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- W2009918603 abstract "We use an extended Gifmmode bar{o}else ={o}fi{} model, in unfrustrated and frustrated variants, to study the energy landscape and the fluctuations of a model protein. The model exhibits two transitions, folding and dynamical transitions, when changing the temperature. The inherent structures corresponding to the minima of the landscape are analyzed and we show how their energy density can be obtained from simulations around the folding temperature. The scaling of this energy density is found to reflect the folding transition. Moreover, this approach allows us to build a reduced thermodynamics in the inherent structure landscape. Equilibrium studies, from full molecular dynamics (MD) simulations and from the reduced thermodynamics, detect the features of a dynamical transition at low temperature and we analyze the location and time scale of the fluctuations of the protein, showing the need of some frustration in the model to get realistic results. The frustrated model also shows the presence of a kinetic trap which strongly affects the dynamics of folding." @default.
- W2009918603 created "2016-06-24" @default.
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- W2009918603 date "2006-10-25" @default.
- W2009918603 modified "2023-10-03" @default.
- W2009918603 title "Modeling protein thermodynamics and fluctuations at the mesoscale" @default.
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- W2009918603 doi "https://doi.org/10.1103/physreve.74.041916" @default.
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