High field electrophoresis - computer simulations
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 N = 442 reptons. The results are compared with those from a modified version of the one-dimensional automaton (IDA), 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 (N much greater than 1) the velocity v tends to a constant both for IDA 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 y = D/(Lv), where L = Na is the molecule length and a is the stiffness length. The discussion of y reveals the role of the length fluctuations. (C) 2004 Elsevier B.V. All rights reserved.
simulation dna transport biased diffusion