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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 nd and sample the rare transient events. We describe here an ecient 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 nonequilibrium
simulations. We give toy examples.
molecular simulations are slow to nd and sample the rare transient events. We describe here an ecient 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 nonequilibrium
simulations. We give toy examples.
