The main goal of this thesis is to study and compare electron microscopy images of Nicotiana Occidentalis chloroplasts, obtained from two types of transmission electron microscopes,which work with different accelerating voltage of 80kV and 5kV. The two instruments, TEM JEOL 1010 and low voltage electron microscope LVEM5 are employed for experiments. In the first theoretical part, principle of electron microscopy and chloroplast morphology is described. In experimental part, electron microscopy images of chloroplast under different conditions of sample preparation are shown and discussed.

Content: A comprehensive analysis of the molecular and structural components of deer skin and cow hide was undertaken. These skins known to be strong, however they derive their strength from different combinations of molecular and structural properties. Firstly, the physical properties of deer skin and cow hide including the tensile strength, tear strength and denaturation temperature were measured. Secondly, the structure of the collagen fibrils and glycosaminoglycans was investigated using transmission electron microscopy (TEM), and small angle X-ray scattering (SAXS). Finally, the chemical composition of deer skin and cow hide such as amino acids, crosslinks and glycosaminoglycans were analysed. Our results showed that physical properties of deer skin and cow hide are derived from different combinations of several chemical components resulting in different architecture. It was found that the large and “wavy” collagen fibres in deer skin made up of collagen fibrils with small diameters. Additionally, deer skin fibrils appeared to be linked by regular arrays of filaments of large glycosaminoglycans that are distributed uniformly. Deer skin contained higher proportion of trivalent collagen crosslinks. In contrast, the collagen fibrils in cow hide were large, contained a diverse glycosaminoglycan distribution and a higher proportion of tetravalent collagen crosslinks, resulting in straight collagen fibres. This study suggests that although deer skin and cow hide are both strong, they have different structural and molecular features. Take-Away: Deer skin and cow hide have different structural and molecular make up which are reflected in their physical properties particularly strength. Glycosaminoglycans are important for the organisation of collagen fibrils in deer skin and cow hide. Deer skin and cow hide contain different ratios of collagen natural crosslinks which are essential collagen stability.

Tato Diplomová práce je zaměřena na odstranění šumu ze snímků získaných pomocí Transmisního elektronového mikroskopu. V práci jsou popsány principy digitalizace výsledných snímků a popis jednotlivých šumových složek, které vznikají při digitalizaci snímků. Tyto nechtěné složky ovlivňují kvalitu výsledného snímku. Proto byly vybrány filtrační metody založené na minimalizaci totální variace, jejichž principy jsou v této práci popsány. Jako referenční filtrační metoda byla vybrána filtrace pomocí Non-local means filtru. Tento filtr byl vybrán, jelikož v dnešní dobře patří mezi nejvíce využívané metody, které mají vysokou účinnost. Pro objektivní hodnocení kvality filtrací byly použity tyto hodnotící kritéria – SNR, PSNR a SSIM. V závěru této práce, jsou všechny získané výsledky zobrazeny a jsou diskutovány účinnosti jednotlivých filtrační metod.

Irradiation of metals with energetic particles causes heavy damage effects in microstructure and mechanical properties, which is closely associated with irradiation conditions, presence of impurities, and microstructural features. It has been proposed that the radiation tolerance of a certain material can be enhanced by introducing a high density of interfaces, acting as ‘sinks’ that can frequently involve in attracting, absorbing and annihilating defects. Nanostructured materials with large volume fraction of interfaces, therefore, are assumed to be more radiation tolerant than conventional materials. This thesis focuses on the radiation damage effects in nanostructured Cu via the methods of in-situ TEM (transmission electron microscope) radiation experiments, postirradiation TEM analyses, small-mechanical tests (nanoindentation and micro-pillar compression), and computer simulations (molecular dynamics and phase-field modeling). We design and fabricate nanostructured Cu using direct current (DC) magnetron sputtering deposition technique, a typica physical vapor deposition (PVD) method and a bottom-up way to construct various nanostructured metals. High-density twin boundaries (TBs) and nanovoids (NVs) are introduced into two distinct nanostructured Cu films, including nanovoid-nanotwinned (NVNT) Cu (111) and nanovoid (NV) Cu (110). The in-situ high-energy Kr⁺⁺ (1 MeV) and ex-situ low energy He⁺ (< 200 keV) irradiations are subsequently preformed on the as-deposited Cu samples. On the one hand, the in-situ TEM observations suggest that TBs and NVs can influence the formation, distribution and stability of radiation-induced defects. Meanwhile, the preexisting microstructures also undergo structural change through void shrinkage and twin boundary migration. On the other hand, the ex-situ micro-pillar compression tests reveal that the Heirradiated NV-NT Cu contains less defect clusters but experiences more radiation-induced hardening. The underlying mechanisms of void shrinkage, twin boundary migration, and radiationinduced hardening are fully discussed based on post-irradiation analyses and computer simulations.

<p>Ni-base superalloys are among the highest temperature capable alloys and are used pervasively throughout the transportation, energy, and nuclear industries. However, their microstructures have been largely limited to containing the γ´ (cubic) and γ´´ (tetragonal) phases to enable high strength at elevated temperatures, and this fixation has restricted alloy development opportunities. In the past three decades, a new set of alloys, strengthened by the γ´´´ (orthorhombic) phase, was developed by Haynes International. The alloys exhibit comparable strength to existing Ni-based superalloys and show a 25% decrease in the thermal expansion coefficient, designed for tighter clearances (thus improving engine efficiency) and help to reduce thermally induced fatigue from engine cycling. </p> <p>The newest iteration of such alloys, HAYNES^® 244^®, has a nominal composition of Ni-22.5Mo-8Cr-6W (wt.%), and each alloying element is used to help precipitate the γ´´´-Ni₂(Cr, Mo, W) phase. The deformation mechanisms of this material are currently unknown. Previous studies investigating the predecessor alloy, HAYNES^® 242^® alloy, showed deformation twinning to be the dominant deformation mechanism during mechanical testing, but the physical phenomena responsible for this mode of deformation were not clearly elucidated. As a result, the primary motivation of this project is to understand the deformation behavior of the 244 alloy from the atomistic level and upwards. </p> <p>This work details efforts to elucidate these deformation mechanisms using an integrated computational and experimental approach. First-principles calculations were performed to determine the entire generalized stacking fault energy (GSFE) surface and slip pathways of the γ´´´ phase for dislocation slip. The various planar defects that could form from dislocation slip were predicted to provide significant barriers for dislocation motion due to their very high planar defect energies (~1000 mJ/m²), likely precluding shearing of the precipitates. We incorporated these results into phase field dislocation dynamics (PFDD) to simulate dislocation-precipitate interactions of finite size. These results showed that the planar defect energies of the γ´´´ phase largely govern the deformation behavior and critical resolved shear stress for precipitate shearing, regardless of precipitate shape, size, or orientation. Extensive mechanical testing conducted from room temperature up to 760 ºC over strain rates ranging from 10^-9 s^-1 to 10^-4 s^-1 combined with transmission electron microscopy validated the predicted deformation structures of creep and tensile samples. Shearing of individual precipitates by intrinsic and extrinsic stacking faults, as well as extensive deforming twinning, was observed. The integrated GSFE and PFDD simulations showed that the precipitates would resist dislocation shearing and favor twinning as the preferred deformation mechanism at all temperatures and strain rates investigated. These results provide pathways for microstructural and composition modification to further increase the strength of γ´´´ strengthened alloys in the future.</p> <p><br></p>

Les techniques d'analyse des images présentées dans cette thèse sont élaborées dans le cadre du Projet Européen dédié au développement d'une plateforme automatique pour l'évaluation de la cristallisation des protéines membranaires. Un grand nombre d'échantillons est simultanément produit et évalué par microscopie électronique en transmission (MET). Pour rendre cette tache automatique, une analyse en ligne des images acquises est indispensable ; des régions d'intérêt essentielles pour le pilotage du microscope sont progressivement sélectionnées afin d'évaluer les cristaux de protéines a fort grossissement.L'observation de l'échantillon à moyen grossissement fournit des informations nécessaires pour la caractérisation du succès de la cristallisation 2D. Les objets résultants, et en particulier le gris. De plus, ces membranes sont pratiquement transparentes aux électrons et donc, apparaissent faiblement contrastées.Cette thèse présente un ensemble de techniques de traitement d'images pour leur analyse à moyen grossissement (5-15 nm/pixel). La contribution originale de ce travail est située sur i) une évaluation statistique des contours en mesurant la corrélation entre les niveaux de gris proche du contour et un filtre de gradient pour réduire le sur segmentation, ii) la reconnaissance des objets de l'image, iii) une étude préliminaire de classification. Cette chaîne est en cours de validation sur un prototype. / The image analysis techniques presented in the présent thesis have been developed as part of a European projeet dedicated to the development of an automatic membrane protein crystallization pipeline. A large number of samples is simultaneously produced and assessed by transmission electron microscope (TEM) screening. Automating this fast step implicates an on-fine analysis of acquired images to assure the microscope control by selecting the regions to be observed at high magnification and identify the components for specimen characterization.The observation of the sample at medium magnification provides the information that is essential to characterize the success of the 2D crystallization. The resulting objects, and especially the artificial membranes, are identifiable at this scale. These latter present only a few characteristic signatures, appearing in an extremely noisy context with gray-level fluctuations. Moreover they are practically transparent to electrons yielding low contrast. This thesis presents an ensemble of image processing techniques to analyze medium magnification images (5-15 nm/pixel). The original contribution of this work lies in: i) a statistical evaluation of contours by measuring the correlation between gray-levels of neighbouring pixels to the contour and a gradient signal for over-segmentation reduction, ii) the recognition of foreground entities of the image and iii) an initial study for their classification. This chain has been already tested on-line on a prototype and is currently evaluated.

<p>Gold nanoparticles exhibit remarkable optical properties and could prove useful in sensitive biosensing applications. Upon illumination gold nanoparticles produce localized surface plasmons, which influence nearby fluorophores and an enhancement in their fluorescence intensity can be observed. This property makes gold nanoparticles attractive for enhancing optical signals.</p><p>In this project gold nanoparticles were functionalized with an antibody and immobilized to the surface of an existing biochip platform based on fluorescence. The aim was to investigate the possibility of obtaining an increased fluorescence signal from the gold nanoparticles. Two different conjugation procedures were investigated, direct physisorption and covalent attachment of the antibodies to the particles. Activity of bound antibodies was confirmed in both cases.</p><p>The on-chip fluorescence intensity produced by the different conjugates was monitored by use a specialized fluorescence reader designed for point-of-care use. AFM and SEM were used to determine the surface concentration of particles. A correlation between the produced fluorescence intensity and the surface concentration could be seen.</p>

Gold nanoparticles exhibit remarkable optical properties and could prove useful in sensitive biosensing applications. Upon illumination gold nanoparticles produce localized surface plasmons, which influence nearby fluorophores and an enhancement in their fluorescence intensity can be observed. This property makes gold nanoparticles attractive for enhancing optical signals. In this project gold nanoparticles were functionalized with an antibody and immobilized to the surface of an existing biochip platform based on fluorescence. The aim was to investigate the possibility of obtaining an increased fluorescence signal from the gold nanoparticles. Two different conjugation procedures were investigated, direct physisorption and covalent attachment of the antibodies to the particles. Activity of bound antibodies was confirmed in both cases. The on-chip fluorescence intensity produced by the different conjugates was monitored by use a specialized fluorescence reader designed for point-of-care use. AFM and SEM were used to determine the surface concentration of particles. A correlation between the produced fluorescence intensity and the surface concentration could be seen.

Le poly(3-hexylthiophène) régiorégulier (rr-P3HT) est l’un des matériaux phare pour les applications en électronique plastique. Afin d’améliorer les performances des dispositifs, il est important de comprendre et de contrôler la structure et la morphologie de la couche active. Des films minces de rr-P3HT cristallins et orientés peuvent être obtenus par epitaxie directionnelle par cristallisation (DEC) de 1,3,5-trichlorobenzène (TCB). Dans ce travail de thèse, nous présentons les avantages de la méthode DEC pour (i) déterminer la structure cristalline du rr-P3HT et pour (ii) étudier les fibres « shish-kebab », une morphologie alternative du rr-P3HT. La première partie de ce manuscrit consiste en l’analyse structurale par diffraction électronique de la forme I du P3HT obtenue dans les films epitaxiés. Afin d’affiner le modèle structural, nous avons fait varier la conformation des chaînes latérales. Dans un deuxième temps, nous avons appliqué ce même protocole afin de résoudre la structure du second polymorphe du P3HT (forme II) grâce à l’obtention de monocristaux parself-seeding. La deuxième partie du manuscrit est consacrée à l’élaboration de fibres orientées dites en « shish-kebab » par épitaxie dans un mélange TCB/Pyridine. La cinétique de croissance ainsi que l’orientation des chaînes de P3HT sont étudiés afin d’optimiser la méthode de préparation des fibres. L’effet de la masse moléculaire sur leur formation a également été évalué. Finalement les propriétés de transport de charges au sein de ces fibres ont été étudiées grâce à l’élaboration de transistors à effet de champ. / Regioregular poly(3-hexylthiophene) (rr-P3HT) is one of the promising materials for plastic electronic applications. Understanding as well as controlling the structure and morphology of the active layer is essential to improve the device efficiency. Highly crystalline and highly oriented rr-P3HT thin films can be obtained via directional epitaxial crystallization (DEC) in 1,3,5-trichlorobenzene (TCB). In this dissertation, we present the benefits of DEC method to (i) determine the crystal structure of rr-P3HT and (ii) to study shish-kebab fibers, an alternative morphology of rr-P3HT. The first part of this dissertation is related to the structural analysis of rr-P3HT form-I by using electron diffraction analysis on the epitaxied film. Furthermore, the modification of side chain conformation is used to improve the structural model. Finally, the determination protocol is also applied to resolve the preliminary crystal structure of rr-P3HT form II prepared by self-seeding method. The second part of thisdissertation is related to highly oriented shish-kebab fibers of rr-P3HT prepared by epitaxial crystallization in a mixture of TCB and pyridine. The investigations of growth kinetics and orientation of P3HT chains in the fiber are performed in order to determine the optimization of preparation conditions and growth mechanism of the fibers. In addition, the effect of molecular weight on the formation of the fibers is investigated. Finally, the charge transport properties of the fibers are measured by using the field effect transistor configuration.

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