Physics Commons^™

The Profound Photophysical Effects Of Organic Chromophore Connectivity And Coupling, David J. Walwark Jr

Nanoscience and Microsystems ETDs

Through-bond and through-space interactions between chromophores are shown to have wide-ranging effects on photophysical outcomes upon light absorption in organic molecules. In collapsed poly(3-hexylthiophene), through-space coupling creates hybrid chromophores that act as energy sinks for nearby excitons and favorable sites for molecular oxygen to dock. Upon excitation with visible light the highly-coupled chromophores react with the docked oxygen and subsequently do not quench nearby excitons as efficiently. In tetramer arrays of perylene diimide chromophores the central moiety through-bond connectivity is synthesized in two variants which exhibit vastly different single-molecule blinking behavior and theoretically-predicted electronic transition character. In the more-connected tetramer …

Bayesian Analysis Of Single Molecule Fluorescence Microscopy Data, Mohamadreza Fazel

Physics & Astronomy ETDs

The diffraction limit can be circumvent by creating and exploiting independent behaviors of the sample at lengths scale below the diffraction limit. In fluorescence microscopy, the independence arises from individual fluorescent labels switching between dark and fluorescence states. The fluorophores can then be localized employing the generated sparse image frames. Finally, the resulting list of coordinates is utilized to generate high resolution images or to gain quantitative insight into the underlying biological structures. Therefore image processing and post-processing are essential stages of SMLM techniques.

In this dissertation, Reversible Jump Markov Chain Monte Carlo was employed to implement Bayesian analysis of …

Applications Of The Negatively-Charged Silicon Vacancy Color Center In Diamond, Forrest A. Hubert

Optical Science and Engineering ETDs

The spatial resolution and fluorescence signal amplitude in stimulated emission depletion (STED) microscopy is limited by the photostability of available fluorophores. Here, we show that negatively-charged silicon vacancy (SiV) centers in diamond are promising fluorophores for STED microscopy, owing to their photostable, near-infrared emission and favorable photophysical properties. A home-built pulsed STED microscope was used to image shallow implanted SiV centers in bulk diamond at room temperature. We performed STED microscopy on isolated SiV centers and observed a lateral full-width-at-half-maximum spot size of 89 ± 2 nm, limited by the low available STED laser pulse energy (0.4 nJ). For a …

High-Throughput Automated Multi-Target Super-Resolution Imaging, Farzin Farzam

Physics & Astronomy ETDs

Super-resolution microscopy techniques developed through the past few decades enable us to surpass the classical diffraction limit of light, and thus open new doors to investigate the formerly inaccessible world of nanometer-sized objects. Most importantly, by using super-resolution microscopy, one can visualize sub-cellular structures in the range of 10 to 200 nm. At this range, we can investigate exciting problems in biology and medicine by visualizing protein-protein interactions and spatiotemporal analysis of structures of interest on the surface or inside cells. These techniques (collectively known as nanoscopy) have a high impact on understanding and solving biological questions. This dissertation starts …