Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions

We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter kappa(b) considered in this paper, we observe that the mean first passage time <tau > increases as <tau(kappa(b))> similar to <tau(kappa(b) = 0)> l(p)(aN), where kappa(b) and l(p) are the stiffness parameter and persistence length, respectively, and a(N) is a constant that has a weak N dependence. We monitor the time dependence of the last monomer x(N)(t) at the cis compartment and calculate the tension propagation time (TP) t(tp) directly from simulation data for < x(N)(t)> similar to t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007)] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure t(tp) from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of t(tp) on chain persistence length l(p) and show that the ratio t(tp)/<tau > is independent of the bias F. (C) 2013 AIP Publishing LLC.