Non-Markovian dynamics of reaction coordinate in polymer folding

Abstract

We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary parts which can bind to each other. At the critical temperature, the (un) zipping is unbiased and the two strands open and close as a zipper. The number of broken base pairs n(t) displays a subdiffusive motion characterized by a variance growing as < Dn(2)(t)> similar to t(alpha) with alpha < 1 at long times. Our theory provides an estimate of both the asymptotic anomalous exponent alpha and of the subleading correction term, which are both in excellent agreement with numerical simulations. The results indicate that the tension propagation theory captures the relevant features of the dynamics and shed some new insights on related polymer problems characterized by anomalous dynamical behavior.