Viktor Drugge
Grand canonical study of the thermodynamics of a toy model for amyloid formation
Bachelor Thesis in Theoretical Physics
Abstract:
The aggregation of proteins into amyloid fibrils via erroneous folding,
also known as misfolding, occurs in several diseases. As a consequence,
the study of the kinetics and thermodynamics of this process is
currently intensely pursued. Here, we study a minimalistic
lattice-based model for amyloid formation using Monte Carlo techniques
to sample the grand canonical ensemble, where the chemical potential, volume and temperature describe the system. The
coarse-grained model uses orientation-dependent nearest-neighbour
interactions. A previous study of this model in the canonical ensemble,
where the number of peptides rather than the chemical potential is
given, identified two distinct phases, one consisting of smaller
aggregates and the other with elongated multilayered fibril-like
aggregates.
At a certain value of the chemical potential, the model exhibits an abrupt jump in concentration, indicating a bimodal distribution of the number of peptides, N. To be able to determine the shape of this distribution in the intermediate region of suppressed N values, an artificial ω-ensemble is introduced, where the distribution of N is approximately uniform. Using this ensemble, a cusp in the Helmholtz free energy is identified, viewed as a function of N. It is concluded that this cusp is a manifestation of the phase transition previously observed in canonical simulations.
LU TP 15-40