov state models from non-equilibrium molecular dynamics data, specifically applied to polymer transitions under shear flow.

Findings

Folding/unfolding rates match detailed models

Transitions occur through the same configuration space region

Different cycles characterize folding and unfolding processes

Abstract

We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding/unfolding rates of the coarse-grained model agree with the original detailed model. We demonstrate that the folding/unfolding proceeds through the same narrow region of configuration space but along different cycles.