Electrophoresis of charged polymers: Simulation and scaling in a lattice model of reptation

G. T. Barkema*, J. F. Marko, B. Widom

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

72 Scopus citations

Abstract

We report numerical results on the repton model of Rubinstein [Phys. Rev. Lett. 59, 1946 (1987)] as adapted by Duke [Phys. Rev. Lett. 62, 2877 (1989)] as a model for the gel electrophoresis of DNA. We describe an efficient algorithm with which we have simulated chains of N reptons with N several hundred in some instances. The diffusion coefficient D in the absence of an external electric field is obtained for N≤100; we find N2D=1/3(1+5N-2/3) for large N. The coefficient 1/3 is in accord with the analytical results of Rubinstein and of van Leeuwen and Kooiman [Physica A 184, 79 (1992)]. The drift velocity v in a static field of variable strength E is obtained for various N and NE up to N=30 when NE is as small as 0.01 and up to N=400 when NE is as large as 20. We find that v has a finite, nonzero limit as N→ at fixed E and that this limit is proportional to EE, in accord with the conclusions of Duke, Semenov, and Viovy [Phys. Rev. Lett. 69, 3260 (1992)] for a different but related model. In a scaling limit in which N→ and E→0 the drift velocity in the repton model is fitted well by the formula N2v=NE[(1/3)2+(2NE/5)2]1/2 for all values of the scaling variable NE. We present a scaling analysis complementary to that of Duke, Semenov, and Viovy with which we rationalize the EE behavior of the limiting drift velocity.

Original languageEnglish (US)
Pages (from-to)5303-5309
Number of pages7
JournalPhysical Review E
Volume49
Issue number6
DOIs
StatePublished - 1994

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics

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