Sieving of spherical particles during gel electrophoresis: A new computer simulation algorithm.

Abstract

A new computer simulation algorithm is developed to study the behavior of a hard sphere during gel electrophoresis. The electrophoresis mobility and the diffusion coefficients are presented to show the effects of the field intensity, of the gel concentration, and of the randomness of the gel. The results indicate that previous models are not applicable for either the periodic or the random gel, and that the Einstein relation does not hold because the gel molecules affect the dynamics of the hard sphere. Moreover, the randomness of sieving gels lead to a trapping effect where the longitudinal diffusion coefficient is much larger than expected when the gel is dense and the field intensity is non-negligible. This trapping effect predicts a limit to both the field intensity and the gel concentration that one can use for the separation of particles during gel electrophoresis. Our new algorithm thus opens a door to a detailed study of the process of electrophoretic sieving with potential applications in biology and biotechnology.