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Exploring Dna Translocation Through A Nanopore Via A Multiscale Lattice-Boltzmann Molecular-Dynamics Methodology

Author

Listed:
  • SIMONE MELCHIONNA

    (INFM-SOFT, Department of Physics, Università di Roma La Sapienza, P.le A. Moro 2, 00185 Rome, Italy)

  • MARIA G. FYTA

    (Department of Physics, Harvard University, Cambridge, MA 02138, USA)

  • EFTHIMIOS KAXIRAS

    (Department of Physics and Division of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA)

  • SAURO SUCCI

    (Istituto Applicazioni Calcolo, CNR, Viale del Policlinico 137, 00161, Roma, Italy)

Abstract

A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of various initial configurations and lengths we map the probability distibutions of the passage times of the DNA through the nanopore. A scaling law behavior for the most probable of these times with respect to length is derived, and shown to exhibit an exponent that is in a good agreement with the experimental findings. The essential features of the DNA dynamics as it passes through the pore are explored.

Suggested Citation

  • Simone Melchionna & Maria G. Fyta & Efthimios Kaxiras & Sauro Succi, 2007. "Exploring Dna Translocation Through A Nanopore Via A Multiscale Lattice-Boltzmann Molecular-Dynamics Methodology," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 18(04), pages 685-692.
    • Handle: RePEc:wsi:ijmpcx:v:18:y:2007:i:04:n:s0129183107010942
    DOI: 10.1142/S0129183107010942
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