Tandem mass spectrometry (MS/MS) is the dominant approach for large-scale peptide sequencing in high-throughput proteomic profiling studies. The computational analysis of MS/MS spectra involves the identification of peptides from experimental spectra, especially those with post-translational modifications (PTMs), as well as the inference of protein composition based on the putative identified peptides. In this thesis, we tackled two major challenges associated with an MS/MS analysis: 1) the refinement of PTM predictions from MS/MS spectra and 2) the inference of protein composition based on peptide predictions. We proposed two PTM prediction refinement algorithms, PTMClust and its Bayesian nonparametric extension \emph{i}PTMClust, and a protein identification algorithm, pro-HAP, that is based on a novel two-layer hierarchical clustering approach that leverages prior knowledge about protein function. Individually, we show that our two PTM refinement algorithms outperform the state-of-the-art algorithms and our protein identification algorithm performs at par with the state of the art. Collectively, as a demonstration of our end-to-end MS/MS computational analysis of a human chromatin protein complex study, we show that our analysis pipeline can find high confidence putative novel protein complex members. Moreover, it can provide valuable insights into the formation and regulation of protein complexes by detailing the specificity of different PTMs for the members in each complex.

Optimal control problems are often characterized by discontinuities or switchings in the control variables. One way of accurately capturing the irregularities in the solution is to use a high resolution (dense) uniform grid. This requires a large amount of computational resources both in terms of CPU time and memory. Hence, in order to accurately capture any irregularities in the solution using a few computational resources, one can refine the mesh locally in the region close to an irregularity instead of refining the mesh uniformly over the whole domain. Therefore, a novel multiresolution scheme for data compression has been designed which is shown to outperform similar data compression schemes. Specifically, we have shown that the proposed approach results in fewer grid points in the grid compared to a common multiresolution data compression scheme. The validity of the proposed mesh refinement algorithm has been verified by solving several challenging initial-boundary value problems for evolution equations in 1D. The examples have demonstrated the stability and robustness of the proposed algorithm. Next, a direct multiresolution-based approach for solving trajectory optimization problems is developed. The original optimal control problem is transcribed into a nonlinear programming (NLP) problem that is solved using standard NLP codes. The novelty of the proposed approach hinges on the automatic calculation of a suitable, nonuniform grid over which the NLP problem is solved, which tends to increase numerical efficiency and robustness. Control and/or state constraints are handled with ease, and without any additional computational complexity. The proposed algorithm is based on a simple and intuitive method to balance several conflicting objectives, such as accuracy of the solution, convergence, and speed of the computations. The benefits of the proposed algorithm over uniform grid implementations are demonstrated with the help of several nontrivial examples. Furthermore, two sequential multiresolution trajectory optimization algorithms for solving problems with moving targets and/or dynamically changing environments have been developed.

In order to understand the properties of thin film devices, knowledge of the material's structure is essential. The work presented here combines magnetic and structural characterization of the systems studied to gain a deeper physical understanding. The magnetic properties have been studied with a combination of x-ray magnetic circular dichroism, SQUID magnetometry and magneto-optical Kerr effect. For the structural characterization, x-ray reflectivity and diffraction have been used, complemented by neutron diffraction and transmission electron microscopy. One structural property that affects the magnetic moment in metal-on-metal superlattices is interdiffusion between the layers. This is discussed for bcc Fe/Co(001) and bcc Fe81Ni19/Co(001) superlattices. The effect of interdiffusion was seen as a large region of enhanced magnetic moments as compared to theoretical calculations, which assume perfectly sharp interfaces. For the Fe81Ni19/Co(001) superlattices the chemical interface region, as revealed by neutron diffraction, was in good agreement with the region of magnetic enhancement. Another structural property that has been investigated is the strain in the magnetic layers. This does not affect the spin magnetic moment to a large extent. However the magnetocrystalline anisotropy and the orbital moment are affected by the presence of strain. The effects on the orbital moment from strain and interfaces for Fe in Fe/V superlattices was studied, and it was found that the two contributions were separable. In this context the effect of strain on the out-of-plane magnetocrystalline anisotropy in FeCo/Pt has also been studied. The latter system is interesting from a technological perspective since tetragonally distorted FeCo alloys have the potential to be suitable new materials in computer hard drives. Finally, a computer program, based on the Differential Evolution algorithm, to refine primarily x-ray reflectivity data, is presented.

A new method is developed to determine a set of informative and refined interface assertions satisfied by functions that are represented by feed-forward neural networks. Neural networks have often been criticized for their low degree of comprehensibility.It is difficult to have confidence in software components if they have no clear and valid interface description. Precise and understandable interface assertions for a neural network based software component are required for safety critical applications and for theintegration into larger software systems. The interface assertions we are considering are of the form &quote if the input x of the neural network is in a region (alpha symbol) of the input space then the output f(x) of the neural network will be in the region (beta symbol) of the output space &quote and vice versa. We are interested in computing refined interface assertions, which can be viewed as the computation of the strongest pre- and postconditions a feed-forward neural network fulfills. Unions ofpolyhedra (polyhedra are the generalization of convex polygons in higher dimensional spaces) are well suited for describing arbitrary regions of higher dimensional vector spaces. Additionally, polyhedra are closed under affine transformations. Given a feed-forward neural network, our method produces an annotated neural network, where each layer is annotated with a set of valid linear inequality predicates. The main challenges for the computation of these assertions is to compute the solution of a non-linear optimization problem and the projection of a polyhedron onto a lower-dimensional subspace.

Made available in DSpace on 2014-12-17T15:47:59Z (GMT). No. of bitstreams: 1 MadielSCF_DISSERT.pdf: 1874479 bytes, checksum: dc22e7d8884791a523682f62c1e8c32c (MD5) Previous issue date: 2011-10-07 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The use of increasingly complex software applications is demanding greater investment in the development of such systems to ensure applications with better quality. Therefore, new techniques are being used in Software Engineering, thus making the development process more effective. Among these new approaches, we highlight Formal Methods, which use formal languages that are strongly based on mathematics and have a well-defined semantics and syntax. One of these languages is Circus, which can be used to model concurrent systems. It was developed from the union of concepts from two other specification languages: Z, which specifies systems with complex data, and CSP, which is normally used to model concurrent systems. Circus has an associated refinement calculus, which can be used to develop software in a precise and stepwise fashion. Each step is justified by the application of a refinement law (possibly with the discharge of proof obligations). Sometimes, the same laws can be applied in the same manner in different developments or even in different parts of a single development. A strategy to optimize this calculus is to formalise these application as a refinement tactic, which can then be used as a single transformation rule. CRefine was developed to support the Circus refinement calculus. However, before the work presented here, it did not provide support for refinement tactics. The aim of this work is to provide tool support for refinement tactics. For that, we develop a new module in CRefine, which automates the process of defining and applying refinement tactics that are formalised in the tactic language ArcAngelC. Finally, we validate the extension by applying the new module in a case study, which used the refinement tactics in a refinement strategy for verification of SPARK Ada implementations of control systems. In this work, we apply our module in the first two phases of this strategy / A utiliza??o de aplica??es de software cada vez mais complexas est? exigindo um maior investimento no desenvolvimento de sistemas, garantindo uma melhor qualidade das aplica??es. Diante desse contexto, novas t?cnicas est?o sendo utilizadas na ?rea de Engenharia de Software, tornado o processo de desenvolvimento mais eficaz. Destacam- se, como exemplo dessas novas abordagens, os M?todos Formais. Estes m?todos utilizam linguagens formais que t?m sua base fundamentada na matem?tica, apresentando uma sem?ntica e sintaxe bem definidas. Uma dessas linguagens ? Circus, que possibilita a mo- delagem de sistemas concorrentes. Esta linguagem foi desenvolvida a partir da uni?o dos conceitos das linguagens formais Z (que permitem a modelagem de dados complexos) e CSP Communicating Sequential Processes (que permitem a modelagem de sistemas con- correntes). Adicionalmente, Circus tamb?m possui um c?lculo de refinamento associado, que pode ser utilizado para desenvolver software de forma precisa e gradual. Cada etapa deste c?lculo ? justificada pela aplica??o de uma lei de refinamento (possivelmente com a prova de certas condi??es chamadas de obriga??es de prova). Algumas vezes, as mesmas leis podem ser aplicadas da mesma forma em diferentes desenvolvimentos ou mesmo em partes diferentes de um ?nico desenvolvimento. Uma estrat?gia para otimizar esse c?l- culo ? formalizar estas aplica??es como t?ticas de refinamento, que podem ser utilizadas como uma simples regra de transforma??o. A ferramenta CRefine foi desenvolvida para realizar o suporte a este c?lculo de refinamento de Circus. Entretanto, antes deste traba- lho, essa ferramenta n?o fornecia suporte para as t?ticas. A proposta desta disserta??o ? oferecer um suporte ferramental para a utiliza??o das t?ticas no c?lculo de refinamento de programas Circus. Para tanto, foi desenvolvido um novo m?dulo em CRefine, que auto- matiza o processo de defini??o e aplica??o das t?ticas de refinamento. Nesta extens?o as t?ticas s?o formalizadas na linguagem de t?ticas para sistemas concorrentes, ArcAngelC. Por fim, validamos a extens?o, aplicando o novo m?dulo a um estudo de caso, que utiliza as t?ticas em uma estrat?gia de refinamento para verifica??o de implementa??es SPARK Ada de sistemas de controle. Nesta disserta??o, aplicamos o novo modulo ?s duas fases iniciais desta estrat?gia.

The vehicles industry is facing increasing demands for fuel efficiency and cost reduction due to environmental legislation, sustainability and customer demands. Therefore, there is a great need to develop and produce lightweight components by using materials and processes that offer higher specific strength and/or design optimization. Semi‐solid aluminium casting offers design freedom and castings with lower shrinkage and gas entrapment defects compared to high pressure die castings. The lack of understanding of microstructure and defect formation, and design data, for semi‐solid castings is a barrier for foundries and designers in the vehicles industry to use semi‐solid castings. In this study, the effect of two grain refiners on slurry formation and surface segregation of semi‐solid Al‐7Si‐0.3Mg castings produced by the Rheometal™ process was evaluated. The influence of grain refinement on primary α‐Al grain size, shape factor and solid fraction was analysed in addition to the solute content of the surface segregation layer. The influence of magnesium on the formation of intermetallic phases during solidification and the heat treatment response of Al‐7Si‐Mg semi‐solid castings was investigated. The magnesium content was varied from 0.3 to 0.6wt.% and the semi-solid castings were analysed in the T5 and T6 conditions. Energy dispersive spectroscopy was used to identify the intermetallic phases formed during solidification. Tensile testing was performed and the results were correlated to the magnesium and silicon concentration measured in the interior of the α‐Al globules formed during slurry preparation. The results suggest that the addition of grain refiner decreases the solid fraction obtained in the Rheometal™ process. However, no significant effect was observed on the α‐Al grain size and shape factor. A good correlation was obtained between the magnesium concentration in the interior of the α‐Al globules formed during slurry preparation and the offset yield strength for all alloys. The low magnesium solubility in α‐Al at temperatures in the solidification range of the Al‐7Si‐Mg alloys is suggested to be the reason for the low hardening response for the T5 heat treatment compared to the T6 condition.

Depuis le début du millénaire, la simulation numérique directe est apparue comme un outil précieux capable d'étudier l’atomisation d’une goutte isolée par un écoulement à grande vitesse. L’atomisation peut être divisée en deux phases distinctes : l'éclatement se produit d'abord sous la forme d'aplatissement de la goutte, formant également des filaments, puis il se poursuit via l'obtention d'une multitude de gouttes de tailles réduites ce qui complète le processus d’atomisation. Les principaux objectifs pour le présent travail étaient donc d’établir un modèle et une méthode numérique capables d’étudier au mieux ces phénomènes. L'atomisation d’une goutte isolée est présentée et est accompagnée d’une comparaison avec l’expérience qui confirme les capacités du modèle et de la méthode à simuler numériquement les différents processus physiques mis en jeu. Des informations essentielles quant aux mécanismes d’atomisation, non exploitables avec l’expérience, sont décrites et l’objectif d’obtenir des gouttes de tailles réduites est atteint. / Only at the beginning of the millennium, direct numerical simulation has emerged as a valuable tool capable of studying the atomization of an isolated droplet by a high-speed flow. The atomization can be divided into two distinct phases: the aerobreakup occurs first in the form of flattening of the droplet, also forming filaments, and then it continues via the obtaining of a multitude of reduced sizes droplets what completes the process of atomization. The main objectives of this work were therefore to establish a model and a numerical method able to study these phenomena as well as possible. The atomization of an isolated droplet is presented and is accompanied by a comparison with the experiment which confirms the capacities of the model and the method to numerically simulate the different physical processes involved. Essential information on atomization mechanisms, which cannot be exploited with experiments, is described and the objective of obtaining droplets of reduced sizes is achieved.

Abstract Stabilized ferritic stainless steel grades are attractive alternatives to common austenitic grades in sheet metal applications. Compared with older unstabilized ferritic grades, the mechanical and corrosion properties are usually improved. The impurity level, mainly the amount of interstitial carbon and nitrogen, plays an important role in these steels. There are notable issues in the welding of these steels, the most apparent difference to austenitic steels is the susceptibility to brittle failure. This research focused on the influence of minor elements, especially aluminium, calcium, silicon, titanium, niobium, nitrogen and oxygen, on the weldability of modern intermediate purity level stabilized ferritic stainless steels. The research proceeded in several stages. At first, the general characteristics and performance data about the welds in currently manufactured 11 to 21 mass percent chromium ferritic stainless steels in Europe was obtained. The research then focused on novel high chromium stabilized ferritic stainless steels. Lastly, the influence of various steelmaking practices on weldability were investigated. The results showed that in stabilized ferritic stainless steels, slag islands are frequently seen in the molten weld pools. These islands can have many origins, e.g. deoxidation, calcium treatment and stabilization practices, and they can be roughly assessed from the chemical composition of the steel. The nature and the influence of these slags varies and can be related to irregularities in the weldability and molten metal fluid flow. Large grain size and titanium carbonitride particles impair the toughness of the heat-affected zone. Generally, stabilization with niobium is preferred. However, solely niobium stabilized steel welds run the risk of forming coarse columnar grains in welds deteriorating some of the properties. A breakdown of the columnar grains is possible to achieve in autogenous welds with minor titanium and aluminium alloying, provided that small amounts of nitrogen and oxygen are induced from the shielding gas. However, grain refinement may not improve the properties, if it is accomplished with an increase in the total interstitial content. / Tiivistelmä Stabiloidut ferriittiset ruostumattomat teräkset soveltuvat korvaamaan tavanomaisia austeniittisia ruostumattomia teräksiä ohutlevysovelluksissa. Näillä teräksillä keskeiset mekaaniset ja korroosio-ominaisuudet ovat usein paremmat kuin varhaisilla, stabiloimattomilla ferriittisillä teräksillä. Hiili ja typpi ovat näissä teräksissä kuitenkin epäpuhtauksia. Toisin kuin austeniittiset teräkset, ferriittiset teräkset ovat alttiita haurasmurtumalle, erityisesti hitsatuissa rakenteissa. Tässä väitöstutkimuksessa keskityttiin mikroseosaineiden ja epäpuhtauksien vaikutukseen keskipuhtaiden stabiloitujen ferriittisten teräslajien hitsauksessa. Tutkimus kohdistui erityisesti alumiinin, kalsiumin, piin, titaanin, niobin, typen ja hapen vaikutuksiin. Aluksi tutkittiin kaupallisten terästen hitsien keskeisiä ominaisuuksia. Tämän jälkeen tutkittiin uusia ns. korkeakromisia stabiloituja ferriittisiä teräslajeja. Lopuksi tutkittiin teräksen valmistuksen vaikutuksia stabiloitujen ferriittisten ruostumattomien terästen hitsattavuuteen. Tutkituilla teräksillä hitsauksen aikana muodostui runsaasti kuonalauttoja. Näillä kuonilla on monta alkuperää, esim. deoksidointi, kalsiumkäsittely ja stabilointiaineet. Hitsien kuonaisuutta voidaan karkeasti arvioida teräksen kemiallisen koostumuksen perusteella. Muodostuvilla kuonilla on useita vaikutuksia hitsauksessa, mm. epäjatkuvuuksiin ja sulan virtauksiin. Hitsauksessa muodostuva suuri raekoko ja stabiloinnin titaanikarbonitridipartikkelit heikentävät oleellisesti hitsin muutosvyöhykkeen sitkeyttä. Stabilointi käyttäen pääasiassa niobia on toivottavaa, mutta jos stabilointiin käytetään vain niobia, tulee hitsin mikrorakenteesta karkea ja hitsin ominaisuudet voivat heikentyä. Karkean mikrorakenteen hienontaminen on mahdollista käyttäen suojakaasuna argonia, jossa on hieman typpeä ja happea, mikäli teräkseen on seostettu hieman alumiinia ja titaania. Raerakenteen hienontaminen ei kuitenkaan yksiselitteisesti paranna hitsin ominaisuuksia, mikäli hienontaminen saavutetaan kasvattamalla epäpuhtauspitoisuutta tarpeettoman korkeaksi.

Neste trabalho desenvolveu-se e implementou-se um modelo computacional paralelo multifísica para a simulação do transporte de substâncias e do escoamento hidrodinâmico, bidimensional (2D) e tridimensional (3D), em corpos de água. Sua motivação está centrada no fato de que as margens e zonas costeiras de rios, lagos, estuários, mares e oceanos são locais de aglomerações de seres humanos, dada a sua importância para as atividades econômica, de transporte e de lazer, causando desequilíbrios a esses ecossistemas. Esse fato impulsiona o desenvolvimento de pesquisas relativas a esta temática. Portanto, o objetivo deste trabalho é o de construir um modelo computacional com alta qualidade numérica, que possibilite simular os comportamentos da hidrodinâmica e do transporte escalar de substâncias em corpos de água com complexa configuração geométrica, visando a contribuir para seu manejo racional. Visto que a ênfase nessa tese são os aspectos numéricos e computacionais dos algoritmos, analisaram-se as características e propriedades numérico-computacionais que as soluções devem contemplar, tais como a estabilidade, a monotonicidade, a positividade e a conservação da massa. As estratégias de soluções enfocam os termos advectivos e difusivos, horizontais e verticais, da equação do transporte. Desse modo, a advecção horizontal é resolvida empregando o método da limitação dos fluxos de Sweby, e o transporte vertical (advecção e difusão) é resolvido com os métodos beta de Gross e de Crank-Nicolson. São empregadas malhas com distintas resoluções para a solução do problema multifísica. O esquema numérico resultante é semi-implícito, computacionalmente eficiente, estável e fornece acurácia espacial e temporal de segunda ordem. Os sistemas de equações resultantes da discretização, em diferenças finitas, das equações do escoamento e do transporte 3D, são de grande porte, lineares, esparsos e simétricos definidos-positivos (SDP). No caso 2D os sistemas são lineares, mas os sistemas de equações para a equação do transporte não são simétricos. Assim, para a solução de sistemas de equações SDP e dos sistemas não simétricos empregam-se, respectivamente, os métodos do subespaço de Krylov do gradiente conjugado e do resíduo mínimo generalizado. No caso da solução dos sistemas 3-diagonal, utiliza-se o algoritmo de Thomas e o algoritmo de Cholesky. A solução paralela foi obtida sob duas abordagens. A decomposição ou particionamento de dados, onde as operações e os dados são distribuídos entre os processos disponíveis e são resolvidos em paralelo. E, a decomposição de domínio, onde obtém-se a solução do problema global combinando as soluções de subproblemas locais. Em particular, emprega-se neste trabalho, o método de decomposição de domínio aditivo de Schwarz, como método de solução, e como pré-condicionador. Para maximizar a relação computação/comunicação, visto que a eficiência computacional da solução paralela depende diretamente do balanceamento de carga e da minimização da comunicação entre os processos, empregou-se algoritmos de particionamento de grafos para obter localmente os subproblemas, ou as partes dos dados. O modelo computacional paralelo resultante mostrou-se computacionalmente eficiente e com alta qualidade numérica. / A multi-physics parallel computational model was developed and implemented for the simulation of substance transport and for the two-dimensional (2D) and threedimensional (3D) hydrodynamic flow in water bodies. The motivation for this work is focused in the fact that the margins and coastal zones of rivers, lakes, estuaries, seas and oceans are places of human agglomeration, because of their importance for economic, transport, and leisure activities causing ecosystem disequilibrium. This fact stimulates the researches related to this topic. Therefore, the goal of this work is to build a computational model of high numerical quality, that allows the simulation of hydrodynamics and of scalar transport of substances behavior in water bodies of complex configuration, aiming at their rational management. Since the focuses of this thesis are the numerical and computational aspects of the algorithms, the main numerical-computational characteristics and properties that the solutions need to fulfill were analyzed. That is: stability, monotonicity, positivity and mass conservation. Solution strategies focus on advective and diffusive terms, horizontal and vertical terms of the transport equation. In this way, horizontal advection is solved using Sweby’s flow limiting method; and the vertical transport (advection and diffusion) is solved with Gross and Crank-Nicolson’s beta methods. Meshes of different resolutions are employed in the solution of the multi-physics problem. The resulting numerical scheme is semi-implicit, computationally efficient, stable and provides second order accuracy in space and in time. The equation systems resulting of the discretization, in finite differences, of the flow and 3D transport are of large scale, linear, sparse and symmetric positive definite (SPD). In the 2D case, the systems are linear, but the equation systems for the transport equation are not symmetric. Therefore, for the solution of SPD equation systems and of the non-symmetric systems we employ, respectively, the methods of Krylov’s sub-space of the conjugate gradient and of the generalized minimum residue. In the case of the solution of 3-diagonal systems, Thomas algorithm and Cholesky algorithm are used. The parallel solution was obtained through two approaches. In data decomposition or partitioning, operation and data are distributed among the processes available and are solved in parallel. In domain decomposition the solution of the global problem is obtained combining the solutions of the local sub-problems. In particular, in this work, Schwarz additive domain decomposition method is used as solution method and as preconditioner. In order to maximize the computation/communication relation, since the computational efficiency of the parallel solution depends directly of the load balancing and of the minimization of the communication between processes, graph-partitioning algorithms were used to obtain the sub-problems or part of the data locally. The resulting parallel computational model is computationally efficient and of high numerical quality.

Previsões meteorológicas para longos períodos de tempo estão se tornando cada vez mais importantes. A preocupação mundial com as consequências da mudança do clima tem estimulado pesquisas para determinar o seu comportamento nas próximas décadas. Ao mesmo tempo, os passos necessários para definir uma melhor modelagem e simulação do clima e/ou tempo estão longe da precisão desejada. Aumentar o refinamento da superfície terrestre e, consequentemente, aumentar o número de pontos discretos (utilizados para a representação da atmosfera) na modelagem climática e precisão das soluções computadas é uma meta que está em conflito com o desempenho das aplicações numéricas. Aplicações que envolvem a interação de longos períodos de tempo e incluem um grande número de operações possuem um tempo de execução inviável para as arquiteturas de computadores tradicionais. Para superar esta situação, um modelo climatológico pode adotar diferentes níveis de refinamento da superfície terrestre, utilizando mais pontos discretos somente em regiões onde uma maior precisão é requerida. Este é o caso de Ocean-Land-AtmosphereModel, que permite o refinamento estático de uma determinada região no início da execução do código. No entanto, um refinamento dinâmico possibilitaria uma melhor compreensão das condições climáticas específicas de qualquer região da superfície terrestre que se tivesse interesse, sem a necessidade de reiniciar a execução da aplicação. Com o surgimento das arquiteturas multi-core e a adoção de GPUs para a computação de propósito geral, existem diferentes níveis de paralelismo. Hoje há paralelismo interno ao processador, entre processadores e entre computadores. Com o objetivo de extrair ao máximo a performance dos computadores atuais, é necessário utilizar todos os níveis de paralelismo disponíveis durante o desenvolvimento de aplicações concorrentes. No entanto, nenhuma interface de programação paralela explora simultaneamente bem os diferentes níveis de paralelismo existentes. Baseado neste contexto, esta tese investiga como explorar diferentes níveis de paralelismo em modelos climatológicos usando interfaces clássicas de programação paralela de forma combinada e como é possível prover refinamento de malhas em tempo de execução para estes modelos. Os resultados obtidos a partir de implementações realizadas mostraram que é possível reduzir o tempo de execução de uma simulação atmosférica utilizando diferentes níveis de paralelismo, através do uso combinado de interfaces de programação paralela. Além disso, foi possível prover maior desempenho na execução de aplicações climatológicas que utilizam refinamento de malhas em tempo de execução. Com isso, uma malha de maior resolução para a representação da atmosfera terrestre pode ser adotada e, consequentemente, as previsões numéricas serão mais precisas. / Weather forecasts for long periods of time has emerged as increasingly important. The global concern with the consequences of climate changes has stimulated researches to determine the climate in coming decades. At the same time the steps needed to better defining the modeling and the simulation of climate/weather is far of the desired accuracy. Upscaling the land surface and consequently to increase the number of points used in climate modeling and the precision of the computed solutions is a goal that conflicts with the performance of numerical applications. Applications that include the interaction of long periods of time and involve a large number of operations become the expectation for results infeasible in traditional computers. To overcome this situation, a climatic model can take different levels of refinement of the Earth’s surface, using more discretized elements only in regions where more precision are required. This is the case of Ocean-Land- Atmosphere Model, which allows the static refinement of a particular region of the Earth in the early execution of the code. However, a dynamic mesh refinement could allow to better understand specific climatic conditions that appear at execution time of any region of the Earth’s surface, without restarting execution. With the introduction of multi-core processors and GPU boards, computers architectures have many parallel layers. Today, there are parallelism inside the processor, among processors and among computers. In order to use the best performance of the computers it is necessary to consider all parallel levels to distribute a concurrent application. However, nothing parallel programming interface abstracts all these different parallel levels. Based in this context, this thesis investigates how to explore different levels of parallelism in climatological models using mixed interfaces of parallel programming and how these models can provide mesh refinement at execution time. The performance results show that is possible to reduce the execution time of atmospheric simulations using different levels of parallelism, through the combined use of parallel programming interfaces. Higher performance for the execution of atmospheric applications that use online mesh refinement was also provided. Therefore, more mesh resolution to describe the Earth’s atmosphere can be adopted, and consequently the numerical forecasts are more accurate.