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

TL;DR

This paper extends a theoretical framework to predict the nonequilibrium relaxation dynamics of flexible chain molecules, validated by simulations on pentadecane, and aims to apply it to biologically relevant processes like protein folding.

Contribution

The authors develop a new extension of their existing theory to describe nonequilibrium relaxation in flexible molecules, validated against simulations, and demonstrate significant computational efficiency.

Findings

Theory accurately predicts pentadecane relaxation dynamics.

Predictions agree well with Brownian dynamics simulations.

Method offers substantial computational savings.

Abstract

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.