Explicit methods are widely used in finite element analysis as efficient ways to solve differential equations. The efficiency of explicit methods relies on the economical evaluation of internal forces at each time step. The greatest efficiency can be provided by one-point quadrature. However, instability arises because of the shortcomings in the use of one-point quadrature. The instability is called hourglass mode, or spurious singular mode. An effective method to control the instability is to add “hourglass stiffness” to an element integrated by one-point quadrature. Explicit methods often require a very small time step to ensure stability. Thus, for complex problem with refined meshes, a very large number of timesteps will be required to complete the analysis. Minimizing the number of operations per time step can provide significant improvement on efficiency of the methods. Since hourglass terms typically require more computational operations than one-point quadrature terms, we are very interested in reducing the number of operations on hourglass control. In addition, considerable approximation is involved with hourglass control, and hence overall accuracy may not be seriously affected by relaxing the precision of the temporal integration of the hourglass force. Consequently, there is a possibility of trading some accuracy of the hourglass control for computational efficiency. A subcycling approach is applied to the hourglass portion of explicit methods. Namely, instead of updating hourglass forces every time step, we update hourglass forces every two steps. The proposed approach is examined with the use of mass-spring models. The applicability to more complex models is demonstrated on a 3-D model with the subcycling approach implemented into an explicit finite element code. Efficiency, stability and accuracy are discussed as important issues of the proposed approach. The mass-spring models and finite element implementation show that a beating instability can be introduced by the subcycling approach, and additional restriction is placed on the stable time step for the central difference operator. However, sufficient damping can restore the usual stability conditions. Thus, the proposed subcycling approach is seen to be highly advantageous where damping can be used, and it can cut computation time by 30% or more without significantly affecting the overall accuracy of the solution. / Thesis / Master of Applied Science (MASc)

abstract: Urbanization provides an excellent opportunity to examine the effects of human-induced rapid environmental change (HIREC) on natural ecosystems. Certain species can dominate in urban habitats at the expense of biodiversity. Phenotypic plasticity may be the mechanism by which these 'urban exploiters' flourish in urban areas. Color displays and condition-dependent phenotypes are known to be highly plastic. However, conspicuous color displays are perplexing in that they can be costly to produce and may increase detection by enemies. The Western black widow spider () is a superabundant pest species that forms dense aggregations throughout metropolitan Phoenix, Arizona, USA. Adult female display a red hourglass on their abdomen, which is speculated to function as a conspicuous warning signal to enemies. Here, I performed field studies to identify how widow morphology and hourglass color differ between urban and desert subpopulations. I also conducted laboratory experiments to examine the dietary sensitivity of hourglass coloration and to identify its functional role in the contexts of agonism, mating, and predator defense. My field data reveal significant spatial variation across urban and desert subpopulations in ecology and color. Furthermore, hourglass coloration was significantly influenced by environmental factors unique to urban habitats. Desert spiders were found to be smaller and less colorful than urban spiders. Throughout, I observed a positive correlation between body condition and hourglass size. Laboratory diet manipulations empirically confirm the condition-dependence of hourglass size. Additionally, widows with extreme body conditions exhibited condition-dependent coloration. However, hourglass obstruction and enlargement did not produce any effects on the outcome of agonistic encounters, male courtship, or predator deterrence. This work offers important insights into the effects of urbanization on the ecology and coloration of a superabundant pest species. While the function of the hourglass remains undetermined, my findings characterize the black widow's hourglass as extremely plastic. Plastic responses to novel environmental conditions can modify the targets of natural selection and subsequently influence evolutionary outcomes. Therefore, assuming a heritable component to this plasticity, the response of hourglass plasticity to the abrupt environmental changes in urban habitats may result in the rapid evolution of this phenotype. / Dissertation/Thesis / M.S. Biology 2014

Le recours aux logiciels de simulation basés sur la méthode des éléments finis devenant de plus en plus systématique dans les différents secteurs de l'industrie, l'efficacité et la précision de ces derniers deviennent des propriétés déterminantes. Dans les situations les plus courantes, les structures minces nécessitent une analyse précise et efficace, rendue possible par les éléments coques. En présence de structures dans lesquelles coexistent des parties minces et des zones plus épaisses, l'utilisation de ces éléments est encore plus cruciale. Ce travail est une contribution au développement et à la validation d'éléments finis solide-coques. Les déplacements nodaux sont les seuls degrés de liberté et ils sont munis d'un ensemble de points d'intégration distribués le long d'une direction préférentielle, désignée comme “l'épaisseur”. Une intégration réduite dans le plan moyen est utilisée. La loi élastique 3D est modifiée pour s'approcher de la situation coque et atténuer les verrouillages. Grâce à ses formulations particulières, ces éléments solide-coques se connectent naturellement aux éléments 3D et présentent une bonne performance dans des applications de structures minces et pour des problèmes dominés par la flexion. Il s'agit des trois nouveaux éléments isoparamétriques SHB6, SHB15, et SHB20. L'analyse détaillée d'une potentielle déficience du rang de la matrice de raideur a révélé que ces derniers ne possèdent pas de modes à énergie nulle et qu'aucune stabilisation n'est donc nécessaire. Néanmoins, nous proposons des modifications basées sur la méthode bien connue “Assumed Strain”, pour l'opérateur gradient discrétisé de l'élément SHB6, dans le but d'améliorer sa vitesse de convergence. Pour illustrer les capacités de ces éléments, ses performances sont évaluées sur un ensemble de cas tests en configurations linéaire ou non-linéaire, communément utilisés dans la littérature pour tester les éléments finis de type coques. En particulier, il est montré que le nouvel élément SHB6 joue un rôle très utile en tant que complément à l'élément hexaèdre SHB8PS, ce qui nous permet ainsi de mailler des géométries arbitraires.

Essential genes are those whose presence is imperative for an organism's survival, whereas the functions of non-essential genes may be useful but not critical. Abnormal functionality of essential genes may lead to defects or death at an early stage of life. Knowledge of essential genes is therefore key to understanding development, maintenance of major cellular processes and tissue-specific functions that are crucial for life. Existing experimental techniques for identifying essential genes are accurate, but most of them are time consuming and expensive. Predicting essential genes using computational methods, therefore, would be of great value as they circumvent experimental constraints. Our research is based on the hypothesis that mammalian essential (lethal) and non-essential (viable) genes are distinguishable by various properties. We examined a wide range of features of Mus musculus genes, including sequence, protein-protein interactions, gene expression and function, and found 75 features that were statistically discriminative between lethal and viable genes. These features were used as inputs to create a novel machine learning classifier, allowing the prediction of a mouse gene as lethal or viable with the cross-validation and blind test accuracies of ∼91% and ∼93%, respectively. The prediction results are promising, indicating that our classifier is an effective mammalian essential gene prediction method. We further developed the mouse gene essentiality study by analysing the association between essentiality and gene duplication. Mouse genes were labelled as singletons or duplicates, and their expression patterns over 13 developmental stages were examined. We found that lethal genes originating from duplicates are considerably lower in proportion than singletons. At all developmental stages a significantly higher proportion of singletons and lethal genes are expressed than duplicates and viable genes. Lethal genes were also found to be more ancient than viable genes. In addition, we observed that duplicate pairs with similar patterns of developmental co-expression are more likely to be viable; lethal gene duplicate pairs do not have such a trend. Overall, these results suggest that duplicate genes in mouse are less likely to be essential than singletons. Finally, we investigated the evolutionary age of mouse genes across development to see if the morphological hourglass pattern exists in the mouse. We found that in mouse embryos, genes expressed in early and late stages are evolutionarily younger than those expressed in mid-embryogenesis, thus yielding an hourglass pattern. However, the oldest genes are not expressed at the phylotypic stage stated in prior studies, but instead at an earlier time point - the egg cylinder stage. These results question the application of the hourglass model to mouse development.

Apresenta-se uma formulação de adaptação de malha para problemas com grandes deformações. A formulação Arbitrária Lagrangeana-Euleraina (ALE) permite manter a qualidade dos elementos finitos durante o processo de cálculo através de rearranjo ou movimento de malha independente do movimento material. Nas formulações Lagrangeanas a malha fica “colada” ao corpo durante toda a análise, logo quando este sofre grandes deformações diferenciais o mesmo se reproduz numa malha distorcida. A formulação ALE desacoplada consta de dois passos: O passo Lagrangeano onde são aplicados os incrementos de carga, a malha permanece “colada” à matéria durante a análise. E cada certo “tempo” o passo Euleriano onde “descola-se” a malha da matéria e efetua-se o movimento de malha que se ajusta melhor ao corpo deformado. São apresentados assim métodos de realocação da malha e transferência ou atualização das variáveis necessárias para, depois do passo Euleriano, continuar a análise com a nova malha sem grandes distorções dos elementos. Os problemas de grandes deformações e deslocamentos são acompanhados de não linearidades físicas e geométricas, assim, são abordados os métodos para o tratamento destas não linearidades. Trabalha-se com o elemento hexaédrico tri-linear com integração reduzida e controle dos modos espúrios que tem demostrado um bom comportamento frente a grandes não linearidades geométricas assim como para as não linearidades físicas. A formulação ALE tem ganhando seu espaço na mecânica dos sólidos, em problemas de conformação mecânica e impacto, devido às grandes deformações e na última década está abrindo-se passo na área da geomecânica tratando problemas recalque e penetração de fundações em solos. / This work presents remeshing techniques for finite element simulation and investigates their performance for large deformation problems. Lagrangian formulation generally results in excessive mesh distortion owing to its attachment to the material. Meanwhile, the Lagrangian- Eulerian (ALE) formulation alouds to keep the finite element quality through the arbitrarily rearrangement or movement of the mesh, to optimize the element’s shape. The decoupled Arbitrary Lagrangian-Eulerian approach consists in a sequence of Lagrangian and Eulerian steps. The mesh is “coupled” to the material during the Lagrangian steps. From step to step, mesh is decoupled from the system material (Eulerian step), the nodes corresponding to free boundaries are relocated using an analytical approach, remeshing is performed and finally the state variables are remapped. Rearrangements methods for the element’s node are presented, as well as the variables remapping algorithms at the new quadrature points, in order to continue with the finite element analysis without altering the element topology of the original mesh. Special attention is given to methods dealing with geometric and physical nonlinearities. A trilinear hexahedral element is used with reduced integration and hourglass control. This combination has shown well behavior in front of large geometric and physical nonlinearities. ALE formulation field has considerably grown in geotechnical research, especially in impact and mechanical extrusion problems. Over the last decade, geomechanic is dealing with settlement problems and foundation penetration in soils.

Apresenta-se uma formulação de adaptação de malha para problemas com grandes deformações. A formulação Arbitrária Lagrangeana-Euleraina (ALE) permite manter a qualidade dos elementos finitos durante o processo de cálculo através de rearranjo ou movimento de malha independente do movimento material. Nas formulações Lagrangeanas a malha fica “colada” ao corpo durante toda a análise, logo quando este sofre grandes deformações diferenciais o mesmo se reproduz numa malha distorcida. A formulação ALE desacoplada consta de dois passos: O passo Lagrangeano onde são aplicados os incrementos de carga, a malha permanece “colada” à matéria durante a análise. E cada certo “tempo” o passo Euleriano onde “descola-se” a malha da matéria e efetua-se o movimento de malha que se ajusta melhor ao corpo deformado. São apresentados assim métodos de realocação da malha e transferência ou atualização das variáveis necessárias para, depois do passo Euleriano, continuar a análise com a nova malha sem grandes distorções dos elementos. Os problemas de grandes deformações e deslocamentos são acompanhados de não linearidades físicas e geométricas, assim, são abordados os métodos para o tratamento destas não linearidades. Trabalha-se com o elemento hexaédrico tri-linear com integração reduzida e controle dos modos espúrios que tem demostrado um bom comportamento frente a grandes não linearidades geométricas assim como para as não linearidades físicas. A formulação ALE tem ganhando seu espaço na mecânica dos sólidos, em problemas de conformação mecânica e impacto, devido às grandes deformações e na última década está abrindo-se passo na área da geomecânica tratando problemas recalque e penetração de fundações em solos. / This work presents remeshing techniques for finite element simulation and investigates their performance for large deformation problems. Lagrangian formulation generally results in excessive mesh distortion owing to its attachment to the material. Meanwhile, the Lagrangian- Eulerian (ALE) formulation alouds to keep the finite element quality through the arbitrarily rearrangement or movement of the mesh, to optimize the element’s shape. The decoupled Arbitrary Lagrangian-Eulerian approach consists in a sequence of Lagrangian and Eulerian steps. The mesh is “coupled” to the material during the Lagrangian steps. From step to step, mesh is decoupled from the system material (Eulerian step), the nodes corresponding to free boundaries are relocated using an analytical approach, remeshing is performed and finally the state variables are remapped. Rearrangements methods for the element’s node are presented, as well as the variables remapping algorithms at the new quadrature points, in order to continue with the finite element analysis without altering the element topology of the original mesh. Special attention is given to methods dealing with geometric and physical nonlinearities. A trilinear hexahedral element is used with reduced integration and hourglass control. This combination has shown well behavior in front of large geometric and physical nonlinearities. ALE formulation field has considerably grown in geotechnical research, especially in impact and mechanical extrusion problems. Over the last decade, geomechanic is dealing with settlement problems and foundation penetration in soils.

Apresenta-se uma formulação de adaptação de malha para problemas com grandes deformações. A formulação Arbitrária Lagrangeana-Euleraina (ALE) permite manter a qualidade dos elementos finitos durante o processo de cálculo através de rearranjo ou movimento de malha independente do movimento material. Nas formulações Lagrangeanas a malha fica “colada” ao corpo durante toda a análise, logo quando este sofre grandes deformações diferenciais o mesmo se reproduz numa malha distorcida. A formulação ALE desacoplada consta de dois passos: O passo Lagrangeano onde são aplicados os incrementos de carga, a malha permanece “colada” à matéria durante a análise. E cada certo “tempo” o passo Euleriano onde “descola-se” a malha da matéria e efetua-se o movimento de malha que se ajusta melhor ao corpo deformado. São apresentados assim métodos de realocação da malha e transferência ou atualização das variáveis necessárias para, depois do passo Euleriano, continuar a análise com a nova malha sem grandes distorções dos elementos. Os problemas de grandes deformações e deslocamentos são acompanhados de não linearidades físicas e geométricas, assim, são abordados os métodos para o tratamento destas não linearidades. Trabalha-se com o elemento hexaédrico tri-linear com integração reduzida e controle dos modos espúrios que tem demostrado um bom comportamento frente a grandes não linearidades geométricas assim como para as não linearidades físicas. A formulação ALE tem ganhando seu espaço na mecânica dos sólidos, em problemas de conformação mecânica e impacto, devido às grandes deformações e na última década está abrindo-se passo na área da geomecânica tratando problemas recalque e penetração de fundações em solos. / This work presents remeshing techniques for finite element simulation and investigates their performance for large deformation problems. Lagrangian formulation generally results in excessive mesh distortion owing to its attachment to the material. Meanwhile, the Lagrangian- Eulerian (ALE) formulation alouds to keep the finite element quality through the arbitrarily rearrangement or movement of the mesh, to optimize the element’s shape. The decoupled Arbitrary Lagrangian-Eulerian approach consists in a sequence of Lagrangian and Eulerian steps. The mesh is “coupled” to the material during the Lagrangian steps. From step to step, mesh is decoupled from the system material (Eulerian step), the nodes corresponding to free boundaries are relocated using an analytical approach, remeshing is performed and finally the state variables are remapped. Rearrangements methods for the element’s node are presented, as well as the variables remapping algorithms at the new quadrature points, in order to continue with the finite element analysis without altering the element topology of the original mesh. Special attention is given to methods dealing with geometric and physical nonlinearities. A trilinear hexahedral element is used with reduced integration and hourglass control. This combination has shown well behavior in front of large geometric and physical nonlinearities. ALE formulation field has considerably grown in geotechnical research, especially in impact and mechanical extrusion problems. Over the last decade, geomechanic is dealing with settlement problems and foundation penetration in soils.

The contents of this graduation thesis is design and assessment of the load-bearing structure of the observation tower situated between the village of Horni Lhota and Provodov. The construction was designed as a steel structure in two variants. Type A is cuboid shape with a side lenght ground plan 6,8 m and height of 37,7 m. Type B is an hourglass shape with a height of 39 m. Ground plan is a regular octagon shape with variable diameter. Detailed static calculation and drawing documentation was processed only for option B.

Cette thèse étudie quelques situations dans lesquelles un système actif, composé de particules auto-propulsées, est soumis à des contraintes extérieures. Dans un premier chapitre, nous étudions le comportement d'une assemblée de bactéries magnétotactiques —capables de s'aligner sur un champ magnétique extérieur— forcées au travers d'une constriction en forme de sablier. Nous caractérisons les propriétés dynamiques de ce système, à l'échelle individuelle mais également à celle de l'embouteillage formé et du jet émergeant. En particulier, nous montrons dans les zones concentrées en bactéries des couplages reliant densité en bactéries, vitesse de nage et forçage magnétique beaucoup plus complexes que ce qui avait été considéré jusqu'à maintenant dans les modèles théoriques.Le deuxième chapitre aborde un nouveau système actif constitué de disques de camphres posés à la surface de l'eau. Dans une première étape, nous avons étudié en détails les propriétés de nage individuelle de ces objets qui brisent spontanément la symétrie du système pour se mettre en mouvement. En particulier, nous montrons que les données recueillies peuvent être rationnalisées à l'aide d'une approche théorique très simple de ce problème couplé d'hydrodynamique et de transport de tensio-actif. Dans un troisième chapitre, nous avons abordé la dynamique d'une assemblée de ces nageurs interfaciaux interagissant via les champs hydrodynamiques et chimiques qu'ils génèrent. À concentration intermédiaire en nageurs, un régime de nage intermittente caractérisé par des bouffées pseudo-périodiques d'activité des nageurs apparaît. En utilisant des outils et concepts issus du domaine de la turbulence nous montrons que de façon remarquable, ce système très simple exhibe des comportements canoniques de la turbulence tels que prédits par Kolmogorov (1941), ouvrant ainsi des perspectives concrètes sur des analogies très riches entre turbulence et systèmes actifs / This work address different situations where active matter, made out of self-propelled particles, is submitted to external constraints.In a first part, we consider the response of magnetotactic bacteria –capable of swim alignment along magnetic field lines- directed through an hourglass shape geometry. We characterize the dynamic properties of the system, both at the individual bacteria scale and at the scale of the jammed region or of the induced outgoing jet. We show that in high density regions, couplings between the bacteria interactions, swim velocity and magnetic forcing take a much more complex form than had been considered so far in theoretical models.In a second chapter, we are addressing a new active system made out of camphor disks lying at the air-water interface. First of all, we study in details the individual swim properties of such particles, which spontaneously break the system symmetry to start moving. In particular, we show that all experimental data can be rationalized within the framework of a very simple model of this complex problem where hydrodynamic flows and surfactant transports are coupled through Marangoni stress.In a last chapter, we addressed the collective dynamics of an assembly of such interfacial swimmers that interact through the flow and chemical fields they generate. At intermediate swimmers concentrations, an intermittent swim regime appears characterized by pseudo-periodic activity bursts. Using tools and concepts from the turbulence domain, we show that, remarkably, this simple system exhibits dynamical properties matching the ones of canonical turbulence as predicted by Kolmogorov in the 40s. This demonstration opens up rich perspectives in the historical domain of turbulence together with in the emerging one of active matter

Double-sided module exhibits electrical and thermal characteristics that are superior to wire-bonded counterpart. Such structure, however, induces more than twice the thermo-mechanical stress in a single-layer structure. Compressive posts have been developed and integrated into the double-sided module to reduce the stress to a level acceptable by silicon dice. For a 14 mm x 21 mm module carrying 6.6 mm x 6.6 mm die, finite-element simulation suggested an optimal design having four posts located 1 mm from the die; the z-direction stress at the chip was reduced from 17 MPa to 0.6 MPa. / Ph. D.