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

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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 \( \varepsilon\) and the globule size N G is observed. We find two distinct dynamical regimes: a liquid-like regime (for \( \varepsilon\) < \( \varepsilon_{{\rm s}}^{}\) with fast internal dynamics and a solid-like regime (for \( \varepsilon\) > \( \varepsilon_{{\rm s}}^{}\) with slow internal dynamics. The cohesion strength \( \varepsilon_{{\rm s}}^{}\) 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 \( \varepsilon\) 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.

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Einert, T.R., Sing, C.E., Alexander-Katz, A. et al. Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations. Eur. Phys. J. E 34, 130 (2011). https://doi.org/10.1140/epje/i2011-11130-8

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