One-dimensional migration of DNA in the presence of point particle traps

Abstract

This paper studies the one-dimensional motion of a DNA molecule through a microchannel with a series of point particle electric traps. The three particle molecule model uses three beads connected via harmonic springs in the presence of a Weeks-Chandler-Andersen repulsive potential and a Brownian force. Using the stochastic fourth order Runge-Kutta method, the trajectory of the center of mass is observed as the field strengths were varied. System parameters are identified that can impede the flow of a DNA molecule.