PMID: 11909019Mar 23, 2002Paper

Glassy behavior of a homopolymer from molecular dynamics simulations

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Nikolay V DokholyanH Eugene Stanley

Abstract

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics. The main quantities of interest are the average root mean square displacement of the monomers below the theta point, and the structure factor, as a function of time. The observation of these quantities show a close resemblance to those measured in structural glasses and suggest that the polymer chain in its low temperature phase is in a glassy phase, with its dynamics dominated by traps. In equilibrium, at low temperature, we observe the trapping of the monomers and a slowing down of the overall motion of the polymer as well as nonexponential relaxation of the structure factor. Out of equilibrium, at low temperatures, we compute the two-time quantities and observe breaking of ergodicity in a range of waiting times, with the onset of aging.

References

Jan 16, 1999·Folding & Design·N V DokholyanE I Shakhnovich
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Apr 24, 2002·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·G E CrooksY Bar-Yam

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Citations

Jul 26, 2005·Trends in Biotechnology·Feng Ding, Nikolay V Dokholyan
Jul 9, 2004·Biophysical Journal·Jose M BorregueroNikolay V Dokholyan
Jul 23, 2004·The Journal of Chemical Physics·Michael Bachmann, Wolfhard Janke
Jan 21, 2017·Soft Matter·Suman MajumderWolfhard Janke
Aug 18, 2018·Physical Review Letters·Vittore F ScolariJulien Mozziconacci
Apr 15, 2016·Physical Review. E·Suman Majumder, Wolfhard Janke
Sep 10, 2017·The Journal of Chemical Physics·Henrik ChristiansenWolfhard Janke
Nov 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Thomas Frisch, Alberto Verga
Mar 15, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·S L NarasimhanK P N Murthy
Apr 17, 2021·Physical Review Letters·Hyun Woo ChoD Thirumalai
Nov 1, 2011·Journal of the American Chemical Society·Loukas PetridisJeremy C Smith

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