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Kinetics Of Polymer Ejection From Capsid Confinement: Scaling Considerations And Computer Experiment

Author

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  • A. MILCHEV

    (Institute for Physical Chemistry, Bulgarian Academy of Science, 1113 Sofia, Bulgaria;
    Institut für Physik, Johannes Gutenberg Universität Mainz, Staudinger Weg 7, 55099 Mainz, Germany)

  • K. BINDER

    (Institut für Physik, Johannes Gutenberg Universität Mainz, Staudinger Weg 7, 55099 Mainz, Germany)

Abstract

We investigate the ejection dynamics of a flexible polymer chain out of confined environment by means of scaling considerations and Monte Carlo simulations. Situations of this kind arise in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. In the case of cylindric confinement the entropic driving force which pulls the chain out of the pore is argued to be constant once a few persistent lengths are out of the pore. We demonstrate that in this case the ejection dynamics follows a$\sqrt{t}$-law with elapsed timet. The mean ejection time τ depends nonmonotonically on chain lengthN. However, if the geometric constraints comprise a wider capsid chamber attached to a narrow exit tube, the mechanism of ejection changes and involves the surmounting of an activation barrier. The driving force then varies in time. One finds good agreement of theory and computer simulation with recent experiments with DNA.

Suggested Citation

  • A. Milchev & K. Binder, 2012. "Kinetics Of Polymer Ejection From Capsid Confinement: Scaling Considerations And Computer Experiment," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 23(08), pages 1-11.
    • Handle: RePEc:wsi:ijmpcx:v:23:y:2012:i:08:n:s0129183112400050
    DOI: 10.1142/S0129183112400050
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