High field electrophoresis—computer simulations Original Research Article

We describe for the first time the results, obtained by means of a new two-dimensional version of a cellular automaton (2DA), designed for the simulation of the gel electrophoresis at high fields. The calculations are performed up to image reptons. The results are compared with those from a modified version of the one-dimensional automaton (1DA), which has been constructed previously. The modification is that the movements of different parts of a molecule of DNA are treated as statistically independent events. This approach is applied also for 2DA. Main results are: (i) for long molecules image the velocity v tends to a constant both for 1DA and 2DA; (ii) the diffusion coefficient D for 2DA increases with N; (iii) 2DA enables the formation of so-called hernias, i.e. fragments of DNA locally perpendicular to the molecule, and (iv) a direct observation of the geometration effect. The results (i) and (ii) mimic the experimental behavior at high electric fields. We also calculate a dimensionless quantity image, where image is the molecule length and a is the stiffness length. The discussion of y reveals the role of the length fluctuations.