Simulation of DNA Motion in Entropic Trapping

Abstract

Electrophoresis is a method of separating molecules with an applied electric field. An example of a molecule that can be separated by electrophoresis is the DNA, where its short strands are separated from the longer strands. Electrophoresis can be implemented with the use of a gel or with the use of entropic traps. Between these two methods, gel electrophoresis is more commonly used. Since entropic trapping is less familiar to many, much effort is presently being undertaken for further studies of this method. The development of computer simulations will indeed be of great help in such studies.

The Simulation of DNA Motion in Entropic Trapping is a stand-alone application developed in Java that calculates the position of a particle within an entropic trapping environment under certain parameters. The graph provided by JFreeChart is a visual representation of the position versus time plot of the simulation. Through the graph, the behavior, particularly the motion of the DNA whether it is trapped or not can be observed.