Femtosecond electron diffraction experiments were performed on solid state iron(II) tris(2,2'-bipyridine) bis(hexafluorophosphate). The cation is known to undergo a spin crossover process when solvated in water and irradiated with 400 nm coherent light which results in a transition from a low spin to high spin state within a picosecond which is accompanied by a uniform 0.2 Å Fe-N bond elongation. A femtosecond diffraction experiment was performed on the solid sample and was unable to find evidence of a fast spin crossover transition. Suspecting this may be due to limitations of the apparatus, an ultrafast transient absorption experiment was performed. Emulating the liquid study by Gawelda et al, the pump probe experiment found evidence of spin crossover in the solid state sample. This result awaits verification by an improved transient absorption apparatus and has inspired efforts to perform an improved femtosecond electron diffraction experiment.

Femtosecond electron diffraction experiments were performed on solid state iron(II) tris(2,2'-bipyridine) bis(hexafluorophosphate). The cation is known to undergo a spin crossover process when solvated in water and irradiated with 400 nm coherent light which results in a transition from a low spin to high spin state within a picosecond which is accompanied by a uniform 0.2 Å Fe-N bond elongation. A femtosecond diffraction experiment was performed on the solid sample and was unable to find evidence of a fast spin crossover transition. Suspecting this may be due to limitations of the apparatus, an ultrafast transient absorption experiment was performed. Emulating the liquid study by Gawelda et al, the pump probe experiment found evidence of spin crossover in the solid state sample. This result awaits verification by an improved transient absorption apparatus and has inspired efforts to perform an improved femtosecond electron diffraction experiment.

Monte Carlo (MC) simulations are widely used in the field of medical biophysics, particularly for modelling light propagation in biological tissue. The iterative nature of MC simulations and their high computation time currently limit their use to solving the forward solution for a given set of source characteristics and tissue optical properties. However, applications such as photodynamic therapy treatment planning or image reconstruction in diffuse optical tomography require solving the inverse problem given a desired light dose distribution or absorber distribution, respectively. A faster means for performing MC simulations would enable the use of MC-based models for such tasks. In this thesis, a gold standard MC code called MCML was accelerated using two distinct hardware-based approaches, namely designing custom hardware on field-programmable gate arrays (FPGAs) and programming commodity graphics processing units (GPUs). Currently, the GPU-based approach is promising, offering approximately 1000-fold speedup with 4 GPUs compared to an Intel Xeon CPU.

Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities were developed for quantitative structural investigations of nano and micro-sized architectures. Non-invasive extraction of crystallographic information in microscopic samples will have a number of potential benefits, for example, in clinical applications, allowing observations of disease states inside tissues without the need for biopsy. Industrial nanotechnology will benefit from fast determination of nanostructures with nonlinear microscopy that will improve quality of nanodevices.

La spectroscopie Raman est un outil non destructif fort utile lors de la caractérisation de matériau. Cette technique consiste essentiellement à faire l’analyse de la diffusion inélastique de lumière par un matériau. Les performances d’un système de spectroscopie Raman proviennent en majeure partie de deux filtres ; l’un pour purifier la raie incidente (habituellement un laser) et l’autre pour atténuer la raie élastique du faisceau de signal. En spectroscopie Raman résonante (SRR), l’énergie (la longueur d’onde) d’excitation est accordée de façon à être voisine d’une transition électronique permise dans le matériau à l’étude. La section efficace d’un processus Raman peut alors être augmentée d’un facteur allant jusqu’à 106. La technologie actuelle est limitée au niveau des filtres accordables en longueur d’onde. La SRR est donc une technique complexe et pour l’instant fastidieuse à mettre en œuvre. Ce mémoire présente la conception et la construction d’un système de spectroscopie Raman accordable en longueur d’onde basé sur des filtres à réseaux de Bragg en volume. Ce système vise une utilisation dans le proche infrarouge afin d’étudier les résonances de nanotubes de carbone. Les étapes menant à la mise en fonction du système sont décrites. Elles couvrent les aspects de conceptualisation, de fabrication, de caractérisation ainsi que de l’optimisation du système. Ce projet fut réalisé en étroite collaboration avec une petite entreprise d’ici, Photon etc. De cette coopération sont nés les filtres accordables permettant avec facilité de changer la longueur d’onde d’excitation. Ces filtres ont été combinés à un laser titane : saphir accordable de 700 à 1100 nm, à un microscope «maison» ainsi qu’à un système de détection utilisant une caméra CCD et un spectromètre à réseau. Sont d’abord présentés les aspects théoriques entourant la SRR. Par la suite, les nanotubes de carbone (NTC) sont décrits et utilisés pour montrer la pertinence d’une telle technique. Ensuite, le principe de fonctionnement des filtres est décrit pour être suivi de l’article où sont parus les principaux résultats de ce travail. On y trouvera entre autres la caractérisation optique des filtres. Les limites de basses fréquences du système sont démontrées en effectuant des mesures sur un échantillon de soufre dont la raie à 27 cm-1 est clairement résolue. La simplicité d’accordabilité est quant à elle démontrée par l’utilisation d’un échantillon de NTC en poudre. En variant la longueur d’onde (l’énergie d’excitation), différentes chiralités sont observées et par le fait même, différentes raies sont présentes dans les spectres. Finalement, des précisions sur l’alignement, l’optimisation et l’opération du système sont décrites. La faible acceptance angulaire est l’inconvénient majeur de l’utilisation de ce type de filtre. Elle se répercute en problème d’atténuation ce qui est critique plus particulièrement pour le filtre coupe-bande. Des améliorations possibles face à cette limitation sont étudiées. / Raman spectroscopy is a useful and non-destructive tool for material characterization. It uses inelastic light scattering interaction with matter to investigate materials. The major part of the performances in a Raman spectroscopy system comes from two light filter units: the first shapes the light source (usually a laser) and the other attenuates the elastic scattered light in the signal beam. In resonant Raman spectroscopy (RRS), the excitation energy (wavelength) is tuned to match an electronic transition of the sample. When in resonance, the Raman cross section is increased by a factor up to 106. Current RRS setups are limited by filtering devices technology. RRS is a complex technique which, for the moment, remains tedious to implement. This master thesis presents the construction of a tunable Raman spectroscopy system based on volume Bragg gratings light filters. The setup is designed to operate in the near infrared region so as to study carbon nanotubes resonances. Steps leading to the operation of the system are described. They cover conceptualization, fabrication, characterization and optimisation of the setup. Collaboration with a local small company, Photon etc, led to the building of two new light filters that allow to tune easily the excitation wavelength. These filters have been adapted to work with a tunable titanium-sapphire laser (tunable from 700 to 1100 nm) and assembled with a homemade microscope and a detection system combining a CCD camera with a grating spectrometer. This document is arranged as follow: First are presented the theoretical aspects surrounding RRS. Carbon nanotubes (CNT) are than described to illustrate the relevance of such technique applied to material science. Principles behind the use of the Bragg filters are described to be followed by a scientific paper in which the main results of this work are presented. These include the optical characterisation of the filters and measurements with the system. Low frequency limits of the system are demonstrated using a sulphur powder where the 27 cm-1 line is clearly resolved. The tunability of the setup is also demonstrated using a bulk carbon nanotube sample. By changing the excitation wavelength, different nanotube chiralities become resonant, leading to different signals in the Raman spectra. Finally, clarifications regarding the alignment, optimisation and operation of the system are described. Low angular acceptance has been found to be the main drawback of the system leading to attenuation problems especially critical for the notch filter. Possible improvements on this limitation are discussed.

Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities were developed for quantitative structural investigations of nano and micro-sized architectures. Non-invasive extraction of crystallographic information in microscopic samples will have a number of potential benefits, for example, in clinical applications, allowing observations of disease states inside tissues without the need for biopsy. Industrial nanotechnology will benefit from fast determination of nanostructures with nonlinear microscopy that will improve quality of nanodevices.

The design of a photonics-based multi-gas sensor is presented. Absorption spectroscopy theory has been analyzed to derive key requirements for effective gas concentration measurements. HITRAN spectral analyses have determined appropriate ranges for single and multi-gas sensing. A discussion of two setups (large-scale setup and portable prototype) outlines relevant results for the development of innovative data processing algorithms (floating-point technique (FPT)). Eight absorption lines were experimentally detected (761 nm range), facilitating the recognition of oxygen spectra with surety. The FPT was used to measure oxygen concentration with an approx. 2.5% error when scanning one absorption line. Strategies to reduce the error to below 0.1% and to improve the prototype are presented. The sensor is expected to operate in an inhomogeneous network. The network utilizes different sensors capable of cross-using information to achieve high reliability and accuracy, in order to predict, prevent, and recognize man-made and natural threats.

This thesis examines second-order optical nonlinear wave mixing processes in domain-disordered quasi-phase matching waveguides and evaluates their potential use in compact, monolithically integrated wavelength conversion devices. The devices are based on a GaAs/AlGaAs superlattice-core waveguide structure with an improved design over previous generations. Quantum-well intermixing by ion-implantation is used to create the quasi-phase matching gratings in which the nonlinear susceptibility is periodically suppressed. Photoluminescence experiments showed a large band gap energy blue shift around 70 nm after intermixing. Measured two-photon absorption coefficients showed a significant polarization dependence and suppression of up to 80% after intermixing. Similar polarization dependencies and suppression were observed in three-photon absorption and nonlinear refraction. Advanced modeling of second-harmonic generation showed reductions of over 50% in efficiency due to linear losses alone. Self-phase modulation was found to be the dominant parasitic nonlinear effect on the conversion efficiency, with reductions of over 60%. Simulations of group velocity mismatch showed modest reductions in efficiency of less than 10%. Experiments on second-harmonic generation showed improvements in efficiency over previous generations due to low linear loss and improved intermixing. The improvements permitted demonstration of continuous wave second-harmonic generation for the first time in such structures with output power exceeding 1 µW. Also, Type-II phase matching was demonstrated for the first time. Saturation was observed as the power was increased, which, as predicted, was the result of self-phase modulation when using 2 ps pulses. By using 20 ps pulses instead, saturation effects were avoided. Thermo-optically induced bistability was observed in continuous wave experiments. Difference frequency generation was demonstrated with wavelengths from the optical C-band being converted to the L- and U-bands with continuous waves. Conversion for Type-I phase matching was demonstrated over 20 nm with signal and idler wavelengths being separated by over 100 nm. Type-II phase matched conversion was also observed. Using the experimental data for analysis, self-pumped conversion devices were found to require external amplification to reach practical output powers. Threshold pump powers for optical parametric oscillators were calculated to be impractically large. Proposed improvements to the device design are predicted to allow more practical operation of integrated conversion devices based on quasi-phase matching superlattice waveguides.

The design of a photonics-based multi-gas sensor is presented. Absorption spectroscopy theory has been analyzed to derive key requirements for effective gas concentration measurements. HITRAN spectral analyses have determined appropriate ranges for single and multi-gas sensing. A discussion of two setups (large-scale setup and portable prototype) outlines relevant results for the development of innovative data processing algorithms (floating-point technique (FPT)). Eight absorption lines were experimentally detected (761 nm range), facilitating the recognition of oxygen spectra with surety. The FPT was used to measure oxygen concentration with an approx. 2.5% error when scanning one absorption line. Strategies to reduce the error to below 0.1% and to improve the prototype are presented. The sensor is expected to operate in an inhomogeneous network. The network utilizes different sensors capable of cross-using information to achieve high reliability and accuracy, in order to predict, prevent, and recognize man-made and natural threats.

Monte Carlo (MC) simulations are widely used in the field of medical biophysics, particularly for modelling light propagation in biological tissue. The iterative nature of MC simulations and their high computation time currently limit their use to solving the forward solution for a given set of source characteristics and tissue optical properties. However, applications such as photodynamic therapy treatment planning or image reconstruction in diffuse optical tomography require solving the inverse problem given a desired light dose distribution or absorber distribution, respectively. A faster means for performing MC simulations would enable the use of MC-based models for such tasks. In this thesis, a gold standard MC code called MCML was accelerated using two distinct hardware-based approaches, namely designing custom hardware on field-programmable gate arrays (FPGAs) and programming commodity graphics processing units (GPUs). Currently, the GPU-based approach is promising, offering approximately 1000-fold speedup with 4 GPUs compared to an Intel Xeon CPU.