Submitted by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2016-09-09T19:43:53Z No. of bitstreams: 2 CECILIA ISABEL INES URQUIZA MACHADO PAVIN.pdf: 662363 bytes, checksum: ba4999290c4e1737856e3587e64e850d (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Approved for entry into archive by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2016-09-09T19:44:24Z (GMT) No. of bitstreams: 2 CECILIA ISABEL INES URQUIZA MACHADO PAVIN.pdf: 662363 bytes, checksum: ba4999290c4e1737856e3587e64e850d (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2016-09-09T19:44:24Z (GMT). No. of bitstreams: 2 CECILIA ISABEL INES URQUIZA MACHADO PAVIN.pdf: 662363 bytes, checksum: ba4999290c4e1737856e3587e64e850d (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2016-08-05 / Os métodos de seleção espermática são utilizados com o objetivo de isolar uma maior população de espermatozoides morfologicamente melhor, além de permitir a capacitação destes, incrementando a taxa de embriões produzidos in vitro. Entre os métodos de seleção, o mais utilizado comercialmente na produção in vitro (PIV) de embriões bovinos é o método de Gradiente Descontínuo de Percoll® (GDP). No entanto, apesar da praticidade desta técnica, a etapa de centrifugação é prejudicial, sendo responsável por danos estruturais as células espermáticas, bem como a diminuição da motilidade e da taxa de recuperação, interferindo assim, nas taxas de fecundação in vitro (FIV). Este estudo objetivou avaliar a centrifugação com amortecimento utilizando uma solução de iodixanol durante a seleção espermática para a PIV de embriões bovinos. No experimento I, o sêmen foi descongelado e dividido em quatro grupos, e os espermatozoides submetidos a separação espermática pelo método de GDP com ou sem a solução colóide; sendo o amortecimento testado na primeira (C1), segunda (C2) ou ambas centrifugações (C1-2). Em seguida, foram avaliadas a taxa de recuperação, a cinética espermática, e a produção de espécies reativas de oxigênio (EROs). No experimento II foi avaliada a taxa de fecundação e a cinética de desenvolvimento embrionário dos grupos C e C1, que foram os tratamentos que demonstraram os melhores resultados para a cinética espermática, taxa de recuperação e análise bioquímica no primeiro experimento. Neste estudo, o grupo com amortecimento obteve um aumento na taxa de fecundação e clivagem, quando comparado ao grupo controle (60,5 vs 48,55 e 80,0 vs 64,7%, respectivamente). Com base nestes resultados foi possível concluir que o uso de 9 uma solução de amortecimento durante a etapa de centrifugação para a seleção espermática permitiu a preservação da cinética e da integridade da membrana dos espermatozoides, sem reduzir a taxa de recuperação. Adicionalmente, foi demonstrado pela primeira vez que o uso da centrifugação com amortecimento incrementa, não apenas a taxa de fecundação e clivagem, mas também o número de embriões que clivam mais cedo. / In order to optimize bovine in vitro fertilization (IVF), sperm selection methods have been used to isolate sperm subpopulations with high fertilizing capacity for use in animal breeding. Among the methods of sperm selection, the most common method used is the Discontinuous Percoll® Gradients (DPG). However, again despite the practicality of this technique, the centrifugation step is harmful, accounting for structural damage in sperm and decrease in motility and sperm recovery rate, as well as interfering with in vitro fertilization rates. This study aimed to evaluate the cushioned centrifugation using an iodixanol solution on sperm selection for in vitro production (IVP) of bovine embryos. In experiment I, the thawed semen was divided into four groups and the sperm subjected to the separation method by discontinuous Percoll® gradients with and without a colloid solution, where the cushioning was tested in the first (C1), second (C2), and both centrifugations (C1-2). Then, the recovery rate, sperm kinetics, and production of reactive oxygen species (ROS) were evaluated. Experiment II evaluated the fertilization rate and embryonic development kinetics of C and C1 groups; who were the treatments that have shown the best results for motion kinetics, recovery rate, and biochemical analysis in Experiment I. In this assay, the group with cushioning obtained an increase in the fertilization and cleavage rate when compared with the control (60.5 vs 48.55 and 80.0 vs 64.7%, respectively). With this study, we can conclude that the use of a cushion solution during centrifugation on sperm selection had preserved the motion properties of spermatozoa and the 11 integrity of the sperm membrane without lowering the recovery rate. Furthermore, it was demonstrated for the first time that the use of cushioned centrifugation increases not only the cleavage rate but the number of embryos previously cleaved.

Dans cette thèse, nous nous intéressons à l’amélioration des performances numériques dela méthode Galerkin Discontinu en Domaine Temporel (GDDT), afin de valoriser son emploi industrielpour des problèmes de propagation d’ondes électromagnétiques. Pour ce faire, nous cherchons à réduire lenombre d’éléments des maillages utilisés en appliquant une stratégie de h-déraffinement/p-enrichissement.Dans un premier temps, nous montrons que si ce type de stratégie permet d’améliorer significativementl’efficacité numérique des résolutions dans un cadre conforme, son extension aux maillages non-conformespeut s’accompagner de contre-performances rédhibitoires limitant fortement leur intérêt pratique. Aprèsavoir identifié que ces dernières sont causées par le traitement des termes de flux non-conformes, nousproposons une méthode originale de condensation afin de retrouver des performances avantageuses. Cellecise base sur une redéfinition des flux non-conformes à partir d’un opérateur de reconstruction de traces,permettant de recréer une conformité d’espaces, et d’un produit scalaire condensé, assurant un calculapproché efficace. La stabilité et la consistance du schéma GDDT ainsi défini sont établies sous certainesconditions portant sur ces deux quantités. Dans un deuxième temps, nous détaillons la construction desopérateurs de trace et des produits scalaires associés. Nous proposons alors des flux condensés pourplusieurs configurations non-conformes, et validons numériquement la convergence du schéma GDDT résultant.Puis, nous cherchons à concevoir un algorithme de h-déraffinement/p-enrichissement automatisé,dans le but de générer des maillages hp minimisant les coûts de calcul du schéma. Ce processus est traduitsous la forme d’un problème d’optimisation combinatoire sous plusieurs contraintes de natures trèsdiverses. Nous présentons alors un algorithme de post-maillage basé sur un parcours efficace de l’arbrede recherche des configurations admissibles, associé à un processus de déraffinement hiérarchique. Enfin,nous mettons en œuvre la chaîne de calcul développée sur plusieurs cas-tests d’intérêt industriel, etévaluons son apport en termes de performances numériques. / This thesis is devoted to improving the numerical efficiency of the Discontinuous Galerkinin Time Domain (DGDT) method, in order to enhance its suitability for industrial use. One can noticethat, in an hp-conforming context, increasing correlatively the approximation order and the mesh sizeis a powerful strategy to reduce numerical costs. However, in complex geometries, the mesh can beconstrainted by the presence of small-scale inner elements, leading to hp-nonconforming configurationswith hanging nodes. The first issue we are dealing with is related to the nonconforming fluxes involvedin these configurations, whose high computational costs can deter the use of hp-coarsening strategies.In order to recover a satisfactory performance level, an original flux-lumping technique is set up. Thistechnique relies on recasting hybrid fluxes into conforming ones, and is performed by introducing twoingredients : a reconstruction operator designed to map traces from each side of a nonconforming interfaceinto the same functional space, and a lumped scalar product granting efficient integral computations.The resulting DGTD scheme is then proved to be stable and consistent, under some assumptions on thelatter two elements. Subsequently, we develop a lumped flux construction routine, and show numericalconvergence results on basic hybrid configurations. In a second part, we implement an automated strategyaiming at generating efficient hp-nonconforming meshes, well-suited to the previous DGDT scheme. To doso, a post-meshing process is formalized into a constrained optimization problem. We then put forward aheuristic hp-coarsening algorithm, based on a hierarchical coarsening approach coupled with an efficientsearch over the feasible configuration tree. Lastly, we present several numerical examples related toelectromagnetic wave propagation problems, and evaluate computational cost improvements.

The first ocean general circulation models developed in the late sixties were based on finite differences schemes on structured grids. Many improvements in the fields of engineering have been achieved since three decades with the developments of new numerical methods based on unstructured meshes. Some components of the first models may now seem out of date and new second generation models are therefore under study, with the aim of taking advantage of the potential of modern numerical techniques such as finite elements. In particular, unstructured meshes are believed to be more efficient to resolve the large range of time and space scales present in the ocean. Besides the classical continuous finite element or finite volume methods, another popular new trend in engineering applications is the Discontinuous Galerkin (DG) method, i.e. discontinuous finite elements presenting many interesting numerical properties in terms of dispersion and dissipation, errors convergence rates, advection schemes, mesh adaptation, etc. The method is especially efficient at high polynomial orders. The motivation for this PhD research is therefore to investigate the use of the high-order DG method for geophysical flow modeling. A first part of the thesis is devoted to the mesh adaptation using the DG method. The inter-element jumps of the fields are used as error estimators. New mesh size fields or polynomial orders are then derived and local h- or p-adaptation is performed. The technique is applied to standard benchmarks and computations in more realistic domains as the Gulf of Mexico. A second part deals with the use of the high order DG method with high-order representation of geometrical features. On one hand, a method is proposed to deal with complex representations of the coastlines. Computations are performed using high-order mappings around the Rattray island, located in the Great Barier Reef. Numerical results are then compared to in-situ measurements. On the other hand, a new method is proposed to deal with curved manifolds in order to represents oceanic or atmospheric flows on the sphere. The approach is based on the use of a local high-order non-orthogonal basis, and is equivalent to the use of vectorial shape and test functions to represent the vectorial conservation laws on the manifold's surface. A method is finally proposed to analyze the dispersion and dissipation properties of any numerical scheme on any kind of grid, possibly unstructured. The DG method is then compared to other techniques as the mixed non-conforming linear elements, and the impact of unstructured meshes is studied.

To simulate real world problems modeled by differential equations, it is often not sufficient to  consider and tackle a single equation. Rather, complex phenomena are modeled by several partial dierential equations that are coupled to each other. For example, a heart beat involve electric activity, mechanics of the movement of the walls and valves, as well as blood fow - a true multiphysics problem. There may also be ordinary differential equations modeling the reactions on a cellular level, and these may act on a much finer scale in both space and time. Determining efficient and accurate simulation tools for such multiscalar multiphysics problems is a challenge. The five scientific papers constituting this thesis investigate and present solutions to issues regarding accurate and efficient simulation using adaptive finite element methods. These include handling local accuracy through submodeling, analyzing error propagation in time-dependent  multiphysics problems, developing efficient algorithms for adaptivity in time and space, and deriving error analysis for coupled PDE-ODE systems. In all these examples, the error is analyzed and controlled using the framework of dual-weighted residuals, and the spatial meshes are handled using octree based data structures. However, few realistic geometries fit such grid and to address this issue a discontinuous Galerkin Nitsche method is presented and analyzed.

Delay differential equations (DDEs) are a class of differential equations that have received considerable recent attention and been shown to model many real life problems, traditionally formulated as systems of ordinary differential equations (ODEs), more naturally and more accurately. Ideally a DDE modeling package should provide facilities for approximating the solution, performing a sensitivity analysis and estimating unknown parameters. In this thesis we propose new techniques for efficient simulation, accurate sensitivity analysis and reliable parameter estimation of DDEs. We propose a new framework for designing a delay differential equation (DDE) solver which works with any supplied initial value problem (IVP) solver that is based on a general linear method (GLM) and can provide dense output. This is done by treating a general DDE as a special example of a discontinuous IVP. We identify a precise process for the numerical techniques used when solving the implicit equations that arise on a time step, such as when the underlying IVP solver is implicit or the delay vanishes. We introduce an equation governing the dynamics of sensitivities for the most general system of parametric DDEs. Then, having a similar view as the simulation (DDEs as discontinuous ODEs), we introduce a formula for finding the size of jumps that appear at discontinuity points when the sensitivity equations are integrated. This leads to an algorithm which can compute sensitivities for various kind of parameters very accurately. We also develop an algorithm for reliable parameter identification of DDEs. We propose a method for adding extra constraints to the optimization problem, changing a possibly non-smooth optimization to a smooth problem. These constraints are effectively handled using information from the simulator and the sensitivity analyzer. Finally, we discuss the structure of our evolving modeling package DDEM. We present a process that has been used for incorporating existing codes to reduce the implementation time. We discuss the object-oriented paradigm as a way of having a manageable design with reusable and customizable components. The package is programmed in C++ and provides a user-friendly calling sequences. The numerical results are very encouraging and show the effectiveness of the techniques.

Delay differential equations (DDEs) are a class of differential equations that have received considerable recent attention and been shown to model many real life problems, traditionally formulated as systems of ordinary differential equations (ODEs), more naturally and more accurately. Ideally a DDE modeling package should provide facilities for approximating the solution, performing a sensitivity analysis and estimating unknown parameters. In this thesis we propose new techniques for efficient simulation, accurate sensitivity analysis and reliable parameter estimation of DDEs. We propose a new framework for designing a delay differential equation (DDE) solver which works with any supplied initial value problem (IVP) solver that is based on a general linear method (GLM) and can provide dense output. This is done by treating a general DDE as a special example of a discontinuous IVP. We identify a precise process for the numerical techniques used when solving the implicit equations that arise on a time step, such as when the underlying IVP solver is implicit or the delay vanishes. We introduce an equation governing the dynamics of sensitivities for the most general system of parametric DDEs. Then, having a similar view as the simulation (DDEs as discontinuous ODEs), we introduce a formula for finding the size of jumps that appear at discontinuity points when the sensitivity equations are integrated. This leads to an algorithm which can compute sensitivities for various kind of parameters very accurately. We also develop an algorithm for reliable parameter identification of DDEs. We propose a method for adding extra constraints to the optimization problem, changing a possibly non-smooth optimization to a smooth problem. These constraints are effectively handled using information from the simulator and the sensitivity analyzer. Finally, we discuss the structure of our evolving modeling package DDEM. We present a process that has been used for incorporating existing codes to reduce the implementation time. We discuss the object-oriented paradigm as a way of having a manageable design with reusable and customizable components. The package is programmed in C++ and provides a user-friendly calling sequences. The numerical results are very encouraging and show the effectiveness of the techniques.

Aquesta tesi doctoral proposa formulacions de Galerkin discontinu (DG) d'alt ordre per fluxos viscosos incompressibles. Es desenvolupa un nou mètode de DG amb penalti interior (IPM-DG), que condueix a una forma feble simètrica i coerciva pel terme de difusió, i que permet assolir una aproximació espacial d'alt ordre. Aquest mètode s'aplica per resoldre les equacions de Stokes i Navier-Stokes. L'espai d'aproximació de la velocitat es descompon dins de cada element en una part solenoidal i una altra irrotacional, de manera que es pot dividir la forma dèbil IPM-DG en dos problemes desacoblats. El primer permet el càlcul de les velocitats i de les pressions híbrides, mentre que el segon calcula les pressions en l'interior dels elements. Aquest desacoblament permet una reducció important del número de graus de llibertat tant per velocitat com per pressió. S'introdueix també un paràmetre extra de penalti resultant en una formulació DG alternativa per calcular les velocitats solenoidales, on les pressions no apareixen. Les pressions es poden calcular com un post-procés de la solució de les velocitats. Es contemplen altres formulacions DG, com per exemple el mètode Compact Discontinuous Galerkin, i es comparen al mètode IPM-DG. Es proposen mètodes implícits de Runge-Kutta d'alt ordre per problemes transitoris incompressibles, permetent obtenir esquemes incondicionalment estables i amb alt ordre de precisió temporal. Les equacions de Navier-Stokes incompressibles transitòries s'interpreten com un sistema de Equacions Algebraiques Diferencials, és a dir, un sistema d'equacions diferencials ordinàries corresponent a la equació de conservació del moment, més les restriccions algebraiques corresponent a la condició d'incompressibilitat. Mitjançant exemples numèrics es mostra l'aplicabilitat de les metodologies proposades i es comparen la seva eficiència i precisió. / This PhD thesis proposes divergence-free Discontinuous Galerkin formulations providing high orders of accuracy for incompressible viscous flows. A new Interior Penalty Discontinuous Galerkin (IPM-DG) formulation is developed, leading to a symmetric and coercive bilinear weak form for the diffusion term, and achieving high-order spatial approximations. It is applied to the solution of the Stokes and Navier-Stokes equations. The velocity approximation space is decomposed in every element into a solenoidal part and an irrotational part. This allows to split the IPM weak form in two uncoupled problems. The first one solves for velocity and hybrid pressure, and the second one allows the evaluation of pressures in the interior of the elements. This results in an important reduction of the total number of degrees of freedom for both velocity and pressure. The introduction of an extra penalty parameter leads to an alternative DG formulation for the computation of solenoidal velocities with no presence of pressure terms. Pressure can then be computed as a post-process of the velocity solution. Other DG formulations, such as the Compact Discontinuous Galerkin method, are contemplated and compared to IPM-DG. High-order Implicit Runge-Kutta methods are then proposed to solve transient incompressible problems, allowing to obtain unconditionally stable schemes with high orders of accuracy in time. For this purpose, the unsteady incompressible Navier-Stokes equations are interpreted as a system of Differential Algebraic Equations, that is, a system of ordinary differential equations corresponding to the conservation of momentum equation, plus algebraic constraints corresponding to the incompressibility condition. Numerical examples demonstrate the applicability of the proposed methodologies and compare their efficiency and accuracy.

<p>In this study we propose a fast hybrid spectral-element time-domain (SETD) / finite-element time-domain (FETD) method for transient analysis of multiscale electromagnetic problems, where electrically fine structures with details much smaller than a typical wavelength and electrically coarse structures comparable to or larger than a typical wavelength coexist.</p><p>Simulations of multiscale electromagnetic problems, such as electromagnetic interference (EMI), electromagnetic compatibility (EMC), and electronic packaging, can be very challenging for conventional numerical methods. In terms of spatial discretization, conventional methods use a single mesh for the whole structure, thus a high discretization density required to capture the geometric characteristics of electrically fine structures will inevitably lead to a large number of wasted unknowns in the electrically coarse parts. This issue will become especially severe for orthogonal grids used by the popular finite-difference time-domain (FDTD) method. In terms of temporal integration, dense meshes in electrically fine domains will make the time step size extremely small for numerical methods with explicit time-stepping schemes. Implicit schemes can surpass stability criterion limited by the Courant-Friedrichs-Levy (CFL) condition. However, due to the large system matrices generated by conventional methods, it is almost impossible to employ implicit schemes to the whole structure for time-stepping.</p><p>To address these challenges, we propose an efficient hybrid SETD/FETD method for transient electromagnetic simulations by taking advantages of the strengths of these two methods while avoiding their weaknesses in multiscale problems. More specifically, a multiscale structure is divided into several subdomains based on the electrical size of each part, and a hybrid spectral-element / finite-element scheme is proposed for spatial discretization. The hexahedron-based spectral elements with higher interpolation degrees are efficient in modeling electrically coarse structures, and the tetrahedron-based finite elements with lower interpolation degrees are flexible in discretizing electrically fine structures with complex shapes. A non-spurious finite element method (FEM) as well as a non-spurious spectral element method (SEM) is proposed to make the hybrid SEM/FEM discretization work. For time integration we employ hybrid implicit / explicit (IMEX) time-stepping schemes, where explicit schemes are used for electrically coarse subdomains discretized by coarse spectral element meshes, and implicit schemes are used to overcome the CFL limit for electrically fine subdomains discretized by dense finite element meshes. Numerical examples show that the proposed hybrid SETD/FETD method is free of spurious modes, is flexible in discretizing sophisticated structure, and is more efficient than conventional methods for multiscale electromagnetic simulations.</p> / Dissertation

Preconditioners based upon sweeps and diffusion-synthetic acceleration (DSA) have been constructed and applied to the zeroth and first spatial moments of the 1-D transport equation using SN angular discretization and a strictly positive nonlinear spatial closure (the CSZ method). The sweep preconditioner was applied using the linear discontinuous Galerkin (LD) sweep operator and the nonlinear CSZ sweep operator. DSA preconditioning was applied using the linear LD S2 equations and the nonlinear CSZ S2 equations. These preconditioners were applied in conjunction with a Jacobian-free Newton Krylov (JFNK) method utilizing Flexible GMRES. The action of the Jacobian on the Krylov vector was difficult to evaluate numerically with a finite difference approximation because the angular flux spanned many orders of magnitude. The evaluation of the perturbed residual required constructing the nonlinear CSZ operators based upon the angular flux plus some perturbation. For cases in which the magnitude of the perturbation was comparable to the local angular flux, these nonlinear operators were very sensitive to the perturbation and were significantly different than the unperturbed operators. To resolve this shortcoming in the finite difference approximation, in these cases the residual evaluation was performed using nonlinear operators "frozen" at the unperturbed local psi. This was a Newton method with a perturbation fixup. Alternatively, an entirely frozen method always performed the Jacobian evaluation using the unperturbed nonlinear operators. This frozen JFNK method was actually a Picard iteration scheme. The perturbed Newton's method proved to be slightly less expensive than the Picard iteration scheme. The CSZ sweep preconditioner was significantly more effective than preconditioning with the LD sweep. Furthermore, the LD sweep is always more expensive to apply than the CSZ sweep. The CSZ sweep is superior to the LD sweep as a preconditioner. The DSA preconditioners were applied in conjunction with the CSZ sweep. The nonlinear CSZ DSA preconditioner did not form a more effective preconditioner than the linear DSA preconditioner in this 1-D analysis. As it is very difficult to construct a CSZ diffusion equation in more than one dimension, it will be very beneficial if the results regarding the effectiveness of the LD DSA preconditioner are applicable to multi-dimensional problems.

Distributed optimal control problems with transient convection dominated diffusion convection reaction equations are considered. The problem is discretized in space by using three types of discontinuous Galerkin (DG) method: symmetric interior penalty Galerkin (SIPG), nonsymmetric interior penalty Galerkin (NIPG), incomplete interior penalty Galerkin (IIPG). For time discretization, Crank-Nicolson and backward Euler methods are used. The discretize-then-optimize approach is used to obtain the finite dimensional problem. For one-dimensional unconstrained problem, Newton-Conjugate Gradient method with Armijo line-search. For two-dimensional control constrained problem, active-set method is applied. A priori error estimates are derived for full discretized optimal control problem. Numerical results for one and two-dimensional distributed optimal control problems for diffusion convection equations with boundary layers confirm the predicted orders derived by a priori error estimates.