Bond fluctuation method for a polymer undergoing gel electrophoresis

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Abstract
We present a computational methodology for the investigation of gel electrophoresis of polyelectrolytes. We have developed the method initially to incorporate sliding motion of tight parts of a polymer pulled by an electric field into the bond fluctuation method (BFM). Such motion due to tensile force over distances much larger than the persistent length is realized by nonlocal movement of a slack monomer at either end of the tight part. The latter movement is introduced stochastically. This new BFM overcomes the well-known difficulty in the conventional BFM that polymers are trapped by gel fibers in relatively large fields. At the same time it also reproduces properly equilibrium properties of a polymer in a vanishing field limit. The new BFM thus turns out to be an efficient computational method to study gel electrophoresis in a wide range of the electric field strength.
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