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

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.

References in corpus (2)

• Thermodynamic uncertainty relation for biomolecular processes
• Entropy production and coarse-graining in Markov processes

Cited by in corpus (3)

• Coarse-Grained Modelling Out of Equilibrium
• Towards a Benchmark for Markov State Models: The Folding of HP35
• Modeling of biomolecular machines in non-equilibrium steady states