Dorfman Group
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We are located in the Department of Chemical Engineering and Materials Science at the University of Minnesota - Twin Cities. Take a look at our current research interests or our recent publications at our group web site: http://research.cems.umn.edu/dorfman/index.html
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Browsing Dorfman Group by Author "Bhandari, Aditya Bikram"
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Item Data and code supporting: Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA(2019-08-12) Bhandari, Aditya Bikram; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; DorfmanHairpins in the conformation of DNA confined in nanochannels close to their persistence length cause the distribution of their fractional extensions to be heavily left skewed. A recent theory rationalizes these skewed distributions using a correlated telegraph process, which can be solved exactly in the asymptotic limit of small but frequent hairpin formation. Pruned-enriched Rosenbluth method simulations of the fractional extension distribution for a channel-confined wormlike chain confirm the predictions of the telegraph model. Remarkably, the asymptotic result of the telegraph model remains robust well outside the asymptotic limit. As a result, the approximations in the theory required to map it to the polymer model and solve it in the asymptotic limit are not the source of discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA during genome mapping. The agreement between theory and simulations motivates future work to determine the source of the remaining discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA in nanochannels used for genome mapping.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: Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels(2018) Gupta, Damini; Bhandari, Aditya Bikram; Dorfman, Kevin DItem Data from: Limitations of the equivalent neutral polymer assumption for theories describing nanochannel-confined DNA(2020) Bhandari, Aditya Bikram; Dorfman, Kevin DItem A simple model for the wall depletion length of nanoconfined DNA (preprint)(2018-05-17) Bhandari, Aditya Bikram; Reifenberger, Jeffrey G; Chuang, Hui-Min; Cao, Han; Dorfman, Kevin D