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

Materials. 2013;6(9):3989-4000 DOI 10.3390/ma6093989

 

Journal Homepage

Journal Title: Materials

ISSN: 1996-1944 (Print)

Publisher: MDPI AG

LCC Subject Category: Technology: Electrical engineering. Electronics. Nuclear engineering | Technology: Engineering (General). Civil engineering (General) | Science: Natural history (General): Microscopy | Science: Physics: Descriptive and experimental mechanics

Country of publisher: Switzerland

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Yong Kweon Suh
Woo Seong Che
Suresh Alapati

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 11 weeks

 

Abstract | Full Text

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.