Monte Carlo Simulation of Amyloid Protofibril Formation

Aggregation processes of amyloid protofibrils are studied using the replica-exchange Wang-Landau (REWL)\footnote{T. Vogel, Y. W. Li, T. W\"ust, and D. P. Landau, Phys. Rev. E \textbf{90}, 023302 (2014).} algorithm to simulate multiple interacting model peptides. The H0P model\footnote{G. Shi, T. W\"ust, Y. W. Li, and D. P. Landau, J. Phys.: Conf. Ser. \textbf{640}, 012017 (2015).}, which adds an additional neutral polarity group to the classic hydrophobic-polar (HP) model\footnote{K. A. Dill, Biochemistry \textbf{24}, 1501 (1985); K. F. Lau and K. A. Dill, Macromolecules \textbf{22}, 3986 (1989).}, is used for simplicity and efficiency. Constituent peptides are modeled as short, intrinsically disordered H0P sequences, which do not form globular structures individually but self-assemble to form various aggregated structures. Using the parallelized sampling framework, the density of states is determined and the minimal energy state is identified. From thermodynamic quantities, the effects of peptide concentration are studied for the formation of protofibrillar structures.