DNA detection technology has developed rapidly due to its extensive application in clinical diagnostics, bioengineering, environmental monitoring, and food science areas. Currently developed methods such as surface Plasmon resonance (SPR) methods, fluorescent dye labeled methods and electrochemical methods, usually have the problems of bulky size, high equipment cost and time-consuming algorithms, so limiting their application for in vivo detection. In this work, an intrinsic Fabry-Perot interferometric (IFPI) based DNA sensor is presented with the intrinsic advantages of small size, low cost and corrosion-tolerance. This sensor has experimentally demonstrated its high sensitivity and selectivity. In theory, DNA detection is realized by interrogating the sensor's optical cavity length variation resulting from hybridization event. First, a microgap structure based IFPI sensor is fabricated with simple etching and splicing technology. Subsequently, considering the sugar phosphate backbone of DNA, layer-by-layer electrostatic self-assembly technique is adopted to attach the single strand capture DNA to the sensor endface. When the target DNA strand binds to the single-stranded DNA successfully, the optical cavity length of sensor will be increased. Finally, by demodulating the sensor spectrum, DNA hybridization event can be judged qualitatively. This sensor can realize DNA detection without attached label, which save the experiment expense and time. Also the hybridization detection is finished within a few minutes. This quick response feature makes it more attractive in diagnose application. Since the sensitivity and specificity are the most widely used statistics to describe a diagnostic test, so these characteristics are used to evaluate this biosensor. Experimental results demonstrate that this sensor has a sensitivity of 6nmol/ml and can identify a 2 bp mismatch. Since this sensor is optical fiber based, it has robust structure and small size ( 125μm ). If extra etching process is applied to the sensor, the size can be further reduced. This promises the sensor potential application of in-cell detection. Further investigation can be focused on the nanofabrication of this DNA sensor, and this is very meaningful topic not only for diagnostic test but also in many other applications such as food industry, environment monitoring. / Master of Science

Sapphire fiber based temperature sensors are exceptional in their ability to operate at temperatures above 1000C and as high as 1800C. Sapphire fiber technology is emerging and the fiber is available commercially. Sapphire fiber has a high loss, is highly multi-mode and does not have a solid cladding, but it is nonetheless very useful in high temperature applications. Of the available interferometer configurations, Fabry-Perot interferometers are distinguished in their high accuracy and great isolation from sources of error. In this thesis, improvements are reported to an existing design to enhance its reliability and to reduce possible modes of failure. The existing high temperature sensor design has shown a lot of potential in the past by continuously measuring the temperature in a coal gasifier for 7 months, but its true potential has not yet been realized. The goal of this work and the work of many others is to extend the working life and reliability of high-temperature optical sapphire temperature sensors in harsh environments by exploring a solid cladding for sapphire fiber, improved fringe visibility sapphire wafers and a new sensor design. This project is supported by the National Energy and Technology Laboratory of the Department of Energy. / Master of Science

The motivation of this research is to meet the growing demand for the measurand high-resolution, high-spatial resolution, attenuation insensitive and low-cost quasi-distributed temperature and strain sensors that can reliably work under harsh environment or in extended structures. There are two main drives for distributed fiber sensor research. The first is to lower cost-per-sensor so that the fiber sensors may become price-competitive against electrical sensors in order to gain widespread acceptance. The second is to obtain spatial distribution of the measurand. This dissertation presents detailed research on the design, modeling, analysis, system implementation, sensor fabrication, performance evaluation, sensor field test and noise analysis of a quasi-distributed intrinsic Fabry-Perot interferometric (IFPI) fiber sensor suitable for temperature and strain measurement. For the first time to our knowledge, an IFPI sensor using a different type of fiber spliced in between two single-mode fibers is proposed and tested. The proposed sensor has high measurement accuracy, excellent repeatability, a large working range and a low insertion-loss. It requests no annealing after the sensor is made, and the sensor is calibration-free. The sensor fabrication is low-cost and has a high yield rate. The goal for this research is to bring this sensor to a level where it will become commercially viable for quasi-distributed sensing applications. / Ph. D.

This dissertation proposes a miniaturized optical fiber based sensor system for the measurement of 3-dimensional vector magnetic fields. The operation of the sensor system is based on the detection of magnetostrictive dimensional changes in the sensor gage using a modified extrinsic Fabry-Perot Interferometer configuration. Because of the magnetostrictive reflector the gap length depends on the magnetic fields applied to the sensor. Since the diameter of the magnetostrictive sensor gage is 125 micrometer which is the same as that of the input/output fiber, the sensor is simply constructed by inserting the sensor gage and the input/output fiber into a small glass tube. The glass tube serves as both an aligner for the sensor gage and input/out fiber, and a passive temperature compensator. In addition, it also enhances the mechanical strength and compactness of the sensor. This sensor design shows 98 percent suppression of the thermally induced sensor output changes. The linear output of the sensor system is enhanced by transverse field annealing which increases magnetostrictive induction in the ferromagnetic sensor gage material and controls the sensor gage geometry. A 5-times increase in sensor sensitivity is obtained with the transverse field annealing and the use of a new magnetostrictive material. A modified sensor gage endface demonstrates 92 percent of fringe visibility, which further improves the performance of the interferometer. The signal fading in the interferometric sensors at the peak or bottom of a fringe is reduced by using a quadrature signal demodulation method. The system has been shown to have a resolution better than 100 nT over a measurement range from 100 to 40,000 nT. This research is supported financially by the Phillips Laboratory of the U.S. Air Force. / Ph. D.

In this report, detailed and systematic theoretical and experimental study of low-finesse extrinsic Fabry-Perot interferometric (EFPI) fiber optic sensors together with their signal processing methods for white-light systems are presented. The work aims to provide a better understanding of the operational principle of EFPI fiber optic sensors, and is useful and important in the design, optimization, fabrication and application of single mode fiber(SMF) EFPI (SMF-EFPI) and multimode fiber (MMF) EFPI (MMF-EFPI) sensor systems. The cases for SMF-EFPI and MMF-EFPI sensors are separately considered. In the analysis of SMF-EFPI sensors, the light transmitted in the fiber is approximated by a Gaussian beam and the obtained spectral transfer function of the sensors includes an extra phase shift due to the light coupling in the fiber end-face. This extra phase shift has not been addressed by previous researchers and is of great importance for high accuracy and high resolution signal processing of white-light SMF-EFPI systems. Fringe visibility degradation due to gap-length increase and sensor imperfections is studied. The results indicate that the fringe visibility of a SMF-EFPI sensor is relatively insensitive to the gap-length change and sensor imperfections. Based on the spectral fringe pattern predicated by the theory of SMF-EFPI sensors, a novel curve fitting signal processing method (Type 1 curve-fitting method) is presented for white-light SMF-EFPI sensor systems. Other spectral domain signal processing methods including the wavelength-tracking, the Type 2-3 curve fitting, Fourier transform, and two-point interrogation methods are reviewed and systematically analyzed. Experiments were carried out to compare the performances of these signal processing methods. The results have shown that the Type 1 curve fitting method achieves high accuracy, high resolution, large dynamic range, and the capability of absolute measurement at the same time, while others either have less resolution, or are not capable of absolute measurement. Very different from SMF-EFPI sensors, MMF-EFPI sensors with high fringe visibility usually are more difficult to obtain in practice because the fringe visibility of a MMF-EFPI sensor is much more sensitive to gap-length change and sensor head imperfections. %Previously, only geometric-optics are available to analyze MMF-EFPI sensors which approximate the light in MMF as rays propagating in different directions. Geometric-optics theory has fundenmental limitations because it is approximate and only valid for limited conditions. Moreover, geometric-optics theory is not capable of poviding the exact fringe pattern which is important in the signal processing of white light MMF-EFPI sensor systems. In this report, Previous mathematical models for MMF-EFPI sensors are all based on geometric optics; therefore their applications have many limitations. In this report, a modal theory is developed that can be used in any situations and is more accurate. The mathematical description of the spectral fringes of MMF-EFPI sensors is obtained by the modal theory. Effect on the fringe visibility of system parameters, including the sensor head structure, the fiber parameters, and the mode power distribution in the MMF of the MMF-EFPI sensors, is analyzed. Experiments were carried out to validate the theory. Fundamental mechanism that causes the degradation of the fringe visibility in MMF-EFPI sensors are revealed. It is shown that, in some situations at which the fringe visibility is important and difficult to achieve, a simple method of launching the light into the MMF-EFPI sensor system from the output of a SMF could be used to improve the fringe visibility and to ease the fabrication difficulties of MMF-EFPI sensors. Signal processing methods that are well-understood in white-light SMF-EFPI sensor systems may exhibit new aspects when they are applied to white-light MMF-EFPI sensor systems. This report reveals that the variations of mode power distribution (MPD) in the MMF could cause phase variations of the spectral fringes from a MMF-EFPI sensor and introduce measurement errors for a signal processing method in which the phase information is used. This MPD effect on the wavelength-tracking method in white-light MMF-EFPI sensors is theoretically analyzed. The fringe phases changes caused by MPD variations were experimentally observed and thus the MFD effect is validated. / Ph. D.

Optical fiber sensor multiplexing reduces cost per sensor by designing a system that minimizes the expensive system components (sources, spectrometers, etc.) needed for a set number of sensors. The market for multiplexed optical sensors is growing as fiberoptic sensors are finding application in automated factories, mines, offshore platforms, air, sea, land, and space vehicles, energy distribution systems, medical patient surveillance systems, etc. Optical path length multiplexing (OPLM) is a modification to traditional white-light interferometry techniques to multiplex extrinsic Fabry-Perot interferometers and optical path length two-mode sensors. Additionally, OPLM techniques can be used to design an optical fiber sensor to detect pressure/force/acceleration and temperature simultaneously at a single point. While power losses and operating range restrictions limit the broadscale applicability of OPLM, it provides a way to easily double or quadruple the number of sensors by modifying the demodulation algorithm. The exciting aspect of OPLM is that no additional hardware is needed to multiplex a few sensors. In this way OPLM works with conventional technology and algorithms to drastically increase their efficiency. [1] / Master of Science

Miniature pressure sensors which can endure harsh environments are a highly sought after goal in industrial, medical and research fields. Microelectromechanical systems (MEMS) are the current methods to fabricate such small sensors. However, they suffer from low sensitivity and poor mechanical properties. To fulfill the need for robust and reliable miniature pressure sensors that can operate under high temperatures, a novel type of optical fiber tip sensor only 125μm in diameter is presented in this thesis. The essential element is a piece of hollow fiber which connects the fiber end and a diaphragm to form a Fabry-Pérot cavity. The all-fused-silica structure fabricated directly on a fiber tip has little temperature dependence and can function very well with high resolution and accuracy at temperatures up to 600 °C. In addition to its miniature size, its advantages include superior mechanical properties, biocompatibility, immunity to electromagnetic interference, disposability and cost-effective fabrication. The principle of operation, design analysis, fabrication implementation and performance evaluation of the sensor are discussed in detail in the following chapters. / Master of Science

O objetivo do presente trabalho foi o estudo e análise da resposta óptica de dispositivos de cristal fotônico uni-dimensional (1D) fabricados através do uso da tecnologia de silício poroso. Os resultados obtidos neste trabalho apresentam contribuições significativas no desenvolvimento de uma tecnologia para a fabricação de dispositivos ópticos em silício. As principais contribuições deste trabalho estão direcionadas ao aprimoramento dos processos de fabricação de cristais fotônicos 1D e processos de tratamento térmico. Os resultados da análise estrutural através de microscopia óptica de varredura (MEV) e da resposta óptica (refletância ou absorbância) mostraram que dispositivos de cristal fotônico fabricados em soluções altamente diluídas de HF apresentam melhor desempenho, tendo sido otimizado o processo de fabricação utilizando-se uma célula de duplo compartimento (célula dupla). A otimização da resposta óptica dos dispositivos foi atribuída ao efeito de minimização das rugosidades de interface e minimização de efeitos de anisotropia na taxa de corrosão durante o processo de anodização eletroquímica. O processo eletroquímico utilizado para a fabricação de cristais fotônicos 1D apresentou limitação quanto ao número máximo de camadas, sendo observado que dispositivos com número de camadas acima de 60 apresentavam degradação das suas camadas superficiais, comprometendo a resposta óptica do dispositivo. Este resultado foi atribuído a efeitos de diluição química das camadas expostas à solução por longos períodos de processo. Os dispositivos fotônicos 1D mostraram-se sensíveis a processos de recozimento térmico, deslocando suas bandas fotônicas proibidas para regiões de menor comprimento de onda devido à mudança do índice de refração das camadas e aos efeitos de expansão e compressão das camadas constitutivas do dispositivo. Os dispositivos de micocavidade Fabry-Perot mostraram-se mais sensíveis aos processos de recozimento térmico. Os resultados obtidos no presente trabalho vislumbram grandes possibilidades de aplicação dos cristais fotônicos de PS na fabricação de dispositivos ópticos na tecnologia de silício como filtros, lentes, cavidades ressonantes, guias de ondas, grades de difração e dispositivos sensores. / The aim of the present work was to study and analyze the optical response of one- dimensional (1D) photonic crystal devices obtained by using the porous silicon technology. The experimental results obtained from this work showed the significant contribution to the development of a technological process for optical device fabrication in the silicon substrate. The most important contributions of the work are pointed out to improve the electrochemical process for device fabrication and thermal annealing process in order to improve the optical response of the devices. The results obtained from Scanning electronic microscopy (SEM) and from the optical response of the devices, showed that devices fabricated in the double cell and diluted HF solution improved their optical response due to minimization of the anisotropy of corrosion rate and decreasing of the surface roughness between layers. The electrochemical process used for device fabrication showed the existence of limitation on the numbers of layers because of the existence of chemical dissolution effect that became important for long time process. The 1D photonic crystal devices in PS technology showed high sensibility to thermal annealing process, due to the refraction index change after thermal annealing the photonic band gap position shift down to low wavelength region. The Fabry-Perot devices showed higher sensibility to thermal annealing process improving their optical response after annealing process. The results obtained from the present work showed that the PS 1D photonic device could be applied to optical devices fabrication in silicon technology such as optical filters, lenses, resonant cavities, wave-guide devices, diffraction grade and optical sensor device.

Cette thèse a pour but l’étude théorique de métamatériaux métalliques empilés. Ces structures sont actuellement proposées pour améliorer et élargir les fonctionnalités des métamatériaux métalliques. Nous portons un intérêt particulier aux propriétés de polarisation de ces structures métalliques empilées.En premier lieu, nous précisons le type de métamatériaux que nous étudions et nous présentons la méthode modale qui nous permet de décrire les propriétés électromagnétiques de la structure. A l’aide d’un Formalisme de Jones Etendu (FJE), développé récemment dans notre équipe, nous faisons ressortir les principales propriétés de polarisation linéaire de ces métamatériaux métallique.En alliant le FJE à l’algorithme de propagation de la matrice S, nous étudions un empilement de deux métamatériaux vus comme un montage polariseur-analyseur. Nous établissons ensuite une expression de la transmission de la structure: la loi de Malus étendue. Cela nous permet notamment de démontrer les résonances de type Fabry-Perot qui ont lieu entre les métamatériaux.Pour des structures plus conséquentes, nous montrons qu’il est possible de réaliser une rotation de la polarisation, à très faible perte et spectralement agile, grâce aux résonances de type Fabry-Perot.Fondamentalement, nous révélons une nouvelle façon d’exciter des résonances Fano qui sont induites par les propriétés de polarisation des métamatériaux. Ces résonances peuvent être utilisées pour des applications de capteur ou de filtrage. De plus, ces résonances Fano induites par la polarisation ouvrent de nouvelles possibilités d’applications pour les empilement de métamatériaux métalliques. / This PhD thesis deals with the theoretical study of stacked metallic metamaterials. Such structures are currently investigated to extend the functionalities offered by single metallic metamaterials. We especially focus on the specific polarization properties of the stacked metallic metamaterials.We first present the type of metamaterial that we consider, and we describe the modal method that is used to model its electromagnetic properties. We outline the linear polarization properties characterizing the metamaterial thanks to an Extended Jones Formalism (EJF) recently developed by our team.In combination with the EJF, we apply the S-matrix algorithm to the study of a stack of two metallic metamaterials in a polarizer-analyzer configuration. We derive an analytical expression for the transmission response of the stacked structure: the Extended Malus Law. Mainly, it highlights the Fabry-Perot-like resonances located between the metamaterials.Using larger stacked structures, we demonstrate that spectrally tunable and low loss polarization rotation can be achieved owing to these Fabry-Perot-like resonances.In essence, we reveal a new way of realizing Fano resonances which are induced by the specific polarization properties of the metamaterials. We show that such resonances can be engineered for sensing or filtering applications. Moreover, the polarization-induced Fano resonances expand the possibilities of stacked metallic metamaterials.

O objetivo do presente trabalho foi o estudo e análise da resposta óptica de dispositivos de cristal fotônico uni-dimensional (1D) fabricados através do uso da tecnologia de silício poroso. Os resultados obtidos neste trabalho apresentam contribuições significativas no desenvolvimento de uma tecnologia para a fabricação de dispositivos ópticos em silício. As principais contribuições deste trabalho estão direcionadas ao aprimoramento dos processos de fabricação de cristais fotônicos 1D e processos de tratamento térmico. Os resultados da análise estrutural através de microscopia óptica de varredura (MEV) e da resposta óptica (refletância ou absorbância) mostraram que dispositivos de cristal fotônico fabricados em soluções altamente diluídas de HF apresentam melhor desempenho, tendo sido otimizado o processo de fabricação utilizando-se uma célula de duplo compartimento (célula dupla). A otimização da resposta óptica dos dispositivos foi atribuída ao efeito de minimização das rugosidades de interface e minimização de efeitos de anisotropia na taxa de corrosão durante o processo de anodização eletroquímica. O processo eletroquímico utilizado para a fabricação de cristais fotônicos 1D apresentou limitação quanto ao número máximo de camadas, sendo observado que dispositivos com número de camadas acima de 60 apresentavam degradação das suas camadas superficiais, comprometendo a resposta óptica do dispositivo. Este resultado foi atribuído a efeitos de diluição química das camadas expostas à solução por longos períodos de processo. Os dispositivos fotônicos 1D mostraram-se sensíveis a processos de recozimento térmico, deslocando suas bandas fotônicas proibidas para regiões de menor comprimento de onda devido à mudança do índice de refração das camadas e aos efeitos de expansão e compressão das camadas constitutivas do dispositivo. Os dispositivos de micocavidade Fabry-Perot mostraram-se mais sensíveis aos processos de recozimento térmico. Os resultados obtidos no presente trabalho vislumbram grandes possibilidades de aplicação dos cristais fotônicos de PS na fabricação de dispositivos ópticos na tecnologia de silício como filtros, lentes, cavidades ressonantes, guias de ondas, grades de difração e dispositivos sensores. / The aim of the present work was to study and analyze the optical response of one- dimensional (1D) photonic crystal devices obtained by using the porous silicon technology. The experimental results obtained from this work showed the significant contribution to the development of a technological process for optical device fabrication in the silicon substrate. The most important contributions of the work are pointed out to improve the electrochemical process for device fabrication and thermal annealing process in order to improve the optical response of the devices. The results obtained from Scanning electronic microscopy (SEM) and from the optical response of the devices, showed that devices fabricated in the double cell and diluted HF solution improved their optical response due to minimization of the anisotropy of corrosion rate and decreasing of the surface roughness between layers. The electrochemical process used for device fabrication showed the existence of limitation on the numbers of layers because of the existence of chemical dissolution effect that became important for long time process. The 1D photonic crystal devices in PS technology showed high sensibility to thermal annealing process, due to the refraction index change after thermal annealing the photonic band gap position shift down to low wavelength region. The Fabry-Perot devices showed higher sensibility to thermal annealing process improving their optical response after annealing process. The results obtained from the present work showed that the PS 1D photonic device could be applied to optical devices fabrication in silicon technology such as optical filters, lenses, resonant cavities, wave-guide devices, diffraction grade and optical sensor device.