Thesis (M.S.)--State University of New York at Binghamton, Department of Computer Science, Thomas J. Watson School of Engineering and Applied Science, 2007. / Includes bibliographical references.

Thesis (Ph. D.)--Ohio State University, 2004. / Document formatted into pages; contains 218 p. Includes bibliographical references. Abstract available online via OhioLINK's ETD Center; full text release delayed at author's request until 209 March 29.

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Laser beams can be manipulated by volume diffractive elements in addition to conventional optical elements like mirrors, lenses, and beam splitters. Conventional optical elements can be described by applying the basic laws of reflection and refraction at the surfaces of the elements. Even diffraction by surface gratings utilizes relatively simple mathematics. This is to be contrasted with the volume diffraction, which requires coupled wave theory in the slowly varying envelope approximation (SVEA) to obtain accurate results. Efficient spatially distributed diffraction of laser beams is possible due to the high coherence of laser light, and it occurs at specific resonant Bragg conditions. This research work is inspired and driven by the successful development of recording technology for robust, high-efficiency volume Bragg gratings (VBGs) in photo-thermo-refractive (PTR) glass. Mostly VBGs of the reflective type are discussed in this dissertation. Starting with an analysis of electro-magnetic wave propagation in layered media, we have reformulated Fresnel and volume reflection phenomena in terms of a convenient parameter – strength of reflection. The influence that the different non-uniformities inside a VBG have on its spectral properties has been examined. One important result of this work is the proposal of moiré VBG and the derivation of an analytical expression for its bandwidth. A multiplexed VBG used as a coherent combiner is discussed as well. Beam distortion via transmission through and/or reflection by a heated VBG due to residual absorption is analyzed.

Single-stranded DNA binding proteins (SSB) bind to single-stranded DNA (ssDNA) that is generated by molecular machines such as helicases and polymerases. SSBs play crucial roles in DNA translation, replication and repair and their importance is demonstrated by their inclusion across all domains of life. The homotetrameric E. coli SSB and the heterotrimeric human RPA demonstrate how SSBs can vary structurally, but all fulfil their roles by employing oligonucleotide/oligosaccharide binding (OB) folds. Nucleofilaments of SSB proteins bound to ssDNA sequester the ssDNA strands, and in doing so protect exposed bases, keep the ssDNA in conformations favoured by other proteins that metabolise DNA and also recruit other proteins to bind to ssDNA. This thesis focuses on the SSB from the archaeon S. solfataricus (SsoSSB), and has found SsoSSB to be a monomer that binds cooperatively to ssDNA with a binding site size of 4-5 nucleotides. Tagging ssDNA and SsoSSB with fluorescent labels allowed the real time observation of single molecule interactions during the initial nucleation event and subsequent binding of an adjacent SsoSSB monomer. This was achieved by interpreting fluorescent traces that have recorded combinations of FRET, protein induced fluorescent enhancement (PIFE) and quenching events. This novel analysis gave precise measurements of the dynamics of the first and second monomers binding to ssDNA, which allowed affinity and cooperativity constants to be quantified for this important molecular process. SsoSSB was also found to have a similar affinity for RNA, demonstrating a promiscuity not found in other SSBs and suggesting further roles for SsoSSB in the cell - possibly exploiting its capacity to protect nucleic acids from degradation. The extreme temperatures that S. solfataricus experiences and the strength of the interaction with ssDNA and RNA make exploring the application of SsoSSB for industrial uses an interesting prospect; and its rare monomeric structure provides an opportunity to investigate the action of OB folds in a more isolated environment than in higher order structures.

The Clement Ader Institute of Albi and the von Karman Institute follow<p>since numerous years works about IR radiometry with the aim to do quantitative<p>thermography (true temperature measurement without contact). These works allowed<p>to explore potentiality several spectral bands :8-12µm, 3-5µm and recently the<p>0.75-1.7µm band (near IR) with the help of CCD camera (Si) or VisGaAs camera.<p>Studies done in this specific domain have underlined some perturbations emphasized<p>at high-temperature (T>800◦C). This work has to deal in details with the<p>treatment of parameters playing a role in camera measurements. The first of these<p>parameters is the emissivity, this treatment is made in another thesis. The second<p>parameter affects particularly the hot spot location and the spatial distortion. This<p>perturbation comes from convective effect present around every hot objects.The<p>purpose of this thesis is to analyze this effect and to correct it. Indeed, when a hot<p>object is in a colder surrounding media, a temperature gradient is shaped around<p>the object and thus a refractive index gradient too. This phenomena brings inevitably<p>distortions of the spatial information received by the camera. The goal of this<p>work will be to estimate and correct error made on temperature and/or distortion<p>measurement by CCD or VisGaAs camera on hot object.We chose to focus our work<p>on the convective plume created by a hot horizontal disk. This study will be done<p>with an experimental and a numerical approach. For the numerical approach, a raytracing<p>code has been developed in order to obtain numerically the displacement<p>due to the light deviation occurring in the perturbation. The input data of the code<p>is the refractive index of the hot air present around the object. This refractive index,<p>depending on the wavelength, can be found directly from the temperature thanks<p>to the Gladstone-Dale law. The temperature is given by a CFD software such as<p>FLUENT. Experimentally, we will use the Background Oriented Schlieren (BOS)<p>method in order to retrieve the displacement. We can see that the displacement can<p>reach 4 pixels in the plume (corresponding to 1mm in this case). This perturbation<p>has been studied for several spectral bands (visible, near infrared, infrared). Finally,<p>some solutions of correction are given, like using the inverse Abel Transform<p>in order to retrieve from the 2D displacement, a 3D (axisymmetric) refractive index<p>field that we will implement in the ray-tracing code and consequently predict the<p>displacement for any kind of wavelength or distance (distance between the camera<p>and the object)./L’Institut Clément Ader Albi (ICAA) et l’Institut von Karman (IVK)<p>mènent depuis un certain nombre d’années des travaux sur la radiométrie IR dans<p>le but de faire de la thermographie quantitative (mesure de température vraie sans<p>contact). Ces travaux ont permis d’explorer les potentialités de plusieurs bandes<p>spectrales :8-12µm, 3-5µm et plus récemment la bande 0,75-1,7µm (proche IR) à<p>l’aide de caméras CCD (Si) ou VisGaAs. Les travaux effectués dans ce domaine<p>spectral ont permis de mettre en évidence un certains nombre de perturbations<p>renforcées par les hautes températures (T>800◦C). Cette thèse aborde de façon détaillée<p>le traitement d’un certain nombre de grandeurs d’influence liées à la mesure<p>de différents paramètres dans le domaine du proche IR mais également étendus aux<p>domaines du visible et de l’IR. La première de ces grandeurs est l’émissivité dont le<p>traitement a déjà été abordé par d’autres études. La seconde grandeur d’influence<p>touche plus particulièrement à la localisation des points chauds sur l’objet et la distorsion<p>du champ de température apportée par les effets convectifs présents autour<p>d’un objet à haute température, elle est le coeur de cette thèse. En effet, lorsqu’une<p>pièce chaude se trouve dans un milieu ambiant beaucoup plus froid, il se crée un<p>gradient de température et donc d’indice de réfraction autour de la pièce. Or les<p>caméras travaillant dans les différentes bandes spectrales vont être plus ou moins<p>sensibles à ces variations d’indices de réfraction du fait de la dépendance de l’indice<p>optique avec la longueur d’onde et de la résolution spatiale de la caméra utilisée.<p>Ce phénomène, appelé effet mirage, entraîne inévitablement une déformation des<p>informations spatiales reçues par la caméra. Le but de cette thèse a donc été d’estimer<p>et de proposer une première approche pour corriger l’erreur faite sur la mesure<p>de température et/ou de déformation faites par caméras sur des pièces chaudes.<p>La démarche générale du travail a donc été dans un premier temps de calculer le<p>champ de température autour de l’objet considéré en se ramenant d’abord à des cas<p>simplifiés. On en a déduit alors le champ de réfraction entraînant une « déformation<p>» de l’objet, en faisant le lien entre T et n. Cette étape correspond à l’approche<p>numérique de notre étude. Cette étape numérique a été réalisé à l’aide d’un outil de<p>lancer de rayons développée à l’ICA. L’approche expérimentale a consisté à l’utilisation<p>de méthodes telle que la BOS (Background Oriented Schlieren), la PIV,<p>la srtioscopie afin de déduire le champ de déplacements provoqué par le panache<p>convectif. Ces résultats ont été comparés à la méthode numérique et ceci pour différentes<p>longueurs d’ondes. Enfin, une stratégie de correction d’images perturbées<p>a été abordé à l’aide de méthodes telles que la transformée d’Abel inverse afin de<p>remonter au champ d’indice de réfraction 2D axisymétrique à partir d’une déformation<p>plane. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished