Simulation of fibril formation in a coarse-grained model

Molecular dynamics simulation of amyloid fibril formation performed with a coarse-grained model of a polypeptide in a periodic box. Initially the 125 monomers condensate into micellar aggregates, which, after a long lag phase, interconvert to a fibril through an irreversible nucleation step. The fibril elongates and reaches a mature form that is in equilibrium with isolated monomers. Remaining micellar aggregates dissolve while the fibril is elongating, and disappear at the end of the simulation. The green square is the simulation box, while the red and blue colors are used for monomers in the amyloid-competent and amyloid-protected states,respectively.

Publication Link: 
Interpreting the aggregation kinetics of amyloid peptides
Pathways and intermediates of amyloid fibril formation
Link to video file: 
fibril.mp4