A abordagem de modos normais de baixa frequência na descrição das flutuações conformacionais dos estados nativos das proteínas globulares tem ajudado na caracterização das suas funções biológicas. Vários métodos teóricos e experimentais têm sido empregados para a determinação destas flutuações internas. Estes movimentos podem ser caracterizados pelo fator Debye-Waller (fator-B), correspondente à mobilidade local do resíduo em nível atômico. A análise de modos normais utilizando os modelos de rede elástica (ENM) demonstra ser uma técnica robusta. Fatores-B experimentais são reproduzidos teoricamente por meio desta técnica em tempos computacionais relativamente curtos, mostrando-se competitiva com as técnicas mais sofisticadas. O modelo de rede elástica é uma abordagem t ipo coarse-grain na qual a proteína no seu estado enovelado é representada por uma rede elástica tridimensional de carbonos conectados por molas. As molas representam as interações ligantes e não ligantes entre os carbonos . Neste trabalho, inicialmente, estudamos os modelos de rede elástica já conhecidos na literatura. Em seguida, realizamos um estudo comparativo entre eles. Neste estudo, comprovamos que os modelos pfGNM e pfANM apresentam melhor correlação com os fatores-B experimentais que os os modelos GNM e ANM tradicionais. Desenvolvemos também uma nova abordagem, a qual intitulamos número de contatos ponderados anisotrópica (AWCN). Mostramos que a abordagem AWCN apresenta um desempenho significativamente melhor que o modelo de rede elástica anisotrópica tradicional. Por fim, realizamos um estudo de caráter investigativo do comportamento do peso das interações entre resíduos. Este estudo re velou que, para os modelos WCN e AWCN, a correlação exibe o seu valor máximo para interações ponderadas $1/R^p$, entre resíduos $i$ e $j$j, para valores de $p$ em torno de 2. Nos modelos pfGNM e pfANM a correlação é maximizada para dois valores de $p$, o primeiro em torno de 2 e o segundo em torno de 4,75, indicando que a ponderação pelo recíproco do quadrado da distância, usualmente empregada na literatura, pode não ser adequada para obter a melhor correlação. / Low frequency normal mode approach to describe conformational fluctuations of globular proteins has helped to characterize their biological functions. Various theoretical and experimental methods have been employed to det ermine the magnitudes of those internal motions. Those motions can be characterized by the Debye-Waller factor (B-factor), co rresponding to the local mobility of the residue at the atomic level. Normal mode analysis using elastic network models (ENM) has demonstrated to be a robust technique. Experimental B-factors has been reproduced theoretically by means of this techniq ue in a short computational time and it has been shown to be competitive with more sophisticated techniques. The ENM is a coarse-grained approach in which the protein is represented by a three-dimensional elastic network of alpha-carbon atoms connect ed by springs. Springs represent bonded and non-bonded interactions between the alpha-carbon atoms. In this work, we study th e elastic network models known in the literature. Next, we perform a comparative study between them. We show that the pfGNM a nd pfANM models present better correlation with experimental B-factors than the traditional GNM and ANM models. We also devel op a new approach, which we entitled anisotropic weighted contact number (AWCN). We show that it presents results significantly better than the traditional anisotropic elastic network model. Finally, we perform a study of investigative character of the behavior for the weight of the interactions between residues. This study revealed that, for the WCN and AWCN models, the correlation exhibits its maximum value for weighted interactions $1/R^p$, between residues $i$ and $j$, for values of $p$ around 2. In the pfGNM and pfANM models the correlation is max imized for two values of $p$, the first one around 2 and the second one around 4.75. This indicates that the weighting by the reciprocal of the square of the distance, usually employed in the literature, may not be appropriate to obtain the best correlation.

Geological storage of carbon dioxide (CO2) in deep saline aquifers is one approach to mitigate release from large point sources to the atmosphere. Understanding of in-situ processes providing trapping is important to the development of realistic models and the planning of future storage projects. This thesis covers both field- and pore-scale numerical modeling studies of such geohydrological processes, with focus on residual trapping. The setting is a CO2-injection experiment at the Heletz test site, conducted within the frame of the EU FP7 MUSTANG and TRUST projects. The objectives of the thesis are to develop and analyze alternative experimental characterization test sequences for determining in-situ residual CO2 saturation (Sgr), as well as to analyze the impact of the injection strategy on trapping, the effect of model assumptions (coupled wellbore-reservoir flow, geological heterogeneity, trapping model) on the predicted trapping, and to develop a pore-network model (PNM) for simulating and analyzing pore-scale mechanisms. The results include a comparison of alternative characterization test sequences for estimating Sgr. The estimates were retrieved through parameter estimation. The effect on the estimate of including various data sets was determined. A new method, using withdrawal and an indicator-tracer, for obtaining a residual zone in-situ was also introduced. Simulations were made of the CO2 partitioning between layers in a multi-layered formation, and parameters influencing this were identified. The results showed the importance of accounting for coupled wellbore-reservoir flow in simulations of such scenarios. Simulations also showed that adding chase-fluid stages after a conventional CO2 injection enhances the (residual and dissolution) trapping. Including geological heterogeneity generally decreased the estimated trapping. The choice of trapping model may largely effect the quantity of the predicted residual trapping (although most of them produced similar results). The use of an appropriate trapping model and description of geological heterogeneity for a site when simulating CO2 sequestration is vital, as different assumptions may give significant discrepancies in predicted trapping. The result also includes a PNM code, for multiphase quasi-static flow and trapping in porous materials. It was used to investigate trapping and obtain an estimated trapping (IR) curve for Heletz sandstone.

L’objectif de cette thèse est de modéliser en temps réel la propagation d’un incendie dans des ensembles comportant un grand nombre de locaux. Un modèle semi-physique de réseau polydisperse amorphe prenant en compte les connexions à courte et longue distances entre sites, est proposé. Les phénomènes physiques liés au développement du feu dans un local et à sa transmission entre locaux par les parois sont simulés par des lois normales de probabilité. Les durées moyennes de transmission par les parois sont déterminées à l’aide d’un modèle à zones prenant en compte les spécificités du local en feu. Des expérimentations spécifiques dans un caisson en acier, représentatif d’un local de la Marine Nationale, ont permis de valider le modèle à zones. Un exemple détaillé du calcul par le modèle de réseau de la propagation d’un feu dans une maquette de navire à échelle un est ensuite décrit et analysé pour différents scénarios. Une analyse de sensibilité utilisant un plan factoriel complet à deux niveaux permet de hiérarchiser les paramètres du modèle et d’étudier la sensibilité de la solution aux variations de ces paramètres. Une étude statistique est conduite afin d’établir une cartographie du risque incendie à bord du navire. La transmission du feu par les gaines de ventilation est simulée par une loi normale de probabilité où la durée moyenne de transmission est déterminée à l’aide d’un code à champ unidimensionnel. Après avoir validé ce code sur des mesures obtenues par DGA dans une conduite cylindrique différentiellement chauffée, l’influence de ce mode de transmission sur la propagation du feu dans le navire est analysée. / This thesis work is devoted to the development of a semi-physical network model to predict real-time fire spread in polydisperse amorphous massively multi-compartmented spaces. This model takes into account short-range and long-range connections between adjacent and remote network sites. The physical phenomena of fire ignition and flashover, and of fire transmissions through the walls are simulated using time-dependent normal probability distributions. Mean durations of transmission though the walls are determined by a two-zone model which takes into account the fuel load, the room size and the thermal properties of walls. Specific experiments were conducted in a steel room, representative of a naval vessel compartment, in order to validate the zone model. Then a proof of concept is developed by applying the network model to different fire scenarios in a full-scale vessel mockup. A sensitivity analysis using a two-level full factorial design is performed to identify the most influential model parameters and to evaluate the sensitivity of the solution to variations of these parameters. A statistical study is conducted to produce fire risk maps. Finally, a special emphasis is put on the fire transmission by the ventilation ducts. This phenomenon is simulated using a time-dependent normal probability distribution where the mean duration is determined by means of a one-dimensional CFD model. This model is first validated using data obtained by DGA in a differentially heated duct and second, the influence of fire transmission through ventilation duct on its propagation throughout the vessel is investigated.

The first step of Master's thesis was to gain knowledge about technologies Adobe Flex SDK and Google Maps API. Knowledge was used to develop an application, which let users create, generate and modify graphical wireless network model. Position and characteristics of each single unit are monitored either in a map interface or in building plans. Dates are gathered from forms filled by current user, from external file or periodically from connected database system. Theoretical part enlightens technologies that were used. It describes program development and solutions, which were made, along with examples of the source code. Included are printscreens of graphical user interface as well as description of how does it all work.

In manufacturing of paper and paperboard, optimized fiber usage has crucial importance for process efficiency and profitability. Dry strength of paper is one of the important quality criteria, which can be improved by adding dry strength additive that affect fiber to fiber bonding. This study is using the micromechanical simulations which assist interpretation of the experimental results concerning the effect of strength additives. A finite element model for 3D dry fiber network was constructed to study the effect of bond strength, bond area and the number of bonds numerically on the strength of paper products. In the network, fibers’ geometrical properties such as wall thickness, diameter, length and curl were assigned according to fiber characterization of the pulp and SEM analyses of dry paper cross-section. The numerical network was created by depositing the fibers onto a flat surface which should mimic the handsheet-making procedure. In the FE model, each fiber was represented with a number of quadratic Timoshenko beam elements where fiber to fiber bonds were modelled by beam-to-beam contact. The contact model is represented by cohesive zone model, which needs bond strength and bond stiffness in normal and shear directions. To get a reasonable estimate of the bond stiffness, a detailed finite element model of a fiber bond was used. Additionally, the effect of different fiber and bond geometries on bond stiffness were examined by this model since the previous work [13] indicated that the bond stiffness can have a considerable effect on dry strength of paper. The network simulation results show that the effect of the strength additive comes through improving the bond strength primarily. Furthermore, with the considered sheet structure, both the fiber bond compliance and the number of bonds affect the stiffness of paper. Finally, the results of the analyses indicated that the AFM measurements of the fiber adhesion could not be used directly to relate the corresponding changes in the bond strength. The fiber bond simulation concluded that fiber wall thickness has the most significant effect on the fiber bond compliance. It was also affected by micro-fibril orientation angle, bond orientation and the degree of pressing.

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This study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.

The purpose of this research is to determine if it is possible to validate the new 1D method for measuring pulse wave velocity in the aorta in vivo and estimate compliance. Arterial pressure and blood flow characterize the traveling of blood from the heart to the arterial system and have played a significant role in the evaluation of cardiovascular diseases. Blood vessel distensibility can give some information on the evolution of cardiovascular disease. A patient’s aorta cannot be explanted to measure compliance; therefore we are using a flow phantom model to validate the 1D pulse wave velocity technique to estimate compliance.

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