Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2009-12-06
Progress of Theoretical Physics Supplement No. 184 (2010) pp. 339-350
Physics
Condensed Matter
Soft Condensed Matter
Proceedings of the "YKIS 2009 : Frontiers in Nonequilibrium Physics" conference in Kyoto, August 2009. To appear in Progress o
Scientific paper
10.1143/PTPS.184.339
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.
Imparato Alberto
Luccioli Stefano
Torcini Alessandro
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