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.
Categories: cond-mat.soft cond-mat.stat-mech