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Building Markov State Models Using Optimal Transport Theory
Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because<br>molecular simulations are slow to nd and sample the rare transient events. We describe here an e cient 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<br>networks) to patchdoi:10.26434/chemrxiv.7498229.v1 fatcat:7mhb6ovrcvfvpdii4crtuna7sq