UC Berkeley

Optical methods, including light and fluorescence microscopies, have seen widespread

application in the characterization of materials and biology, but are not equally applicable to all

such systems. This dissertation aims to describe new developments in select optical methods, and

their subsequent application to answering scientific questions about material and biological

systems that were intractable using previous methodologies. We first develop a novel label-free

interference-based optical method for characterizing thin films on transparent substrates and

subsequently apply it to reveal reaction dynamics of graphene films in real time. We next

develop novel methods in a different optical technique, point-localization super-resolution

fluorescence microscopy. These include the application of spectrally-resolved super-resolution

microscopy to organic adlayers on surfaces and the development of a remote focusing technique

to image oblique planes through thick biological samples. We then combine our developments in

optical methods and super-resolution microscopy to describe a novel correlative super-resolution

imaging methodology, and overview the challenges and opportunities inherent to correlative

super-resolution methods. We conclude with concrete applications of super-resolution

fluorescence microscopy to biological systems and shed light on long-standing biological

questions. These include elucidation of the structure of meiotic chromosome axes in C. Elegans,

a mechanism for crossover-interference and crossover-regulation in the same meiotic

chromosomes, discovery of a novel structural arrangement for nuclear pore complexes in meiotic

cells, and discovery of a tube-shaped structure spanning the nucleus of breast cancer-like cells.