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theses

Biopolymers are the molecular building blocks of the natural world and are a focal point of many areas of active research. Despite their universality, many of their properties are still poorly understood because these properties are associated with a level of detail that is far beyond experimental characterization. Molecular dynamics (MD) simulations offer the opportunity to study these ubiquitous macromolecules with femtosecond accuracy and angstrom resolution. In this work, we examine methodologies that are crucial to accurate, representative, and meaningful results to MD simulations of biopolymers. We conduct simulations using replica-exchange molecular dynamics, implicit and explicit solvent, and umbrella sampling in order to characterize these systems. We explore methods of validating empirical potential energy functions and use the results to characterize the effects of phosphorylation and its experimental counterpart pseudophosphorylation on the conformational ensemble of the tau-derived protein PHF43 in the early stages of aggregation in Alzheimer’s disease. We then consider how MD methodologies can bolster theoretical models and be applied to the production of biomaterials from tunable biopolymer mixtures by modeling the dissolution and regeneration process of cellulose in ionic liquids.

ETD_8963

M.S.

Includes bibliographical references

by John W. Whittaker

doi:10.7282/T3KS6VWK

ETD graduate

The author owns the copyright to this work.