Approximating nonequilibrium processes using a collection of surrogate diffusion models

Details Approximating nonequilibrium processes using a collection of surrogate diffusion models Approximating nonequilibrium processes using a collection of surrogate diffusion models

2008-01-28

arxiv.org/abs/0801.4281v1

J. Chem. Phys. (2008) no. 145103 vol. 128

Physics

Condensed Matter

Statistical Mechanics

13 pages, 7 figures

Scientific paper

10.1063/1.2903439

The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300 K. The RC dynamics, which correspond to the evolution of the end-to-end distance of the polypeptide, are produced by steered molecular dynamics (SMD) simulations and approximated using overdamped diffusion models. We show that the collection of (estimated) SPA models contain structural information "orthogonal" to the RC monitored in this study. Functional data analysis ideas are used to correlate functions associated with the fitted SPA models with the work done on the system in SMD simulations. It is demonstrated that the shape of the nonequilibrium work distributions for the unfolding and refolding processes of deca-alanine can be predicted with functional data analysis ideas using a relatively small number of simulated SMD paths for calibrating the SPA diffusion models.

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