Anomalous zipping dynamics and forced polymer translocation

Abstract

We investigate by means of Monte Carlo simulations the zipping and unzipping dynamicsof two polymers connected at one end and subject to an attractive interaction betweencomplementary monomers. In zipping, the polymers are quenched from a hightemperature equilibrium configuration to a low temperature state, such that the twostrands zip up by closing up a ‘Y’-fork. In unzipping, the polymers are broughtfrom a low temperature double-stranded configuration to high temperatures,such that the two strands separate. Simulations show that the unzipping time,τu, scales as a function of the polymer length asτu ∼ L, while the zipping is characterized by the anomalous dynamicsτz ∼ Lα withα = 1.37(2). Thisexponent is in good agreement with simulation results and theoretical predictions for the scaling ofthe translocation time of a forced polymer passing through a narrow pore. We find that the exponentα is robust against variations of parameters and temperature, whereas the scaling ofτz as a function of the driving force shows the existence of two different regimes: the weak forcing (τz ∼ 1/F) and strongforcing (τz independent of F) regimes. The crossover region is possibly characterized by a non-trivial scaling inF, matching the prediction of recent theories of polymer translocation. Although thegeometrical setups are different, zipping and translocation share thus the same type ofanomalous dynamics. Systems where this dynamics could be experimentally investigatedinclude DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins’closing times, but not for the opening times.