Figure 17.
Aβ16-22 aggregation simulations under several conditions. Top panels. Pictorial representation of monomer aggregation for several simulation schemes: i) Langevin dynamics, ii) Langevin dynamics with Hydrodynamics Interactions (HI), and iii) Langevin dynamics with HI and longitudinal shear, shear rate Δv/Δz=108 s-1. The time-evolutions show the effect of HI on the aggregation kinetics. When shear-flow is activated also the details of the aggregation change: i.e. first two separate aggregates form and their relative motion in the shear flow (translation and rotation) guides their further encounter and fusion. Bottom panels. Time evolution of key parameters describing the aggregation process in shear-flow for different values of the shear rate Δv/Δz (0,108,109,1010 s-1): the gyration radius Rg (left panel), the number of inter-peptide hydrogen bonds formed between backbone NH and O groups (mid panel) and number of inter-peptide side-chain contacts (right panel). The system is composed of 18 peptides placed in a cubic box of L=65 Å and the shear gradient is generated along the Z direction.