Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions
Abbreviated Journal Title
J. Chem. Phys.
FORCED POLYMER TRANSLOCATION; SOLID-STATE NANOPORE; EXCLUDED-VOLUME; MONTE-CARLO; NARROW PORE; MODEL; FABRICATION; MOLECULES; EXPONENTS; BREAKDOWN; Physics, Atomic, Molecular & Chemical
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 increases as similar to 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)/ is independent of the bias F. (C) 2013 AIP Publishing LLC.
Journal of Chemical Physics
"Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions" (2013). Faculty Bibliography 2010s. 3589.