Model Amyloid Protofibrils Simulated with Replica-Exchange Wang-Landau

As neurological diseases associated with toxic peptide aggregates emerge, the research of aggregate and fibril formation has become a prominent, yet extremely challenging problem. The ability to form an amyloid state has been posited as a general feature of peptide systems, and is considered in this study by simulating a collection of coarse-grained, generic model peptides. The H0P model¹ adds an additional neutral polarity group to the classic hydrophobic-polar (HP) model² , and is used for simplicity and efficiency. With the replica-exchange Wang-Landau (REWL) algorithm and an efficient trial move set³, the density of states is determined for multiple interacting model peptides. We observe the formation of fibrillar structures in two continuous transitions that separate three phases: dissolved peptides, disordered oligomers, and crystalline aggregate structures. Additional structural observables are calculated in a post-simulation production run to further study the physical behavior during the observed transitions.



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