Brownian dynamics simulations of polyelectrolyte molecules traveling through an entropic trap array during electrophoresis

Using Brownian dynamics simulations of wormlike chain bead-spring models, the dynamics of linear and star-branched polyelectrolyte molecules traveling through an array of entropic traps during electrophoresis have been investigated. First, the effectiveness of using coarse-grained bead-spring systems for linear molecules to model the electrophoretic process was demonstrated and compared to previous bead-rod (Kramers) chain simulations by Panwar and Kumar Macromolecules 39, 1297 (2006)]. Second, the coarse-grained bead-spring model has been extended to investigate the effect of branching on the dynamics of molecules through the entropic trap array. Initial studies indicate the reduced mobility of star-branched molecules as compared to equivalent linear molecules. The radius of gyration of the polymer molecule appears to be the dominating factor governing the time scales encountered during traversal of the entropic trapping array.