Lorentz TEM observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials of the sample. These potentials can be extracted from the electron wave phase shift by separating electrostatic and magnetic phase shifts, followed by 3D tomographic reconstructions. In past, Vector Field Electron Tomography (VFET) was utilized to perform the reconstruction. However, VFET is based on a conventional tomography method called filtered back-projection (FBP). Consequently, the VFET approach tends to produce inconsistencies that are prominent along the edges of the sample. We propose a model-based iterative reconstruction (MBIR) approach to improve the reconstruction of magnetic vector potential, A(r). In the case of scalar tomography, the MBIR method is known to yield better reconstructions than the conventional FBP approach, due to the fact that MBIR can incorporate prior knowledge about the system to be reconstructed. For the same reason, we seek to use the MBIR approach to optimize vector field tomographic reconstructions via incorporation of prior knowledge. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to deduce the vector potential. A detailed study of reconstructions from simulated as well as experimental data sets is provided to establish the superiority of the MBIR approach over the VFET approach.

The doctoral thesis is focused on research, design, implementation and testing of systems for the application of magnetic vector potential to biological materials. The main objective was to analyze and design systems which could generate magnetic vector potential without the presence of other unwanted fields or at least amplify its intensity. Moreover, the systems designed had to eliminate other foreign effects on the biological samples, especially the influence of waste heat from the coils. Toroidal coils were employed to generate the vector potential, because they confine the unwanted magnetic induction inside their core thanks to their shape. The thesis employed coils with two different outer diameters, specifically 102 and 600 mm. To excite the coils, four current pulse generators capable of delivering currents of up to 100 A were constructed. The systems’ generated fields were comprehensively analyzed with the help of finite-element simulations in ANSYS. To simplify the design phase, analytical equations for the calculation of vector potential intensity at an arbitrary point around the toroidal coils were also derived. A method employing electromagnetic shielding made of two different materials was developed to suppress the unwanted fields. To eliminate the influence of heat, the 102 mm system employed air cooling and the 600 mm system employed a closed water loop to equalize the temperatures of biological samples. The biological effects of both systems were tested on genetically modified bio-luminescent bacteria Escherichia coli K12 luxABCDEamp. The thesis was created in connection with the research project of The Ministry of Education, Youth and Sports of the Czech Republic named “Research into the effect of a combination of substances for targeted therapy and inhibitory action of the field pulse vector magnetic potential on oncogenous diseases”, No. 2B08063.

Les machines électriques sont modélisées pour prédire leurs performances et optimiser leur rendement. Cette modélisation peut être faite par des simulations avec la méthode des éléments finis. En particulier, les machines asynchrones nécessitent des simulations 3D pour prendre en compte les courants de Foucault et les têtes de bobines. Dans le logiciel Flux®, des formulations 3D basées sur le potentiel scalaire magnétique sont utilisées avec succès depuis de nombreuses années. Néanmoins, des coupures mathématiques artificielles sont nécessaires, lorsque le domaine n'est pas simplement connexe.Afin de se libérer de ces contraintes de connexité, des formulations en potentiel vecteur magnétique ont été étudiées et développées. En 3D, leur mise en œuvre nécessite l'utilisation d'éléments finis d'arêtes afin de respecter la nature des champs. Avec les éléments d'arêtes, les formulations sont généralement résolues avec une condition de jauge pour les solveurs directs comme pour les solveurs itératifs. De nouvelles formulations en potentiel vecteur magnétique auto-jaugées ont été développées permettant la prise en compte des bobines maillées et des bobines non maillées. La prise en compte du mouvement est relativement simple à mettre en œuvre pour les formulations en potentiel scalaire magnétique avec l'interpolation nodale.Avec les éléments d'arête, l'interpolation est plus délicate. C'est pourquoi la méthode des éléments avec joints a été développée pour prendre en compte le mouvement dans un cas général. / Electric machines are modeled in order to predict their performance and to optimize their output. This modeling can be done by simulation with the finite element method. In particular, induction machines require 3D simulation to take into account eddy currents and coils overhangs. In the Flux® software, 3D formulations based on magnetic scalar potential has been used with success for many years. Nevertheless, artificial mathematical cuts are necessary, when the domain is not simply connected.In order to avoid connection constraints, magnetic vector potential formulations have been studied and developed. In 3D, their implementation requires the use of edge elements to respect the nature of fields. With edge elements, formulations are generally solved with a gauge condition for direct solvers as well as for iterative solvers. New auto-gauged magnetic vector potential formulations have been developed to take into account meshed coils and non-meshed coils. Consideration of movement is relatively simple to implement for magnetic scalar potential formulations with nodal interpolation. With edge elements, the interpolation is more delicate. For this reason, the mortar method has been developed to take into account movement in a general case.

L'objectif principal de cette thèse concerne la mise en oeuvre d'une méthoded'éléments finis stabilisés pour la simulation des plasmas de fusion. Pour cela,nous avons d'abord dérivé les modèles magnétohydrodynamiques depuis lemodèle cinétique. Les modèles MHD sont généralement utilisés pour simuler lesinstabilités macroscopiques des plasmas. Nous nous sommes concentrés sur lemodèles de la MHD complète. Ensuite, l'approche numérique est décrite dans lecadre de la stabilisation Variationelle Multi-Échelles (VMS). Cette stabilisationvient ajouter un terme à la formulation faible pour mimer les effets des échellesnon-résolues sur celles résolues. Si les effets de ces sous-échelles ne sont paspris en compte lorsque l'on traite des écoulements dominés par convection,comme dans le cadre des plasmas de fusion, le schéma numérique conduit àdes résultats non-physiques. Une étude détaillée de l'instabilité de « Kinkinterne » a été faite ainsi qu'une étude préliminaire des plasmas avec point-Xayant pour but la validation du schéma numérique développé ici / The main objective of this thesis concerns the implementation of a robuststabilized finite element method for simulating fusion plasmas. For that, we firstderive the magnetohydrodynamic models from the kinetic model. MHD modelsare generally used for macroscopic simulations of plasma instabilities. Weconcentrate ou efforts on the full MHD model. Next, the numerical approach isdescribed in the context of the Variational Multi-Scale (VMS) stabilization. Thisstabilization comes to add a term to the weak formulation to mimics the effectsof the unresolved scales over the coarse scales. If the effects of these subscalesare not taken into account when dealing with fluxes dominated byconvection, as it is the cases for fusion plasmas, the numerical scheme canlead to unphysical results. A detailed study of the resistive internal kinkinstability has been done as well as an introductory study of the so called Xpointplasmas in order to validate the numerical scheme developed here