Simple model of trapping electrophoresis with complicated transient dynamics

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Abstract
A simple reptation model of DNA trapping gel electrophoresis is shown to lead to surprisingly complicated transient dynamics. The DNA has a big neutral object attached to one of its ends; electrophoretic migration is thus slowed by trapping when it occurs in random gels. The detrapping process is thermally driven and its dependence upon the instantaneous molecular conformation gives rise to anomalous transport properties in our computer simulations. The electric field affects the molecular conformations and thus modifies the nature of the transient dynamics in nontrivial ways. The phenomenon is analyzed in terms of a directed walk through a periodic lattice of traps with a broad release time distribution. For large molecular sizes, we estimate that it is actually impossible to reach the steady state in an (experimentally) reasonable period of time.