Cette thèse porte sur l’élaboration d’un outil de capture d’ADN permettant d’identifier une mutation génétique (SNP) grâce à la formation de sandwichs avec des particules de carboxylatex biofonctionnalisées avec des oligonucléotides couplée à une détection de la fluorescence. Le modèle biologique choisi pour ce projet est le génotypage plaquettaire et plus particulièrement la recherche du gène biallélique HPA-1. Le principal objectif de ce travail a été d’optimiser un outil de capture préalablement développé dans l’équipe (Trévisan, 2011) afin de réduire le nombre d’étapes et de simplifier la mise en oeuvre globale du test en modifiant les interactions moléculaires utilisée pour capturer l’ADN cible et en utilisant des particules fluorescentes comme élément de détection. En présence d’ADN cible, des sandwichs sont formés entre les particules fluorescentes et les particules magnétiques biofonctionnalisées. Ces sandwichs sont purifiés par séparation magnétique et la fluorescence est détectée par trois méthodes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (détection par ondes évanescentes). Dans un premier temps, les paramètres de fonctionnalisation chimique et biologique des différentes particules (magnétiques et fluorescentes) ont été déterminés et optimisés ainsi que les conditions d’hybridation pour la capture de l’ADN cible. Ensuite, la formation des sandwichs et leur détection ont été suivies par des mesures de fluorescence en utilisant trois méthodes différentes : la cytométrie en flux, l’imagerie de fluorescence et l’Evareader (capteur à ondes évanescentes). Les résultats obtenus avec les différentes méthodes de détection sont concordants et montrent que l’outil de capture d’ADN développé permet de capturer la cible synthétique (oligonucléotide) HPA-1 en réduisant le temps d’analyse de 45 min. Dans nos conditions, le test permet de discriminer l’allèle a de l’allèle b du gène HPA-1 qui ne diffère que d’un nucléotide. Le rapport des signaux de fluorescence issus du sandwich spécifique et du sandwich non spécifique est d’environ 2,5 à 3. Ce rapport devra être amélioré par la suite, en optimisant les conditions de formation des sandwichs. La prochaine étape consistera à optimiser le système de capture d’ADN développé pour gagner en spécificité et déterminer la limite de détection du test. Ce test devra également être validé avec des échantillons biologiques. A plus long terme, la fluorescence pourra être détectée par un photodétecteur miniaturisé actuellement développé à l’Université de Sherbrooke. Des études préliminaires présentées dans ce manuscrit montrent les potentialités de ce nouveau transducteur. / This thesis is about the development of a new assay to capture DNA. This assay is based on the formation of sandwiches between biofunctionnalized with oligonucleotides carboxylatex microparticles combined with fluorescence detection. It should be able to discriminate single nucleotide polymorphism (SNP). This assay is designed to be applied to platelet genotyping for the research of the gene HPA-1. The main goal of this work was to improve an assay previously developed (Trévisan, 2011) by INL and EFS Rhône-Alpes. The objectives are to reduce the number of steps and to simplify the test. To do so, the molecular interactions used in order to capture target DNA are modified and fluorescent microparticles are used for the detection. In the presence of target DNA, sandwiches are formed between both biofunctionnalized fluorescent and magnetic particles. Those sandwiches are purified through magnetic separation. Then, fluorescence is detected by three methods: flow cytometry, fluorescence imaging and Evareader (detection with an evanescent wave). First, chemical and biological parameters for the functionalization of the different particles (magnetic and fluorescent) are determined. The conditions for the capture of target DNA were optimized. Then, the formation and the detection of the sandwiches were estimated by measuring the fluorescence using three different methods: flow cytometry, fluorescence imaging and Evareader. The results obtained with the three methods are consistent. They show that the new system enables to capture synthetic target (oligonucleotide) HPA-1 with a reduction of total time analysis of 45 min. In our conditions, SNP can be discriminated for HPA-1 gene. For this discrimination, the fluorescence signal ratio about 2.5 to 3. This ratio should be improved by optimizing the conditions of sandwiches formation. Next step will consist in the optimization of the system developed to capture DNA in order to gain specificity and to determine the limit of detection. This test should also be validated with biological samples. In the long term, fluorescence could be detected by a miniaturized photodetector developed in the University of Sherbrook. Preliminary studies presented in this manuscript show the potentialities of this new transducer.

Depuis une vingtaine d’années, l’optique bénéficie des avancées considérables de la microélectronique.Ainsi, il est maintenant possible de produire, guider, confiner ou encore ralentirla lumière sur puce à une échelle sub-longueur d’onde. Dans cette thèse, nous étudions de telscomposants par l’intermédiaire d’un microscope en champ proche optique (SNOM).La première partie présente une vision d’ensemble de la situation actuelle en nanophotoniqueintégrée sur substrat diélectrique. Elle expose plusieurs enjeux et faits marquants récents dansce domaine. Elle introduit également le principe physique et le fonctionnement d’un SNOMdans les grandes lignes.La seconde partie est consacrée à la microscopie en champ proche optique d’un point devue instrumental. Après une analyse physique, nous détaillons le montage de notre propremicroscope sur le banc de caractérisation optique du laboratoire, avant d’analyser la formationdes images optiques obtenues avec cette technique.La troisième partie concerne l’étude de guides d’onde couplés en Silicium sur isolant (SOI),dans lesquels s’intègrent des nano-cavités optiques. Les phénomènes de couplage par recouvrementde champs évanescents sont étudiés numériquement et analytiquement. L’analyse de cesstructures grâce au SNOM nous a permis d’une part de vérifier la validité de ces modèles, etd’autre part d’observer directement le guidage et le confinement de la lumière dans un milieude faible indice de réfraction. Nous montrons cependant que ces résultats restent très sensiblesaux aléas de fabrication. Enfin, nous mettons en évidence grâce au SNOM et à des mesuresspectrales que la description de structures de N cavités juxtaposées peut être approchée par lathéorie des modes couplés. / Since the end of the XXth century, optics benefits from significant breakthrough comingfrom the micro-electronic technologies. It is thus now possible to produce, guide, slow downor even trap light on a chip at a sub-wavelength scale. In this thesis, we study such opticalcomponents thanks to a Scanning Near-Field Optical Microscope (SNOM).The first part exposes an overall view of the current situation in the field of dielectricsubstrate integrated nanophotonics. Some of the recent outstanding issues and results are hereintroduced, as well as the general principle and the necessary tools to operate a SNOM.The second part is dedicated to optical near-field microscopy, technically speaking. Thephysical rules are here developed. Then we detail the instrumental set up of our own SNOMon our optical characterization bench. We end by analysing the optical images formation witha SNOM.The third part bears upon the study of Silicon-on-Insulator (SOI) coupled waveguides whereoptical nano-cavities could be inserted, by resorting to the previously implemented SNOM.Overlapping evanescent fields induced coupling phenomena are numerically and analyticallystudied. The use of the SNOM allowed us here to check the validity of our models. Besides,we have directly observed thanks to this instrument the guiding and confinement of light ina low refractive index media. However, we show that this phenomenon is highly subjected tofabrication uncertainties. Finally, we use the SNOM and spectral measurements in order todemonstrate that systems of N coupled nanocavities could be described with a simple coupledmodes model.

Reliability and sensitive information protection are critical aspects of integrated circuits. A novel technique using near-field evanescent wave coupling from two subwavelength gratings (SWGs), with the input laser source delivered through an optical fiber is presented for tamper evidence of electronic components. The first grating of the pair of coupled subwavelength gratings (CSWGs) was milled directly on the output facet of the silica fiber using focused ion beam (FIB) etching. The second grating was patterned using e-beam lithography and etched into a glass substrate using reactive ion etching (RIE). The slightest intrusion attempt would separate the CSWGs and eliminate near-field coupling between the gratings. Tampering, therefore, would become evident. Computer simulations guided the design for optimal operation of the security solution. The physical dimensions of the SWGs, i.e. period and thickness, were optimized, for a 650 nm illuminating wavelength. The optimal dimensions resulted in a 560 nm grating period for the first grating etched in the silica optical fiber and 420 nm for the second grating etched in borosilicate glass. The incident light beam had a half-width at half-maximum (HWHM) of at least 7 µm to allow discernible higher transmission orders, and a HWHM of 28 µm for minimum noise. The minimum number of individual grating lines present on the optical fiber facet was identified as 15 lines. Grating rotation due to the cylindrical geometry of the fiber resulted in a rotation of the far-field pattern, corresponding to the rotation angle of moiré fringes. With the goal of later adding authentication to tamper evidence, the concept of CSWGs signature was also modeled by introducing random and planned variations in the glass grating. The fiber was placed on a stage supported by a nanomanipulator, which permitted three-dimensional displacement while maintaining the fiber tip normal to the surface of the glass substrate. A 650 nm diode laser was fixed to a translation mount that transmitted the light source through the optical fiber, and the output intensity was measured using a silicon photodiode. The evanescent wave coupling output results for the CSWGs were measured and compared to the simulation results.

El control de las propiedades acústicas de los cristales de sonido (CS) necesita del estudio de la distribución de dispersores en la propia estructura y de las propiedades acústicas intrínsecas de dichos dispersores. En este trabajo se presenta un estudio exhaustivo de diferentes distribuciones, así como el estudio de la mejora de las propiedades acústicas de CS constituidos por dispersores con propiedades absorbentes y/o resonantes. Estos dos procedimientos, tanto independientemente como conjuntamente, introducen posibilidades reales para el control de la propagación de ondas acústicas a través de los CS. Desde el punto de vista teórico, la propagación de ondas a través de estructuras periódicas y quasiperiódicas se ha analizado mediante los métodos de la dispersión múltiple, de la expansión en ondas planas y de los elementos finitos. En este trabajo se presenta una novedosa extensión del método de la expansión en ondas planas que permite obtener las relaciones complejas de dispersión para los CS. Esta técnica complementa la información obtenida por los métodos clásicos y permite conocer el comportamiento evanescente de los modos en el interior de las bandas de propagación prohibida del CS, así como de los modos localizados alrededor de posibles defectos puntuales en CS. La necesidad de medidas precisas de las propiedades acústicas de los CS ha provocado el desarrollo de un novedoso sistema tridimensional que sincroniza el movimiento del receptor y la adquisición de señales temporales. Los resultados experimentales obtenidos en este trabajo muestran una gran similitud con los resultados teóricos. La actuación conjunta de distribuciones de dispersores optimizadas y de las propiedades intrínsecas de éstos, se aplica para la generación de dispositivos que presentan un rango amplio de frecuencias atenuadas. Se presenta una alternativa a las barreras acústicas tradicionales basada en CS donde se puede controlar el paso de ondas a su través. Los resultados ayudan a entender correctamente el funcionamiento de los CS para la localización de sonido, y para el guiado y filtrado de ondas acústicas. / Romero García, V. (2010). On the control of propagating acoustic waves in sonic crystals: analytical, numerical and optimization techniques [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8982 / Palancia

This thesis deals with a measurement and interpretation of NIR spectra of bacterial cells and design of biosensor using this analytical technique. In the first chapter, there is introduction of current state of knowledge in the field of NIR spectroscopy in microbiology and technology of fiber optic biosensors. The summary of this chapter shows that NIR is a suitable technique for direct molecular analysis of bacteria, but it suffers from low sensitivity and insufficient interpretation of bacterial spectra. In the next part of the thesis, there is a theoretical background of spectral analysis techniques and technology of fiber optic sensors. In the practical part of this work, there is suggested the elimination of disadvantages of NIR spectroscopy in microbiology by a series of experiments used for interpretation of NIR spectra of bacteria and design of fiber optic sensor to increase sensitivity of this technique. In this work, spectral regions important for the identification of bacterial strains were determined and partially interpreted and the sensor for bacterial analysis capable of classifying strains based on 105 captured cells was designed. Therefore, the objectives of this work were fulfilled.

This Master thesis examines a phenomenon that occurs in the upper polar atmosphere, namely, Polar Mesospheric Winter Echoes, or PMWEs. PMWEs are radar echoes observed by Very High Frequency Mesosphere Stratosphere Troposphere (VHF MST) radar, from altitudes of 60 to 76 km at 7 to 15 UT, in the winter months from the middle of September to the beginning of May. The aforementioned specifications are the partial results of this thesis.PMWEs are generally understood to be caused by turbulence; however, radar data indicate some rare cases where PMWEs can be created with velocities exceeding the speed of sound, which is not possible with current turbulence theory. Kirkwood et al., 2006 and Belova, Kirkwood, and Sergienko, 2013 hypothesised that infrasound could generate the necessary conditions for PMWEs with velocities equal to or exceeding the speed of sound. Observations of PMWEs presented in this thesis have been carried out by the MST radar ESRAD, located at Esrange (67 56’N, 21 04’E) near Kiruna in northern Sweden. The radar operates at 52 MHz and has been performing continuous radar observations since Dec 1996. Observations of the infrasounds presented in this thesis were carried out by a microbarometer located close to Rymdcampus in Kiruna. Access to the data is restricted, but through university administration, this master’s thesis has been granted permission to use the data for the study of PMWEs. The instrument performed continuous infrasound measurements from the 24th of May 2016 and forward. This thesis will perform a full analysis of all radar data from the 17th of Dec 1996 until the 31st of Jan 2021 to assess the altitude interval, diurnal interval and yearly interval. The data given in the first section are a result of this work. Additionally, space weather parameters relation with the occurrence of PMWEs is analysed. Space weather parameters are very important for the chemistry and conditions present in the mesosphere. It is shown thatt here is a strong relation between solar wind and PMWE occurrence, decent relation with Kp index and no to weak relation with solar particle event (SPE). Correlating space weather and PMWEs in greater detail could be the subject of other studies. Last but most interesting, microbarometer data will be analysed for days where high-speed PMWEs are detected. Because of the rarity of these high-speed PMWEs, only seven total cases were found from 24 May 2016 onward, making the analysis of the infrasound measurements very limited, and no connection was found. However, it was found that days with high-speed PMWEs had an abnormally low amount of infrasound detections, further making analysis difficult but raising questions of why. This could mean that infrasound signals might be hindered from reaching the ground on days where we have high-speed PMWEs. No further conclusions can be made, as this indicates relation but not causation. Airborne infrasound instruments could be used to detect weaker infrasound signals due to being unaffected by wind disturbance at the ground.

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase. Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes. A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.

Integration and miniaturisation in electronics has undoubtedly revolutionised the modern world. In biotechnology, emerging lab-on-a-chip (LOC) methodologies promise all-integrated laboratory processes, to perform complete biochemical or medical synthesis and analysis encapsulated on small microchips. The integration of electrical, optical and physical sensors, and control devices, with fluid handling, is creating a new class of functional chip-based systems. Scaled down onto a chip, reagent and sample consumption is reduced, point-of-care or in-the-field usage is enabled through portability, costs are reduced, automation increases the ease of use, and favourable scaling laws can be exploited, such as improved fluid control. The capacity to manipulate single cells on-chip has applications across the life sciences, in biotechnology, pharmacology, medical diagnostics and drug discovery. This thesis explores multiple applications of optical manipulation within microfluidic chips. Used in combination with microfluidic systems, optics adds powerful functionalities to emerging LOC technologies. These include particle management such as immobilising, sorting, concentrating, and transportation of cell-sized objects, along with sensing, spectroscopic interrogation, and cell treatment. The work in this thesis brings several key applications of optical techniques for manipulating and porating cell-sized microscopic particles to within microfluidic chips. The fields of optical trapping, optical tweezers and optical sorting are reviewed in the context of lab-on-a-chip application, and the physics of the laminar fluid flow exhibited at this size scale is detailed. Microfluidic chip fabrication methods are presented, including a robust method for the introduction of optical fibres for laser beam delivery, which is demonstrated in a dual-beam optical trap chip and in optical chromatography using photonic crystal fibre. The use of a total internal reflection microscope objective lens is utilised in a novel demonstration of propelling particles within fluid flow. The size and refractive index dependency is modelled and experimentally characterised, before presenting continuous passive optical sorting of microparticles based on these intrinsic optical properties, in a microfluidic chip. Finally, a microfluidic system is utilised in the delivery of mammalian cells to a focused femtosecond laser beam for continuous, high throughput photoporation. The optical injection efficiency of inserting a fluorescent dye is determined and the cell viability is evaluated. This could form the basis for ultra-high throughput, efficient transfection of cells, with the advantages of single cell treatment and unrivalled viability using this optical technique.

A near-field technique known as evanescent interferometric lithography allows for high resolution imaging. However its primary limitation is that the image exponentially decays within the photoresist due to physical limits. This thesis aims to overcome this limitation and presents a method to considerably enhance the depth of focus of images created using evanescent interferometric lithography by using a material underlay beneath the photoresist. A key enabler of this is the understanding that evanescent fields couple to surface states and operating within proximity of a resonance, the strength of the coupling allows for considerable energy extraction from the incident beam and redistribution of this energy in a photoresist cavity. This led to the analysis of the Fresnel equations, which suggested that such coupling was in fact the result of an enhanced reflectance that takes place at boundaries of carefully chosen materials. While it is known that metals and lossy dielectrics result in surface plasmon polaritons (SPP) and surface exciton polaritons (SEP) as conventional solutions to the Fresnel reflection equations for the TM polarization of light, there is no such naturally occurring surface state that allows evanescent wave enhancement with the TE polarization of light. Further investigation of the Fresnel reflection equations revealed both for TM and TE that in fact another solution exists that is but unconventional to enhance the reflectivity. This solution requires that one of the media have a negative loss. This is a new type of surface resonance that requires that one of the media be a gain medium; not one in the optical pumped sense but one that would naturally supply energy to a wave to make it grow. This new surface resonance is also a key result of this thesis. Clearly, however this is only a hypothetical solution as a real gain medium would violate the conservation of energy. However, as it is only the reflectance of this gain medium that is useful for evanescent wave enhancement, in fact a multilayered stack consisting of naturally occurring materials is one way to achieve the desired reflectivity. This would of course be only an emulation of the reflectivity aspect of the gain medium. This multilayered stack is then an effective gain medium for the reflectivity purposes when imaging is carried out at a particular NA at a particular wavelength. This proposal is also a key idea of this thesis. At λ = 193 nm, this method was used to propose a feasible design to image high resolution structures, NA = 1.85 at an aspect ratio of ~3.2. To experimentally demonstrate the enhancements, a new type of solid immersion test bed, the solid immersion Lloyd's mirror interference lithography test-bed was constructed. High quality line and space patterns with a half-pitch of 55.5 nm were created using λ = 405 nm, corresponding to a NA of 1.824, that is well in the evanescent regime of light. Image depths of 33-40 nm were seen. Next, the evanescent image was coupled to an effective gain medium made up of a thin layer of hafnium oxide (HfO) upon silicon dioxide (SiO2). This resulted in a considerable depth enhancement, and 105 nm tall structures were imaged. The work in this thesis details the construction of the solid immersion lithography test-bed, describes the implementation of the modeling tools, details the theory and analysis required to achieve the relevant solutions and understanding of the physical mechanism and finally experimentally demonstrates an enhancement that allows evanescent interferometric lithography beyond conventional limits.

This thesis describes the development and application of condensed-phase cavity-based spectroscopic techniques - namely cavity ring-down spectroscopy (CRDS); cavity enhanced absorption spectroscopy (CEAS); broadband cavity enhanced absorption spectroscopy (BBCEAS) and evanescent wave (EW) variants of all three. The recently-developed cavity technique of EW-broadband cavity enhanced absorption spectroscopy (EW-BBCEAS) has been used—in combination with a supercontinuum source (SC) and a sensitive, fast readout CCD detector—to record of the full visible spectrum (400–700 nm) of a silica-liquid interfacial layer (with an effective thickness ca. 1 µm), at rapid acquisition rates (> 600 Hz) that are sufficient to follow fast kinetics in the condensed phase, in real time. The sensitivity achieved (A_min= 3.9 x 10^-5) is comparable with previous EW-CRDS and EW-CEAS studies, but the spectral region accessed in this broadband variant is much larger. The study of liquid|air interfaces using EW cavity-based techniques is also illustrated for the first time. The first application of BBCEAS to the analysis of microfluidic samples, flowing through a microfluidic chip, is illustrated. Proof-of-principle experiments are presented, demonstrating the technique’s ability to provide full visible broadband spectral measurements of flowing microfluidic droplets, with both high detection sensitivity (α_min < 10^-2 cm^-1) and excellent spatial and temporal resolution: an SC light source and sensitive, fast readout CCD allowed measurement repetition rates of 273 Hz, whilst probing a very small sample volume (ca. 90 nL). A significant portion of this thesis is devoted to demonstrating the powerful capabilities of CEAS, CRDS and BBCEAS in monitoring radical recombination reactions and associated magnetic field effects (MFEs) in solution. The efficacy of CEAS as a high-sensitivity MFE detection method has been established in a proof-of-principle study, using narrow band CEAS in combination with phase-sensitive detection: MFE-induced absorbance changes of ca. 10^-6 could be detected using the modulated CEAS technique and the data are shown to be superior to those obtained using conventional transient absorption (TA) methods typically employed for MFE measurements. The powerful capabilities of CRDS in monitoring radical recombination reactions and associated MFEs are also demonstrated. In particular, a pump-probe CRDS variant allows not only high sensitivity (A_min on the order 10^-6), but also sub-microsecond time-resolution. Combined, these features represent significant advantages over TA. Finally, SC-BBCEAS is used to measure full visible spectra of photoinduced reactions and their MFEs. The applicability of this approach to in vitro MFE studies of Drosophila cryptochrome is demonstrated—the results mark the first in vitro observation of a magnetic field response in an animal cryptochrome, a key result supporting the hypothesis that cryptochromes are involved in the magnetic sense in animals.