O ganho crescen te de desempenho nos computadores modernos tem impulsionado os trabalhos científicos nas áreas de simulação computacional. Muitos autores utilizam em suas pesquisas ferramentas comerciais que limitam seus trabalhos ao esconder os algoritmos internos destas ferramentas e dificultam a adição de dados in-vivo nestes trabalhos. Este trabalho explora esta lacuna deixada por aqueles autores. Elaboramos um arcabouço computacional capaz de reproduzir os fenômenos óticos e fisiológicos do sistema visual. Construímos com superfícies quádricas os modelos esquemáticos do olho humano e propomos um algoritmo de traçado de raio realístico. Então realizamos um estudo nos modelos esquemáticos e a partir deles mais a adição de dados in-vivo obtidos de um topógrafo de córnea extraímos informações óticas destes modelos. Calculamos os coeficientes e Zernike dos modelos para tamanhos diversos de pupila e obtivemos medidas de aberração do olho humano. Os resultados encontrados estão de acordo com os trabalhos relacionados e as simulações com dados in-vivo estão consoantes com as produzidas por um aparelho de frente de onda comerciais. Este trabalho é um esforço em aproveitar as informações adquiridas pelos equipamentos modernos de oftalmologia, além de auxiliar o entendimento de sistemas visuais biológicos acabam também em auxiliar a elaboração de sistemas de visão artificial e os projetistas de sistemas óticos / The increase in performance of the modern computers has driven scientific work in the areas of computer simulation. Many authors use in their research commercial tools that use embedding algorithms, which sources are not provided, and it makes harder and sometimes impossible, the development of novel theories or experiments. This work explores this gap left for those authors. We present a computational framework capable to reproduce the optical and physiological phenomena of the human visual system. We construct schematical models of the human eye from quadrics surfaces and consider an algorithm of realistic ray tracing. Afterward, we performed a study on schematics models and in addition we introduce, in these models, in-vivo data obtained from corneal topography machine and extract optical information. We calculate the Zernike coefficients in the models for different sizes of pupil and measures of aberration of the human eye. The results are in agreement with related work and simulations with in-vivo data are according with the produced by a commercial wave-front device. This work is an effort in using to advantage the information acquired for the modern equipment of ophthalmology, besides assisting the understanding of biological visual systems, it also helps the development of artificial vision systems and the designing of optical systems

The main problem addressed by this dissertation is the accurate and automated determination of electron microscope imaging conditions. This enables the restoration of the object wave, which confers direct structural information about the specimen, from sets of differently aberrated images. An important member in the imaging chain is the image recording device, in many cases now a charge-coupled device (CCD) camera. Previous characterisations of these cameras often relied on the unjustified assumption that the Modulation Transfer Function (MTF) also correctly describes the spatial frequency dependent attenuation of the electron shot noise. A new theory is therefore presented that distinguishes between signal and noise transfer. This facilitates the evaluation of both properties using a detailed Monte-Carlo simulation model for the electron and photon scattering in the scintillator of the camera. Furthermore, methods for the accurate experimental determination of the signal and noise transfer functions are presented. In agreement with the Monte-Carlo simulations, experimental results for commercially available CCD cameras show that the signal transfer is significantly poorer than the noise transfer. The centrepiece of this dissertation is the development of new methods for determining the relative aberrations in a set of images and the absolute symmetric aberrations in the restored wave. Both are based on the analysis of the phase information in the Fourier domain and give each Fourier component a weight independent of its strength. This makes the method suitable even for largely crystalline samples with little amorphous contamination, where conventional methods, such as automated diffractogram fitting, usually fail. The method is then extended to also cover the antisymmetric aberrations, using combined beam tilt and focal series. The applicability of the new method is demonstrated with object wave restorations from tilt and focal series of complex inorganic block oxides and of carbon nanotubes filled with one-dimensional inorganic crystals. The latter specimens allowed for the first time a direct comparison between the phase shift in the restored object wave of a specimen with precisely known thickness and the value predicted by simulations.

O ganho crescen te de desempenho nos computadores modernos tem impulsionado os trabalhos científicos nas áreas de simulação computacional. Muitos autores utilizam em suas pesquisas ferramentas comerciais que limitam seus trabalhos ao esconder os algoritmos internos destas ferramentas e dificultam a adição de dados in-vivo nestes trabalhos. Este trabalho explora esta lacuna deixada por aqueles autores. Elaboramos um arcabouço computacional capaz de reproduzir os fenômenos óticos e fisiológicos do sistema visual. Construímos com superfícies quádricas os modelos esquemáticos do olho humano e propomos um algoritmo de traçado de raio realístico. Então realizamos um estudo nos modelos esquemáticos e a partir deles mais a adição de dados in-vivo obtidos de um topógrafo de córnea extraímos informações óticas destes modelos. Calculamos os coeficientes e Zernike dos modelos para tamanhos diversos de pupila e obtivemos medidas de aberração do olho humano. Os resultados encontrados estão de acordo com os trabalhos relacionados e as simulações com dados in-vivo estão consoantes com as produzidas por um aparelho de frente de onda comerciais. Este trabalho é um esforço em aproveitar as informações adquiridas pelos equipamentos modernos de oftalmologia, além de auxiliar o entendimento de sistemas visuais biológicos acabam também em auxiliar a elaboração de sistemas de visão artificial e os projetistas de sistemas óticos / The increase in performance of the modern computers has driven scientific work in the areas of computer simulation. Many authors use in their research commercial tools that use embedding algorithms, which sources are not provided, and it makes harder and sometimes impossible, the development of novel theories or experiments. This work explores this gap left for those authors. We present a computational framework capable to reproduce the optical and physiological phenomena of the human visual system. We construct schematical models of the human eye from quadrics surfaces and consider an algorithm of realistic ray tracing. Afterward, we performed a study on schematics models and in addition we introduce, in these models, in-vivo data obtained from corneal topography machine and extract optical information. We calculate the Zernike coefficients in the models for different sizes of pupil and measures of aberration of the human eye. The results are in agreement with related work and simulations with in-vivo data are according with the produced by a commercial wave-front device. This work is an effort in using to advantage the information acquired for the modern equipment of ophthalmology, besides assisting the understanding of biological visual systems, it also helps the development of artificial vision systems and the designing of optical systems

The main problem addressed by this dissertation is the accurate and automated determination of electron microscope imaging conditions. This enables the restoration of the object wave, which confers direct structural information about the specimen, from sets of differently aberrated images. An important member in the imaging chain is the image recording device, in many cases now a charge-coupled device (CCD) camera. Previous characterisations of these cameras often relied on the unjustified assumption that the Modulation Transfer Function (MTF) also correctly describes the spatial frequency dependent attenuation of the electron shot noise. A new theory is therefore presented that distinguishes between signal and noise transfer. This facilitates the evaluation of both properties using a detailed Monte-Carlo simulation model for the electron and photon scattering in the scintillator of the camera. Furthermore, methods for the accurate experimental determination of the signal and noise transfer functions are presented. In agreement with the Monte-Carlo simulations, experimental results for commercially available CCD cameras show that the signal transfer is significantly poorer than the noise transfer. The centrepiece of this dissertation is the development of new methods for determining the relative aberrations in a set of images and the absolute symmetric aberrations in the restored wave. Both are based on the analysis of the phase information in the Fourier domain and give each Fourier component a weight independent of its strength. This makes the method suitable even for largely crystalline samples with little amorphous contamination, where conventional methods, such as automated diffractogram fitting, usually fail. The method is then extended to also cover the antisymmetric aberrations, using combined beam tilt and focal series. The applicability of the new method is demonstrated with object wave restorations from tilt and focal series of complex inorganic block oxides and of carbon nanotubes filled with one-dimensional inorganic crystals. The latter specimens allowed for the first time a direct comparison between the phase shift in the restored object wave of a specimen with precisely known thickness and the value predicted by simulations.

The pursuit of high quality, large area graphene has been a major research focus of contemporary materials science research, in the wake of the discovery of the multitude of exceptional properties exhibited by the material. The DPhil project was undertaken with the objective of developing an understanding of the growth of large graphene sheets by chemical vapour deposition (CVD), and also in the subsequent characterisation of their material properties. By conducting atmospheric pressure CVD growth at high methane flow rates, it was found that few-layered graphene (FLG) could be deposited on a copper catalyst. It is demonstrated that the self-limiting property of a copper catalyst is not universal to all deposition conditions, and shown that FLG grows in a terrace-like configuration. In depth transmission electron microscopy (TEM) studies were carried out on FLG. By selective image reconstruction from the inverse power spectrum of the TEM images, it was possible to elucidate the inter-grain connectivity of few-layer graphenes. It was determined that there were two possible inter-grain configurations possible; specifically an overlap of graphene layers or a discrete atomic bonding edge. The perturbation of the few-layer structure when subject to an out of plane distortion was found to incur a shift in the conventional AB-Bernal stacking of FLG. By utilising the aberration corrected TEM (AC-TEM) at Oxford it was possible to resolve atomic detail in CVD synthesised monolayer films, including atomic bond rotations and vacancies. The use of a high current density at low accelerating voltage (80 kV) was demonstrated to allow for the controlled defect creation in graphene sheets. This permitted the creation of monovacancies and iron doped vacancy complexes suitable for further study. The behaviour of these two defect types under electron beam irradiation was subsequently studied.

L'instrument SNIFS a été conçu pour l'observation des Supernovae de type Ia à bas redshit afin de mieu connaître et caractériser ces objets. Le but étant de savoir si ces objets peuvent être utilisés comme des chandelles standards afin de contraindre les paramètres cosmologiques. La première partie de cette thèse porte sur le développement d'une simulation numérique détaillée de l'instrument SNIFS. Cette simulation reproduit les données issues de l'instrument de la manière la plus réaliste possible en tenant compte de toutes les aberrations présentes, ce qui inclut l'instrument mais aussi l'atmosphère. A terme ces images pourront être utilisées pour préparer la calibration de l'instrument. Le seconde partie tente d'établir une méthode capable d'analyser les résultats produits par l'instrument SNIFS. En se basant sur des outils morphométriques, cette méthode montrera comment l'on peut comparer des séries temporelles de spectre de supernovae et extraire des informations statistiques de celles ci.

El establecimiento de correlaciones entre fenotipo y genotipo es uno de los principales objetivos de la genética. La obtención de un diagnóstico ajustado facilita el manejo clínico del paciente, así como poder ofrecer un correcto consejo genético, con asesoramiento reproductivo a las familias de pacientes con enfermedades genéticas. La identificación de genes asociados a patología desde alteraciones citogenéticas asociadas a fenotipo es uno de los métodos de clonación posicional. En este trabajo nos hemos basado en dos tipos de modelos de anomalías citogenéticas: balanceadas y no balanceadas (translocaciones y cromosomas marcadores). Hemos caracterizado las alteraciones citogenéticas de cinco pacientes de cada modelo con fenotipos diversos, empleando una combinación de técnicas citogenéticas y moleculares, con el objetivo de proponer genes candidatos asociados a cada fenotipo. / One of the main objectives of Genetics is the establishment of phenotype-genotype correlations. A correct diagnosis facilitates the clinical management of the patient and the possibility to offer a genetic counselling, with reproductive assessment to the families with a patient with a genetic disease. The identification of genes associated to pathology from cytogenetic alterations associated to phenotype is one of the methods of positional cloning. In this work we have based in two different models of cytogenetic alterations: balanced and unbalanced anomalies (translocations and marker chromosomes). We have characterized five patients of each group with different phenotypes, using a combination of cytogenetic and molecular techniques, with the objective of establish candidate genes associated to disease.

No description available.

Actuellement, la presbytie peut être corrigée chirurgicalement à l’aide d’implants intraoculaires réfractifs ou diffractifs multifocaux (chirurgie endoculaire invasive et irréversible) ou en intracornéen avec une correction multifocale réfractive (correction laser irréversible, ou insertion d’un implant dans le stroma). L’objectif de ce travail est de développer un nouvel implant permettant de corriger la presbytie, qui allie l’innocuité et la réversibilité d’une correction intracornéenne, à l’efficacité du diffractif. Le design des profils optiques bifocaux a été permis grâce au développement d’outils de simulation optique. Les efficacités de diffraction sont calculées à partir de la propagation du champ électrique par spectre angulaire. La qualité optique est déterminée d’après les simulations de Fonction de Transfert de Modulation obtenues sous Zemax. Des simulations de rendu d’images permettent de visualiser les effets de différents profils envisagés. Les paramètres critiques du design optique sont déterminés. Le choix du matériau dépend des contraintes de biocompatibilité de l’implant et des techniques de fabrication. La solution retenue est un hydrogel à forte teneur en eau, couplé à une nouvelle architecture de l’implant. L’hydrogel est obtenu par polymérisation radicalaire de macromonomères difonctionnels de poly(éthylène glycol) de masses molaires de l’ordre de 8000 g.mol‐1 qui conduisent à des propriétés mécaniques et une perméabilité aux nutriments compatibles avec l’application. La réalisation, la stérilisation et la caractérisation optique de prototypes ont abouti à la preuve du concept d’un implant bifocal diffractif intracornéen / Presbyopia can be corrected with surgery by means of refractive or diffractive multifocal intraocular lenses (which imply an irreversible and invasive endocular surgery) or by intracorneal multifocal refractive correction (irreversible laser correction, or insertion of an intrastromal implant). This work aims at developing a new implant to correct presbyopia, which takes advantage of both the harmlessness and the reversibility of an intracorneal correction, and the efficiency of diffractive optics. The design of the bifocal optical profiles was based on the development of optical simulation tools. The diffractive efficiencies are calculated from the distribution of the electric field with the method of angular spectrum. The optical quality is determined according to the simulations of Modulation Transfer Function obtained with Zemax. Images simulations show the effects of the different profiles studied. The critical parameters of the optical design are also determined. The choice of the material depends on several constraints such as biocompatibility and techniques of manufacturing. The adopted solution relies on the used of an hydrogel with high water content and the design of a new implant architecture. The hydrogel is obtained by radical polymerization of difunctional macromonomers of poly(ethylene glycol) with molar masses around 8000 g.mol‐1, allowing mechanical properties and permeability to nutriments compatible with the application. The realization, the sterilization and the characterization of prototypes showed the proof of the concept of a diffractive bifocal intracorneal implant

This diploma thesis considers with human vision and human eye. It takes into account both anatomic view and physiology standpoints. There is, among others, description of optical processes occurring in the organ of the sight mentioned in the work. The human eye suffers from optical defects – aberrations – that are able to degrade the retinal image and ultimately visual performance. Substantial part of the text deals with these aberrations. There are also analysed possibilities of their elimination using an inverse aberration. Work also assumes opportunity to optical modeling to calculate distorted images from ocular aberration data. Practical part consist of software application created using Matlab environment ver. 6.5 as well as full documentation. The examples of outputs procured using this application are published. Both software application and detail documentation are included on CD.