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Polymers 2016, 8(3), 79; doi:10.3390/polym8030079

The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels

Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA
Current address: Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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Author to whom correspondence should be addressed.
Academic Editor: Martin Krőger
Received: 26 January 2016 / Revised: 5 February 2016 / Accepted: 7 March 2016 / Published: 14 March 2016
(This article belongs to the Special Issue Semiflexible Polymers)
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Abstract

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 chains. In the course of this analysis, we also computed the global persistence length of ideal wormlike chains for the modestly rectangular channels that are used in many experimental systems. The results are relevant to genomic mapping systems that confine DNA in channel sizes around 50 nm, since fabrication constraints generally lead to rectangular cross-sections. View Full-Text
Keywords: DNA; confinement; genome mapping; nanochannels; Flory theory; backfolding; hairpin; Odijk; rectangular channels; semiflexible polymers DNA; confinement; genome mapping; nanochannels; Flory theory; backfolding; hairpin; Odijk; rectangular channels; semiflexible polymers
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Muralidhar, A.; Quevillon, M.J.; Dorfman, K.D. The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels. Polymers 2016, 8, 79.

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