L'omniprésence du collagène dans le corps humain et les nombreuses pathologies qui sont associées à ses anomalies de structure en font un objet d'étude de premier plan. Le collagène possède dans sa séquence primaire de nombreux cycles pyrrolidines stabilisant une structure secondaire de type polyproline II (PPII) et une structure tertiaire en triple hélice correspondant à un superenroulement de trois chaines peptidiques. Lors de ce travail, nous nous sommes intéressés à la synthèse et la caractérisation structurale de peptides mimes de collagène (CMP), seuls ou en présence de collagène de type I. Pour appréhender les différents niveaux de structuration des CMP: conformation locale, structures secondaires, assemblages trimériques et supramoléculaires, nous avons privilégié une approche muti-échelle. Les études que nous avons menées par dichroïsme circulaire et RMN ont visé à analyser en détail les relations entre triples hélices et les différentes espèces monomériques présentes en solution. Grâce à l'utilisation de peptides modèles marqués, nous avons pu mesurer par RMN des paramètres structuraux locaux et les comparer à des simulations de dynamique moléculaire. La présence d'assemblages supramoléculaires a été mise en évidence et analysé d'un point de vue qualitatif, quantitatif et cinétique par des études de DLS, RMN et par différentes approches de microscopies. Enfin, l'ensemble de nos observations nous ont conduit à proposer de nouvelles molécules CMP. Nous avons ainsi entrepris la synthèse de peptidomimétiques fluorés en vue d'améliorer la cinétique de formation et la stabilité de la triple hélice et pour également favoriser des assemblages supramoléculaires ordonnés. / The collagen is omnipresent in the human body and many diseases are associated with its structural anomalies, these are the main reasons to study its stability. Collagen has in its primary sequence many pyrrolidine cycles, which stabilize a secondary structure such polyproline II (PPII), and a triple helix structure where three left-handed helical polypeptide chains are supercoiled. In this work, we focused on the synthesis and structural characterization of collagen model peptides (CMP), alone or in the presence of type I collagen. To understand the different levels of CMP structuration: local conformation, secondary structures, trimeric and supramolecular assemblies, we favoured a multi-scale approach. The studies we conducted by circular dichroism and NMR aimed to analyze the relationship between triple helices and the different monomeric species present in solution. Through the use of labeled peptides models, we were able to measure NMR local structural parameters and compare them to molecular dynamics simulations. The presence of supramolecular assemblies was demonstrated and analyzed from a qualitative, quantitative and kinectics point of view by DLS, NMR and different microscopies approaches. Finally, all of our observations have led us to propose new CMP molecules. We undertook the synthesis of fluorinated peptidomimetics to improve the kinetics formation and stability of the triple helix, and also promote ordered supramolecular assemblies.

Doctor of Philosophy / Department of Biology / Keith B. Gido / A large scale habitat manipulation was conducted to assess the effects of establishing an emergent macrophyte, American water willow Justicia americana, on littoral reservoir communities. Coves in three large (>1,800 ha) Kansas impoundments were chosen and half planted with water willow. Sampling was conducted during the summer from 2001 to 2004. I found that water willow coves had more complex habitat as well as higher abundance and diversity of fishes, macroinvertebrates, and zooplankton than control coves. However, strong temporal variation in water levels influenced the amount of inundated water willow available in these systems. The effects of water willow on density, growth, condition, and diet of age-0 largemouth bass Micropterus salmoides were assessed. Significantly higher densities of age-0 largemouth bass were found in water willow coves, but growth, condition, and diet did not differ between water willow and control coves. Therefore, water willow was able to support higher abundances of age-0 largemouth bass than control coves without affecting growth, condition, or diet. Characteristics of age-0 largemouth bass from the water willow coves were compared to those from two small impoundments (<80 ha) with abundant macrophyte and healthy largemouth bass populations. Small impoundments had higher densities of age-0 largemouth bass than water willow coves in the three large impoundments, but individuals on average also had lower growth, condition, and fewer fish in their diet. Thus, largemouth bass populations in small impoundments may be more regulated by density dependent factors than populations in large impoundments. Overall, water willow is beneficial to littoral areas, supporting an increase in both abundance and diversity of assemblages. Finally, I used a field experiment to test the inundation and desiccation tolerance of water willow for different depths and durations. Water willow was susceptible to inundation, but resistant to desiccation. My findings provide information that can be used to select candidate reservoirs for water willow establishment based on expected water-level fluctuations.

Les travaux de thèse s'inscrivent dans le cadre du projet de recherche européen MAAXIMUS (More Affordable Aircraft through eXtended, Integrated and Mature nUmerical Sizing) et portent sur la simulation numérique de problèmes d'assemblages de composants en matériaux composites stratifiés. Ces assemblages sont sources de deux types de non-linéarités. D'une part, l'interface entre les pièce conduit au traitement de non-linéarités fortes (contact, frottement). D'autre part, dans les composants de l'assemblage, le comportement du matériau stratifié est complexe, du fait des nombreux phénomènes de dégradations interagissant entre eux. Ces deux aspects ont une influence forte sur la réponse globale de l'assemblage, ce qui implique la résolution de systèmes de très grandes tailles, nécessitant généralement l'utilisation de moyens de calcul parallèles.Le couplage entre ces deux problématiques nécessite donc l'utilisation d'algorithmes de calcul parallèle dédiés et robustes, à même de traiter de nombreuses non-linéarités très fortes. Pour cela, la méthode LATIN (pour LArge Time INcrement) présente de nombreux avantages, déjà mis en évidence dans le cas de calcul d'assemblages de pièces élastiques lors de travaux précédents. Le but de ces travaux est donc d'élargir le cadre de la méthode au cas des pièces au comportement endommageable et anélastique.Un dernier aspect, qui sera abordé au sein de ces travaux, traite des fortes variabilités des coefficients intervenant dans les lois non-linéaires. Par conséquent, il est nécessaire de pouvoir traiter un très grand nombre de problèmes affectés de valeurs de coefficients différents. Pour cela, la stratégie multiparamétrique, intimement liée à la méthode LATIN, doit être étendue au cas de comportements matériau non-linéaires. Elle sera alors appliquée au travers de plusieurs paramètres variables : coefficients de frottement, précharges des éléments de fixation, seuil d'endommagement des matériaux... / The presented work, within the framework of the European research project MAAXIMUS (More Affordable Aircraft through eXtended, Integrated and Mature nUmerical Sizing), is dedicated to the numerical simulation of assemblies with components made of laminated composites. These assemblies involve two types of high non-linearities. First ones are linked to the interfaces between parts (unilateral contact and friction). Second ones are linked to the constitutive material behaviour, from its initial properties to the complex evolution of degradations. These two non-linearities have a strong influence on the response of the assembly, which involves solving systems with a high number of degrees of freedom and generally requires the use of parallel computing resources.The coupling between the two sources of non-linearities requires dedicated and robust algorithms, able to run on parallel architectures and to deal with many very strong non-linearities. The efficiency of the LATIN method (LArge Time INcrement) has already been highlighted in the case of assemblies with elastic components. A first aim of this work is thus to extend the method to the case of damageable and anelastic components' behaviour.A second aim is to deal with the variability of the coefficients involved in the non-linear laws. Each set of parameters (friction coefficients, preload of fasteners, damage threshold of material laws...) requiring a given calculation, the multiparametric strategy of the LATIN method must be extended to the case of non-linear materials in order to efficiently reduce the computation time.

MEnvSC / Department of Zoology

Les bandes magnétiques sont des assemblages multicouches utilisant des réseaux polyuréthanes. Ces matériaux organiques sont utilisés en tant que revêtement protecteur contenant des pigments ou en tant que liant assurant la cohésion des charges magnétiques utilisées pour le codage d’informations. Parmi les défauts, dont l’apparition nécessite une meilleure compréhension des réactions chimiques mises en jeu lors de l’élaboration de ces assemblages, le développement d’une adhésion excessive entre les bandes et des plaques de PVC pouvant conduire à une dégradation par arrachement a été ciblé pour cette étude.L’influence des conditions de réactions (atmosphère, température et rapports molaires alcool/isocyanate) sur la cinétique de réticulation de systèmes polyuréthanes modèles a permis de quantifier les espèces réactives résiduelles à l’issue de la formation du réseau et de mettre en évidence l’implication des fonctions isocyanate dans des réactions secondaires, et une inhibition de leur réactivité lorsque les réactions ne sont pas conduites en conditions inertes. La présence d’eau dans le milieu réactionnel a été reliée l’implication des fonctions isocyanate dans la formation de liaisons urée. Enfin, la réalisation d’assemblages modèles n’a pas permis de reproduire les arrachements mais l’étude d’assemblages fournis par l’industriel suggère que le procédé utilisé pour la mise en forme de la couche de protection soit la cause de ce défaut. / Magnetic tapes are multilayer assemblies using polyurethane networks. These organic materials are used as a protective coating containing pigments or as a binder ensuring the cohesion of the magnetic charges used for the information coding. Among the defects, the appearance of which requires a better chemical reactions involved in these assemblies development understanding, an excessive adhesion development between the strips and PVC plates which can lead to degradation by tearing been targeted for this study.The reaction conditions influence (atmosphere, temperature and alcohol / isocyanate molar ratios) on the crosslinking kinetics of model polyurethane systems made it possible to quantify the residual reactive species at the network formation end and to prove the isocyanate functions involvement in side reactions, and their reactivity inhibition when the reactions are not conducted under inert conditions. The water presence in the reaction environment was related to the isocyanate functions involvement in the urea bonds formation. Finally, the model assemblies realization did not make it possible to reproduce the stripping but the assemblies provided by the industrialist study suggests that the process used for the protective layer shaping is the defect cause.

The thesis presents systematical study and taphonomical evaluation of fusite wood specimens collected in the middle bench of the main lignite seam in the Bilina mine. In the introduction part, there are a general characteristic of the Most Basin and its geological setting with respect to the main lignite seam. Consequently, the charcoal is described in detail. Generally, the charcoaled wood, which was produced during wildfires in the Tertiary forests, shows well preserved anatomical details. The final part resumes systematics and taphonomy of the charcoal specimens collected by the author.

Orientador: Paulo José dos Reis Pereira / Resumo: A literatura acadêmica sobre “criminalidade organizada transnacional” tem uma ampla e crescente produção na área de Relações Internacionais, enquanto a dimensão transnacional do crime, que tal literatura leva no nome, ainda não ultrapassou as epistemologias analíticas tradicionais do campo da Segurança Internacional, muitas vezes presas a um aporte “Estadocêntrico” do território para analisar a suposta transnacionalidade do crime. O objetivo da pesquisa é criticar essa literatura e introduzir uma abordagem alternativa capaz de analisar o crime e sua dimensão transnacional. Tal abordagem irá focalizar os ordenamentos, os conjuntos, de relações entre atores, e o foco será em como tais relações constroem uma dimensão transnacional para análise do crime, e como o “local” é expressão dessa transnacionalidade. Criticada as abordagens tradicionais de “crime organizado transnacional”, o entendimento de mercados ilícitos transnacionais servirá como suporte para entender essa abordagem alternativa e a dimensão transnacional, pois os mercados ilícitos focalizam em diferentes atores e suas formas de relação para manter uma estrutura mercadológica e de fluxos ilícitos funcionando. Empiricamente, o grupo central dessa análise é o mexicano Los Zetas, e seu papel na Guatemala, a partir de 2008 até 2015, para explicar que o grupo faz parte de um mercado ilícito transnacional, e que a partir de suas relações, também formam uma dimensão transnacional, e partes da Guatemala são expressões das di... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The academic literature about “transnational organized crime” has a wide and growing production in the International Relations discipline, although the transnational dimension of crime, which said literature takes in its name, still hasn’t trespassed traditional epistemological and analytical perspectives in the International Security field, often stuck to a “Statecentric” approach about territory for the supposed transnationality of crime. The goal of this research is to criticize this literature and introduce an alternative approach capable of analysing crime and its transnational dimension. This new approach will focus on orderings, collectives, of relations between actors, and how these relations build up a dimension of their own, to analyse crime and their transnational flows, and how the “local” is an expression of this transnationality. After criticizing the traditional approaches of “transnational organized crime”, the knowledge of “transnational illicit markets” will serve as a support to understand this alternative approach and the transnational dimension, because these illicit markets focus on different actors and their relations to maintain a market structure of flows working on. Empirically, the central group of this analysis is the Mexican Los Zetas, and its role in Guatemala, from 2008 until 2015, to explain that the group was part of a transnational illicit market, and through their relations, also made up a transnational dimension, and portions of Guatemalan ... (Complete abstract click electronic access below) / Resumen: La literatura académica sobre “crimen organizado transnacional” tiene una amplia y creciente producción en el área de Relaciones Internacionales, en cuanto la dimensión transnacional del crimen, que tal literatura lleva en su nombre, todavía no ultrapasó las epistemologías analíticas tradicionales del campo de Seguridad Internacional, muchas veces focalizadas a un aporte “Estadocéntrico” del territorio para analizar la supuesta transnacionalidad del crimen. El objetivo de la investigación es criticar estas literaturas e introducir un nuevo abordaje capaz de analizar el crimen y su dimensión transnacional. Tal abordaje irá focalizar los ordenamientos, los colectivos de relaciones entre actores, y su foco será en como tales relaciones construyen una dimensión transnacional propria para el análisis del crimen y sus flujos transnacionales, y como el “local” es una expresión de las dinámicas transnacionales. Criticados los abordajes tradicionales del “crimen organizado transnacional”, la comprensión de mercados ilícitos transnacionales servirá como soporte para comprender ese abordaje alternativo y la dimensión transnacional, porque los mercados ilícitos transnacionales focalizan diferentes actores y sus formas de relación para mantener funcionando una estructura mercadológica de flujos transnacionales. Empíricamente, el grupo central de este análisis es lo mexicano Los Zetas, y su papel en Guatemala, a partir de 2008 hasta 2015, para explicar que el grupo hace parte de un mercado... (Resumen completo clicar acceso eletrônico abajo) / Mestre

Despite the increases in the intensity and frequency of disturbances on coral reefs in the Red Sea over the past decade, patterns of variability in fish communities are still poorly understood. This study aims to contribute to a better understanding of how fish communities vary along multiple spatial scales (10-100’ of kilometers) and to provide a baseline for future comparisons, fundamental to assess responses to climate change and other disturbances. Coral reefs along the Saudi Arabian Red Sea coast were surveyed from 2017 to 2019. The reefs ranged from 28° N to 18 °N and were categorized according their geographical location and grouped within three regions, namely north (24-28.5°N; 12 reefs), central (20.4-22.3°N; 11 reefs), and south (18.5-21.2°N; 30 reefs). The quantification of spatial patterns was conducted based on both taxonomic- and trait-based approaches. Considering the dependence of fish communities on the benthic habitat the relationship between different attributes of the fish assemblages and coral cover was also investigated. A consistent pattern of separation between assemblages of the northern and central region from the ones in the south was observed in nearshore reefs but was not evident for offshore reefs. The southern region supported higher densities, biomass, and species richness than the other two regions. The analysis showed that transect and reef scales contributed to the greatest variation in fish communities, suggesting higher levels of variability within small spatial scales. Several parameters of the fish community (total species, total density, total biomass, total functional entities, functional richness, functional redundancy) were positively correlated to coral cover, particularly in the northern region. Responses were not consistent across the Red Sea basin, suggesting that management plans should be regionally based. This study can be helpful to design management strategies as it provides a current baseline from both taxonomic and trait perspectives for Red Sea reefs that can be used to evaluate future changes due to natural and human-based disturbances.

The recent addition to Stockholm’s built environment in the shape of the new Slussen bridge, or Guldbron as most locals call it, has been both a source of controversy and admiration. This reaction is typical of any infrastructure that reshapes our surroundings. However, this interaction is not unidirectional. Similar projects may be affected by the very relations they might trigger in the first place. Building upon the conjunction of crucial concepts from actor-network theory and assemblage thinking, this study intends to identify the co-producing nature of the bridge as a technical artefact and the relations surrounding the project. To that end, I employ a qualitative research technique combining various methods of interviews and observation. The research primarily identifies the desired nature of the bridge and its ability to stabilize relations as a heterogeneous assemblage. Ultimately, the everchanging state of affairs or fluid character of this piece of infrastructure is discussed. The thesis concludes by arguing that the exploration of similar projects from a relational perspective challenges the conceptualization of megaprojects as taken- for-granted entities. Such an understanding brings to the forefront the crucial importance of interactions to define whether a project can be considered as ‘mega’, as opposed to employing a prescribed set of criteria.

Due to intensive coastal development, a combination of local (e.g. pollution, fishing) and global pressures (such as climate change) is affecting marine habitats worldwide. This is a pressing issue in Saudi Arabia, particularly considering the plans for the expansion of sea-related activities within the Saudi Arabia's Vision 2030 framework. Sustaining some of those activities, such as tourism, is dependent upon the maintenance of good ecosystem health. National monitoring programs in Saudi Arabia are scarce and a lack of sound knowledge on how marine organisms change in space and time and what the main factors driving their responses are, limits the contribution of scientists to the management and conservation of the Red Sea. Here we provide baseline knowledge, that can be critical for assessing changes associated with current and future coastal development as well as climate change by collecting data across multiple spatial (including multiple habitats) and temporal scales for the analysis of macroinvertebrate organisms and environmental drivers. One of the most striking findings is related to the low densities observed for macroinvertebrates, making populations potentially vulnerable to disturbance. We also highlight the contribution of different habitats within the seascape and the need to prioritize the features of the bottoms for management and conservation purposes. Each habitat has a unique ecological signature but they are connected to adjacent habitats through a subset of species able to utilize different biotopes within the seascape. Disrupting this ecological network may affect biodiversity patterns from local to regional levels. Within each habitat, temporal variability should be taken into account as patterns change on a seasonal and annual scale. The aim of the thesis is to contribute to the sustainable development of the Red Sea, a unique resource shared among several countries, which will result in a long-term benefit to the Kingdom of Saudi Arabia, and other countries. Information provided is critical as previous knowledge for the region was almost inexistent and allows for future studies to investigate and predict the impacts of intense coastal development and inform conservation and management decisions.