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.

L'objet de cette thèse est l'étude de l'interaction d'un laser femtoseconde avec un support photosensible particulier: un verre phosphate dopé à l'argent appelé verre photo-luminescent (PL). Une nouvelle approche permettant de réaliser en trois dimensions dans un verre PL des nanostructures d'argent aux dimensions bien inférieures à la limite de diffraction est tout d'abord présentée. La mesure des propriétés optiques et structurales pour différentes échelles (spatiales et temporelles) a permis de proposer un mécanisme de formation des structures photo-induites qui est basé sur un jeu subtil entre les phénomènes d’absorption non-linéaire et de thermo-diffusion. La deuxième partie de cette thèse sera orientée sur les propriétés optiques (linéaires et non-linéaires) et les applications des ces nanostructures d’argent. En particulier, l’exaltation des propriétés non-linéaires des agrégats d’argent sera exploitée pour stocker optiquement de l’information en trois dimentions. / The aim of this work is the study of the interaction between a femtosecond laser and a special photosensitive medium: a silver containing phosphate glass, also called photo-luminescent (PL) glass. A new approach allowing to write, inside the PL glass, 3D silver nanostructures with feature size down to the diffraction limit is presented. Based on optical and structural measurments at different time and spacial scales, the mechanism of the formation of these nanostructures is described. A subtle interplay between nonlinear absorption and thermo-diffusion effects is found to be the key of the mechanism. The second part of this work relies on the optical properties (linear and nonlinear) and few applications of the silver nanostructures. More particulary, the enhancement of their nonlinear properties is used for three dimentional optical data storage.