Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-04-11T19:27:27Z No. of bitstreams: 1 daianaaparecidarodrigues.pdf: 8225936 bytes, checksum: 96ec323f343f92c319f4e261145f9c6a (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-04-24T03:34:16Z (GMT) No. of bitstreams: 1 daianaaparecidarodrigues.pdf: 8225936 bytes, checksum: 96ec323f343f92c319f4e261145f9c6a (MD5) / Made available in DSpace on 2016-04-24T03:34:16Z (GMT). No. of bitstreams: 1 daianaaparecidarodrigues.pdf: 8225936 bytes, checksum: 96ec323f343f92c319f4e261145f9c6a (MD5) Previous issue date: 2013-08-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Fenômenos biológicos são todo e qualquer evento que possa ser observado nos seres vivos. O estudo desses fenômenos permite propor explicações para o seu mecanismo, a m de entender as causas e efeitos. Pode-se citar como exemplos de fenômenos biológicos o comportamento das células como respiração, reprodução, metabolismo e morte celular. Equações de reação-difusão são frequentemente utilizadas para modelar fenômenos bioló- gicos. Sistemas de reação-difusão podem produzir padrões espaciais estáveis a partir de uma distribuição inicial uniforme esse fenômeno é conhecido como instabilidade de Turing. Este trabalho apresenta a análise da instabilidade de Turing bem como resultados numéricos para a solução de três modelos biológicos, modelo de Schnakenberg, modelo de glicólise e modelo da coagulação sanguínea. O modelo de Schnakenberg é utilizado para descrever uma reação química autocatalítica e o modelo de glicólise é relativo ao processo de degradação metabólica da molécula de glicose para proporcionar energia para o metabolismo celular, esses dois modelos são frequentemente relatados na literatura. O terceiro modelo é mais recente e descreve o fenômeno da coagulação sanguínea. Nas soluções numéricas se utiliza o método das linhas onde a discretização espacial é feita através de um esquema de diferenças nitas. O sistema de equações diferencias ordinárias resultante é resolvido por um esquema de integração adaptativo, com a utilização de pacote para computação cientí ca da linguagem Python, Scipy. / Biological phenomena are all and any event that can be observed in living beings. The study of these phenomena enables us to propose explanations for its mechanisms in order to understand causes and e ects. One can cite as examples of biological phenomena the behavior of cells as respiration, reproduction, metabolism and cell death. Reactiondi usion equations are often used to model biological phenomena. Reaction-di usion systems can produce stable spatial patterns from a uniform initial distribution, this phenomenon is known as Turing instability. This dissertation presents an analysis of the Turing instability as well as numerical results for the solution of three biological models, model Schnakenberg, model of glycolysis and model of blood coagulation. The Schnakenberg model is used to describe an autocatalytic chemical reaction and glycolysis model refers to the process of metabolic breakdown of the glucose molecule to provide energy for cellular metabolism, these two models are frequently reported in the literature. The third model is newer and describes the phenomenon of blood coagulation. The method of lines is used in the numerical solutions, where the spatial discretization is done through a nite di erence scheme. The resulting system of ordinary di erential equations is then solved by an adaptive integration scheme with the use of the package for scienti c computing of Python language, Scipy.

Cette thèse porte sur le développement de méthodes de Monte-Carlo pour calculer des représentations Feynman-Kac impliquant des opérateurs sous forme divergence avec un coefficient de diffusion constant par morceaux. Les méthodes proposées sont des variantes de la marche sur les sphères à l'intérieur des zones avec un coefficient de diffusion constant et des techniques de différences finies stochastiques pour traiter les conditions aux interfaces aussi bien que les conditions aux limites de différents types. En combinant ces deux techniques, on obtient des marches aléatoires dont le score calculé le long du chemin fourni un estimateur biaisé de la solution de l'équation aux dérivées partielles considérée. On montre que le biais global de notre algorithme est en général d'ordre deux par rapport au pas de différences finies. Ces méthodes sont ensuite appliquées au problème direct lié à la tomographie par impédance électrique pour la détection de tumeurs. Une technique de réduction de variance est également proposée dans ce cadre. On traite finalement du problème inverse de la détection de tumeurs à partir de mesures de surfaces à l'aide de deux algorithmes stochastiques basés sur une représentation paramétrique de la tumeur ou des tumeurs sous forme d'une ou plusieurs sphères. De nombreux essais numériques sont proposés et montrent des résultats probants dans la localisation des tumeurs. / This thesis deals with the development of Monte-Carlo methods to compute Feynman-Kac representations involving divergence form operators with a piecewise constant diffusion coefficient. The proposed methods are variations around the walk on spheres method inside the regions with a constant diffusion coefficient and stochastic finite differences techniques to treat the interface conditions as well as the different kinds of boundary conditions. By combining these two techniques, we build random walks which score computed along the walk gives us a biased estimator of the solution of the partial differential equation we consider. We prove that the global bias is in general of order two with respect to the finite difference step. These methods are then applied for tumour detection to the forward problem in electrical impedance tomography. A variance reduction technique is also proposed in this case. Finally, we treat the inverse problem of tumours detection from surface measurements using two stochastics algorithms based on a spherical parametric representation of the tumours. Many numerical tests are proposed and show convincing results in the localization of the tumours.

Cette thèse porte sur les fronts de transition pour des équations de réaction-diffusion dans différents milieux. Les fronts de transition généralisent les notions habituelles de fronts progressifs ou pulsatoires. Les principaux résultats sont les suivants. Pour des réactions bistables, nous prouvons la monotonie en temps de tous les fronts de transition avec vitesse globale moyenne non nulle. Pour des réactions bistables périodiques en temps ou pour des réactions de type combustion, nous prouvons l’existence et l’unicité de la vitesse globale moyenne d’un front. De plus, nous montrons que les fronts presque plans sont en réalité plans et nous montrons l’existence de fronts de transitions non standard. Pour des réactions bistables périodiques en espace, nous montrons la continuité et la différentiabilité des vitesses et des profils de ces fronts pulsatoires par rapport à la direction e en supposant l’existence de fronts pulsatoires à vitesse non nulle dans toutes les directions $e$. Ensuite, nous prouvons que la vitesse de propagation d’un front de transition quelconque est comprise entre les vitesses minimales et maximales des fronts pulsatoires. Enfin, nous étudions les vitesses globales moyennes des fronts de transition bistables dans des domaines non bornés : domaines extérieurs ou domaines à branches multiples cylindriques. Dans ces deux types de domaines, nous prouvons l’existence et l’unicité de la vitesse globale moyenne de tous les fronts de transition sous certaines hypothèses. / This dissertation is concerned with transition fronts in various media, which generalize the standard notions of traveling fronts. The main results are as following. For bistable reaction, we prove the time monotonicity of all transition fronts with non-zero global mean speed, whatever shape their level sets may have. For time-periodic bistable reaction and combustion-type reaction, we prove the existence and the uniqueness of the global mean speed. Meantime, we show that almost-planar fronts are actually planar and we show the existence of non-standard transitions fronts in $\mathbb{R}^N$. For spatially periodic bistable reaction, we show some continuity and differentiability properties of the front speeds and profiles with respect to the direction $e$ by providing the existence of pulsating fronts with nonzero speed in all directions $e$. Then, we prove that the propagating speed of any transition front is bounded by the minimal speed and the maximal speed of pulsating fronts. Finally, we study the mean speed of bistable transition fronts in unbounded domains: exterior domains and domains with multiple cylindrical branches. In both domains, we prove the existence and uniqueness of the global mean speed of any transition front under some assumptions.

Cette thèse s'inscrit dans le cadre général de l'étude de la dynamique de populations. Elle porte sur la modélisation et l'analyse mathématique de l'hématopoïèse, le processus de production et de régulation des cellules sanguines. La population de cellules est perçue comme un milieu continu avec une structuration en âge et en espace. Nous avons commencé par analyser des modèles d'équations différentielles et aux différences à retard discret et distribué. Ces modèles à retard permettent de mettre en évidence des comportements particuliers tels que l'existence de solutions périodiques. Ensuite, nous avons pris en compte l'aspect spatial et la diffusion des cellules dans ces modèles, tout en sachant que la structuration en espace, dans le cas de l'hématopoïèse, a été très peu abordée par le passé. Un nouveau modèle a été obtenu du point de vue mathématique. Une étude d'existence d'ondes progressives est effectuée lorsque le domaine est non borné et lorsque le domaine est borné une étude de stabilité des états stationnaires ainsi que de l'existence d'une bifurcation de Hopf est réalisée / This thesis focuses on the study of population dynamics. It is devoted to the mathematical analysis and modeling of hematopoiesis, which is the process leading to the production and regulation of blood cells. The cell's population is seen as a continuous medium structured in age and space. We analyzed models of differential-difference system with discrete- and distributed -delay. These models can exhibit specific behaviors such as the existence of periodic solutions. Then we consider a space structuration and the diffusion of cells in such models, knowing that the space structure has not been widely studied in the case of hematopoiesis. A new model is obtained from the mathematical point of view. We studied the existence of traveling waves when the domain is unbounded. When the domain is bounded, the stability of stationary solutions and the existence of a Hopf bifurcation are obtained

Le but de ce travail est l'étude d'un problème de transmission en dynamique de population entre deux habitats juxtaposés. Dans chacun des habitats, on considère une équation aux dérivées partielles, modélisant la dispersion généralisée, formée par une combinaison linéaire du laplacien et du bilaplacien. On commence d'abord par étudier et résoudre la même équation avec diverses conditions aux limites posée dans un seul habitat. Cette étude est effectuée grâce à une formulation opérationnelle du problème: on réécrit cette EDP sous forme d'équation différentielle, posée dans un espace de Banach construit sur les espaces Lp avec 1 < p < +∞, où les coefficients sont des opérateurs linéaires non bornés. Grâce au calcul fonctionnel, à la théorie des semi-groupes analytiques et à la théorie de l'interpolation, on obtient des résultats optimaux d'existence, d'unicité et de régularité maximale de la solution classique si et seulement si les données sont dans certains espaces d'interpolation. / The aim of this work is the study of a transmission problem in population dynamics between two juxtaposed habitats. In each habitat, we consider a partial differential equation, modeling the generalized dispersion, made up of a linear combination of Laplacian and Bilaplacian operators. We begin by studying and solving the same equation with various boundary conditions in a single habitat. This study is carried out using an operational formulation of the problem: we rewrite this PDE as a differential equation, set in a Banach space built on the spaces Lp with 1 < p < +∞, where the coefficients are unbounded linear operators. Thanks to functional calculus, analytic semigroup theory and interpolation theory, we obtain optimal results of existence, uniqueness and maximum regularity of the classical solution if and only if the data are in some interpolation spaces.

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No. of bitstreams: 1 nunesneto_o_dr_bauru.pdf: 4276326 bytes, checksum: e73a2086ffde0d12d2f5875fb168f8c1 (MD5) Previous issue date: 2016-04-28 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Materiais e dispositivos baseados em compostos orgânicos desempenham um importante papel em diversas áreas da aplicação tecnológica devido às suas interessantes propriedades eletro-magneto- ópticas, adicionadas às suas características mecânicas únicas, facilidade de processamento, versatilidade de síntese e baixo custo relativo. Apesar do proeminente campo de aplicação destes materiais, muitos aspectos associados à sua ciência básica são ainda pouco compreendidos. Nesse cenário destaca-se o fenômeno de Magnetoresistência Orgânica (OMAR, da sigla em inglês). Tal fenômeno encontra-se associado a variações significativas da condutividade elétrica de dispositivos orgânicos induzidas por pequenos campos magnéticos externos em temperatura ambiente e tem sido observado em diversificados materiais poliméricos e moleculares. No presente trabalho avaliou-se o fenômeno de OMAR apresentado por um Diodo Emissor de Luz baseado na molécula de Alq3. Medidas de Espectroscopia de Impedância Elétrica na presença de um Campo Magnético estático externo (EIE-CM) foram realizadas sobre o referido dispositivo para diferentes temperaturas. Métodos diferenciados de aquisição e manipulação de dados foram empregados a fim de remover a dependência temporal dos sinais tipicamente observados. Os seguintes Efeitos de Campo Magnético (MFE, da sigla em inglês) foram observados sobre a resposta elétrica do dispositivo: (i) redução de cerca de 1% na resistência, efeito praticamente constante para todo o espectro de frequência e; (ii) variações significativas na capacitância, com intensificação do efeito de Capacitância Negativa em baixas frequências. Como suporte para a interpretação dos resultados experimentais foram realizadas simulações empregando-se duas abordagens: Circuitos Equivalentes e Análise de perturbações de pequenos sinais (em inglês, Small Signal Analysis ) via soluções numéricas das equações de transporte de Boltzmann numa aproximação por Drift-Diffusion empregando-se dispositivos simplificados. As análises sugerem que os MFE evidenciados podem estar associados a um aumento da mobilidade efetiva dos portadores de carga e a uma redução na taxa de recombinação bimolecular no dispositivo. Os resultados foram interpretados em termos dos modelos atualmente aceitos para o fenômeno de OMAR. Esta tese também apresenta um estudo de processos de geração e transferência de carga em corantes Cianinas, materiais promissores para aplicações em células solares com absorção no infravermelho. Técnicas de Ressonância de Spin Eletrônico induzida por Luz foram empregadas em blendas destes corantes com o polímero MEH-PPV e com o fulereno (C60) a fim de avaliar, respectivamente, o caráter aceitador e doador de elétrons das Cianinas. / Materials and devices based on organic compounds play an important role in various technological applications, mainly due to their interesting electrical-magneto-optical properties combined with their unique mechanical properties, easy processing, versatility of synthesis and relatively low cost. Despite the prominent application field of these materials many aspects associated with their basic science are still not well understood. In this context the Organic Magnetoresistance phenomenon (OMAR) deserves to be highlighted. This phenomenon is associated with significant changes in the electrical conductivity of organic devices induced by the presence of small external magnetic fields at room temperature, being observed in various polymeric and molecular materials. In this study we have investigated the OMAR phenomenon in Alq3-based OLEDs. Electrical impedance spectroscopy technique in the presence of an external static magnetic field (EIS-MF) was employed in the experiments; distinct temperatures were considered. Differentiated methods of acquisition and data manipulation were employed to remove the typically observed signal time dependence. The following magnetic field effects (MFE) were observed on the electrical response of the device: (i) a constant reduction of around 1% in the resistance over the entire frequency spectrum and; (ii) significant changes in the capacitance followed by an intensification of the negative capacitance effect at low frequencies. Simulations employing two different approaches were carried out for the interpretation of the experimental results: (i) Equivalent Circuits and (ii) Small Signal Analysis via numerical solutions of the Boltzmann transport equations by Drift-Diffusion approach. The results suggest that the observed MFE can be associated with an increase in the effective mobility of the charge carriers and a reduction in the bimolecular recombination rate in the device. The results were interpreted in terms of the currently accepted models for the OMAR phenomenon. This thesis also presents a study about generation and charge transfer processes in cyanine dyes (near infrared absorbing compounds) which are promising materials for applications in solar cells. Light induced Electron Spin Resonance (L-ESR) technique was employed to study the presence/formation of paramagnetic centers in blends of these dyes with MEH-PPV polymer and fullerene (C60) to evaluate, respectively, the electron acceptor and donor character of cyanine dyes. / FAPESP: 2011/21830-6 / CNPq: 204432/2013-8

Problems governed by partial differential equations (PDEs) in deformable domains, t Rd; d = 2; 3; are of fundamental importance in science and engineering. They are of particular relevance in the design of many engineering systems e.g., aircrafts and bridges as well as to the analysis of several biological phenomena e.g., blood ow in arteries. However, developing numerical scheme for such problems is still very challenging even when the deformation of the boundary of domain is prescribed a priori. Possibility of excessive mesh distortion is one of the major challenge when solving such problems with numerical methods using boundary tted meshes. The arbitrary Lagrangian- Eulerian (ALE) approach is a way to overcome this difficulty. Numerical simulations of convection-dominated problems have for long been the subject to many researchers. Galerkin formulations, which yield the best approximations for differential equations with high diffusivity, tend to induce spurious oscillations in the numerical solution of convection dominated equations. Though such spurious oscillations can be avoided by adaptive meshing, which is computationally very expensive on ne grids. Alternatively, stabilization methods can be used to suppress the spurious oscillations. In this work, the considered equation is designed within the framework of ALE formulation. In the first part, Streamline Upwind Petrov-Galerkin (SUPG) finite element method with conservative ALE formulation is proposed. Further, the first order backward Euler and the second order Crank-Nicolson methods are used for the temporal discretization. It is shown that the stability of the semi-discrete (continuous in time) ALE-SUPG equation is independent of the mesh velocity, whereas the stability of the fully discrete problem is unconditionally stable for implicit Euler method and is only conditionally stable for Crank-Nicolson time discretization. Numerical results are presented to support the stability estimates and to show the influence of the SUPG stabilization parameter in a time-dependent domain. In the second part of this work, SUPG stabilization method with non-conservative ALE formulation is proposed. The implicit Euler, Crank-Nicolson and backward difference methods are used for the temporal discretization. At the discrete level in time, the ALE map influences the stability of the corresponding discrete scheme with different time discretizations, and it leads to schemes where conservative and non-conservative formulations are no longer equivalent. The stability of the fully discrete scheme, irrespective of the temporal discretization, is only conditionally stable. It is observed from numerical results that the Crank-Nicolson scheme induces high oscillations in the numerical solution compare to the implicit Euler and the backward difference time discretiza-tions. Moreover, the backward difference scheme is more sensitive to the stabilization parameter k than the other time discretizations. Further, the difference between the solutions obtained with the conservative and non-conservative ALE forms is significant when the deformation of domain is large, whereas it is negligible in domains with small deformation. Finally, the local projection stabilization (LPS) and the higher order dG time stepping scheme are studied for convection dominated problems. The analysis is based on the quadrature formula for approximating the integrals in time. We considered the exact integration in time, which is impractical to implement and the Radau quadrature in time, which can be used in practice. The stability and error estimates are shown for the mathematical basis of considered numerical scheme with both time integration methods. The numerical analysis reveals that the proposed stabilized scheme with exact integration in time is unconditionally stable, whereas Radau quadrature in time is conditionally stable with time-step restriction depending on the ALE map. The theoretical estimates are illustrated with appropriate numerical examples with distinct features. The second order dG(1) time discretization is unconditionally stable while Crank-Nicolson gives the conditional stable estimates only. The convergence order for dG(1) is two which supports the error estimate.

Understanding and characterising the diffusive transport of capillary oxygen and nutrients in striated muscles is key to assessing angiogenesis and investigating the efficacy of experimental and therapeutic interventions for numerous pathological conditions, such as chronic ischaemia. In articular, the influence of both muscle tissue and microvascular heterogeneities on capillary oxygen supply is poorly understood. The objective of this thesis is to develop mathematical and computational modelling frameworks for the purpose of extending and generalising the current use of histology in estimating the regions of tissue supplied by individual capillaries to facilitate the exploration of functional capillary oxygen supply in striated muscles. In particular, we aim to investigate the balance between local capillary supply of oxygen and oxygen demand in the presence of various anatomical and functional heterogeneities, by capturing tissue details from histological imaging and estimating or predicting regions of capillary supply. Our computational method throughout is based on a finite element framework that captures the anatomical details of tissue cross sections. In Chapter 1 we introduce the problem. In Chapter 2 we develop a theoretical model to describe oxygen transport from capillaries to uniform muscle tissues (e.g. cardiac muscle). Transport is then explored in terms of oxygen levels and capillary supply regions. In Chapter 3 we extend this modelling framework to explore the influence of the surrounding tissue by accounting for the spatial anisotropies of fibre oxygen demand and diffusivity and the heterogeneity in fibre size and shape, as exemplified by mixed muscle tissues (e.g. skeletal muscle). We additionally explore the effects of diffusion through the interstitium, facilitated--diffusion by myoglobin, and Michaelis--Menten kinetics of tissue oxygen consumption. In Chapter 4, a further extension is pursued to account for intracellular heterogeneities in mitochondrial distribution and diffusive parameters. As a demonstration of the potential of the models derived in Chapters 2--4, in Chapter 5 we simulate oxygen transport in myocardial tissue biopsies from rats with either impaired angiogenesis or impaired arteriolar perfusion. Quantitative predictions are made to help explain and support experimental measurements of cardiac performance and metabolism. In the final chapter we summarize the main results and indicate directions for further work.

<p>Doktorska disertacija je posvećena re&scaron;avanju Ko&scaron;ijevog problema odabranih klasa frakcionih diferencijalnih jednačina u okviru Kolomboovih prostora uop&scaron;tenih funkcija. U prvom delu disertacije razmatrane su nehomogene evolucione jednačine sa prostorno frakcionim diferencijalnim operatorima reda 0 &lt; &alpha; &lt; 2 i koeficijentima koji zavise od x i t. Ova klasa jednačina je aproksimativno re&scaron;avana, tako &scaron;to je umesto početne jednačine razmatrana aproksimativna jednačina data preko regularizovanih frakcionih izvoda, odnosno, njihovih regularizovanih množitelja. Za re&scaron;avanje smo koristili dobro poznate uop&scaron;tene uniformno neprekidne polugrupe operatora. U drugom delu disertacije aproksimativno su re&scaron;avane nehomogene frakcione evolucione jednačine sa Kaputovim<br />frakcionim izvodom reda 0 &lt; &alpha; &lt; 2, linearnim, zatvorenim i gusto definisanim<br />operatorom na prostoru Soboljeva celobrojnog reda i koeficijentima koji zavise<br />od x. Odgovarajuća aproksimativna jednačina sadrži uop&scaron;teni operator asociran sa polaznim operatorom, dok su re&scaron;enja dobijena primenom, za tu svrhu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br />u disertaciji konstruisanih, uop&scaron;tenih uniformno neprekidnih operatora re&scaron;enja.<br />U oba slučaja ispitivani su uslovi koji obezbeduju egzistenciju i jedinstvenost<br />re&scaron;enja Ko&scaron;ijevog problema na odgovarajućem Kolomboovom prostoru.</p> / <p>Colombeau spaces of generalized functions. In the firs part, we studied inhomogeneous evolution equations with space fractional differential operators of order 0 &lt; &alpha; &lt; 2 and variable coefficients depending on x and t. This class of equations is solved&nbsp; approximately, in such a way that instead of the originate equation we considered the corresponding approximate equation given by regularized fractional derivatives, i.e. their&nbsp; regularized multipliers. In the solving procedure we used a well-known generalized uniformly continuous semigroups of operators. In the second part, we solved approximately inhomogeneous fractional evolution equations with Caputo fractional derivative of order 0 &lt; &alpha; &lt; 2, linear, closed and densely defined operator in Sobolev space of integer order and variable coefficients depending on x. The corresponding approximate equation&nbsp;&nbsp; is a given by the generalized operator associated to the originate&nbsp; operator, while the solutions are obtained by using generalized uniformly continuous solution operators, introduced and developed for that purpose. In both cases, we provided the conditions that ensure the existence and uniqueness solutions of the Cauchy problem in some Colombeau spaces.</p>