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, ${\tau }_u$, scales as a function of the polymer length as ${\tau }_u\sim L$, while the zipping is characterized by anomalous dynamics ${\tau }_z\sim L^{\alpha }$ with $\alpha =1.37(2)$. 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 $\alpha$ is robust against variations of parameters and temperature, whereas the scaling of ${\tau }_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing (${\tau }_z\sim 1/F$) and strong forcing (${\tau }_z$ 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.

15 pages, 9 figures

References in corpus (21)

• Anomalous Dynamics of Forced Translocation
• Nonequilibrium dynamics of polymer translocation and straightening
• Pulling Pinned Polymers and Unzipping DNA
• Force and kinetic barriers in unzipping of DNA
• Langevin Dynamics Simulations of Polymer Translocation through Nanopores
• Dynamical scaling of the DNA unzipping transition
• Driven polymer translocation through nanopores: slow versus fast dynamics
• Anomalous Dynamics of Unbiased Polymer Translocation through a Narrow Pore
• Confinement-driven translocation of a flexible polymer
• Pore-blockade Times for Field-Driven Polymer Translocation
• Scaling exponents of Forced Polymer Translocation through a nano-pore
• Polymer translocation through a nanopore under a pulling force
• Pulling a polymer out of a potential well and the mechanical unzipping of DNA
• Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore
• Non-Equilibrium Dynamics of Single polymer Adsorption to Solid Surfaces
• Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network
• Zipping and collapse of diblock copolymers
• Adsorption Kinetics of a Single Polymer on a Solid Plane
• Statistical mechanics of RNA folding: a lattice approach
• Unwinding dynamics of double-stranded polymers
• A lattice polymer study of DNA renaturation dynamics

Cited by in corpus (8)

• Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation
• Anomalous dynamics of DNA hairpin folding
• Fractional Brownian motion and the critical dynamics of zipping polymers
• Unzipping DNA by a periodic force: Hysteresis loop area and its scaling
• Non-Markovian dynamics of reaction coordinate in polymer folding
• Strand diffusion-limited closure of denaturation bubbles in DNA
• Role of helicity in DNA hairping folding dynamics
• Effect of grafting on the binding transition of two flexible polymers