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The objectives of the work presented were to 1) fabricate reproducible nanorod array SERS substrates, 2) detection of bacteria using nanorod substrates, 3) detection of DNA hybridization using nanorod substrates and 4) critically evaluate the sensing method. Important findings from this work are as follows. A novel method for batch fabrication of substrates for surface enhanced Raman scattering (SERS) has been developed using a modified platen machined to fit in a commercial electron beam evaporator. The use of this holder enables simultaneous deposition of silver nanorod (AgNR) arrays onto six microscope slide substrates utilizing glancing angle deposition. In addition to multiple substrate fabrication, patterning of the AgNR substrates with 36 wells allows for physical isolation of low volume samples. The well-to-well, slide-to-slide, and batch-to-batch variability in both physical characteristics and SERS response of substrates prepared via this method was nominal. A critical issue in the continued development of AgNR substrates is their stability over time, and the potential impact on the SERS response. The thermal stability of the arrays was investigated and changes in surface morphology were evaluated using scanning electron microscopy and x-ray diffraction and correlated with changes in SERS enhancement. The findings suggest that the shelf-life of AgNR arrays is limited by migration of silver on the surface. Continued characterization of the AgNR arrays was carried out using fluorescent polystyrene microspheres of two different sizes. Theory suggests that enhancement between nanorods would be significantly greater than at the tops due to contributing electromagnetic fields from each nanostructure. In contrast to the theory, SERS response of microspheres confined to the tops of the AgNR array was significantly greater than that for beads located within the array. The location of the microspheres was established using optical fluorescence and scanning electron microscopy. The application of SERS to characterizing pathogens such as bacteria and viruses is an active area of investigation. AgNR array-based SERS substrates have enabled detection of pathogens present in biofluids. Specifically, several publications have focused on determining the spectral bands characteristic of bacteria from different species and cell lines. Studies were carried out on three strains of bacteria as well as the medium in which the bacteria were grown. The spectra of the bacteria and medium were surprisingly similar, so additional spectra were acquired for commonly used bacterial growth media. In many instances, these spectra were similar to published spectra purportedly characteristic of specific bacterial species. In addition to bacterial samples, nucleic acid hybridization assays were investigated. Oligonucleotide pairs specifically designed to detect respiratory syncytial virus (RSV) in nasal fluids were prepared and evaluated. SERS spectra acquired on oligos, alone or in combination, contain the known spectral signatures of the nucleosides that comprise the oligo. However, spectra acquired on an oligo with a 5'- or 3' thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting some control over the orientation of the oligo on the nanorod surface. The signal enhancement in SERS depends markedly upon the location of the probe relative to the substrate surface. By systematic placement of nucleotide markers along the oligo chain, the point at which the nucleotide disappears from the spectrum was identified. The overall findings for AgNR SERS substrates suggest that the applicability of SERS for detecting nucleic acid hybridization is limited. The strong distance dependence coupled with the lack of substrate stability at temperatures required for annealing oligos during hybridization suggest that AgNRs are not the platform to use for hybridization assays.

Optically active helical microparticles are studied in the forms of thin films, suspensions and powders. From fabricated helical porous thin films, microparticle suspensions are obtained by removing the microparticles (film columns) from their substrates and dispersing them into water. For removing microparticles, four methods are explored and compared: sacrificial NaCl layer, gold (Au) layer, buffered oxide etching, and direct ultrasonic agitation. The primary film material studied in this work is amorphous silicon (Si). Physical morphology of the microparticles is examined with scanning electron microscopy (SEM). Methods employed to characterize optical activity of the microparticles include: polarimetry, spectrophotometry, and spectroscopic ellipsometry (SE). The produced chiral microparticles exhibit optical activity: optical rotation (OR) and circular dichroism (CD - in the form of differential circular transmission (DCT)). Significant findings include: (a) we observe the largest optical rotatory power ever reported in scientific literature, 11◦/μm at 610 nm wavelength for a Si film; (b) for the helical thin films, there is one dominant DCT band in the measured wavelength range; however for microparticle suspensions and powders, there exist two DCT bands: one broad band at long wavelengths, and one narrow band in the short wavelength range; compared to their thin film forms, microparticle suspensions and powders have inverted sign for the broad DCT band. A discrete dipole approximation (DDA) model is employed to calculate optical response (e.g. extinction, scattering, and absorption cross-sections) of the microparticles, so as to enable us to understand the effects of different structural parameters of the microparticles on their optical response. Calculation confirms that optical activity of chiral microparticles is due to coherent light scatterings with the chiral structures of the particles. The inversion in sign of the broad DCT bands of microparticle suspensions and powders is likely due to the averaging effect from random orientation of the helical microparticles, as is indicated both from experimental results and from calculation. / Thesis (Ph.D, Physics, Engineering Physics and Astronomy) -- Queen's University, 2012-07-06 09:59:20.751

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Un microgyromètre 3 axes permet avec une structure unique de mesurer la vitesse de rotation d’un objet autour des trois axes de l’espace. Les micro-gyromètres 3 axes existants sont peu nombreux et typiquement résonants, fabriqués en technologie silicium par micro-usinage de surface, à transductions électro-statiques, et conçus pour des applications de fort volume ou la taille et le coût sont des critères majeurs. Dans cette thèse nous avons étudié la transduction et le procédé de fabrication d’un gyromètre résonant 3 axes à actionnement et détection piézoélectriques, fabriqué par micro-usinage de volume dans du GaAs semi-isolant, et dont les performances sont potentiellement très supérieures à l’état de l’art tout en conservant une taille et un coût limité. Ce microgyromètre nécessite une transduction piézoélectrique 3D et un routage des connexions électriques qui ont été modélisés et optimisés pour réduire les couplages parasites entre les modes de détection et le mode pilote. Un procédé original de fabrication collective du microgyromètre a été développé, modélisé et caractérisé. Ce procédé utilise notamment une gravure ionique réactive très profonde et traversante du GaAs dans un plasma BCl3-Cl2. Il est démontré pour la première fois qu’une gravure anisotrope traversante de tranchées de 450 μm de profondeur peut être réalisée grâce à une optimisation des paramètres de gravure et à l’utilisation d’un masque en résine. Un procédé original de dépôt et de délimitation d’électrodes Au/Cr sur les flancs verticaux d’une structure gravée par évaporation sous incidence oblique avec rotation du substrat et à travers un masque pochoir en film sec photosensible a aussi été étudié en détail. Une caractérisation fine de la structure cristalline, de la résistivité et des contraintes mécaniques avant, pendant et après recuit des couches Au/Cr poreuses évaporées sous incidence oblique a été menée. Des micro-gyromètres complets avec tout le système de transduction 3D ont été réalisés. Des premières caractérisations par vibrométrie optique hors du plan et dans le plan des gyromètres réalisés démontrent des résultats encourageants. Enfin, différentes voies d’amélioration de la conception et du procédé sont proposées. / A 3 axis gyroscope allows, with a single mechanical structure, the measurement of rotation rates of an object around 3 perpendicular spatial axes. Existing 3 axis microgyroscopes are scarce and typically resonating, made in silicon technology by surface micromachining, use electrostatic transductions and are designed for high volume applications where size and cost are major characteristics. In this thesis we investigated the transduction and fabrication process of a resonating 3 axis microgyroscope having piezoelectric actuation and detection, made in semi-insulating GaAs by bulk micromachining, and with performances potentially much higher than state of the art while limiting the size and cost. This microgyroscope requires a 3D piezoelectric transduction and circuitry which were modelled and optimized to reduce cross-talks effects. An original batch fabrication process was developed, modelled and characterized. This process notably makes use of very deep through wafer reactive ion etching of GaAs in a BCl3-Cl2 plasma. It is demonstrated for the first time that a through wafer highly anisotropic etching of 450 μm deep trenches can be realized owing to etching parameters optimization and the use of a resist masking layer. An original deposition and patterning process of Au/Cr electrodes on the vertical walls of an etched structure by oblique evaporation on rotated substrate through a dry film shadow mask has also been investigated in details. A fine characterization of the crystallographic structure, resistivity and mechanical stress before, during and after annealing of Au/Cr films evaporated under oblique incidence has been performed. Full microgyroscopes with the whole 3D tranduction system were realized. Preliminary characterizations of realized gyroscopes by out-of-plane and in-plane optical vibrometry demonstrated promising results. Finally, different ways to improve the design and fabrication process are proposed.

Metallic thin films consisting of separated nanostructures are fabricated by evaporative glancing angle deposition at room temperature. The columnar microstructure of the Ti and Cr columns is investigated by high resolution transmission electron microscopy and selective area electron diffraction. The morphology of the sculptured metallic films is studied by scanning electron microscopy. It is found that tilted Ti and Cr columns grow with a single crystalline morphology, while upright Cr columns are polycrystalline. Further, the influence of continuous substrate rotation on the shaping of Al, Ti, Cr and Mo nanostructures is studied with view to surface diffusion and the shadowing effect. It is observed that sculptured metallic thin films deposited without substrate rotation grow faster compared to those grown with continuous substrate rotation. A theoretical model is provided to describe this effect

Thin films are produced from layers of materials ranging from nanometres to micrometres in height. They are increasingly common and are being used in integrated circuit design, optical coatings, protective coatings, and environmental sensing. Thin films can be fabricated using a variety of methods involving chemical reactions or physical transport of matter. Glancing angle deposition (GLAD) thin films are produced using physical vapour deposition techniques under high vacuum conditions where exploitation of the geometric conditions between the source and the substrate causes enhanced atomic self shadowing to produce structured thin films. This work deals with the modification of these films, emph{in situ} by altering growing conditions through substrate temperatures control, or post-deposition through reactive ion etching (RIE). The first part of the thesis deals with the modification of TiO$_2$ GLAD humidity sensors using RIE with CF$_4$. The data presented demonstrates improved response times to step changes in humidity. Characterization revealed response times of better then 50~ms (instrument-limited measurement). An etch recipe for complete removal of TiO$_2$ was also demonstrated with shadow masking to transfer patterns into GLAD films. The subsequent chapter focuses on modification of thin film growth conditions by increasing adatom mobility. A radiative heating system was designed and implemented with the ability to achieve chuck temperatures of 400$^circ$C. Capping layers on top of GLAD films were grown to demonstrate effects of emph{in situ} heating, and a quantitative analysis of crack reduction with increased temperatures is presented. Lithographic pattern transfer onto a capped GLAD film was demonstrated. Opposite to the goal of the preceding chapter, the focus of the final experimental chapter was to limit adatom mobility. A LN$_2$-based cooling system was designed and implemented for the purpose of studying the growth by GLAD of lower melting point materials, which under regular growth conditions do not form well-defined structures. Chuck temperatures of $-60$$^circ$C can be achieved during deposition while still allowing substrate rotation. The growth of helical copper films was used to demonstrate the effects of emph{in situ} substrate cooling. / Micro-Electro-Mechanical Systems (MEMS) and Nanotechnology

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Cette thèse participe à l'étude générale et à la compréhension des relations structure- propriétés optiques de couches minces d'oxyde de tungstène, nanostructurées lors de leur dépôt par la technique Glancing Angle Déposition. Cette technique repose sur le contrôle de l'orientation relative du substrat vis à vis de la source de vapeur.[...] / This thesis contributes to the general study and understanding of the relationship between structure and optical properties of nanostructured tungsten oxide by Glancing Angle Déposition technique. this technique relies on the control of the relative orientation of the substrate to the vapor source.[...]