Brownian Dynamics modeling of electrophoretic dsDNA-molecule separation using nanofluidic devices

We present a Brownian Dynamics model of electrophoretic separation of short (up to 7 persistence lengths) dsDNA molecules in nanofluidic devices. Our formulation uses the Worm-Like-Chain model with hydrodynamic interactions. Our simulation results are in good agreement with the experimental results of Fu et al. [{\it Phys. Rev. Lett.}, {\bf 97}, 018103, 2006] for realistic values of all physical parameters. We also find good agreement between our simulation results and the theoretical model of Li et al. [{\it Anal. Bioanal. Chem.}, {\bf 394}, 427, 2009] who proposed an asymmetric separation device that operates under the effect of an alternating electric field.