Building Markov State Models Using Optimal Transport Theory [post]

Purushottam Dixit, Ken Dill
2018 unpublished
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 patch
more » ... ogether transient dynamical information from multiple nonequilibrium<br>simulations. We give toy examples.
doi:10.26434/chemrxiv.7498229.v1 fatcat:7mhb6ovrcvfvpdii4crtuna7sq