Dynamics and energetics of a molecular zipper under external driving

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.