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Full-Text Articles in Chemical Engineering
Interplay Between Chain Stiffness And Excluded Volume Of Semiflexible Polymers Confined In Nanochannels, Abhiram Muralidhar, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Interplay Between Chain Stiffness And Excluded Volume Of Semiflexible Polymers Confined In Nanochannels, Abhiram Muralidhar, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Faculty Publications
The properties of channel-confined semiflexible polymers are determined by a complicated interplay of chain stiffness and excluded volume effects. Using Pruned-Enriched Rosenbluth Method (PERM) simulations, we study the equilibrium properties of channel-confined polymers by systematically controlling chain stiffness and excluded volume. Our calculations of chain extension and confinement free energy for freely jointed chains with and without excluded volume show excellent agreement with theoretical predictions. For ideal wormlike chains, the extension is seen to crossover from Odijk behavior in strong confinement to zero-stretching, bulk-like behavior in weak confinement. In contrast, for self-avoiding wormlike chains, we always observe that the linear …
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 …
Resolution Limit For Dna Barcodes In The Odijk Regime, Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Resolution Limit For Dna Barcodes In The Odijk Regime, Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Faculty Publications
We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of …
Simulation Of Dna Extension In Nanochannels, Yanwei Wang, Douglas R. Tree, Kevin D. Dorfman
Simulation Of Dna Extension In Nanochannels, Yanwei Wang, Douglas R. Tree, Kevin D. Dorfman
Faculty Publications
We have used a realistic model for double-stranded DNA and Monte Carlo simulations to compute the extension (mean span) of a DNA molecule confined in a nanochannel over the full range of confinement in a high ionic strength buffer. The simulation data for square nanochannels resolve the apparent contradiction between prior simulation studies and the predictions from Flory theory, demonstrating the existence of two transition regimes between weak confinement (the de Gennes regime) and strong confinement (the Odijk regime). The simulation data for rectangular nanochannels support the use of the geometric mean for mapping data obtained in rectangular channels onto …