Simulation of DNA mobility in one-dimension using the bead-spring model


Proceedings of the 26th Samahang Pisika ng Pilipinas Physics Congress, University of the Phlippines Baguio, Baguio City, 22–24 Oct 2008, SPP-2008-138.


This paper studies the one-dimensional motion of a DNA molecule through a microchannel with a single electric trap. 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 spring constant is sought that allows motion through the microchannel without overlap between the three beads.