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This dissertation details an investigation into the use of laser pulses from a titanium:sapphire regenerative amplifier laser system to vaporize analytes in ambient air for mass spectral analysis. The laser system was modified to operate in one of two distinct modes. In femtosecond (fs) mode the laser produced 2.5 mJ, ~60 fs laser pulses centered at 800 nm. In nanosecond (ns) mode the laser produced 2.4 mJ, ~10 ns laser pulses centered at 800 nm. Using appropriate optical components the laser pulse energy was attenuated to achieve pulses varying from 0.15 mJ to 2.0 mJ. Laser pulses were used to vaporize liquid and solid samples on different substrates. The laser vaporized material was captured and ionized by an electrospray source and then detected via a mass spectrometer instrument. It was discovered that samples on glass substrate could be vaporized by fs laser pulses, but not by ns laser pulses. Samples on metal substrate were successfully vaporized by both fs and ns laser pulses. Low energy ns laser pulses were less efficient than fs laser pulses of the same energy for vaporizing off metal substrate. A comparison of vaporization from aluminum, copper and stainless steel substrates revealed limited vaporization from copper by ns laser pulses. The electrospray ionization (ESI) mass spectral response of wet and dry proteins on stainless steel was similar for both fs and ns laser pulses. Experiments to test the capabilities of ns laser electrospray mass spectrometry (ns-LEMS) revealed that sample vaporization was limited to analysis on metal surfaces. This dissertation details methods for femtosecond laser electrospray ionization (fs-LEMS) to be used to quantify non-covalent protein-ligand interactions. Hen egg white lysozyme (HEWL) and N,N’,N”-triacetylchitotriose (NAG3) interactions were quantified via dissociation constant (Kd) measurements. The Kd for HEWL and N,N’,N”,N”’-tetraacetylchitotetraose (NAG4) were also measured. This dissertation also reports a miniaturized flowing atmospheric pressure afterglow (micro-FAPA) for use as an alternative ionization source of fs-laser vaporized analytes. Loratadine pills were vaporized and reacted with the gas stream from the micro-FAPA source to generate ions which were then detected by a mass analyzer. The ions detected varied in distribution as a response to the distance the sample was vaporized from the ion source. Complexed samples were tested and molecular assignments were difficult due to the numerous pathways for ion formation. The use of an ion filter to decrease the energy imparted on sample molecules during the ionization process of the micro-FAPA is also reported. / Chemistry

This dissertation elucidates the instrumentation and application of a hybrid ambient ionization source, laser electrospray mass spectrometry (LEMS), for the direct analysis and molecular imaging of biological tissue without matrix deposition. In LEMS, laser pulses from a Ti:Sapphire laser amplifier (60 fs, 800 nm, and 1 mJ) interact with surface analytes and transfer them from the condensed phase into the gas phase without the requirement of either exogenous matrix or endogenous water in the sample. The laser vaporized analytes are captured and ionized by an electrospray source, and finally detected by a mass analyzer. It was found that a turn-key, robust femtosecond fiber laser with longer wavelength, longer duration, and lower pulse energy at 1042 nm, 425 fs, and 50 µJ, respectively, provided comparable results with the Ti:Sapphire laser. Vaporization of intact, dried or aqueous cytochrome c and lysozyme samples was demonstrated by the fiber laser. A charge states distribution at lower charge states indicating folded conformation of proteins and the hemoglobin α subunit-heme complex from whole blood was observed. Endogenous anthocyanins, sugars, and other metabolites were detected and revealed the anticipated metabolite profile for the flower petal and leaf samples by the fiber laser. Phospholipids, especially phosphatidylcholine, were identified from a fresh mouse brain section sample. These lipid features were suppressed in both the fiber laser and Ti:Sapphire LEMS measurement in the presence of optimal cutting temperature compounds which are commonly used in animal tissue cryosectioning. This dissertation also details the design of an automated mass spectrometry imaging source based on the Ti:Sapphire LEMS. The laser, translation stage, and mass analyzer are synchronized and controlled using a customized user interface to enable step-by-step scanning of the area of interest on a given tissue sample. The imaging source is coupled with a high resolution accurate mass quadrupole time-of-flight (QTOF) mass analyzer with tandem mass analysis capability. A lateral resolution of 60 µm was demonstrated on a patterned ink film by LEMS imaging. Plant metabolites including sugar and anthocyanins were directly imaged from a leaf sample. Small metabolites, lipids and proteins were simultaneously imaged from a single tissue section of a pig liver sample. Biomarkers of blood-brain barrier damage and traumatic brain injury (TBI) that occurred during the injury were detected and imaged from a TBI mouse brain. The loading values from principal component analysis (PCA) were shown to be useful for identification of features of interest from the large LEMS imaging dataset. / Chemistry

During the past decades, femtosecond laser micro-fabrication has gained growing interests owing to its several unique features including direct and maskless fabrication, flexible choice of materials and geometries, and truly three-dimensional fabrication. Moreover, fiber-optic sensors have demonstrated distinct advantages over traditional electrical sensors such as the immunity to electromagnetic interference, miniature footprint, robust performance, and high sensitivity. Therefore, the marriage between femtosecond laser micro-fabrication and optical fibers have enabled and will continue to offer vast opportunities to create novel structures for sensing applications. This dissertation focuses on design, fabrication and characterization of optical-fiber based interferometric devices for sensing applications. Three novel devices have been proposed and realized, including point-damage-based Fiber Bragg gratings in single-crystal sapphire fibers, all-sapphire fiber-tip Fabry-Pérot cavity, and in-fiber Whispering-Gallery mode resonator / Doctor of Philosophy / Optical fibers are an optical platform with cylindrical symmetry with overall diameter typically within 50 to 500 μm. The miniature footprint and large aspect ratio make it attractive in sensing applications, where intrusion, flexibility, robustness and small size are key design parameters. Beyond that, fiber-optic sensors also possess distinct operational advantages over traditional electrical sensors such as high sensitivity, immunity to electromagnetic interference (EMI), and fully distributed deployment. Owing to the above advances, fiber-optic sensors have been one of the key technologies in the broader sensing field for the past decades. However, the unique cylindrical shape of optical fiber makes it naturally less compatible to those well-developed fabrication technologies in the current sophisticated semiconductor industry. During the past decades, the possibility of three-dimensional (3D) writing inside transparent materials with tightly focused ultrafast laser pulses has attracted attention widely among the academy as well as the industry. Therefore, the marriage between ultrafast laser micro-fabrication and optical fibers have enabled and will continue to offer vast opportunities to create novel structures for sensing applications. This dissertation focuses on design, fabrication and characterization of optical-fiber based interferometric devices for sensing applications. Three novel devices have been proposed and realized, including point-damage-based Fiber Bragg gratings in single-crystal sapphire fibers, all-sapphire fiber-tip Fabry-Pérot cavity, and in-fiber Whispering-Gallery mode resonator.

Thesis (MSc)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: The selective excitation of an arbitrary vibrational level of a polyatomic molecule, without passage through an intermediary electronic excited state is demonstrated. This was achieved by simulating the interaction of a shaped, femtosecond pulse with one vibrational mode of the molecule. The carrier frequency of the pulse is chosen near resonant to the ground-to- rst-excited vibrational transition of the mode, and the pulse shape is optimized via closed-loop feedback. The simulation concentrates on the rst few vibrationally excited states since the density of states is still low, thus ensuring that the inter-vibrational decoherence time is relatively long compared to the pulse length. While various molecules were investigated this study focuses onUF6 for which detailed spectroscopic data for the v3 vibrational mode is available in literature. A multilevel model was developed and can be adapted for any number of levels. The model reported here was limited to a vibrational quantum number of four. The spectroscopic data included anharmonic splitting as well as forbidden transitions. The effect of rotational levels was not included. A density matrix approach was followed because this will allow for the introduction of dephasing of the coherent excitation via thermalizing collisions with the reservoir, as well as inter-vibrational relaxation. The time evolution of the density matrix is given by the Von Neumann equations. / AFRIKAANSE OPSOMMING: Die selektiewe opwekking van 'n arbitrêre vibrasionele vlak van 'n poliatomies molekule sonder oorgang na 'n intermediëre elektroniese opgewekte toetstand word gedemonstreer. Dit was bereik deur die interaksie te simuleer van 'n gevormde, femtosekonde pulse met een vibrasionele mode van 'n molekule. Die draer frekwensie van die pulse is so gekies dat dit naby resonansie van die grond-tot-eerste-opgewekte vibrasionele oorgang van die mode is, die puls vorm word geoptimeer deur 'n geslote-lus terugvoer. Die simulasie konsentreer op die eerste paar vibrasionele opgewekte toestande, omdat die digtheid van toestande nog steeds laag is, dus verseker dit dat inter-vibrasionele de-koherensie tyd relatief lank is in vergelyking met die puls se lengte. Verskillende molekules was ondersoek vir die studie. Die fokus is op UF6 waarvoor gedetaileerde spektroskopiese data vir die v3 vibrasionele beskikbaar is in die literatuur. 'n Multivlak model was ontwikkel en kan aangepas word vir enige aantal van vlakke. Die model wat hier aangemeld is, is beperk tot die vibrasionele kwantum getal van vier. Die spektroskopiese data het anharmonies splitting so wel as nie toegelaatbare oorgange bevat. Die effek van rotasionele vlakke was nie in berekening geneem nie. 'n Digtheids matriks benadering was gevolg, omdat dit toelaat vir die dekoherensie. Die tyd evolusie van die digtheids matriks word gegee deur die Von Neumann vergelykings.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

La structuration laser femtoseconde en trois dimensions rencontre un intérêt grandissant du fait de sa facilité de mise en œuvre et des nombreuses applications qu’elle peut couvrir dans le domaine des composants photoniques. Des structures telles que des guides d’onde, des réseaux de diffraction, des mémoires optiques ou des cristaux photoniques peuvent être fabriquées grâce à cette technique. Son emploi sur des verres oxydes est prometteur car ces derniers présentent des avantages certains ; ils sont très résistants au flux et au vieillissement, leur composition chimique peut être changée facilement afin de s’adapter à un cahier des charges précis. On les retrouve déjà dans les amplificateurs Raman, les fibres optiques, les lasers à fibres, etc… Le travail de cette thèse s’articule autour de deux grands axes. Le premier axe consiste à caractériser les propriétés optiques linéaires et non-linéaires de matériaux vitreux massifs afin d’optimiser leur composition en vue d’une application particulière. Dans ce contexte, les propriétés optiques non-linéaires, leurs origines physiques (électronique et nucléaire) ainsi que leurs temps de réponse caractéristiques (de quelques femtosecondes à quelques centaines de picosecondes) sont décrits dans le cadre de l’approximation de Born-Oppenheimer. Ainsi, la silice fondue et plusieurs verres sodo-borophosphates contenant différentes concentrations en oxyde de niobium ont été étudiés. Les résultats montrent que les propriétés optiques non-linéaires dans la silice fondue sont majoritairement d’origine électronique, alors que dans les verres sodo-borophosphates, la contribution d’origine nucléaire peut devenir prépondérante lorsque la concentration en oxyde de niobium dépasse 30%. Le second axe s’articule autour de la structuration des matériaux. Trois échantillons commerciaux de silice fondue présentant des conditions de fabrication différentes (donc des taux d’impuretés distincts) et irradiés avec un laser femtoseconde proche infrarouge ont été étudiés. Les défauts induits par laser ont été identifiés au moyen de plusieurs techniques de spectroscopie. Elles ont montré la formation de centres colorés ainsi qu’une densification au niveau de la zone irradiée. Leurs propriétés optiques linéaire (indice de réfraction) et non-linéaire (susceptibilité du troisième ordre) ont été mesurées. De plus, la structuration de la silice fondue à l’échelle sub-micrométrique sous forme de « nano-réseaux » est observée et la biréfringence de forme induite par ces structures est discutée. En plus des échantillons de silice fondue, plusieurs verres oxydes présentant des compositions chimiques très distinctes ont été étudiés. Un verre sodo-borophosphate contenant de l’oxyde de niobium exhibe des micro-craquelures et des nano-crystallites après irradiation. Un verre silicate contenant ou non de l’argent dévoile des structures en anneau fluorescentes ou en « nano-réseaux ». Un verre zinc phosphate contenant de l’argent présente lui aussi des structures en anneau fluorescentes, d’une taille de l’ordre de 80 nm, bien inférieure à la limite de diffraction. Des techniques pompe-sonde sous microscope ont été mises en œuvre sur ce dernier verre pour étudier l’interaction laser-verre. Le mécanisme d’absorption de l’énergie lumineuse pour ce verre est l’absorption à quatre photons. La densité d’électrons libres générée est de l’ordre de 1017 cm-3, ce qui permet de conclure qu’un gaz d’électrons plutôt qu’un plasma se forme pendant l’irradiation laser. / Three-dimensional femtosecond laser structuring has a growing interest because of its ease of implementation and the numerous possible applications in the domain of photonic components. Structures such as waveguides, diffraction gratings, optical memories or photonic crystals can be fabricated thanks to this technique. Its use with oxide glasses is promising because of several advantages; they are resistant to flux and ageing, their chemical composition can easily be changed to fit the well-defined requirements of an application. They can already be found in Raman amplifiers, optical fibers, fiber lasers, and other devices. This thesis is based on two axes. The first axis consists in characterizing the linear and nonlinear optical properties of bulk vitreous materials in order to optimize their composition with a particular application in view. Within this context, the nonlinear optical properties, their physical origins (electronic and nuclear) as well as their characteristic response times (from a few femtoseconds to a few hundreds of picoseconds) are described within the Born-Oppenheimer approximation. Fused silica and several sodium-borophosphate glasses containing different concentrations in niobium oxide have been studied. Results show that the nonlinear optical properties of fused silica are mainly from electronic origin, whereas in the sodium-borophosphate glasses, the contribution from nuclear origin becomes predominant when the concentration of niobium oxide exceeds 30%. The second axis is based on the structuring of materials. Three commercially available fused silica samples presenting different fabrication conditions (therefore distinct impurity levels) and irradiated with a near infrared femtosecond laser have been studied. The laser induced defects have been identified by means of several spectroscopic techniques. They show the formation of color centers as well as a densification inside the irradiated area. Their linear refractive index and nonlinear third-order susceptibility properties have been measured. Moreover, the structuring of fused silica at the subwavelength scale into “nanogratings” is observed and the form of birefringence induced by these structures is discussed. In addition to the fused silica samples, several oxide glasses presenting very distinct chemical compositions have been studied. A sodium-borophosphate glass containing niobium oxide exhibits micro-cracks and nano-crystallites following irradiation. A silicate glass with or without a silver component reveals fluorescent rings or “nanograting” structures. A zinc phosphate glass containing silver also presents fluorescent ring structures, with a size of the order of 80 nm, well below the diffraction limit. Pump-probe microscope techniques have been performed on this glass to investigate the laser-glass interaction. The absorption mechanism is determined to be four-photon absorption. The generated free electron density is ~ 1017 cm-3, which suggests the conclusion that an electron gas rather than a plasma is formed during the laser irradiation.

Mon travail pendant cette thèse a d’abord été le développement d’une source de génération d’harmoniques d’ordre élevé basée sur une chaîne laser femtoseconde amplifiée (Saphir-Titane) fonctionnant à une cadence de 1 kHz (AURORE). Une ligne de lumière construite au CELIA permet de fournir un faisceau focalisé VUV-XUV femtoseconde, monochromatique dans une région spectrale comprise entre 10 nm et 73 nm environ (17 eV à 120 eV). Cette installation expérimentale est en fonctionnement et est parmi les toutes premières lignes à être mise en service pour la communauté scientifique française et étrangère. J’ai également mis en place une installation d'étude des cinétiques de luminescence avec résolution temporelle sub-picoseconde (450 fs) par mélange de fréquences. Le thème général de ce travail est l’étude des processus de relaxation et d'interaction entre les excitations électroniques créées par des impulsions ultra brèves femtosecondes de photons IR, UV et VUV-XUV dans les solides diélectriques massifs et des nano particules. L’observable principale utilisée est la luminescence émise par ces systèmes, résolue spectralement et en temps sur des échelles allant de la µs à des temps sub picosecondes. Ce travail a abouti à une avancée sensible de la description des processus principaux de formation et d’évolution des excitations électroniques. La comparaison et l’interprétation des données expérimentales obtenues pour des nano particules et des cristaux ont permis d’élucider certaines propriétés spécifiques de ces systèmes. / The work during this Ph.D. was a development of a source of high order harmonics generation based on amplified Ti:Sapphire femtosecond laser with repetition rate 1kHz (AURORE). The beam line constructed in CELIA has on its exit a VUV-XUV focalized beam; it may has wide spectrum or monochromatic in spectral range from 10nm up to 73nm (17-120eV). This beam line is in operation and is using for experiments for solid state VUV spectroscopy, photoelectron spectroscopy etc. Also it was installed a system for detection of luminescence with sub-picosecond time resolution (450fs) based on the nonlinear effect – generation of sum of two light frequencies. The main subject of this work was the study of processes of relaxation and interaction of electronic excitations, created by ultra-short pulse of IR, UV or XUV in dielectric crystals and nanoparticles. Out method is based on observation of luminescence with spectral and time resolution up to sub-picosecond temporal resolution. This study has given new experimental results for description of fundamental processes of creation and evolution of electronic excitations. Comparison and interpretation of experimental data of semiconductor nano-particles and monocrystals gave some interpretations of extra-fast luminescence of these systems.

La capacité de la tomographie par cohérence optique (OCT) à délivrer des images tomographiques de tissus biologiques in vivo, de manière non invasive et en temps réel, a suscité un intérêt croissant pour de nombreuses applications biomédicales, principalement en ophtalmologie pour l’imagerie de la rétine et du segment antérieur de l’œil. Toutefois, pour l’imagerie à haute résolution de tissus biologiques fortement diffusants, comme la sclérotique et la cornée œdémateuse, la technique nécessitait des améliorations technologiques. Dans cette thèse, un système d’OCT « Fourier-domain » (FD-OCT) à très haute résolution spatiale (< 4 µm), à la longueur d’onde de 1,3 µm, a été développé dans la Laboratoire Charles Fabry – Institute d’Optique Graduate School. Avec ce système original, nous avons réussi, pour la première fois, à visualiser correctement le canal de Schlemm de l’œil humain qui se trouve à une profondeur d’environ 0,8 mm dans le limbe de la cornée, milieu fortement diffusant. L’imagerie du canal de Schlemm est capitale afin d’envisager la chirurgie par laser du glaucome, qui consiste à inciser cette partie de l’œil afin d’améliorer l’écoulement de l’humeur aqueuse. Par ailleurs, en collaboration avec le Laboratoire d’Optique Appliquée de l’ENSTA ParisTech, nous avons démontré la possibilité de contrôler en temps réel par OCT des découpes par laser femtoseconde pratiquées dans la cornée humaine in vitro. Ces travaux ont montré que l’opération du Glaucome par laser femtoseconde, contrôlée par OCT, devrait être possible. / The ability of optical coherence tomography (OCT) to deliver tomographic images of biological tissues in vivo non-invasively and in real-time has been a growing interest in many biomedical applications, mainly in ophthalmology for imaging the retina and the anterior segment of the eye. However, developing high-resolution OCT for imaging strongly scattering biological tissues like sclera and edematous cornea has still been the main challenge. In this PhD work, an ultrahigh-resolution (< 4 µm) Fourier-domain OCT (FD-OCT) system optimized at 1.3 µm center wavelength was developed in Laboratoire Charles Fabry – Institut d’Optique Graduate School. Using this OCT system, we have, for the first time, properly visualized the Schlemm’s canal of the human eye that is located in the strongly scattering corneal limbus at depth of ~ 0.8 mm. Schlemm’s canal has been our target for OCT imaging because it plays an important role for the management of the aqueous humor that is responsible for causing glaucoma - an eye disease that can potentially lead to blindness. In collaboration with Laboratoire d’Optique Appliquée at ENSTA ParisTech, we have also demonstrated real-time OCT imaging of the femtosecond laser surgery in excised human cornea. These studies have thus shown that the surgery of glaucoma by femtosecond laser, monitored by OCT, would be possible.