Approximating nonequilibrium processes using a collection of surrogate diffusion models

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dc.creatorCalderon, Christopher P.
dc.creatorChelli, Riccardo
dc.date2008-01-28
dc.date.accessioned2026-07-07T09:32:37Z
dc.date.available2026-07-07T09:32:37Z
dc.descriptionThe 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.
dc.description13 pages, 7 figures
dc.identifierhttps://arxiv.org/abs/0801.4281
dc.identifierhttp://arxiv.org/abs/0801.4281
dc.identifierJ. Chem. Phys. (2008) no. 145103 vol. 128
dc.identifierdoi:10.1063/1.2903439
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/158839
dc.subjectStatistical Mechanics
dc.titleApproximating nonequilibrium processes using a collection of surrogate diffusion models
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