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Abstract: Polymer translocation through a nano-pore in a thin membrane is studied usinga coarse-grained bead-spring model and Langevin dynamics simulation with aparticular emphasis to explore out of equilibrium characteristics of thetranslocating chain. We analyze the out of equilibrium chain conformations bothat the $cis$ and the $trans$ side separately either as a function of the timeduring the translocation process or as as function of the monomer index $m$inside the pore. A detailed picture of translocation emerges by monitoring thecenter of mass of the translocating chain, longitudinal and transversecomponents of the gyration radii and the end to end vector. We observe thatpolymer configurations at the $cis$ side are distinctly different from those atthe $trans$ side. During the translocation, and immediately afterwards, thechain is clearly out of equilibrium, as different parts of the chain arecharacterized by a series of effective Flory exponents. We further notice thatimmediately after the translocation the last set of beads that have justtranslocated take a relatively compact structure compared to the first set ofbeads that translocated earlier, and the chain immediately after translocationis described by an effective Flory exponent $0.45 \pm 0.01$. The analysis ofthese results is further strengthened by looking at the conformations of chainsegments of equal length as they cross from the $cis$ to the $trans$ side, Wediscuss implications of these results to the theoretical estimates andnumerical simulation studies of the translocation exponent reported by variousgroups.



Author: Aniket Bhattacharya, Kurt Binder

Source: https://arxiv.org/







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