Scaling exponents of forced polymer translocation through a nanopore

    Authors

    A. Bhattacharya; W. H. Morrison; K. Luo; T. Ala-Nissila; S. C. Ying; A. Milchev;K. Binder

    Comments

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    Abbreviated Journal Title

    Eur. Phys. J. E

    Keywords

    MOLECULAR-DYNAMICS SIMULATION; NARROW PORE; ADSORPTION; MEMBRANE; Chemistry, Physical; Materials Science, Multidisciplinary; Physics, ; Applied; Polymer Science

    Abstract

    We investigate several properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulations in three dimensions (3D). Motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we estimate the exponents describing the scaling with chain length (N) of the average translocation time < tau >, the average velocity of the center of mass < upsilon(CM) > , and the effective radius of gyration < R-g > during the translocation process defined as < tau > similar to N-alpha, < upsilon(CM) > similar to N-delta, and R-g similar to N-(nu) over bar. respectively, and the exponent of the translocation coordinate (s-coordinate) as a function of the translocation time < s(2)(t) > similar to t(beta). We find alpha = 1.36 +/- 0.01, beta = 1.60 +/- 0.01 for < s(2)(t) > similar to tau(beta) and (beta) over bar = 1.44 +/- 0.02 for < Delta s(2)(t) > similar to tau((beta) over bar), delta = 0.81 +/- 0.04, and (nu) over bar similar or equal to nu = 0.59 +/- 0.01, where nu is the equilibrium Flory exponent in 3D. Therefore, we find that < tau > similar to N-1.36 is consistent with the estimate of < tau > similar to < R-g > / < upsilon(CM) > . However, as observed previously in Monte Carlo (MC) calculations by Kantor and Kardar (Y. Kantor, M. Kardar, Phys. Rev. E 69, 021806 (2004)) we also find the exponent alpha = 1.36 +/- 0.01 < 1 + nu. Further, we find that the parallel and perpendicular components of the gyration radii, where one considers the "cis" and "trans" parts of the chain separately, exhibit distinct out-of-equilibrium effects. We also discuss the dependence of the effective exponents on the pore geometry for the range of N studied here.

    Journal Title

    European Physical Journal E

    Volume

    29

    Issue/Number

    4

    Publication Date

    1-1-2009

    Document Type

    Article

    Language

    English

    First Page

    423

    Last Page

    429

    WOS Identifier

    WOS:000269973600008

    ISSN

    1292-8941

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