Neste trabalho apresentamos uma investigação desenvolvida ao longo de três anos em cursos introdutórios de Física da Universidade Federal do Rio Grande. O objetivo foi minimizar a dicotomia observada entre teoria e laboratório. A estratégia de ensino utilizada nas disciplinas de Física Geral para Engenharia fez uso do Vê de Gowin, um dispositivo heurístico capaz de explicitar como se dá o processo de produção do conhecimento científico. A construção de diagramas Vê foi utilizada para auxiliar na compreensão de textos nas aulas teóricas e como alternativa aos tradicionais relatórios nas aulas experimentais. A professora também fez uso dos Vês para organizar o ensino, em especial das aulas de laboratório. Alicerçados na teoria da aprendizagem significativa de Ausubel e Novak e nas teorias de ensino de Gowin e Moreira, e fundamentados em algumas idéias-chave de epistemólogos e filósofos da ciência contemporâneos, procuramos estimular uma integração entre teoria e experimentação, buscando contribuir para uma compreensão mais efetiva dos conceitos físicos e das concepções epistemológicas veiculadas nas aulas de Física. Na pesquisa, optamos por uma metodologia interpretativa, de imersão, mas também fizemos uso de vários dados quantitativos, procurando indícios da validade da estratégia. Os resultados mostraram que a eficácia do instrumento, para promover a desejada integração, depende da atuação decidida do professor. Indicaram também que as concepções dos estudantes sobre a ciência, o cientista e o modo como se dá a construção do conhecimento, ensinadas muitas vezes de forma implícita em aula, são persistentes e capazes de interferir na aprendizagem de teorias físicas. / In this paper, we presents a research carried out over three years in Physics introductory courses at Federal University of Rio Grande. The aim of the present study was to minimize the observed dichotomy between theory and lab. The teaching strategy in General Physics disciplines for Engineering has made use of Gowin's Vee, a heuristic device able to explain the process of scientific knowledge production. The construction of Vee diagrams was used to assist understanding of texts in theory classes and as an alternative to traditional reports in the experimental classes. The teacher also made use of it to organize the education, especially for laboratory classes. We based our work on the theory of Ausubel and Novak's meaningful learning and on Gowin and Moreira's theories of teaching and we also grounded it on some key ideas of contemporary epistemology and philosophy of science. We want to promote theory-experiment integration, seeking to contribute to a more effective comprehension of physical concepts and epistemological conceptions expressed in Physics classes. In research, we opted for an interpretative methodology, but we also made use of several quantitative data, looking for evidence of strategy's validity. The results showed that the effectiveness of the instrument performance to promote the desired integration depends on the teacher's decisive role. They also indicated that the students conceptions about science, the scientist and how the knowledge construction is made, that are taught many times implicitly in class, are persistent and can interfere in the physical theories learning.

AN ABSTRACT OF THE DISSERTATION OF PRAGYAN P. MOHANTY, for the Doctor of Philosophy degree in ELECTRICAL AND COMPUTER ENGINEERING, presented on June 11, 2015, at Southern Illinois University Carbondale. TITLE: FUNCTION-BASED ALGORITHMS FOR BIOLOGICAL SEQUENCES MAJOR PROFESSOR: Dr. Spyros Tragoudas Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented methods is the use of binary decision diagrams that store and manipulate binary functions. Searching for a particular pattern in a very large DNA database, is a fundamental and essential component in computational biology. In the biological world, pattern matching is required for finding repeats in a particular DNA sequence, finding motif and aligning sequences etc. Due to immense amount and continuous increase of biological data, the searching process requires very fast algorithms. This also requires encoding schemes for efficient storage of these search processes to operate on. Due to continuous progress in genome sequencing, genome rearrangements and construction of evolutionary genome graphs, which represent the relationships between genomes, become challenging tasks. Previous approaches are largely based on distance measure so that relationship between more phylogenetic species can be established with some specifically required rearrangement operations and hence within certain computational time. However because of the large volume of the available data, storage space and construction time for this evolutionary graph is still a problem. In addition, it is important to keep track of all possible rearrangement operations for a particular genome as biological processes are uncertain. This study presents a binary function-based tool set for efficient DNA sequence storage. A novel scalable method is also developed for fast offline pattern searches in large DNA sequences. This study also presents a method which efficiently stores all the gene sequences associated with all possible genome rearrangements such as transpositions and construct the evolutionary genome structure much faster for multiple species. The developed methods benefit from the use of Boolean functions; their compact storage using canonical data structure and the existence of built-in operators for these data structures. The time complexities depend on the size of the data structures used for storing the functions that represent the DNA sequences and/or gene sequences. It is shown that the presented approaches exhibit sub linear time complexity to the sequence size. The number of nodes present in the DNA data structure, string search time on these data structures, depths of the genome graph structure, and the time of the rearrangement operations are reported. Experiments on DNA sequences from the NCBI database are conducted for DNA sequence storage and search process. Experiments on large gene order data sets such as: human mitochondrial data and plant chloroplast data are conducted and depth of this structure was studied for evolutionary processes on gene sequences. The results show that the developed approaches are scalable.

RAMOS, Igor Rochaid Oliveira. Study of strongly correlated colloidal systems. 2014. 113 f. Tese (Doutorado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2014. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-04-09T20:37:08Z No. of bitstreams: 1 2014_tese_iroramos.pdf: 4160505 bytes, checksum: 1c5b95406b1be080fece98a7bc0bf05a (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-04-10T20:54:10Z (GMT) No. of bitstreams: 1 2014_tese_iroramos.pdf: 4160505 bytes, checksum: 1c5b95406b1be080fece98a7bc0bf05a (MD5) / Made available in DSpace on 2015-04-10T20:54:10Z (GMT). No. of bitstreams: 1 2014_tese_iroramos.pdf: 4160505 bytes, checksum: 1c5b95406b1be080fece98a7bc0bf05a (MD5) Previous issue date: 2014 / This thesis presents the study of the structural and dynamical properties, as well as, melting of colloidal systems. Initially, we study the structure and phonon spectrum of a system of charged magnetic dipoles, organized in a bilayer structure and oriented perpendicular to the plane of the layers. This system can be tuned through six different crystalline phases by changing parameters such as the interlayer separation and/or the charge and/or dipole moment of the particles. The presence of the electric charge on the dipole particles is responsible for the nucleation of five staggered phases and a disordered phase which are not found in the magnetic dipole bilayer system previously presented in the literature. These extra phases are a consequence of the competition between the repulsive Coulomb and the attractive dipole interlayer interaction. The minimum energy structures are summarized in a phase diagram associated to the separation between the layers and to the relative importance between the magnetic and electric interactions. We determine the order of the structural phase transitions. The phonon spectrum of the system was calculated within the harmonic approximation. A non-monotonic behavior of the phonon spectrum is found as a function of the effective strength of the inter-particle interaction. The thermodynamic stability of the different phases is determined. Then, we study the bilayer system of charged magnetic dipoles for nonzero temperatures, investigating the melting behavior of the system through the modified Lindemann criterion, as a function of the parameters: (i) the distance between the layers η and (ii) the relative intensity of the magnetic interaction with respect to the electric interaction λ. For large enough λ, one of the phases (the matching hexagonal phase) exhibits a re-entrant melting behavior as a function of η. Since the charges and the magnetic dipole moment of the colloidal particles can be altered, for example, by changing the pH of the solution in which they are immersed or an external magnetic field, respectively, this system can be in principle verified experimentally. Last, a two-dimensional (2D) binary colloidal system consisting of interacting dipoles is investigated. Within the harmonic approximation, we obtained the phonon spectrum of the system as a function of the composition, dipole moment ratio and mass ratio between the small and big particles. Through a systematic analysis of the phonon spectra, we are able to determine the stability region of the different lattice structures of colloidal alloys. The gaps in the phonon frequency spectrum, the optical frequencies in the long-wavelength limit and the sound velocity are discussed as well. Using the modified Lindemann criterion and within the harmonic approximation, we estimated the melting temperature of the sub-lattice generated by the big particles. / Nesta tese, estudamos as propriedades estruturais e dinâmicas, bem como, a fusão de sistemas coloidais. Inicialmente, abordamos o problema de determinar as estruturas de mínima energia e o espectro de fônons de um sistema de dipolos magnéticos carregados, organizados em uma estrutura de bicamadas e orientados perpendicularmente ao plano das camadas. Este sistema pode ser sintonizado através de seis diferentes fases cristalinas, através da variação de parâmetros tais como a separação entre as camadas e/ou a carga e/ou o momento de dipolo das partículas. A presença de carga elétrica nas partículas dipolares é responsável pela nucleação de cinco fases onde as camadas não estão alinhadas verticalmente e uma fase desordenada, que não são encontradas no sistema em bicamadas de dipolos magnéticos previamente apresentado na literatura. Estas fases extras são uma consequência da competição entre a repulsão coulombiana e a interação atrativa entre os dipolos em diferentes camadas. As estruturas de mínima energia são sumarizadas em um diagrama de fases associado à separação entre camadas e a importância relativa entre as interações elétrica e magnética. Determinamos, ainda, a ordem das transições estruturais entre as várias configurações de mínima energia. O espectro de fônons do sistema foi calculado usando a aproximação harmônica. Um comportamento não-monotônico do espectro de fônons é encontrado como função da interação efetiva entre as partículas. A estabilidade termodinâmica das diferentes fases é determinada. Em seguida, estudamos o sistema de bicamadas de dipolos magnéticos carregados para temperaturas diferentes de zero, investigando a fusão do sistema através do critério de Lindemann modificado, em função dos parâmetros: (i) a distância entre as camadas η e (ii) a intensidade relativa da interação magnética com respeito à interação elétrica λ. Para λ suficientemente grande, uma das fases (a fase hexagonal com alinhamento vertical) exibe um comportamento reentrante na temperatura de fusão em função de η. Uma vez que a carga e o momento de dipolo magnético das partículas coloidais pode ser alterado, por exemplo, pela variação do pH da solução na qual estão imersos e por um campo magnético externo, respectivamente, este sistema pode ser em princípio verificado experimentalmente. Por último, um sistema bidimensional (2D) coloidal binário consistindo de dipolos interagentes é investigado. Dentro da aproximação harmônica, calculamos o espectro de fônons do sistema em função da composição, da razão entre os momentos de dipolo e da razão entre as massas das partículas pequenas e grandes. Através de uma análise sistemática dos espectros de fônons, determinamos a região de estabilidade das diferentes estruturas das ligas coloidais. As lacunas no espectro de frequência dos fônons, as frequências óticas no limite de longos comprimentos de onda e a velocidade do som são também discutidos. Usando o critério de Lindemann modificado e dentro da aproximação harmônica, estimamos a temperatura de fusão da sub-rede gerada pelas partículas grandes.

Neste trabalho apresentamos uma investigação desenvolvida ao longo de três anos em cursos introdutórios de Física da Universidade Federal do Rio Grande. O objetivo foi minimizar a dicotomia observada entre teoria e laboratório. A estratégia de ensino utilizada nas disciplinas de Física Geral para Engenharia fez uso do Vê de Gowin, um dispositivo heurístico capaz de explicitar como se dá o processo de produção do conhecimento científico. A construção de diagramas Vê foi utilizada para auxiliar na compreensão de textos nas aulas teóricas e como alternativa aos tradicionais relatórios nas aulas experimentais. A professora também fez uso dos Vês para organizar o ensino, em especial das aulas de laboratório. Alicerçados na teoria da aprendizagem significativa de Ausubel e Novak e nas teorias de ensino de Gowin e Moreira, e fundamentados em algumas idéias-chave de epistemólogos e filósofos da ciência contemporâneos, procuramos estimular uma integração entre teoria e experimentação, buscando contribuir para uma compreensão mais efetiva dos conceitos físicos e das concepções epistemológicas veiculadas nas aulas de Física. Na pesquisa, optamos por uma metodologia interpretativa, de imersão, mas também fizemos uso de vários dados quantitativos, procurando indícios da validade da estratégia. Os resultados mostraram que a eficácia do instrumento, para promover a desejada integração, depende da atuação decidida do professor. Indicaram também que as concepções dos estudantes sobre a ciência, o cientista e o modo como se dá a construção do conhecimento, ensinadas muitas vezes de forma implícita em aula, são persistentes e capazes de interferir na aprendizagem de teorias físicas. / In this paper, we presents a research carried out over three years in Physics introductory courses at Federal University of Rio Grande. The aim of the present study was to minimize the observed dichotomy between theory and lab. The teaching strategy in General Physics disciplines for Engineering has made use of Gowin's Vee, a heuristic device able to explain the process of scientific knowledge production. The construction of Vee diagrams was used to assist understanding of texts in theory classes and as an alternative to traditional reports in the experimental classes. The teacher also made use of it to organize the education, especially for laboratory classes. We based our work on the theory of Ausubel and Novak's meaningful learning and on Gowin and Moreira's theories of teaching and we also grounded it on some key ideas of contemporary epistemology and philosophy of science. We want to promote theory-experiment integration, seeking to contribute to a more effective comprehension of physical concepts and epistemological conceptions expressed in Physics classes. In research, we opted for an interpretative methodology, but we also made use of several quantitative data, looking for evidence of strategy's validity. The results showed that the effectiveness of the instrument performance to promote the desired integration depends on the teacher's decisive role. They also indicated that the students conceptions about science, the scientist and how the knowledge construction is made, that are taught many times implicitly in class, are persistent and can interfere in the physical theories learning.

Vias biológicas representam interações entre entidades químicas complexas (proteínas, substratos, metabólitos etc.) que ocorrem no nível molecular das células. A representação e compreensão do comportamento destas vias é o principal alvo de estudos da Biologia Sistêmica. Esta área de estudos envolve a construção de modelos matemáticos que possam simular in silico (computacionalmente) o comportamento destes sistemas biológicos verificados in vivo (experimentalmente). Do ponto de vista computacional é evidente que tais sistemas são complexos para abordar e descrever de modo intuitivo. São necessários modelos com valor preditivo, isto é, que permitam descrever os comportamentos do sistema que são experimentalmente verificáveis. Algumas notações gráficas foram propostas para descrever vias biológicas. Entre elas, os diagramas de processos tem sido amplamente utilizados. Um diagrama de processos é essencialmente um grafo no qual vértices e arestas representam componentes biológicos, e há uma notação gráfica associada com cada elemento. Nesta dissertação propomos uma fundamentação formal para a linguagem dos diagramas de processos definindo a sintaxe usando gramática de grafos. Nós definimos primeiramente um grafo chamado BioProc, descrevendo o meta-modelo dos diagramas de processos. Instâncias do grafo BioProc são portanto diagramas de processos modelando vias biológicas. Para descrever a semântica foi proposta uma tradução algébrica dos grafos BioProc para redes de Petri estocásticas generalizadas (GSPNs) já amplamente utilizadas na modelagem de processos biológicos. O uso de gramática de grafos como formalismo intermediário na tradução habilita a verificação sintática da via com a checagem dos tipos válidos que podem ser definidos para cada reação antes da simulação na rede de Petri e usá-las posteriormente para explorar propriedades estruturais e estocásticas do modelo. Além disso serve como base para a evolução do modelo proposto. Isto é relevante já que modelos frequentemente são construídos incrementalmente para se adaptar a novos requisitos e/ou incluir novas características. / Biological pathways represent interactions between complex chemical entities (proteins, substrates, metabolites, etc.) that occur at the molecular level of cells. The representation and comprehension of biological pathways behavior is the main target of research in the field of Systems Biology. This area investigates the construction of mathematical models that can simulate in silico (computationally) the behavior of biological systems checked in vivo (experimentally). From a computational view point it is clear that such systems are too complex to analyze and describe in an intuitiveway. Models with predictive value are needed, describing the behaviors that are experimentally verifiable. There are some graphical notations to describe biological pathways. Among them, process diagrams have been widely used. A process diagram is essentially a graph in which vertices and edges represent biological components, and there is a graphical notation associated with each element. In this master thesis we give a formal foundation for biological process diagrams, by defining their (concrete and abstract) syntax and semantics using a formalism called graph grammars. We first build a graph called BioProc Graph, describing the meta-model of process diagrams. Instances of this BioProc graph are concrete process diagrams modeling biological pathways. To describe the semantics we proposed a translation of BioProc diagrams to generalized stochastic Petri networks (GSPNs) already widely used in modeling biological processes. The use of graph grammar formalism as a basis for translation enables the syntatic verification to check the valid types that can be defined for each reaction after the simulation of Petri net and before that to explore structural and stochastic properties of the model. In addition it serves as the basis for model evolution proposed. This is relevant because models are often built incrementally to adapt to new requirements and/or include new features.

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abstract: Multimodal presentations have been found to facilitate learning, however, may be a disadvantage for low spatial ability students if they require spatial visualization. This disadvantage stems from their limited capacity to spatially visualize and retain information from both text and diagrams for integration. Similarly, working memory capacity (WMC) likely plays a key role in a learner's ability to retain information presented to them via both modalities. The present study investigated whether or not the act of self-explaining helps resolve deficits in learning caused by individual differences in spatial ability, working memory capacity, and prior knowledge when learning with text, or text and diagrams. No interactions were found, but prior knowledge consistently predicted performance on like posttests. The author presents methodological and theoretical explanations as to the null results of the present study. / Dissertation/Thesis / M.S. Applied Psychology 2014

Dans cette thèse, nous décrivons comment on peut utiliser un diagramme de séquence UML avec des contraintes de temps MARTE pour spécifier complètement le comportement des systèmes à base de composants tout en faisant abstraction des rôles fonctionnels des composants. Nous avons proposé une approche qui permet d'analyser ces spécifications d'une manière modulaire. Pour cela, nous avons attribué une sémantique opérationnelle aux diagrammes de séquence en les traduisant vers les TIOSTS qui sont des automates symbolique et temporisé. Nous avons utilisé des techniques d'exécution symbolique pour calculer les exécutions du système sous la forme d'un arbre symbolique. Nous avons défini des mécanismes de projection pour extraire l'arbre d'exécution associé à un composant sous-jacent. L'arbre résultant de la projection caractérise les comportements attendus du composant et peut être utilisé comme une référence pour valider le système bout par bout. Pour ce faire, nous nous sommes intéressés à des techniques de test. Nous avons présenté un résultat qui ramène la conformité du système à la conformité des composants qui le composent. Sur la base de ces résultats, nous avons proposé une méthodologie incrémentale de test basé sur des spécifications décrites sous la forme de diagrammes de séquence. / In this thesis, we describe how to use UML sequence diagrams with MARTE timing constraints to specify entirely the behavior of component-based systems while abstracting as much as possible the functional roles of components composing it. We have shown how to conduct compositional analysis of such specifications. For this, we have defined operational semantics to sequence diagrams by translating them into TIOSTS which are symbolic automata with timing constraints. We have used symbolic execution techniques to compute possible executions of the system in the form of a symbolic tree. We have defined projection mechanisms to extract the execution tree associated with any distinguished component. The resulting projected tree characterizes the possible behaviors of the component with respect to the context of the whole system specification. As such, it represents a constraint to be satisfied by the component and it can be used as a correctness reference to validate the system in a compositional manner. For that purpose, we have grounded our validation framework on testing techniques. We have presented compositional results relating the correctness of a system to the correctness of components. Based on these results, we have defined an incremental approach for testing from sequence diagrams.