Replica-Exchange Wang-Landau Simulations of Lattice Peptide Aggregation

The computational study of interacting biomolecules is a challenging endeavor due to the large range of time and length scales associated with the relevant physical transitions. In order to analyze the general, qualitative statistical physics of such systems as they transition from dissolved to aggregated crystalline states, we use the H0P lattice protein model^1,2 simulated on simple cubic and face centered cubic lattices. Utilizing the parallel Replica-Exchange Wang-Landau³ Monte Carlo algorithm, the energy states and density of states are calculated for multiple interacting H0P peptides. Thermodynamic quantities are studied for short (< 20 residues) model peptides at a range of concentrations and temperatures as structures such as disordered oligomers, amyloid fibrils, and aggregates are formed. Additional structural observables such as the cluster size distribution are calculated in a post-simulation production run, and used to further elucidate the physical behavior during transitions.

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