Simuler la Dynamique des Protéines: Simulation Protein Dynamics

The study of protein dynamics has expanded considerably in the last ten years, in large part because of the wider availability of parallel supercomputers. But the growth in computing power is not sufficient: new numerical approaches must also be developed that allow for a more efficient sampling of configuration space. In this presentation, I will present some recent progress on the methodological side - including the replica method and the activation/relaxation technique - and on the description of potentials - internal coordinates representation and coarse-grained force fields. I will also present some applications of these methods to the folding of the A protein, a chain of 60 amino acids used as a toy model, and to amyloid aggregation. As we shall see, despite the recent progress, many challenges remain. The results presented were obtained in collaboration with Philippe Derreumaux, Wei Chen, Xiao Dong, Lilianne Dupuis, Rozita Laghaei, Jean-Francois St-Pierre et Guanghong Wei.