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Polymer in a double well: dynamics of translocation of short chains over a barrier

Sebastian, KL and Debnath, Ananya (2006) Polymer in a double well: dynamics of translocation of short chains over a barrier. In: Workshop on Biopolymers 2005, MAY 30-JUN 03, 2005, Trieste, ITALY.

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Abstract

We consider the dynamics of a short chain polymer crossing over a free energy barrier in space. Adopting the continuum version of the Rouse model, we find exact expressions for the activation energy and the rate of crossing. For this model, the analysis of barrier crossing is analogous to semiclassical treatment of quantum tunnelling. Finding the saddle point for the process requires solving a Newton-like equation of motion for a fictitious particle. The analysis shows that short chains would cross the barrier as a globule. The activation free energy for this would increase linearly with the number of units N in the polymer. The saddle point for longer chains is an extended conformation, in which the chain is stretched out. The stretching out lowers the energy and hence the activation free energy is no longer linear in N. The rates in both the cases are calculated using a multidimensional approach and analytical expressions are derived, using a new formula for evaluating the infinite products. However, due to the harmonic approximation made in the derivation, the rates are found to diverge at the point where the saddle point changes over from the globule to the stretched out conformation. The reason for this is identified to be the bifurcation of the saddle to give two new saddles, and a correction formula is derived for the rate in the vicinity of this point. Numerical results using the formulae are presented. As a function of N, it is possible for the rate to have a minimum. This is due to confinement effects in the initial state

Item Type: Conference Paper
Additional Information: Copyright of this article belongs to Iop Publishing Ltd.
Department/Centre: Division of Chemical Sciences > Inorganic & Physical Chemistry
Date Deposited: 06 Apr 2009 09:49
Last Modified: 19 Sep 2010 04:58
URI: http://eprints.iisc.ernet.in/id/eprint/17774

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