Simulation of DNA electrophoresis by lattice reptation models

The cage model for reptation is extended to describe the dynamics of a polymer in a gel, under the influence of a homogeneous electric field. This model gives results that agree qualitatively with experiments on DNA strands in agarose gels, provided the polymer's persistence length, a measure of its rigidity, is large compared to its diameter, and of the same order of magnitude as the pore size of the gel. This manuscript describes the proposed model, and compares it to another model for electrophoresis, the DukeRubinstein model. An e#cient sequential and parallel implementation is presented to calculate the drift velocity of the polymer numerically exactly, and results for polymers up to twelve persistence lengths are reported. From these results, numerically exact results are also obtained for the di#usion constant. Contents 1 Introduction 5 1.1 Gel electrophoresis of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2 Motion of DNA strands in a gel . . . . ....