Realistic Brownian Dynamics simulations of biological molecule separation in nanofluidic devices

Abstract

We present a Brownian Dynamics model of biological molecule separation in periodic nanofilter arrays. The biological molecules are modeled using the Worm-Like-Chain model with Hydrodynamic Interactions. We focus on short dsDNA molecules; this places the separation process either in the Ogston sieving regime or the transition region between Ogston sieving and entropic trapping. Our simulation results are validated using the experimental results of Fu et al. (Phys Rev Lett 97:018103, 2006); particular attention is paid to the model’s ability to quantitatively capture experimental results using realistic values of all physical parameters. Our simulation results showed that molecule mobility is sensitive to the device geometry. Moreover, our model is used for validating the theoretical prediction of Li et al. (Anal Bioanal Chem 394:427–435, 2009) who proposed a separation process featuring an asymmetric device and an electric field of alternating polarity. Good agreement is found between our simulation results and the predictions of the theoretical model of Li et al.