Polymer translocation through a nanopore: A two-dimensional Monte Carlo study

Abstract

Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model J. Chem. Phys. 121, 6042 (2004); 10.1063/1.1785776 This article is copyrighted as indicated in the article. Reuse of AIP content is subject to the terms at: http://scitation. We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time required for the polymer to completely exit the pore on either end. We find numerically that scales with the chain length N as ϳ N 1+2 , where is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R g . For L Ӷ R g , we numerically verify that asymptotically ϳ N 1+2 . For L ӷ R g , we find ϳ N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R ʈ Ϸ L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.

Fractional Brownian motion approach to polymer translocation: The governing equation of motion

“…Meanwhile, many interesting experimental and theoretical findings have been reported [2]. A number of important observations have been gained by means of computer simulations [3][4][5][6][7][8][9]. However, notwithstanding the significance of translocation phenomena both as a possible technological application and from the standpoint of basic research, the understanding of the polymer translocation through a narrow pore is still elusive and, in some respects, controversial [10].…”

Langevin dynamics simulations of polymer translocation through nanopores

“…Inspired by the experiments, 7,11,17 a number of recent theories [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] have been developed for the dynamics of polymer translocation. Even for the field-free case, polymer translocation remains a challenging problem.…”

“…A quadratic dependence of on N is predicted in their theory and confirmed by their simulations. 33 Most recently, we have investigated both free 35 and forced 36 translocations using the two-dimensional fluctuating bond ͑FB͒ model with single-segment Monte Carlo moves. For the free translocation, to overcome the entropic barrier without artificial restrictions we considered a polymer, which is initially placed in the middle of the pore, and examined the escape time e required for the polymer to completely exit the pore on either end.…”

“…Particularly, the scaling of translocation time with the chain length N is an important measure of the underlying dynamics of polymer translocation. As a result, recently a considerable number of experimental, 7-17 theoretical, [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] and numerical studies [32][33][34][35][36][37][38][39][40][41][42][43][44][45] have been carried out.…”

Sequence Dependence of DNA Translocation through a Nanopore

“…Similar experiments have been done recently using solid state nanopores with more precisely controlled dimensions. Triggered by these experiments and potential technological applications [1,2], such as rapid DNA sequencing, gene therapy, and controlled drug delivery, the translocation of biopolymers through a nanopore has become the subject of intensive experimental [3][4][5][6][7][8] and theoretical [8][9][10][11][12][13][14][15][16][17][18][19][20][21] studies. A particular important question is if DNA translocation through a nanopore can be used to determine the detailed sequence structure of the molecule [2 -4,18].…”