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Hydrodynamics regulates protein motion in crowding environments, that is, in conditions similar to the cell interior. Here diffusion is greatly reduced if compared to dilute conditions and the slowdown takes place at both long and short timescales, millisecond and nanosecond, respectively. Another typical examples is the aggregation process of peptides at the onset of Alzheimer disease, a phenomenon that is greatly accelerated by solvent-mediated interactions.
Notwithstanding the huge number of particles in the system we are interested in the dynamics of a relatively small set of degrees of freedom and we approach them by a multi scale method where drag force, fluctuations and thermodynamic forces can be incorporated. The limits of validity and the possible extensions of the simulation framework will be presented, together with presenting results on protein diffusion and peptide aggregations.
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