Several scientific and technological advancements in radiation oncology have resulted in dramatic improvements in dose conformity and delivery to the target volumes using external beam radiation therapy (EBRT). However, radiation therapy acts as a double-edged sword leading to drastic side-effects, one of them being secondary malignant neoplasms in cancer survivors. The latency time for the occurrence of second cancers is around $10$-$20$ years. Therefore, it is very important to evaluate the risks associated with various types of clinically relevant radiation treatment protocols, to minimize the second cancer risks to critical structures without impairing treatment to the primary tumor volume. A widely used biologically motivated model (known as the initiation-inactivation-proliferation model) with heterogeneous dose volume distributions of Hodgkin's lymphoma survivors is used to evaluate the excess relative risks (ERR). There has been a paradigm shift in radiation therapy from purely photon therapy to other particle therapies in cancer treatments. The extension of the model to include the dependence of linear energy transfer (LET) on the radio-biological parameters and mutation rate for charged particle therapy is discussed. Due to the increase in the use of combined modality regimens to treat several cancers, it is extremely important to evaluate the second cancer risks associated with these anti-cancer therapies. The extension of the model to include chemotherapy induced effects is also discussed. There have been several clinical studies on early and late relapses of cancerous tumors. A tumor control probability (TCP) model with recurrence dynamics in conjunction with the second cancer model is developed in order to enable design of efficient radiation regimens to increase the tumor control probability and relapse time, and at the same time decrease secondary cancer risks. Evolutionary dynamics has played an important role in modeling cancer progression of primary cancers. Spatial models of evolutionary dynamics are considered to be more appropriate to understand cancer progression for obvious reasons. In this context, a spatial evolutionary framework on lattices and unstructured meshes is developed to investigate the effect of cellular motility on the fixation probability. In the later part of this work, this model is extended to incorporate random fitness distributions into the lattices to explore the dynamics of invasion probability in the presence and absence of migration.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A partir da análise das diversas versões de Malhas da Liberdade (1976-2008), obra de Cildo Meireles, o ensaio Cama de gato traça um percurso rizomático por entre as transformações e inflexões das estratégias políticas e de alteridade da produção do artista e, de modo mais amplo, de parte da recente arte brasileira. Atravessando aspectos como a história da arte, a subjetividade, a economia e a história, o ensaio faz uma leitura sobre as metaformoses dos modos de participação ativados e propostos pela prática artística, atentando para suas implicações políticas e ideológicas. Por entre a cama de gato de ideias e interpretações do ensaio estão, ainda, reflexões sobre a historiografia da arte brasileira e seu processo de internacionalização, além de uma preocupação com a relação entre arte, participação, alteridade, topologia, espaço social e democracia / Departing from the analysis of the various versions of Meshes of Freedom(1976-2008), artwork of Cildo Meireles, the essay Cats Cradle traces a rhizomatic path through the transformations and inflections of political and otherness strategies of the artist's work and, more broadly, of part of Brazilian recent art. Tresspassing aspects such as art history, subjectivity, economics and history, the essay reflects upon the metaformoses of the modes of participation proposed and activated by artistic practice, paying attention to their political and ideological implications. Through the cat bed of ideas and interpretations of this essay are also reflections on the historiography of Brazilian art and its internationalization process, as well as a concern with the relationship between art, participation, otherness, topology, social space and democracy

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A partir da análise das diversas versões de Malhas da Liberdade (1976-2008), obra de Cildo Meireles, o ensaio Cama de gato traça um percurso rizomático por entre as transformações e inflexões das estratégias políticas e de alteridade da produção do artista e, de modo mais amplo, de parte da recente arte brasileira. Atravessando aspectos como a história da arte, a subjetividade, a economia e a história, o ensaio faz uma leitura sobre as metaformoses dos modos de participação ativados e propostos pela prática artística, atentando para suas implicações políticas e ideológicas. Por entre a cama de gato de ideias e interpretações do ensaio estão, ainda, reflexões sobre a historiografia da arte brasileira e seu processo de internacionalização, além de uma preocupação com a relação entre arte, participação, alteridade, topologia, espaço social e democracia / Departing from the analysis of the various versions of Meshes of Freedom(1976-2008), artwork of Cildo Meireles, the essay Cats Cradle traces a rhizomatic path through the transformations and inflections of political and otherness strategies of the artist's work and, more broadly, of part of Brazilian recent art. Tresspassing aspects such as art history, subjectivity, economics and history, the essay reflects upon the metaformoses of the modes of participation proposed and activated by artistic practice, paying attention to their political and ideological implications. Through the cat bed of ideas and interpretations of this essay are also reflections on the historiography of Brazilian art and its internationalization process, as well as a concern with the relationship between art, participation, otherness, topology, social space and democracy

Dans le cadre du projet européen ENVISION (2010-2014) et en collaboration avec l'équipe CAS-PHABIO de l'IPNL, cette thèse constitue une contribution méthodologique et technique dans le domaine de la dosimétrie et de l'imagerie de contrôle par émission des positons (TEP) pour les organes en mouvement. Les méthodes actuelles utilisent le recalage déformable d'images CT pour estimer le mouvement des organes internes. Le recalage déformable permet d'estimer le déplacement de chaque voxel d'une image à une autre. La dose radio-thérapeutique ainsi que l'activité TEP sont accumulées sur des voxels. Ces approches ont des difficultés quand il s'agit de prendre en compte la variation de densité à l'intérieur des organes et l'aspect non-répétitif du mouvement respiratoire. Les travaux antérieurs de l'équipe ont permis de développer un premier modèle biomécanique complet du système respiratoire qui, corrélé avec des signaux externes, pourrait prendre en compte la variabilité du mouvement respiratoire. Cette thèse présente une approche qui permet d'intégrer un tel modèle biomécanique dans un système de planification de traitement pour l'hadronthérapie. Dans cette thèse, nous avons choisi d'investiguer de près l'utilisation des maillages tétraédriques déformables dans la dosimétrie et la reconstruction d'images TEP afin d'estimer les avantages et inconvénients de ce type de géométrie. En conclusion, notre approche peut être utilisée avec n'importe quel modèle de déformation basé sur une géométrie tétraédrique et dont le mouvement est décrit par le déplacement des nœuds des maillages et donc contrairement aux méthodes basés images, notre approche n'est pas nécessairement dépendante de l'existence des images internes à tout moment. Dans le futur, les méthodes développées dans cette thèse pourraient être utilisées avec un modèle biomécanique complet du système respiratoire afin de quantifier, par exemple, les effets de la variabilité de la respiration sur le dépôt de dose / Respiratory-induced organ motion is a technical challenge to nuclear imaging and to charged particle therapy dose calculations for lung cancer treatment in particular. Internal organ tissue displacements and deformations induced by breathing need to be taken into account when calculating Monte Carlo dose distributions as well as when performing tomographic reconstructions for PET imaging. Current techniques based on Deformable Image Registration (DIR) cannot fully take into account the density variations of the tissues nor the fact that respiratory motion is not reproducible. As part of the ENVISION (2010-2014) European project, in collaboration with the CAS-PHABIO team from IPNL (the Nuclear Physics Institute from Lyon), this PhD project presents a methodological contribution to physical dose calculations and PET-based treatment verification for hadron therapy in the case of moving tumours. Contrary to DIR-based methods where motion is described by relative voxel displacement, each organ is represented as a deformable grid of tetrahedra where internal motion is described by mesh vertex transformations calculated using continuum mechanics. First, this PhD project proposes a new method to calculate four dimensional dose distribution over tetrahedral meshes, which are deformed using biomechanical modeling based on Finite Element Analysis (FEA). The second part of the PhD is focused on motion compensation for PET image reconstruction using deformable tetrahedral meshes

Spatial statistics methods are widely used since several areas of knowledge such as environmental sciences, geology, agronomy, among others, involve the understanding of the spatial distribution of processes from spatially referenced data. With the advancement of Geographic Information Systems and the Global Positioning Systems this use has been extended. Many methods used in spatial statistics are computationally demanding, and therefore, the development of more computationally efficient methods has received a lot of attention in recent years. One such important development is the introduction of the integrated nested Laplace approximation method which is able to carry out Bayesian analysis in a more efficient way. The use of this method for geostatistical data is commonly done considering the stochastic partial differential equation approach that requires the creation of a mesh overlying the study area. This is the first and an important step since all results will depend on the choice of this mesh. As there is no formal and close way to specify the mesh, we investigate possible guidelines on how a suitable mesh is chosen for a specific problem. Through simulations studies, we tried to create guidelines for the construction of the mesh for random, regular and cluster data set and we aplly this guidelines in real data set. / Métodos de estatística espacial são amplamente utilizados, uma vez que várias áreas do conhecimento, como ciências ambientais, geologia, agronomia, entre outros, envolvem a compreensão da distribuição espacial de processos a partir de dados referenciados espacialmente. Com o avanço dos Sistemas de Informação Geográfica e dos Sistemas de Posicionamento Global, esse uso foi ampliado. Muitos métodos utilizados na estatística espacial são computacionalmente exigentes e, portanto, o desenvolvimento de métodos mais eficientes recebeu muita atenção nos últimos anos. Um desenvolvimento importante foi a introdução do método de aproximação de Laplace aninhado integrado, capaz de realizar análises Bayesianas de forma mais eficiente. O uso deste método para dados geoestatísticos é comumente feito considerando a abordagem de equações diferenciais parciais estocásticas que requer a criação de uma malha que cobre a área de estudo. Este é o primeiro e um importante passo, pois todos os resultados dependerão da escolha desta malha. Como não existe uma maneira formal e direta de especificar a malha, investigamos possíveis diretrizes sobre como uma malha adequada é escolhida para um problema específico. Através de estudos de simulações, tentamos criar diretrizes para a construção da malha para conjunto de dados aleatórios, regulares e de cluster e aplicamos essas diretrizes em conjunto de dados reais.

Measuring visual closeness of 3-D models is an important issue for different problems and there is still no standardized metric or algorithm to do it. The normal of a surface plays a vital role in the shading of a 3-D object. Motivated by this, we developed two applications to measure visualcloseness, introducing normal difference as a parameter in a weighted metric in Metro’s sampling approach to obtain the maximum and mean distance between 3-D models using 3-D and 6-D correspondence search structures. A visual closeness metric should provide accurate information on what the human observers would perceive as visually close objects. We performed a validation study with a group of people to evaluate the correlation of our metrics with subjective perception. The results were positive since the metrics predicted the subjective rankings more accurately than the Hausdorff distance.

In this thesis, we present new superconvergence properties of discontinuous Galerkin (DG) methods for two-dimensional hyperbolic problems. We investigate the superconvergence properties of the DG method applied to scalar first-order hyperbolic partial differential equations on triangular meshes. We study the effect of finite element spaces on the superconvergence properties of DG solutions on three types of triangular elements. Superconvergence is described for structured and unstructured meshes. We show that the DG solution is O(hp+1) superconvergent at Legendre points on the outflow edge on triangles having one outflow edge using three p- degree polynomial spaces. For triangles having two outflow edges the finite element error is O(hp+1) superconvergent at the end points of the inflow edge for an augmented space of degree p. Furthermore, we discovered additional mesh-orientation dependent superconvergence points in the interior of triangles. The dependence of these points on orientation is explicitly given. We also established a global superconvergence result on meshes consisting of triangles having one inflow and one outflow edges. Applying a local error analysis, we construct simple, efficient and asymptotically correct a posteriori error estimates for discontinuous finite element solutions of hyperbolic problems on triangular meshes. A posteriori error estimates are needed to guide adaptive enrichment and to provide a measure of solution accuracy for any numerical method. We develop an inexpensive superconvergence-based a posteriori error estimation technique for the DG solutions of conservation laws. We explicitly write the basis functions for the error spaces corresponding to several finite element solution spaces. The leading term of the discretization error on each triangle is estimated by solving a local problem where no boundary conditions are needed. The computed error estimates are shown to converge to the true error under mesh refinement in smooth solution regions. We further present a numerical study of superconvergence properties for the DG method applied to time-dependent convection problems. We also construct asymptotically correct a posteriori error estimates by solving local hyperbolic problems with no boundary conditions on general unstructured meshes. The global superconvergence results are numerically confirmed. Finally, the a posteriori error estimates are tested on several linear and nonlinear problems to show their efficiency and accuracy under mesh refinement. / Ph. D.

This Ph.D. thesis specifically deals with the issue of metamorphosis of 3D objects represented as 3D triangular meshes. The objective is to elaborate a complete 3D mesh morphing methodology which ensures high quality transition sequences, smooth and gradual, consistent with respect to both geometry and topology, and visually pleasant. Our first contributions concern the two different approaches of parameterization: a new barycentric mapping algorithm based on the preservation of the mesh length ratios, and a spherical parameterization technique, exploiting a Gaussian curvature criterion. The experimental evaluation, carried out on 3D models of various shapes, demonstrated a considerably improvement in terms of mesh distortion for both methods. In order to align the features of the two input models, we have considered a warping technique based on the CTPS C2a radial basis function suitable to deform the models embeddings in the parametric domain maintaining a valid mapping through the entire movement process. We show how this technique has to be adapted in order to warp meshes specified in the parametric domains. A final contribution consists of a novel algorithm for constructing a pseudo-metamesh that avoids the complex process of edge intersections encountered in the state-of-the-art. The obtained mesh structure is characterized by a small number of vertices and it is able to approximate both the source and target shapes. The entire mesh morphing framework has been integrated in an interactive application that allows the user to control and visualize all the stages of the morphing process

Triangle meshes have become an increasingly popular shape representation. Given the ease of standardization it allows and the proliferation of devices (scanners, range images ) that capture and output shape information as meshes, this representation is now used in applications such as virtual reality, medical imaging, rapid prototyping, digital art and entertainment, simulation and analysis, product design and development. In product development manipulation of mesh models is required in applications such as visualization, analysis, simulation and rapid prototyping. The nature of manipulation of the mesh includes annotation, interactive viewing, slicing, re-meshing, mesh optimization, mesh segmentation, simplification and editing. Of these editing has received the least attention. Mesh model often requires editing either locally or globally based on the application. With the increased use of meshes it is desirable to have formal reasoning tools that enable manipulation of mesh models in product development. The mesh model may contain artifacts like self-intersection, overlapping triangles, inconsistent normal’s of triangles and gaps or holes with or without islands. It is necessary to repair the mesh before further processing the mesh model. An automatic algorithm is proposed to repair and fill arbitrary holes while maintaining curvature continuity across the boundaries of the hole. The algorithm uses slices across the hole to first identify curves that bridge the hole. These curves are then used to find the surface patch that would fill the hole. The proposed algorithm works for arbitrary holes in any mesh model irrespective of the type of underlying surface and is able to preserve features in the mesh model that are missing in the input information. Since editing during product development is mostly feature based, an automatic algorithm to recognize shape features by directly clustering the triangles constituting a feature in a mesh model is proposed. Shape features addressed in the thesis are volumetric features that are associated with either addition or removal of a finite volume. The algorithm involves two steps – isolating features in 2D slices followed by a 3D traversal to cluster all the triangles in the feature. Editing a mesh model mainly implies editing local volumetric features in that model. An automatic algorithm is proposed for parametric editing of volumetric features in the mesh model. The proposed algorithm eliminates the need of original CAD model while manipulating any volumetric feature in the mesh model based on feature parameters. An automatic algorithm to manipulate global shape parameters of the object using the mesh model is developed. Global shape parameters include thickness, drafts and axes of symmetry. As the mesh models do not explicitly carry this information global editing of mesh models (other than for visualization) has not been attempted thus far. This thesis proposes the use of mid-surface to identify and manipulate global shape parameters for a class of objects that are classified as thin walled objects. Mid-curves are first identified on slices of the part and then the mid-surface is obtained from these mid-curves. Results of implementation are presented and discussed along with the scope for future work.

Cette thèse de doctorat aborde spécifiquement le problème de la métamorphose entre différents maillages 3D, qui peut assurer un niveau élevé de qualité pour la séquence de transition, qui devrait être aussi lisse et progressive que possible, cohérente par rapport à la géométrie et la topologie, et visuellement agréable. Les différentes étapes impliquées dans le processus de transformation sont développées dans cette thèse. Nos premières contributions concernent deux approches différentes des paramétrisations: un algorithme de mappage barycentrique basé sur la préservation des rapports de longueur et une technique de paramétrisation sphérique, exploitant la courbure Gaussien. L'évaluation expérimentale, effectuées sur des modèles 3D de formes variées, démontré une amélioration considérable en termes de distorsion maillage pour les deux méthodes. Afin d’aligner les caractéristiques des deux modèles d'entrée, nous avons considéré une technique de déformation basée sur la fonction radial CTPS C2a approprié pour déformer le mappage dans le domaine paramétrique et maintenir un mappage valide a travers le processus de mouvement. La dernière contribution consiste d’une une nouvelle méthode qui construit un pseudo metamaillage qui évite l'exécution et le suivi des intersections d’arêtes comme rencontrées dans l'état-of-the-art. En outre, notre méthode permet de réduire de manière drastique le nombre de sommets normalement nécessaires dans une structure supermesh. Le cadre générale de métamorphose a été intégré dans une application prototype de morphing qui permet à l'utilisateur d'opérer de façon interactive avec des modèles 3D et de contrôler chaque étape du processus / This Ph.D. thesis specifically deals with the issue of metamorphosis of 3D objects represented as 3D triangular meshes. The objective is to elaborate a complete 3D mesh morphing methodology which ensures high quality transition sequences, smooth and gradual, consistent with respect to both geometry and topology, and visually pleasant. Our first contributions concern the two different approaches of parameterization: a new barycentric mapping algorithm based on the preservation of the mesh length ratios, and a spherical parameterization technique, exploiting a Gaussian curvature criterion. The experimental evaluation, carried out on 3D models of various shapes, demonstrated a considerably improvement in terms of mesh distortion for both methods. In order to align the features of the two input models, we have considered a warping technique based on the CTPS C2a radial basis function suitable to deform the models embeddings in the parametric domain maintaining a valid mapping through the entire movement process. We show how this technique has to be adapted in order to warp meshes specified in the parametric domains. A final contribution consists of a novel algorithm for constructing a pseudo-metamesh that avoids the complex process of edge intersections encountered in the state-of-the-art. The obtained mesh structure is characterized by a small number of vertices and it is able to approximate both the source and target shapes. The entire mesh morphing framework has been integrated in an interactive application that allows the user to control and visualize all the stages of the morphing process