Download the full-sized PDF of DNA separation in nanoporous microfluidic devicesDownload the full-sized PDF



Permanent link (DOI):


Export to: EndNote  |  Zotero  |  Mendeley


This file is in the following communities:

Graduate Studies and Research, Faculty of


This file is in the following collections:

Theses and Dissertations

DNA separation in nanoporous microfluidic devices Open Access


Other title
DNA separation
colloidal crystals
pulsed field electrophoresis
Type of item
Degree grantor
University of Alberta
Author or creator
Nazemifard, Neda
Supervisor and department
Harrison, D. Jed (Chemistry)
Examining committee member and department
Nobes, David (Mechanical Engineering)
Harrison, D. Jed (Chemistry)
Slater, Gary W. (Physics, University of Ottawa)
Bhattacharjee, Subir (Mechanical Engineering)
Masliyah, Jacob H. (Chemical and Material Engineering)
Lucy, Charles (Chemistry)
Department of Mechanical Engineering

Date accepted
Graduation date
Doctor of Philosophy
Degree level
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 self-assembly, 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.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication

File Details

Date Uploaded
Date Modified
Audit Status
Audits have not yet been run on this file.
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 6613236
Last modified: 2015:10:12 16:56:10-06:00
Filename: Nazemifard_Neda_Spring2011.pdf
Original checksum: a45f48eecadb2bca94bc4e767b76400a
Well formed: true
Valid: true
Status message: Too many fonts to report; some fonts omitted. Total fonts = 1122
File title: Microsoft Word - titlewithout
File author: neda
Page count: 195
Activity of users you follow
User Activity Date