We present a Brownian Dynamics model of dsDNA-molecule separation using periodic nanofilter arrays. Particular attention is paid to the model's ability to capture relevant experimental results. The effect of various device parameters on molecule selectivity is investigated. 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.
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