The main objective of the present research work is to fabricate three dimensional photonic nanostructures in photo-sensitive polymers using a novel diffractive optical element (DOE) based lithography technique. A diffractive optical element is a promising alternative device for 3D fabrication where one DOE creates multiple laser beams in various diffraction orders that are inherently phase-locked and stable for reproducible creation of 3D near-field diffraction patterns from a single laser beam. These near-field patterns are captured inside a photosensitive material like photoresist to fabricate 3D photonic crystal templates. We have demonstrated fabrication of a wide range of 3D structures having different crystal symmetries and different relative crystal axis ratios. The present work has provided 3D photonic crystal nanostructures with uniform optical and structural properties over large sample area (~3-4 mm diameter) and through large 15-50 micron thickness with large number of layers (> 40) having period 550 nm - 650 nm and feature sizes between 200 nm and 300 nm. The short exposure time and small number of process steps shows promise for scaling to very large volume fabrication, dramatically improving the throughput, quality and structural uniformity of 3D periodic nanostructures, especially over that provided by tedious and costly semiconductor processing technology. The diffractive optics lithography is a parallel processing method that is easily scalable to generate centimeter-scale 3D nanostructures having large number of layers in several seconds. Due to low refractive index contrasts these polymer templates possess partial stopgaps along several crystallographic directions which can be practically used in several device or sensor applications where complete bandgap is not necessary. The potential usefulness of these partial stopbands for refractive index sensing of liquids has been demonstrated. These low refractive index polymer structures have been inverted with amorphous silica to convert a "soft" polymer structure to a robust "hard" structure. Further, few preliminary tests were done in fabricating 3D nanostructures into micro-fluidic channels for potential chromatography applications. The practical merits of this 3D fabrication technique will enable new practical manufacturing methods for optical and MEMS applications of 3D micro and nano structures.

Röntgen Freie Elektronen Laser ermöglichen es Doppel-K-Schalen Löchern in Molekülen in aufeinanderfolgenden mehrfachen Ionisationsschritten in bedeutender Anzahl zu erzeugen. Die Eigenschaften dieser zweifach ionisierten Zustände ist insbesondere relevant für die Strahlungsschäden bei Beugungsexperimenten mit kohärenter Röntgenstrahlung zur Bildgebung einzelner Moleküle. In dieser Arbeit wird der Auger Zerfall doppelt K-Schalen ionisierter Moleküle mittels quantenchemischer ab-initio Methoden untersucht. Zur Beschreibung des emittierten Auger Elektrons im kontinuierlichen Energiespektrum wird dabei die Ein-Zentrums Methode verwendet, in der die elektronische Wellenfunktion auf einem radialen Gitter beschrieben wird unter Verwendung von sphärischen Harmonischen. Wie anhand desWassermoleküls gezeigt wird, ergeben sich durch die Doppel-K-Loch induzierte Protonendynamik in dem Auger Spektrum ausgeprägte Flanken im höherenergetischen Teil jeder Spektralspitze. Die Lebensdauer von Doppel-K-Schalen Löchern in Molekülen ist deutlich verringert im Vergleich zu einfachen K-Löchern durch die K-Loch induzierten Abschirmeffekte der Valenzelektronen. Dieser Mechanismus wird durch ein einfaches Modell erklärt aus dem eine Beziehung zwischen Zerfallsrate und Valenzelektronenpopulation abgeleitet. Mögliche Konsequenzen dieser Ergebnisse für Röntgenbeugungsexperimente sind: Erstens, auch für Röntgenpulse kürzer als 10fs wird das Beugungsbild durch die K-Loch induzierten Umstrukturierungen der Valenzelektronen beeinflußt. Zweitens, die Gesamt-Ionisationsrate ist erhöht aufgrund der schnelleren Neubesetzung der K-Löcher.

Röntgenlicht-Freie-Elektronen-Laser (XFEL) schaffen neue Möglichkeiten für die molekulare Strukturbestimmung in Einzelmolekülexperimenten. In dieser Arbeit stelle ich zwei alternative bayessche Verfahren vor, das Orientational Bayes und das Structural Bayes Verfahren, die das Extrahieren der Strukturinformationen aus dünn besetzten und verrauschten Streuungsbildern ermöglichen. Im ersten Verfahren wird ein "Seed"-Modell verwendet, um die zugrunde liegende molekulare Orientierung für jedes aufgezeichnete Streuungsbild separat zu bestimmen. Eine verbesserte molekulare Transformation der bestrahlten Moleküle wird durch Ausrichten und Mitteln dieser Bilder im dreidimensionalen reziproken Raum erhalten. Im Structural Bayes Verfahren wird ein Realraum-Strukturmodell optimiert, sodass es am besten zum gesamten Streuungsbildersatz passt. Auf diese Weise wird ermöglicht, zwischen verschiedenen Strukturmodellen zu unterscheiden. Ich habe die Auflösung bei der Abbildung einzelner Moleküle mit unterschiedlichen Massen für verschiedene XFEL Strahlintensitäten abgeschätzt. Die Ergebnisse zeigen, dass die erreichbare strukturelle Auflösung mit der Molekülmasse wie M^{-1/ 6} steigt. Laut dieser Skalierung ist hierbei, im Gegensatz zur traditionellen Röntgenkristallographie, die hochaufgelöste Strukturbestimmung kleiner Einzelmoleküle, im Vergleich zu großen Molekülen, schwieriger. Als Machbarkeitsnachweis des Orientational Bayes Verfahrens wurde beispielhaft die Elektronendichte eines Glutathion-Moleküls aus 20.000 synthetischen Streuungsbildern, mit durchschnittlich 82 aufgezeichneten elastisch gestreuten Photonen und bis zu 50% zusätzlichem Hintergrundrauschen pro Bild, berechnet. Um die Anwendbarkeit des Structural Bayes Verfahrens in einer de novo Strukturbestimmung zu testen, wurde zudem die Struktur des Glutathion-Moleküls in einer Monte Carlo-Verfeinerungs-Simulation gelöst, für die zufällige Aminosäure-Konformationen als Ausgangsmaterial verwendet wurden. Um zusätzlich zu prüfen, ob mehrere Längenskalen umfassende Strukturänderungen in einem komplexen Molekül unter Verwendung des Structural Bayes Verfahrens rückverfolgbar sind, wurden Konformationsänderungen von drei Immunglobulin-Domänen eines Titin-Moleküls sowie der tRNA-Translokationsvorgang im Ribosom untersucht. Die Ergebnisse zeigen, dass es möglich ist sowohl zwischen unterschiedlichen molekularen Konformationen zu unterscheiden als auch kleinere strukturelle Änderungen, die mit der tRNA-Translokation assoziiert sind, zu erkennen. Insgesamt betrachtet deuten die Ergebnisse dieser Arbeit darauf hin, dass sich mithilfe der beiden hier vorgestellten bayesschen Verfahren die Struktur einzelner Moleküle mit atomarer Auflösung von dünn besetzten und verrauschten Röntgenstreuungsbildern aus XFEL-Einzelmolekülexperimenten für ein breites Spektrum von Molekülmassen bestimmen lässt.

A la suite de la première démonstration de l'écriture de guide d'onde au sein de verres en 1996 par laser femtoseconde, l'écriture direct par Laser Femtoseconde (Femtoseconde Direct Laser Writing - FLDW) est apparu comme une technique souple pour la fabrication de structure photonique en trois dimensions au sein de matériaux pour l'optique. La thèse a porté sur l'inscription par laser femtoseconde de fonctionnalités optiques au sein de verres. Des éléments diffractifs par modification de l'indice de réfraction et des structures présentant des propriétés de luminescence ou d'optique non linéaire d'ordre deux ont pu être obtenus au sein de matériaux vitreux et étudiés. / Since the first demonstration of femtosecond laser written waveguides in 1996, femtosecond laser direct writing (FLDW) has been providing a versatile means to fabricate embedded 3-D microstructures in transparent materials. The key mechanisms are nonlinear absorption processes that occur when a laser beam is tightly focused into a material and the intensity of the focused beam reaches the range creating enough free electrons to induce structural modification. This dissertation was an attempt to make an improvement on the existing FLDW technique to achieve a reliable fabrication protocol for integrated optical devices involving micro diffractive optical elements and laser-structures exhibiting second order nonlinear optical properties. Relaxation processes of directly-written structures in chalcogenide glasses have been also investigated.

La thèse porte sur un nouveau concept pour les afficheurs de réalité augmentée placés près de l’œil, notamment pour améliorer les champs de vision. Deux guides d'ondes sont empilés avec un petit espace d'air entre eux. La lumière couplée dans le premier guide d'ondes par le coupleur d’entrée se propage par réflexion interne totale jusqu'à atteindre un miroir cylindrique à l'extrémité du guide. Puis, la lumière réfléchie est couplée dans le second guide d'ondes avant d'atteindre le coupleur de sortie. Un système similaire basé sur des micro-prismes est aussi décrit. Les conceptions ont été simulées avec le logiciel Zemax. Les champs de vision horizontal et vertical obtenus sont respectivement de 30° et 60°. La Fonction de Transfert de Modulation pour tous les champs objets est supérieure à 30% pour 33 npl/mm, ce qui est suffisant pour un système visuel. De plus, un grand volume de déplacement admissible pour l’œil (Eye-box) d'environ 10×8 mm a été obtenu. / We propose a new concept to improve notably the fields-of-view (FOV) of the near to eye displays (NEDs) for augmented reality. Two waveguides are stacked with a small air gap between them. The light coupled in the first waveguide by the in-coupler propagates by total internal reflection until it reaches a cylindrical mirror at the end of the guide. Then, the reflected light is coupled in the second waveguide before to reach the out-coupler. A similar system based on micro-prisms is also described. The designs were simulated with Zemax software. The obtained horizontal and vertical FOV are respectively 30° and 60°. The Modulation Transfer Function for all object fields is greater than 30% for 33 npl/mm, which is sufficient for a visual system. In addition, a large Eye-box of approximately 10 × 8 mm was obtained.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho apresenta medidas de duas razões de produção difrativa envolvendo sabores pesados, através de um estudo em uma amostra reconstruída de J/ψ → μ+ μ- em colisões pp a raiz quadrada de s= 1,96 TeV com o uso do detector DØ situado no Fermilab. Estes eventos foram selecionados com o uso dos detectores do Monitor de Luminosidade, o sistema de calorimetria e o sistema de m Ão ons do DØ, em uma região de pseudo-rapidez 2,7 ≤|η|≤ 4 ,4 . As razões medidas foram NJϕdiff/Nj/ϕtotal = (1,74 0,16 (estat) 0,13 (sist)) % e N b dif / N b total = 0,79 0,11(estat) 0,23 (sist))% / This work presents measurements of two diffractive production ratio for heavy flavour physics on sat with the use of are constructed J/ψ → μ + μ sample in pp collisions at s= 1. 96 TeV using the DØ detector at Fermilab Tevatron. These events were selected using the Luminosity Monitor detectors, the calorimeter system and the muon system in a pseudo-rapidity region with range 2 . 7 ≤|η|≤ 4, 4 . The measured ratio were estimated to be NJϕdiff/Nj/ϕtotal = (1,74 0,16 (estat) 0,13 (sist)) % and Nb dif / Nb total = 0,79 0,11(estat) 0,23 (sist))%

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O presente trabalho refere-se ao estudo sobre a razão da produção difrativa e total de B+ decaindo em J=y +K+, no ambiente do experimento CMS do colisor de prótons LHC do CERN, contribuindo assim com a compreensão geral do Modelo Padrão (SM) como a teoria das interações fundamentais entre as partículas elementares. Inicialmente, é apresentada uma análise com o intuito de selecionar os eventos que possuem um méson B+, uma vez que o canal de decaimento mencionado: poderá ser a primeira medida da produção exclusiva do méson B à escala de energia do LHC; é um dos principais canais de fundo para outras análises; e possibilita a utilização de um canal limpo para a calibração do CMS. Em seguida, é apresentada a forma de se identificar eventos difrativos no CMS, utilizando a baixa multiplicidade de torres ativas nos calorímetros CASTOR e HF. Esse estudo foi baseado em simulações computacionais, as quais reproduziram as condições físicas esperadas para o CMS/LHC, à energia de centro de massa de 10 TeV. Utilizou-se na geração de eventos o Monte Carlo POMWIG para as amostras difrativas e o PYTHIA para as demais. / This work concerns the study of the diffractive production ratio of the B+ meson decaying into J=y + K+, in the CMS/LHC environment, thus contributing to an general understanding of the Standard Model (SM) as the theory of fundamental interactions between elementary particles. To begin with, an analysis is done in order to select the events that have B+, as the study of the mentioned channel could provide the first measurement of the exclusive production of B mesons at the energy scale of the LHC. Also, it is an important channel both for further analysis and to make CMS calibrations. Furthermore, we show how to identify diffractive events in CMS, using low multiplicity of active cells in the forward calorimeters, HF and CASTOR. This study was based on computer simulations, which reproduce the Physics conditions expected for CMS at 10 TeV. The POMWIG generator was used to produce the diffractive samples and the others were done with PYTHIA.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Neste trabalho estudamos as características das distribuições da lacuna de rapidez em amostras de eventos de minimum bias de colisões pp a ps=7 TeV no CMS/LHC. Tais eventos são constituídos por processos difrativos, além de processos de QCD mole. São investigados o tamanho e a localização das lacunas, assim como as correlações entre as distribuições obtidas a partir dos objetos reconstruídos no detector e as distribuições obtidas a partir das partículas geradas via simulação Monte Carlo. Uma boa compreensão dessas distribuições pode, eventualmente, possibilitar a caracterização de eventos difrativos nos dados. / Rapidity gap distributions in minimum bias events from pp collisions at ps = 7TeV are studied. Minimum bias events are composed by diffractive processes and soft QCD processes. Gap size and position, as well as correlations between reconstructed distributions and Monte Carlo simulated distributions are investigated. A good understanding of such distributions may, eventually, make it possible characterize diffractive events in real data.

abstract: Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing the phase information. The measurement of amplitude alone is insufficient to solve the structure. Therefore, phase retrieval is essential to structure determination with X-ray diffractive imaging. So far, many experimental as well as algorithmic approaches have been developed to address the phase problem. The experimental phasing methods, such as MAD, SAD etc, exploit the phase relation in vector space. They usually demand a lot of efforts to prepare the samples and require much more data. On the other hand, iterative phasing algorithms make use of the prior knowledge and various constraints in real and reciprocal space. In this thesis, new approaches to the problem of direct digital phasing of X-ray diffraction patterns from two-dimensional organic crystals were presented. The phase problem for Bragg diffraction from two-dimensional (2D) crystalline monolayer in transmission may be solved by imposing a compact support that sets the density to zero outside the monolayer. By iterating between the measured stucture factor magnitudes along reciprocal space rods (starting with random phases) and a density of the correct sign, the complex scattered amplitudes may be found (J. Struct Biol 144, 209 (2003)). However this one-dimensional support function fails to link the rod phases correctly unless a low-resolution real-space map is also available. Minimum prior information required for successful three-dimensional (3D) structure retrieval from a 2D crystal XFEL diffraction dataset were investigated, when using the HIO algorithm. This method provides an alternative way to phase 2D crystal dataset, with less dependence on the high quality model used in the molecular replacement method. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho apresenta medidas de duas razões de produção difrativa envolvendo sabores pesados, através de um estudo em uma amostra reconstruída de J/ψ → μ+ μ- em colisões pp a raiz quadrada de s= 1,96 TeV com o uso do detector DØ situado no Fermilab. Estes eventos foram selecionados com o uso dos detectores do Monitor de Luminosidade, o sistema de calorimetria e o sistema de m Ão ons do DØ, em uma região de pseudo-rapidez 2,7 ≤|η|≤ 4 ,4 . As razões medidas foram NJϕdiff/Nj/ϕtotal = (1,74 0,16 (estat) 0,13 (sist)) % e N b dif / N b total = 0,79 0,11(estat) 0,23 (sist))% / This work presents measurements of two diffractive production ratio for heavy flavour physics on sat with the use of are constructed J/ψ → μ + μ sample in pp collisions at s= 1. 96 TeV using the DØ detector at Fermilab Tevatron. These events were selected using the Luminosity Monitor detectors, the calorimeter system and the muon system in a pseudo-rapidity region with range 2 . 7 ≤|η|≤ 4, 4 . The measured ratio were estimated to be NJϕdiff/Nj/ϕtotal = (1,74 0,16 (estat) 0,13 (sist)) % and Nb dif / Nb total = 0,79 0,11(estat) 0,23 (sist))%