Wall depletion length of a channel-confined polymer

Guo Kang Cheong, Xiaolan Li, and Kevin D. Dorfman
Phys. Rev. E 95, 022501 – Published 15 February 2017

Abstract

Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.

  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Received 19 December 2016

DOI:https://doi.org/10.1103/PhysRevE.95.022501

©2017 American Physical Society

Physics Subject Headings (PhySH)

  1. Research Areas
  1. Physical Systems
Physics of Living SystemsPolymers & Soft Matter

Authors & Affiliations

Guo Kang Cheong, Xiaolan Li, and Kevin D. Dorfman*

  • Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA

  • *dorfman@umn.edu

Article Text (Subscription Required)

Click to Expand

References (Subscription Required)

Click to Expand
Issue

Vol. 95, Iss. 2 — February 2017

Reuse & Permissions
Access Options
CHORUS

Article Available via CHORUS

Download Accepted Manuscript
Author publication services for translation and copyediting assistance advertisement

Authorization Required


×
×

Images

×

Sign up to receive regular email alerts from Physical Review E

Log In

Cancel
×

Search


Article Lookup

Paste a citation or DOI

Enter a citation
×