Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group


First Advisor

Zahra Fakhraai

Second Advisor

Tobias Baumgart


Amyloid fibrils spontaneously formed by the aggregation of a diverse class of polypeptides and proteins are the hallmarks of numerous neurodegenerative diseases (e.g. Alzheimer’s disease and Parkinson’s disease) and nonneuropathic localized diseases (e.g. Type II diabetes). Among those proteins, amyloid-beta (Aβ) peptides are the most well-known species because of their fibrillar aggregations constituted the insoluble amyloid deposits in the brain of Alzheimer's patients. After years of studies, the mechanism by which they nucleate and extend to form amyloid fibrils remains unclear, as so does their fibrillar structures. In this thesis, I mainly perform atomic force microscopy (AFM) to (1) investigate the kinetics of surface effects on Aβ12-28 fibril growth and (2) quantitatively characterize the polymorphism (polymorphic structures) of Aβ40 fibrils in mesoscale using imaging analysis techniques. The first section demonstrates that the surface-mediated fibrillization can rapidly happen while incubating the low-concentrated Aβ12-28 peptide solution on the mica substrate within one hour. The formation of surface-mediated fibrils with one-peptide thickness feature, ~0.5 nm, can be imaged by AFM after drying the samples with an appropriate spin-coating procedure. Furthermore, the incubation time controls reveal the evolution of the length of surface-mediated fibrils during kinetic growth on the surface. A proposed two-dimensional diffusion-limited aggregation model can predict the experimental length evolution that suggests a diffusion limited aggregation mechanism behind the surface-mediated fibrillization. In the second section, two distinct methods are developed to quantitatively study the polymorphism of Aβ40 fibrils at various length scales. One utilizes the height histograms of AFM images to correct for the tip-dilation effect and provide the relative volume content of various species at mesoscale. The other is performed the high-resolution AFM equipped with ultrasharp tip to identify the molecular basis of various polymorphs at molecular-level. Overall, our AFM works provide a guideline for accurate studies on aggregation mechanism, amyloid polymorphism, and fibrillar structures, that are critical in advancing the field.

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