Three-Dimensional Molecular Simulation of Electrophoretic Separations

A three-dimensional stochastic simulation has been developed for electrophoretic separations. This simulation follows the trajectories of individual molecules by applying the fundamental equations of motion for diffusion, electroosmotic flow, and electrophoretic migration. The molecular zone profile may then be examined and characterized at any specified time or distance. The stochastic simulation has been validated by comparison with classical transport models, having average relative errors for the mean zone distance and variance of 0.01−0.04% and 2.67−4.36%, respectively. The simulation also shows excellent agreement with experimental results for the electrophoretic separation of the nucleotide monophosphates in phosphate buffer solution, having average relative errors for the mean zone distance and variance of 1.65% and 12.99%, respectively. This stochastic simulation provides an accurate and versatile means to examine and characterize transport processes in complex electrophoretic systems.