DNA electrophoresis studied with the cage model

Authors:
A. van Heukelum;G. T. Barkema;R. H. Bisseling
Affiliations:
Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands;Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands;Mathematical Institute, Utrecht University, P.O. Box 80010, 3508 TA Utrecht, The Netherlands
Venue:
Journal of Computational Physics
Year:
2002

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Abstract

The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15 monomers. The computations show the Nernst-Einstein regime (υ ∼ E) followed by a regime where the velocity decreases exponentially with the applied electric field strength. In agreement with de Gennes' reptation arguments, we find that asymptotically for large polymers the diffusion coefficient D decreases quadratically with polymer length; for the cage model, the proportionality coefficient is DL2 = 0.175(2). Additionally we find that the leading correction term for finite polymer lengths scales as N-1/2, where N = L - 1 is the number of bonds.