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arXiv · 1109.5387

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

Thomas R. Einert·Charles E. Sing·Alfredo Alexander-Katz·Roland R. Netz
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Abstract

We study the conformational dynamics within homo-polymer 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 NG 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 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 {\epsilon} 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.

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Thomas R. Einert, Charles E. Sing, Alfredo Alexander-Katz, Roland R. Netz. 2011-09-25. Conformational dynamics and internal friction in homo-polymer globules: equilibrium vs. non-equilibrium simulations. https://arxiv.org/abs/1109.5387

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