title: Theoretical study of the transpore velocity control of single-stranded DNA.
abstract: 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.
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. qian@bnf.me.es.osaka-u.ac.jp.
authors.forename: Weixin
authors.initials: W
authors.lastname: Qian
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. doi@me.es.osaka-u.ac.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Doi
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. uehara@paris.ifs.tohoku.ac.jp.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Uehara
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. morita@bnf.me.es.osaka-u.ac.jp.
authors.forename: Kaito
authors.initials: K
authors.lastname: Morita
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. kawano@me.es.osaka-u.ac.jp.
authors.forename: Satoyuki
authors.initials: S
authors.lastname: Kawano
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry*; D004560:Electricity; D044085:Microfluidics; D008962:Models, Theoretical; D058608:Nanopores
chemical_list: D004277:DNA, Single-Stranded