title: Opening of a weak link in a semiflexible ring polymer.
abstract: The dynamics of contact formation between different parts of a long chain molecule is of considerable interest in biology. The related processes of opening of a loop or closing to form a loop also are of considerable interest and have attracted the attention of experimentalists/theorists. For closing, results are available in the completely flexible limit. However, this limit is not realized in many cases. Recently, there have been investigations for the semiflexible case too. We develop an approach, which leads to an easy description of the dynamics, incorporating semiflexibility rigorously into account. With this approach, the dynamics of a semiflexible polymer ring formed by a weak bond between the two ends can be modeled as the escape of a particle over a barrier in a multidimensional potential energy surface. We then calculate the rate of opening using a multidimensional transition state theory. Effects of friction on the rate are also taken into account using the standard coupling to a bath of harmonic oscillators. We find that for shorter chains (i.e., semiflexible), the rate of opening is strongly length dependent and is well described by the equation A(L/lp)v exp(Blp/L), with L as the length, and lp as the persistence length, A, B as the constants, and v approximately 1.2.
authors.affiliation: Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India.
authors.forename: K P
authors.initials: KP
authors.lastname: Santo
authors.forename: K L
authors.initials: KL
authors.lastname: Sebastian
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D013314:Stress, Mechanical
chemical_list: D001704:Biopolymers