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Materials 2013, 6(9), 3989-4000; doi:10.3390/ma6093989

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

1 Department of Mechatronics Engineering, Kyungsung University, 309 Suyeong-ro, Nam-gu, Busan 608-736, Korea 2 Department of Mechanical Engineering, Dong-A University, 840 Hadan-dong, Saha-gu, Busan 604-714, Korea
* Author to whom correspondence should be addressed.
Received: 30 May 2013 / Revised: 25 July 2013 / Accepted: 29 August 2013 / Published: 11 September 2013
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In this study, we simulate the electrophoretic motion of a bio-polymer through a synthetic nanopore in the presence of an external bias voltage by considering the hydrodynamic interactions between the polymer and the fluid explicitly. The motion of the polymer is simulated by 3D Langevin dynamics technique by modeling the polymer as a worm-like-chain, while the hydrodynamic interactions are incorporated by the lattice Boltzmann equation. We report the simulation results for three different lengths of the nanopore. The translocation time increases with the pore length even though the electrophoretic force on the polymer is the same irrespective of the pore length. This is attributed to the fact that the translocation velocity of each bead inside the nanopore decreases with the pore length due to the increased fluid resistance force caused by the increase in the straightened portion of the polymer. We confirmed this using a theoretical formula.
Keywords: translocation motion; bio-polymer; nanopore length; lattice Boltzmann method translocation motion; bio-polymer; nanopore length; lattice Boltzmann method
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Alapati, S.; Che, W.S.; Suh, Y.K. Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study. Materials 2013, 6, 3989-4000.

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