Modeling the Electrophoretic Separation of Short Biological Molecules in Nanofluidic Devices

Abstract

Via comparisons with rigid-rod and wormlike-chain Brownian dynamics (BD) simulations and the experimental results of Fu et al. (2006, “Molecular Sieving in Periodic Free-Energy Landscapes Created by Patterned Nanofilter Arrays,” Phys. Rev. Lett., 97(1), p. 018103), we demonstrate that, for the purposes of low-to-medium field electrophoretic separation, sufficiently short biomolecules can be modeled as point particles, with their orientational degrees of freedom accounted for using partition coefficients. This observation is used in the present work to build an efficient BD simulation method. Particular attention is paid to the model's ability to quantitatively capture experimental results using realistic values of all physical parameters.