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Journal of Chemical Physics / Volume 135 / Issue 24 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 245102 (2011); http://dx.doi.org/10.1063/1.3669427 (8 pages)

First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases

Rouhollah Haji Abdolvahab1, Ralf Metzler2,3, and Mohammad Reza Ejtehadi1

1Physics Department, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
2Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
3Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland

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(Received 8 June 2011; accepted 21 November 2011; published online 23 December 2011)

Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Péclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Péclet number. We investigate the effect of the chaperone size on the translocation process. In particular, for large chaperone size, the translocation progress and the mean waiting time as function of the reaction coordinate exhibit pronounced sawtooth-shapes. The effects of a heterogeneous polymer sequence on the translocation dynamics is studied in terms of the translocation velocity, the probability distribution for the translocation progress, and the monomer waiting times.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. DRIFT-DIFFUSION MODEL
  3. COMPARISON WITH SIMULATIONS
    1. Homopolymer chain
    2. Heteropolymer chain
  4. SAWTOOTH BEHAVIOR OF TRANSLOCATION DYNAMICS FOR λ > 6
  5. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biochemistry, biodiffusion, molecular biophysics, Monte Carlo methods, nanobiotechnology, nanoporous materials, polymers, probability

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3669427

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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    M. Muthukumar, J. Chem. Phys. 111, 10371 (1999)JCPSA6000111000022010371000001;, Phys. Rev. Lett. 86, 3188 (2001)
    J. Chem. Phys. 118, 5174 (2003)JCPSA6000118000011005174000001.

    K. Luo, R. Metzler, T. Ala-Nissila, and S.-C. Yung, Phys. Rev. E 80, 021907 (2009).

    Y. Kantor and M. Kardar, Phys. Rev. E 69, 021806 (2004).

    S. Matysiak, A. Montesi, M. Pasquali, A. B. Kolomeisky, and C. Clementi, Phys. Rev. Lett. 96, 118103 (2006).

    J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 65, 011802 (2001).

    K. Luo and R. Metzler, J. Chem. Phys. 134, 135102 (2011)JCPSA6000134000013135102000001.

    W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996).

    R. H. Abdolvahab, F. Roshani, A. Nourmohammad, M. Sahimi, and M. R. R. Tabar, J. Chem. Phys. 129, 5102 (2008)JCPSA6000129000023235102000001.

    C. Chatelain, Y. Kantor, and M. Kardar, Phys. Rev. E 78, 021129 (2008).

    K. Luo, T. Ala-Nissila, S.-C. Ying, and A. Bhattacharya, Phys. Rev. Lett. 100, 058101 (2008)
    J. Chem. Phys. 126, 145101 (2007)JCPSA6000126000014145101000001.


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