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Modeling The Relaxation Time Of Dna Confined In A Nanochannel, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Modeling The Relaxation Time Of Dna Confined In A Nanochannel, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Faculty Publications
Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 …
Entropic Depletion Of Dna In Triangular Nanochannels, Wesley F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Entropic Depletion Of Dna In Triangular Nanochannels, Wesley F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Faculty Publications
Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the …