Langevin Dynamics Simulations of Polymer Translocation through Nanopores

Ilkka Huopaniemi; Kaifu Luo; Tapio Ala-Nissila; See-Chen Ying

doi:10.1063/1.2357118

paper

Langevin Dynamics Simulations of Polymer Translocation through Nanopores

arXiv:cond-mat/0608506 · doi:10.1063/1.2357118

Abstract

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time $τ_{e}$ required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that $τ_{e}$ scales with the chain length $N$ as $τ_{e} \sim N^{1 + 2 ν}$ , where $ν$ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient $ξ$ , the driving force $E$ and the length of the chain $N$ on the translocation time $τ$ , which is defind as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and $τ \sim E^{- 1}$ . The influence of $ξ$ depends on the ratio between the driving and frictional forces. For intermediate $ξ$ , we find a crossover scaling for $τ$ with $N$ from $τ \sim N^{2 ν}$ for relatively short chains to $τ \sim N^{1 + ν}$ for longer chains. However, for higher $ξ$ , only $τ \sim N^{1 + ν}$ is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing $ξ$ increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveals additional features of dependency on friction.

submitted to J. Chem. Phys., 8 pages with 10 figures

Langevin Dynamics Simulations of Polymer Translocation through Nanopores

Abstract

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