This thesis presents a detailed study of complementary metal-oxide-semiconductor (CMOS) compatible silicon waveguide and ring resonator technologies. The project specifically focuses on a range of slotted ring resonator configurations comprised of rib-style waveguides. Single ring resonators and Mach-Zehnder interferometers with double rings and central drop port channels have been successfully characterised. Thermal tuning techniques using on-chip heaters were used to determine their sensitivities. A stringent signal cleaning method was also developed to remove systematic background noise. Analysing the transmission signals produced by the Mach-Zehnder interferometers with double rings and a central drop port, it was revealed that coupled resonator induced transparency (CRIT) is created along with Fano-type resonances when the resonant peaks of the two ring resonators are tuned to overlap. The tuning of these features revealed a 2.7 and 2-fold improvement in device sensitivity. A 3x3 transfer matrix model has been developed to simulate the behaviour of light travelling through this configuration. Modelling suggests that effective refractive index and relative phase are the key factors in determining this behaviour. When tuned to close proximity, a resonant ‘superstate’ is achieved in which a modified model is required. Applying the single ring resonators to biosensing applications, basic refractive index testing and a glucose sensing calibration were conducted. A polydimethylsiloxane (PDMS) based microfluidics system was also developed to improve the reliability of sensing and enable automation. Using silicon nitride ring resonators with inkjet-printed upconverting nanoparticles, it was found that the evanescent field of the rings could stimulate the upconversion process revealing visible spectrum emission around the rings.

A simple, but innovative microfluidic Lab-on-a-chip (LOC) device which is broadly applicable in point of care diagnostics of biological pathogens was designed, fabricated and assembled utilising explicit microfluidic techniques. The purpose of this design was to develop a cartridge with the capability to perform multiplex DNA amplification reactions on a single device. To achieve this outcome, conventional laboratory protocols for sample preparation; involving DNA extraction, purification and elution were miniaturized to suit this lab-on-a-chip device of 75mm X 50mm cross-sectional area. The extraction process was carried out in a uniquely designed microchamber embedded with chitosan membrane that binds DNA at pH 5.0 and elutes when a different solution at pH 9.0 flows through. Likewise, purification protocol that occurs in the designed waste reservoir is very significant in biomedical field because it is concerned with waste treatment and cartridge disposability, was performed with a super absorbent powder that converts liquid to a gel like substance. This powder is known as sodium polyacrylate, which is also they treated with anti-bacterial chemicals to prevent environmental contamination. Furthermore, this process also employed the use of a passive valve for a precise fluid handling operation involving flow regulation from extraction to waste reservoir. In order to achieve the intended multiplexing function a multiplexer was created to distribute flow simultaneously through a bifurcated network of channels connected to six similar amplification microchambers. Prior to fabrication, computational fluid dynamics (CFD) simulation was utilized at flowrates less than 10μL/s as the means to test the effectiveness of each design components and also to specifically deduct empirical values that can be analyzed to improve or understand the relationship between the fluid and geometrical constraints of the microfluidic modular elements. The device produced was a hybrid cartridge composed of PDMS and glass which is the most widely used materials microfluidics research due to their low cost and simplicity of fabrication by soft lithography technique. The choice of material also took into account the various physical and chemical properties advantages and disadvantages in their bio-medical applications. Such properties include but not limited to surface energy that determines the wetting fluid characteristics, biocompatibility, optical transparency. Subsequently, after a prototype cartridge was developed fluid flow experimentation using liquid coloured dye was used on the fully fabricated cartridge to test the efficacy of its microfluidic functionalities before expensive DNA amplification reagents were utilised at similar flowrates to the CFD simulations. This gave rise to comparison between similar and dissimilar flow Peculiarities in the microfluidic circuit of both experiments. The final experiment was performed with the aid of a recent molecular technique in DNA amplification known as of RPA kit (recombinase polymerase amplification reaction). It involved performing two main reaction experiments; first, was the positive experiment that bears the sample DNA and the latter, negative that served as the control without DNA. In the end, quantitative analysis of results was done using an agarose gel that showed 143 base pairs, for the positive samples, thus validating the amplification experiment.

The objective of this work presented here is to extend the capabilities of siloxane waveguide technology in the field of biochemical sensing. Recent advances in the integration of polymeric optical waveguides with electronics onto standard printed circuit boards (PCBs) allow the formation of cost-effective lab-on-achip modules suitable for mass production. This technology has been primarily designed for on-board data communication. The focus of this research is to investigate the possibility of realising a Siloxane polymer based lab-on-chip sensor. Different siloxane-polymer-based optical waveguide sensor structures have been designed and analysed from the aspect of biochemical sensing. An evanescent-wave absorption sensor based on mode-selective asymmetric waveguide junctions is proposed for the first time. The device mitigates the common optical effect of spurious response in absorption sensors due to the analyte transport fluid. Head injury is the leading cause of death in the population of people under 40 years. Currently, 3 out of 5 deaths in emergency rooms are due to severe brain injuries in the developed world. Researchers at the Neurosciences Critical Care Unit (NCCU) at Addenbrooke's Hospital have managed to correlate biochemical changes with the severeness of the injury and the likelihood of patient recovery. Considerable progress has been made to develop a lab-on-chip sensor capable of continuously monitoring glucose, lactate and pyruvate concentrations in the brain fluid, hence the contribution to the current trend in the advancement of portable lab-on-chip technologies for the deployment of point-of-care diagnostic tools. A novel recognition layer has been developed based on porphyrin in combination with glucose, lactate and pyruvate oxidase for measuring all the analytes, enabling fast and reversible chemical reactions to be monitored by optical interrogation. The operational wavelength of the developed recognition layer is 425 nm, which required the formation of polymer features that were beyond the fabrication capabilities at the time. Through considerable process development and the adoption of nanoimprinting lithography, siloxane polymer based optical waveguides were fabricated allowing the realisation of highly sensitive optical sensors. Based on the results that are presented here, it can be concluded the functionalization of siloxane polymer waveguide have a potential for realising biochemical sensors in the future. The new fabrication technique will allow the formation of more robust and complex lab-on-chip sensors based on this material.

This thesis describes the design, fabrication, and testing process for a microfluidic phosphate colorimeter utilized for water quality analysis. The device can be powered by, and interfaced for data collection with, a common cell phone or laptop to dramatically reduce costs. Unlike commercially available colorimeters, this device does not require the user to measure or mix sample and reagent. A disposable poly(dimethylsiloxane) (PDMS) microfluid chip, powered by an absorption pumping mechanism, was used to draw water samples, mix the sample at a specific ratio with a molybdovanadate reagent, and load both fluids into an onboard cuvette for colorimetric analysis. A series of capillary retention valves, channels, and diffusion pumping surfaces passively controls the microfluidic chip so that no user input is required. The microfluidic chip was fabricated using a modified SU-8 soft lithography process to produce a 1.67mm light absorbance pathlength for optimal Beer Lambert Law color absorbance. Preliminary calibration curves for the device produced from standard phosphate solutions indicate a range of detection between 5 to 30mg/L for reactive orthophosphate with a linearity of R²=91.3% and precision of 2.6ppm. The performance of the PDMS absorption driven pumping process was investigated using flow image analysis and indicates an effective pumping rate up to approximately 7µL/min to load a 36µL sample.

The main objective of this thesis is to perform a study of and optimize the most direct and practical gas mixture composition inside the Radial Time Projection Chamber for the Barely-Offshell Nucleon Structure (BONuS 12) detector for use in the CLAS 12 detector in Experimental Hall B at Thomas Jefferson National Accelerator Facility (JLab). The optimization of these conditions will enhance the performance and resolution of the detector. The original BONuS 6 experiment utilized a gas composition of 80 % He and 20% Dimethyl Ether (DME). With the extensive 12 GeV energy upgrade constructed at JLab and the new BONuS 12 detector established , it is imperative that the gas composition utilized, is best suited to facilitate the experimental needs and demands. BONuS 12 is an experiment designed to measure the momentum of recoiling spectator protons down to 70 MeV/c. This technique will extract the structure function Fn 2 at large x from 0.1 up to 0.8 over a significant range in Q2 and W from the nucleon mass, with a beam energy of 11 GeV, enabling us to essentially select free neutrons.

The CEBAF Large Acceptance Spectrometer for the 12 GeV era, known as CLAS12, uses the time of flight (TOF) system to identify charged particles from scattering events between the beam and target. The TOF system is divided into two parts: The Forward time of flight system, and the Central time of flight system. These two sub-systems subtend different polar angles of the detector geometry for wide acceptance of scattered particles. Reconstruction is the service used to identify particles from the interactions between the beam and target, called as a vertex or the point where the interaction occurs. The vertex position is traced back using the tracking system and the TOF system. The resolution of the detector affects the accuracy of the reconstructed vertex location. This paper’s goal will be to develop software for validation suite for CLAS12, which will include central and forward tracking plots. Plots will be developed to check the precision of the reconstructed vertices in both the central and forward detectors. This will be done assuming a target with zero dimension at 𝑣𝑧 = 0, and an extended target of 5 cm at 𝑣𝑧 = 0. This paper will also look at the TOF resolution, and identify particles using the TOF detectors and the effect of the vertex correction on the velocity vs. momentum plots.

L’intérêt des ultrasons pour la caractérisation de milieux ou pour l’actionnement à plus forte puissance n’est plus à démontrer. L’intégration de fonctions acoustiques substrats de silicium soulève en revanche de nombreux problèmes technologiques. Le travail de thèse présenté fait suite aux premiers développements technologiques qui ont permis la validation du concept de caractérisation acoustique haute fréquence en canal microfluidique. Les principales avancées de ce travail concernent l’optimisation du transfert de l’énergie acoustique dans le canal microfluidique dans une bande de fréquence allant de 500 à 1000 MHz. Des dépôts de couches minces sur les miroirs et le développement de transducteurs en couches épaisses constituent les principales avancées. Une première évaluation de l’actionnement de fluides ou de particules en canal microfluidique est également présentée ainsi qu’une application du système à la mesure de température en canal microfluidique par ultrasons. / The interest of ultrasounds for media characterization or for actuation when using more power is well known. Nevertheless, the integration of these acoustic functions in silicon based Lab-on-chips requires specific technological developments. The possibility to use high frequency bulk acoustic waves in this kind of systems for characterization or detection has been presented previously in another PhD work. The main objective of this work was to optimize acoustic energy transfer to a microfluidic channel in a frequency range between 500 MHz and 1000 MHz. To do that, the main technological developments achieved among others concern the coating of the guiding mirrors to avoid acoustic mode conversion and ZnO thick films sputtering for the fabrication of piezoelectric transducers. The developed system has been used for particles detection or concentration evaluation. Moreover, a first evaluation of fluids/particles actuation was demonstrated, along with temperature evaluation using ultrasound were achieved in microfluidic channels.

Les Kazakhs sont des consommateurs traditionnels de lait d'espèces non-conventionnelles comme la chamelle. Pour autant, les régions d'élevage camelin dans ce pays, bien que basées sur un mode extensif et un accès à des ressources naturelles, n'en sont pas moins fragilisées par les risques de pollution, l'environnement du pays étant affectées par la présence de métaux lourds, pesticides et radionucléides. L'objectif de la thèse a été (a) d'évaluer l'impact de cette pollution sur la qualité du lait de chamelle et du shubat (lait fermenté), et (b) d'évaluer les capacités de détoxification des produits laitiers.Pour aborder la question de l'impact de la pollution, plusieurs niveaux d'analyses ont été mis en œuvre:(i) A l'échelle régionale, des cartes d'indice de pollution ont été établies autour de 13 fermes de zones polluées (Almaty, Sud Kazakhstan, Atyraou et Kyzylorda) afin de comparer le niveau de pollution des différentes matrices (sol, eau, plante) selon la distance aux sources de pollution.(ii) A l'échelle des matrices environnementales (sol, plante, eau), deux métaux lourds majeurs (Pb et Cd) ont été déterminés dans les échantillons de sols (7,76-131,08 ppm et 0,08-0,39 ppm, respectivement), l'eau (Pb entre 5,9-13,6 ppm et Cd 0,05-0,25 ppm), les plantes (0,50-2,30 ppm et >0,05-0,56 ppm, respectivement). Un lien entre indice de pollution et métaux dans les sols a été observé, montrant l'impact de la proximité et de la nature des sources de polluants sur la contamination des sols. On observe également une corrélation étroite entre teneur en Pb et Cd au sein des différentes matrices. Cependant, les teneurs dans le sol sont indépendantes des teneurs dans l'eau ou les plantes. Les teneurs en pesticides dans l'eau sont inférieures à celles des normes internationales. Dans les fourrages, le DDT et ses dérivés ont été plus élevés que dans le sol. Cela signifie que les résidus de pesticides peuvent être également d'origine atmosphérique et donc inhalés par les animaux(iii) Dans le lait et le shubat, la concentration en métaux lourds dans cinq régions (Almaty, Atyraou, Kyzylorda, Taraz et Sud Kazakhstan) a été en moyenne faible en Cu (< 0,05 ppm), normale en Zn (près de 5 ppm) et Cd, mais un peu élevée pour Pb. Nos résultats ont été relativement élevés pour le DDT total dans le lait de toutes les régions sauf Kyzylorda et supérieurs pour le HCH total dans le lait des régions d'Almaty et d'Atyraou.(iv) Les relations entre environnement et lait ont été testées montrant l'absence de lien entre contamination de l'environnement en métaux lourds et celle du lait et shubat. Aucune relation non plus n'a été observée pour les pesticides, à l'exception du lindane et 4,4-DDD.Pour tester l'effet détoxifiant, il a été procédé en deux étapes. D'abord l'isolement et l'identification des souches de bactéries lactiques (BAL) du shubat afin de tester leur capacité à fixer Pb et Cd. Au total, 138 souches ont été isolées à partir de 25 échantillons laitiers. Une étude qualitative pour détecter la capacité des BAL à fixer les métaux lourds a été réalisée. Parmi 118 souches testées, seules 5,1% d'entre elles n'ont poussé ni sur Pb ni sur Cd, 36 % ayant eu la capacité de fixer Pb ou Cd, et 9% les deux. Les 52 souches montrant les meilleurs résultats ont été retenues pour identification par des méthodes moléculaires (rRNA16S). Selon les résultats de séquençage, la plupart de souches étaient de genre Enterococcus et Lactobacillus, secondairement Lactococcus et Leuconostoc.Dans un second temps, un test physiologique (in vivo) a été réalisé sur 80 cobayes divisés en 8 groupes traités par le Pb et des souches de BAL. La quantité de Pb dans les fèces des groupes traités par le lait fermenté ayant contenu ou pas du Pb était relativement élevé par rapport aux groupes témoin et celui recevant de l'eau enrichie de Pb (groupe EauPb). La distribution du Pb dans les organismes de cobayes du groupe EauPb s'est révélée dans l'ordre croissant: rate / The Kazakh people are traditional consumers of milk from non-conventional species like camel. However, the camel-rearing areas in this country, although based on an extensive mode and an access to natural resources, are affected by the risks of pollution, the environment of the country being affected by the presence of heavy metals, pesticides and radionuclides. The objective of the thesis was (a) to evaluate the impact of this pollution on the quality of the camel milk and shubat (fermented milk), and (b) to evaluate the abilitiy of detoxification by the dairy products. To answer to the question of the impact of pollution, several levels of analyses were implemented:(i) At the regional level, maps of pollution index were established around 13 farms from polluted zones (Almaty, Southern Kazakhstan, Atyraou and Kyzylorda) in order to compare the level of pollution of the various matrices (soil, water, plant) according to the distance to the polluting sources.(ii) On environmental matrix level (soil, plant, water), two major heavy metals (Pb and Cd) were determined in the soil (7,76-131,08 ppm and 0,08-0,39 ppm, respectively), water (Pb 5,9-13,6 ppm and Cd 0,05-0,25 ppm), the plants (0,50-2,30 ppm and >0,05-0,56 ppm, respectively) samples. A correlation between pollution index and metals in soils was observed, showing the impact of the proximity and the nature of the polluting sources on the contamination of the soils. A close correlation between Pb and Cd content within the various matrices was also observed. However, the contents in the soil were independent of the contents in water or plants. The contents of pesticides in water were lower than those of the international standards. In fodder, the DDT and its derivatives were higher than in the soil. That means that the pesticides residues can be also of atmospheric origin and thus inhaled by the animals(iii) In milk and shubat, the heavy metal concentration in five areas (Almaty, Atyraou, Kyzylorda, Taraz and Sud Kazakhstan) was on average low in Cu (< 0,05 ppm), normal for Zn (nearly 5 ppm) and Cd, but a little high for Pb. Our results were relatively high for the total DDT in the milk of all the areas except Kyzylorda and superiors for the total HCH in the milk of Almaty and Atyraou areas.(iv) The relations between environment and milk were tested showing the absence of link between environmental contamination of the heavy metals and that of milk and shubat. No relation either was observed for the pesticides, except for lindane and 4,4-DDD.To test the detoxification effect, it was proceeded in two stages: initially the isolation and identification of the strains of lactic bacteria (LAB) of the shubat in order to test their capacity to fix Pb and Cd. On the whole, 138 strains were isolated starting from 25 dairy samples. A qualitative study to detect the capacity of the LAB to fix heavy metals was carried out. Among 118 tested strains, only 5.1% of them pushed neither on Pb nor on Cd, 36% having had the capacity to fix Pb or Cd, and 9% both. The 52 strains showing the best results were retained for identification by molecular methods (rRNA16S). According to results' of sequencing, the majority of strains were of genus Enterococcus and Lactobacillus, secondarily Lactococcus and Leuconostoc. In the second time, a physiological test (in vivo) was carried out on 80 guinea-pigs divided into 8 groups treated by strains of LAB containing or not some Pb. The quantity of Pb in feces of the groups treated by fermented milk having contained or not Pb was relatively high compared to the reference groups and that receiving from the water enriched by Pb (WaterPb group). The distribution of Pb in the organes of guinea-pigs of the WaterPb group appeared in the ascending order: spleen> blood> heart> lungs> liver> kidneys. There was no significant correlation between organs.The results obtained on the identification of the isolated strains, gave the possibilities of studying

Photonic crystals serve as powerful building blocks for the development of lab-on-chip devices. Currently they are used for a wide range of miniaturized optical components such as extremely compact waveguides to refractive-index based optical sensors. Here we propose a new technique for analyzing and characterizing cells through the design of a micro-flow cytometer using photonic crystals. While lab scale flow cytometers have been critical to many developments in cellular biology they are not portable, difficult to use and relatively expensive. By making a miniature sensor capable of replicating the same functionality as the large scale units with photonic crystals, we hope to produce a device that can be easily integrated into a lab-on-chip and inexpensively mass produced for use outside of the lab. Using specialized FDTD software, the proposed technique has been studied, and multiple important flow cytometry functions have been established. As individual cells flow near the crystal surface, transmission of light through the photonic crystal is influenced accordingly. By analyzing the resulting changes in transmission, information such as cell counting and shape characterization have been demonstrated. Furthermore, correlations for simultaneously determining the size and refractive indices of cells has been shown by applying the statistical concepts of central moments.

CPAP is the most common treatment for moderate to severe sleep apnea in adults. Despite its efficacy, patients’ safety, comfort and compliance are issues to be considered and improved in CPAP design. The issues include condensation, carbon dioxide in inhaled air, humidity and temperature of inhaled air. When a CPAP user breaths deeply, there will be some air not fully expelled and may be driven back into the heated air delivery tube (HADT). An interest has existed in what impacts this so called reverse flow may bring about to the CPAP use. The main objectives of this research are to quantify the reverse flow and its influence on carbon dioxide re-breathing, delivered humidity to the patient and condensation in the HADT. Within this thesis, two computer models of the CPAP system have been constructed on Simulink™ in the Matlab™ environment. One is about the CPAP fluid dynamic performance and carbon dioxide re-breathing and the other is on thermodynamic performance. The models can predict the dynamic behaviour of the CPAP machine. They are able to mimic the breath induced airflow fluctuation, and flow direction changes over wide real working ranges of ambient conditions, settings and coefficients. These models can be used for future analysis, development, improvement and design of the machine. The fluid dynamic and thermodynamic models were experimentally validated and they have proved to be valuable tool in the work. The main conclusions drawn from this study are: • Reverse flow increases when breaths load increases and pressure setting decreases. • Reverse flow does not definitely add exhaled air to the next inhalation unless the reverse flow is relatively too much. • Mask capacity does not influence the reverse flow. • The exhaled air re-breathed is mainly due to that stays in the mask, therefore larger mask capacity increases the exhaled air re-breath and the percentage of exhaled air in next inhalation drops when the breath load increases. • Deep breathing does not significantly change the total evaporation in chamber. • When deep breathing induced reverse flow occurs, condensation occurs or worsens in the HADT near the mask. This happens only when the humidity of the airflow from the CPAP is much lower than that of the exhaled air and the tube wall temperature is low enough for condensation to occur. • The deep breathing and reverse flow do not significantly influence the average inhaled air temperature. • The overall specific humidity in inhaled air is lower under deep breathing. • Mask capacity does not influence the thermal conditions in the HADT and the inhaled air specific humidity. Also the mask capacity does not significantly influences the inhaled air temperature.