The term amyloid describes misfolded protein aggregates in which a highly ordered cross β-sheet pattern is adopted. While there exist functional amyloids, the majority of known amyloids are associated with diseases in multicellular organisms. One example is the association is that between Amyloid β (Aβ) and Alzheimer’s disease, a neurodegenerative disorder in humans. Several mechanisms of toxicity have been proposed, yet a lack of dynamic data prevents a full molecular explanation for the toxicity of Aβ and other amyloid systems. Mutational effects often increase the degree of polymorphism in observable structures, compounding the issues with a molecular level examination. In this thesis, Molecular Dynamic (MD) simulations of wild-type and mutant sequences of both Aβ and Prion proteins are performed to explore the structural dynamics of amyloids and amyloid-like systems. The data generated will provide physics-based explanations of the traits of amyloids on a molecular level which may guide further physical experimentation into the mechanism of amyloid toxicity and formation.