Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
Physik Department, Technische Universität München, James-Franck-Straße, 85748, Garching, Germany
2 Department of Materials Science and Engineering, Massachusetts Institute of Technology, MA 02139-4307, Cambridge, USA
3 Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
Accepted: 3 November 2011
Published online: 14 December 2011
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 and the globule size N G is observed. We find two distinct dynamical regimes: a liquid-like regime (for < with fast internal dynamics and a solid-like regime (for > with slow internal dynamics. The cohesion strength 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 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.
© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg, 2011