Cette thèse propose l’étude d’une méthode numérique permettant de simuler un plasma. On considère un ensemble de particules, dont le mouvement est régi par l’équation de Vlasov, et qui est sensible aux forces électromagnétiques, qui proviennent des équations de Maxwell. La résolution numérique des équations de Vlasov-Maxwell est réalisée par une méthode Particle In Cell (PIC). La résolution des équations de Maxwell nécessite un maillage suffisamment fin afin de modéliser correctement les problémes multi-échelles que nous souhaitons traiter. Cependant, mailler finement tout le domaine de calcul a un coût. La nouveauté de cette thèse est de proposer un solveur PIC sur des maillages cartésiens localement raffinés, des maillages non conformes, afin de garantir la bonne modélisation du phénomène physique et d’éviter une trop forte pénalisation des temps de calcul.Nous utilisons une méthode Galerkin Discontinue en domaine temporelle (GDDT), qui offre l’avantage d’être d'une grande flexibilité dans le choix du maillage et qui est une méthode d’ordre élevé. Un point fondamental dans l’étude des solveurs PIC concerne le respect de la conservation de la charge. Nous proposons deux approches afin de traiter cet aspect. La première concerne les méthodes utilisant un système de Maxwell augmenté, dont la nouveauté a été de les étendre aux maillages non conformes. La seconde approche repose sur une méthode originale de pré-traitement du calcul du terme source de courant. / This thesis deals with the study of a numerical method to simulate a plasma. We consider a set of particles whose displacement is governed by the Vlasov equation and which creates an electromagnetic field thanks to Maxwell equations. The numerical resolution of the Vlasov-Maxwell system is performed by a Particle In Cell (PIC) method. The resolution of Maxwell equations needs a sufficiently fine mesh to correctly simulate the multi scaled problems that we have to face. Yet, a uniform fine mesh of the whole domain has a prohibitive cost. The novelty of this thesis is a PIC solver on locally refined Cartesian meshes : non conforming meshes, to guarantee the good modeling of the physical phenomena and to avoid too large CPU time. We use the Discontinuous Galerkin in Time Domain (DGTD) method which has the advantage of a great flexibility in the choice of the mesh and which is a high order method. A fundamental point in the study of PIC solvers is the respect of the charge conserving law. We propose two approaches to tackle this point. The first one deals with augmented Maxwell systems, that we have adapted to non conforming meshes. The second one deals with an original method of preprocessing of the calculation of the current source term.

Dans un contexte de changement climatique, il est essentiel de prévoir comment les organismes peuvent être affectés dans leurs relations physiques avec l'environnement. Les amphibiens représentent le groupe des vertébrés le plus sensible aux changements environnementaux, en raison d'une perte en eau par évaporation transépidermique (PEET) permanente. Ma thèse vise à mettre en place des approches pour mesurer et modéliser avec précision les surfaces de la peau contribuant à la PEET; établir les lois de transfert d'eau amphibien-environnement; et fournir une meilleure compréhension des réponses physiologiques face au pathogène Batrachochytrium dendrobatidis. Ces expériences ont été réalisées sur des tritons palmés (Lissotriton helveticus) mâles adultes en phase terrestre. Nos résultats suggèrent que L. helveticus ne présente aucune adaptation physiologique pour limiter la PEET, les moyens étant limités à l'expression d'une posture en forme de "$". Une méthode de reconstruction 3D basée sur l'lmagerie par Résonance Magnétique a été utilisée pour générer des géométries 3D des tritons utilisables pour mesurer leur surface, et à des fins de simulation. Nous avons ainsi réalisé une analyse numérique en 3D des PEET, et avons proposé une relation pour estimer cette perte dans une large gamme de conditions climatiques. Enfin, nos résultats supportent l'hypothèse de dysfonctionnement épidermique, suggérant que B. dendrobatidis compromet la capacité des amphibiens à se réhydrater. Ma thèse devrait contribuer à développer de nouvelles approches en sciences des relations eau-amphibiens, et à améliorer nos connaissances sur les effets des changements environnementaux sur les organismes / Ln a context of climate change, it is critical to predict how organisms might be affected in their physical relations with environment. Amphibians are among the vertebrate groups the most affected by ecological changes, because of permanent transepidermal evaporative water loss (TEWL) through their skin. My thesis aims at setting up approaches to measure and model accurately the functional skin surface areas that contribute to TEWL, establishing laws of water transfer between an amphibian and its physical environment, and providing understanding on physiological responses to the skin pathogen Batrachochytrium dendrobatidis. We conducted experiments on adult males of the palmate newt (Lissotriton helveticus) during their terrestrial phase. Our results suggest that L. helveticus did not show any physiological adaptations to restrain TEWL. The ways to reduce TEWL result essentially in the expression of a stereotyped "$"-shaped water-conserving posture. We used a Magnetic Resonance lmaging-based 3D reconstruction method to generate 3D geometries of newt that is suitable for measuring skin surface areas, and for simulation purposes. We successfully performed 3D numerical analysis of TEWL, and proposed an original relationship to estimate TEWL rates in a large range of temperature and humidity. Finally, our results support the epidermal dysfunction hypothesis, which suggests that B. dendrobatidis compromises the ability of amphibians to rehydrate. My thesis would contribute to open new approaches to the science of amphibian water relations, and improve our knowledge of the effects of ecological changes on organisms

Water pollution in drinking water is a major concern in rural areas that depend on local surface and ground water supplies. The Amazon river, for example, has800 thousand rural inhabitants, many of whom do not have access to treated water. Reaching the Amazon River to collect these water samples is already a complicated task. With constantly changing floodplains, and therefore water quality, the ability to collect water samples remotely and autonomously can help rural areas monitor their drinking water. There have been several studies investigating different unmanned surface vehicle (USV)prototypes and data collection methods. However, none have specifically made a compact USV to maneuver in rivers, while aiming to conserve energy to drive longer distances. This paper describes an in-depth design, fabrication, and automation process for a USV to drive in the Wabash River. The USV monitors its own location, speed, and battery voltage for power consumption analysis. As proof of concept, the USV measures water depth during field studies performed in Lake Harner, Indiana and the Wabash River. These field studies yield affirming results for the controls logic and power conservation of the designed USV.<br>

<p>Breast cancer is the most commonly diagnosed cancer type worldwide. Given high survivorship, increased focus has been placed on long-term treatment outcomes and patient quality of life. While breast-conserving surgery (BCS) is the preferred treatment strategy for early-stage breast cancer, anticipated healing and breast deformation (cosmetic) outcomes weigh heavily on surgeon and patient selection between BCS and more aggressive mastectomy procedures. Unfortunately, surgical outcomes following BCS are difficult to predict, owing to the complexity of the tissue repair process and significant patient-to-patient variability. To overcome this challenge, we developed a predictive computational mechanobiological model that simulates breast healing and deformation following BCS. The coupled biochemical-biomechanical model incorporates multi-scale cell and tissue mechanics, including collagen deposition and remodeling, collagen-dependent cell migration and contractility, and tissue plastic deformation. Available human clinical data evaluating cavity contraction and histopathological data from an experimental porcine lumpectomy study were used for model calibration. The computational model was successfully fit to data by optimizing biochemical and mechanobiological parameters through the Gaussian Process. The calibrated model was then applied to define key mechanobiological parameters and relationships influencing healing and breast deformation outcomes. Variability in patient characteristics including cavity-to-breast volume percentage and breast composition were further evaluated to determine effects on cavity contraction and breast cosmetic outcomes, with simulation outcomes aligning well with previously reported human studies. The proposed model has the potential to assist surgeons and their patients in developing and discussing individualized treatment plans that lead to more satisfying post-surgical outcomes and improved quality of life.</p>

Bakgrund: Bröstcancer är idag den vanligaste typen av cancer i världen hos kvinnor. Att drabbas av bröstcancer är en stor omställning i livet. Bra kontakt med omvårdnadspersonalen är viktigt för behandlingen och återhämtningen. Kvinnors upplevelser finns beskrivet i forskning och behöver sammanställas för att ge en överblick på kunskapsläget. Syfte: Syftet med denna litteraturstudie var att beskriva kvinnors upplevelse av att drabbas av bröstcancer, synen på omvårdnad och genomgå kirurgisk behandling.  Metod: Studien baserades på åtta studier som har genomförts med kvalitativ metod. Artiklarna kvalitetsgranskades med stöd av Olsson och Sörensens (2011) granskningstabell för att därefter analyseras med hjälp av Hsieh och Shannons (2005) analysmodell. Resultat: Resultatet kategoriserades i tre huvudteman: nyuppkomna känslor, kommunikation från omvårdnadspersonal och relationen med omvårdnadspersonalen med sammanlagt sex subteman. Kvinnorna som gjort kirurgisk behandling vid bröstcancer önskade stöd från omvårdnadspersonalen, förbättrad kommunikation och individanpassad information om operationen och vad som kommer hända sen. Konklusion: För att kunna ge kvinnorna bästa möjliga omvårdnad behöver omvårdnadspersonalen ha ett mer personcentrerat tankesätt med fokus på stöd och kommunikation samt ge individanpassad information. / Background: Breast cancer is the most common cancer among women all over the world. To be diagnosed with breast cancer is a big challenge. Good contact with healthcare professionals is important for treatment and recovery. The experience of women is described in research and need to be compiled to provide an overview of the state of knowledge  Aim: The purpose of this literature study was to examine women's experiences of suffering from breast cancer, their view of nursing care and undergoing surgical treatment. Methods: A qualitative method was used based on eight scientific articles reviewed with Olsson and Sörensen’s (2011) review table. The analysis process was inspired of Hsieh and Shannon’s (2005) analysis form. Results: The results were categorized into three main themes: new emotions, communication with nursing staff, and the relationship with nursing staff, altogether with six sub-themes. Women who have gone through surgical treatment due to breast cancer wanted support from the nursing staff, improved communication, personalized information about the surgery and what will happen post surgery. Conclusion: To be able to provide women with the best possible care, the nursing staff need to have a more person-centered mindset with a focus on support and communication and provide individualized information.

Yes / The need for desalinated seawater and reclaimed wastewater is increasing rapidly with the rising demands for drinkable water required for the world with continuously growing population. Reverse Osmosis (RO) processes are now among the most promising technologies used to remove chemicals from industrial effluents. N-nitrosamine compounds and especially N-nitrosodimethylamine (NDMA) are human carcinogens and can be found in industrial effluents of many industries. Particularly, NDMA is one of the by-products of disinfection process of secondary-treated wastewater effluent with chloramines, chlorines, and ozone (inhibitors). However, multi-stage RO processes with permeate reprocessing and recycling has not yet been considered for the removal of N-nitrosodimethylamine from wastewater. This research therefore, begins by investigating a number of multi-stage RO processes with permeate-reprocessing to remove N-nitrosodimethylamine (NDMA) from wastewater and finds the best configuration in terms of rejection, recovery and energy consumption via optimisation. For the first time we have applied Species Conserving Genetic Algorithm (SCGA) in optimising RO process conditions for wastewater treatment. Finally, permeate recycling is added to the best configuration and its performance is evaluated as a function of the amount of permeate being recycled via simulation. For this purpose, a mathematical model is developed based on the solution diffusion model, which is used for both optimisation and simulation. A number of model parameters have been estimated using experimental data of Fujioka et al. (Journal of Membrane Science 454 (2014) 212–219), so that the model can be used for simulation and optimisation with high accuracy and confidence.

Breast cancer is the most common cancer among women in the United States with over 60% of cases diagnosed as early stage disease. For those women without prohibiting clinical or cosmetic concerns, a choice between breast-conserving surgery and mastectomy can be made. Either choice confers equivalent survival. The decision-making process also involves consideration of recurrence risk as well as management of the unaffected, contralateral breast for both future surveillance and risk reduction. In recent years, increasing rates of mastectomy with contralateral prophylactic mastectomy have been reported among women with unilateral, early stage breast cancer. If eligible for a choice among surgical options, a woman’s decision becomes one of personal preference. The decision-making process is complex and involves consideration of potential benefits and harms with each option. The purpose of this dissertation was to: 1) analyze the psychometric properties of the Anxiety Subscale of the Depression Anxiety Stress Scale, 2) critically review Decisional Conflict Scales and 3) prospectively identify demographic, clinical, cognitive and affective factors influencing a woman’s decision to choose either breast conserving surgery or mastectomy with contralateral prophylactic mastectomy and to identify self-reported sources of information in the surgical decision-making process. Three manuscripts make up the dissertation. A secondary data analysis was conducted to test the psychometric properties of the Anxiety Subscale of the Depression Anxiety Stress Scale (DASS). The results of this analysis supported the reliability and validity of the DASS anxiety subscale. A critical review of decisional conflict measures for use with early stage breast cancer patients making surgical treatment decisions was conducted. The results of this review supported the use of Decisional Conflict Scales from a clinical and research perspective. Existing Decisional Conflict Scales show moderate to acceptable reliability. The first two manuscripts provided background and support for the use of scales included in the research study described in the third manuscript. This study was a prospective, exploratory, cross-sectional, mixed-methods study describing factors influencing preference for surgical choice among women with early stage breast cancer. A sample of 78 participants enrolled in the study, 47 who chose breast conserving surgery and 31 who chose mastectomy with contralateral prophylactic mastectomy. Differences were tested between the groups. Women who chose mastectomy with contralateral prophylactic mastectomy were younger, more likely to work full or part-time, had larger tumors and participated in preoperative genetic counselling. Women who chose breast conserving surgery were more likely to have participated in preoperative breast magnetic resonance imaging. Overall, women choosing either surgery were not experiencing severe levels of distress, depression, anxiety or stress although there were individual variations. Women choosing mastectomy with contralateral prophylactic mastectomy were more anxious and had more frequent intrusive thoughts about the diagnosis. They also had less decisional conflict as compared to women choosing breast conserving surgery. Information sources were similar but the most influential information source differed among the two groups. In both groups, intention for surgical choice was matched by the final decision. There are many factors influencing surgical choice among women with early stage breast cancer. Previous work has focused on clinical, demographic and diagnostic processes influencing the decision. With this study, evidence regarding the influence of cognitive and affective factors is described.

Small kinematics assumption in classical engineering has been in the center of consideration in structural analysis for decennaries. In the recent years the interest for sustainable and optimized structures, lightweight structures and new materials has grown rapidly as a consequence of desire to archive economical sustainability. These issues involve non-linear constitutive response of materials and can only be accessed on the basis of geometrically and materially non-linear analysis. Numerical simulations have become a conventional tool in modern engineering and have proven accuracy in computation and are on the verge of superseding time consuming and costly experiments.\newlineConsequently, this work presents a numerical computational framework for modeling of geometrically non-linear large deformation of isotropic and orthotropic materials under static and dynamic loading. The numerical model is applied on isotropic steel in plane strain and orthotropic wood in 3D under static and dynamic loading. In plane strain Total Lagrangian, Updated Lagrangian, Newmark-$\beta$ and Energy Conserving Algorithm time-integration methods are compared and evaluated. In 3D, a Total Lagrangian static approach and a Total Lagrangian based dynamic approach with Newmark-$\beta$ time-integration method is proposed to numerically predict deformation of wood under static and dynamic loading. The numerical model's accuracy is validated through an experiment where a knot-free pine wood board under large deformation is studied. The results indicate accuracy and capability of the numerical model in predicting static and dynamic behaviour of wood under large deformation. Contrastingly, classical engineering solution proves its inaccuracy and incapability of predicting kinematics of the wood board under studied conditions. / Små kinematikantaganden inom klassisk ingenjörsteknik har varit centralt för konstruktionslösningar under decennier. Under de senaste åren har intresset för hållbara och optimerade strukturer, lättviktskonstruktioner och nya material ökat kraftigt till följd av önskan att uppnå ekonomisk hållbarhet. Dessa nya konstruktionslösningar involverar icke-linjär konstitutiv respons hos material och kan endast studeras baserad på geometriskt och materiellt olinjär analys. Numeriska simuleringar har blivit ett konventionellt verktyg inom modern ingenjörsteknik och visat sig ge noggrannhet i beräkning och kan på sikt ersätta tidskrävande och kostsamma experiment.\newlineDetta examensarbete presenterar ett numeriskt beräkningsramverk för modellering av geometrisk olinjäritet med stora deformationer hos isotropa och ortotropa material vid statisk och dynamisk belastning. Den numeriska modellen appliceras på isotropiskt stål i plantöjning och ortotropisk trä i 3D vid statisk och dynamisk belastning. I fallet med plantöjning jämförs och utvärderas den Totala Lagrangianen, Uppdaterade Lagrangianen, Newmark-$\beta$ och Energi Konserverings Algoritm metoderna. I 3D föreslås en statisk Total Lagrangian metod och en dynamisk Total Lagrangian-baserad metod med Newmark-$\beta$ tidsintegreringsmetod för att numeriskt förutse statisk och dynamisk deformation hos trä. Den numeriska modellens noggrannhet valideras genom ett experiment där en kvistfri furuplanka studeras under stora deformationer. Resultaten bekräftar noggrannhet och förmåga hos den numeriska modellen att förutse statiska och dynamiska processer hos trä vid stora deformationer. Däremot, visar klassisk ingenjörslösning brist på förmåga att förutse trä plankans kinematik under studerade förhållanden.

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This thesis presents some theoretical studies dealing with quantum interference effects in electron transport through single molecule magnet transistors and a study on optical non-conserving spin transitions in the Nitrogen-vacancy center in diamond. The thesis starts with a brief general introduction to the physics of quantum transport through single electron transistors. Afterwards, the main body of the thesis is divided into three studies: (i) In chapter (2) we describe the properties of single molecule magnets and the Berry phase interference present in this nanomagnets. We then propose a way to detect quantum interference experimentally in the current of a single molecule magnet transistor using polarized leads. We apply our theoretical results to the newly synthesized nanomagnet Ni4. (ii) In chapter (3) we review the Kondo effect and present a microscopic derivation of the Kondo Hamiltonian suitable for full and half integer spin nanomagnets. We then calculate the conductance of the single molecule magnet transistor in the presence of the Kondo effect for Ni4 and show how the Berry phase interference becomes temperature dependent. (iii) We conclude in chapter (4) with a theoretical study of the single Nitrogen vacancy defect center in diamond. We show that it is possible to have spin non-conserving transitions via the hyperfine interaction and propose a way to write and read quantum information using circularly polarized light by means of optical Lambda transitions in this solid state system.