Orientador: Ricardo Aparicio / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-24T05:53:06Z (GMT). No. of bitstreams: 1 Reis_MarceloAugustodos_D.pdf: 42698206 bytes, checksum: fa5cd41ff5c44a71b42dd07db4a8fd79 (MD5) Previous issue date: 2013 / Resumo: Neste trabalho de tese, o problema da caracterização estrutural de proteínas foi abordado de maneira contextualizada e com um viés em modelagem computacional utilizando vínculos experimentais obtidos com a técnica de espalhamento de raios X a baixos ângulos (SAXS, Small-Angle X-ray Scattering). Parte das pesquisas foram concentradas na caracterização estrutural da proteína SurE de Xylella fastidiosa (XfSurE) por técnicas experimentais e computacionais. Estudos estruturais da XfSurE realizados com a técnica de SAXS apontaram para um arranjo tetramérico da enzima apo e, do nosso conhecimento, foi a primeira estrutura em solução descrita na literatura para esta família de proteínas. Quando associada às técnicas computacionais ¿ como, por exemplo, análise de modos normais de vibração¿a interpretação das análises por SAXS foi realçada. Neste caso, o vínculo experimental imposto pela curva I(q) possibilitou que uma estrutura em solução fosse modelada apenas com o uso de um único modo normal, cujo efeito estaria relacionado com as possíveis transições alostéricas de XfSurE. Em outra frente de trabalho, um novo programa denominado SAXSTER foi desenvolvido. SAXSTER tem a habilidade de gerar modelos estruturais mais prováveis para uma proteína-alvo a partir de alinhamentos ótimos obtidos por threading e de estruturas similares identificadas em um banco de dados, com o auxílio de SAXS. A partir dos dados de entrada, é realizada uma busca no Protein Data Bank para que a estrutura da proteína-alvo possa ser predita. O programa foi testado para 553 proteínas não redundantes. Foi demonstrado que SAXSTER pode melhorar consistentemente o resultado global da classificação dos alinhamentos, com p-valores que variam de 10 a 10. De acordo com TM-score médio, conclui-se que SAXSTER tende a melhorar o desempenho preditivo conforme a estrutura da proteína-alvo se afasta da forma globular / Abstract: In this work, the protein structure problem was approached from two different perspectives: from the computational modeling to the experimental data mainly collected by Small-Angle X-ray Scattering technique (SAXS) whose data were also used as constraint for modelling. Part of the research was focused on the structural characterization of the protein SurE of Xylella fastidiosa (XfSurE) by experimental and computational techniques. Structural studies of XfSurE performed by SAXS technique indicated a tetrameric arrangement of the apo enzyme and to our knowledge, this was the first solution structure of a SurE protein described in the literature. When combined with computational techniques ¿ for instance, normal mode analysis ¿ the interpretation of SAXS analysis was enhanced. In that case, the experimental constraints imposed by the I(q) curve allowed to reach a new structure model that fits the SAXS profile using only a single normal mode. This effect would be associated with the possible allosteric transitions of the XfSurE. It was also developed a new program called SAXSTER (SAXS-assisted multi-source ThreadER). SAXSTER has the ability to generate more likely structural models for the target protein from optimal alignments obtained by threading and similar structures identified in the Protein Data Bank aided by SAXS. The program was tested on 553 nonredundant proteins. It was shown that SAXSTER can consistently improve the overall classification of the alignments, with p-values ranging from 10 to 10. According to average TM-score, a more promising use of the SAXSTER algorithm would be to improve the template recognition results for protein whose structure is more rod-like than globular-like ones / Doutorado / Físico-Química / Doutor em Ciências

Cette thèse porte sur la modélisation thermomécanique 3D en configuration de fraisage. Afin de déterminer, pour chaque orientation de la plaquette et à chaque position angulaire de l’outil, le torseur d’action complet (efforts et moments) trois grandes parties ont été développées dans ce manuscrit.En se basant sur les lignes de glissement dans les trois zones de coupe, un modèle de coupe orthogonale a été développé. Le rayon d’acuité est intégré dans la modélisation et les résultats du modèle sont sensibles à ce paramètre. Le modèle a été validé par une confrontation avec des essais de rabotage.Pour deux types de plaquette, à arêtes droite et ronde, l’étude cinématique le long de l’arête de coupe a menée à la détermination du torseur cinématique instantanée en chaque point. Cette partie a permis de définir une nouvelle composante de vitesse de coupe dépendante de la position angulaire de l’outil. L’inclinaison de l’arête génère une vitesse parallèle à l’arête de coupe (perpendiculaire au plan de coupe en configuration orthogonale) qui participe au comportement cinématique de la matière dans les zones de cisaillement primaire et secondaire.Une modélisation volumique 3D dans les deux zones de coupe primaire et secondaire a permis de définir la cartographie de déformation et de vitesse de déformation. Cette approche a été basée sur les données cinématiques et les conditions aux limites appropriées. Les gradients de contraintes et de vitesses trouvés sont à l’origine de l’apparition des moments de coupe. / This thesis is focused on 3D thermomechanical modeling in milling configuration. In order to determine, for each insert orientation and each tool angular position, the complete actions torsor (forces and moments) three parts have been developed in this work.Based on the slip lines in the three cutting areas, an orthogonal cutting model was developed. The tool edge radius is built in modeling and model results are sensitive to this parameter. The model was validated by comparison with experimental tests.For two types of insert, with straight and round edge, the kinematic study along the cutting edge allowed to determine the instantaneous kinematic torsor at each point. This part has defined a new cutting velocity component dependent of tool angular position. The inclination of the edge generates a parallel velocity to the cutting edge (perpendicular to the cutting plane in orthogonal configuration) that participates in the kinematic behavior of the material in the primary and secondary shear zones.A 3D solid modeling in the primary and secondary cutting zones helped to define the cartography of strain and strain rate. This approach was based on kinematic data and appropriate boundary conditions. The gradients of stresses and velocities are the source of the appearance of the cutting moments.

Making 3D models with polygon modeling is the most common technique used for a 3D animated movie production, but there are also other good modeling techniques to work with. The aim of this thesis is to examine which of three chosen modeling technique is most appropriate to use for modeling a chair for a 3D animated movie production. I made three models of the same chair design and compared the results. The modeling technique used is polygon modeling, NURBS modeling and digital sculpting. A few factors were considered when I judged which one of the three techniques that was most suitable: The model's geometry, the workflow and the rendering (material and lightning). The three chairs were rendered in the same scene with the same lightning and settings. The results showed that the model's geometry and how smooth it is to work with the modeling technique matter most for judging which technique is the most appropriate. In addition, the results show that how the light falls and reflects the surface depends on how the geometry was placed on the model rather than which of the other modeling techniques that was used.

We consume more and more which also have led to an increase in the waste we most handle. In public environment, common solution have been to increase the size of the waste bin, but that’s not always an option. To big and it may interfere with the environment it placed in. Another approach is to compress the disposed waste and so increase the waste bins capacity without increasing the volume of the wastebin itself. BigBelly is one product which have embraced this apprach. It is a solar driven compressing waste bin commonly seen in big cities around the world. The problem is that some miner municipalities and private companies still are in need of a solution but don’t have the resources to obtain BigBellys or other similar solutions. One way to approach this market is to develop a waste bin without the electric usually expensive components and develop a less expensive compressible waste bin that’s still an effective choice. To understand the needs, both of those who dispose of waste publicly but also those who manage the waste bins, have interviews, observations, questionaries and focus groups been used to gather valuable data. This data have then been remade in terms of user needs and ranked according to importance by the users themselves and the project manager. Some highly ranked needs are: the waste bin is steady and robust, the waste bin can only be opened by those who handle/empty the waste bins, a manual compression can be performed by those who throw the waste, and a manual compression can be performed without any major effort.  By the method Design by analogies and a workshop held at Luleå University of Technology was ideas created. The three concepts with the highest potential were selected via Pugh’s selection matrix and tested according to efficiency and effectivity. The concept with the highest result was developed in Simens NX a CAD-program and then used as a template for the construction of a functional prototype. By testing and analyzing the prototype a product specification could be created. The final result, which is based on the prototype and the specification, consist of two rendered waste bins, developed towards compression in public environment. The compactor is based on a scissor-lift design modified to expand and so compress waste by gravity and contract by the energy of the users. Both models are estimated to enhance the capacity of 170-200% compared with a waste bin none-compressing waste bin of the same size. Model 1 requires a force of 196N from the user during use while model 2 requires force of 123N.

Ce travail de thèse concerne l'articulation trapézométacarpienne. La première partie du travail a concerné l'étude de la morphogénèse de l'arche palmaire par modélisation géométrique 3D. Cinq embryons ont été utilisés. Les résultats de cette étude montre le caractère asymétrique et l'opposition précoce du pouce chez l'embryon humain. La deuxième partie a consisté à partir d'un protocole IRM spécifique sur 5 sujets sains à déterminer la cinématique 3D de l'articulation trapézo-métacarpienne en utilisant les axes hélicoïdaux. La troisième partie, suivant le même protocole sur sujets pathologiques à partir d'image scanner a permis d'évaluer l'effet des différents types de traitement en cas de rhizarthrose. Les résultats trouvent leur application dans l'évaluation quantitative des pathologies de l'articulation trapézo-métacarpienne ainsi que dans le développement des prothèses. / This work concerned the first carpo-metacarpal joint. The first part of this work was the study of the morphogenesis of the palmar arch using three-dimensional geometrie modeling. Five embryos were used for this study. The results of this study support the hypothesis that opposition and asymmetry of the thumb appears early in embryological development. In the second part, with specifie MRI protocol on 5 normal subjects, the objective was to quantify the 3D motion of the trapezo-metacarpal joint using helical axes theory. In the last part, using the same protocol on pathological subjects (CT scan images), the objective was to evaluate the effect of different type of treatment of the first carpo­ metacarpal arthritis.The results of the work are of interest for the quantitative evaluation of pathological trapezo-metacarpal joint and in the development of prosthesis.

Orientador: Maria Gabriela Caffarena Celani / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Civil, Arquitetura e Urbanismo / Made available in DSpace on 2018-08-24T11:31:11Z (GMT). No. of bitstreams: 1 BarbosaNeto_Wilson_M.pdf: 18612146 bytes, checksum: d8fbaaa3aaa7ff8e9008c22519dc03e7 (MD5) Previous issue date: 2013 / Resumo: A utilização de técnicas de Fabricação Digital está cada vez mais presente no campo da arquitetura e construção por todo o mundo, devido aos avanços tecnológicos que os sistemas CAD (Computer-aided Design) e CAM (Computer-aided Manufacturing) têm proporcionado aos processos de concepção e produção da obra arquitetônica. As possibilidades que essas ferramentas oferecem aos arquitetos e projetistas abrem caminho para novas abordagens de projeto, que permitem o uso da produção automatizada sem a necessidade de uma padronização tão rígida como aquela imposta pelo sistema industrial. Entretanto, nota-se que a aplicação dos métodos de Fabricação Digital no processo de produção do espaço edificado no Brasil é lento, quando comparado a outros países onde a tecnologia necessária para o exercício da técnica já se encontra amplamente difundida. A presente pesquisa tem como foco investigar a aplicação da Fabricação Digital, por intermédio de processos file-to-factory na produção arquitetônica de elementos para a construção civil, mais especificamente com o uso de técnicas subtrativas de corte 2D. Após um levantamento sobre o estado da arte da área e o desenvolvimento de dois estudos de caso, o método utilizado foi a pesquisa-ação, por meio de um exercício de aplicação do conceito file-to-factory. O processo de projeto foi documentado detalhadamente e analisado para a sistematização dos procedimentos, que servirão de referência para futuras aplicações no campo da arquitetura. Espera-se, com isso, contribuir para a divulgação dessas novas tecnologias na produção arquitetônica no cenário brasileiro / Abstract: The use of Digital Fabrication techniques is increasingly present in the field of architecture and construction throughout the world. Systems such as CAD (Computer-aided Design) and CAM (Computer-aided Manufacturing) have provided technological advances to the architectural design and production process. The possibilities that these tools provide to architects and designers introduce new design approaches, which allow the use of automated production without the rigid standardization imposed by the industrial system. However, it can be noticed that the use of Digital Fabrication methods in the built environment production process in Brazil is slow when compared to other countries where the technology is widely incorporated. This research focuses on investigating the application of Digital Fabrication, through file-to-factory processes in the production of architectural elements for the construction industry, specifically with the use of 2D subtractive cutting techniques. After a survey on the state of the art in the field and two case studies, the method used was an action research through a file-to-factory exercise. The design process was documented in detail and analyzed in order to systematize the procedures as a reference for future applications in architecture. As a result we expect to contribute to the dissemination of these new technologies in architectural production in the Brazilian scenario / Mestrado / Arquitetura, Tecnologia e Cidade / Mestre em Arquitetura, Tecnologia e Cidade

The work deals with the modeling of the parameters of solar power plants and the issue of solar energy with its use in the photovoltaic power plants. It uses the geographic information system named ArcGIS. In the beginning of the work, there is the theory. This theory is necessary to understanding the function of the photovoltaic cells, from the beginning to the photovoltaic panels construction. There were analyzed the conditions of the location of the photovoltaic panels in the Czech Republic. Furthermore, the work approaches the ArcGIS and its 3D modeling possibilities. The part of the work deals with the proposal for the selection process of the most suitable location to the photovoltaic panels installing. The main part of the work is the visualization of the 3D models of the locations of interest.

This diploma thesis deals with geometrical surfaces and their engineering aplications. The teoretic parts are focused on the definitions of basic concepts and mathematical descriptions of curves, surfaces and trans- formations. Further, the classification of geometrical surfaces is described as well as examples of their usage in technical practice with deep focus on screws, tools, gears and other parts of machines. The last part describes cre- ation process of four models for education. We used 3D printing technology and 3D modeling in Rhinoceros 3D software for the production of these mo- dels. Source codes and files with the 3D models can be found in electronic attachment. The thesis also includes photographic attachment with pictures of created models. 1

Electrical impedance imaging is an imaging technique which has the capability of revealing the spatial distribution of the electrical impedance inside biological tissues. Classical electrical impedance imaging including Electrical Impedance Tomography (EIT) typically has low resolution. Advances in electrical impedance imaging typically involve methods that either increase image resolution or image contrast. This study investigates the possibility of the resolution improvement for electrical impedance imaging using motion, and presents a novel high-resolution and calibrated impedance imaging method called Scanning electrical Impedance Imaging (SII). SII uses an electrical probe held at a known voltage and scanned over a thin sample immersed in a conductive medium on a grounded conducting plane to obtain high-resolution calibrated impedance images of samples. For system improvement and image reconstruction, a numerical model is developed to describe the SII system. This model simulates the measurement process by solving a 3-D electrostatic field at each scanning position using a modified approach of the finite difference method (FDM). The simulation consists of a quasi-statics problem involving inhomogeneous media with a complicated boundary condition. This 3-D model is used to optimize both the probe height and the shield-spacing for probe fabrication and also to evaluate system parameters including the frequency and the resistor in the peripheral circuit. Based on this model, an approach is also developed to quantifying conductivity values using the SII system. However, a large computational cost due to the motion involved in SII leads to challenges for a fast and accurate image reconstruction based on this 3-D model. Alternative fast models are derived as a replacement of the 3-D model for quick image reconstruction. In particular, the Modified Linear Approximation (MLA) involving two conductivity-weighted convolutions based on the reciprocity principle, explains the function of the special shield design introduced in the SII system reasonably well. Based on the MLA a nonlinear inverse method using total variation regularization and the Polak-Ribi'{e}re variant of the nonlinear conjugate-gradient method is developed for fast image reconstruction of the SII system. The inverse method is accelerated using convolution which eliminates the requirement of a numerical solver for the 3-D electrostatic field. 2-D images of small biological tissues and cells are measured using the SII system. The corresponding conductivity images are reconstructed using the MLA method. The successful improvement of resolution shown in both simulation and experimental results demonstrates that the idea of this approach can potentially be expanded to other imaging modalities for resolution improvement using motion.

<p>High-throughput phenotyping is a recent multidisciplinary research field that investigates the accurate acquisition and analysis of multidimensional phenotypes on large and diverse populations of plants. High-throughput phenotyping is at the crossroad between plant biology and computer vision, and profits from advances in plant modeling, plant reconstruction, and plant structure understanding. So far, most of the data analysis is done on 2D images, yet plants are inherently 3D shapes, and measurements made in 2D can be biased. For example, leaf angles change when they are reprojected in 2D images. Although some research works investigate the 3D reconstruction of plants, high-throughput phenotyping is still limited in its ability to automatically measure a large population of plants in 3D. In fact, plants are difficult to 3D reconstruct because they look self-similar, feature highly irregular geometries, and self-occlusion. </p> <p><br></p> <p>In this dissertation, we investigate the research question \textit{whether we can design and validate high-throughput phenotyping algorithms that take advantage of the 3D nature of the plants to outperform existing algorithms based on 2D images?} We present four contributions that address this question. First, we show a voxel 3D reconstruction pipeline and measure phenotypic traits related to canopy architecture over a population of 351 sorghum plants. Second, we show a machine learning-based skeletonization and segmentation algorithm for sorghum plants, which automatically learns from a set of 100 manually annotated plants. Third, we estimate individual leaf angles over a population of 1,098 sorghum plants. Finally, we present a sparse 3D reconstruction algorithm that can triangulate thousands of points of interest from up to 15 views without correspondences, even in the presence of noise and occlusion. We show that our approach outperforms single-view methods by using multiple views for sorghum leaf counting.</p> <p><br></p> <p>Progress made towards improving high-throughput phenotyping has the potential to benefit society with a better adaptation of crops to climate change, which will limit food insecurity in the world.</p>