Theory for the nonequilibrium dynamics of flexible chain molecules: relaxation to equilibrium of pentadecane from an all-trans conformation

Details Theory for the nonequilibrium dynamics of flexible chain molecules: relaxation to equilibrium of pentadecane from an all-trans conformation Theory for the nonequilibrium dynamics of flexible chain molecules: relaxation to equilibrium of pentadecane from an all-trans conformation

1998-02-25

arxiv.org/abs/cond-mat/9802277v1

Physics

Condensed Matter

Soft Condensed Matter

11 pages total, including 2 Postscript figures; submitted to Journal of Chemical Physics

Scientific paper

10.1063/1.476302

We extend to nonequilibrium processes our recent theory for the long time dynamics of flexible chain molecules. While the previous theory describes the equilibrium motions for any bond or interatomic separation in (bio)polymers by time correlation functions, the present extension of the theory enables the prediction of the nonequilibrium relaxation that occurs in processes, such as T-jump experiments, where there are sudden transitions between, for example, different equilibrium states. As a test of the theory, we consider the ``unfolding'' of pentadecane when it is transported from a constrained all-trans conformation to a random-coil state at thermal equilibrium. The time evolution of the mean-square end-to-end distance after release of the constraint is computed both from the theory and from Brownian dynamics (BD) simulations. The predictions of the theory agree very well with the BD simulations. Furthermore, the theory produces enormous savings in computer time. This work is a starting point for the application of the new method to nonequilibrium processes with biological importance such as the helix-coil transition and protein folding.

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