Conformational dynamics and internal friction in homopolymer globules: Equilibrium vs. non-equilibrium simulations

T. R. Einert, C. E. Sing, A. Alexander-Katz, R. R. Netz

Research output: Contribution to journalArticlepeer-review

Abstract

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size NG is observed. We find two distinct dynamical regimes: a liquidlike regime (for ε < ε s) with fast internal dynamics and a solid-like regime (for ε > ε s) with slow internal dynamics. The cohesion strength ε s of this freezing transition depends on NG. Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in NG. This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Original languageEnglish (US)
Article number130
JournalEuropean Physical Journal E
Volume34
Issue number12
DOIs
StatePublished - Dec 1 2011
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Chemistry(all)
  • Materials Science(all)
  • Surfaces and Interfaces

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