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Adaptive conformational sampling based on replicas

Curuksu, Jeremy

In: Journal of Mathematical Biology, 2012, vol. 64, no. 6, p. 917-931

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    Title
    • Adaptive conformational sampling based on replicas
    Author
    • Curuksu, Jeremy. Institute of Mathematics, Ecole Polytechnique Fédérale de Lausanne (EPFL), MATHGEOM, LCVMM, Station 8, MAC1 615, 1015, Lausanne, Switzerland
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:309656
    Summary
    Computer simulations of biomolecules such as molecular dynamics simulations are limited by the time scale of conformational rearrangements. Several sampling techniques are available to search the multi-minima free energy landscape but most efficient, time-dependent methods do generally not produce a canonical ensemble. A sampling algorithm based on a self-regulating ladder of searching copies in the dihedral subspace is developped in this paper. The learning process using short- and long-term memory functions allows an efficient search in phase space while combining a deterministic dynamics and stochastic swaps with the searching copies conserves a canonical limit. The sampling efficiency and accuracy are indicated by comparing the ansatz with conventional molecular dynamics and replica exchange simulations