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Building Markov State Models Using Optimal Transport Theory

preprint
submitted on 21.12.2018 and posted on 21.12.2018 by Purushottam Dixit, Ken Dill
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.

History

Email Address of Submitting Author

dixitpd@gmail.com

Institution

Columbia University

Country

United States

ORCID For Submitting Author

0000-0003-3282-0866

Declaration of Conflict of Interest

no conflict of interest

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in The Journal of Chemical Physics

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