A new bond fluctuation method for a polymer undergoing gel electrophoresis

Details A new bond fluctuation method for a polymer undergoing gel electrophoresis A new bond fluctuation method for a polymer undergoing gel electrophoresis

1998-08-12

arxiv.org/abs/cond-mat/9808122v1

Physics

Condensed Matter

Soft Condensed Matter

15 pages, 11 figures

Scientific paper

10.1103/PhysRevE.59.650

We present a new 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 non-local movement of a slack monomer at an 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 filed limit. The new BFM thus turns out an efficient computational method to study gel electrophoresis in a wide range of the electric field strength.

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