Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
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Alexander-Katz_Conformational dynamics.pdf
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Author(s)
Einert, Thomas R.
Netz, Roland R.
Sing, Charles E.
Alexander-Katz, Alfredo
Date Issued
December 2011
Journal
The European Physical Journal E
Publisher
Springer-Verlag
Citation
Einert, T. R., C. E. Sing, A. Alexander-Katz, and R. R. Netz. Conformational Dynamics and Internal Friction in Homopolymer Globules: Equilibrium Vs. Non-equilibrium Simulations. The European Physical Journal E 34, no. 12 (December 14, 2011).
Version
Author's final manuscript
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 N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < εs with fast internal dynamics and a solid-like regime (for ε > ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . 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 N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.
MIT Department
Massachusetts Institute of Technology. Department of Materials Science and Engineering
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DOI of Published Version
https://doi.org/10.1140/epje/i2011-11130-8
