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A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations

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Meshfree Methods for Partial Differential Equations VI

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 89))

Abstract

Markov State Models (MSMs) are widely used to represent molecular conformational changes as jump-like transitions between subsets of the conformational state space. However, the simulation of peptide folding in explicit water is usually said to be unsuitable for the MSM framework. In this article, we summarize the theoretical background of MSMs and indicate that explicit water simulations do not contradict these principles. The algorithmic framework of a meshless conformational space discretization is applied to an explicit water system and the sampling results are compared to a long-term molecular dynamics trajectory. The meshless discretization approach is based on spectral clustering of stochastic matrices (MSMs) and allows for a parallelization of MD simulations. In our example of Trialanine we were able to compute the same distribution of a long term simulation in less computing time.

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Authors and Affiliations

  1. Zuse Institute Berlin (ZIB), Takustraße 7, 14195, Berlin, Germany

    Konstantin Fackeldey, Alexander Bujotzek & Marcus Weber

Authors
  1. Konstantin Fackeldey
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  2. Alexander Bujotzek
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  3. Marcus Weber
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Correspondence to Konstantin Fackeldey .

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Editors and Affiliations

  1. , Institut für Numerische Simulation, Universität Bonn, Wegelerstr. 6, City, 53115, Germany

    Michael Griebel

  2. Institut für Parallele, und Verteilte Systeme, Universität Stuttgart, Universitätsstraße 38, Stuttgart, 70569, Germany

    Marc Alexander Schweitzer

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Fackeldey, K., Bujotzek, A., Weber, M. (2013). A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations. In: Griebel, M., Schweitzer, M. (eds) Meshfree Methods for Partial Differential Equations VI. Lecture Notes in Computational Science and Engineering, vol 89. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32979-1_9

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