Translocation dynamics of a short polymer driven by an oscillating force

Nicola Pizzolato,Alessandro Fiasconaro,Dominique Persano Adorno,Bernardo Spagnolo

doi:10.1063/1.4789016

Abstract

We study the translocation dynamics of a short polymer moving in a noisy environment and driven by an oscillating force. The dynamics is numerically investigated by solving a Langevin equation in a two-dimensional domain. We consider a phenomenological cubic potential with a metastable state to model the polymer-pore interaction and the entropic free energy barrier characterizing the translocation process. The mean first translocation time of the center of inertia of polymers shows a nonmonotonic behavior, with a minimum, as a function of the number of the monomers. The dependence of the mean translocation time on the polymer chain length shows a monotonically increasing behavior for high values of the number of monomers. Moreover, the translocation time shows a minimum as a function of the frequency of the oscillating forcing field for all the polymer lengths investigated. This finding represents the evidence of the resonant activation phenomenon in the dynamics of polymer translocation, whose occurrence is maintained for different values of the noise intensity.

Highlights

The transport of molecules across membranes and the translocation of a polymer through a nanopore represent very important processes in the science of the living systems
In this regime the mean first translocation time (MFTT) is equal to the average of the crossing times over the upper and lower configurations of the barrier, and the slower processes critically affect the value of the mean crossing time
In this work we investigate the influence of a phenomenological oscillating potential on the translocation dynamics of polymers, with different lengths, embedded in a noisy environment

Summary

INTRODUCTION

The transport of molecules across membranes and the translocation of a polymer through a nanopore represent very important processes in the science of the living systems. In spite of the experimental and theoretical work done, the complicated boundary conditions, and out of equilibrium translocation dynamics due to the biological environment, make the problem of biopolymer translocation still far from being completely understood In this framework, a detailed description of the transport dynamics of short polymers driven by an oscillating driving field is missing. The role of the polymer chain length and frequency of the oscillating forcing field on the mean first translocation time (MFTT) is investigated. This nonmonotonic behavior confirms the occurrence of the resonant activation (RA) phenomenon in polymer translocation This phenomenon is characterized by the presence of a minimum in the mean time as a function of the frequency of the force, spent by a single Brownian particle in surmounting a potential barrier.. The phenomenological potential profile with a metastable state of Eq (4) is used to model the polymer-pore

POLYMER DYNAMICS MODEL

RESULTS AND DISCUSSION

CONCLUSIONS