The newly emerging Stimulated Raman Scattering (SRS) Microscopy has been proved to be a powerful tool in biomedical research. This advanced imaging platform offers high spatiotemporal resolution and chemical specificity, which greatly empowers the label-free biomedical imaging and small molecule metabolite tracing. Throughout the research introduced in this thesis, we focus on the exploration of more applications of SRS microscopy beyond aforementioned. Particularly, this new expedition involves more chemistry and answered two major questions: what SRS can do for chemistry and what chemistry can do for SRS. Chapter 1 introduces the basics of SRS microscopy, such as the physical fundamentals and start-of-art instrumentations. Besides, this chapter discusses the design principles of vibrational reporters through a chemistry view. Chapter 2 introduces one of the major progresses of SRS microscopy beyond biomedical study. We use SRS microscopy to study the ion transportation and concentration polarization phenomena in lithium metal batteries (LMBs), with a strong focus in solid-state polymer electrolyte. A self-induced phase separation process over lithium metal electrode is observed and correlated with local lithium ion concentrations, which inspires a protection mechanism for durable LMB design. Chapter 3 discusses the use of SRS microscopy for in-vivo drug tracing in mammalian cells. A novel alkyne tag is incorporated into bio-engineered natural depsi-peptides and serves as Raman reporter. The mode-of-action of the labeled drug is visualized with SRS microscopy. Chapter 4 heavily focuses on the development of synthetic molecular probes for super-multiplexed optical imaging. We systematically synthesize a library of molecular probes based on 9-cyanopyronin, and their Raman features are characterized to build a model that correlates photophysical properties with structures. The Raman shifts of probes can be tuned with high precision. The multiplexing capability of the new library is demonstrated in labeling fixed and living cell samples.

The nonapoptotic form of regulated cell death known as ferroptosis is an attractive target for combating numerous diseases. Ferroptosis is an iron-dependent death of cells by lipid peroxidation. Pharmacological inhibition of anti-ferroptotic pathways is a promising therapeutic avenue for treatment of cancer, and death by ferroptosis has been implicated in numerous neurodegenerative and ischemia-reperfusion-driven diseases. Therefore, demystifying the dynamics of lipid peroxidation in this cell death process opens a window to understanding disease processes and how to treat them. This dissertation makes use of ferroptosis-modulating compounds as chemical probes to elucidate the roles of different subcellular membranes in ferroptotic lipid peroxidation. Chapters two and three explore the structure-activity-distribution relationship of fatty acids and the ferroptosis inducer FINO2, respectively, and together demonstrate the endoplasmic reticulum as a driver of lipid peroxidation in ferroptosis. Chapter two makes use of stimulated Raman scattering imaging, while chapter three uses confocal fluorescence imaging. Chapter four shifts gears to focus on development of FINO2 as a drug lead, performing structure activity relationship analysis to increase the potency and pharmacological properties of the analogs. Altogether, this work answers questions about how cells die by ferroptosis, and provides footwork for how we can better modulate ferroptosis against cancer and other illnesses.

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1. A two prism spectrograph has been designed and oonstruoted with which it is believed Raman spectra may be obtained. 2. Attempts have been made using the spectrograph to obtain Raman spectra. These attempts, are as yet unsuccessful. / M.S.

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The development of state-of-the-art AlGaN/GaN high electron mobility transistors (HEMTs) has shown much promise for advancing future RF and microwave communication systems. These revolutionary devices demonstrate great potential and superior performance and many commercial companies have demonstrated excellent reliability results based on multiple temperature accelerated stress testing. However, a physical understanding of the various reliability limiting mechanisms is lacking and the role and relative contribution of the various intrinsic material factors, such as physical stress and strain has not been clearly explained in the literature. Part of issues that impact device reliability are the mechanical stresses induced in the devices as well as the self-heating that also limit device performance. Thus, quantification of stress and temperature in AlGaN/GaN HEMTs is of great importance. To address some of the needs for metrology to quantify stress in AlGaN/GaN HEMTs, micro-Raman spectroscopy and micro-photoluminescence (micro-PL) were utilized to quantify the residual stress in these devices. Through the use of micro-Raman and micro-PL optical characterization methods, mapping of the vertical and lateral stress distributions in the device channels was performed. Results show that stress can be influenced by the substrate material as well as patterned structures including metal electrodes and passivation layers. Previously developed and reported micro-Raman thermometry methods require an extensive calibration process for each device investigated. To improve the implementation of micro-Raman thermometry, a method was developed which offers both experimental simplicity and high accuracy in temperature results utilizing a universal calibration method that can be applied to a broad range of GaN based devices. This eliminates the need for performing calibration on different devices. By utilizing this technique, it was revealed that under identical power dissipation levels, the bias conditions (combination of Vgs and Vds) alter the heat generation profile across the conductive channel and thus influence the degree of device peak temperature. The role of stress in the degradation of AlGaN/GaN HEMTs was also explored. A combined analysis using micro-Raman spectroscopy, coupled electro-thermo-mechanical simulation, and electrical step stress tests was conducted to investigate the link between performance degradation and the evolution of total stress in devices. It was found that in addition to stresses arising from the inverse piezoelectric effect, the substrate induced residual stress and the operational themo-elastic stress in the AlGaN layer play a major role in determining the onset of mechanically driven device degradation. Overall, these experiments were the first to suggest that a critical level of stress may exist at which point device degradation will start to occur. The optical characterization methods developed in this study show the ability to reveal unprecedented relationships between temperature/stress and device performance/reliability. They can be used as effective tools for facilitating improvement of the reliability of future AlGaN/GaN HEMTs.

G-quadruplexes (G4s) are nucleic acid structures formed from π-stacked planar sets of four Hoogsteen hydrogen bonded guanine bases. G4s emerged as potential therapeutic targets based on their ability to modulate gene expression and inhibit the ability of telomerase to elongate chromosomal telomeres. Raman spectroscopy, polarized Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS), and other optical spectroscopic techniques were used to characterize the G4s formed by four different DNA sequences: human telomeric (HT), thrombin-binding aptamer (TBA), nuclease hypersensitive element III1 region of the c- Myc gene promoter (Myc), and a single loop-isomer of Myc (MycL1). / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Over the last 50 years, flow cytometry has evolved from a modest cell counter into an invaluable analytical tool that measures an ever-expanding variety of phenotypes. Flow cytometers interrogate passing samples with laser light and measure the elastically scattered photons to ascertain information about sample size, granularity, and basic morphology. Obtaining molecular information, however, requires the addition of exogenous fluorescent labels. These labels, although a power tool, have numerous challenges and limitations such as large emission spectra and cellular toxicity. To move beyond fluorescent labels in microscopy, a variety of techniques that probe the intrinsic Raman vibrations within a sample have been developed, such as coherent anti-Stokes Raman scattering (CARS) and Raman microspectroscopy. In this dissertation, I present the first development of a label-free flow cytometer that measures the elastically scattered photons and probes the intrinsic Raman vibrations of passing samples using multiplex coherent anti-Stokes Raman scattering (MCARS). MCARS, a coherent Raman technique that probes a large region of the Raman spectrum simultaneously, provides rich molecularly-sensitive information. Furthermore, I present its application to sorting polymer microparticles and its use in two example biological applications: monitoring lipid bodies within cultures of Saccharomyces cerevisiae, a model yeast with numerous human homologs, and monitoring the affect of nitrogen starvation on Phaeodactylum tricornutum, a diatom, which is being genetically engineered to efficiently produce biofuels.

Once diagnosed, cancer is treated by surgical resection, chemotherapy, radiation therapy, or a combination of these therapies. It is intuitive that physically and completely removing a solid tumor would be an effective treatment. A complete resection of the tumor mass, defined by surgical margins that are clear of neoplasia, is prognostic for a decreased chance of cancer recurrence and an increased survival rate. In practice, complete resection is difficult. A surgeon primarily has only their senses of touch and sight to provide "real-time" guidance in the removal of a tumor while in the operating room. Preoperative imaging can guide a surgeon to a tumor but does not give a continuous update of surgical progress. Intraoperative pathology is limited to a few slides worth of samples: a product of its time-consuming nature and the limited time a patient can remain under general anesthesia. Technologies to guide a surgeon in effecting complete resection of a tumor mass during the surgical procedure would greatly increase cancer survival rates by lowering rates of cancer recurrence; such a technology would also reduce the need for follow-up chemotherapy or radiation therapy. Here, we describe a prototype instrumentation system that can provide intraoperative guidance with exogenous optical contrast agents. The instrumentation combines interactive point excitation, local spectroscopy, and widefield fluorescence imaging to enable low-cost surgical guidance using FDA-approved fluorescent dyes, semiconductor quantum dots (QDs), or surface-enhanced Raman scattering (SERS) nanoparticles. The utility of this surgical system is demonstrated in rodent tumor models using an FDA-approved fluorescent dye, indocyanine green (ICG), and is then more extensively demonstrated with a pre-clinical study of spontaneous tumors in companion canines. The pre-clinical studies show a high sensitivity in detecting a variety of canine tumors with a low false positive rate, as verified by pathology. We also present a fundamental study on the behavior of quantum dots. QDs are a promising fluorophore for biological applications, including as a surgical contrast agent. To use QDs for in vivo human imaging, toxicity concerns must be addressed first. Although it is suspected that QDs may be toxic to an organism based on the heavy-metal elemental composition of QDs, overt organism toxicity is not seen in long-term animal model studies. We have found that some reactive oxygen species (ROS) generated by the host inflammatory response can rapidly degrade QDs; in the case of hypochlorous acid, optical changes to the QDs are suggestive of degradation occurring within seconds. It is well-known that QDs are sequestered by the immune system when used in vivo---we therefore believe that QD degradation through an inflammatory response may represent a realizable in vivo mechanism for QD degradation. We demonstrate in an in vitro cell culture model that immune cells can degrade QDs through ROS exposure. Knowledge of the degradative processes that QDs would be subject to when used in vivo informs on adaptations that can be made to the QDs to resist degradation. Such adaptations will be important in developing QD-based contrast agents for image guided surgery.

L’expansion de nouvelles technologies et la demande incessante d’une transmission d’informations plus rapide font que les systèmes de télécommunications nécessitent plus de débit sur de plus longues distances. L’amplification optique et notamment l’amplification optique par effet Raman représente une intéressante possibilité à repousser les limites de distance et de debit.Les verres à base d’oxyde de tellure sont des matériaux prometteurs pour les applications d’amplification optique par effet Raman; en particulier grâce à leurs fortes propriétés optiques linéaires et non linéaires, leurs fenêtres de transparence allant dans le proche et milieu infra-rouge du spectre de transmission. De plus, leurs propriétés thermiques et en particulier leurs faibles temperatures de transition vitreuse permettent une facilité de fibrage. L’estimation de l’intensité du gain Raman et sa zone spectrale mise en jeu sont généralement approchées à partir du spectre de diffusion Raman spontanée du matériaux. La compréhension des relations existantes entre la structure vitreuse, la réponse vibrationnelle et les propriétés d’optique non linéaire, représente un point clé au développement et à l’optimisation des verres de tellure pour l’amplification Raman. Cette dissertation apporte une réponse détaillée à la question fondamentale de l’étude doctorale: “Quel est l’impact de la structure vitreuse sur les propriétés d’amplification Raman dans les verres d’oxyde de tellure?” / Tellurite-based oxide glasses have been investigated as promising materials for Raman gain applications, due to their good linear and nonlinear optical properties and their wide transparency windows in the near- and midwave infrared spectral region. Furthermore, their interesting thermal properties, i.e. low glass transition temperature and ability to be drawn into optical fibers, make tellurite-based glasses excellent candidates for optical fiber amplifiers. The estimation of the strength and spectral distribution of Raman gain in materials is commonly approximated from the spontaneous Raman scattering cross-section measurement. For development of tellurite-based glasses as Raman amplifiers, understanding the relationship between glass structure, vibrational response, and nonlinear optical properties (NLO) represents a key point. This dissertation provides an answer to the fundamental question of the PhD study: “What is the impact of the glass structure on Raman gain properties of tellurite glasses?”