<p> Metamaterials operating at terahertz (THz) region of the electromagnetic spectrum have remained have remained a promising area of study not only for realizing technologies in a historically underdeveloped spectral regime, but also as a scientific tool for exploring and controlling fundamental physical phenomena at meV energy scales in a variety of condensed matter systems. In this thesis, I will present several projects in which metamaterials and more traditional condensed matter systems are integrated into hybrid metamaterial systems. We leverage these systems to realize new practical THz devices, as well as to couple to and control quantum phenomena in condensed matter systems. I will begin with an introduction to the conceptual, numerical, and experimental techniques in the THz metamaterial toolbox. The first research endeavor I will discuss is a metamaterial system that incorporates perhaps the simplest material; air. This metamaterial perfect absorber with a continuously tunable air dielectric layer allows for comprehensive exploration of metamaterial absorber systems, and demonstrates some unique phenomena owing to its lossless dielectric layer. Next I will introduce an applications oriented device; an electrically actuated broadband terahertz switch which transitions from a non-reflective, transmissive state to a fully absorptive state. It employs an all dielectric metamaterial layer to suppress reflections and trap light, and an electrically actuated phase change material, <i>VO</i>₂ to transition between states. The final section of this dissertation will explore strong coupling effects between a metamaterial and the superconducting c-axis Josephson plasmon in the layered cuprate, <i>La_2&ndash;xSr_xCuO₄</i>. Preliminary measurements are first presented then followed by high field THz measurements in which complex nonlinear behavior is observed.</p><p>

<p> X-ray computed tomography (CT)&mdash;more commonly known as CAT scan&mdash;has recently evolved from the world of medical imaging and nondestructive evaluation to the field of dimensional metrology; the CT technique can now be used to measure a specimen&rsquo;s geometrical dimensions (of both internal and external features). As a result, CT presently contributes to the areas of dimensional inspection and geometric analysis for technology companies that produce manufactured parts for a variety of industries such as automotive, aerospace, medical devices, electronics, metalworking, injection molding plastics, composite materials, ceramics, and 3D printing or additive manufacturing. While dimensional accuracy is not crucial for medical diagnoses or other qualitative analyses, accurate dimensional quantification is the essence of X-ray CT metrology. Despite increasing advances in this technology, the current state of the art of CT metrology still confronts challenges when trying to estimate measurement uncertainties, mainly due to the plethora of influencing factors contributing to the CT measurement process. Gradual progress has occurred over the last decade toward a better understanding of some of these influencing factors that were illuminated by a series of collaborative research initiatives between a collective of several universities and institutions (predominantly located in the European Union) committed to the advancement and development of industrial CT scanning as a measuring technology. In an effort to further understand phenomenologically the role of variables affecting the precision and accuracy of CT dimensional measurements, this dissertation presents a series of experimental studies that evaluate the performance of cone-beam CT measurements, and their uncertainty estimates, in comparison with reference measurements generally obtained from tactile coordinate measurement machines (CMMs). In some cases, the results are contrasted against simulations performed in Matlab software (to compute fan-beam projection data) and an additional simulation tool called &ldquo;Dreamcaster&rdquo; (for ray casting and Radon-space analysis). The main CT variables investigated were: temperature in the X-ray CT enclosure, number of projections for a CT scan, workpiece tilt orientation, sample magnification, material thickness influences, software post-filtration, threshold determination, and measurement strategies. For dimensions of geometric features ranging from 0.5 mm to 65 mm, a comparison between dimensional CT and CMM measurements, performed at optimized conditions, typically resulted in differences of approximately 5 &micro;m or less for data associated with dimensional lengths (length, width, height, and diameters) and around 5 to 50 &micro;m for data associated with measurements of form, while expanded uncertainties computed for the CT measurements ranged from 1 to over 50 &micro;m. Methods for estimating measurement uncertainty of CT scanning are also assessed in this work. Special attention is paid to the current state of measurement comparisons (in the field of dimensional X-ray CT) by presenting a comprehensive study of metrics used for proficiency testing, including rigorous tests of statistical consistency (null-hypothesis testing) performed with Monte Carlo simulation, and particularly applied to results from two recent CT interlaboratory comparisons. This latter study contributes to the knowledge of methods for performance assessment in measurement comparisons. In particular, it is shown that the use of the En-metric in the current state of CT interlaboratory comparisons could be difficult to interpret when used to evaluate performance and/or statistical consistency of CT measurement sets.</p><p>

<p> Coupled mechanical oscillators have long been an archetypical system for understanding eigcnmodes and coupled dynamics. But in the last few decades, the study of open systems (i.e. those open to loss or gain) has brought a fresh interest and perspective to such simple systems, revealing a surprisingly rich set of physical phenomena. Specifically, it was realized that degeneracies in open systems ('exceptional points', or EPs) possess a non-trivial topology, with interesting implications for closed adiabatic cycles. The theoretical properties of EPs have been made increasingly clear over the last 20 years, but experimental progress has generally been limited to spectroscopy, with no demonstrations of the predicted dynamical behavior. Here, I'll present work in which we use a cavity optomechanical system as a convenient, highly tunable platform for studying this multimode physics.</p><p> I'll begin with a pedagogical introduction to cavity optomechanics, including our particular experimental realization: a Si₃N₄ membrane coupled to a high-finesse optical cavity. Then, the physics of exceptional points will be reviewed using a toy model, before seeing how these features are accessible in our optomechanical system. I'll then present our study of time-dependent perturbations of this system, which provided the first experimental demonstration of adiabatic (and non-adiabatic) behavior near, an EP. These perturbations can be used to affect energy transfer which is both topology-dependent and non-reciprocal. This demonstration relies on a somewhat fortunate symmetry in our system, but in the final chapter, we'll see that this restriction can be lifted, to enable this energy transfer in a broad class of systems.</p><p>

<p> The light collecting apertures of space telescopes are currently limited in part by the size and weight restrictions of launch vehicles, ultimately limiting the spatial resolution that can be achieved by the observatory. A technique that can overcome these limitations and provide superior spatial resolution is interferometric imaging, whereby multiple small telescopes can be combined to produce a spatial resolution comparable to a much larger monolithic telescope. In astronomy, the spectrum of the sources in the scene are crucial to understanding the material composition of the sources. So, the ultimate goal is to have high-spatial-resolution imagery and obtain sufficient spectral resolution for all points in the scene. This goal can be accomplished through spatio-spectral interferometric imaging, which combines the aperture synthesis aspects of a Michelson stellar interferometer with the spectral capabilities of Fourier transform spectroscopy. </p><p> Spatio-spectral interferometric imaging can be extended to a wide-field imaging modality, which increases the collecting efficiency of the technique. This is the basis for NASA&rsquo;s Wide-field Imaging Interferometry Testbed (WIIT). For such an interferometer, there are two light collecting apertures separated by a variable distance known as the baseline length. The optical path in one of the arms of the interferometer is variable, while the other path delay is fixed. The beams from both apertures are subsequently combined and imaged onto a detector. For a fixed baseline length, the result is many low-spatial-resolution images at a slew of optical path differences, and the process is repeated for many different baseline lengths and orientations. Image processing and synthesis techniques are required to reduce the large dataset into a single high-spatial-resolution hyperspectral image. </p><p> Our contributions to spatio-spectral interferometry include various aspects of theory, simulation, image synthesis, and processing of experimental data, with the end goal of better understanding the nature of the technique. We present the theory behind the measurement model for spatio-spectral interferometry, as well as the direct approach to image synthesis. We have developed a pipeline to preprocess experimental data to remove unwanted signatures in the data and register all image measurements to a single orientation, which leverages information about the optical system&rsquo;s point spread function. In an experimental setup, such as WIIT, the reference frame for the path difference measured for each baseline is unknown and must be accounted for. To overcome this obstacle, we created a phase referencing technique that leverages point sources within the scene of known separation in order to recover unknown information regarding the measurements in a laboratory setting. We also provide a method that allows for the measurement of spatially and spectrally complicated scenes with WIIT by decomposing them prior to scene projection.</p><p>

<p> The work of this thesis is devoted to examining the impact of silicon dioxide (silica or SiO₂) planarization on the optical properties and laser damage resistance of thin-film coatings. SiO₂ planarization is a process to smooth out fluence limiting nodular defects within multilayer coatings for high-energy laser applications. Mitigating these defects will improve the power handling abilities and improve the lifetime of laser coatings. </p><p> Presented here is a combination of work with the aim of evaluating the optical and laser damage properties of SiO₂ planarization within single layers, bilayers, and multilayers. As compared to control (non-planarized) samples, a 2&ndash;3x increase in the thin-film absorption, which decreases with post-process annealing, was discovered for SiO₂ planarized samples. This suggests that planarization creates oxygen-related defects which can be annealed out and little impurity implantation. Investigations of laser damage resistance were carried out at &lambda; = 1030nm and pulse durations of &tau; = 220ps and 9ps. The laser damage of single and bilayer coatings is known to be dependent on the substrate-coating interface and this is further evidenced within this thesis. This is because the effects of planarization are masked by the extrinsic laser damage processes within the single and bilayers. Slight change (&lt; 15%) in the laser induced damage threshold (LIDT) at 220ps and 9ps was observed for planarized single and bilayers. Depending on coating design, post-process annealing was shown to increase the LIDT by ~10% to ~75% at 220ps and ~10% to ~45% at 9ps. Although the fused silica substrate surface LIDT was shown to follow the &radic;&tau; pulse scaling law for pulses above ~10ps, the single and bilayer coatings do not follow this pulse scaling. The divergence from the &radic;&tau; pulse scaling on the coatings suggests a variation in the laser damage initiation mechanisms between 220ps and 9ps. </p><p> Multilayer high-reflecting (HR) mirrors with varying planarization design were also damage tested. A 6&ndash;7 J/cm² LIDT, with 220ps, was observed for HR coatings with SiO₂ planarization layers within high electric-field areas within the coating. However, SiO₂ planarization at the substrate-coating interface, where the electric-field is minimal, and control (non-planarized) was shown to have a LIDT of 63 &plusmn; 1.2 J/cm² and 21.5 &plusmn; 0.5 J/cm² for 220ps, respectively. At 9ps, the LIDT varied less than 90% difference between the various planarization designs. The substrate-coating planarization multilayer and control coating had an equal LIDT of 9.6 &plusmn; .3 J/cm² at 9ps.</p><p>

<p> Efficiency of solar cells is degraded by deposition of mineral dust as well as other particles, and experiments reveal that losses can be significant (up to ~85%) depending on various factors. However, little is known about the role of light scattering and absorption in reducing optical transmission to the solar cell semiconductor. This dissertation first develops a fundamental model of optical losses due to particle-on-substrate scattering for light propagating into the forward direction. We use discrete dipole approximation with surface interaction (DDA-SI), which is a numerical solution of light scattering for an arbitrarily shaped particle-on-substrate. Using DDA-SI, we studied transmission losses due to hemispheric backward scattering (HBS) and absorption. A parameter called the fraction of power lost, defined as the ratio of HBS efficiency plus absorption efficiency to extinction efficiency, was found appropriate to describe optical losses into the forward direction. We found that fine particles lead to higher losses (per optical depth or layer optical thickness) than coarser ones. Losses into the forward direction are maximized when the ratio of skin depth to particles diameter approaches unity. </p><p> In addition, we conducted a resuspension-deposition experiment with two types of mineral dust, optically absorbing and non-absorbing dust. The dust samples were suspended and deposited onto glass slides, acting as surrogates for solar cells. Dust-deposited glass slides with increasing amounts of mass per area were spectroscopically characterized using a spectrophotometer with an integrating sphere (SIS) detector system. The SIS device allowed us to measure forward-hemisphere scattering, HBS, and direct beam transmission. Transmission into the forward direction was found to decrease as function of optical depth, depending on the absorptivity of the dust. Multiple-scattering radiative transfer theory, specifically the two-stream model as well as Monte Carlo stochastic calculations, were used to describe transmission as function of optical depth for both absorbing and nonabsorbing dust, yielding good agreement with experimental results within ~5%. Two-stream model and Monte Carlo techniques yield a multiple-scattering transmission calculation that depends on the single-scattering parameters of albedo and asymmetry parameter. </p><p> This study has the potential to help with solar energy forecasting, aiding smart power grids in predicting and adapting to variations in solar cell energy output due to aerosol deposition. In addition, this study can help optimize cleaning procedures and schedules to save water in desert and semi-arid regions by describing transmission losses as function of dust type. </p><p>

Complex information within biological systems is being uncovered at an unprecedented speed thanks to the rapid technical development of a wide variety of research tools, among which imaging and sequencing technologies are attracting big attention in recent years. Optical imaging enables the visualization of the spatial distribution of biomolecules at cellular level, allowing deeper understanding of the structure and dynamics of biological systems. Fluorescence microscopy has contributed greatly to our understanding of these processes, but it relies on the use of fluorescent labels or dyes. These labels may perturb the studied systems especially for imaging small molecules, and the photobleaching problem also limits the long-term biological dynamics observation within living cells. In the first part of this dissertation, we introduce the recent development of Stimulated Raman scattering (SRS) microscopy as a noninvasive imaging technique with superior sensitivity, molecular specificity at video-rate imaging speed. It has superseded coherent anti-Stokes Raman scattering (CARS) microscopy due to the absence of non-resonant background and automatic phase matching. However, SRS imaging has been mostly demonstrated for the visualization of lipid and protein with long vibrational wavenumbers. We extend the detectability of SRS imaging into the crowded fingerprint region with characteristic signatures of more biomolecules such as nucleic acids in live cells (Chapter 2), unsaturated lipid and aromatic amino acid in multiphasic food products (Chapter 3). Noninvasiveness of SRS imaging also brings new opportunities to biomedical applications and we demonstrate its feasibility as a potential pathology diagnostic tool by generating comparable image contrast as golden standard H&E staining in human brain frozen sections (Chapter 4). We further extend SRS imaging to real-time multiband detection using a novel modulation multiplex approach (Chapter 5). The rapid development of high throughput sequencing technologies has enabled whole genome and transcriptome wide analysis at faster speed and affordable cost, but a large number of cells are often still required for these analyses. However, cell-to-cell variation is significant and may carry important indication to the study of complex wiring in the nervous systems. In this second part of the dissertation, we explore the heterogeneity of retina using a recently developed single cell transcriptome amplification technique based on Multiple Annealing Looping Based Amplification Cycles (MALBAC), which is superior to other single cell techniques with its low amplification bias, high reproducibility rate and low dropout rate. We first classify different retinal cell populations (photoreceptor cells vs. retinal ganglion cells) and closely related subpopulations (different direction selective retinal ganglion cells) (Chapter6). We further study the molecular divergence of an unsolved ON-OFF retina circuit responsible for direction selectivity function. We show that the inhibitory interneurons responsible for this function can be classified into two clusters based on the single cell transcriptome data. This clustering result strongly correlates with the ON-OFF starburst amacrine cells (SACs) based on the immunostaining results of the identified differential genes. The newly reported differential genes can potentially be used as molecular markers for ON-OFF SACs with more validation underway (Chapter 7). These new findings open up more opportunities for the functional studies on the direction-selective circuit in retina. / Engineering and Applied Sciences - Applied Physics

Adoptive Immunotherapy has long been explored as a possible cure for challenging diseases including cancer and HIV infection. The key step in such therapies is to identify and select disease-specific effector cells, which in the past have relied on well-plate based bulk manipulations. But as effector cells against a specific disease are often scarce, bulk studies are ineffective at identifying and selecting the rare effector cells with accuracy. It also takes weeks to prepare a desired population. Though recent advances such as genetically engineered T cell technology and the mutation selection technology have shown great promises, the former is limited by the difficulty in identifying the receptor and antigen, the latter is limited by the direct cell surface fluorescent tagging which could impairs the functional epitomes of surface activation marker and the ineffectiveness of the surface activation marker based selection. Thus I developed a microfluidic system to identify and select effector cells with unprecedented accuracy and speed, by probing the dynamic single cell immune response through co assessing single cell cytokine secretion and cytolysis in picoliter droplets. / Engineering and Applied Sciences - Applied Physics

The study of quantum mechanics, together with the ability to coherently control and manipulate quantum systems in the lab has led to a myriad of discoveries and real world applications. In this thesis we present experiments demonstrating precise control of an individual long-lived spin qubit as well as sensing applications for biology and investigation of quantum many-body dynamics. Stable quantum bits, capable both of storing quantum information for macroscopic time scales and of integration inside small portable devices, are an essential building block for an array of potential applications. In the second chapter of this thesis we demonstrate high-fidelity control of a solid-state qubit, which preserves its polarization for several minutes and features coherence lifetimes exceeding 1 second at room temperature. Sensitive probing of temperature variations on nanometer scales is an outstanding challenge in many areas of modern science and technology. In chapter three we show how nitrogen vacancy centers in diamond can be used as a robust, high sensitivity temperature probe. We furthermore demonstrate biological compatibility by introducing nano-sized diamonds into living cells and measuring externally induced sub-cellular temperature gradients. Understanding the dynamics of interacting many-body quantum systems with on-site potential disorder has proven one of the biggest challenges in quantum physics to investigate both in theory and experiment. In chapter four we demonstrate how coherent control techniques can be utilized to probe the many-body dynamics of a strongly interacting NV spin ensemble. Specifically, we show how a long-range interacting dipolar spin system exhibits characteristically slow thermalization in the presence of tunable disorder. The presented works offer up many new areas to investigate, including complex quantum many-body effects of large, disordered spin systems, as well as applications of NV centers as bio-compatible nano-scale temperature probes. / Physics

Brillouin scattering based distributed fiber optic sensing as a novel technique has attracted much attention in both research and application for the past ten years. The fiber optic group at the University of Ottawa has developed an advanced automatic Brillouin sensing system and improved it continuously. This thesis presents the characterization and optimization of this sensing system and a series of successful applications both in the laboratory and in the field. Several parameters have been studied around the pulse generation subsystem: such as, bias, leakage, PW voltage, pulsewidth, and repetition frequency. Bias is found to be the most important parameter. We also discuss the relationships between the system repeatability and control parameters such as bias, polarization states, averages and frequency lock methods. Four successful applications of the distributed Brillouin sensing system are reported in the thesis. They are strain measurement in a reinforced concrete beam, simultaneous strain and temperature monitoring of composite curing process, strain and temperature monitoring of a concrete structure, and temperature compensated strain measurement of the load test on the Rollinsford Bridge.