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

TitleConformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
Publication TypeJournal Article
Year of Publication2011
AuthorsEinert, TR, Sing, CE, Alexander-Katz, A, Netz, RR
JournalEuropean Physical Journal E
Volume34
Issue12
Date Published2011/12//
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 epsilon and the globule size N-G is observed. We find two distinct dynamical regimes: a liquid-like regime (for epsilon < epsilon(s)) with fast internal dynamics and a solid-like regime (for epsilon > epsilon(s)) with slow internal dynamics. The cohesion strength epsilon(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 epsilon and scales extensive in N-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.