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Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States

  • E. Meerbach
  • E. Dittmer
  • I. Horenko
  • C. Schütte
Chapter
Part of the Lecture Notes in Physics book series (LNP, volume 703)

Abstract

We report on a novel approach to the automatic identification of metastablestates from long term simulation of complex molecular systems. The new approachis based on a hierarchical concept of metastability: metastable statesare understood as subsets of state or configuration space from which the dynamicsexits only very rarely; subsets with the smallest exit probabilities areof most interest, their further decomposition then may reveal subsets fromwhich exiting is less but comparably difficult for the system under investigation.The article gives a survey of the theoretical foundation of the approachand its algorithmic realization that generalizes the well-known concept of HiddenMarkov Models. The performance of the resulting algorithm is illustratedby an application to a 100 ns simulation of penta-alanine with explicit water.We demonstrate that the resulting metastable states allow to reveal theconformation dynamics of the molecule.

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Copyright information

© Springer 2006

Authors and Affiliations

  • E. Meerbach
    • 1
  • E. Dittmer
    • 1
  • I. Horenko
    • 1
  • C. Schütte
    • 1
  1. 1.Institut für Mathematik IIFreie Universität BerlinBerlinGermany

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