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Alborghetti, Marcos Rodrigo. "Proteínas da família FEZ (Fasciculation and Elongation protein Zeta) como adaptadoras bivalentes do transporte = aspectos funcionais, estruturais e evolutivos." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314365.
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Orientador: Jörg KobargTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: As proteínas humanas FEZ1 e FEZ2 (fasciculation and elongation protein zeta) são ortólogas da proteína UNC-76 de C. elegans e estão envolvidas no crescimento e na fasciculação dos axônios através de interações que envolvem kinesinas, mitocôndrias e vesículas sinápticas. Além disso, algumas evidências sugerem a participação de FEZ1 na etiologia da esquizofrenia, no ciclo viral, além da resistência à quimioterápicos. Sua estrutura intrinsecamente desordenada, com coiled-coil ao longo da sequência, pode contribuir para sua função. Nós exploramos a evolução molecular da família de proteínas FEZ com ênfase no ramo dos vertebrados. Através do perfil do interactoma comparado entre FEZ1 e FEZ2 de Homo sapiens e UNC-76 de C. elegans foi observado um padrão de conservação das interações proteínaproteína entre FEZ1 e UNC-76, que explicam a capacidade de FEZ1 resgatar os defeitos causados por mutações em unc-76 em nematoides, de acordo com o descrito por Bloom e colaboradores em 1997. Além disso, caracterizamos a interação entre FEZ1 e SCOCO (short coil-coiled) por SAXS (Small Angle X-ray Scattering). Essa interação já foi descrita previamente entre os seus ortólogos UNC-76 e UNC-69, que cooperam no crescimento axonal. Um estado de heterotetramérico foi observado, consistindo de duas moléculas GST-SCOCO interagindo com duas moléculas de 6xHis-FEZ1 dimerizadas. Por PAGE (Polyacrylamide Gel Electrophoresis, eletroforese em gel de poli-acrilamida), SAXS, Espectrometria de Massas e Ressonância Magnética Nuclear, constatamos que FEZ1 dimeriza envolvendo a formação de ponte dissulfeto. In vivo, este estado dimérico de forma covalente pode ser importante para o transporte mediado por kinesinas de proteínas ao longo dos microtúbulos. Assim, FEZ1 pode ser classificada como uma proteína adaptadora do transporte, dimérica e bivalente, essencial para o crescimento axonal e organização pré-sináptica normal e transporte de cargas. A agregação de novos parceiros de interação encontrada para a proteína FEZ2 poderia ser interpretada como aquisição de novas funções moleculares e pode ter ocorrido nos primeiros estágios da evolução dos cordados
Abstract: The human proteins FEZ1 and FEZ2 (fasciculation and elongation protein zeta 1) are orthologs of the protein UNC-76 from C. elegans, involved in growth and fasciculation of axons, through interactions that involve kinesins, mitochondria and synaptic vesicles. Moreover, some evidence suggests involvement of FEZ1 in the etiology of schizophrenia, in addition to the viral cycle and resistance to chemotherapy. Its structure intrinsically disordered, with coiled-coil along the sequence, can contribute to its function. We have explored the molecular evolution of the FEZ protein family with emphasis on the vertebrata branch. Analyzing the interactome profile of the FEZ1 and FEZ2 from Homo sapiens and UNC-76 from C. elegans we observed a conserved pattern of protein-protein interactions among FEZ1 and UNC-76 that explain the ability of FEZ1 to rescue the defects caused by unc-76 mutations in nematodes, according to Bloom and co-workers in 1997. Furthermore, we characterized the interaction between FEZ1 and SCOCO (short coiled-coil protein) by SAXS (Small Angle X-ray Scattering). This interaction has been previously reported between their orthologs UNC-76 and UNC-69 that cooperate in axonal outgrowth. A heterotetrameric state was observed, which consists of two GST-SCOCO molecules attached to two FEZ1 molecules. By PAGE (Polyacrylamide Gel Electrophoresis), SAXS, Mass Spectrometry and Nuclear Magnetic Resonance we defined that FEZ1 dimerizes involving formation of disulfide bond. In vivo this covalent mediated dimeric state could be important for kinesin mediated protein transport along the microtubule. Thereby, FEZ1 may be classified as a dimeric and bivalent transport adaptor, essential to axon outgrowth and normal pre-synaptic organization and transport of cargoes. The aggregation of new interaction partners found for the FEZ2 protein could be interpreted as the acquisition of new molecular functions and may have occurred in the early stages of chordate evolution
Doutorado
Bioquimica
Doutor em Biologia Funcional e Molecular
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Foulkes, William Matthew Colwyn. "Interatomic forces in solids." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328669.
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Gerdy, James Joseph Goddard William A. "Accurate interatomic potentials for simulations." Diss., Pasadena, Calif. : California Institute of Technology, 1996. http://resolver.caltech.edu/CaltechTHESIS:10212009-150813700.
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Schwarz, Michael Heinz. "Interative and evolutionary identification and control." Thesis, University of Sunderland, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.398549.
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Gray, Benjamin R. "Accurate interatomic potentials for ion-neutral systems." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.478962.
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Dzingina, Benjamin Harr. "Richer Web : interative dynamic graphics for web applications /." Leeds : University of Leeds, School of Computer Studies, 2008. http://www.comp.leeds.ac.uk/fyproj/reports/0708/Dzingina.pdf.
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Hobday, Steven. "Artificial intelligence and simulations applied to interatomic potentials." Thesis, Loughborough University, 1998. https://dspace.lboro.ac.uk/2134/33255.
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The interatomic potential is a mathematical model that describes the chemistry occurring at the atomic level. It provides a functional mapping between the atomic nuclei coordinates and the total potential energy of a system. This thesis investigates three aspects of interatomic potentials, the first of which is the simulation of materials at the atomic scale using classical molecular dynamics (MD). Molecular dynamics code is used to follow the evolution of a system of discrete particles through time and is employed here to model the bombardment of fullerite films modified with low dose Argon ion impacts.
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CHAOUBAH, ALFREDO. "INTERATIVE METHODS FOR SERVOMECHANISM DESIGN BASED ON H2 OPTIMIZATION." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 1993. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=9278@1.
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COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIORConsidera-se, neste trabalho, um problema de controle ótimo no qual o critério ( relativo à atenuação de sinais de perturbação) e a restrição (relativa à margem de estabilidade) são, respectivamente, normas e H2 e H(infinito) ponderadas de funções de transferência em malha fechada. Um procedimento iterativo para o obtenção de soluções aproximadas, no qual somente problemas H2 irrestritos são resolvidos, é apresentado. Vários exemplos de aplicação deste procedimento são discutidos.
In this work an optimal control problem is considered in which the cost function (pertaining to disturbance attenuation) and the constraint (due to unstructured, stability margin requirements) are, respectively, weighted H2 e H(infinity) norms of closed-loop transfer functions. An iterative scheme is described for generating aproximate soluctions in which only unconstrained H2 problems are solved. Some numerical examples are then discussed.
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LOPES, JOSE MARCOS. "INTERATIVE METHODS FOR LINEAR COMPLEMENTARITY PROBLEMS AND LEAST NORM." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 1992. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=8250@1.
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UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHOApresentamos nesta dissertação novos métodos interativos para resolver o Problema de Complementaridade Linear (PCL) e Problemas de Norma Mínima. Após uma revisão geral sobre métodos interativos para o PCL, apresentaremos no Capítulo 2, uma forma de aceleração aplicada a métodos clássicos para o PCL simétrico, através de uma decomposição (Splitting) conveniente da matriz associada ao problema. A aceleração para os novos métodos consiste em calcular uma direção de avanço usando o método básico mais uma minimização unidimensional que respeite as condições de não negatividade, provas de convergência forte são apresentadas. No Capítulo 3 comparamos algoritmos do tipo seqüencial e paralelo para solução de um Problema de Programação Linear e Problemas de Norma Mínima em l 1: para o segundo problema os métodos iterativos são aplicados no dual do problema original penalizado com um termo quadrático. Introduzimos um novo método paralelo para o Problema de Norma mínima em l 1 e provamos sua convergência. Propomos no capítulo 4, novos métodos iterativos paralelos para Problemas de Norma Mínima, convenientes para problemas de grande porte, provas de convergência são fornecidas. Finalmente, no capítulo 5 baseados sobre uma combinação da iteração de ponto proximal e métodos iterativos clássicos, propomos novos métodos iterativos para a solução de um PCL monótono não simétrico. Ilustramos todos os algoritmos apresentados, em diferentes versões, com um extensa experimentação numérica.
We present in this dissertation new iterative methods for solving Linear Complementarity (LCP) and Least Norm (LNP) Problems. After a general overview on iterative methods for the LCP, in chapter 2 we present an acceleration techinique applied to classic methods for symmetric LCP generated by considering appropriate splittings of the associated matrix. The acceleration gives rise to new methods consisting of computing a search direction using the basic method plus a one dimensional minimization taking into account the nonnegative constraints. Strong convergence proofs are given. In chapter 3 we compare sequential and parallel algorithms for solving Linear Programming and least 1-Norm Problems obtained by applying iterative methods to a dual of the original problem penalized with a quadratic term. We introduce a new parallel method for the Least 1-Norm Problem, proving its convergence. In chapter 4, we present new parallel iterative methods for solving large LNP, giving convergence proofs. Finally, in chapter 5 we propose new iterative methods for solving monotone nonsymmetric LCp based on a combination of proximal point iterations and classic iterative methods. All the algorithms, in their different versions are illustrated and compared through many numerical experiments.
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Batzner, Simon Lutz. "Learning symmetry-preserving interatomic force fields for atomistic simulations." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122525.
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Thesis: S.M., Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2019Cataloged from PDF version of thesis.
Includes bibliographical references.
Machine-Learning Interatomic Force-Fields have shown great promise in increasing time- and length-scales in atomistic simulations while retaining the high accuracy of the reference calculations that they are trained on. Most proposed models aim to learn the potential energy surface of a system of atoms as a function of atomic coordinates and species and obtain the forces acting on the atoms as the negative of the gradient of the global energy with respect to the atomic positions. For the time evolution of an atomistic system in molecular dynamics, however, only atomic forces are required. This thesis examines the construction of a direct approach for learning atomic forces, thereby bypassing the need for learning an energy-based model. Predicting atomic forces directly requires the careful consideration of incorporating the symmetries of 3D space into the model. The construction of an efficient, direct, and symmetry-preserving deep learning model that can predict atomic forces in a fully end-to-end fashion is shown. The model's accuracy, its computational efficiency for training as well as its computational efficiency at time of prediction are evaluated. Finally, the approach is used in the simulation of different small organic molecules and the resulting Molecular Dynamics simulations are analyzed.
by Simon Lutz Batzner.
S.M.
S.M. Massachusetts Institute of Technology, Computation for Design and Optimization Program
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Ehemann, Robert Christopher. "Force-matched interatomic potentials for tungsten and titanium-niobium." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1511363152728115.
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Vieira, Sylvio André Garcia. "IDENTIFICAÇÃO DE PADRÕES DE EXPRESSÃO EM DOENÇAS GENÉTICAS USANDO UMA REDE DE INTEGRAÇÃO DE VIAS DE MANUTENÇÃO DO GENOMA, ANGIOGÊNESE, HIPÓXIA EVIGILÂNCIA IMUNOLÓGICA." Centro Universitário Franciscano, 2016. http://www.tede.universidadefranciscana.edu.br:8080/handle/UFN-BDTD/571.
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The analysis of the biological formations through computer programs has been turning the interpretation of information quicker, more practical, and more reliable. There are a great number of data stored in specialized databases all over the world, that need to be analyzed and interpreted. On the biological databases, there are data obtained from a variety of ways of research in organisms affected by illnesses such as adenoma and carcinoma. There are also data related to the processes of maintenance of the organism in various levels, called pathways. These pathways act in the organism in a different way in every stage, such as in its normality or in the presence of some genetic disease. This study aims at using graphs in order to develop a model of pathway interaction network that incorporate the maintenance of the genome and other activities of the organism conveyed in adenoma and carcinoma of the adrenal cortex, identifying those who are active in the organism in the presence of gene mutation. In order to determine which pathways are modified in the presence of each disease was used a calculus of relative activity of the route associated to the statistical test Z. To visualize the results, graphs were used, whose junctions represent the pathways and whose edges represent the interactions. Through the computer program developed, it was possible to identify the differences that the organism presents in these conditions, allowing the suggestion of employment of this technique to identify modifications that the organism may present when a new nanoencapsulated drug is used.
A análise de informações biológicas por meios computacionais vem tornando as atividades de interpretação das informações mais rápida, prática e confiável. Existem muitos dados depositados em bancos especializados ao redor do mundo, que precisam ser avaliados e interpretados. Nestes bancos de dados de informações biológicas há informações resultantes de várias formas de pesquisas em organismos acometidos de doenças, como adenomas e carcinomas. A evolução dessas doenças ocorre através da ativação de vias muito específicas. Estas vias atuam no organismo de forma diferente em cada estado, como na sua normalidade ou na presença de alguma doença genética. Este trabalho tem por objetivo utilizar grafos para desenvolver um modelo de redes de interação de vias que envolvam a manutenção do genoma e outras atividades do organismo expressas em adenoma e carcinoma de córtex adrenal, identificando as vias expressas no organismo na presença de mutações. Para determinar quais vias estariam com a sua expressão alterada na presença de cada doença, foi utilizado o cálculo de atividade relativa da via associado ao teste estatístico Z. Para visualização dos resultados foram utilizados grafos, cujos nós representam as vias e as arestas representam as interações. Por meio do sistema computacional desenvolvido foi possível identificar as diferenças que o organismo apresenta nestas condições, permitido a sugestão de utilização desta técnica para a identificação das modificações que o organismo possa apresentar quando da utilização de um novo fármaco nanoencapsulado.
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Sukhomlinov, Sergey. "Development of effective interatomic potentials for computer simulation of oxides." Thesis, Lille 1, 2012. http://www.theses.fr/2012LIL10092/document.
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Le modèle de potentiels effectifs d'interactions interatomiques (champ de forces) pour la modélisation d'oxydes a été développé avec l'utilisation de calculs ab initio basés sur la théorie de la fonctionnelle de la densité. Le champ de forces décrit l'énergie potentielle totale du système par la somme de l'énergie électrostatique, celle de dispersion, et l'énergie d'interactions à courte portée. L'énergie électrostatique a été décrite par le modèle d'équilibration des tranferts de charge (SQE) basé sur l'approche d'égalisation du potentiel chimique (CPE). Le calcul de coefficients de dispersion, qui déterminent les interactions de dispersion, a été réalisé avec l'utilisation de fonctions Wannier maximalement localisées (MLWF). Dans les oxydes la position des centres des MLWF près d'atomes permet de calculer les coefficients de dispersion pour chaque atome. Les calculs de ces coefficients ont montré que leur valeur dépend du nombre d'atomes et du rayon de la première sphère de coordination. Le développement de potentiels d'interactions à courte portée a été réalisé avec l'utilisation de la méthode "force-matching", ce qui a permis de choisir la forme analytique des potentiels. Les paramètres des composants du champ de force ont été obtenus sur la base de calculs de chimie quantique de systèmes isolés et périodiques de structures de silicates. Les paramètres du modèle SQE on été calibrés en utilisant le potentiel électrostatique comme la grandeur de référence. Le champ de forces complet a été testé par simulation de polymorphes cristallins de la silice par la méthode de la dynamique moléculaire. Les résultats des calculs ont permis de choisir le meilleur modèle. Le champ de forces sélectionné reproduit bien les caractéristiques structurelles de α-quartz et α-cristobalite. Le calcul de spectres vibrationnels des systèmes montre que le champ de forces sous-estime les constantes de forces Si-O, ce qui conduit à un déplacement de spectres vibrationnels vers les basses fréquences par rapport aux spectres expérimentaux. Des voies visant l'amélioration de la performance du champ de forces sont proposéesThe effective interatomic potential model (force field) for the atomistic modeling of oxide materials was developed with the extensive use of ab initio density functional calculations. The force field represents the total potential energy of system as a sum of the long-range electrostatic, dispersion, and short-range energy contributions. The long-range energy electrostatic energy was described with the use of split-charge equilibration (SQE) model based on the chemical potential equalization (CPE) approach. The electrostatic potential was used as the reference quantity for the calibration of parameters of the SQE model. The computation of dispersion coefficients, which determine the magnitude of the dispersion interactions, was carried out with the use of maximally localized Wannier functions (MLWF). The position of MLWF centers close to the nuclei in oxides permits the computation of the dispersion coefficients in an atom-wise manner. The values of the dispersion coefficients were found to be affected by the coordination number and the radius of the first coordination sphere of atom. The short-range (SR) interaction potentials were designed with the use of force-matching method, which has allowed a judicious choice of the functional form of the SR potentials. The parametrization of the force field components was performed on the basis of extensive quantum-chemical calculations of isolated and periodic silicate systems. The complete force field was tested in the molecular dynamics simulations of crystalline silica polymorphs. Results of the calculations allowed to choose the best model. The selected force field well reproduces structural characteristics of the α-quartz and α-cristobalite polymorphs. The calculation of the vibrational spectra of the systems has shown that the model underestimates the Si-O force constants that leads to a downward shift of the vibrational spectra in comparison with the experimental data. A number of ways aimed at improving the force field's performance are suggested
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Cabral, Heleno Carmo Borges. "A DEFINIÇÃO DE UMA ONTOLOGIA PARA INTEGRAR DADOS DE INTERATOMA E TRANSCRIPTOMA DE CÂNCER." Universidade Franciscana, 2010. http://tede.universidadefranciscana.edu.br:8080/handle/UFN-BDTD/247.
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Previous issue date: 2010-06-23Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Ontocancro is an ontology stored in a knowledge database designed to be a source of information to integrate transcriptomics and interatomics data involved in gene pathways of genome maintenance/stability mechanisms (GMM). Genome maintenance mechanisms are shown to be critical for cell homeostasis since their malfunctioning can predispose to cancer. Repair, apoptosis and chromosome stability pathways comprise the cornerstone of GMM. The information about these pathways are disseminated in various databases as NCI-Nature, BioCarta, KEGG, Reactome, Prosite, GO and others. Ontocancro was created with the intention of integratin the information of genes involved in GMM from several curated databases. This data integration is difficult for biological data lack a unified vocabulary and need constant update what is provided by Ontocancro. Additionally, it allows the integration of transcriptome data provided by some Affymetrix microarrays platforms with interactome data from the STRING database, which has information about protein interactions. So, this work shows the integration of data from biological information systems using the ontology paradigm, in order to integrate transcriptomics and interatomics data involved in gene pathways of genome stability.
A Ontocancro é uma ontologia armazenada em um banco de dados de conhecimento projetada para ser a fonte de informação referente a integração de dados de interatoma e transcriptoma envolvidos em vias metabólicas de mecanismo de manutenção do genoma humano (GMM). Esse mecanismo de manutenção são críticos para homeostase celular desde o seu mau funcionamento, o que pode causar câncer. O reparo, a apoptose e as vias de estabilidade cromossômicas compreendem o cerne do GMM. A informação sobre essas vias metabólicas são disseminadas em vários bancos de dados, como o NCI-Nature, o BioCarta, o KEGG, o Reactome, o Prosite e o GO, entre outros. A ontologia Ontocancro foi criada com a intenção de integrar a informação sobre os genes envolvidos em GMM a partir de diversos bancos de dados curados. Essa integração de dados é complexa pela falta de um vocabulário sobre os dados biológicos e a necessidade constante de atualização destes dados. Para sanar essas duas dificuldades, a Ontocancro foi criada. Adicionalmente, ela permite a integração de dados oriundos de transcriptoma obtidos a partir da plataforma Affymetrix com os dados de interatoma obtidos a partir do banco de dados chamado STRING, o qual possui informação sobre as interações entre as proteínas. Portanto, este trabalho apresenta a integração de dados obtidos de sistemas de informação biológicos usando o paradigma ontológico, de forma a integrar os dados envolvidos em interatoma e transcriptoma em vias metabólicas de estabilidade do genoma.
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Szlachta, Wojciech Jerzy. "First principles interatomic potential for tungsten based on Gaussian process regression." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648779.
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MOREIRA, Ícaro Valgueiro Malta. "Reconstrução tomográfica utilizando o FPSIRT (Fast Article System Interative Reconstruction Technique)." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/13963.
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O PSIRT - Particle System Iterative Reconstruction Technique – é um método de reconstrução tomográfica de imagens primariamente desenvolvido para configurações compatíveis com aplicações industriais. Sistema de partícula é uma técnica de otimização inspirada em características da real física de sistemas que associa ao material reconstruído um conjunto de partículas com certas características físicas, sujeitas a um campo de força, que pode produzir movimento. O sistema constantemente atualiza a rede de partículas reposicionando-as numa forma que elas se aproximam do equilíbrio. A potencial elástica ao longo de um raio é uma função da diferença do coeficiente de atenuação de uma determinada configuração e a entrada correspondente. O PSIRT tem sido usado com sucesso para reconstruir objetos simulados e reais para configurações paralelas e fanbeam em diferentes ângulos, representando os arranjos comuns de tomografia de raios gama. Uma das limitações do PSIRT era o seu desempenho muito aquém da reconstrução em tempo real, e assim, neste trabalho a sua modelagem computacional foi inteiramente reformulada, dando origem ao FPSIRT - Fast System Iterative Reconstruction Technique, capaz de aumentar sua velocidade por um fator de até 200 vezes em alguns experimentos mantendo a mesma qualidade de reconstrução.
The PSIRT – Particle System Iterative Reconstruction Technique– is a method of tomographic image reconstruction primarily designed to work with configurations suitable for industrial applications. A particle system is an optimization technique inspired in real physical systems that associates to the reconstructing material a set of particles with certain physical features, subject to a force field, which can produce movement. The system constantly updates the set of particles by repositioning them in such a way as to approach the equilibrium. The elastic potential along a trajectory is a function of the difference between the attenuation coefficient in the current configuration and the corresponding input data. PSIRT has been successfully used to reconstruct simulated and real objects subject to sets of parallel and fanbeam lines in different angles, representing typical gamma-ray tomographic arrangements. One of the limitations was that its performance performance is very slow when compared to real time. In this dissertation, PSIRT is totally redesigned, giving origin to FPSIRT – Fast System Iterative Reconstruction Technique. The FPSIRT can reconstruct until 200 times faster than PSIRT in some experiments.
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Bahmanpour, Laila. "Theory of ultrafast interatomic (intermolecular) electronic decay processes in polyatomic clusters." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/24869.
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This thesis is devoted to the study of the non-radiative process of Interatomic (Intermolecular) Coulombic Decay (ICD) in clusters. The aims of this thesis are two-fold: firstly we study ICD in the inner-valence-ionised endohedral fullerene complexes, such as (2s^1)Ne^+@C_60, where it is ultrafast due to the many available decay channels. We investigate the open question of the dependence of the ICD rate on the location of the endohedrally confined ion. Qualitative analysis shows that once the symmetry of the endohedral system is lowered by the departure of a rare gas atom from its equilibrium position in the centre of the cage, multipole plasmon resonances can be excited by energy transfer from the inner-valence-ionised ion to the cage. Nevertheless, our quantitative analytical and ab initio numerical studies lead to the conclusion that the total ICD width is remarkably stable across broad range of geometries. It turns out that the multipole plasmon excitation is negligible and the well-known dipole fullerene plasmon is the one defining the ICD time scale. Secondly we focus our attention onto inner-valence vacancies that are not energetic enough to decay via ICD. We propose that under such conditions, an ICD-like electronic process may still be induced by an incident photon. We call the new process single photon laser-enabled ICD (spLEICD). We for the first time investigate spLEICD in a series of van der Waals and hydrogen-bonded clusters. Our results demonstrate that the spLEICD cross-sections in hydrogen-bonded systems are larger than in van der Waals ones, whereas polyatomic van der Waals clusters lead to a more efficient spLEICD process than the van der Waals diatoms. We analyse the dependence of the spLEICD cross-section on the inter-atomic distance in a cluster showing analytically that it obeys the 1/R^6 law at large distances. This analysis is confirmed by our \textit{ab initio} numerical calculations. This strong distance-dependence may allow spLEICD to be used as a novel spectroscopic technique for the study of processes which occur in different spatial regions of molecules or clusters.
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Mastrocola, Vicente Martin. "Comunicação, Consumo e entretenimento: o interator na ficção seriada Star Wars." Associação Escola Superior de Propaganda e Marketing, 2011. http://tede2.espm.br/handle/tede/99.
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Previous issue date: 2011-03-22This project delimitates the concept of transmedia storytelling: a kind of narrative which develops into multiple mediatic platforms, such as internet, books, videogames, comics, television, cinema etc., examining the use of strategy in the entertainment industry and understanding how the consume and communication strategies materialize in this scenario. The object of this project is: to examine the strategic appropriation of transmediatic narratives in the industry of entertainment; to study the systematic use of multiple platforms on the biggest mediatic series worldwide, using an established example in the industry of entertainment: the Star Wars fiction series. Finally, we will investigate the participation of a digital social network in the consolidation of the success of this series through user-generated (interactor) content and distribution. It is used in this project a multimethodological approach wherein will be highlighted a netnographic character observation, following interactors among diverse social networks and digital platforms where they are found.
Neste projeto, procura-se examinar as narrativas transmidiáticas: um tipo de narrativa que se desdobra em múltiplas plataformas midiáticas, como internet, livros, videogames, quadrinhos, televisão, cinema etc., analisando sua utilização estratégica na indústria de entretenimento e visando compreender como se materializam as estratégias de comunicação e consumo nesse cenário. Pretende-se, com este trabalho: cartografar a apropriação estratégica de narrativas transmidiáticas na indústria do entretenimento; estudar a utilização sistemática de múltiplas plataformas nas grandes séries midiáticas de âmbito global, servindo-se de um exemplo consagrado da indústria do entretenimento: a ficção seriada Star Wars. Por fim, investiga-se a participação de uma rede social digital na consolidação do sucesso desta série por meio da distribuição e geração de conteúdo do usuário (interator). Utiliza-se neste projeto uma abordagem multimetodológica em que se destaca uma observação de caráter netnográfico na internet acompanhando os interatores nas diversas redes sociais e plataformas digitais onde se encontram.
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Belgrade, Diana Stojanovic. "Interative multistage maximum likelihood decoding algorithm for multilevel codes and its applications." Thesis, University of Hawaii at Manoa, 2003. http://hdl.handle.net/10125/6876.
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The role of channel coding in digital communication system is to provide reliability, that is, a successful information transmission in the presence of noise and interference, with as small an error rate as required. Half a century of research in Information Theory and Communications resulted in construction of many good codes and classes of codes. In general, longer codes achieve better performance, but the required time, memory, and amount of computation needed for successful decoding of these codes may in practice be infeasible. Thus the search for an efficient decoding algorithm is as important as the search for a good code. A good trade-off between the performance, measured by the low error probability, and efficiency, measured by the low decoding complexity, is set as a criterion. Multistage decoding is devised for decoding codes with multilevel structure to achieve an efficient trade-off between error performance and decoding complexity. Multilevel code structure is used to simplify decoding. Component codes are decoded level-by-level in series of decoding stages, with the decoded information passed between them. Optimal for the codes of small and medium lengths and number of decoding stages, this technique shows a significant drop in performance when applied to longer codes, thus sacrificing performance to achieve efficiency. In this dissertation, we develop an efficient soft-decision iterative multistage decoding algorithm for decoding decomposable and multilevel concatenated codes. This algorithm achieves maXImum likelihood (ML) performance through iterations with optimality tests at each decoding stage. It is the first proposed multistage decoding algorithm that achieves ML performance, and at the same time has a significant reduction in average decoding complexity compared to other known ML decoding algorithms, such as ViterlJi algorithm. The application of the algorithm to two general classes of multilevel codes, decomposable linear block codes, on the example of Reed-Muller codes, and multilevel block coded modulation codes, is presented. The results show that this new algorithm achieves excellent performance-complexity trade-off.xi, 113 leaves
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Steele, Brad. "Non-equilibrium melting and sublimation of graphene simulated with two interatomic potentials." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4586.
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The mechanisms of the sublimation of graphene at zero pressure and the condensation of carbon vapor is investigated by molecular dynamics (MD) simulations. The interatomic interactions are described by the Reactive Empirical Bond Order potential (REBO). It is found that graphene sublimates at a temperature of 5,200 K. At the onset of sublimation, defects that contain several pentagons and heptagons are formed, that are shown to evolve from double vacancies and stone wales defects. These defects consisting of pentagons and heptagons act as nucleation sites for the gaseous phase. The influence of the interatomic interactions on the sublimation process are also investigated by comparing the results using the REBO potential with the Screened Environment Dependent (SED)-REBO potential. Two-dimensional MD simulations are also performed, and it is found that graphene melts at a much higher temperature and forms many more point defects than in three dimensions. It is also observed that carbon chains make up the two-dimensional molten state.
The isothermal equation of state of gaseous and liquid carbon, as well as the coexistence of the two phases is calculated at 6,000 K and up to a few GPa. The analysis shows that the material that forms immediately following the phase transformation in graphene is actually a coexistence of liquid and gaseous phases, but it is primarily two-fold coordinated, so it is mostly a gas, hence the identification of the phase transformation as sublimation. The coexistence pressure for liquid and gaseous carbon is found using the Maxwell Construction to be 0.0365 GPa at 6,000 K. It was previously believed that carbon vapor consists exclusively of carbon chains. We find that under compression, at a pressure lower than the coexistence pressure, carbon vapor develops a small amount (6 %) of sp2 bonds indicating a slight non-chain bonding character. The diffusion coefficient of this dense gas is calculated to be in between that of the liquid and gaseous phases.
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Bartók-Pártay, Albert. "Gaussian approximation potential : an interatomic potential derived from first principles Quantum Mechanics." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608570.
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Hauschild, Timo. "Investigating interatomic solid state potentials using Crystal-GRID: a study of applicability; Dissertation." Forschungszentrum Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:d120-qucosa-29729.
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Hauschild, Timo. "Investigating interatomic solid state potentials using Crystal-GRID: a study of applicability; Dissertation." Forschungszentrum Rossendorf, 2001. https://hzdr.qucosa.de/id/qucosa%3A21799.
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Toft, Malcolm. "The reduction tomography of materials-forming processes." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299421.
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Mason, Colin Raymond. "An evaluation of model potential and pseudopotential methods for the calculation of interatomic potentials." Thesis, University College London (University of London), 1991. http://discovery.ucl.ac.uk/1363642/.
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This thesis presents an evaluation of the model potential and pseudopotential methods for the calculation of atom-atom interaction curves. At University College London, Peach has computed interatomic potential curves for several alkali-rare gas pairs using both the model potential and pseudopotential methods in a completely self-consistent manner. The value of these calculations is that any differences between the interatomic potential curves obtained from the model potential and pseudopotential methods can be attributed unambiguously to the theoretical representations of the Pauli exclusion principle which differentiate the two methods. The work of Peach thus allows the utility of these two representations to be compared directly and their effect on the quality of the resulting interatomic potentials to be assessed. The present study has developed a suite of computer programs designed to calculate observable quantities which are sensitive to the interatomic potentials. Calculations of the profiles, widths and shifts of the alkali resonance line when perturbed by rare gases, together with cross sections for fine structure state changing transitions within the alkali excited state multiplet, are reported and comparisons are made with experimental measurements of these observables. It is demonstrated that the theoretical representation of the Pauli exclusion principle has a significant effect on the quality of the resulting interatomic potentials. Observables calculated on the basis of interatomic potentials obtained via the model potential method are in better agreement with the available experimental data than those calculated on the basis of pseudopotential interaction curves. From this it may be inferred that the interatomic potentials obtained by the model potential method represent the actual interaction between alkali and rare gas atoms more accurately than do interatomic potentials obtained by the pseudopotential method. The results of this study provide strong evidence for the superiority of the model potential method for the calculation of interatomic potentials.
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Kopelke, Sören [Verfasser], and Lorenz S. [Akademischer Betreuer] Cederbaum. "Quenching of Molecular Photodissociation by Interatomic Coulombic Decay / Sören Kopelke ; Betreuer: Lorenz S. Cederbaum." Heidelberg : Universitätsbibliothek Heidelberg, 2011. http://d-nb.info/117978300X/34.
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Molle, Axel [Verfasser]. "Electron Dynamics of Interatomic Coulombic Electron Capture in Artificial and Real Atoms / Axel Molle." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1199937428/34.
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Notari, Daniel Luís. "Desenvolvimento de workflows científicos para a geração e análise de diferentes redes de interatomas." reponame:Repositório Institucional da UCS, 2012. https://repositorio.ucs.br/handle/11338/694.
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Workflows científicos são projetados para realizar experimentos in silico com o
intuito de processar e analisar uma grande quantidade de dados usando simulação
computacional. Os experimentos são organizados como uma sequência de etapas que
caracterizam um fluxo de execução, onde em cada etapa utilizam-se diferentes
softwares. Estes softwares não possuem um modelo de representação de dados comum.
Por isto, quando um workflow científico é construído com o objetivo de integrar e
processar dados, cada etapa precisa analisar a estrutura dos dados, processá-los e
preparar os mesmos de acordo com a estrutura necessária para a execução da próxima
etapa do workflow. Desta maneira, os workflows científicos usam diferentes algoritmos
provenientes das áreas da matemática e da ciência da computação, os quais são capazes
de processar, armazenar e transformar os dados utilizados em informação útil para
diferentes análises de pesquisadores de biologia. Adicionalmente, a biologia de sistemas
é uma subárea da bioinformática que ajuda a compreender as interações observadas
entre populações de moléculas, células e organismos resultantes do aumento da
complexidade biológica. Assim, nesta tese de doutorado, buscou-se desenvolver
workflows científicos utilizando-se ferramentas de bioinformática e biologia de sistemas
para comparar processos biológicos através da geração de redes de interação proteínaproteína.
Para tanto, o programa Dis2PPI foi gerado por meio de um workflow científico
que possibilitou integrar os bancos de dados de doenças monogênicas OMIM (Online
Mendelian Inheritance in Man) com o programa de metabuscas STRING (Search Tool
for the Retrieval of Interacting Genes/Proteins). O objetivo desta integração foi gerar
uma rede de interação proteína-proteína associada com doenças de natureza
monogênica. Como prova de conceito, o programa Dis2PPI foi utilizado para a
obtenção de redes de interação para as síndromes xeroderma pigmentosa e de Cockayne, duas doenças monogênicas raras e cujos fenótipos estão associados com
acúmulos de danos de DNA, câncer, progeria e neurodegeneração. Uma vez geradas,
estas redes foram avaliadas com o uso ferramentas de biologia de sistemas para análise
de ontologia gênica e de centralidade no programa Cytoscape. Da mesma forma, o
programa Net2Homology foi gerado através de um desenho de um workflow científico
que possibilitasse integrar o resultado de um alinhamento de sequências de proteínas,
usando o programa NCBI PSI-BLAST, com o programa de metabuscas STRING. Neste
sentido, o programa Net2Homology possibilitou recuperar duas redes de interação
proteína-proteína associada a dois organismos diferentes. Este mesmo programa foi
utilizado para a obtenção de redes de interação para a doença xeroderma pigmentosa e
para a enzima ciclo-oxigenase-1 cruzando as informações dos organismos Homo
sapiens e Mus musculus. As redes de interação obtidas foram comparadas visando obter
os processos biológicos evolutivamente conservados.Submitted by Marcelo Teixeira (mvteixeira@ucs.br) on 2014-06-17T12:38:59Z No. of bitstreams: 1 Tese Daniel Luis Notari.pdf: 7846140 bytes, checksum: ebfd645042f867b8840d5ab9083411bc (MD5)
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Scientific workflows can be used to design in silico experiments to process and analyse a great amount of data using computational simulation. In this sense, all in silico experiments are organized as a sequence of steps that characterize an execution flow, where each steps employ different softwares. It is important to note that these softwares do not employ a common structure or model to represent data. Thus, taking into account the diversity of softwares and data representation, a scientific workflow should be built to integrate and process data, where each step must be able to analyse the data structure, to process these data and finally generate a new data structure that provide the requirements needed to execute the next step of the workflow. It is important to note that scientific workflows use mathematics and computer sciences methods capable to process, storage, and transform these data into useful information. In addition, a subarea of Bioinformatics termed Systems biology helps to understand the interactions observed between populations of molecules, cells and organisms as the result of the increase of biological complexity. Thus, the purpose of this work was to develop scientific workflows using bioinformatics and system biology softwares with the purpose to compare different biological processes from the generation of proteinprotein interaction (PPI) networks. In this sense, the Dis2PPI software was design as a scientific workflow to integrate OMIM (Online Mendelian Inheritance in Man) database with metasearch program STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) in order to retrieve protein-protein interaction networks associated to monogenic diseases. The Dis2PPI was used to generate PPI networks for xeroderma pigmentosum and cockayne syndromes, two rare monogenic diseases associated with DNA damage, cancer, progeria, and neurodegeneration. The PPI networks generated were analyzed with Cytoscape program and specific plugins that evaluate gene ontologies and centrality analysis. By its turn, Net2Homology program was designed as a scientific workflow to integrate NCBI PSI-BLAST sequence alignments with STRING metasearch program to recovery PPI networks associate with two different species. In this sense, Net2Homology was used to obtain PPI network for xeroderma pigmentosum disease and cyclooxigenase-1 enzyme by crossing Homo sapiens and Mus musculus information. A comparison between these networks was realized to verify the major evolutively conserved biological process.
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Takahashi, Akira. "Construction of interatomic potentials using large sets of DFT calculations and linear regression method." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225594.
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Tseng, Chien H. "Iterative algorithms for envelope-constrained filter design." Curtin University of Technology, Australian Telecommunications Research Institute, 1999. http://espace.library.curtin.edu.au:80/R/?func=dbin-jump-full&object_id=10453.
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The design of envelope-constrained (EC) filters is considered for the time-domain synthesis of filters for signal processing problems. The objective is to achieve minimal noise enhancement where the shape of the filter output to a specified input signal is constrained to lie within prescribed upper and lower bounds. Traditionally, problems of this type were treated by using the least-square (LS) approach. However, in many practical signal processing problems, this "soft" least-square approach is unsatisfactory because large narrow excursions from the desired shape occur so that the norm of the filter can be large and the choice of an appropriate weighting function is not obvious. Moreover, the solution can be sensitive to the detailed structure of the desired pulse, and it is usually not obvious how the shape of the desired pulse should be altered in order to improve on the solution. The "hard" EC filter formulation is more relevant than the "soft" LS approach in a variety of signal processing fields such as robust antenna and filter design, communication channel equalization, and pulse compression in radar and sonar. The distinctive feature is the set of inequality constraints on the output waveform: rather than attempting to match a specific desired pulse, we deal with a whole set of allowable outputs and seek an optimal point of that set.The EC optimal filter design problems involve a convex quadratic cost function and a number of linear inequality constraints. These EC filtering problems are classified into: discrete-time EC filtering problem, continuous-time EC filtering problem, and adaptive discrete-time EC filtering problem.The discrete-time EC filtering problem is handled using the discrete Lagrangian duality theory in combination with the space transformation function. The optimal solution of the dual problem can be computed by finding the limiting point of ++an ordinary differential equation given in terms of the gradient flow. Two iterative algorithms utilizing the simple structure of the gradient flow are developed via discretizing the differential equations. Their convergence properties are derived for a deterministic environment. From the primal-dual relationship, the corresponding sequence of approximate solutions to the original discrete-time EC filtering problem is obtained.The continuous-time EC filtering problem (semi-infinite convex programming problem) is handled using the continuous Lagrangian duality theory and Caratheodory's dimensionality theory. Several important properties are derived and discussed in relation to practical engineering requirements. These include the observation that the continuous-time optimal filter via orthonormal filters has the structure of a matched filter in cascade with another filter. Furthermore, the semi-infinite convex programming problem is converted into an equivalent finite dual optimization problem, which can be solved by the optimization methods developed. Another issue, which relates to the continuous-time optimal filter design problem, is the design of robust optimal EC filters. The robustness issue arises because the solution of the EC filtering problem lies on the boundary of the feasible region. Thus, any disturbance in the prescribed input signal or errors in the implementation of the optimal filter are likely to result in the output constraints being violated. A detailed formulation and a corresponding design method for improving the robustness of optimal EC filters are given.Finally, an adaptive algorithm suitable for a stochastic environment is presented. The convergence properties of the algorithm in a stochastic environment are established.
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Martin, Leonardo Curi. "Identificação de SNPs para uma anomalia de desenvolvimento em E. grandis e seus efeitos na estrutura proteica e interatoma /." Botucatu, 2015. http://hdl.handle.net/11449/132200.
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Orientador: Celso Luís MarinoCoorientador: Marcio Luis Acencio
Banca: Douglas Silva Domingues
Banca: Iraê Amaral Guerrini
Banca: Esteban Roberto Gonzales
Banca: Edson Luiz Furtado
Resumo: Espécies de Eucalyptus têm sido utilizadas com sucesso para plantios florestais devido ao seu rápido crescimento, sua capacidade de adaptação às diversas condições climáticas e pelo seu potencial econômico na produção de energia, fibra e madeira sólida, reduzindo assim a pressão sobre as florestas tropicais e a biodiversidade associada. Investimentos em pesquisas e desenvolvimento estão sendo realizados pelo setor florestal, no intuito de aumentar os ganhos de produtividade através da pesquisa na área da biologia molecular. Visto que características anômalas nas progênies podem gerar perdas na produtividade, a identificação e caracterização dos genes relacionados a anomalias são muito importantes no auxílio em programas de melhoramento genético. Ao realizar um cruzamento controlado de Eucalyptus grandis, a empresa Suzano Papel e Celulose detectou uma anomalia com segregação mendeliana 3:1 (normais:anômalas) na progênie. As características eram bem significativas se comparadas com as plantas normais, tais como diferenças na altura, diâmetro da base do caule, tamanho das folhas e morte em poucos meses. Estudos anteriores identificaram uma marca molecular ligada à anomalia, e análises de comparação da sequência contra o banco de dados de eucalipto demonstrou identidade com proteínas da família Bet v1 PR10 (Pathogenesis-related protein 10), embora não estivesse claro o envolvimento deste gene no desenvolvimento da anomalia. Outros estudos traçaram o perfil transcricional dos fenótipos contrastantes pela técnica de RNAseq. Dentre os genes diferencialmente expressos, através do enriquecimento funcional, destacaram-se os pertencentes as famílias Bet v1, quitinase classe I e taumatina, todos relacionados à resposta contra patógenos, sugerindo que a anomalia seja causada pela ativação do sistema imune da planta (resposta autoimune). Com o intuito de se obter mais informações sobre à patogênese da...
Abstract: Eucalyptus species have been successfully used for forest plantations. Some intrinsic features such as rapid growth, adaptability to various weather conditions and economic potential in energy production, fiber and solid wood, help to reduce pressure on tropical forests and associated biodiversity. Investments in research and development on molecular biology arebeing carried out by forestry sector in order to increase productivity gains. Since anomalous characteristics of progeny may generate productivity loss, gene identification linked to abnormalities are crucial for breeding programs. During a controlled crossing with Eucalyptus grandis, the Suzano Papel e Celulose enterprise detected an atypical Mendelian segregation 3: 1 (normal: abnormal). Significant phenotypic differences concerning height, stem base diameter, and leaf size appeared, as well as an unusual early death, when compared to normal plants. Previous studies identified a molecular tag attached to this anomaly. Sequence comparison analysis of eucalyptus database showed identity with Bet v1 PR10 protein family (Pathogenesis-related protein 10). However, gene involvement in developing such aberration is undetermined. Other studies found a transcriptional profile of contrasting phenotypes by RNAseq technique. Among differentially expressed genes by functional enrichment highlighted those belonging to Bet v1 families, chitinases class I, and thaumatin, all related to pathogenic response. This fact suggests that aberration is caused by the plant immune system activation (autoimmune response). To investigate the pathogenesis of such genetic disorder, three approaches were adopted: (i) SNPs identification among the differentially expressed genes of Bet v1 families, chitinase, and thaumatin, (ii) miRNAs identification with potential binding to mRNAs differentially expressed genes, and (iii) check of possible influence of differentially expressed gene products on ...
Doutor
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Martin, Leonardo Curi [UNESP]. "Identificação de SNPs para uma anomalia de desenvolvimento em E. grandis e seus efeitos na estrutura proteica e interatoma." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/132200.
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000851181.pdf: 995768 bytes, checksum: 291b7a6204ae963d850eb7c3b74f4c19 (MD5)Espécies de Eucalyptus têm sido utilizadas com sucesso para plantios florestais devido ao seu rápido crescimento, sua capacidade de adaptação às diversas condições climáticas e pelo seu potencial econômico na produção de energia, fibra e madeira sólida, reduzindo assim a pressão sobre as florestas tropicais e a biodiversidade associada. Investimentos em pesquisas e desenvolvimento estão sendo realizados pelo setor florestal, no intuito de aumentar os ganhos de produtividade através da pesquisa na área da biologia molecular. Visto que características anômalas nas progênies podem gerar perdas na produtividade, a identificação e caracterização dos genes relacionados a anomalias são muito importantes no auxílio em programas de melhoramento genético. Ao realizar um cruzamento controlado de Eucalyptus grandis, a empresa Suzano Papel e Celulose detectou uma anomalia com segregação mendeliana 3:1 (normais:anômalas) na progênie. As características eram bem significativas se comparadas com as plantas normais, tais como diferenças na altura, diâmetro da base do caule, tamanho das folhas e morte em poucos meses. Estudos anteriores identificaram uma marca molecular ligada à anomalia, e análises de comparação da sequência contra o banco de dados de eucalipto demonstrou identidade com proteínas da família Bet v1 PR10 (Pathogenesis-related protein 10), embora não estivesse claro o envolvimento deste gene no desenvolvimento da anomalia. Outros estudos traçaram o perfil transcricional dos fenótipos contrastantes pela técnica de RNAseq. Dentre os genes diferencialmente expressos, através do enriquecimento funcional, destacaram-se os pertencentes as famílias Bet v1, quitinase classe I e taumatina, todos relacionados à resposta contra patógenos, sugerindo que a anomalia seja causada pela ativação do sistema imune da planta (resposta autoimune). Com o intuito de se obter mais informações sobre à patogênese da...
Eucalyptus species have been successfully used for forest plantations. Some intrinsic features such as rapid growth, adaptability to various weather conditions and economic potential in energy production, fiber and solid wood, help to reduce pressure on tropical forests and associated biodiversity. Investments in research and development on molecular biology arebeing carried out by forestry sector in order to increase productivity gains. Since anomalous characteristics of progeny may generate productivity loss, gene identification linked to abnormalities are crucial for breeding programs. During a controlled crossing with Eucalyptus grandis, the Suzano Papel e Celulose enterprise detected an atypical Mendelian segregation 3: 1 (normal: abnormal). Significant phenotypic differences concerning height, stem base diameter, and leaf size appeared, as well as an unusual early death, when compared to normal plants. Previous studies identified a molecular tag attached to this anomaly. Sequence comparison analysis of eucalyptus database showed identity with Bet v1 PR10 protein family (Pathogenesis-related protein 10). However, gene involvement in developing such aberration is undetermined. Other studies found a transcriptional profile of contrasting phenotypes by RNAseq technique. Among differentially expressed genes by functional enrichment highlighted those belonging to Bet v1 families, chitinases class I, and thaumatin, all related to pathogenic response. This fact suggests that aberration is caused by the plant immune system activation (autoimmune response). To investigate the pathogenesis of such genetic disorder, three approaches were adopted: (i) SNPs identification among the differentially expressed genes of Bet v1 families, chitinase, and thaumatin, (ii) miRNAs identification with potential binding to mRNAs differentially expressed genes, and (iii) check of possible influence of differentially expressed gene products on ...
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Karimi, Fawad [Verfasser]. "Towards Realtime Observation of Interatomic Coulombic Decay via XUV Pump - THz Probe Streaking / Fawad Karimi." München : Verlag Dr. Hut, 2019. http://d-nb.info/1190421941/34.
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Moualek, Idir. "Intelligent decision support systems for interative decision making in complex environments applied to regional planning." Thesis, University of Nottingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243349.
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Spoladore, Larissa. "Identificação de interatores putativos envolvidos na localização de proteínas de duplo direcionamento em Arabidopsis thaliana." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-28062011-153024/.
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A maioria das proteínas organelares são codificadas pelo núcleo, sintetizadas no citosol e direcionadas especificamente ao seu destino final. O direcionamento aos diferentes subcompartimentos subcelulares é feito por uma complexa e ampla maquinaria que envolve sequências de direcionamento, proteínas citossólicas e receptores organelares específicos. Entretanto, relativamente pouco se conhece sobre o processo na qual uma proteína recém sintetizada é transportada ao seu destino final. Parte significativa das proteínas destinadas às organelas possui a informação necessária ao seu transporte localizada na extremidade N-terminal. Vários estudos têm buscado caracterizar as etapas que envolvem a localização de uma proteína, desde os estágios iniciais após a sua síntese até os fatores que regulam o seu correto endereçamento. Modificações pós-traducionais, regiões 5-UTR, região C-terminal, transporte por vias alternativas e interações proteína-proteína podem agir na localização subcelular de proteínas. O estudo de redes biomoleculares se tornou um dos focos de estudo da biologia de sistemas e demonstra um enorme potencial na descoberta de diversos processos biológicos, como as interações proteína-proteína. As proteínas que possuem duplo direcionamento (DD) em Arabidopsis thaliana foram analisadas em redes de interação proteína-proteína (PPI) e proteínas que interagem com proteínas de DD foram escolhidas quanto a função e localização para a verificação de um eventual papel dessas proteínas na localização subcelular de outras proteínas. Para tanto, foram realizadas varreduras em ensaios de duplo-híbrido em levedura para os genes de GRF9 (14-3-3) e ATH7 (tiorredoxina tipo h). Os resultados para GRF9 incluem as proteínas peroxidase PRXR1 e dihidrolipoamida acetiltransferase. Já os resultados para ATH7 mostram a interação com glutamina sintetase (AT5G35630.3). A combinação dos estudos in silico com a varredura via duplo-híbrido de levedura abrem novas perspectivas no entendimento do controle da localização subcelular de proteínas.Most organellar proteins are nuclear encoded, synthesized in the cytosol and then targeted to their destination. Specific subcellular targeting is conducted by a complex machinery for the specific localization of the proteins, which includes targeting sequences, cytosolic proteins and specific organelar receptors. However, little is known about the process that happens from the synthesis of a protein and the transport to its final destination. Most organellar proteins contain the information for their localization in the N-terminal sequence. Many studies have searched to characterize the steps involved in protein targeting, from the early stages after its synthesis to the cytosolic factors regulating its correct localization. Post-translational modifications, 5-UTR regions, the C-terminal extension on the protein, alternative transport pathways and proteinprotein interactions may influence the subcellular location of some proteins. The use of biomolecular netwoks has become one of the main focus of systems biology studies and possess a major potential in the discovery of several biological processes, such as protein-protein interactions (PPI). Dual-targeted (DT) proteins in Arabidopsis thaliana were analyzed through a PPI network, and the proteins displaying interactions with DT proteins were selected by their funtion and location. The selected proteins were analyzed for their eventual role in the subcellular targeting of other proteins. Screenings in yeast two-hibrid assays were performed for the genes GRF9 (14-3-3) and ATH7 (h-type thioredoxin). The results for GRF9 include a peroxidase (PRXR1) and dihydrolipamide acetyltransferase. The results for ATH7 include glutamine synthetase (AT5G35630.3). Combination of in silico analysis with yeast two-hibrid screenings provide new perspectives for understanding the control of subcellular localization.
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Perriot, Romain. "Development of Interatomic Potentials for Large Scale Molecular Dynamics Simulations of Carbon Materials under Extreme Conditions." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4384.
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The goal of this PhD research project is to devise a robust interatomic potential for large scale molecular dynamics simulations of carbon materials under extreme conditions. This screened-environment dependent reactive empirical bond order potential (SED-REBO) is specifically designed to describe carbon materials under extreme compressive or tensile stresses. Based on the original REBO potential by Brenner and co workers, SED-REBO includes reparametrized pairwise interaction terms and a new screening term, which serves the role of a variable cutoff. The SED-REBO potential overcomes the deficiencies found with the most commonly used interatomic potentials for carbon: the appearance of artificial forces due to short cutoff that are known to create erroneous phenomena including ductile fracture of graphene and carbon nanotubes, which contradicts the experimentally observed brittle character of these materials. SED-REBO was applied in large scale molecular dynamics simulations of nanoindentation of graphene membranes and shock-induced compression of diamond. It was shown in the first computational experiment that graphene membranes exhibit a non-linear response to large magnitude of indentation, followed by a brittle fracture in agreement with experiments. The strength of graphene was determined using the kinetic theory of fracture, and the crack propagation mechanisms in the material were identified. It was found in large-scale shock simulations that SED-REBO improves the predictive power of MD simulations of carbon materials at extreme conditions.
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Bock, Florian. "Active learning of interatomic potentials to investigate thermodynamic and elastic properties of Ti0.5Al0.5N at elevated temperature." Thesis, Linköpings universitet, Teoretisk Fysik, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-176587.
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With the immense increase in the computational power available for the material science community in recent years, a range of new discoveries were made possible. Accurate investigations of large scale atomic systems, however, still come with an extremely high computational demand. While the recent development of Graphics Processing Unit (GPU) accelerated supercomputing might offer a solution to some extent, most well known electronic structure codes have yet to be fully ported to utilize this new power. With a soaring demand for new and better materials from both science and industry, a more efficient approach for the investigation of material properties needs to be implemented. The use of Machine Learning (ML) to obtain Interatomic Potentials (IP) which far outperform the classical potentials has increased greatly in recent years. With successful implementation of ML methods utilizing neural networks or Gaussian basis functions, the accuracy of ab-initio methods can be achieved at the demand of simulations with empirical potentials. Most ML approaches, however, require high accuracy data sets to be trained sufficiently. If no such data is available for the system of interest, the immense cost of creating a viable data set from scratch can quickly negate the benefit of using ML. In this diploma project, the elastic and thermodynamic properties of the Ti0.5Al0.5N random alloy at elevated temperature are therefore investigated using an Active Learning (AL) approach with the Machine Learning Interatomic Potentials (MLIP) package. The obtained material properties are found to be in good agreement with results from computationally demanding ab-initio studies of Ti0.5Al0.5N, at a mere fraction of the demand. The AL approach requires no high accuracy data sets or previous knowledge about the system, as the model is initially trained on low accuracy data which is removed from the training set (TS) at a later stage. This allows for an iterative process of improving and expanding the data set used to train the IP, without the need for large amounts of data.
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Cade, Steven C. "An investigation of the interatomic bonding characteristics of a Ti - 51at.% Al alloy by X-ray diffraction." Thesis, Monterey, California. Naval Postgraduate School, 1991. http://hdl.handle.net/10945/28311.
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Orlat, Simon. "Development of an interatomic potential for the study of the thermodynamic properties of oxide coumpounds containing americium." Thesis, KTH, Fysik, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-288982.
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For the purpose of americium recycling, the effect of americium content on the nuclear fuel behaviour needs to be investigated. Atomic scale simulations and classical molecular dynamic simulations provide a tool of choice for the study of thermophysical properties of the nuclear fuel. In this work, we fitted a new interatomic empirical potential for (U,Am)O2 based on the CRG formalism. Our work enabled us to propose at the same time a new potential for the study of the Am-O system. The proposed potentials show good agreement with lattice parameters and enthalpy increments. We finally computed the heat capacity of (U,Am)O2 from 350 K to 3200 K for 0, 10, 20, 30, 40 and 50% americium contents using the potential obtained. The heat capacities calculated reveal a Bredig transition, as seen in UO2 and (U,Pu)O2. This transition shifts toward lower temperatures and its peak decreases in intensity when the Am content increases.För americium-återvinning måste effekten av americiuminnehåll på kärnbränslets beteende undersökas. Simulering på atomskala med klassisk molekylärdynamik utgör ett utmärkt verktyg för att studera kärnbränslets termofysikaliska egenskaper. I detta arbete anpassade vi en ny interatomär empirisk potential för (U,Am)O2 baserat på CRG-formalismen. Vårt arbete gjorde det möjligt för oss att samtidigt föreslå en ny potential för studier av Am-O-systemet. De föreslagna potentialerna visade bra överensstämmelse med gitterparametrar och entalpitillskott under valideringen. Vi beräknade slutligen värmekapaciteten för (U,Am)O2 från 350 K till 3200 K för 0, 10, 20, 30, 40 och 50% amerciuminnehåll med den nya potentialen. Den beräknade värmekapaciteten avslöjade att en Bredig-övergång som ses i UO2 och (U,Pu)O2. Denna övergång växlar till lägre temperaturer och dess topp minskar i intensitet när americiuminnehållet ökar.
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Wu, Lulu. "Um método para modificar vias de sinalização molecular por meio de análise de banco de dados de interatomas." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-22082015-085947/.
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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.
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Fellinger, Michael Richard. "First Principles-Based Interatomic Potentials for Modeling the Body-Centered Cubic Metals V, Nb, Ta, Mo, and W." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1365516163.
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Schnorr, Kirsten [Verfasser], and Robert [Akademischer Betreuer] Moshammer. "XUV Pump-Probe Experiments on Electron Rearrangement and Interatomic Coulombic Decay in Diatomic Molecules / Kirsten Schnorr ; Betreuer: Robert Moshammer." Heidelberg : Universitätsbibliothek Heidelberg, 2014. http://d-nb.info/1177811189/34.
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Stumpf, Vasili [Verfasser], and Lorenz S. [Akademischer Betreuer] Cederbaum. "Neutralization and relaxation of cations in an environment driven by interatomic decay processes / Vasili Stumpf ; Betreuer: Lorenz S. Cederbaum." Heidelberg : Universitätsbibliothek Heidelberg, 2017. http://d-nb.info/1180738772/34.
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Tian, Yongzhe. "Applications of Slattery - Lagoudas' theory for the stress deformation behavior." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4252.
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The thermodynamics of three-dimensional, single-component elastic crystalline
solids was developed by Slattery and Lagoudas (2005). Considering the inïnitesimal
deformations, the stress can be expressed as a function of the lattice vectors and
density in the reference configuration and ù(I;mn), which is defined as the derivative of
specific Helmoholtz free energy with respect to the I(mn). Using the Cauchy - Born rule
to connect the interatomic potential energy and the specific Helmholtz free energy, it is
possible to calculate the elastic properties of both nano-scale materials such as carbon
nanotubes and macro-scale materials such as diamond and silicon. In this study, we
used Tersoî (1988a) - Brenner (1990b) Potential, Tersoî (1988b) potential and Finnis
and Sinclair (1984) potential for carbon, silicon, and vanadium systems respectively.
Using the interatomic potentials to describe the specific Helmholtz free energy, the
elastic properties of graphite, diamond, silicon and vanadium were calculated. This
method was also extended to the calculation of Young's modulus of single-walled
carbon nanotubes (SWCNTs), which are composed of a two dimensional array of
carbon atoms. For SWCNT, we get good agreement with the available experimental
data. For diamond and silicon, C11 and C12 were consistent with both the superelastic
model and the experimental data. The difference of C44 between the calculation and
experimental data was due to accuracy of the potential functions.
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Sousa, Jaqueline Zaia de. "InterVis: um sistema para geração e exploração interativas de visualizações de informação." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/100/100131/tde-24112016-123123/.
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Devido ao crescimento acelerado da quantidade de dados disponíveis para análise hoje, é comum lidar com grandes conjuntos de dados, por vezes complexos demais para serem interpretados na sua forma bruta. Por isso, as técnicas de Visualização de Informação têm o objetivo de facilitar para o ser humano a tarefa de análise e interação dos dados por meio da sua abstração em forma gráfica. Justificado pela necessidade de dar autonomia ao usuário final na criação de visualizações, este trabalho pretende delinear a importância da participação do usuário na criação e suporte à abstração da informação em forma gráfica. Para isso, foi desenvolvido o InterVis um sistema para criação interativa de visualizações de informação a partir de dados dinâmicos, que visa a permitir que o usuário final possa gerar e editar visualizações de acordo com a sua necessidade, independentemente da natureza da informação que deve ser analisada. O sistema foi testado utilizando o questionário USE a fim de verificar se a criação interativa de visualizações de informação, sem programação, aliada ao conhecimento do usuário sobre o domínio da aplicação, é mais eficiente da perspectiva da usabilidade sem perda significativa de flexibilidade. Os testes envolveram a execução de tarefas por indivíduos de um grupo de usuários. Todos os usuários conseguiram realizar todas as tarefas de criação e exploração em tempo hábil e avaliaram positivamente o sistema, além de terem sugerido diversas melhorias e novas funcionalidades. É possível concluir que o InterVis atualmente já atende às expectativas iniciais do trabalho, ainda que haja pontos a serem aprimorados em trabalhos futurosBecause of the growing amount of data available for analysis today, it is common to deal with large data sets, often too complex to be interpreted in their brute form. That is why Information Visualization techniques exist, to facilitate the analysis and interaction with data by humans through graphical abstractions. Motivated by the need to allow end users the autonomy to generate and edit visualizations, this work aims to underscore the importance of end user participation in the creation and support of these graphical abstractions of data. For this purpose, it was developed a system for interactive creation of Information Visualizations based on dynamic data, which aims to allow the final user to generate e edit visualizations according to their need and independently of the nature of the information that should be analyzed. This system was tested using the USE questionnaire, to verify whether this interactive creation of Information Visualizations, without programming, allied to the user knowledge of each applications domain, will be more efficient from the perspective of usability without significant loss of flexibility, as expected. The tests were compound of the tasks execution by individuals of a users group. All the users were able to conclude all tasks of creation and exploration in due time and evaluated positively the system, besides they have been suggested diverse improvement and new functionalities. It is possible to conclude that InterVis already fulfills the initial expectations of this work, although there are still points to be refined in future work
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Ben, Ltaief Ltaief [Verfasser]. "Interatomic Coulombic decay in noble gas clusters of varying sizes investigated by photon-induced (dispersed) fluorescence spectrometry / Ltaief Ben Ltaief." Kassel : Universitätsbibliothek Kassel, 2018. http://d-nb.info/1162155019/34.
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Emami, Fatemesadat. "Thermodynamically Consistent Interatomic Potentials for Silica to Design Specifically Binding Peptides: Role of Surface Chemistry, PH, and Amino Acid Sequence." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1366597654.
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Acharya, Sudip. "Development of embedded atom method interatomic potentials for Ge-Sn-Si ternary and constituent binary alloys for modeling material crystallization." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1598820359123203.
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Groth, Gerson Eduardo. "Attribute field K-means : clustering trajectories with attribute by fitting multiple fields." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2016. http://hdl.handle.net/10183/150038.
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A enorme quantidade de trajetórias contendo múltiplas dimensões, e o aumento de complexidade que esses dados ocasionam, impõem desafios ao visualizar e analisar estas informações. Visualização de Trajetórias deve lidar com alterações tanto na dimensão de espaço quanto na dimensão de tempo. Porém, os atributos de cada trajetória podem ocasionar uma melhor compreensão sobre seus comportamentos e características. Dessa forma, eles não deveriam ser neglicenciados. Neste trabalho, nós abordamos este problema interpretando séries temporais multivariadas com foco nos atributos das trajetórias, em um espaço de configuração que codifica um explícito relacionamento entre as variáveis das séries temporais. Nós propomos uma técnica original de clusterização de trajetórias, chamada Attribute Field k-means (AFKM). Ela usa um espaço de configuração dinâmica para gerar clusters baseados nos atributos e parâmetros definidos pelo usuário. Além disso, incorporando uma interface de sketching, nosso método é capaz de encontrar clusters que aproximam os exemplos de trajetórias desenhados pelo usuário. Nós também desenvolvemos um protótipo para explorar as trajetórias e clusters gerados pelo AFKM, de um modo interativo. Nossos resultados, em sintéticos e reais conjuntos de dados de séries temporais, provam a eficiência e o poder de visualização do nosso método.The amount of high-dimensional trajectory data and its increasing complexity imposes a challenge when visualizing and analysing this information. Trajectory Visualization must deal with changes both in space and time dimensions, but the attributes of each trajectory may provide insights about its behavior and important aspects. Thus, they should not be neglected. In this work, we tackle this problem by interpreting multivariate time series as attribute-rich trajectories in a configuration space that encodes an explicit relationship among the time series variables. We propose a novel trajectory-clustering technique called Attribute Field k-means (AFKM). It uses a dynamic configuration space to generate clusters based on attributes and parameters set by the user. Furthermore, by incorporating a sketching-based interface, our approach is capable of finding clusters that approximates the input sketches. In addiction, we developed a prototype to explore the trajectories and clusters generated by AFKM in an interactive manner. Our results on synthetic and real time series datasets prove the efficiency and visualization power of our approach.
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GONDHALEKAR, ROHIT H. "A CONSTITUTIVE MODEL FOR NANOSTRUCTURES BASED ON SPATIAL SECANT." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1120144896.
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