Modeling and prediction of gene-expression patterns has an important place in computational biology and bioinformatics. The measure of gene expression is determined from the genomic analysis at the mRNA level by means of microarray technologies. Thus, mRNA analysis informs us not only about genetic viewpoints of an organism but also about the dynamic changes in environment of that organism. Different mathematical methods have been developed for analyzing experimental data. In this study, we discuss the modeling approaches and the reasons why we concentrate on models derived from differential equations and improve the pioneering works in this field by including affine terms on the right-hand side of the nonlinear differential equations and by using Runge- Kutta instead of Euler discretization, especially, with Heun&rsquo / s method. Herewith, for stability analysis we apply modified Brayton and Tong algorithm to time-discrete dynamics in an extended space.

An efficient simulation technique for calculating the current distribution in a Vertical Cavity Surface Emitting Laser (VCSEL) is proposed and implemented. The technique consists of a hybrid 1D/3D approach to the problem. The 3D aspect of simulation is essential for devices like a photonic crystal VCSEL where the existing 2D simulation techniques are inadequate. The modular approach of the technique is advantageous, as it provides exibility in dealing with device simulations of varying complexity. It also provides a relatively short simulation time, beneficial for exploring a large design parameter space. The box integration technique is used for discretizing the equations and sparse matrix methods are used in solving the matrices. Simulation results and comparisons are provided for various aspects and modules of the simulator. The results for a few sample simulations indicate that the analysis has reasonable agreement with experimental results. The simulation error can be reduced using more accurate models for the active region of the laser.

Neste trabalho, calculam-se o calor específico e a entropia do Modelo de Anderson simétrico de uma impureza usando o Grupo de Renormalização Numérico (GRN). O método é baseado na discretização logarítmica da banda de condução do metal hospedeiro a qual a impureza está acoplada. Porém, esta discretização introduz oscilações nas propriedades termodinâmicas. Esta inconveniência, inerente ao método, é contornável para a suscetibilidade magnética, mas é crítica para o calor específico, restringindo o alcance do GRN. Para sobrepor essa dificuldade, é usado o novo procedimento denominado intercalado que foi desenvolvido para o cálculo da suscetibilidade magnética de modelos de duas impurezas. Para reduzir as matrizes e o tempo computacional, é usado, também, o operador carga axial, recentemente definido no contexto do Modelo de Kondo de duas impurezas, e que é conservado pelo Hamiltoniano de Anderson simétrico. As curvas obtidas são comparadas com resultados exatos obtidos por ansatz de Bethe e pelo Modelo de Nível Ressonante. / The specific heat and the entropy of the one-impurity symmetric Anderson Model are calculated using the Numerical Renormalization Group (NRG). The heart of the method is the logarithmic discretization of the metal conduction band where the impurity is coupled. However, this discretization, inherent in the method, introduces oscillations in the thermodynamical properties. For the susceptibility it is not so critical but for the specific heat the usual calculation is prohibitive. To overcome this difficulty, we use the new procedure called interleaved that was developed to calculate the susceptibility of two-impurity models. In order to reduce the matrices and computation time, use is made of the axial charge operator recently defined in the two-impurity Kondo Model context and that is conserved by the symmetric Anderson Hamiltonian. The curves obtained are compared with exacts results of Bethe ansatz and Resonant Level Model.

Orientador: Philippe Remy Bernard Devloo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Civil, Arquitetura e Urbanismo / Made available in DSpace on 2018-08-13T10:14:35Z (GMT). No. of bitstreams: 1 Lucci_PauloCesardeAlvarenga_M.pdf: 6661587 bytes, checksum: b77bb456093ce1f153056c6b2fa89626 (MD5) Previous issue date: 2009 / Resumo: Este trabalho é dedicado ao desenvolvimento de uma metodologia específica de mapeamento curvo aplicável a qualquer tipo de elemento geométrico regular. Trata-se de uma generalização do modelo matemático de representação geométrica apresentado em 1967 por Steven Anson Coons, denominado "Bilinearly Blended Coons Patches", o qual ajusta uma superfície retangular em um contorno delimitado por quatro curvas arbitrárias. A generalização proposta permitirá a utilização deste tipo de interpolação geométrica em elementos de qualquer topologia, através de uma sistemática única e consistente. / Abstract: In this work a methodology is developed for mathematical representation of curved domains, applicable to any type of finite element geometry. This methodology is a generalization of the mathematical model of a geometric representation presented in 1967 by Steven Anson Coons, called "Bilinearly Blended Coons Patches", which patch a rectangular surface in four arbitrary boundary curves. The proposed methodology is a kind of geometric transfinite interpolation applicable to elements of any topology, using a single and consistent systematic. / Mestrado / Estruturas / Mestre em Engenharia Civil

Muitos grupos de pesquisa já trabalharam com o desenvolvimento de conjuntos de bases, no intuito de obter melhores resultados em tempo e custo de cálculo computacional reduzidos. Para tal finalidade, o tamanho e a precisão são fatores a ser considerados, para que o número de funções do conjunto gerado proporcione uma boa descrição do sistema em estudo, num tempo de convergência reduzido. Esta dissertação tem como objetivo apresentar os conjuntos de bases obtidos pelo Método da Coordenada Geradora, para os átomos Na, Mg, Al, Si, P, S e Cl, e avaliar a qualidade de tais conjuntos pela comparação da energia eletrônica total, em nível atômico e molecular. Foi realizada uma busca para a obtenção do melhor conjunto contraído e do melhor conjunto de funções de polarização. A qualidade do conjunto gerado foi avaliada pelo cálculo DFT-B3LYP, cujos resultados foram comparados aos valores obtidos por cálculos que utilizam funções de bases conhecidas na literatura, tais como: cc-pVXZ do Dunning e pc-n do Jensen. Pelos resultados obtidos, pode-se notar que os conjuntos de bases gerados neste trabalho, denominados MCG-3d2f, podem representar sistemas atômicos ou moleculares. Tanto os valores de energia quanto os de tempo computacional são equivalentes e, em alguns casos, melhores que os obtidos aqui com os conjuntos de bases escolhidos como referência (conjuntos de Dunning e Jensen). / Many research groups have been working with the development of basis sets in order to get the best results in reduced time and cost of computational calculation. It is known that for such purpose, size and accuracy are the primary factors to be considered, so that the number of the generated set of functions allows a good description of the system being studied in a small convergence time. This essay aims to present the basis sets obtained by the Generator Coordinate Method for the atoms Na, Mg, Al, Si, P, S and Cl, as well as evaluating the quality of such clusters by comparing the electron energy at atomic and molecular levels. A research was also performed to obtain the best set contracted as well as the best set of polarization functions. The quality of the generated set was evaluated by calculating DFT-B3LYP results, which were compared to values obtained through calculation using basis functions such as cc-pVXZ of Dunning and pcn of Jensen. It can be noted, from the results obtained, that the basis sets generated in this study, named MCG-3d2f, may well represent atomic or molecular systems. Energy values and the computational time are equivalent and in some cases, even better than those obtained with the sets of bases chosen here as reference sets (Dunning and Jensen).

Simuler les réservoirs souterrains permet d’optimiser la production d’hydrocarbures. Les réservoirs naturellement ou hydrauliquement fracturés détiennent une part importante des réserves et exhibent un degré élevé d’hétérogénéité : les fractures, difficiles à détecter, impactent fortement la production via des réseaux préférentiels d’écoulement. Une modélisation précise de ces forts contrastes permettrait d’optimiser l’exploitation des ressources tout en maîtrisant mieux les risques environnementaux. L’enjeu est de prédire les processus d’écoulement multi échelles par un modèle simplement paramétrable. Une stratégie de simulations, qui améliore la fiabilité et les temps de calculs est mise au point dans cette thèse. Elle permet de simuler numériquement ou analytiquement la complexité d’un réservoir fracturé à grande échelle. Ces techniques dont l’intérêt est démontré sur un réservoir de roche mère trouvent des applications en géothermie ou dans la gestion des ressources en eau. / Fluid flow simulation is used to optimize oil and gas production. Naturally or hydraulically fractured reservoirs hold a significant part of reserves, difficult to assess. Fractures may create preferential flow paths heavily impacting fluid flow. Accurate modeling of fractured media accounting for strong contrasts would allow operators to optimize resources exploitation while better controlling environmental risks. Integrating sparse available data, we aim at predicting fluid flow processes occurring in the earth’s subsurface accounting for multi-scale fractures with a simply parameterized model. Improving the computational time and results reliability, we propose a full integrated strategy suitable for fractured reservoir specificities by simulating the fractures complexity on large scales. The techniques developed in this thesis, whose interest is demonstrated in an unconventional field case study, can find other applications in geothermal engineering and water resources management

La plupart des méthodes pour la modélisation des réservoirs fracturés reposent sur le modèle de Warren et Root (1963). Mais ce modèle reste limité par : l'hypothèse d'un volume élémentaire représentatif, l'évaluation des transferts matrice-fractures, l’idéalisation du système fracturé, l'emploi de conditions aux limites locales. La méthode développée répond à ces quatre points. Un réseau de fractures et une grille de matrice sont discrétisés conjointement, puis un changement d'échelle est réalisé. Un ensemble de nœuds représentatifs est sélectionné, et un système simplifié équivalent est construit par décimation des autres nœuds en assurant la conservation des pressions et des débits sans imposer de conditions aux limites. Enfin le nombre de connexions est réduit et les transmissibilités restantes sont calculées par une procédure d'optimisation. Ces systèmes simplifiés ont été résolus plus rapidement lors de simulations d’écoulement tout en reproduisant le comportement du modèle fin / Most methods for modeling fractured reservoirs rely on the model of Warren and Root (1963). But this model is limited by: the assumption of a representative elementary volume, the evaluation of matrix-fracture transfers, the idealization of the fractured system, the use of local boundary conditions. The developed method overcomes these four points. A fracture network and a matrix grid are jointly discretized, then an upscaling is carried out. A set of representative nodes is selected, and an equivalent simplified system is built by decimating the other nodes while ensuring the preservation of pressure and flow rate and without imposing any boundary conditions. Finally the number of connexions is reduced and the remaining transmissibilities are evaluated by an optimization procedure. These simplified systems have been solved more quickly by the flow simulator while reproducing the fine model behavior

Cette thèse est consacrée à l'étude de la méthode PAW (projector augmented-wave) et d'une de ses modifications, baptisée méthode PAW variationnelle (VPAW), pour le calcul de l'état fondamental d'Hamiltoniens en géométrie périodique. Ces méthodes visent à améliorer la vitesse de convergence des méthodes d'ondes planes (ou méthodes de Fourier) en appliquant une transformation inversible au problème aux valeurs propres initial agissant au voisinage de chaque site atomique. Cette transformation permet de capter une partie des difficultés dues aux singularités coulombiennes. La méthode VPAW est analysée pour un opérateur de Schr\"odinger unidimensionnel avec des potentiels de Dirac. Les fonctions propres de ce modèle comprennent des sauts de dérivées similaires aux cusps électroniques. Le saut de dérivée des fonctions propres du problème aux valeurs propres issu de la méthode VPAW est réduit de façon importante. Cela entraîne une accélération de convergence en ondes planes du calcul des valeurs propres corroborée par une étude numérique. Une étude de la méthode VPAW est conduite pour des Hamiltoniens 3D périodiques avec des singularités coulombiennes, parvenant à des conclusions similaires. Pour la méthode PAW, la transformation inversible comporte des sommes infinies qui sont tronquées en pratique. Ceci introduit une erreur, qui est rarement quantifiée en pratique. Elle est analysée dans le cas de l'opérateur de Schrödinger unidimensionnel avec des potentiels de Dirac. Des bornes sur la plus basse valeur propre en fonction des paramètres PAW sont prouvées conformes aux tests numériques. / This thesis is devoted to the study of the PAW method (projector augmented-wave) and of a variant called the variational PAW method (VPAW). These methods aim to accelerate the convergence of plane-wave methods in electronic structure calculations. They rely on an invertible transformation applied to the eigenvalue problem, which acts in a neighborhood of each atomic site. The transformation captures some difficulties caused by the Coulomb singularities. The VPAW method is applied to a periodic one-dimensional Schr\"odinger operator with Dirac potentials and analyzed in this setting. Eigenfunctions of this model have derivative jumps similar to the electronic cusps. The derivative jumps of eigenfunctions of the VPAW eigenvalue problem are significantly reduced. Hence, a smaller plane-wave cut-off is required for a given accuracy level. The study of the VPAW method is also carried out for 3D periodic Hamiltonians with Coulomb singularities yielding similar results. In the PAW method, the invertible transformation has infinite sums that are truncated in practice. The induced error is analyzed in the case of the periodic one-dimensional Schrödinger operator with Dirac potentials. Error bounds on the lowest eigenvalue are proved depending on the PAW parameters.

The presented work highlights the remarkable potential of physical discretization – lattice model FyDiK in three-dimensional modelling of non-linear problems in structural mechanics. To achieve the objectives a software application, that implements the model FyDiK along with the 3D graphical user interface has been developed and thus is able to assemble a spring network model. Such a model was used for modelling the formation of cracks and fracture in the concrete specimens and also to model a plastic behaviour of steel I-beam. The calculations were performed by a massive parallelization on CUDA platform. In the first part the basic principles on which the work is based are introduced. Subsequently, a detailed description of individual parts of the model and the issue of parallelization by graphics cards are presented. In the next part the creation of the required software and improving of the model properties of mentioned materials are described. That is followed by evaluation of the achieved results with the comparison of other modelling software. The conclusion summarizes the achievements and suggestions for the further development possibilities of the presented method of modelling.

Les moteurs diesel sont largement utilisés pour la propulsion automobile, grâce à leur rendement élevé. Les émissions polluantes les plus importantes des moteurs diesel sont les NOx et les particules (en combustion Dieselconventionnelle). Il est difficile de réduire et contrôler ces émissions parce que la diminution d’un polluant entraine l’augmentation de l’autre. Une voie est la combustion Diesel LTC (Combustion à basse température) qui peut réduireces deux polluants, mais d’autres polluants apparaissent alors, comme CO et HC. Une façon d’arriver à desconditions LTC est l’utilisation de l’injection multiple (pilote/main, split injection, etc.). La caractérisation de cesinjections multiples est particulièrement complexe, en raison des interactions entre les différentes injections.Cette thèse a pour but de réaliser un modèle 1D de spray qui peut simuler l’injection multiple et la combustioncorrespondante dans un moteur diesel de type automobile, suite à la thèse de G. Ma soutenue au LHEEA en 2013,qui a développé un modèle de combustion basé sur le modèle de spray 1D eulérien de Musculus et Kattke (sprayinerte). Une comparaison de ce modèle avec un modèle lagrangien (Hiroyasu, Poetsch), qui a un traitement pseudo2D pour le spray de carburant, est menée pour évaluer les différences entre les approches et déterminer l’approche lamieux adaptée aux cas envisagés.L’interaction du spray avec une paroi, essentielle pour modéliser les conditions dans un moteur automobile faitégalement l’objet d’une étude bibliographique et de premières tentatives de modélisation. Une modélisation pseudo-2D pour le modèle Eulérien est faite pour améliorer le calcul du dégagement de chaleur et de délai d’inflammation. Lavalidation de ces différentes évolutions est faite en confrontant les résultats du modèle avec des résultatsexpérimentaux obtenus sur la base de données de l’ECN (Engine Combustion Network), mais aussi avec des relevéseffectués par des autres auteurs. Des développements spécifiques sont également introduits pour traiter le casd’injection multiple et l’injection dans une chambre de combustion à géométrie variable (le système piston-cylindre). / Diesel engines are largely used in automotive propulsion due to their elevated efficiency. The most important pollutant emissions of diesel engines are NOx and particulate matter (in the case of conventional Diesel combustion). It is difficult to reduce and control these emissions because reducing one pollutant emission increases the other one. One way to try to achieve reduction in both pollutant emissions is called LTC (Low Temperature Combustion), which can reduce these two pollutants, but other pollutant emissions appear, as CO and HC. One way to achieve LTC conditions is using multiple injections (pilot/main, split injection, etc.). Modeling these injections is particularly complex, mainly due to their interactions.The objective of this thesis is to make a 1D spray model that can simulate multiple injections and the correspondingcombustion in an automobile diesel engine, continuing the work of G. Ma in his thesis defended at LHEEA in 2013,which developed a combustion model based in the 1D Eulerian spray of Musculus and Kattke (inert spray). Acomparison is made of this model and a Lagrangian model (Hiroyasu, Poetsch), which has a pseudo-2D treatment ofthe fuel spray, to evaluate the differences between the approaches and determine the best one suited for the foreseencases.The spray-wall interaction, essential to model the conditions inside an automotive engine, is subject to a bibliographyreview and coarse modeling. A pseudo-2D modeling for the Eulerian model is made, to improve the heat release rateand ignition delay calculation. The validation of these different evolutions is made by comparing the model results withexperimental results obtained from the ECN (Engine Combustion Network) data base, and also with data obtainedfrom the TSM test engines. Specific developments are also introduced to treat the multiple injection case and injectionin a variable geometry combustion chamber (the piston-cylinder system).