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摘要
Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N = 21-61. The rate of translocation is controlled by a tunable friction coefficient, gamma(0p), for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length as <tau(1)> similar to (N -Np)(alpha), where N-p is the average number of monomers in the nanopore. The exponent approaches the value alpha = 2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low gamma(0p). However, the chain approaches conformational quasi-equilibrium for sufficiently large gamma(0p). In this limit the observed scaling of <tau(1)> with driving force and chain length supports the Fokker-Planck (FP) prediction that <tau(1)> proportional to N/f(d) for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the FP equation to calculate translocation time distributions. At sufficiently high gamma(0p), the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.
- 出版日期2014-5-14
