Simulation study on the translocation of a partially charged polymer through a nanopore

The translocation of a partially charged polymer through a neutral nanopore under external electrical field is studied by using dynamic Monte Carlo method on a simple cubic lattice. One monomer in the polymer is charged and it suffers a driving force when it locates inside the pore. Two time scales, mean first passage time tau(FP) with the first monomer restricted to never draw back into cis side and translocation time tau for polymer continuously threading through nanopore, are calculated. The first passage time tau(FP) decreases with the increase in the driving force f, and the dependence of tau(FP) on the position of charged monomer M is in agreement with the theoretical results using Fokker-Planck equation [A. Mohan, A. B. Kolomeisky, and M. Pasquali, J. Chem. Phys. 128, 125104 (2008)]. But the dependence of tau on M shows a different behavior: It increases with f for M < N/2 with N the polymer length. The novel behavior of tau is explained qualitatively from dynamics of polymer during the translocation process and from the free energy landscape. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4737929]