This research proposes a novel polymer-based optical waveguide made with Polydimethylsiloxane (PDMS) for optical detection applications. Alternative to other fiber-based sensor, the proposed optical sensor uses PDMS waveguide as the main sensing component. PDMS has excellent optical properties which is essential for bio-photonic detection, including highly optical transparency, good flexibility and high bio-compatibility. Uncured PDMS polymer is cast in a Teflon tubing to form the PDMS rod. Since the reflective index of PDMS is as high as 1.43, that the bare PDMS can be an optical waveguide while the reflective index of the surrounding media is smaller than 1.43. The cast PDMS waveguide is then connect with plastic optical fibers to form the proposed optical waveguide system. In order to improve the optical performance of the PDMS waveguide, a surface coating process is used to reduce the surface roughness of the PDMS waveguide. The measured insertion loss with and without performing the surface coating procedure is 1.14 and 1.71dB/cm, respectively. Once the PDMS waveguide is formed, Au nanoparticles (Au-Nps) were coated on the PDMS surface with the assistance of a positive charge polymer of PDDA to form an optical waveguide capable of localized SPR detection. In addition, an atmospheric plasma treating process is used to enhance the coating ratio and speed of Au-Nps. UV-VIS spectrum and the SEM observation of the Au-particle coated PDMS waveguide confirm that the plasma treatment process significantly improves the coating results of Au-Nps. Liquid samples with different refractive index were used to demonstrate the LSPR sensing ability of the fabricated optical waveguide. The label free DNA detection was demonstrated by the system. The thiolated single strand DNA was modify on the PDMS optical waveguide as a DNA probe and bound with target DNA by DNA hybridization. The detection limit is as low as 10 pM. This research provides a simple and fast fabrication method to fabricate waveguide-based LSPR sensors.

Many phenomena associated with nonlinear optics are produced by the light-matter interaction in liquid crystals. Nematic liquid crystals possess the properties of the birefringence and that refractive indexes of nematic liquid crystal vary with temperature. As a light beam propagates in liquid crystals, the light beam experiences changes of refractive indexes because the optical field reorientates molecules or the optical intensity changes the temperature of liquid crystal. Then, some interesting phenomena of optical nonlinearity produce in liquid crystals. This study investigates mainly the nonlinear behaviors in nematic liquid crystals. By etching ITO glasses to control distribution of electric field, we discuss applications in photo-electric field. These works are described as follows: First, a low voltage was applied to a planar nematic liquid crystal cell; the director field can be reoriented using a low intensity. Then, the self-focusing effect produces due to a variation of refractive indexes. The light beam in nematic liquid crystal forms a spatial soliton by producing the effect of the self-focusing to balance the diffraction. Additionally, we study the interaction between solitons. One soliton creates a potential well of refractive index, anther one will be attracted in the potential well. As the separated distance between two solitons and the pumping angle are appropriate, two solitons propagate in the form of spiral. Second, we study the behavior of light in a periodic refractive index medium. The director field of the nematic liquid crystal (NLC) is reorientated in a grating¡Vlike indium-tin-oxide electrode cell by applying a controllable-voltage. The variation of refractive index with voltage varied 0v to 10v was observed by a conoscopic method. Numerical simulations have reproduced the main features of the gradient distribution of refractive index in the waveguide. Several phenomena of a polarized laser beam that propagated in the waveguide with different incident angles and positions have observed by a CCD camera, including solitons, undulate beam, the total internal reflection and beam coupling. Third, at the temperature close to nematic-isotropic phase transition temperature, the variation of refractive index in the liquid crystal becomes obvious to the change of temperature. And, a laser beam can easily reorientate molecules. We changed beam intensity in liquid crystal cell, different nonlinear phenomena were observed. Besides, A combined microscopic and conoscopic technique was used in experiments as a convenient way to analyze the optical nonlinearity that is associated with the molecular configuration of nematic liquid crystal.

The current techniques and methodologies used in the field of material characterization are well documented and widely accepted as reliable and accurate. However, literature describing these techniques focuses on the algorithms used during material characterization; few studies have reposted on the design of, and the selection criteria for, the test fixtures themselves. This research focuses on the measurement cell with the goal of determining the sensitivity of the measurement cell to the addition of a thin film material. Microstrip and coplanar waveguide were chosen for the analysis, which included three configurations of each transmission line geometry: a reference with no additional thin film material, one with the thin film on top of the conductors and one with the thin film beneath the conductors but on top of the transmission line substrate. The scattering parameters for the reference cell are compared to the scattering parameters of the test cell with the thin film material. The additional thin film material changes the effective dielectric constant of the reference cell; this change is evident in the phase and amplitude of S21. The optimum measurement cell is the one that experiences the greatest change to the effective dielectric constant with the addition of the thin film. Thus the greatest difference in S21 between the reference cell and the test cell is indicative of the reference cell's sensitivity. The figure of merit (FOM) to determine the structure's sensitivity is the integration over frequency of the magnitude of the vector difference of S21. The analysis shows that the double-layered CPW measurement cell was the most sensitive. Once the optimum structure was determined an analysis of the sensitivity of the FOM to changes in the physical and electrical properties of the reference structure was conducted. The most important factors in the selection of the reference cell as evident by the FOM's sensitivity are the substrate to thin film dielectric constant ratio and the CPW conductor aspect ratio to the thin film thickness. In particular, thinner films require a smaller conductor gap while wider gaps are preferable for thicker films. Measurement of four different CPW geometries, each covered in a 300 micron Polydimethylsiloxane thick film, validate the analysis process. The measurement cells differ in the conductor aspect ratio. The values of the measured FOMs trend as predicted by the simulation analysis.

A novel capture matrix utilizing human serum albumin (HSA) and streptococcal Protein G (PG), which possesses an albumin binding domain (ABD), was used to immobilize antibodies for improved bacterial capture efficiency in immunoassays. Enzyme linked immunosorbent assays (ELISA) were used to characterize and optimize a specific protocol for the HSA-PG capture matrix; which revealed several critical factors that should be considered. The Fc binding domain, on PG, should have high affinity for the species of capture antibody used in the assay. Goat and rabbit species antibodies bound strongly to the Fc binding domain of PG. Displacement of the capture antibody, by the detector antibody should be avoided to reduce background signals. The Fc binding domain on PG should have equivalent or lower affinity for the detector antibody, when compared to the capture antibody. Goat species antibody, used as a detector antibody, did not displace the same-species capture antibody. ELISA analysis showed detection of Escherichia coli O157:H7 cells at 1.0 x 104 CFU/ml using HSA-PG and goat antibody raised against Escherichia coli O157:H7; unlabeled antibody was used for capture while HRP labeled antibody was used for detection. Studies were performed on an automated fiber optic biosensor, RAPTOR, which was used for the rapid detection of pathogens. Biosensor assays showed detection of E. coli O157:H7 at 1.0 x 10³ CFU/ml in PBS and 1.0 x 105 CFU/ml in homogenized ground beef supernatant. Capture efficiency of the HSA-PG capture matrix was studied using the biosensor and GFP-E. coli O157:H7. The amount of cells captured was less than one percent of the sample concentration. This limit of detection and capture efficiency was comparable to the streptavidin-biotin capture matrix.

Waveguides are desirable components for energy transmission throughout the electromagnetic spectrum. This thesis experimentally examines a thick slot waveguide for THz guiding and field enhancement. The waveguide is machined from planar copper sheets using the novel technique of femtosecond laser micromachining. In-plane photoconductive THz coupling to a thick slot waveguide is demonstrated using Discontinuous Galerkin Time Domain (DGTD) simulation. The results reveal positive implications for broadband low-loss/dispersion transmission lines up to 1.5 THz. / Graduate / 0544 / 0607 / 0756 / levismith3@hotmail.com

The design and use of metamaterials have shown exciting applications in electrical engineering, physics, optics, and other science fields that are expanding our physical understanding and leading to unprecedented performance of many standard devices such as antennas, microwave circuits, and sensors. The manufacturing of metamaterials, while ingenious, has typically been exotic and depended on the inclusion of sub-wavelength particles in a host medium to tailor the effective characteristics of a material. This work verifies a much more simple approach to realizing a kind of metamaterial, the epsilon-near-zero (ENZ) metamaterial. The intriguing aspect of this metamaterial is that while it is simple to realize, it is a novel approach to many practical applications such as the tunneling energy through highly discontinuous bends and abruptions, cloaking of sensors, miniaturization of microwave components, and design of highly directive antennas. Further, the physics and mathematical formulation of these ENZ materials is both intriguing and counterintuitive. / text

This dissertation covers a broad range of research topics all towards the ultimate goal establishing of a novel type of biosensor in which the biocompatible membrane structure reconstituted with functional transmembrane proteins is utilized as the sensing element. It focuses on 1) examining the activity of a model transmembrane protein, bovine rhodopsin (Rho) when reconstituted into stabilized lipid membranes and 2) the instrumentation of a novel type of optical spectroscopy, plasmon waveguide resonance (PWR), which is a surface sensitive technique and its application in sensing biological events.Lipid membrane play crucial roles in cell function. Their biophysical properties affect the activity of a large amount of transmembrane receptors. They are great candidates for biosensing/ biomedical coating. However, the intrinsic instability of natural or fluid membranes prevents them to be used in a device. Studies have been done to show indirect evidence that the activity of Rho maybe maintained in polymerized membrane composed of bis-SorbPC lipids. The activity of Rho reconstituted into vesicular membranes comprised of various lipids was studied by a more direct technique, UV-Vis. It was found Rho activity was maintained to 66% of that in natural Egg PC lipid in the mixture of Egg PC:(poly)bis-SorbPC (1:1 mol:mol) as opposed to minimal values in 100 % (poly)lipids.A new type of spectral PWR was developed. The working concept, technical characterization and comparisons with similar techniques were discussed and compared in this work. A modified version of angular PWR in which lipid bilayers were formed by vesicle fusion was also developed. This method excludes possible effects from a high boiling point organic solvent on either the lipid bilayer itself or the membrane proteins associated with it. A calculating program NphaseAll for PWR was developed to do predictions of waveguide properties can be made to provide guidance for waveguide design. Theoretical calculations were done for PWR and experimental results were compared with the theoretical predictions.PWR was used to detect the formation of a biological lipid membrane, the association of alpha synuclein with membranes and the binding activity of human melanarcortin to its ligands in fluid and polymerized/dried membranes.

Integrated optics present a potentially low cost and higher performance alternative to electronics in optical communication systems. Surface plasmon waveguides (SPWGs) offer a new approach for manipulating light in integrated optical chips. SPWGs provide several advantages over dielectric waveguides. In this study, a fabrication process for SPWGs is developed. SPWGs are fabricated with various lengths and bend radii to allow for study of absorption and bending losses in the waveguides at telecommunications wavelengths (~1550nm). Finite-element method models of straight, bent, and optically coupled waveguides are developed and analyzed.

The study and applications of surface plasmon polaritons (SP) – also known as plasmonics – has attracted the interest of a wide range of researchers in various fields such as biology, physics, and engineering. Unfortunately, the large propagation losses of the SP severely limit the usefulness of plasmonics for many practical applications. In this dissertation a new wave guiding mechanism is proposed in order to address the large propagation losses of the plasmonic guides. Possible applications of this guiding scheme are also investigated. The proposed hybrid plasmonic waveguide (HPWG) consists of a metal layer separated from a high index slab by a low index spacer. A detailed analysis is carried out to clarify the wave guiding mechanism and it is established that the mode guided by the HPWG results from the coupling of a SP mode and a dielectric waveguide mode. A two dimensional HPWG is proposed and the effects of various parameters on the HPWG performance are analyzed in detail. This structure offers the possibility of integrating plasmonic devices on a silicon platform. The proposed waveguide supports two different modes: a hybrid TM mode and a conventional TE mode. The hybrid TM mode is concentrated in the low index layer, whereas the conventional TE mode is concentrated in the high index region. This polarization diversity is used to design a TM- and a TE-pass polarizer and a polarization independent coupler on a silicon-on-insulator (SOI) platform. Moreover, the performance of a HPWG bend is investigated and is compared with plasmonic waveguide bends. The proposed devices are very compact and outperform previously reported designs. The application of HPWG for biosensing is also explored. By utilizing the polarization diversity, the HPWG biosensor can overcome some of the limitations of plasmonic sensors. For example, unlike plasmonic sensors, the HPWG biosensor can remove the interfering bulk and surface effects.

The limit of current technology for mobile base station filters is the multimode filter, in which each cavity supports two (or possibly three) independent degenerate resonances. Shielded dielectric resonators with a rectangular cross-section are useful in this application. In the design of these filters, manufacturers are using software packages employing finite element or finite difference time domain techniques. However, for sufficient accuracy these procedures require large numbers of points or elements and can be very time consuming. Over the last decade research using the mode matching technique has been used to solve this kind of difficulty for various types of filter design and waveguide problems. In this thesis a mode matching method and computer program is developed to calculate the propagation coefficients and field patterns of the modes in a shielded rectangular dielectric rod waveguide. Propagating, complex, evanescent and backward wave modes are included and the work shows the presence of a dominant mode, and other fundamental modes, not previously identified. The effect of the shield proximity on the propagation characteristics and mode spectrum is investigated, together with the limitations on the accuracy of the mode matching method. In addition, the fields within the shielded rectangular dielectric rod waveguide, are used to calculate the attenuation coefficient of the dominant and fundamental modes. The influence on the attenuation coefficient of the proximity of the shield to the rod is also evaluated for these modes and limitations on accuracy are discussed. The calculated numerical results for the propagation and attenuation coefficient values are verified by measurement. The propagation coefficients results are typically within 2% of those measured. Verification of the attenuation coefficient results is achieved by comparing calculated and measured Q at the resonant frequencies of a number of shielded rectangular dielectric rod resonators. The difference between calculated and measured Q values is on average less than 4%. In the absence of a full solution of the shielded rectangular dielectric rod resonator, these results provide useful design information for this structure. In addition, the work reported in this thesis provides a basis for a full electromagnetic solution of this type of resonator. This would encompass the cubic dielectric resonator in a cubical cavity.