The backfolded Odijk regime for wormlike chains confined in rectangular nanochannels

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

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16 Scopus citations

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.

Original languageEnglish (US)
Article number79
JournalPolymers
Volume8
Issue number3
DOIs
StatePublished - Mar 14 2016

Bibliographical note

Funding Information:
We thank Walter Reisner (McGill University) for discussion on fabrication of nanochannel devices. This work was supported by the National Science Foundation (NSF) grant CBET-1262286. Computational resources were provided in part by the University of Minnesota Supercomputing Institute.

Keywords

  • Backfolding
  • Confinement
  • DNA
  • Flory theory
  • Genome mapping
  • Hairpin
  • Nanochannels
  • Odijk
  • Rectangular channels
  • Semiflexible polymers

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