Building Markov State Models Using Optimal Transport Theory
Keyword(s):
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 together transient dynamical information from multiple nonequilibrium<br>simulations. We give toy examples.
2018 ◽
2019 ◽
Vol 150
(5)
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pp. 054105
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2018 ◽
Vol 148
(24)
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pp. 241731
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2014 ◽
Vol 25
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pp. 135-144
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2014 ◽
Vol 11
(1)
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pp. 17-27
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2020 ◽
2016 ◽
Vol 18
(44)
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pp. 30228-30235
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2013 ◽
Vol 9
(7)
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pp. 2900-2906
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