Compression and Stretching of a Self-Avoiding Chain in Cylindrical Nanopores

Suckjoon Jun, D. Thirumalai, and Bae-Yeun Ha
Phys. Rev. Lett. 101, 138101 – Published 22 September 2008

Abstract

Force-induced deformations of a self-avoiding chain confined inside a cylindrical cavity, with diameter D, are probed using molecular dynamics simulations, scaling analysis, and analytical calculations. We obtain and confirm a simple scaling relation fDR9/4 in the strong-compression regime, while for weak deformations, we find fD=A(R/R0)+B(R/R0)2, where A and B are constants, f the external force, and R the chain extension (with R0 its unperturbed value). For a strong stretch, we present a universal, analytical force-extension relation. Our results can be used to analyze the behavior of biomolecules in confinement.

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  • Received 26 May 2008

DOI:https://doi.org/10.1103/PhysRevLett.101.138101

©2008 American Physical Society

Authors & Affiliations

Suckjoon Jun

  • FAS Center for Systems Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA

D. Thirumalai

  • Biophysics Program, IPST and Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, USA

Bae-Yeun Ha

  • Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada

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Vol. 101, Iss. 13 — 26 September 2008

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