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Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables

Please always quote using this URN:urn:nbn:de:0296-matheon-10907
  • Markov (state) models (MSMs) have attracted a lot of interest recently as they (1) can probe long-term molecular kinetics based on short-time simulations, (2) offer a way to analyze great amounts of simulation data with relatively little subjectivity of the analyst, (3) provide insight into microscopic quantities such as the ensemble of transition pathways, and (4) allow simulation data to be reconciled with measurement data in a rigorous and explicit way. Here we sketch our current perspective of Markov models and explain in short their theoretical basis and assumptions. We describe transition path theory which allows the entire ensemble of protein folding pathways to be investigated and that combines naturally with Markov models. Experimental observations can be naturally linked to Markov models with the dynamical fingerprint theory, by which experimentally observable timescales can be equipped with an understanding of the structural rearrangement processes that take place at these timescales. The concepts of this paper are illustrated by a simple kinetic model of protein folding.

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Metadaten
Author:Jan-Hendrik Prinz, Bettina Keller, Frank Noe
URN:urn:nbn:de:0296-matheon-10907
Referee:Christof Schütte
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/02/27
Release Date:2012/02/27
Tag:MSM; Markov (state) models; Molecular kinetics; Spectroscopy; Temperature jump; Transition path theory; Transition pathways
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:62-XX STATISTICS / 62Mxx Inference from stochastic processes / 62M05 Markov processes: estimation
Preprint Number:934
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