The European Physical Journal Special Topics

, Volume 224, Issue 12, pp 2445–2462 | Cite as

A critical appraisal of Markov state models

Review B. Bridging of Time Scales and Methods for Rare Events
Part of the following topical collections:
  1. Discussion and Debate: Recurrent Problems in Scale Bridging Techniques in Molecular Simulation – What are the Current Options?

Abstract

Markov State Modelling as a concept for a coarse grained description of the essential kinetics of a molecular system in equilibrium has gained a lot of attention recently. The last 10 years have seen an ever increasing publication activity on how to construct Markov State Models (MSMs) for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecular sensors to molecular aggregation. Simultaneously the accompanying theory behind MSM building and approximation quality has been developed well beyond the concepts and ideas used in practical applications. This article reviews the main theoretical results, provides links to crucial new developments, outlines the full power of MSM building today, and discusses the essential limitations still to overcome.

Keywords

European Physical Journal Special Topic Transfer Operator Collocation Point Discretization Error Dominant Eigenvalue 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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© EDP Sciences and Springer 2015

Authors and Affiliations

  1. 1.Institut für MathematikFreie Universität BerlinBerlinGermany
  2. 2.Zuse Institute BerlinBerlinGermany

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