Dès sa découverte, le graphène oxydé (GO), le plus accessible des précurseurs du graphène, a été largement utilisé pour des applications en science et technologie. La motivation de ce travail est d'étudier, d'un point de vue fondamental, le couplage entre des bicouches amphiphiles auto-associées (lesquelles peuvent être vues comme une matrice anisotrope formée d'objets bidimensionnels) et un objet lui-même bidimensionnel, en l'occurrence le feuillet de graphène oxydé, quand ils sont dispersés dans un solvant commun. La compétition entre les élasticités intrinsèques des bicouches et des feuillets de GO, ainsi que les interactions directes bicouche-bicouche, bicouche-GO et GO-GO, permet d'envisager un riche polymorphisme en fonction de la composition du système. Après avoir développé une procédure destinée à contrôler, dans une gamme étendue de teneur en GO, le système binaire GO-eau, le domaine confiné des dispersions aqueuses de GO a été exploré et, par la suite, le diagramme de phases ternaire a été construit. Les systèmes obtenus ont été caractérisés par des techniques comme la microscopie optique et la diffusion du rayonnement (diffusion dynamique de la lumière et diffusion des rayons-X aux petits angles). Les propriétés élastiques et thermodynamiques ont été décrites par l'application de modèles initialement conçus pour les phases lamellaires à deux constituants et adaptés dans le cadre de cette étude. / Since the discovery of graphene oxide (GO), the most accessible of the precursors of graphene, this material has been widely studied for applications in science and technology. The motivation of this work is to study with a fundamental perspective the coupling between amphiphilic bilayers, which can be seen as an anisotropic matrix formed of two-dimensional objects, and another two-dimensional object, namely the graphene oxide sheet when they are dispersed in a common solvent. The competition between the intrinsic elasticities of the bilayers and GO sheets, as well as between direct bilayer-bilayer, bilayer-GO and GO-GO interactions allows us to envisage a rich polymorphism, depending on the composition of the system. Following the development of a dedicated procedure for controlling in an extended range of GO content the binary GO-water system, the confined domain of aqueous GO dispersions was first investigated, and the ternary phase diagram then constructed. The obtained systems have been characterised, using techniques such as optical microscopy, light and x-ray scattering. Elastic and thermodynamic properties have been described by applying, and adapting to the scope of this study, models for two-component lamellar stacks. / Desde sua descoberta, o grafeno oxidado (GO), o mais acessível dos precursores do grafeno,tem sido amplamente utilizado para aplicações na ciéncia e tecnologia. A motivação destetrabalho é de estudar, de um ponto de vista fundamental, o acoplamento entre bicamadas anfifílicas auto-organizadas (que podem ser vistas como uma matriz anisotrópica formada por objetos bidimensionais) e um objeto ele mesmo bidimensional, neste caso a folha de óxido de grafeno, quando estão dispersados em um solvente comum.A competição entre as elasticidades intrínsecas das bicamas e das folhas de GO, assimcomo as interaçãoes diretas bicamada-bicamada, bicamada-GO e GO-GO, permitem esperar um rico polimorfismo em função da composição do sistema. Seguindo o desenvolvimento de um procedimento destinado ao controle, em um intervalo extendido da quantidade de GO, o sistema binário GO-água, o domínio confinado de dispersões aquosas de GO foi explorado e, em seguida, o diagrama de fases ternário contruído.Os sistemas obtidos foram caracterizados por t_ecnicas como microscopia ótica, espalhamento dinâmico de luz e espalhamento de raios-x à baixos ângulos. As propriedadeselásticas e termodinâmicas foram descritas pela aplicação de modelos inicialmente concebidos para fases lamelares à dois constituintes e adaptados ao escopo deste estudo.

Nesta dissertação discorremos acerca do crescimento e caracterização de filmes finos de carbeto de silício amorfo hidrogenado (a-Si1-xCx:H), crescidos pelo método de deposição química de vapor assistida por plasma (PECVD) no regime de baixa densidade de potência a partir de misturas de silano e metano. Foram analisadas e correlacionadas as propriedades ópticas, morfológicas e composicionais de filmes depositados em diferentes condições de fluxo de silano e concentração de metano. Os resultados não apenas confirmaram dados anteriores obtidos em filmes de a-Si1-xCx:H similares, mas possibilitaram uma melhor compreensão das características deste material. Para a obtenção de um composto de alto gap, alto conteúdo de carbono, química e morfologicamente homogêneo é necessário utilizar baixos fluxos de silano e alta concentração de metano, condições de deposição conhecidas como regime de \"plasma faminto por silano\". Neste regime são crescidos filmes com Eg > 3 eV, x > 0,5, maior concentração de ligações Si-C, concentração de hidrogênio de 50 at.%, menor proporção de radicais CH3 e menor densidade de poros. / In this work we describe the growth and characterization of hydrogenated amorphous silicon carbide (a-Si1-xCx:H) thin films deposited by plasma enhanced chemical vapor deposition (PECVD) in the low power density regime from mixtures of silane and methane. The optical, morphological and compositional properties of films deposited under different silane flow and methane concentration were analyzed and correlated. The results not only confirmed previous data obtained on similar a-Si1-xCx:H films, but improved the comprehension of their characteristics. In order to obtain a compound with high optical gap, high carbon content, chemically and morphologically homogeneous, it is necessary to work with low silane flow and high methane concentration; deposition conditions known as \"silane starving plasma\" regime. In this regime, films with Eg > 3 eV, x > 0.5, higher concentration of Si-C bonds, hydrogen concentration of 50 at.%, smaller proportion of CH3 radicals and smaller density of pores are produced.

Phosphate transfer is ubiquitous in nature, however the occurance of phosphomutases is rare. Their uniqueness can be attributed to the complex and malleable substrate recognition scheme that allows the enzyme to perform two similar, yet distinct, catalytic steps while maintaining strict fidelity for substrate versus water. The complexity of developing this mechanism is highlighted in that, while phosphomutase function has independently evolved in most larger phosphotransferase superfamilies, very little diversification of this function has developed. As such, phosphomutases provide a rich framework to study the intricate specificity mechanisms employed by enzymes. β-Phosphoglucomutase (bPGM) catalyzes the interconversion between β-glucose 1-phosphate (βG1P) and glucose 6-phosphate (G6P) via a β-glucose 1,6 bisphosphate (βG16P) intermediate. βPGM is in one of two subfamilies that have independently acquired phosphomutase activity within the ubiquitous Haloalkanoate Dehalogenase superfamily (HADSF) of phosphotransferases. The enzyme has been observed to undergo a large conformational change upon binding βG16P as well as a repositioning of the general acid/base catalyst residue Asp10. In addition, the mechanism involves cycling of the protonation state of Asp10, which requires a significant pKa shift. The importance of Asp10 and its activation of the enzyme have been discussed previously, however a clear understanding of the interplay between the conformational and catalytic activation mechanisms for βPGM has not been described. This work uses aqueous phase techniques, solution X-ray scattering and molecular dynamics, to probe the effect of individual ligand moieties on the conformational state of the enzyme and free energy molecular dynamics and electrostatic calculations determine the interplay between conformation, protonation and Asp10 activation. The results implicate a model where the ligand-induced conformational change is governed by the non-catalytic phosphate site, and this transition induces correct positioning of Asp10, which, in turn induces the pKa shift, forming the catalytically competent complex.

Biogenesis of the multivesicular body (MVB) organelle is an important process for regulation of signalling in the cell. Signal receptors embedded within the outer MVB membrane can be sorted into intralumenal vesicles which bud away from the cytosol to within the MVB preventing further signalling. Sorting of receptors, invagination of the membrane and release of vesicles into the MVB lumen are mediated by the endosomal sorting complexes required for transport (ESCRT) along with a range of accessory proteins including histidine domain protein tyrosine phosphatase (HD-PTP). HD-PTP is a multidomain protein which makes several interactions with ESCRT partners, including ESCRT-0, ESCRT-I and ESCRT-III. This thesis focusses specifically on the interaction between HD-PTP CC domain and Ubap1 (ESCRT-I), and the two interactions of HD-PTP Bro and PRR domains with STAM2 (ESCRT-0) SH3 and Core domains. To address the structure of HD-PTP, multiple techniques were used: X-ray crystallography, which gives high resolution structural information; small angle X-ray scattering (SAXS), which gives low resolution data for large non-crystallisable units in their solution state; and double electron-electron resonance (DEER) spectroscopy, which gives high resolution nanometre-range distance constraints between cysteines labelled with methanethiosulfonate spin label (MTSL). It was shown by X-ray crystallography that HD-PTP has an elongated CC domain, in stark contrast to its homologues ALIX and Bro1 which both have V-shaped CC domains. The CC domain showed limited flexibility both by SAXS and DEER. Further investigation showed that there was no significant conformational change upon binding its ESCRT-I partner Ubap1. The multidomain structure of HD-PTP Bro1-CC-PRR was described by SAXS, showing that these domains form an extended arrangement in solution. In addition, SAXS was also used to analyse the structure of these domains in complex with STAM2 (ESCRT-0), which showed that STAM2 is simultaneously tethered by the Bro1 domain and PRR. The Bro-CC-PRR portion of HD-PTP, has 9 cysteines, so with the aim of measuring local structural information in the CC domain alone, alternative spin labelling methods were investigated. Use of a bromoacrylaldehyde spin label (BASL), instead of MTSL, allowed more selective labelling of surface exposed cysteines, and avoided labelling most of the cysteines in the Bro1 domain. This novel method allowed the shape of the CC domain to be monitored during STAM2 binding and showed that there is no induced conformational change.

Nesta dissertação discorremos acerca do crescimento e caracterização de filmes finos de carbeto de silício amorfo hidrogenado (a-Si1-xCx:H), crescidos pelo método de deposição química de vapor assistida por plasma (PECVD) no regime de baixa densidade de potência a partir de misturas de silano e metano. Foram analisadas e correlacionadas as propriedades ópticas, morfológicas e composicionais de filmes depositados em diferentes condições de fluxo de silano e concentração de metano. Os resultados não apenas confirmaram dados anteriores obtidos em filmes de a-Si1-xCx:H similares, mas possibilitaram uma melhor compreensão das características deste material. Para a obtenção de um composto de alto gap, alto conteúdo de carbono, química e morfologicamente homogêneo é necessário utilizar baixos fluxos de silano e alta concentração de metano, condições de deposição conhecidas como regime de \"plasma faminto por silano\". Neste regime são crescidos filmes com Eg > 3 eV, x > 0,5, maior concentração de ligações Si-C, concentração de hidrogênio de 50 at.%, menor proporção de radicais CH3 e menor densidade de poros. / In this work we describe the growth and characterization of hydrogenated amorphous silicon carbide (a-Si1-xCx:H) thin films deposited by plasma enhanced chemical vapor deposition (PECVD) in the low power density regime from mixtures of silane and methane. The optical, morphological and compositional properties of films deposited under different silane flow and methane concentration were analyzed and correlated. The results not only confirmed previous data obtained on similar a-Si1-xCx:H films, but improved the comprehension of their characteristics. In order to obtain a compound with high optical gap, high carbon content, chemically and morphologically homogeneous, it is necessary to work with low silane flow and high methane concentration; deposition conditions known as \"silane starving plasma\" regime. In this regime, films with Eg > 3 eV, x > 0.5, higher concentration of Si-C bonds, hydrogen concentration of 50 at.%, smaller proportion of CH3 radicals and smaller density of pores are produced.

Understanding the mechanism of zeolite nucleation and crystallization will enable the zeolite science community to tune zeolite properties during synthesis in order to accommodate the purposes of various applications. Thus there has been considerable research effort in "deciphering" the mechanism by studying the growth course of tetrapropylammonium (TPA)-mediated silicalite-1 using several techniques, such as dynamic light scattering (DLS), small-angle X-ray/neutron scattering (SAXS/SANS), and nuclear magnetic resonance (NMR). While these studies have generated a more comprehensive picture on the silicalite-1 growth mechanism, the general application of the mechanism and how it could be applied to other zeolite systems have not been addressed. This work initially tried to apply the insights developed from the TPAsilicalite- 1 clear solution synthesis by investigating the nanoparticles formation and zeolite growth in several tetraethyl orthosilicate (TEOS)-organocation-water solutions heated at 368 K using SAXS. The results are in contrast to TEOS-TPAOH-water mixtures that rapidly form silicalite-1 at 368 K. These results imply that the developed TPA-silicalite-1 nucleation and crystallization mechanism is not universally applicable to other zeolite systems and TPA-silicalite-1 itself could be a special case. With this in mind, the next goal of this work uses in situ SAXS to revisit silicalite-1 growth kinetics prepared by using several TPA-mimic organocations and some asymmetric geometry organocations. The results clearly show the TPA cation is an extraordinarily efficient structure-directing agent (SDA) due to its moderate hydrophobicity and perfect symmetric geometry. Any perturbation of the hydrophobicity and symmetry of SDA leads to a deterioration of zeolite growth. This work further investigates the influences of alcohol identity and content on silicalite-1 growth from clear solutions at 368 K using in situ SAXS. Several tetraalkyl orthosilicates (Si(OR)4, R = Me, Pr, and Bu) are used as the alternative silica sources to TEOS in synthesizing silicalite-1. Increasing the alcohol identity hydrophobicity or lowering the alcohol content enhances silicalite-1 growth kinetics. This implies that the alcohol identity and content do affect the strength of 1) hydrophobic hydration of the SDA and 2) the water-alcohol interaction, through changing the efficiency of the interchanges between clathrated water molecules and solvated silicate species.

Structured RNAs are pervasive in biology, spanning a functional repertoire that includes messengers, regulators of gene expression and catalysts of translation and splicing. From the relatively simple tRNAs and riboswitches to the highly structured ribosomal RNAs, the ability of RNAs to function is dependent on well-defined secondary and tertiary structures. However, studies of RNA folding in vitro have revealed an extreme propensity to form alternative structures, which can be long-lived and interfere with function. In the cell, a diverse array of RNA binding proteins and RNA chaperones guide RNAs towards the correct structure and disrupt misfolded intermediates. Among these proteins, DEAD-box protein family stands out as one of the largest groups, with its members ubiquitously involved in RNA metabolism across all domains of life. DEAD-box proteins can function as both specific and general RNA chaperones by disrupting RNA structures in an ATP-dependent manner. Here I describe my work studying the general RNA chaperone mechanism of the Neurospora crassa protein CYT-19, a model DEAD-box protein and a biological RNA chaperone that is required for efficient folding of self-splicing group I intron RNAs in vivo. After an introduction to DEAD-box proteins and their mechanisms as RNA remodelers (Chapter 1), I will first describe studies of group I intron unfolding by CYT-19, focusing on the effects of RNA tertiary structure stability on CYT-19 activity and targeting to RNA substrates (Chapter 2). I will then describe the characterization of ATP-dependent mechanisms during CYT-19-mediated refolding of the misfolded group I intron (Chapter 3). In Chapter 4, I will present small-angle X-ray scattering (SAXS) studies of structural features of DEAD-box proteins that allow them to efficiently interact with large structured RNA substrates. Finally, I will turn to studies of DEAD-box protein involvement during early steps of RNA compaction and folding, using SAXS and activity-based approaches (Chapter 5). I will conclude with a general discussion of superfamily 2 RNA helicases, which include DEAD-box and related proteins, and their functions and mechanisms as remodelers of structured RNAs and RNPs. / text

The controlled, _ne-grained microstructure of thermomechanically processed Nb microalloyed linepipe steels is destroyed in the vicinity of welds used in fabricating pipelines. There are conflicting views on the influence of niobium in the `heat-affected zone', particularly in the region closest to the weld fusion line which is most dramatically impacted by the thermal cycling that occurs during welding. Consequently, there is a need to fully characterise the influence of niobium on the evolution of structures and properties in this zone. The aim of the work presented in this thesis was to quantify and characterise precipitates of niobium and dissolved niobium across sub-zones of the weld heat-affected zone, in order to develop a better understanding of the effects of niobium across the region. In order to achieve this, heat treatments were undertaken for the first time to simulate each sub-zone of the heat affected zone such that unique states of dissolved niobium and precipitated niobium was developed. A novel technique as designed and applied for the first time to measure and quantify the precipitate sizes and size distributions in bulk samples of Nb micro-alloyed steels. In addition, measurements of the dissolved niobium across the heat-affected zone were completed in order to ensure that the discrete effects of all states of niobium were subjected to analysis. Weld simulations of the coarse-grained heat-affected zone, the region closest to the weld fusion line, were conducted and assessed against the measured states of niobium. This was followed by the manufacture of commercial welds in order to assess the variation of structures and properties across the heat-affected zone for different plate conditions generated by heat treatment prior to welding. This work established that that a wide range of niobium carbide precipitate sizes were crucial in assuring the excellent mechanical properties in the line-pipe steel, coarser precipitates were found to control the austenite grain size that evolved in the coarse-grain heat affected zone, while fine precipitates dissolved in the thermal cycles close to the weld fusion line, and produced finer microstructures.

The Enhanced Actinide Removal Plant (EARP), located on the Sellafield site, is one of the UK's most crucial radioactive effluent treatment plants. EARP removes actinides and select fission products from routine reprocessing effluents by association with a ferric iron oxyhydroxide floc, which is precipitated from acidic effluent streams by the addition of NaOH. The effluent compositions that EARP receives will change in character as the Sellafield site transitions from its current routine reprocessing operations to post-operational clean-out and accelerated decommissioning activities over the next few years. An enhanced understanding of the iron oxyhydroxide formation processes occurring in EARP would help underpin optimisation of current plant efficiency and allow better prediction of changes in efficiency as effluent composition varies. In this study, iron oxyhydroxide formation, properties and evolution with time under EARP-relevant conditions were characterized. These processes were investigated in a pure ferric nitrate system and systems with added sulfate, phosphate and boric acid using a range of techniques including SAXS, TEM and FTIR. In all the experimental systems the iron oxyhydroxide floc was composed of nanoparticulate ferrihydrite aggregated into extensive mass fractal structures. In situ SAXS experiments showed that formation proceeded via a precursor cluster pathway whereby Fe(III) clusters ~ 0.45 nm in radius form rapidly at pH 0.12 - pH 1.5 upon dropwise addition of strong NaOH to the acidic effluent simulants. Further analysis indicates these clusters are Fe13 Keggin clusters, which have previously been shown to be an important structural motif in the ferrihydrite structure. With further pH increase, cluster aggregation occurs along with precipitation of low molecular weight Fe(III) species (mostly monomers), leading to formation of ferrihydrite nanoparticles which preserve the Keggin cluster in the core. Phosphate, sulfate and boric acid exhibit varying interactions with the solid phase throughout the formation process, with both inner and outer sphere adsorption observed for different species. Ageing experiments show that the ferrihydrite floc readily undergoes transformation leading to predominantly hematite formation, except in the presence of phosphate (concentrations > 10 ppm) where transformation is entirely inhibited due to phosphate adsorption to the floc. These results progress the fundamental understanding of the iron oxyhydroxide formation and ageing processes occurring in EARP.

Gold nanoparticles (AuNPs) have garnered considerable attention for their interesting size-dependent properties. These properties have fueled applications that span a continuum ranging from simple to sophisticated. Applications for these materials have grown more complex as syntheses for these materials have improved. For simple applications, current synthetic processes are sufficient. However, development of syntheses that generate well-defined particle sizes with specifically tailored surface functionalities is an on-going challenge for chemists. The aim of this dissertation is to improve upon current AuNP syntheses to produce sophisticated materials needed to discover new material properties, and provide efficient access to materials to develop new advanced applications. The research described in this dissertation improves upon current methods for AuNP production by using a microreactor to provide enhanced mixing and synthetic control, and small angle X-ray scattering (SAXS) as a precise, rapid, solution-based method for size distribution determination. Using four ligand-stabilized AuNP samples as reference materials, SAXS analysis was compared to traditional microscopic size determination. SAXS analysis provided similar average diameters while avoiding deposition artifacts, probing a larger number of particles, and reducing analysis time. Next, the limits of SAXS size analysis was evaluated, focusing on identifying multiple distributions in solution. Utilizing binary and ternary mixtures of well-defined AuNP reference samples, SAXS analysis was shown to be effective at identifying multiple distributions. While microscopy has limited ability to differentiate these modes, SAXS analysis is more rapid and introduces less researcher bias. Because AuNP size and ligand functionality are interdependent, accessing desired core sizes with varied functionality is challenging. To address this, a new microfluidic synthetic method was developed to produce thiolate-passivated AuNPs with targeted core sizes from 1.5 - 12 nm with tailored functionality. This ability to control size while independently varying surface functionality is unprecedented. Lastly, AuNP core formation was probed by simultaneous in situ SAXS and UV/visible spectroscopy. A coalescence mechanism for AuNP growth was observed when using Bunte salt ligands. This finding compares well to observed coalescence in other systems using weakly-passivating ligands, and supports the hypothesis that Bunte salts passivate ionically during particle growth while resulting in covalent linkages. / 2015-10-10