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Markov State Models for Rare Events in Molecular Dynamics
Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, Berlin 14195, Germany
Zuse Institute Berlin, Takustr. 7, Berlin 14195, Germany
* Author to whom correspondence should be addressed.
Received: 18 September 2013; in revised form: 3 December 2013 / Accepted: 9 December 2013 / Published: 30 December 2013
Abstract: Rare, but important, transition events between long-lived states are a key feature of many molecular systems. In many cases, the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible, even on the most powerful computers, because of the immensely long simulation timescales needed. Recently, a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore, we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls.
Keywords: rare events; Markov State Models; long timescales; optimal control
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MDPI and ACS Style
Sarich, M.; Banisch, R.; Hartmann, C.; Schütte, C. Markov State Models for Rare Events in Molecular Dynamics. Entropy 2014, 16, 258-286.
Sarich M, Banisch R, Hartmann C, Schütte C. Markov State Models for Rare Events in Molecular Dynamics. Entropy. 2014; 16(1):258-286.
Sarich, Marco; Banisch, Ralf; Hartmann, Carsten; Schütte, Christof. 2014. "Markov State Models for Rare Events in Molecular Dynamics." Entropy 16, no. 1: 258-286.