Theoretical study of the transpore velocity control of single-stranded DNA

Weixin Qian, Kentaro Doi, Satoshi Uehara, Kaito Morita, Satoyuki Kawano

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

Original languageEnglish
Pages (from-to)13817-13832
Number of pages16
JournalInternational journal of molecular sciences
Issue number8
Publication statusPublished - 2014 Aug 11


  • Coarse-graining
  • Langevin dynamics simulation
  • Micro/nanofluidics
  • Transpore dynamics
  • ssDNA

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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