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Building Markov State Models for Periodically Driven Non-Equilibrium Systems

Please always quote using this URN: urn:nbn:de:0297-zib-53167
  • Recent years have seen an increased interest in non-equilibrium molecular dynamics (NEMD) simulations, especially for molecular systems with periodic forcing by external fields, e.g., in the context of studying effects of electromagnetic radiation on the human body tissue. Lately, an NEMD methods with local thermostating has been proposed that allows for studying non-equilibrium processes in a statistically reliable and thermodynamically consistent way. In this article, we demonstrate how to construct Markov State Models (MSMs) for such NEMD simulations. MSM building has been well-established for systems in equilibrium where MSMs with just a few (macro-)states allow for accurate reproduction of the essential kinetics of the molecular system under consideration. Non-equilibrium MSMs have been lacking so far. The article presents how to construct such MSMs and illustrates their validity and usefulness for the case of conformation dynamics of alanine dipeptide in an external electric field.

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Author:Han Wang, Christof Schütte
Document Type:ZIB-Report
Tag:Alanine dipeptide; Electric field; Floquet theory; Markov states model; Non-equilibrium
MSC-Classification:65-XX NUMERICAL ANALYSIS / 65Cxx Probabilistic methods, simulation and stochastic differential equations (For theoretical aspects, see 68U20 and 60H35) / 65C40 Computational Markov chains
82-XX STATISTICAL MECHANICS, STRUCTURE OF MATTER / 82Cxx Time-dependent statistical mechanics (dynamic and nonequilibrium) / 82C05 Classical dynamic and nonequilibrium statistical mechanics (general)
Date of first Publication:2014/11/11
Series (Serial Number):ZIB-Report (14-46)
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