The modelling of transport processes in biological systems is one of the main theoretical challenges in physics, chemistry and biology. This is motivated by their essential role in the emergence of diseases, like tumour metastases, which originate from the spontaneous migration of cancer cells. Thus, improvements in their understanding could potentially pave the way for an outstanding innovation of present-day techniques in medicine. These processes often exhibit anomalous properties, which are qualitatively described by the power-law scaling of their mean square displacement, compared to the linear one of normal diffusion. Such behaviour has been often successfully explained by the celebrated continuous-time random walk model. However, recent experimental studies revealed the existence of both more complicated mean square displacement behaviour and anomalous features in other characteristic observables, e.g. the position-velocity statistics or the two point correlation functions of either the velocity or the position. Thus, in order to understand the anomalous diffusion recorded in these experiments and assess the microscopic processes underlying the observed macroscopic dynamics, one needs to have a complete tool-kit of techniques and models that can be readily compared with the experimental datasets. In this Thesis, we contribute to the construction of such a complete framework by fully characterising anomalous processes, which are described by means of a continuoustime random walk with general waiting time distributions and/or external forces that are exerted both during the jumps (as in the original model) and the waiting times. In the first case we derive both the joint statistics of these processes and their observables, specifically by obtaining a generalised fractional Feynman-Kac formula, and their multipoint correlation functions and employ them to fit the mean square displacement data of diffusing mitochondria. This result supports the experimental relevance of our formalism, which comprises general formulas for several quantities that can provide readily predictable tests to be checked in experiments. In the second case, we characterise the new anomalous processes by means of Langevin equations driven by a novel type of non Gaussian noise, which reproduces the typical fluctuations of a free diffusive continuous-time random walk. For a constant external force, we also obtain the fractional evolution equations of their position probability density function and show that, contrarily to continuous-time random walks, they are weak Galilean invariant, i.e., their position distribution in different Galilean frames is obtained by shifting the sample variable according to the relative motion of the frames. Thus, these processes provide a suitable frame-invariant framework, that could be employed to investigate the stochastic thermodynamics of anomalous diffusive processes.

Nesta Tese de Doutoramento investigamos a influência das órbitas em regime de stickiness, para com a dinâmica de alguns sistemas dinâmicos clássicos. Tais órbitas são caracterizadas como aprisionamentos de tempo finito ao redor de estrututas de regularidade no espaço de fases. Esse comportamento ao longo da dinâmica, pode afetar propriedades estatísticas, de difusão e de transporte, dependendo do ensemble de condições iniciais e parâmetros de controle. Caracterizamos a influência deste fenômeno em três sistemas dinâmicos: (i) modelo Fermi-Ulam (FUM), onde órbitas em regime de stickiness produzem decaimento de correlações em forma de exponencial esticada e de lei de potência, e toda uma análise estatística ao longo da dinâmica é feita, tanto analítica quanto numericamente; (ii) no modelo Bouncer, essas órbitas são caracterizadas via expoentes de Lyapunov e decaimento de correlações, onde elas funcionam como um mecanismo para atrasar a difusão ilimitada de energia; e finalmente (iii) no bilhar Stadium, onde aliado a ressonância, o stickiness atua como um facilitador na troca de comportamento de órbitas, onde as mesmas sofrem uma transição de difusão ilimitada, para platô estacionário, perto da criticalidade ressonante. / In this Doctorate Thesis we investigate how the sticky orbits influence the dynamics of some classical dynamical systems. These orbits are characterized as finite-time trapping around stability islands in the phase space. This behaviour along the dynamics, may affect statistical properties, diffusion and transport, depending on the ensemble of energies, initial conditions and control parameters. We characterize this stickiness influence in three dynamical systems: (i) in the Fermi-Ulam Model (FUM), where orbits in sticky regime produce a decay of correlations, of a stretched exponential and power law kinds and a whole statistics analysis is made concerning numerical and analytical approaches; (ii) in the Bouncer model, these orbits are characterized along the dynamics via Lyapunov exponents and decay of correlations, where they play the role of a mechanism to slow down the unlimited diffusion of energy; and finally (iii) in the Stadium billiard, where allied with the resonance, stickiness allows a change in the orbits behaviour, where we can set a transition from unlimited diffusion to stationary state, near the critical resonance.

Nesta Tese de Doutoramento investigamos a influência das órbitas em regime de stickiness, para com a dinâmica de alguns sistemas dinâmicos clássicos. Tais órbitas são caracterizadas como aprisionamentos de tempo finito ao redor de estrututas de regularidade no espaço de fases. Esse comportamento ao longo da dinâmica, pode afetar propriedades estatísticas, de difusão e de transporte, dependendo do ensemble de condições iniciais e parâmetros de controle. Caracterizamos a influência deste fenômeno em três sistemas dinâmicos: (i) modelo Fermi-Ulam (FUM), onde órbitas em regime de stickiness produzem decaimento de correlações em forma de exponencial esticada e de lei de potência, e toda uma análise estatística ao longo da dinâmica é feita, tanto analítica quanto numericamente; (ii) no modelo Bouncer, essas órbitas são caracterizadas via expoentes de Lyapunov e decaimento de correlações, onde elas funcionam como um mecanismo para atrasar a difusão ilimitada de energia; e finalmente (iii) no bilhar Stadium, onde aliado a ressonância, o stickiness atua como um facilitador na troca de comportamento de órbitas, onde as mesmas sofrem uma transição de difusão ilimitada, para platô estacionário, perto da criticalidade ressonante. / In this Doctorate Thesis we investigate how the sticky orbits influence the dynamics of some classical dynamical systems. These orbits are characterized as finite-time trapping around stability islands in the phase space. This behaviour along the dynamics, may affect statistical properties, diffusion and transport, depending on the ensemble of energies, initial conditions and control parameters. We characterize this stickiness influence in three dynamical systems: (i) in the Fermi-Ulam Model (FUM), where orbits in sticky regime produce a decay of correlations, of a stretched exponential and power law kinds and a whole statistics analysis is made concerning numerical and analytical approaches; (ii) in the Bouncer model, these orbits are characterized along the dynamics via Lyapunov exponents and decay of correlations, where they play the role of a mechanism to slow down the unlimited diffusion of energy; and finally (iii) in the Stadium billiard, where allied with the resonance, stickiness allows a change in the orbits behaviour, where we can set a transition from unlimited diffusion to stationary state, near the critical resonance.

The requirements of food packages are to ensure food safety and quality, to minimize spoilage, and to provide an easy way to store and handle food. To meet these demands for fibre-based food packages, barrier coatings are generally used to regulate the amount of gases entering a package, as some gases are detrimental to food quality. Oxygen, for example, initiates lipid oxidation in fatty foods. Bakery products may also be sensitive to oxygen. This thesis focused on mass transport of oxygen in order to gain deeper knowledge in the performance of barrier coatings and to develop means to optimize the performance of barrier coatings. This experimental study along with computer modelling characterized the structure of barrier materials with respect to the mass transport process.This project was performed as part of the multidisciplinary industrial graduate school VIPP (www.kau.se/en/vipp) - Values Created in Fibre Based Processes and Products – at Karlstad University, with the financial support from the Knowledge Foundation, Sweden, and Stora Enso. / <p>Artikel 2 "The influence of clay orientation..." ingick som manuskript i avhandlingen, då med titeln: "Influence of clay orientation in dispersion barrier coatings on oxygen permeation". Nu publicerad.</p>

The visualization of a 3D image obtained from computerized tomography examinations has shown itself to be an important factor for increasing the quality of medical diagnoses and, consequently, treatment efficacy. There already exist on the market, several visualization softwares, which use different techniques to show the 3D tomography image. However, to show a high quality 3D image, sophisticated devices must be used to obtain slices, close to one another, thus increasing the incidence of X-ray given to the patient. An interpolation slice method which resulted from the TC examination produces good results, and is able to reduce the X-ray incidence upon the patient. This method must reconstruct the curvature from the patient s internal structures without using slices in close proximity. This work proposes a method of 3D image interpolation, composed of a juxtaposition of the slices from CT examination results. The goal of this method is to increase the quality of 3D visualization through the production of sharp and precise structure contours. This thesis proposes the division of the interpolation method into two steps. In the first step, the goal is to obtain an initial representation of the image in 3D, which is composed of real slices as well as virtual slices which are referred to in this work as initial virtual slices. In the second step, the empty spaces of the structure are recovered by the 3D image inpainting process. This work also proposes a method to obtain the initial virtual slice and two different methods for inpainting the 3D image. These inpainting methods are the transversal slice line prolongation method and the transportation and diffusion of information. Both methods use the differential equation theory. The transportation and diffusion of information method shows better results than other methods proposed in this work, besides this, this method presents better results than the linear interpolation and Goshtasby et al. [1] methods also implemented in this work. Visual and numerical comparisons are used to obtain this conclusion. The numerical measures used are statistical correlation, the PSNR and the Hausdorff distance [2]. The transportation and diffusion of information method shows itself able to produce better results than all the other tested methods. Besides this principal contribution, this work also developed a KIT to implement 2D and 3D CT visualize applications. / A visualização de imagens resultantes de exame de tomografia computadorizada (TC) em 3D ´e um fator importante para o aumento da precisão nos diagnósticos médicos e, consequentemente, na eficácia dos tratamentos. Atualmente existem diversos produtos no mercado, que fazem uso de várias técnicas existentes para apresentação de imagens tomográficas em 3D. Contudo, para se obter maior suavidade e precisão nos contornos das estruturas visualizadas em 3D, utiliza-se equipamentos capazes de produzir fatias paralelas do corpo humano muito próximas uma das outras, aumentando a exposição dos pacientes aos raios X. Um método de interpolação de fatias resultantes de exame de TC que forneça bons resultados, pode reduzir a incidência de raios X no paciente, pois esse método pode recuperar a curvatura das estruturas sem a necessidade de uma grande proximidade entre as fatias. Este trabalho propõe um método para a interpolação de imagem em 3D, formada pela justaposição de fatias de resultados de exames de tomografia computadorizada. O objetivo desse método ´e obter contornos suaves e precisos, melhorando os processos de visualização em 3D. Para isso, esta tese propõe a divisão do processo de interpolação em duas etapas. Na primeira etapa obtém-se uma representação inicial da imagem em 3D composta por fatias reais e por fatias denominadas de fatias virtuais iniciais e, na segunda etapa, restaura-se essas estruturas geradas com um processo de retoque de imagem em 3D. Este trabalho propõe também um método para obtenção da fatia virtual inicial e dois métodos diferentes para a realização do passo de retoque da imagem em 3D resultante da justaposição das fatias reais e virtuais iniciais. Esses métodos são o prolongamento de linhas nas fatias transversais e transporte e difusão de informações. Ambos os métodos utilizam a teoria de equações diferenciais. O método de transporte e difusão de informações demonstrou melhores resultados do que outro método proposto neste trabalho, além de obter melhores resultados do que os métodos de interpolação linear e Goshtasby e outros [1] implementados neste trabalho. Comparações visuais e comparações numéricas utilizando a correlação estatística, a PSNR e a distância de Haussdorff [2] foram realizadas para se obter essas conclusões. O método de transporte e difusão de informações é capaz de gerar contornos mais suaves e precisos que esses outros métodos testados. Além dessa contribuição principal, este trabalho também desenvolveu um KIT para a construção de aplicações visualizadoras de tomografias computadorizadas em 2D e em 3D. / Mestre em Ciências

Dans cette thèse nous regardons plusieurs modèles de populations structurés s’écrivant à l’aide d’équations de transport. Le caractère bien posé ainsi que la positivité des solutions sont montrés de manière systématique au sens des sémiologues dans un cadre L1. Un premier travail est consacré à un système de type proie prédateur structuré en âge. Une étude de stabilité des équilibres nous permet de formuler explicitement un seuil un seuil d’extinction ainsi qu’in seuil pouvant amener à l’explosion des populations. On obtient numériquement la possibilité d’un cycle limite ainsi que la convergence vers un équilibre de coexistence des populations. Dans un cas particulier, ce modèle se réécrit comme un système différentiel à retard. A l’aide de fonctionnelle de Lyapunov, on montre la stabilité globale de cet équilibre sous certaines conditions. On étudie également 2 modèles structuré en taille, issus de la dynamique cellulaire. L’un est composé de deux équations de transport où la cellule peut être soit prolifèrent soit quiescente ; et le deuxième est une équation de type transport/ diffusion avec des conditions aux bords FELLER. On vérifie à chaque fois l’irréductibilité du semi groupe puis des arguments de faibles capacité L1 nous donne l’existence d’un « gap spectral » sous certaines conditions. On démontre ainsi dans certains cas la croissance exponentielle asynchrone du semi groupe / This thesis is dedicated to some structured populations models described with transport or transport-diffusion equations. The well-posedness, in the semigroupes setting in L1 and the positivity of the solutions are systematically shown. A first work is dedicated to an age-structured predator/prey system. A stability study of the equilibria allow us to give explicit formulations of an extinction threshold and an threshold which can lead to explosion of solutions. We numerically obtain the possibility to get a limit cycle and the convergence to a coexistence equilibrium of the populations. In a specific case, this model rewrites as a delay differential system. Using Lyapunov functional, we show the global stability of this equilibrium under some assumptions. We also study two size-structured models that come from cellular dynamics. The first one consists on two transport equations, where the cell can either proliferate or be quiescent, and the second one is a transport-diffusion equation with Feller boundary conditions. The irreducibility of the semigroup governing this latter model is always satisfied using the Hopf maximum principle. However, the irreducibility for the first model is true only under a necessary and sufficient condition that we give. We also show for these two models, using some weak compactness arguments in L1, the existence of a `spectral gap' (essential type strictly less than the type) ensuring the asynchronous exponential growth of the semigroup.