We describe for the first time the results, obtained by means of a new version of the cellular automaton, designed for the simulation of gel #N#electrophoresis. A special purpose of the automaton is to reproduce the geometration effect, i.e. subsequent hookings and release of the molecules of DNA at gel fibres at high electric fields. The starting point is the reptation model [1], where the molecule is represented as a chain of N rigid units, so‐called reptons, connected by flexible bonds. The features of the former, one‐dimensional version [2] of the automaton are: simultaneous movements of many reptons and the conformation‐dependent length of the time step. The present two‐dimensional version enables also the formation of so‐called hernias, i.e. fragments of the DNA molecule locally perpendicular to the molecule. The calculations are performed up to N = 350 reptons. The results are: i) more molecules are trapped at gel fibres, ii) the velocity of the moving fraction of DNA is almost two times smaller, and iii) the diffusion coefficient is about 25 times greater than in the one‐dimensional version. In both cases, the velocity of the moving fraction is inversely proportional to the molecule length, and the diffusion coefficient is proportional to the molecule length. The fraction of trapped molecules decreases with N. The simulation allows for direct observation of the geometration effect.
['Malgorzata J. Krawczyk', 'M. Kopeć', 'K. Kułakowski']
High Field Electrophoresis: Computer Simulations