Computational challenges for the study of amyloid processes
The dominant hypothesis in amyloid diseases considers small amyloid aggregates as one of most important toxic species. Because these structures are out-of-equilibrium, there atomistic properties are difficult to access experimentally. Computer simulations have therefore played an important role for their characterization over the last decade. Yet, full size amyloid aggregates are at the extreme limit of what is accessible by computer today, forcing the use of a wide range of methods to accelerate sampling and simplify their description. In this talk, I will present some of the work we have done on amyloids, using simplified force fields such as the OPEP forcefield and simulations methods ranging from pure MD to the Activation-Relaxation Technique, including systems such as polyglutamine, α-synuclein, IAPP and various fragments of the Aβ protein. I will also discuss ongoing efforts for developing a new coarse-grained forcefield for amyloids.