title: Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations.
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 (G) is observed. We find two distinct dynamical regimes: a liquid-like 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 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 (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.
authors.affiliation: Physik Department, Technische Universität München, James-Franck-Straße, Garching, Germany. einert@ph.tum.de
authors.forename: T R
authors.initials: TR
authors.lastname: Einert
authors.forename: C E
authors.initials: CE
authors.lastname: Sing
authors.forename: A
authors.initials: A
authors.lastname: Alexander-Katz
authors.forename: R R
authors.initials: RR
authors.lastname: Netz
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D017276:Friction; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D013314:Stress, Mechanical
chemical_list: D001704:Biopolymers