Particle simulation of traveling wave gel electrophoresis

This paper describes a 3D particle model to simulate conventional DC and traveling wave gel electrophoresis. Traveling waves sustain much higher fields for increased speed, but require much lower voltage which does not scale with gel dimension. Secondary refinement after initial separation allow for increased resolution. The model is validated for protein migration in both FEF and SDS-PAGE stages of a conventional 2D gel electrophoresis run. Model predictions are verified against two sets of sample proteins. Results from simulations and experiments agree very well for SDS-PAGE. Some discrepancy in the IEF dimension is a constant off-set attributed to the assumption of a linear pH gradient along the IPG strip, and to gel distortion and swelling. This in silica model is successfully used to predict protein migration with traveling wave electrodes.