title: Fractional Brownian motion and the critical dynamics of zipping polymers.
abstract: We consider two complementary polymer strands of length L attached by a common-end monomer. The two strands bind through complementary monomers and at low temperatures form a double-stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature T=T(c) using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as τ∼L(2.26(2)), exceeding the Rouse time ∼L(2.18). We investigate the probability distribution function, velocity autocorrelation function, survival probability, and boundary behavior of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent H=0.44(1). We discuss similarities to and differences from unbiased polymer translocation.
authors.affiliation: Institute for Theoretical Physics, Katholieke Universiteit Leuven, Leuven, Belgium.
authors.forename: J-C
authors.initials: JC
authors.lastname: Walter
authors.forename: A
authors.initials: A
authors.lastname: Ferrantini
authors.forename: E
authors.initials: E
authors.lastname: Carlon
authors.forename: C
authors.initials: C
authors.lastname: Vanderzande
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009038:Motion; D011108:Polymers / Q000737:chemistry*
chemical_list: D011108:Polymers