ELECTROPHORESIS OF TOPOLOGICALLY NONTRIVIAL MACROMOLECULES: MATHEMATICAL AND COMPUTATIONAL STUDIES

Hwa A. Lim ()
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Hwa A. Lim: Bioinformatics, HYSEQ Inc., 670 Almanor Avenue Sunnyvale, California 94086, USA

International Journal of Modern Physics C (IJMPC), 1996, vol. 07, issue 02, 217-271

Abstract: Mathematical and numerical models for studying the electrophoresis of topologically nontrivial molecules in two and three dimensions are presented. The molecules are modeled as polygons residing on a square lattice and a cubic lattice whereas the electrophoretic media of obstacle network are simulated by removing vertices from the lattices at random. The dynamics of the polymeric molecules are modeled by configurational readjustments of segments of the polygons. Configurational readjustments arise from thermal fluctuations and they correspond to piecewise reptation in the simulations. A Metropolis algorithm is introduced to simulate these dynamics, and the algorithms are proven to be reversible and ergodic. Monte Carlo simulations of steady field random obstacle electrophoresis are performed and the results are presented.

Keywords: DNA; Electrophoresis; Knot; Macromolecules; Metropolis Algorithm; Monte Carlo Simulation; Self-Avoiding Walk (search for similar items in EconPapers)
Date: 1996
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DOI: 10.1142/S0129183196000193

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