This thesis reports on the design of an optical relay for use in a color, stereo Head-Mounted Display (HMD) system. / Based on reviews and discussions of the requirements of the human visual system, major factors affecting the visual acuity, the aberration tolerances of the human eye, and optical design limitations, we derive the design criteria for the optical relay. A survey of alternate approaches to the three components of HMDs is presented. / A brief review of first order optics, aberration theory, general design principles, and computer aided lens design is also given. / Two multi-spherical lens systems, a straight structure and a folded layout, are presented. Their aberrations (distortion, coma, lateral color, field curvature and astigmatism) have been well corrected. Each of them has a 20 mm eye relief and an instantaneous field-of-view greater than 60$ sp circ.$

A fast-beam collinear laser spectroscopy apparatus has been designed and tested with the $ sp{23}$Na D$ sb2$ line (wavelength = 589 nm) on continuous atomic beams. / A radio-frequency quadrupole ion trap and its associated electronics have been assembled and successfully operated, trapping $ sp{23}$Na$ sp{+}$ ions from an external source built for the purposes of this work. The bunched ions were extracted and detected; the effect of several injection, bunching and extraction parameters on the extracted bunches' size were studied. A simple model of the ion bunching and losses in the trap is proposed. / From the sensitivity limit of the collinear laser spectroscopy apparatus and the maximum bunched current output from the trap, the possibility of performing fast-beam collinear laser spectroscopy measurements on bunched atomic beams is examined.

<p> The process of capturing solid geometry as 3 dimensional data requires the use of laser based reverse engineering hardware, known as a digitizer. Many digitizers exist as articulated coordinate measuring machines augmented with a laser, which forces the operator into many postures that are not ergonomically sound, particularly in the operator's upper body. This study analyzes the traditional method of laser digitizing using modern methods and technologies. An alternative user interface using an occluded head-mounted monocular display is hypothesized and evaluated.</p>

<p> The Thulium Fiber Laser (TFL) has been studied as a potential alternative to the conventional Holmium:YAG laser (Ho:YAG) for the treatment of kidney stones. The TFL is more ideally suited for laser lithotripsy because of the higher absorption coefficient of the emitted wavelength in water, the superior Gaussian profile of the laser beam, and the ability to operate at arbitrary temporal pulse profiles. The higher absorption of the TFL by water helps translate into higher ablation of urinary stones using less energy. The Gaussian spatial beam profile allows the TFL to couple into fibers much smaller than those currently being used for Ho:YAG lithotripsy. Lastly, the ability of arbitrary pulse operation by the TFL allows energy to be delivered to the stone efficiently so as to avoid negative effects (such as burning or bouncing of the stone) while maximizing ablation. Along with these improvements, the unique properties of the TFL have led to more novel techniques that have currently not been used in the clinic, such as the ability to control the movement of stones based on the manner in which the laser energy is delivered. Lastly, the TFL has led to the development of novel fibers, such as the tapered fiber and removable tip fiber, to be used for lithotripsy which can lead to safer and less expensive treatment of urinary stones. Overall, the TFL has been demonstrated as a viable alternative to the conventional Ho:YAG laser and has the potential to advance methods and tools for treatment of kidney stones. </p>

<p> The energies of protein correlated motions lie in the far infrared or THz frequency range (&lambda; = 1 cm &ndash; 50 mm, f = 0.03 &ndash; 6 THz). The existence of correlated motions has been confirmed by neutron and inelastic x-ray scattering measurements. These techniques require large sample volumes and specialized facilities, limiting their application to systematic studies of changes in correlated motions with functional state and allosteric interactions. Standard terahertz time domain spectroscopy measurements have shown sensitivity to protein-ligand binding, oxidation state, conformation, temperature and hydration. However, the response is broad, in part from the large vibrational density of states and in part from the dielectric response contribution from surface water and side-chains. </p><p> As an overall strategy to measure the correlated structural motions in protein, we use anisotropic and birefringent behavior of molecular crystals to develop a new technique called MOSTS (Modulated Orientation Sensitive Terahertz Spectroscopy). We achieve high sensitivity and mode separation, by using single molecular crystal such as sucrose and oxalic acid, and rapid modulation of the relative alignment of the terahertz polarization and the crystal axes by rotating the sample. By locking into the signal at the rotation frequency, we determine the polarization sensitive signal and map out the optically active vibrational resonances. To illustrate the technique, we compare our measured spectra with the calculated, and find a close agreement. </p><p> We measure dielectric properties of oxalic acid, sucrose and protein crystals and polycarbonate sheet using standard terahertz time domain spectroscopy. We determine the absorbances in oxalic acid and sucrose crystals, using MOSTS technique. We compare the resonances in these two distinct methods. Then, we develop a protein model sample by sticking together two thin plates of sucrose and polycarbonate. We carry out standard THz-TDS and MOSTS measurements on the protein model sample. We show that we are able to isolate the vibrational modes from glassy background in protein model sample by using MOSTS.</p>

<p> The advent of highly-coherent x-ray light sources, such as those now available world-wide in modern third-generation synchrotrons and increasingly available in free-electron lasers, is driving the need for improved analytical and experimental techniques which exploit the coherency of the generated light. As the light illuminating a sample approaches full coherence, a simple Fourier transform describes the diffraction pattern generated by the scattered light in the far field; because the Fourier transform of an object is unique, coherent scattering can directly probe local structure in the scattering object instead of bulk properties.</p><p> In this dissertation, we exploit the coherence of Advanced Light Source beamline 12.0.2 to build three types of novel coherent scattering microscopes. First, we extend the techniques of coherent diffractive imaging and Fourier transform holography, which uses iterative computational methods to invert oversampled coherent speckle patterns, into reflection geometry. This proof-of-principle experiment demonstrates a method by which reflection Bragg peaks, such as those from the orbitally-ordered phase of complex metal oxides, might eventually be imaged. Second, we apply a similar imaging method to the x-ray beam itself to directly image the mutual coherence function with only a single diffraction pattern.</p><p> This technique supersedes the double-slit experiments commonly seen in the scattering literature to measure the mutual intensity function by using a set of apertures which effectively contains all possible double slit geometries. Third, we show how to evaluate the speckle patterns taken from a labyrinthine domain pattern for "hidden" rotational symmetries. For this measurement, we modify the iterative algorithms used to invert speckle patterns to generate a large number of domain configurations with the same incoherent scattering profile as the candidate pattern and then use these simulations as the basis for a statistical inference of the degree of ordering in the domain configuration. We propose extending this measurement to position-resolved speckle patterns, creating a symmetry-sensitive microscope. The three new techniques described herein may be employed at current and future light sources.</p>

In this thesis, I demonstrate the rational design and controllable fabrication of a series of novel plasmonic nanostructures with judiciously tailored optical properties including perfect nanoshells, roughened subwavelength particles, prolate nanoshells known as nanorice, and non-concentric nanoshells known as nanoeggs. All of these nanostructures are very important subwavelength nanoscale optical components that can be utilized to manipulate light in unique ways. The most striking feature of these nanoparticles is their geometrically tunable plasmon resonances, which can be harnessed for widespread applications. I have also utilized these nanostructures as the building blocks to construct self-assembled multinanoparticle systems, such as nanoshell heterodimers, nanosphere arrays and nanoshell arrays. I have further developed multifunctional molecular sensing platforms using these nanoengineered plasmonic structures as substrates for surface-enhanced spectroscopies, realizing integrated analytical chemistry lab-on-a-chip. Applying the Plasmon Hybridization model as design principles to experimentally realizable nanostructures results in a thorough understanding of the origin of the geometry-dependent optical properties observed in these nanosystems. Finite Difference Time Domain (FDTD) method also provides a powerful platform for the numerical simulation of local- and far-field optical properties of these nanostructures.

Optical- and spectroscopic-based screening and imaging strategies possess unique advantages for minimally invasive cancer diagnosis. In this dissertation, we investigated how diagnostic results based on such techniques can be improved by the utilization of both endogenous and nanotechnology-facilitated molecular contrast. First, a diffusion-theory-based inversion reflectance model was constructed for the extraction of intrinsic tissue optical properties from the shape of normalized tissue diffusion reflectance spectra. The accuracy of our diffusion-based inversion algorithm was systematically assessed against Monte Carlo simulation as a function of probe geometry and tissue optical property combinations. By using this method, the spectral absorption and scattering coefficients of normal and cancerous tissue were efficiently retrieved within the center-to-center source-detector fiber separation of 0.5 mm &sim;3 mm, which is compatible with endoscopic specifications. The presented inversion approach is computationally viable for eventual real-time in vivo tissue diagnostic applications. Second, novel quantum dot nanoparticle-based contrast agents were developed for molecular and tissue imaging applications in the visible and near-infrared (NIR) spectral ranges. Specifically, lead sulfide quantum dot bioconjugates were explored as NIR contrast agents for targeted molecular imaging; a protease-activated quantum dot probe was developed to monitor specific molecular targets and pathways through optical strategies; and a phantom study was conducted to assess the utilization of lead sulfide NIR quantum dots as fluorescent contrast agents for deep tissue imaging applications. These nanoengineered exogenous probes were shown to have the potential to significantly improve the implementation of optical/spectroscopic cancer imaging techniques. Taken together, the goal of the combined projects in this dissertation was to demonstrate that photonics-based minimally invasive cancer detection and imaging methods can be greatly advanced by the utilization of both endogenous and nanotechnology-facilitated molecular contrast.

Single particle dark field spectroscopy has been combined with high-resolution scanning electron and atomic force microscopy to study the scattering spectra of individual gold nanoparticles. This technique has been applied to single gold/silica nanoshells, and single gold nanostars. For nanoshells, the plasmon resonant peak energies match those calculated by Mie theory based on the nanoshell geometry. The resonance line widths fit Mie theory without the inclusion of a size-dependent electron surface scattering term, which is often included to fit ensemble measurements. Single particle spectroscopy has also been applied to star-shaped gold nanoparticles which are ca. 100 nm in diameter. The gold nanostars were fabricated by a modified seed-mediated, surfactant-directed synthesis which is similar to a method known to produce gold nanorods in high yield. The yield, monodispersity, and initial investigations into the growth mechanism of the nanostar synthesis are described in detail. Through correlated structural characterization by electron microscopy, each scattering component can be assigned to different points on the nanostars. The plasmon resonances were also found to be extremely sensitive to the local dielectric environment, yielding sensitivities as high as 1.41 eV photon energy shift per refractive index unit. These properties suggest that gold nanostars may be highly valuable for certain biosensing and microscopic imaging paradigms. To test their properties as molecular sensors, single nanostar spectra were monitored upon exposure to alkane thiols (mercaptohexadecanoic acid) and proteins (bovine serum albumin) known to bind gold surfaces. The observed shifts are consistent with the effects of these molecular layers on the surface plasmon resonances in continuous gold films. The results suggest that localized surface plasmon resonance sensing with single nanoparticles is analogous to the well developed field surface plasmon resonance sensors, and will push the limits of sensitivity.

Several significant applications have been realized for light scattering in biomedical imaging. In order to improve imaging results with light scattering-based techniques, a variety of nanoparticles have been investigated as contrast agents, including gold nanoshells. As a method for studying the optical properties of plasmonic gold nanoparticles used as contrast agents for molecular imaging, we developed an automated goniometer instrumentation system. This system, which allows us to specifically study polarized angular-dependent light scattering of plasmonic nanoparticles, allowed us to perform a series of theoretical and experimental step-wise studies. The basic optical properties of the following gold nanoparticles were progressively investigated: (1) bare nanoshells at multipolar plasmonic resonances, (2) nanoshells with PEG modifications, (3) surface-textured nanoshells and (4) immunotargeted nanoshells (nanoshell-antibody bioconjugates) for cancer imaging. Based on the results from these studies, a new technique was developed to quantitatively measure the number of immunotargeted nanoparticles that bind to HER2-positive SKBR3 human breast cancer cells. Preliminary studies of determining the minimal incubation time of immunotargeted nanoshells with SKBR3 cells were also carried out to evaluate the potential clinical application of using gold nanoshells intraoperatively. We, therefore, anticipate that our findings will provide the theoretical groundwork required for further studies aimed at optimizing the application of plasmonic nanoparticles in scattering-based optical imaging techniques.