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Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29–42) peptides

Authors

  • Satoru G. Itoh,

    Corresponding author
    1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
    2. Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
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  • Hisashi Okumura

    1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
    2. Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
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Abstract

We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-β(29–42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-β(29–42) and reveal its dimerization pathways. © 2013 Wiley Periodicals, Inc.

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