Infrared cameras can directly measure the apparent temperature of objects, providing thermal imaging. However, the raw output from most infrared cameras suffers from a strong, often limiting noise source called nonuniformity. Manufacturing imperfections in infrared focal planes lead to high pixel-to-pixel sensitivity to electronic bias, focal plane temperature, and other effects. In turn, different pixels within the focal plane array give a drastically different electronic response to the same irradiance. The resulting imagery can only provide useful thermal imaging after a nonuniformity calibration has been performed. Traditionally, these calibrations are performed by momentarily blocking the field of view with a flat temperature plate or blackbody cavity. However because the pattern is a coupling of manufactured sensitivities with operational variations, periodic recalibration is required, sometimes on the order of tens of seconds. A class of computational methods called Scene-Based Nonuniformity Correction (SBNUC) has been researched for over 20 years where the nonuniformity calibration is estimated in digital processing by analysis of the video stream in the presence of camera motion. The most sophisticated SBNUC methods can completely and robustly eliminate the high-spatial frequency component of nonuniformity with only an initial reference calibration or potentially no physical calibration. I will demonstrate a novel algorithm that advances these SBNUC techniques to support all spatial frequencies of nonuniformity correction. Long-wave infrared microgrid polarimeters are a class of camera that incorporate a microscale per-pixel wire-grid polarizer directly affixed to each pixel of the focal plane. These cameras have the capability of simultaneously measuring thermal imagery and polarization in a robust integrated package with no moving parts. I will describe the necessary adaptations of my SBNUC method to operate on this class of sensor as well as demonstrate SBNUC performance in LWIR polarimetry video collected on the UA mall.

In this work, we develop a many-body theory of electronic transport through single molecule junctions based on nonequilibrium Green’s functions (NEGFs). The central quantity of this theory is the Coulomb self-energy matrix of the junction ∑(C). ∑(C) is evaluated exactly in the sequential-tunneling limit, and the correction due to finite lead-molecule tunneling is evaluated using a conserving approximation based on diagrammatic perturbation theory on the Keldysh contour. In this way, tunneling processes are included to infinite order, meaning that any approximation utilized is a truncation in the physical processes considered rather than in the order of those processes. Our theory reproduces the key features of both the Coulomb blockade and coherent transport regimes simultaneously in a single unified theory. Nonperturbative effects of intramolecular correlations are included, which are necessary to accurately describe the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap, essential for a quantitative theory of transport. This work covers four major topics related to transport in single-molecule junctions. First, we use our many-body theory to calculate the nonlinear electrical response of the archetypal Au-1,4-benzenedithiol-Au junction and find irregularly shaped ‘molecular diamonds’ which have been experimentally observed in some larger molecules but which are inaccessible to existing theoretical approaches. Next, we extend our theory to include heat transport and develop an exact expression for the heat current in an interacting nanostructure. Using this result, we discover that quantum coherence can strongly enhance the thermoelectric response of a device, a result with a number of technological applications. We then develop the formalism to include multi-orbital lead-molecule contacts and multi-channel leads, both of which strongly affect the observable transport. Lastly, we include a dynamic screening correction to ∑(C) and investigate the optoelectric response of several molecular junctions.

The manipulation of molecular structures is an important enabling technology for future advances in nanotechnology. The ability to control the synthesis of nanostructured materials, such as the bond formation and geometry of a molecule is of great significance to nanoscience as nanosystems are constructed from these smaller units. Influencing the assembly of molecular structures at the early stages of material formation can modify the ensuing molecular aggregate structure with the potential for impact in a broad range of optical, chemical, and biological applications. Heteroleptic titanium metal alkoxides (OPy)₂Ti(4MP) ₂ and (OPy)₂Ti(TAP)₂, where OPy = OC₆H₆N, 4MP = OC₆H₄(SH)-4, and TAP = OC₆H₂(CH₂N(CH₃)₂)₃-2,4,6 were investigated as precursors for thin film and solution-based synthesis of oxide materials via the photoactivation of intermolecular reactions (e.g. hydrolysis/condensation) at selected ligand sites about the metal center. Manipulation of the molecular structure of these photosensitive metal alkoxides was achieved through the use of optical irradiation parameters, such as the tuning of the excitation wavelength, total optical fluence, and pulse energy intensity. Irradiating these metal alkoxides with UV-light was seen to cause photodisruption in the ligand groups leading to the formation of Ti-O-Ti linking via hydrolysis and condensation reactions. In spin-coated (OPy)₂Ti(TAP)₂ films, these photoinduced bridge bond formations resulted in an increase in refractive index and film densification as well as produced an insoluble film when rinsed in pyridine. By making use of these photoinduced film properties, the formation of physical relief structures from spin-coated (OPy)₂Ti(TAP)₂ films was demonstrated along with the ability to photopattern sub-micron and nanometer features. In addition, the micro- and nanostructure of thin films were optically manipulated through several deposition methods; a novel dip-coated in-situ photodeposition technique was utilized by illuminating at specific distances above the meniscus to further control the early stages of material formation due to changes in the mobility of the reactants from the evaporation and gravitational draining of the solvent. The ability to manipulate molecular development at the on-set of material formation through different deposition techniques and optical parameters allowed for the creation of several thin film optical devices, such as gratings, micro-optic lenslet arrays, and binary "on-off" patterned devices.

We have investigated ways of modifying a common water soluble CdTe NCs to become non-photobleaching. Such NCs are capable of responding reversibly to an inter-switching of the oxygen and argon environments over multiple hours of photoexcitation. They are found to quench upon exposure to oxygen, but when the system is purged with argon, their photoluminescence (PL) revives to the original intensity. Such discovery could potentially be used as oxygen nanosensors. These PL robust CdTe NCs immobilized on glass substrates also exhibit significant changes in their PL when certain organic/bio molecules are placed in their vicinity (nanoscale). This novel technique also known as NC-organic molecule close proximity imaging (NC-cp imaging) has found to provide contrast ratio greater by a factor of 2-3 compared to conventional fluorescence imaging technique. PL of NCs is recoverable upon removal of these organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors and, upon optimization, ultimately serving as point detectors for purposes of super-resolution microscopy (with proper instrumentation). No solvents are required for this sensing mechanism since all solutions were dried under argon flow. Furthermore, core graded shell CdSe/CdSeₓS(1-x)/CdS giant nanocrystal (g-NCs) were found to have very robust PL temperature response. At a size of 10.2 nm in diameter, these g-NCs undergo PL drop of only 30% at 355K (normalized to PL intensity at 85K). In comparison, the core step shells CdSe/CdS g-NCs at the same diameter exhibit 80% PL drop at 355K. Spectral shifting and broadening were acquired and found to be 5-10 times and 2-4 times smaller respectively than the standard CdSe core and CdSe/CdS core shell NCs. It is also discovered that these core graded shell g-NCs are largely nonblinking and have insignificant photoluminescence decay even after exciting the samples at very high irradiance (44 kW/cm²) for over an hour. These types of g-NCs have great potential to be used as the active medium for temperature insensitive laser devices in the visible range or temperature insensitive bioprobes for bioimaging applications.

Guided-wave integrated optical devices are demonstrated by using various optical materials. First, a novel integrated optical planar waveguide platform for absorption-based biosensing is demonstrated. The platform integrates surface ion-exchanged channel waveguides with one-step UV patterned sol-gel structures to define the probing regions. Cytochrome c protein was utilized to characterize the device performance. Spectroscopically specific attenuation of approximately 2 dB in the guided signal occurred at 532nm for 1.4 cm long probing region. The estimated level of detection is about 1 pmol/cm2 of surface adsorbed cytochrome c. The proposed structure enables environmentally stable, compact, and inexpensive sensing devices that can be applied to a wide range of biological and chemical species. Second, An arrayed waveguide grating (AWG) with a novel S-shaped design for broadband operation is demonstrated for the first time with III-V semiconductors. This device design provided a polarization and temperature insensitive operation. It is also shown that, despite the wide operating range, chromatic dispersion does not degrade the performance of the AWG. The AWG is operational above the absorption edge of the semiconductor (1100nm) and can function for a wide range of wavelengths covering the coarse wavelength multiplexing range from 1270nm to 1610nm. A four channel AWG with this novel design was fabricated and characterized. Finally, simple fabrication of optical waveguides using a novel Photosensitive Polyimide (PSPI) is presented. PSPI has a glass transition temperature (Tg) of 330 oC and is directly patterned by UV exposure and wet chemical development, lending itself to low cost fabrication techniques. The fabricated waveguides posses low optical absorption at 1.3 and 1.5 µm. Single and multimode buried ridge waveguides were made and tested, and a 0.4 dB/cm optical propagation loss is measured at 1.55 µm.

Simulated images can provide insight into the performance of optical systems, especially those with complicated features. Many modern solutions for presbyopia and cataracts feature sophisticated power geometries or diffractive elements. Some intraocular lenses (IOLs) arrive at multifocality through the use of a diffractive surface and multifocal contact lenses have a radially varying power profile. These type of elements induce simultaneous vision as well as affecting vision much differently than a monofocal ophthalmic appliance. With myriad multifocal ophthalmics available on the market it is difficult to compare or assess performance in ways that effect wearers of such appliances. Here we present software and algorithmic metrics that can be used to qualitatively and quantitatively compare ophthalmic element performance, with specific examples of bifocal intraocular lenses (IOLs) and multifocal contact lenses. We anticipate this study, methods, and results to serve as a starting point for more complex models of vision and visual acuity in a setting where modeling is advantageous. Generating simulated images of real- scene scenarios is useful for patients in assessing vision quality with a certain appliance. Visual acuity estimation can serve as an important tool for manufacturing and design of ophthalmic appliances.

The goal of this dissertation research is to develop and demonstrate a functioning snapshot imaging spectropolarimeter for the long wavelength infrared region of the electromagnetic spectrum (wavelengths from 8-12 microns). Such an optical system will be able to simultaneously measure both the spectral and polarimetric signatures of all the spatial locations/targets in a scene with just a single integration period of a camera. This will be accomplished by combining the use of computed tomographic imaging spectrometry (CTIS) and channeled spectropolarimetry. The proposed system will be the first instrument of this type specifically designed to operate in the long wavelength infrared region, as well as being the first demonstration of such a system using an uncooled infrared focal plane array. In addition to the design and construction of the proof-of-concept snapshot imaging spectropolarimeter LWIR system, the dissertation research will also focus on a variety of methods on improving CTIS system performance. These enhancements will include some newly proposed methods of system design, calibration, and reconstruction aimed at improving the speed of reconstructions allowing for the first demonstration of a CTIS system capable of computing reconstructions in 'real time.'

Single-frequency and mode-locked silver film ion-exchanged glass waveguide lasers as well as all-optical clock recovery based on birefringent fiber resonators have been experimentally and theoretically studied. The theory, modeling and fabrication process of silver film ion-exchange techniques, have been discussed and presented.The UV-written gratings on both IOG-1 active and passive glass have been studied. For the first time, with a high quality narrowband grating UV-printed on the passive section of a hybrid glass, a DBR waveguide single-frequency laser is demonstrated with the linewidth less than 1 MHz and the output power of 9 mW.Novel saturable absorbers based on a fiber taper embedded in carbon nanotubes (CNTs)/polymer composite were demonstrated. The saturable absorbers were utilized to build mode-locked fiber lasers, which were studied experimentally. A mode-locked ring laser utilizing an Er-Yb-codoped glass waveguide as the gain medium was also demonstrated. In addition, short cavity mode-locked waveguide lasers with CNTs film on the top were theoretically investigated, which shows a short cavity mode-locked waveguide laser is very promising.A new concept to perform multi-channel multi-rate all-optical clock recovery based on birefringent fiber-optic waveguide resonators was discussed. The concept has been advanced to polarization-insensitive operation. The experimental results, obtained as a proof-of-concept, agree well with numerical simulations.

The ROx is a retinal oximeter under development with the purpose of non-invasively and accurately measuring oxygen saturation (SO₂) in vivo. It is novel in that it utilizes the blue-green oximetry technique with on-axis illumination. ROx calibration tests were performed by inducing hypoxia in live anesthetized swine and comparing ROx measurements to SO₂ values measured by a CO-Oximeter. Calibration was not achieved to the precision required for clinical use, but limiting factors were identified and improved. The ROx was used in a set of sepsis experiments on live pigs with the intention of tracking retinal SO₂ during the development of sepsis. Though conclusions are qualitative due to insufficient calibration of the device, retinal venous SO₂ is shown to trend generally with central venous SO₂ as sepsis develops. The novel sepsis model developed in these experiments is also described. The method of cecal ligation and perforation with additional soiling of the abdomen consistently produced controllable severe sepsis/septic shock in a matter of hours. In addition, the ROx was used to collect retinal images from a healthy human volunteer. These experiments served as a bench test for several of the additions/modifications made to the ROx. This set of experiments specifically served to illuminate problems with various light paths and image acquisition. The analysis procedure for the ROx is under development, particularly automating the process for consistency, accuracy, and time efficiency. The current stage of automation is explained, including data acquisition processes and the automated vessel fit routine. Suggestions for the next generation of device minimization are also described.

Bandwidth demands in global telecommunication infrastructures continue to rise and new optical techniques are needed to deal with massive data flows. Generating high bandwidth signals (> 40 GHz) using conventional modulation techniques is hindered by material limitations and fabrication complexities. Similarly, controlling such high bandwidths in both the temporal and spectral domain becomes more problematic using conventional electronic processes. Advances in electro-optic organic materials, fibers/micro-fluidics integration, and nonlinear optics have significant potential for higher bandwidth modulation and temporal/spectral control. The work presented in this dissertation demonstrates the use of various nonlinear optical effects in new photonic device and system designs towards the generation and manipulation of highspeed optical pulses. First, an all fiber-based system utilizing an integrated carbon disulfide-filled liquidcore optical fiber (i-LCOF) and co-propagating pulses of comparable temporal lengths is presented. The slow light effect was observed in 1-meter of i-LCOF, where 18 ps pulses were delayed up to 34 ps through the use of stimulated Raman scattering. Delays greater than a pulse width indicate a potential application as an ultrafast controllable delay line for time division multiplexing in multi-Gb/s telecommunication systems. Similarly, an optically tunable frequency shift was observed using this system. Pulses experienced a full spectral bandwidth shift at low peak pump powers when utilizing the Raman-induced frequency shift and slow light effects. Numerical simulations of the pulse-propagation equations agree well with the observed shifts. Included in our simulations are the contributions of both the Raman cross-frequency shift and slow light effects to the overall frequency shift. These results make the system suitable for numerous applications including low power wavelength converters. Second, a silica/electro-optic (EO) polymer phase modulator with an embedded bowtie antenna is proposed for use as a microwave radiation receiver. The detection of high-frequency electromagnetic fields has been heavily studied for wireless data transfer. Recently there has been growing interest in the field of microwave photonics. We present the design and optimization of a waveguide with an EO polymer core and silica/sol-gel cladding. The effect of electrodes on the insertion losses and poling efficiency are also analyzed, and conditions for low-loss and high poling efficiency are established. Experimental results for a fabricated device with microwave-response between 10 - 14 GHz are presented. Finally, we present the design for a fast optical switch incorporating silicon as the passive waveguide structure and EO polymer as the active material. The design uses a simple directional coupler with coplanar electrodes and promises to have low cross-talk and high switching speed (on the order of nanoseconds). An initial design for a 1x2 switch is fabricated and tested, and future optimization processes are also presented.