Building Markov state models using optimal transport theory.

Abstract

Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because molecular simulations are slow to find and sample the rare transient events. We describe here an efficient approximate way to determine MSM rate matrices by combining maximum caliber (maximizing path entropies) with optimal transport theory (minimizing some path cost function, as when routing trucks on transportation networks) to patch together transient dynamical information from multiple non-equilibrium simulations. We give toy examples.