Anomalous zipping dynamics and forced polymer translocation

Abstract

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high temperature equilibrium configuration to a low temperature state, so that the two strands zip up by closing up a "Y"-fork. In unzipping, the polymers are brought from a low temperature double stranded configuration to high temperatures, so that the two strands separate. Simulations show that the unzipping time, $τ_u$, scales as a function of the polymer length as $τ_u \sim L$, while the zipping is characterized by anomalous dynamics $τ_z \sim L^α$ with $α= 1.37(2)$. This exponent is in good agreement with simulation results and theoretical predictions for the scaling of the translocation time of a forced polymer passing through a narrow pore. We find that the exponent $α$ is robust against variations of parameters and temperature, whereas the scaling of $τ_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing ($τ_z \sim 1/F$) and strong forcing ($τ_z$ independent of $F$) regimes. The crossover region is possibly characterized by a non-trivial scaling in $F$, matching the prediction of recent theories of polymer translocation. Although the geometrical setup is different, zipping and translocation share thus the same type of anomalous dynamics. Systems where this dynamics could be experimentally investigated are DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins closing times, but not for the opening times.