Browsing by Author "Dorfman, Kevin D."
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Item Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime(2019-09-19) Chuang, Hui-Min; Reifenberger, Jeff G.; Bhandari, Aditya Bikram; Dorfman, Kevin D.; dorfman@umn.edu; Dorfman, Kevin D.; University of Minnesota Dorfman Research LabDNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for lambda -DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.Item Data from: A Boundary Element Method/Brownian Dynamics Approach to Simulating DNA Electrophoresis in Electrically Insulating Microfabricated Devices(2013-07-22) Cho, Jaeseol; Kenward, Martin; Dorfman, Kevin D.Item Data from: Adsorption of Single Polymer Molecules in Shear Flow near a Planar Wall(2013-08-13) Dutta, Sarit; Dorfman, Kevin D.; Kumar, SatishItem Data from: Analysis of a DNA Simulation Model through Hairpin Melting Experiments(2013-07-24) Linak, Margaret C; Dorfman, Kevin D.Item Data from: Backfolding of DNA Confined in Nanotubes: Flory Theory versus the Two-State Cooperativity Model(2016) Muralidhar, Abhiram; Dorfman, Kevin D.Item Data from: Backfolding of wormlike chains confined in nanochannels(2014) Muralidhar, Abhiram; Tree, Douglas R.; Dorfman, Kevin D.Item Data from: Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis and DNA Stretching(2013-08-12) Dorfman, Kevin D.; King, Scott B; Olson, Daniel W.; Thomas, Joel DP; Tree, Douglas RItem Data from: Brownian Dynamics Simulations of Electrophoretic DNA Separations in a Sparse Ordered Post Array(2013-07-23) Cho, Jaeseol; Dorfman, Kevin D.Item Data from: Brownian Dynamics Simulations of Single-Stranded DNA Hairpins(2013-07-22) Kenward, Martin; Dorfman, Kevin D.Item Data from: Coarse Grained Brownian Dynamics Simulations of the 10-23 DNAzyme(2013-07-22) Kenward, Martin; Dorfman, Kevin D.Item Data from: Comparison of Microfabricated Hexagonal and Lamellar Post Arrays for DNA Electrophoresis(2014-03-05) Chen, Zhen; Dorfman, Kevin D.Item Data from: Coupled Flow and Reaction during Natural Convection PCR(2013-07-22) Allen, Joshua W.; Kenward, Martin; Dorfman, Kevin D.Item Data from: Distribution of distances between DNA barcode labels in nanochannels close to the persistence length(2015-02-14) Reinhart, Wesley F; Reifenberger, Jeff G.; Gupta, Damini; Muralidhar, Abhiram; Sheats, Julian; Cao, Han; Dorfman, Kevin D.Item Data from: DNA Electrophoresis in a Sparse Ordered Post Array(2013-07-22) Ou, Jia; Cho, Jaeseol; Olson, Daniel W.; Dorfman, Kevin D.Item Data from: DNA Electrophoresis in Confined, Periodic Geometries: A New Lakes-Straits Model(2013-08-05) Laachi, Nabil; Dorfman, Kevin D.Item Data from: DNA Electrophoresis in Microfluidic Post Arrays under Moderate Electric Fields(2013-07-22) Dorfman, Kevin D.Item Data from: DNA Unhooking from a Single Post as a Deterministic Process: Insights from Translocation Modeling(2013-07-22) Laachi, Nabil; Cho, Jaeseol; Dorfman, Kevin D.Item Data from: Dynamics of Polymer Adsorption from Dilute Solution in Shear Flow near a Planar Wall(2014-02-26) Dutta, Sarit; Dorfman, Kevin D.; Kumar, SatishItem Data from: Effect of excluded volume on the force-extension of wormlike chains in slit confinement(2016) Li, Xiaolan; Dorfman, Kevin D.Item Data from: Electrophoretic Collision of a DNA Molecule with a Small Elliptical Obstacle(2013-07-22) Cho, Jaeseol; Kumar, Satish; Dorfman, Kevin D.
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