A new bond fluctuation method for a polymer undergoing gel electrophoresis

TL;DR

This paper introduces a novel bond fluctuation method that simulates polymer behavior during gel electrophoresis, effectively overcoming previous limitations and accurately modeling polymer dynamics across various electric field strengths.

Contribution

A new bond fluctuation method incorporating non-local slack monomer movement to simulate polymer sliding during gel electrophoresis.

Findings

Overcomes trapping issues in conventional BFM.

Accurately reproduces equilibrium polymer properties.

Efficiently simulates polymer dynamics under various electric fields.

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.