Autonomous oscillation in supramolecular assemblies: Role of free energy landscape and fluctuations

Yuriy V. Sereda and Peter J. Ortoleva

Physica A: Statistical Mechanics and its Applications, 2015, vol. 437, issue C, 442-456

Abstract: Molecular dynamics studies demonstrated that a supramolecular assembly can express autonomous structural oscillations about equilibrium. It is demonstrated here that for nanosystems such oscillations can result from the interplay of free energy landscape and structural fluctuations. Furthermore, these oscillations have intermittent character, reflecting the conflict between a tendency to oscillate due to features in the free energy landscape, and the Second Law’s repression of perpetual oscillation in an isothermal, equilibrium system. The demonstration system is a T=1 icosahedral structure constituted of 12 protein pentamers in contact with a bath at fixed temperature. The oscillations are explained in terms of a Langevin model accounting for interactions among neighboring pentamers. The model is based on a postulated free energy landscape in the 24-dimensional space of variables describing the centrifugal and rotational motion of each pentamer. The model includes features such as basins of attraction and low free energy corridors. When the system is driven slightly out of equilibrium, the oscillations are transformed into a limit cycle, as expressed in terms of power spectrum narrowing.

Keywords: Supramolecular assembly; Autonomous oscillation; The Second Law; Langevin dynamics; Free energy landscape; Limit cycle (search for similar items in EconPapers)
Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:437:y:2015:i:c:p:442-456

DOI: 10.1016/j.physa.2015.05.005

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