Characterization of the low temperature properties of a simplified protein model

Abstract : Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior.
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Johannnes-Geert Hagmann, Naoko Nakagawa, Michel Peyrard. Characterization of the low temperature properties of a simplified protein model. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, American Physical Society, 2014, 89, pp.012705. 〈10.1103/PhysRevE.89.012705〉. 〈ensl-00934624〉

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