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- Douglas R Tree, Abhiram Muralidhar, Patrick S Doyle, Kevin D Dorfman
- Macromolecules
- 2013

The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular… (More)

- Damini Gupta, Jeremy J Miller, Abhiram Muralidhar, Sara Mahshid, Walter Reisner, Kevin D Dorfman
- ACS macro letters
- 2015

We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size… (More)

- Wesley F Reinhart, Jeff G Reifenberger, +4 authors Kevin D Dorfman
- The Journal of chemical physics
- 2015

We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the… (More)

- Damini Gupta, Julian Sheats, +5 authors Walter Reisner
- The Journal of chemical physics
- 2014

We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly… (More)

- Abhiram Muralidhar, Douglas R Tree, Yanwei Wang, Kevin D Dorfman
- The Journal of chemical physics
- 2014

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… (More)

- Abhiram Muralidhar, Michael J. Quevillon, Kevin D. Dorfman
- 2016

The deflection segment length is governed by the smallest channel dimension D and is given by λ D 2/3 L

- Abhiram Muralidhar, Michael J. Quevillon, Kevin D. Dorfman
- 2016

We confirm Odijk's scaling laws for (i) the average chain extension; (ii) the variance about the average extension; and (iii) the confinement free energy of a wormlike chain confined in a rectangular nanochannel smaller than its chain persistence length through pruned-enriched Rosenbluth method (PERM) simulations of asymptotically long, discrete wormlike… (More)

- Abhiram Muralidhar, Kevin D Dorfman
- Macromolecules
- 2015

We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with pruned-enriched Rosenbluth method (PERM) simulations of a… (More)

- Wesley F Reinhart, Jeff G Reifenberger, +4 authors Kevin D Dorfman
- The Journal of chemical physics
- 2017

- Toby St Clere Smithe, Vitalii Iarko, Abhiram Muralidhar, Erik Werner, Kevin D Dorfman, Bernhard Mehlig
- Physical review. E, Statistical, nonlinear, and…
- 2015

Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of… (More)