Dynamics and energetics of a molecular zipper under external driving

TL;DR

This paper models the unzipping dynamics of a molecular zipper under external driving, analyzing how energy and heat distributions evolve over time in different regimes, providing insights into molecular unzipping energetics.

Contribution

It introduces a dynamic model for a molecular zipper driven by external forces, solving probability and energy distribution equations to reveal different behavioral regimes.

Findings

Identification of two distinct regimes based on temperature and unzipped bonds.

Derivation of probability distributions for work and heat during unzipping.

Analysis of how external driving influences molecular energetics.

Abstract

We investigate the dynamics of a single-ended N-state molecular zipper based on a model originally proposed by Kittel. The molecule is driven unidirectionally towards the completely unzipped state with increasing time t, where the driving lowers the energies of states with k unzipped links by an amount proportional to kt. We solve the Pauli rate equation for the state probabilities and the partial differential equations, which yield the probability distributions for the work performed on the zipper and for the heat exchanged with the thermal reservoir. Similarly to the related equilibrium model, two different regimes can be identified at a given temperature with respect to the released molecular degrees of freedom per broken bond. In these two regimes the time evolution of the state probabilities as well as of the work and heat distributions show a qualitatively different behavior.