Polarimetry is one of the principal means of investigating the interaction of light with matter. Theoretical models and experimental techniques are presented in this dissertation for polarimetric characterization of random electromagnetic beams and of signatures of random media in different scattering regimes and configurations. The degree of polarization rather than the full description of the state of polarization is of interest in multiple scattering and free space propagation where the statistical nature and not the deterministic component of light bears the relevant information. A new interferometric technique for determining the degree of polarization by measuring the intensity fluctuations in a Mach-Zehnder interferometric setup is developed. For this type of investigations, one also needs a light source with a controllable degree of polarization. Therefore, also based on a Mach-Zehnder interferometer, we proposed a new method for generating complex random electromagnetic beams. As a direct application of the cross-spectral density matrix formalism, it is shown that the spectral and the polarimetric characteristics of light can be controlled by adjusting the correlations between parallel components of polarization propagating through the two arms of the interferometer. When optical beams are superposed in the previous applications it is desirable to understand how their coherence and polarimetric characteristics are combined. A generalization of the interference laws of Fresnel and Arago is introduced and as a direct application, a new imaging polarimeter based on a modified Sagnac interferometer is demonstrated. The system allows full polarimetric description of complex random electromagnetic beams. In applications such as active illumination sensing or imaging through turbid media, one can control the orientation of the incident state of polarization such that, in a given coordinate system, the intensities are equal along orthogonal directions. In this situation, our novel interferometric technique has a significant advantage over standard Stokes imaging polarimetry: one needs only one image to obtain both the degree of polarization and the retardance, as opposed to at least three required in classical Stokes polarimetry. The measurement of the state of polarization is required for analyzing the polarization transfer through systems that alter it. Two innovative Mueller matrix measurement techniques are developed for characterizing scattering media, either in quasi real-time, or by detection of low level signals. As a practical aspect of Mueller polarimetry, a procedure for selecting the input Stokes vectors is proposed. The polarimetric signatures of different particulate systems are related to their structural properties and to the size distribution, shape, orientation, birefringent or dichroic properties of the particles. Various scattering regimes and different geometries are discussed for applications relevant to the biomedical field, material science, and remote sensing. The analysis is intended to elucidate practical aspects of single and multiple scattering on polydisperse systems that were not investigated before. It seems to be generally accepted that depolarization effects can only be associated to multiple scattering. It is demonstrated in this dissertation that depolarization can also be regarded as an indication of polydispersity in single scattering. In order to quantify the polarizing behavior of partially oriented cylinders, the polarization transfer for systems consisting of individual layers of partially aligned fibers with different degrees of alignment and packing fractions is also analyzed in this dissertation. It is demonstrated that a certain degree of alignment has the effect of a partial polarizer and that the efficiency of this polarizer depends on the degree of alignment and on the packing fraction of the system. In specific applications such as long range target identification, it is important to know what type of polarization is better preserved during propagation. The experimental results demonstrate that for spherical particles smaller than the wavelength of light, linear polarization is better preserved than circular polarization when light propagates through turbulent media. For large particles, the situation is reversed; circular polarization is better preserved. It is also demonstrated here that this is not necessarily true for polyhedral or cylindrical particles, which behave differently. Optical activity manifests as either circular birefringence or circular dichroism. In this dissertation, a study is presented where both the effect of optical activity and that of multiple scattering are considered. This situation is relevant for medical applications and remote sensing of biological material. It is demonstrated here that the output state of polarization strongly depends on the optical density of the scattering medium, the optical rotatory power and the amount of circular dichroism associated to the scattering medium. This study shows that in the circular birefringence case, scattering and optical activity work together in depolarizing light, while in the dichroic case the two effects compete with each other and the result is a preservation of the degree of polarization. To characterize highly diffusive media, a very simple model is developed, in which the scattering is analyzed using the Mueller matrix formalism in terms of surface and volume contributions.

Quadratic spatial soliton interactions were investigated in this Dissertation. The first part deals with characterizing the principal features of multi-soliton generation and soliton self-reflection. The second deals with two beam processes leading to soliton interactions and collisions. These subjects were investigated both theoretically and experimentally. The experiments were performed by using potassium niobate (KNBO3) and periodically poled potassium titanyl phosphate (KTP) crystals. These particular crystals were desirable for these experiments because of their large nonlinear coefficients and, more importantly, because the experiments could be performed under non-critical-phase-matching (NCPM) conditions. The single soliton generation measurements, performed on KNBO3 by launching the fundamental component only, showed a broad angular acceptance bandwidth which was important for the soliton collisions performed later. Furthermore, at high input intensities multi-soliton generation was observed for the first time. The influence on the multi-soliton patterns generated of the input intensity and beam symmetry was investigated. The combined experimental and theoretical efforts indicated that spatial and temporal noise on the input laser beam induced multi-soliton patterns. Another research direction pursued was intensity dependent soliton routing by using of a specially engineered quadratically nonlinear interface within a periodically poled KTP sample. This was the first time demonstration of the self-reflection phenomenon in a system with a quadratic nonlinearity. The feature investigated is believed to have a great potential for soliton routing and manipulation by engineered structures. A detailed investigation was conducted on two soliton interaction and collision processes. Birth of an additional soliton resulting from a two soliton collision was observed and characterized for the special case of a non-planar geometry. A small amount of spiraling, up to 30 degrees rotation, was measured in the experiments performed. The parameters relevant for characterizing soliton collision processes were also studied in detail. Measurements were performed for various collision angles (from 0.2 to 4 degrees), phase mismatch, relative phase between the solitons and the distance to the collision point within the sample (which affects soliton formation). Both the individual and combined effects of these collision variables were investigated. Based on the research conducted, several all-optical switching scenarios were proposed.

A spatial soliton is a shape invariant self guided beam of light or a self induced waveguide. Spatial solitons appear as a result of the balance of diffraction and nonlinear focusing in a system. They have been observed in many different conservative media in the last couple of years. Solitons are ubiquitous, because of the probability of using their interactions in optical data processing, communications etc. Up to now due to the power required to generate the solitons, and the response times of the soliton supporting media, these special waves of nature could not penetrate the applications arena. Semiconductors, with their resonant nonlinearities, are thought to be ideal candidates for fast switching, low power spatial solitons. In this dissertation it is shown theoretically and experimentally that it is possible to observe stable spatial solitons in a periodically patterned semiconductor optical amplifier (PPSOA). The solitons have unique beam profiles that change only with system parameters, like pumping current, etc. Their coherent and incoherent interactions which could lead to all optical devices have been investigated experimentally and theoretically. The formation of filaments or modulational instability has been studied theoretically and yielded analytical formulae for evaluating the filament gain and the maximum spatial frequencies in PPSOA devices. Furthermore, discrete array amplifiers have been analyzed numerically for discrete solitons, and the prospect of using multi peak discrete solitons as laser amplifiers is discussed.

Liquid crystal is an amazing class of soft matters with applications spanning from visible, infrared, millimeter wave, to terahertz. In addition to direct-view displays and projection displays, liquid crystal is also widely used in adaptive optics, tunable-focus lens, and laser beam steering. Although the visible region has well developed materials and mixtures for the vast variety of applications, the midwave infrared (MWIR) region of the electromagnetic spectrum invites much development as only a few materials have been developed with these applications in mind. Unlike visible region, the major challenge for mid-wave infrared liquid crystal is inherently large absorption loss. To reduce absorption, some molecular engineering approaches have been considered, such as deuteration, fluorination, and chlorination. The fluorine and chlorine not only act as the polar group to provide dipole moment but also helps shift some vibration absorption bands outside the MWIR window. Long phenyl ring compounds, fluorinated tolane materials, and chlorinated terphenyl mixtures are explored; as well as a look as the potential bromine might introduce for future development. In this thesis, we first review the current materials and their performance in the mid-wave infrared region, explain the need for higher performing liquid crystals, and then discuss the methodology of compound development and mixture formulation. Some new chlorinated liquid crystal compounds are synthesized, mixture formulated, and their properties evaluated. Finally, we will explain the future work which needs to be performed in this field.

Discrete optical systems are a subgroup of periodic structures in which the evolution of a continuous electromagnetic field can be described by a discrete model. In this model, the total field is the sum of localized, discrete modes. Weakly coupled arrays of single mode channel waveguides have been known to fall into this class of systems since the late 1960's. Nonlinear discrete optics has received a considerable amount of interest in the last few years, triggered by the experimental realization of discrete solitons in a Kerr nonlinear AlGaAs waveguide array by H. Eisenberg and coworkers in 1998. In this work a detailed experimental investigation of discrete nonlinear wave propagation and the interactions between beams, including discrete solitons, in discrete systems is reported for the case of a strong Kerr nonlinearity. The possibility to completely overcome "discrete" diffraction and create highly localized solitons, in a scalar or vector geometry, as well as the limiting factors in the formation of such nonlinear waves is discussed. The reversal of the sign of diffraction over a range of propagation angles leads to the stability of plane waves in a material with positive nonlinearity. This behavior can not be found in continuous self-focusing materials where plane waves are unstable against perturbations. The stability of plane waves in the anomalous diffraction region, even at highest powers, has been experimentally verified. The interaction of high power beams and discrete solitons in arrays has been studied in detail. Of particular interest is the experimental verification of a theoretically predicted unique, all optical switching scheme, based on the interaction of a so called "blocker" soliton with a second beam. This switching method has been experimentally realized for both the coherent and incoherent case. Limitations of such schemes due to nonlinear losses at the required high powers are shown.

This dissertation investigates the monolithic integration of dual optical elements on high power semiconductor lasers for emission around 980nm wavelength. In the proposed configuration, light is coupled out of the AlGaAs/GaAs waveguide by a low reflectivity grating coupler towards the substrate where a second monolithic optical element is integrated to improve the device performance or functionality. A fabrication process based on electron beam lithography and plasma etching was developed to control the grating coupler duty cycle and shape. The near-field intensity profile outcoupled by the grating is modeled using a combination of finite-difference time domain (FDTD) analysis of the nonuniform grating and a self-consistent model of the broad area active region. Improvement of the near-field intensity profile in good agreement with the FDTD model is demonstrated by varying the duty cycle from 20% to 55% and including the aspect ratio dependent etching (ARDE) for sub-micron features. The grating diffraction efficiency is estimated to be higher than 95% using a detailed analysis of the losses mechanisms of the device. The grating reflectivity is estimated to be as low as 2.10-4. The low reflectivity of the light extraction process is shown to increase the device efficiency and efficiently suppress lasing oscillations if both cleaved facets are replaced by grating couplers to produce 1.5W QCW with 11nm bandwidth into a single spot a few mm above the device. Peak power in excess of 30W without visible COMD is achieved in this case. Having optimized, the light extraction process, we demonstrate the integration of three different optical functions on the substrate of the surface-emitting laser. First, a 40 level refractive microlens milled using focused ion beam shows a twofold reduction of the full-width half maximum 1mm above the device, showing potential for monolithic integration of coupling optics on the wafer. We then show that differential quantum efficiency of 65%, the highest reported for a grating-coupled device, can be achieved by lowering the substrate reflectivity using a 200nm period tapered subwavelength grating that has a grating wavevector oriented parallel to the electric field polarization. The low reflectivity structure shows trapezoidal sidewall profiles obtained using a soft mask erosion technique in a single etching step. Finally, we demonstrate that, unlike typical methods reported so far for in-plane beam-shaping of laser diodes, the integration of a beam-splitting element on the device substrate does not affect the device efficiency. The proposed device configuration can be tailored to satisfy a wide range of applications including high power pump lasers, superluminescent diodes, or optical amplifiers applications.

In this dissertation, liquid crystal materials and devices are investigated in meeting the challenges for photonics and communications applications. The first part deals with polymer-stabilized liquid crystal (PSLC) materials and devices. Three polymer-stabilized liquid crystal systems are developed for optical communications. The second part reports the experimental investigation of a novel liquid-crystal-infiltrated photonic crystal fiber (PCF) and explores its applications in fiber-optic communications. The curing temperature is found to have significant effects on the PSLC performance. The electro-optic properties of nematic polymer network liquid crystal (PNLC) at different curing temperatures are investigated experimentally. At high curing temperature, a high contrast, low drive voltage, and small hysteresis PNLC is obtained as a result of the formed large LC micro-domains. With the help of curing temperature effect, it is able to develop PNLC based optical devices with highly desirable performances for optical communications. Such high performance is generally considered difficult to realize for a PNLC. In fact, the poor performance of PNLC, especially at long wavelengths, has hindered it from practical applications for optical communications for a long time. Therefore, the optimal curing temperature effect discovered in this thesis would enable PSLCs for practical industrial applications. Further more, high birefringence LCs play an important role for near infrared photonic devices. The isothiocyanato tolane liquid crystals exhibit a high birefringence and low viscosity. The high birefringence LC dramatically improves the PSLC contrast ratio while keeping a low drive voltage and fast response time. A free-space optical device by PNLC is experimentally demonstrated and its properties characterized. Most LC devices are polarization sensitive. To overcome this drawback, we have investigated the polymer-stabilized cholesteric LC (PSCLC). Combining the curing temperature effect and high birefringence LC, a polarization independent fiber-optical device is realized with over 30 dB attenuation, ~12 Vrms drive voltage and 11/28 milliseconds (rise/decay) response times. A polymer-stabilized twisted nematic LC (PS TNLC) is also proposed as a variable optical attenuator for optical communications. By using the polarization control system, the device is polarization independent. The polymer network in a PS TNLC not only results in a fast response time (0.9/9 milliseconds for rise/decay respectively), but also removes the backflow effect of TNLC which occurs in the high voltage regime.

Optical Coherence Tomography (OCT) is a novel optical imaging technique that has assumed significant importance in bio-medical imaging in the last two decades because it is non-invasive and provides accurate, high resolution images of three dimensional cross-sections of body tissue, exceeding the capabilities of the current predominant imaging technique –ultrasound. In this thesis, high resolution OCT is investigated for in vivo detection of abnormal skin pathology for the early diagnosis of cancer. The technology presented is based on a dynamic focusing microscopic imaging probe conceived for skin imaging and the detection of abnormalities in the epithelium. A novel method for dynamic focusing in the biological sample using liquid crystal (LC) lens technology to obtain three dimensional images with invariant resolution throughout the cross-section and depth of the sample is presented and discussed. Two different skin probe configurations that incorporate dynamic focusing with LC lenses, one involving a reflective microscope objective sub-system, and the other involving an all-refractive immersion microscope objective sub-system are investigated. In order to ensure high resolution imaging, a low coherence broadband source, namely a femtosecond mode-locked Ti: sapphire laser centered at a wavelength of approximately 800nm is used to illuminate the sample. An in-depth description and analysis of the optical design and predicted performance of the two microscope objectives designed for dynamic three dimensional imaging at 5ìm resolution for the chosen broadband spectrum is presented.

The design of high power lasers requires large mode areas to overcome various intensity driven nonlinear effects. Increasing the aperture size within the laser can overcome these effects, but typically result in multi-transverse mode output and reduced beam quality, limiting the brightness of the system. As one possible solution, the angular selectivity of a diffractive optical element is proposed as a spatial filter, allowing for the design of compact high brightness sources not possible with conventional methods of transverse mode selection. This thesis explores the angular selectivity of volume Bragg gratings (VBGs) and their use as spatial transverse mode filters in a laser resonator. Selection of the fundamental mode of a resonator is explored using transmission Bragg gratings (TBGs) as the spatial filter. Simulations and experimental measurements are made for a planar, 1 cm long resonator demonstrating near diffraction limited output (M2 < 1.4) for aperture sizes as large as 2.0 mm. Applications to novel fiber laser designs are explored. Single mode operation of a multi-mode Yb3+ doped ribbon fiber laser (core dimensions of 107.8 ?m x 8.3 ?m) is obtained using a single transmission VBG as the filter in an external cavity resonator. Finally, a novel method of selecting a pure higher order mode to oscillate within the gain medium while simultaneously converting this higher order mode to a fundamental mode at an output coupler is proposed and demonstrated. A multiplexed transmission VBG is used as the mode converting element, selecting the 12th higher order mode for amplifications in an Yb3+ doped ribbon fiber laser, while converting the higher order mode of a laser resonator to a single lobed output beam with diffraction limited divergence.

Bile acids are physiologically important metabolites, which are synthesized in liver as the end products of cholesterol metabolism and then secreted into intestine. They are amphiphilic molecules which play a critical role in the digestion and absorption of fats and fat-soluble vitamins through emulsification. The concentration of bile acids is an indicator for liver function. Individual suffering from liver diseases has a sharp increase in bile acid concentrations. Hence, the concentration level of bile acids has long been used as a biomarker for the early diagnosis of intestinal and liver diseases. Conventional methods of bile acid detection such as chromatography-mass spectrometry and enzymatic reactions are complex and expensive. It is highly desired to have a simple, fast, and low-cost detection of bile acids that is available for self-testing or point-of-care testing. To achieve this goal, we develop a liquid crystal-based biosensor for the detection of bile acids. The sensor platform is based on the anchoring transition of liquid crystals (LCs) at the sodium dodecyl sulfate (SDS)-laden LC/aqueous interface for the detection of bile acids in aqueous solution. The first part of this dissertation focuses on the detection mechanism of bile acids. Our studies show that the displacement of SDS from the LC/aqueous interface by the competitive adsorption of bile acids induces a homeotropic-to-planar anchoring transition of the LC at the interface, providing an optical signature for the simple and rapid detection of bile acids. The adsorption of bile acids on the interface was found to follow Langmuir-Freundlich isotherm. The adsorption kinetics of different bile acids is compared. We find that both the number and position of hydroxyl groups of bile acids affect their adsorption kinetics. The different optical patterns of LC films formed by the adsorption of bile acids are also discussed. The second part of this dissertation studies the effect of solution conditions, surfactants, and liquid crystals on the detection limit of the LC-based biosensor for bile acids. Low pH and high ionic strength in the aqueous solution can reduce the electrostatic interaction between SDS and bile acids, which leads to a decreased detection limit. Surfactants with smaller headgroup and lower packing density also help to reduce the detection limit. To further reduce the detection limit, we investigate the effect of LC structures and find that LCs with a shorter chain length give lower detection limits. Also, by substituting a phenyl ring with a cyclohexane ring, we find that the detection limit is further reduced due to the decrease of the interaction between the phenyl rings of LCs. By mixing different LCs together, the detection limit can be linearly tuned from 160 μM to 1.5 μM, which is comparable to the traditional methods. But the LC-based biosensors have much simpler design and manufacture process. The third part of this dissertation is to apply this LC-based biosensor to the detection of urinary bile acids. We test the influence of several potential interfering species such as urea, creatinine, uric acid and ascorbic acid by conducting experiments in synthetic urine. By adjusting the concentration of SDS, we are able to eliminate the impact of those interfering species, and demonstrate that the LC-based biosensors can selectively detect urinary bile acids in human urine, suggesting its potential for screening liver dysfunctions. The final part of this dissertation is to investigate the application of LC-based biosensors in detecting the lipolysis process by porcine pancreatic lipase (PPL). It has been a long-standing argument over the role of bile salts on the activity of PPL. Thus, we study the time course of the hydrolysis of phospholipid L-dipalmitoylphosphatidylcholine (L-DPPC) by PPL at LC/aqueous interface. The hydrolysis of L-DPPC leads to a homeotropic-to-tilted anchoring transition of the LC at the interface, which allows the hydrolysis process to be monitored by a polarizing optical microscope. The microscopy image analysis reveals a lag-burst kinetics where a lag phase is followed by a burst phase. The effect of bile acids on these two phases is studied. We find that the activity of PPL both in the presence and absence of colipase can be improved by increasing the concentration of bile acids. The improvement becomes more distinct in the presence of colipase.