Markov State Models for Rare Events in Molecular Dynamics

Please always quote using this URN: urn:nbn:de:0297-zib-42420
  • 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.

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Author:Marco Sarich, Ralf Banisch, Carsten Hartmann, Christof Schütte
Document Type:ZIB-Report
Tag:Markov state models; long timescales; optimal control; rare events
MSC-Classification:49-XX CALCULUS OF VARIATIONS AND OPTIMAL CONTROL; OPTIMIZATION [See also 34H05, 34K35, 65Kxx, 90Cxx, 93-XX] / 49Mxx Numerical methods [See also 90Cxx, 65Kxx] / 49M29 Methods involving duality
60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX) / 60Jxx Markov processes / 60J28 Applications of continuous-time Markov processes on discrete state spaces
60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX) / 60Jxx Markov processes / 60J35 Transition functions, generators and resolvents [See also 47D03, 47D07]
93-XX SYSTEMS THEORY; CONTROL (For optimal control, see 49-XX) / 93Exx Stochastic systems and control / 93E20 Optimal stochastic control
Date of first Publication:2013/09/11
Series (Serial Number):ZIB-Report (13-52)
ISSN:1438-0064
Published in:Appeared in: Entropy (spec. issue) 16 (2013) 258-286

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