Information regarding the structure and function of living tissues and cells is instrumental to the advancement of cell biology and biophysics. Nonlinear optical microscopy can provide such information, but only certain biological structures generate nonlinear optical signals. Therefore, structural specificity can be achieved by introducing labels for nonlinear optical microscopy. Few studies exist in the literature about labels that facilitate harmonic generation, coined "harmonophores". This thesis consists of the first major investigation of harmonophores for third harmonic generation (THG) microscopy. Carotenoids and chlorophylls were investigated as potential harmonophores. Their nonlinear optical properties were studied by the THG ratio technique. In addition, a tunable refractometer was built in order to determine their second hyperpolarizability (γ). At 830 nm excitation wavelength, carotenoids and chlorophylls were found to have large negative γ values however, at 1028 nm, the sign of γ reversed for carotenoids and remained negative for chlorophylls. Consequently, at 1028 nm wavelength, THG signal is canceled with mixtures of carotenoids and chlorophylls. Furthermore, when such molecules are covalently bonded as dyads or interact within photosynthetic pigment-protein complexes, it is found that additive effects with the γ values still play a role, however, the overall γ value is also influenced by the intra-pigment and inter-pigment interaction. The nonlinear optical properties of aggregates containing chlorophylls and carotenoids were the target of subsequent investigations. Carotenoid aggregates were imaged with polarization-dependent second harmonic generation and THG microscopy. Both techniques revealed crystallographic information pertaining to H and J aggregates and β-carotene crystalline aggregates found in orange carrot. In order to demonstrate THG enhancement due to labeling, cultured cells were labeled with carotenoid incorporated liposomes. In addition, Drosophila melanogaster larvae muscle as well as keratin structures in the hair cortex were labeled with β-carotene. Polarization-dependent THG studies may be particularly useful in understanding the structural organization that occurs within biological structures containing carotenoids and chlorophylls such as photosynthetic pigment-protein complexes and carotenoid aggregates in plants and alga. Further, artificial labeling with carotenoids and chlorophylls may be useful in clinical applications since they are nontoxic, nutritionally valuable, and they can aid in visualizing structural changes in cellular components.

This research was mainly focused on the design and optimization of aperture-based structures to achieve the greatest third harmonic conversion efficiency. It was discovered that by tuning the localized surface plasmon resonance to the fundamental beam wavelength, and by tuning the propagating surface plasmons resonance to the Bragg resonance of the aperture arrays, both the directivity and conversion efficiency of the third harmonic signal were enhanced. The influence of the gap plasmon resonance on the third harmonic conversion efficiency of the aperture arrays was also investigated. The resulted third harmonic generation (THG) from an array of annular ring apertures as a closed loop structure were compared to arrays of H-shaped, double nanohole and rectangular apertures as open-loop structures. The H-shaped structure had the greatest conversion efficiency at approximately 0.5 %. Moreover, it was discovered that the maximum THG did not result from the smallest gap; instead, the gap sizes where the scattering and absorption cross sections were equal, led to the greatest THG. The finite difference time domain (FDTD) simulations based on the nonlinear scattering theory were also performed. The simulation results were in good agreement with the experimental data. Moreover, a modified quantum-corrected model was developed to study the electron tunneling effect as a limiting factor of the THG from plasmonic structures in the sub-nanometer regime. / Graduate / 0544 / 0794 / 0752 / 0756 / mrnezami@gmail.com

Genetic algorithm is often used to find the global optimum in a multi-dimensional search problem. Inspired by the natural evolution process, this algorithm employs three reproduction strategies -- cloning, crossover and mutation -- combined with selection, to improve the population as the evolution progresses from generation to generation. Femtosecond laser pulse tailoring, with the use of a pulse shaper, has become an important technology which enables applications in femtochemistry, micromachining and surgery, nonlinear microscopy, and telecommunications. Since a particular pulse shape corresponds to a point in a highly-dimensional parameter space, genetic algorithm is a popular technique for optimal pulse shape control in femtosecond laser experiments. We use genetic algorithm to optimize third harmonic generation (THG), and investigate various pulse shaper options. We test our setup by running the experiment with varied initial conditions and study factors that affect convergence of the algorithm to the optimal pulse shape. Our next step is to use the same setup to control coherent anti-Stocks Raman scattering. The results show that the THG signal has been enhanced.

The use of receptor-targeted lipid microbubbles imaged by ultrasound is an innovative method of detecting and localizing disease. However, since ultrasound requires a medium between the transducer and the object being imaged, it is impractical to apply to an exposed surface in a surgical setting where sterile fields need be maintained. Additionally, the application of an ultrasound gel to the imaging surface may cause the bubbles to collapse. Multiphoton microscopy (MPM) is an emerging tool for accurate imaging of tissues and cells with high resolution and contrast. We have recently developed a novel method for detecting targeted microbubble adherence to the upregulated plectin-receptor on pancreatic tumor cells using MPM. Specifically, the third-harmonic generation response can be used to detect bound microbubbles to various cell types presenting MPM as an alternative and useful imaging method. This is an interesting technique that can potentially be translated as a diagnostic tool for the early detection of cancer and inflammatory disorders.

Optical imaging methods have the potential to detect ovarian cancer at an early, curable stage. Optical imaging has the disadvantage that high resolution techniques require access to the tissue of interest, but miniature endoscopes that traverse the natural orifice of the reproductive tract, or access the ovaries and fallopian tubes through a small incision in the vagina wall, can provide a minimally-invasive solution. We have imaged both rodent and human ovaries and fallopian tubes with a variety of endoscope-compatible modalities. The recent development of fiber-coupled femtosecond lasers will enable endoscopic multiphoton microscopy (MPM). We demonstrated two-and three-photon excited fluorescence (2PEF, 3PEF), and second-and third-harmonic generation microscopy (SHG, THG) in human ovarian and fallopian tube tissue. A study was undertaken to understand the mechanisms of contrast in these images. Six patients (normal, cystadenoma, and ovarian adenocarcinoma) provided ovarian and fallopian tube biopsies. The tissue was imaged with three-dimensional optical coherence tomography, multiphoton microscopy, and frozen for histological sectioning. Tissue sections were stained with hematoxylin and eosin, Masson's trichrome, and Sudan black. Approximately 1 mu m resolution images were obtained with an excitation source at 1550 nm. 2PEF signal was absent. SHG signal was mainly from collagen. 3PEF and THG signal came from a variety of sources, including a strong signal from fatty connective tissue and red blood cells. Adenocarcinoma was characterized by loss of SHG signal, whereas cystic abnormalities showed strong SHG. There was limited overlap of two-and three-photon signals, suggesting that three-photon imaging can provide additional information for early diagnosis of ovarian cancer.

The nonlinear optical properties of semiconductor heterostructures, such as GaAsAl/GaAs alloys, are studied with analytic and numerical methods on the basis of quantum mechanics. Particularly, second and third-order nonlinear optical properties of quantum wells described by the various types of confining potentials are considered within the density matrix formalism. We consider a P&ouml / schl-Teller type potential which has been rarely considered in this area. It has a tunable asymmetry parameter, making it a good candidate to investigate the effect of the asymmetry on the nonlinear optical properties. The calculated nonlinear quantities include nonlinear absorption coefficient, second-harmonic generation, optical rectification, third-harmonic generation and the intensity-dependent refractive index. The effects of the DC electric field on the corresponding nonlinearities are also studied. The results are in good agreement with the results obtained in other types of quantum wells, such as square and parabolic quantum wells. The effects of the Coulomb interaction among the electrons on the nonlinear intersubband absorption are considered within the rotating wave approximation. The result is applied to a Si-delta-doped, square quantum well in which the Coulomb interaction among the electrons are relatively important, since there has been no work on the nonlinear absorption spectrum of the Si-delta-doped quantum well. The results are found to be new and interesting, especially when a DC electric field is included in the calculations.

In this study we demonstrate the use of third harmonic (TH) and second harmonic (SH) generation in imaging dental sections. Teeth are the hardest and most indestructible part in human body. The TH and SH greatly facilitate observation of porous structures and collagen within the dental sections, respectively. Strong SH has been found on various biological specimens, such as collagen, potato starch, and skeletal muscles. These materials all possess periodical nano-structures that are often referred as (nonlinear) bio-photonic structures. In particular, collagen is an extra-cellular structural protein and is a major component of bone, cartilage, skin, and other tissues. Collagen fibrils have a triple-helical structure and it is believed that this structure enables collagen to generate SH signal from a wide range of wavelengths in the infrared region. For comparison, microtubule structures within dentin, due to its large index mismatch with surrounding, can be clearly seen with THG imaging. The THG also facilitate observation of prismatic structures in enamel. The successful construction of a multi-photon laser scanning microscope that can operate in both reflection and transmission modes is the key for this study. A femtosecond, sync-pumped optical parametric oscillator (OPO) is used to generate second and third harmonics from dental sections. Dental sections have large index of refraction¡]n~1.68¡^and scatter visible light severely. The employment of excitation wavelength at 1260 nm greatly reduces scattering and absorption within the sample. Its corresponding SH and TH wavelengths are at 630 nm and 420 nm, respectively. Additionally, 3-D structural views are also reconstructed from the optically sectioned images by the use of specialized 3D image processing software.

Histology has long recognized the intimate link between structure and function. Over centuries histologists have utilized an assortment of optical microscopy techniques to elucidate functional attributes of tissues through investigating tissue architecture. This thesis includes developments in the field of nonlinear optical microscopy for use in histology and pathology. The main contributions focused on the study of fibrillar collagen in the extracellular matrix (ECM) with polarization-dependent second harmonic generation (P-SHG) microscopy and the study of harmonophore-stained cellular nuclei with third harmonic generation (THG) microscopy. The P-SHG microscopy technique, “polarization-in, polarization-out” (PIPO), was developed to accurately determine the second-order polarization properties of thin tissue sections. The polarization instrumentation was implemented into a nonlinear optical microscope and a custom fitting algorithm extracted ratios of the second-order nonlinear susceptibility elements at every pixel of an obtained image. Hierarchical organization, at every level of structure, can contribute significantly to the macroscopic second-order polarization properties of fibrillar collagen in the ECM and quantifiable differences between the various tissue architectures were observed. A framework was developed, based on the collagen hierarchical organization, to interpret the submicron polarization properties of various tissues. Complimentary to the P-SHG study of connective tissue, the structure of hematoxylin and eosin (H&E) stained nuclei was revealed by THG microscopy. Imaging the 3D organization of nuclei was possible using the inherent optical sectioning provided by nonlinear microscopy. The origin of THG was investigated with spectrally- and temporally-resolved measurements, as well as the THG ratio method. A rather complex situation involving multiple dye complexes was revealed. The structure of dye aggregates was investigated with THG PIPO microscopy. The techniques of PIPO and harmonophore-stained harmonic generation microscopy show great potential for ultimately furthering understanding of tissue structure and function. H&E stained tissue investigations with THG microscopy has applications as a tool for cancer diagnostics. PIPO can elucidate the symmetry and organization of materials beyond tissues, including starch, nanowires, and protein crystals. In pathology, the developed collagen framework has strong implications, as collagen is recognized as playing a more active role in a number of diseases including idiopathic pulmonary fibrosis, wound repair, and tumour development and progression.

Histology has long recognized the intimate link between structure and function. Over centuries histologists have utilized an assortment of optical microscopy techniques to elucidate functional attributes of tissues through investigating tissue architecture. This thesis includes developments in the field of nonlinear optical microscopy for use in histology and pathology. The main contributions focused on the study of fibrillar collagen in the extracellular matrix (ECM) with polarization-dependent second harmonic generation (P-SHG) microscopy and the study of harmonophore-stained cellular nuclei with third harmonic generation (THG) microscopy. The P-SHG microscopy technique, “polarization-in, polarization-out” (PIPO), was developed to accurately determine the second-order polarization properties of thin tissue sections. The polarization instrumentation was implemented into a nonlinear optical microscope and a custom fitting algorithm extracted ratios of the second-order nonlinear susceptibility elements at every pixel of an obtained image. Hierarchical organization, at every level of structure, can contribute significantly to the macroscopic second-order polarization properties of fibrillar collagen in the ECM and quantifiable differences between the various tissue architectures were observed. A framework was developed, based on the collagen hierarchical organization, to interpret the submicron polarization properties of various tissues. Complimentary to the P-SHG study of connective tissue, the structure of hematoxylin and eosin (H&E) stained nuclei was revealed by THG microscopy. Imaging the 3D organization of nuclei was possible using the inherent optical sectioning provided by nonlinear microscopy. The origin of THG was investigated with spectrally- and temporally-resolved measurements, as well as the THG ratio method. A rather complex situation involving multiple dye complexes was revealed. The structure of dye aggregates was investigated with THG PIPO microscopy. The techniques of PIPO and harmonophore-stained harmonic generation microscopy show great potential for ultimately furthering understanding of tissue structure and function. H&E stained tissue investigations with THG microscopy has applications as a tool for cancer diagnostics. PIPO can elucidate the symmetry and organization of materials beyond tissues, including starch, nanowires, and protein crystals. In pathology, the developed collagen framework has strong implications, as collagen is recognized as playing a more active role in a number of diseases including idiopathic pulmonary fibrosis, wound repair, and tumour development and progression.

Les semi-conducteurs nitrures d'éléments III type GaN, AlN sont des matériaux extrêmement intéressants pour la photonique intégrée sur silicium. Ils sont transparents sur une gamme très étendue et possèdent des susceptibilités non linéaires non nulles, ce qui rend possible les expériences non linéaires d'ordre deux et d'ordre trois. Dans ce contexte, cette thèse a été consacrée à l'étude de circuits photoniques avec des micro-résonateurs tels que les cristaux photoniques et les microdisques en matériau GaN/AlN épitaxiés sur Si. Le dessin des microcavités et des procédés de fabrication ont été optimisés afin d’obtenir un mode résonant dans le proche infrarouge avec un facteur de qualité jusqu'à 34000 pour les cristaux photoniques et 80000 pour les microdisques. J’ai étudié sur ces circuits photoniques les propriétés de conversion harmonique telles que la génération de seconde harmonique (SHG) et la génération de troisième harmonique (THG). En utilisant les propriétés de la THG, en combinant simplement un objectif optique et une caméra CCD, j'ai effectué l'imagerie des modes de cristaux photoniques du proche infrarouge avec une résolution spatiale sub-longueur d'onde (300 nm). J'ai également effectué l'imagerie de SHG sur des microdisques avec une excitation optique en résonance avec un mode de galerie pour le laser pompe. La dernière partie porte sur l'étude de la SHG en accord de phase entre les modes TM-0-0-X et TM-0-2-2X en variant le diamètre du disque avec un pas extrêmement faible (8 nm). Cela a été effectué pour des modes résonants de facteurs de qualité autour de 10000. Ces résultats montrent le potentiel des semi-conducteurs de III-nitrures pour la réalisation de circuits optiques sur silicium à deux dimensions. / Nitride semiconductors are extremely interesting for integrated photonics on silicon. They have a large transparent window and dispose of non zero nonlinear susceptibilities which enable second and third order nonlinear experiments. In this context, this thesis has been devoted to integrated photonic circuits with microresonators such as photonic crystals and microdisks. The microcavity design and the fabrication process have been optimized in order to obtain a near infrared resonant mode with a quality factor up to 34000 for photonic crystals and 80000 for microdisks. I carried out harmonic conversion experiments such as second harmonic generation (SHG) and third harmonic generation (THG). With THG, by combining simply an optical objective and a CCD camera, I carried out near infrared photonic crystal modes imaging with a subwavelength spatial resolution (300 nm). I also did SHG imaging on microdisks with an optical excitation in resonance with the gallery mode for the pump laser. The last part of the work is dedicated to the demonstration of phase-matched SHG in microdisk photonic circuits between the TM-0-0-X and TM-0-2-2X modes by varying the microdisk diameter with a very small step (8 nm). These experiments have been done for resonant modes with quality factors around 10000.These demonstrations show the potential of III-nitride semiconductors for the realization of two dimensional optical circuits on silicon.