New cellular automaton designed to simulate geometration in gel electrophoresis

Abstract

We propose a new kind of cellular automaton to simulate transportation of molecules of DNA through agarose gel. Two processes are taken into account: reptation at strong electric field E, described in the particle model, and geometration, i.e. subsequent hookings and releases of long molecules at and from gel fibres. The automaton rules are deterministic and they are designed to describe both processes within one unified approach. Thermal fluctuations are not taken into account. The number of simultaneous hookings is limited by the molecule length. The features of the automaton are: (i) the size of the cell neighbourhood for the automaton rule varies dynamically, from nearest neighbors to the entire molecule; (ii) the length of the time step is determined at each step according to dynamic rules. Calculations are made up to N = 244 reptons in a molecule. Two subsequent stages of the motion are found. Firstly, an initial set of random configurations of molecules is transformed into a more ordered phase, where most molecules are elongated along the applied field direction. After some transient time, the mobility µ reaches a constant value. Then, it varies with N as 1/N for long molecules. The band dispersion varies with time t approximately as Nt 1/2 . Our results indicate that the well-known plateau of the mobility µ vs. N does not hold at large electric fields.  2002 Elsevier Science B.V. All rights reserved.