Bond fluctuation method for a polymer undergoing gel electrophoresis

Abstract

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.

Diffusion of single long polymers in fixed and low density matrix of obstacles confined to two dimensions

“…The extended-BFM which we have proposed [10] and used in the present study incorporates a non-local movement of the 's-monomer' into the BFM. The s-monomer is defined as the one whose nearest neighbors separate not greater than √ 13 with each other.…”

Modeling the separation of macromolecules: A review of current computer simulation methods

“…In order to solve this problem, one must modify the lattice models by adding nonlocal moves, an idea first implemented by Deutsch and Reger [119] and Duke and Viovy [11] for reptation models. Azuma and Takayama [120] added such moves to the BFA. Although their approach is not very carefully justified, it produces qualitatively reasonable results.…”

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

“…As we increase the field strength or the length of the polymer chain, new physical properties have to be integrated in the models. Some of these, like the sliding motion of the polymers when the chains are stretched by the field, seem to have been successfully added to the simulations [184], but more work has to be done to compare such models to experimental data. In many cases, we still cannot study the very large chain sizes that would allow a useful comparison to data.…”

“…Unfortunately, Monte Carlo methods do not normally include such forces; in fact, chain pinning is then a direct result of the algorithm and has nothing to do with the real physics of the process. Azuma and Takayama [184] developed a new bond fluctuation model (BFM) in which they incorporated a sliding motion of the polymers hooked around the gel fibers. Without this modification, the simulations performed using the traditional BFM show an anomalous trapping of the polymers at high fields.…”