A Multiscale Perturbation Expansion Approach for Markov State Modeling of Nonstationary Molecular Dynamics

Abstract

We investigate metastable dynamical systems subject to nonstationary forcing as they appear in molecular dynamics for systems driven by external fields. We show that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation---a Markov state model---can be assembled by constructing two equilibrium Markov state models, one for the unforced system and one for a slightly perturbed one.