Brownian Dynamics Studies on DNA Gel Electrophoresis. II. `Defect' Dynamics in the Elongation-Contraction Motion
| dc.creator | Azuma, Ryuzo | |
| dc.date | 2001-11-07 | |
| dc.date.accessioned | 2026-07-07T02:43:24Z | |
| dc.date.available | 2026-07-07T02:43:24Z | |
| dc.description | By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in CFGE. The corresponding embodiment, which we call {\it slack beads} (s-beads) is explicitly introduced in our BD model. In equilibrium under a vanishing field the distance between s-beads and their hopping range are found to be randomly distributed following a Poisson distribution. In the strong field range, where a chain undergoes the elongation-contraction motion, s-beads are observed to be alternatively annihilated in elongation and created in contraction of the chain. On the other hand, the distribution of hopping range of s-beads does not differ much from that in equilibrium. The results indicate that the motion of the chain elongated consists of a huge number of random movements of s-beads. We have also confirmed that these features of s-beads agree qualitatively with those of s-monomers in the extended bond fluctuation model (EBFM) which we recently proposed. The coincidence of the two simulations strongly supports the stochastic semi-local movement of s-monomers which we {\it a priori} introduced into the EBFM. | |
| dc.description | 14 pages, 11 figures | |
| dc.identifier | https://arxiv.org/abs/cond-mat/0111100 | |
| dc.identifier | http://arxiv.org/abs/cond-mat/0111100 | |
| dc.identifier | J. Chem. Phys. 117, 6873 (2002) | |
| dc.identifier | doi:10.1063/1.1505868 | |
| dc.identifier.uri | http://salesiana.dossiersoluciones.com/handle/123456789/18486 | |
| dc.subject | Soft Condensed Matter | |
| dc.subject | Statistical Mechanics | |
| dc.title | Brownian Dynamics Studies on DNA Gel Electrophoresis. II. `Defect' Dynamics in the Elongation-Contraction Motion | |
| dc.type | text |