Plectoneme dynamics and statistics in braided polymers

Abstract

Braids composed of two interwoven polymer chains exhibit a "buckling" transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a combination of simulation and analytics, the dynamics of plectoneme formation and their statistics in steady state. The introduction of an order parameter-the plectonemic fraction-allows us to map out the phase boundary between the straight-braid phase and the plectonemic one. We then monitor the formation and the growth of plectonemes, observing events typical of phase separation kinetics for liquid-gas systems (fusion, fission, and one-dimensional Ostwald ripening) but also of DNA supercoiling dynamics (plectonemic hopping). Finally, we propose a stochastic field theory for the coupled dynamics of twist and local writhe which explains the phenomenology found with Brownian dynamics simulations as well as the power laws underlying the coarsening of plectonemes.