Abbreviated Journal Title
Phys. Rev. E
MOLECULAR-DYNAMICS SIMULATION; DRIVEN POLYMER TRANSLOCATION; POLYNUCLEOTIDE MOLECULES; PORE; MEMBRANE; Physics, Fluids & Plasmas; Physics, Mathematical
Polymer translocation through a nanopore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the cis and the trans side separately either as a function of the time during the translocation process or as as function of the monomer index m inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer configurations at the cis side are distinctly different from those at the trans side. During the translocation and immediately afterwards, the chain is clearly out of equilibrium, as different parts of the chain are characterized by a series of effective Flory exponents. We further notice that immediately after the translocation the last set of beads that have just translocated take a relatively compact structure compared to the first set of beads that translocated earlier and the chain immediately after translocation is described by an effective Flory exponent 0.45 +/- 0.01. The analysis of these results is further strengthened by looking at the conformations of chain segments of equal length as they cross from the cis to the trans side, We discuss implications of these results to the theoretical estimates and numerical simulation studies of the translocation exponent reported by various groups.
Physical Review E
Bhattacharya, Aniket and Binder, Kurt, "Out-of-equilibrium characteristics of a forced translocating chain through a nanopore" (2010). Faculty Bibliography 2010s. 6999.