Estudos do mecanismo de reações unimoleculares, das moléculas de acetato de metila e etila, induzidas por absorção multifotônica e de reações bimoleculares com os radicais OH e Cl, usando cálculos ab initio e de funcional de densidade foram realizados neste trabalho. A análise dos cálculos das barreiras de energia e das constantes de velocidade microcanônicas das reações unimoleculares com o formalismo da teoria RRKM, permitiu prever algumas reações cujos produtos não foram determinados experimentalmente. Além disso, semelhanças das geometrias e dos valores de energia de algumas estruturas entre diferentes superfícies de energia, analisadas com cálculos de IRC, permitiram a explicação da viabilidade de determinada via de reação em detrimento de outra. Em outro método, relatado por Forst(1), na determinação das constantes de velocidade variacionais, comparadas com a variação da energia de Gibbs, verificou-se constantes de velocidade microcanônicas menores e a localização dos estados de transição em comprimentos de ligação, também, menores. Nas reações com o radical OH e Cl, a via predominante de reação é o ataque aos hidrogênios do grupo ligado diretamente ao oxigênio da molécula, responsável pelo valor da constante final de mais de 93% nas reações com OH e 99% nas reações com Cl, a 298K, em concordância com os resultados experimentais, em detrimento do ataque ao grupo CH3 da porção carboxilato da molécula. Nas reações com OH, os valores de constante de velocidade calculados mais próximos dos valores experimentais foram obtidos a partir dos resultados com os funcionais mPW1B95-41, para o acetato de metila, e mPW1B95-44, para o acetato de etila, enquanto que nas reações com Cl foram obtidos com o os métodos CCSD(T)//B3LYP para o acetato de metila e CCSD(T)//MP2 para o acetato de etila. Os valores de constante de velocidade da reação com cloro são cerca de dez vezes maiores que aquelas para as reações com radicais OH. As reações com OH e Cl ocorrem em uma única etapa, sem estabilização do intermediário e sem efeito de tunelamento significante. Por sua vez, cálculos da constante de velocidade, pelo método da relação estrutura reatividade (SAR), sobreestimam a reatividade dos hidrogênios dos grupos CH3 na porção carboxilato, em ambos os acetatos, e na porção etóxido do acetato de etila. Este método falha ao descrever a participação de cada grupo na reação com Cl, pois prevê que a reação no grupo CH3 da porção alcóxido passa a ser predominante sobre a reação ao grupo CH2 nas reações do acetato de etila, oposto aos nossos cálculos onde a reação com o grupo CH2 é a predominante. Outra falha do método é na previsão de mesma reatividade para ambos os grupos CH3 no acetato de metila, pois por nossos cálculos a reação ocorre predominantemente no grupo CH3 na porção alcóxido da molécula. / Computational studies on methyl and ethyl acetates molecules using ab initio and density functional calculations exploring the unimolecular mechanism, induced by multiphoton absorption, and the bimolecular reactions with OH and Cl radicals, have been performed in this work. Analysis of the calculated energy barriers and rate constants of unimolecular reactions with the RRKM microcanonical theory, predicts the occurrence of some reactions whose products were not determined experimentally. Furthermore, similarities on geometrical and energetic of some structures between different energy surfaces, analyzed with IRC calculations, allowed the explanation of the viability of a particular reaction pathway over another. Forst\'s method, used to determine variational rate constants, when compared with the variation of Gibbs energy, generates microcanonical rate constants with smaller values and location of transition states in smaller bond lengths. With OH and Cl, the predominant reaction route is the attack on the hydrogens of the group bonded directly to oxygen in the molecule, responsible for more than 93% of the final constant value in reactions with OH and 99% in reactions with Cl , at 298 K, in agreement with the experimental results, while the attack to the CH3 group in the carboxylate portion of the molecule is the less likely to occur. In reactions with OH, the values of the rate constant calculated closer to the experimental values were obtained from the results with functional mPW1B95-41, for methyl acetate, and mPW1B95-44 for ethyl acetate, whereas in reactions with Cl, were obtained with the CCSD(T)//B3LYP method for the methyl acetate and the CCSD(T)//MP2 method for ethyl acetate. The rate constant for the reaction with chlorine are about ten times larger than those for reactions with OH radicals. Reactions with OH and Cl occur in a single step, without stabilization of the intermediary and without significant tunneling effect. The rate constant obtained by the structure-reactivity relationship (SAR) overestimates the reactivity of the hydrogens of the CH3 groups at the carboxylate portion, in both acetates, and at the ethoxide portion of ethyl acetate. This method fails to describe the participation of each group in the reaction with Cl, predicting that the reaction on the CH3 portion of the alkoxide becomes predominant over the reaction on the CH2 group of ethyl acetate, relative to our calculations where the reaction with the CH2 group is predominant. Another flaw by providing the same reactivity for both the CH3 in methyl acetate, is in disagreement with our calculations which indicate that the reaction occurs predominantly in the CH3 group at the alkoxide portion of the molecule.

A gaseificação é um processo de conversão termoquímica que compreende a oxidação parcial de um combustível para convertê-lo em uma mistura gasosa (“syngas”). Geralmente a modelagem desses processos utiliza uma descrição cinética detalhada ou os aproximam ao equilíbrio químico. Ambas as abordagens têm vantagens e desvantagens, bem como limitações. O objetivo deste trabalho foi o desenvolvimento de uma nova modelagem fenomenológica de processos de gaseificação através de um modelo “híbrido” aqui chamado de modelo híbrido adaptativo por zonas (HAZ). Este modelo assumiu que o gaseificador é representado por zonas de dois tipos: uma dominada pela cinética química, representada por um modelo cinético, e outra onde a cinética química é rápida e as espécies químicas estão em equilíbrio químico, representada por um modelo de equilíbrio. Um critério de transição entre as zonas foi proposto através de um número de Damköhler (Da) que relaciona tempos de residência e de reação química. Desta forma, o modelo adapta-se conforme os processos dominantes em cada zona. Em um primeiro momento, um modelo de equilíbrio multifásico (EM) foi desenvolvido e aplicado para um estudo da cogaseificação de carvão mineral e biomassas disponíveis no Brasil. A seguir, o modelo HAZ foi construído através da técnica de rede equivalente de reatores químicos (ERN) a partir do modelo EM e de um modelo cinético, também desenvolvido neste trabalho. Uma metodologia de aplicação do modelo HAZ foi proposta, aplicada e validada para duas configurações de gaseificadores: dois casos de gaseificadores de biomassa em leito fluidizado borbulhante e um caso de gaseificador de carvão mineral em leito de arraste. Para os dois primeiros casos foi estimada que a transição ocorra para Da ≥ 10+5 e para o último caso; chegou-se a Da ≥ 10+3. A aplicação do modelo HAZ se mostrou satisfatória sendo que foi possível a redução do tempo computacional em pelo menos 40% com relação a uma abordagem puramente cinética. Cabe ressaltar ainda que o modelo HAZ possibilitou um maior entendimento físico e químico ao identificar os processos dominantes locais. / Gasification is a thermochemical conversion process consisting of partial oxidation of a fuel to convert it to a gas mixture (“syngas”). Generally, the gasification process modeling uses a kinetic detailed description, or approach it to a chemical equilibrium state. Both approaches have advantages and disadvantages, as well as limitations. The objective of this work was to develop a new phenomenological modeling of gasification processes through a “hybrid” model here called hybrid adaptive zone model (HAZ). This proposed modeling assumed the gasifier is represented by two types of zones: one dominated by chemical kinetics, represented by a kinetic model, and another where chemical kinetics is fast so chemical species are assumed in chemical equilibrium states, represented by an equilibrium model. A transition criterion between zones was defined by a Damköhler number (Da) which relates residence time and chemical reaction time. Therefore, the HAZ model can adapted according to the dominant processes in each zone. Firstly, a multi-phase equilibrium model (ME) was developed and applied to study the coal-biomass co-gasification of Brazilian sources. Hereafter, the HAZ model was built using the technique of equivalent reactor network (ERN) with the ME model and a kinetic model developed in this work. A methodology of use of the HAZ model was proposed, applied and validated for two configurations of gasifiers: two cases of biomass bubbling fluidized-bed gasifiers and one case of coal entrained-flow gasifier. In the first two cases the transition was estimated to occur on Da ≥ 10+5 and in the last case; we estimated on Da ≥ 10+3. The application of the HAZ model proved to be satisfactory since it could reduce the computation time by at least 40% compared to a pure kinetic approach. It should already be emphasized that the HAZ model allowed a better physical and chemical understanding of gasification by identifying the dominant local processes.

La crise environnementale a conduit l’industrie automobile à faire face à des contraintes croissantes tandis que les limitations drastiques de polluants entrent en vigueur. Afin de réduire les émissions polluantes issues de la combustion, l’une des solutions adoptées est de post-traiter les fumées à l’aide de systèmes de post-traitement catalytique à l’image du catalyseur 3 voies (TWC) pour les moteurs à essence ou le catalyseur d’oxydation (DOC)pour les moteurs diesel. Ces appareils présentent une structure en nid d’abeille constituée d’un réseau de canaux à l’échelle millimétrique appelés monolithes et dont les parois intérieures sont recouvertes d’une fine couche de métal précieux aux propriétés catalytiques. Les polluants sont transformés via l’interaction entre les molécules présentes dans la phase gaz et les sites actifs du métal précieux. Etant donné les conditions laminaires d’écoulement au sein des monolithes, un mélange faible et une diffusion moléculaire limitée peuvent être rencontrés au voisinage de la paroi réactive. Le taux de conversion des polluants peut être alors insuffisant pour des conditions opératoires données. Dans le but d’optimiser les transferts,des obstacles peuvent être introduits par déformation mécanique des parois du canal catalytique au cours du processus de fabrication.Les simulations numériques peuvent contribuer à l’émergence de solutions innovantes basées sur une compréhension et une maitrise profonde des phénomènes sous-jacents. Afin d’atteindre cet objectif, le premier élément clé a été de formuler et d’intégrer dans le code de dynamique des fluides AVBP une approche numérique combinant d’une part des conditions aux limites dédiées à la prise en compte de parois réactives,et d’autre part, la résolution de la cinétique chimique gaz et surface via un solveur d’EDP.L’approche a permis la prise en compte de la cinétique détaillée et l’interaction entre la phase gaz et les parois réactives. L’outil développé a été validé en premier lieu à l’aide de calculs de réacteurs hétérogènes zéro-dimensionnels. Les résultats ont montré un parfait accord avec le solveur de référence SENKIN. L’approche a été validée ensuite en l’appliquant à la simulation de deux canaux réactifs aux parois planes et en comparant les résultats numériques aux résultats expérimentaux de Dogwiler et al. L’approche développée s’est révélée être capable de reproduire les principales caractéristiques de la combustion catalytique pour différents points de fonctionnement. Enfin, l’outil développé a été appliqué à l’étude de l’impact de l’introduction d’obstacles pariétaux sur les taux de conversion des systèmes catalytiques. Les résultats ont permis d’ouvrir des perspectives très intéressantes quant à la contribution de la CFD2D et de la chimie hétérogène détaillée à l’optimisation du design des systèmes de post traitement catalytique. En particulier, l’étude de l’influence des obstacles pariétaux a montré que le design de la géométrie des monolithes constitue un fort potentiel d’optimisation de l’efficacité des systèmes de conversion catalytique et ce, à moindre coût grâce à une utilisation optimisée du métal précieux rendue possible par une meilleure interaction entre l'écoulement, les réactions chimiques dans la phase gaz et la paroi réactive. / The environmental emergency has led automotive industry to deal with growing constraints as drastic regulations of pollutant emissions are emerging. In order to reduce emissions resulting from the combustion process, one of the solution adopted is to post process pollutants by the means of catalytic after-treatment systems such as three-way converters (TWC) for gasoline applications oroxidation catalysts (DOC) for Diesel applications. These devices present a honeycomb shape which consists in a grid of millimeter-scale narrow channels called monoliths whose interior wall are coated with precious metals presenting catalytic properties.Pollutants are converted through the chemical interaction involving gas-phase molecules and active precious metal sites. Given the laminar flow encountered within these monoliths, weak mixing and molecular diffusion could occur near the catalytic walls. Pollutant conversion rates may therefore prove insufficient for certain operating conditions. In order to promote transfers, obstacles could be introduced by mechanically deforming the channel wall during the manufacturing process. Numerical simulations can contribute to the emergence of innovative technologies based on a profound understanding and mastering of the underlying phenomena that simulation allows. In order to achieve this goal, a first key element was the formulation and integration into the AVBP CFD code of a numerical approach combining specific boundary conditions for reactive walls and ODE solvers for the gas phase and surface chemistry.The approach allowed to account for detailed kinetics and the interplay between the reactive surface and the gas-phase. The resulting tool was first validated using a zero-dimensional heterogeneous reactor computations. The results were shown to perfectly match the ones obtained with the reference kinetic solver SENKIN.Furthermore, the approach was then validated by applying it to the simulation of two planar reactive channel flows, and comparing the predictions with experimental findings of Dogwiler et al.. The developed approach proved to be able of reproducing main features of the catalytic combustion observed for different operating points. Finally, the developed tool was applied to explore the impact of introducing wall obstacles on the conversion rate of catalytic devices. The resulting findings have proved to open very interesting perspectives for contributing to the optimization of the design of catalytic converters using 2D CFD and detailed heterogeneous chemistry. In particular, the study of the impact of wall obstacles indicates the potential for contributing to further increase the efficiency of catalytic converters via the design of monolith geometries that would allow a more efficient and thus less costly usage of Pt-coating as a consequence of optimized interactions between the gas flow, gas phase chemistry and surface chemistry.

Neste estudo, parâmetros estruturais, energéticos e da frequências vibracionais para os estados X 3Σ- e A 3II do radical CNN e X 2II das espécies iônicas CNN+ e CNN- foram obtidos no nível de teoria CCSD(T)/CBST-5. No estudo termoquímico, os valores para o calor de formação da espécie neutra foram, ΔHf (O K) = 138,89 kcal/mol e ΔHf (298,15 K) = 139,65 kcal/mol. Para o potencial de ionização e a afinidade eletrônica, os resultados deste trabalho são 10,969 e 1,743 eV, respectivamente. Otimizações de geometria para os estados eletrônicos X 3Σ-, A 3II, a 1Δ, b 1Σ+, c 1II, d X 1Σ- e B 3Σ- realizadas com a metodologia MRCI nos permitiram obter valores para Te. Além disso, as energias de transição vertical para 15 estados eletrônicos também foram determinadas. Utilizando o nível de teoria CCSD(T)-F12b/CBSD-Q, geometrias de equilíbrio e frequências vibracionais harmônicas e anarmônicas foram estimadas para a molécula C30 e seu ânion C30-. Uma avaliação dos efeitos que inclusão dos elétrons do caroço no cálculo de diferentes propriedades foi realizada. Descrevemos a primeira determinação do calor de formação para a molécula C3O, ΔHf (0 K) = 79,41 kcal/mol e ΔHf( (298,15 K) = 83,39 kcal/mol, além do cálculo da afinidade eletrônica (1,114 eV). No que se refere à cinética e à dinâmica química, a determinação das constantes de velocidade foi realizada para duas reações de abstração de hidrogênio. Na primeira, as constantes de velocidade para a reação S (3P) + CH4 → SH + CH3, numa ampla faixa de temperaturas (T = 200 - 3000 K), foram determinadas utilizando SS-VTST/MT combinada com cálculos DFT/M05-2X/MG3S. A 1200 K, a constante de velocidade CVT/SCT para este processo (2,85 x 10-14 cm3 molécula-1 s-1) está em excelente concordância com o resultado experimental (8,14 x 10-14 cm3 molécula-1 s-1). Na segunda, o estudo a reação de abstração de hidrogênio do butanoato de metila por hidrogênio atômico foi realizada utilizando a abordagem cinética MS-VTST/MT combidada com cálculos MPWB1K/G- 31+G(d,p). Nesta aproximação cinética, a anarmonicidade associada às torções angulares amortecidas, bem como o acoplamento entre elas foram consideradas no cálculo das constante de velocidade. Neste processo, verificamos que a inclusão da anarmonicidade torcional nas constantes de velocidade aumenta a constante de velocidade em aproximadamente 8-10% a altas temperaturas (T = 1000 -2000 K). A temperaturas mais baixas, os efeitos de tunelamento são predominantes e a constante de velocidade CVT/SCT para a reação CH3CH2CH2COOCH3 + H (2S) → CH2CH2CH2COOCH3 + H (2S) a 300 K (6,17 x 10-18 cm3 molécula-1 s-1) é 8,2 vezes maior que a obtida com CVT (5,07 x 10-17 cm3 molécula-1 s-1). / In this study, the structures, energies and vibrational frequencies for the X 3Σ- e A3II electronic states of CNN, and X 2II of the ions CNN+ and CNN- were obtained at the CCSD(T)/CBST-5 level of theory. Additionally, we also estimated the heats of formation for the neutral species ΔHf (0 K) = 138.89 kcal/mol and ΔHf(298.15 K) = 139.65 kcal/mol. For the ionization potential and electron affinities, this work predicted the values of 10.969 e 1.743 eV, respectively. Geometry optimizations for the electronic states 3Σ-, A 3II, a 1Δ, b 1Σ+, c 1II, d X 1Σ- e B 3Σ- performed with the MRCI approach allowed us to compute the excitation energies (Te). Furthermore, vertical transition energies were also calculated for 15 electronic states. Using the CCSD(T)-F12b/CBSD-Q level of theory, equilibrium geometries, and harmonic and anharmonic vibrational frequencies were estimated for the C3O molecule and the anion C3O-. An assessment of the effects of inclusion of core electrons in the calculation of some properties was also carried out. The determination of the heat of formation of the molecule C3O (ΔHf (0 K) = 79.41 kcal/mol and ΔHf (298.15 K) = 83.39 kcal/mol), and its electron affinity (1,114 eV) were the first ones reported in the literature. In the kinetics investigation, we estimated the rate constants for two hydrogen abstraction reactions. Rate constants for the reaction S(3P) + CH4 → SH + CH3 were predicted for a wide range of temperatures (T = 200 - 3000 K) using VTST/MT combined with DFT/M05-2X/MG3S calculations. At 1200 K, the calculated rate constant CVT/SCT for this process is 2.85 x 10-14 cm3 molecule-1 s-1. For the reaction of hydrogen abstraction from methyl butanoate by a hydrogen atom, the MS-VTST/MT method combined with the density functional MPWB1K/G-31+G(d,p) was employed. In this study, anharmonic torsional hindered rotations were considered in calculations of the rate constants. At high temperatures, the inclusion of torsional anharmonicity increases the rate constants by approximately 8-10%. At low temperatures, tunneling effects are predominant and the rate constant CVT/SCT (6.17 x 10-18 cm3 molécula-1 s-1) is 8.2 times higher than the CVT one (5.07 x 10-17 cm3 molécula-1 s-1 ).

We report here the development of very efficient aryl- and quinolinyl- sulfonate based leaving groups, termed Nucleophile Assisting Leaving Groups (NALGs), which substantially accelerate the rate of nucleophilic substitution reactions with metal halides. Detailed synthesis and kinetics study are described herein. Our synthesized NALGs have shown great reactivity towards poor nucleophiles and/or substrates traditionally considered too hindered to undergo nucleophilic attack. The abundant existence of halide, azide and amine in natural products demands new synthetic pathway. To fulfill this requirement, new mild stereoretentive halogenations (chlorination, bromination and iodination) reactions have also been developed for secondary cyclic alcohols using NALGs involving titanium (IV) reagents. The novel methodology can be extended to Azidation reactions as well with titanium (IV) azide, in which Ti (N3)4 is the first time being engaged in organic synthesis. Beased on the NALGs theory we discover the chlorosulfite can be a simplest NALG and applied as the intermediate in mild one-pot stereoretentive halogenations (chlorination and bromination) using titanium (IV) halides as catalysts or stoichiometric reagents. These reactions were found to be particularly efficient for cyclic alcohols. Finally, an efficient mild bromination and iodination reaction for primary and secondary alcohols with Grignard reagents is also reported. This reaction exhibits the generality with substrates with various leaving groups. The important features of this reaction are that, for the first time, bromide formation using Grignard reagents without the Cu (I) catalysts. / by Songye Li. / Thesis (Ph.D.)--Florida Atlantic University, 2011. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2011. Mode of access: World Wide Web.

Proteins play a major role in living systems and present a wide spectrum of functionalities. Many different types of proteins are involved into biological processes, such as the catalysis of biochemical reactions, cellular membrane transport, immune system response and DNA replication. However, some proteins and peptides might become harmful to living organisms; for example, their abnormal aggregation causes neurodegenerative disorders including Alzheimer disease (AD). One of the causes of AD is the presence of amyloid beta peptides Aβ(1-42), Aβ(1-40), which self-assemble into insoluble fibrils and plaques, which surround neuronal cells impeding synapsis. The number of AD patients is increasing, but a cure has not been founded yet. Therefore, it is crucial to investigate the mechanisms underlying amyloid aggregation and screening for compounds able to prevent this irreversible process. Microfluidics permits characterising the physicochemical properties of proteins, investigate their aggregation and study their interactions with other molecules. Chemical kinetics allows studying the microscopic events occurring during protein self-assembly. The combination of these two techniques provides a powerful tool for the identification of compounds inhibiting the aggregation process. In this thesis by using microfluidics, chemical kinetics and other biophysical assays, I have investigated the proteins isoelectric point (pI) and the inhibition of aberrant Aβ(1-42) self-assembly process. Firstly, I describe the development of a microfluidic platform allowing for the measurement of the protein pI, in a gradient-free manner. This approach overcomes a fundamental limitation of convectional techniques that is the achievement of a stable and well-controlled pH gradient. Secondly, I investigate the inhibiting effect of llama nanobodies on Aβ(1-42) aggregation. The findings from this study show that nanobodies target monomeric species with high affinity whereas interactions with fibril surfaces are weak. Finally, I discuss the use of other compounds inhibiting specific nucleation stages. These include the chaperones clusterin and brichos, as well as soot and pure carbon nanoparticles. Importantly, the addition of both chaperones to Aβ(1-42) solutions has an additive inhibitory effect on aggregation. My findings will improve the characterization of the physicochemical properties of proteins as well as providing promising candidates for the inhibition of specific stages of amyloid beta aggregation opening the way to possible cures for AD disease.

A capacidade das células para responder corretamente a sinais externos e perceber mudanças no seu microambiente é a base do desenvolvimento, reparação de tecidos e de imunidade, bem como a homeostase do tecido normal. Transdução de sinal é o principal meio pelo qual as células respondem a sinais externos de seu ambiente e coordenam alterações celulares complexas. O estudo das vias de sinalização molecular permite-nos tentar compreender o funcionamento dessas transduções de sinais e, consequentemente, as respostas celulares a estímulos externos. Uma abordagem adequada para tais estudos é o uso de modelos matemáticos para simular a cinética das reações químicas que descrevem uma dada via de sinalização, o que nos permite gerar predições testáveis de processos celulares. Construir modelos cinéticos preditivos de vias de sinalização molecular através de dados de alto rendimento produzidos utilizando técnicas ômicas (i.e., genômica, transcriptômica, (fosfo-)proteômica) constitui um dos atuais desafios enfrentados pelos pesquisadores na área de Biologia Molecular. Recentemente, para lidar com este desafio, o arcabouço de e-Science SigNetSim foi introduzido pelo Grupo de Biologia Computacional e de Bioinformática do Instituto Butantan. Esse arcabouço permite fazer a descrição de vias de sinalização molecular através da descrição da estrutura de um modelo através de um conjunto de reações químicas, que por sua vez é mapeado para um sistema de Equações Diferencias Ordinárias (EDOs), numericamente simuladas e avaliadas. Todavia, modificações na estrutura das vias precisam ser feitas manualmente, o qual restringe severamente o número de estruturas da via que precisam ser testadas, especialmente no caso de modelos grandes. Portanto, diante desse panorama, este trabalho propõe o desenvolvimento de um método para modificar vias de sinalização molecular. Esse método se baseia no uso de bancos de dados de interatomas para fornecer um conjunto de espécies químicas candidatas para serem incluídas na via de sinalização. Um componente integrado ao arcabouço SigNetSim capaz de testar diferentes hipóteses de modificação de vias foi desenvolvido neste projeto utilizando a metodologia de heurística incremental. Para avaliar a eficiência do componente implementado, utilizamos como estudo de caso um modelo de vias sinalização de MAPKs e PI3K/Akt para realizar testes experimentais e analisar os resultados obtidos. / The ability of cells to respond correctly external signals and to perceive changes in their microenvironment is the basis for development, tissue repair and immunity as well as normal tissue homeostasis. Signal transduction is the primary means by which cells respond to external signals from their environment and coordinate complex cellular changes. The study of molecular signaling pathways allows us to understand the operation of each process of cellular signal transduction. The use of mathematical models to simulate the kinetics of chemical reactions that describe a given signaling pathway, allow us to generate testable predictions of the cell processos. To Build Kinetic predictive models to molecular signaling pathways through massive data omics produced using modern techniques, Genomics, transcriptomics, (Phospho) proteomics, is one of the current challenges faced by researchers in the field of molecular biology. Recently, the \\textit SigNetSim e-Science was introduced by the Biological Computacional and Bioinformatical Group from the Butantan Institute to face this challenge. This \\textit makes the description of molecular signaling pathways through a set of chemical reactions, which are mapped into a system of ordinary differential equations, this system will be numerically simulated and evaluated . However, changes in the structure of the pathways need to be updated manually presented in this work, which severely restricts the number of track structures that need to be tested, especially for the large models. Therefore, given this background, we present the method to modify the molecular signaling pathways. This method relies on the use of interactome database to provide a set of chemical species candidates to be included in the signaling pathway. An component integrated to SigNetSim framework able to test different hypotheses of pathways modification was developed in this project using the incremental heuristic methodology. To evaluate the implemented component, we used the MAPKs and PI3K/Akt pathways model as case study, in order to perform experimental tests and to analyze the obtained results.

O objetivo central deste trabalho foi investigar como a Cinética Química foi sendo apropriada pelos livros didáticos destinados ao Ensino Médio, em um determinado período de tempo (1929-2004), através do estudo do desenvolvimento histórico dos conceitos químicos envolvidos neste tema. Outro objetivo foi o de identificar as concepções sobre ciência veiculadas pelos livros didáticos ao tratarem o tema Cinética Química. O modelo adotado para a análise dos livros didáticos está baseado na linha de pesquisa desenvolvida por Níaz (2001) e Justi (1997; 1999), que se baseia na história e filosofia da ciência para entender o tratamento dado aos conceitos químicos pelo livro didático. Para isso, foi utilizada a metodologia de Imre Lakatos, da reconstrução racional do conhecimento científico, para analisar a evolução histórica das idéias sobre Cinética Química. A reconstrução histórica foi feita a partir de pesquisas de historiadores da ciência, artigos de pesquisadores e artigos originais dos cientistas que estiveram envolvidos no estudo da cinética química. Foram propostos quatro Programas de Investigação Científica que representam o conhecimento científico sobre a Cinética Química no período de 1850 até 1935, ano em que foi proposta a teoria do estado de transição. Tais Programas foram utilizados para evidenciar os níveis de explicação teórica atingidos em vinte livros didáticos. As concepções de ciência apresentadas pelos livros didáticos foram analisadas sob o ponto de vista de duas perspectivas filosóficas: a empirista/indutivista e a racionalista. Os livros didáticos até a década de 60 se dedicam a explicar a influência de concentração nas reações químicas, apresentando justificativas em termos empíricos e matemáticos, mas não em termos moleculares. A Partir do final dos anos 60 começam a aparecer explicações em termos das teorias de colisão e do estado de transição. As explicações em termos de energia de ativação ou barreira de energia sobre o efeito da temperatura na velocidade das reações também começam a aparecer nos livros a partir do final da década de 60. Com relação às concepções de ciência, pôde-se perceber que e a perspectiva filosófica predominante nos livros didáticos é a empirista/indutivista, independentemente da época em que foram editados, o que parece revelar que os autores não levaram em consideração as mudanças de perspectiva que ocorreram durante esse período. / The main aim of the present study is to investigate how the didactic transposition of knowledge on chemical reactions kinetics happened in high school textbooks published during the period from 1929 to 2004. This work was carried out by an analysis of the historical development of the chemical concepts related to this subject. Another objective was to identify the concepts about science that are conveyed by textbooks to present the subject of chemical kinetics. The model adopted for the analysis of the textbooks is based on the research line of Níaz (2001) and Justi (1997; 1999), which is based in the history and philosophy of science to understand the approach adopted by textbooks to present chemical concepts. The method of rational reconstruction of the scientific knowledge, by Imre Lakatos, was used to analyze the historical evolution of the ideas about chemical kinetics. Four scientific investigation programs that represent the scientific knowledge about chemical kinetics from 1850 to 1935, year when the theory of the transition state was presented, were proposed. These programs were used to highlight the level of theoretical explanation reached in twenty textbooks. The concepts of science presented by the textbooks were examined in the light of two philosophical perspectives: the empirical/inductive and the rationalist. The textbooks published until the sixties were dedicated to explain the effect of concentration on chemical reactions in terms of empirical and mathematical grounds, rather than on a molecular basis. From the end of the sixties, explanations based on the collision and transition state theories began to emerge. Moreover, during this period the concept of activation energy barrier was applied to explain the effect of temperature on chemical reaction rates. The philosophical approach to the concepts of science prevailing in textbooks seems to be the empirical/inductive one regardless of the period when these books were edited, revealing that the authors did not consider the changes in perspective that occurred during this period.

Thesis (Ph.D.)--McMaster University, 2005. / Supervisor: Geoffrey Brooks and Kenneth Coley. Includes bibliographical references (p. 152-164).

The Direct Simulation Monte Carlo method is a computational tool for modelling rarefied flows. The Macroscopic Chemistry Method was developed to simplify the modelling of dissociation and recombination reactions in DSMC. The ability to understand and predict the behaviour of chemically reacting, rarefied flows is a critical aspect in the development of high altitude, high speed bodies such as re-entry craft, high altitude aircraft, space transport vehicles and missiles. Computational methods are an invaluable source of information when experimental techniques are difficult, costly or time-consuming. However, traditional methods of modelling chemical kinetics using DSMC suffer from a number of drawbacks. The Macroscopic Chemistry Method overcomes a number of these problems, but has previously only been applied to simulations of a single diatomic gas. The Macroscopic Chemistry Method (MCM) is extended to consider multiple species and multiple reaction sets, thermal non-equilibrium effects, trace species modelling, unsteady flows, vibrational state specific chemistry, electronic excitation, relaxation and ionization and coupled nonequilibrium radiation emission. The Macroscopic Method is described as a general DSMC modelling philosophy rather than as a single formulated method. That is, the flexibility and utility of the method are shown through examples of applying a macroscopic approach to a number of problems, and by highlighting instances where a macroscopic approach is useful or even necessary. The problems investigated include reservoir relaxation calculations, 1-D shock, expansion and shock-expansion calculations, two-dimensional flows over a vertical step and through a cavity, and axis-symmetric flow about a sphere. The studies demonstrate that although MCM may often present a simplified approach as compared to traditional 'non-macroscopic' methods, it does not necessarily lead to more approximate solutions. On the contrary, the ability of macroscopic methods to combine different models of physical processes with the most recent (verified) data means that they are particularly suited to simulate high altitude, rarefied flows. It is also shown that, like any model approach, the validity of the approximations employed must be justified for a particular problem. In general, macroscopic methods of varying complexity and accuracy may be implemented to model a specific physical process. Adoption of the Macroscopic Chemistry Method in DSMC has the potential to enhance the modelling of chemical kinetics, charged-particle effects and radiation in rarefied hypersonic flows. This capability may be attributed to the simplicity and flexibility which the macroscopic approach affords over methods which seek to avoid the use of collective information. Macroscopic methods have already been employed to model weakly ionized flows. Their further application to model chemical kinetics and other processes would be useful for modelling and understanding the behaviour of objects in rarefied hypersonic flow-fields.