This dissertation investigates the size based separation of DNA molecules in nanoparticle arrays under asymmetric pulsed electrophoresis. Crystalline arrays of nanoparticles within microfluidic channels are fabricated using colloidal selfassembly, yielding structures with pore sizes ranging from a few nanometers to a few hundred nanometers. Angular separation of DNA molecules is achieved in these matrices using asymmetric pulsed field electrophoresis. The DNA migration mechanism in highly confined pores and the impact of pulse frequency and field magnitudes on DNA separation are studied. It is observed that in confinements smaller than the persistence length of DNA, the DNA molecule is fully stretched and can be treated as a persistent chain due to its bending elasticity. The frequency response of DNA separation is also investigated, showing four distinct regions in frequency response curve; a low frequency rise, a plateau, a subsequent decline, and a second plateau at higher frequencies. It is shown that this frequency response is governed by the relation between the pulse time, relaxation time, and the reorientation time of DNA. Real-time videos of single DNA migrating under high frequency pulsed electric field show the DNA no longer follows the ratchet mechanism seen at lower frequencies, but reptates along the average direction of the two electric fields. A freely-jointed-chain model of DNA is developed to calculate the frequency response of a chain under a pulsed external force. The model exhibits a similar variation of angular separation with frequency.;Finally, the role of order within a separation matrix on DNA separation efficiency is studied systematically. Colloidal arrays with two different sized nanoparticles mixed in various proportions are prepared, yielding structures with different degrees of disorder. Radial distribution functions and orientational order parameters are calculated to characterize the scale of disorder. The DNA separation resolution is quantified for each structure, showing a strong dependence on order within the structure. Ordered structures give better separation resolution than highly disordered structures. However, the variation of separation performance with order is not monotonic, showing a small, but statistically significant improvement in structures with short range order compared to those with long range order.
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