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Hierarchical Uncoupling-Coupling of Metastable Conformations

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Computational Methods for Macromolecules: Challenges and Applications

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 24))

Abstract

Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. UCMC aims at avoiding the typical metastable or trapping behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. Therefore, the state space of the chain has to be hierarchically decomposed into its metastable conformations. This is done by means of combining the technique of conformation analysis as recently introduced by the authors, and appropriate annealing strategies. We present a detailed examination of the uncoupling-coupling procedure which uncovers its theoretical background, and illustrates the hierarchical algorithmic approach. Furthermore, application of the UCMC algorithm to the n-pentane molecule allows us to discuss the effect of its crucial steps in a typical molecular scenario.

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Authors and Affiliations

  1. Institut für Mathematik II, Freie Universität Berlin, Arnimallee 2–6, 14195, Berlin, Germany

    Alexander Fischer, Christof Schütte & Peter Deuflhard

  2. Konrad-Zuse-Zentrum, Takustraße 7, 14195, Berlin, Germany

    Peter Deuflhard & Frank Cordes

Authors
  1. Alexander Fischer
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  2. Christof Schütte
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  3. Peter Deuflhard
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  4. Frank Cordes
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Editor information

Editors and Affiliations

  1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

  2. Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

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© 2002 Springer-Verlag Berlin Heidelberg

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Fischer, A., Schütte, C., Deuflhard, P., Cordes, F. (2002). Hierarchical Uncoupling-Coupling of Metastable Conformations. In: Schlick, T., Gan, H.H. (eds) Computational Methods for Macromolecules: Challenges and Applications. Lecture Notes in Computational Science and Engineering, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56080-4_10

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  • DOI: https://doi.org/10.1007/978-3-642-56080-4_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43756-7

  • Online ISBN: 978-3-642-56080-4

  • eBook Packages: Springer Book Archive

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