Repository: Freie Universität Berlin, Math Department

Set-free Markov state model building

Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Set-free Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133.

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Molecular dynamics (MD) simulations face challenging problems since the time scales of interest often are much longer than what is possible to simulate; and even if sufficiently long simulations are possible the complex nature of the resulting simulation data makes interpretation difficult. Markov State Models (MSMs) help to overcome these problems by making experimentally relevant time scales accessible via coarse grained representations that also allow for convenient interpretation. However, standard set-based MSMs exhibit some caveats limiting their approximation quality and statistical significance. One of the main caveats results from the fact that typical MD trajectories repeatedly re-cross the boundary between the sets used to build the MSM which causes statistical bias in estimating the transition probabilities between these sets. In this article, we present a setfree approach to MSM building utilizing smooth overlapping ansatz functions instead of sets and an adaptive refinement approach. This kind of meshless discretization helps to overcome the recrossing problem and yields an adaptive refinement procedure that allows us to improve the quality of the model while exploring state space and inserting new ansatz functions into the MSM.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Mathematics > Applied Mathematics
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:2160
Deposited By: Silvia Hoemke
Deposited On:12 Dec 2017 17:45
Last Modified:13 Dec 2017 08:42

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