The genus Phytophthora comprises numerous plant pathogens in both natural and managed ecosystems. For Phytophthora spp. that infect roots, dispersal occurs in soil water through a combination of advection and swimming of specialized motile propagules (zoospores). Specific biological and physico-chemical processes, however, remain poorly understood, due to difficulties in studying phenomena in opaque media and lack of a theoretical framework for analyzing transport of motile microorganisms. The goal of this research was to elucidate the impacts of advection and swimming on zoospore movement in a saturated, ideal soil. The work was accomplished in two stages, (i) conceptualization of 3-dimensional topography and flow field heterogeneity at the subpore-scale, and (ii) observation of behavior of zoospore suspensions infiltrated into saturated media. Chapter 2 introduces a 3-dimensional particle tracking method and presents two studies investigating particle transport in simplified 'ideal pores'. The first study describes 'avoidance' by latex microspheres of a volume surrounding orthogonal grain contacts and the second describes 'capture', translation, and retention of microspheres under conditions unfavorable to deposition. Chapter 3 expands on the first study and demonstrates, with the aid of computational fluid dynamics, that low flow zones associated with orthogonal grain contacts are minimally connected to the main flow. Thus, probability of entry into these regions for large, non-Brownian particles by advection alone is low. In zoospore infiltration experiments, zoospore plumes 'converged' rather than dispersing as expected. To assess the possibility of zoospore auto-aggregation driving this 'convergence', Chapter 4 delves into the 'pattern swimming' observed in free-swimming zoospore suspensions, concluding that the concentrating is an example of bioconvection. Chapter 5 introduces a conceptual model to explain the anomalous zoospore plume behavior. Random walk simulations replicated plume convergence but were less successful at modeling anisotropic dispersion. At low infiltration rates (<100 μm s⁻¹), simulations predict that zoospores will remain at or near the soil surface, resulting in greater opportunity to find host tissues or to be transported with surface water. Further investigation is necessary to develop a robust theoretical framework with appropriate conceptualization of the subpore hydrodynamic environment for predicting transport of zoospores and other motile microorganisms in porous media. / Graduation date: 2011

This thesis is split in two different topics. Firstly, we study anomalous transport from kinetic models. Secondly, we consider the equations coming from weak wave turbulence theory and we study them via mean-field limits of finite stochastic particle systems. $\textbf{Anomalous transport from kinetic models.}$ The goal is to understand how fractional diffusion arises from kinetic equations. We explain how fractional diffusion corresponds to anomalous transport and its relation to the classical diffusion equation. In previous works it has been seen that particles systems undergoing free transport and scattering with the media can give rise to fractional phenomena in two cases: firstly, if in the dynamics of the particles there is a heavy-tail equilibrium distribution; and secondly, if the scattering rate is degenerate for small velocities. We use these known results in the literature to study the emergence of fractional phenomena for some particular kinetic equations. Firstly, we study BGK-type equations conserving not only mass (as in previous results), but also momentum and energy. In the hydrodynamic limit we obtain a fractional diffusion equation for the temperature and density making use of the Boussinesq relation and we also demonstrate that with the same rescaling fractional diffusion cannot be derived additionally for the momentum. But considering the case of conservation of mass and momentum only, we do obtain the incompressible Stokes equation with fractional diffusion in the hydrodynamic limit for heavy-tailed equilibria. Secondly, we will study diffusion phenomena arising from transport of energy in an anharmonic chain. More precisely, we will consider the so-called FPU-$\beta$ chain, which is a very simple model for a one-dimensional crystal in which atoms are coupled to their nearest neighbours by a harmonic potential, weakly perturbed by a nonlinear quartic potential. The starting point of our mathematical analysis is a kinetic equation; lattice vibrations, responsible for heat transport, are modelled by an interacting gas of phonons whose evolution is described by the Boltzmann Phonon Equation. Our main result is the derivation of an anomalous diffusion equation for the temperature. $\textbf{Weak wave turbulence theory and mean-field limits for stochastic particle systems.}$ The isotropic 4-wave kinetic equation is considered in its weak formulation using model homogeneous kernels. Existence and uniqueness of solutions is proven in a particular setting. We also consider finite stochastic particle systems undergoing instantaneous coagulation-fragmentation phenomena and give conditions in which this system approximates the solution of the equation (mean-field limit).

Nesta tese foi estudado o transporte de partículas na borda do plasma confinado magneticamente em tokamaks a partir de um modelo para ondas de deriva proveniente de flutuaçõoes eletrostáticas geradas pela não uniformidade do plasma. Para investigar esse problema, consideramos o modelo com duas ondas de deriva, que possui uma complexa dinâmica não linear onde podemos encontrar tanto transporte anômalo quanto transporte difusivo. Para a encontras no plano de fases as Estruturas Lagrangianas Coerentes (ELCs) e os jatos, foram confeccionados mapas de Poincaré, diagramas de expoente de Lyapunov a tempo finito, diagramas de deslocamento quadrático, diagramas de autocorrelação da velocidade e o diagrama de retorno. Para avaliar o impacto dessas ELCs no transporte de partículas foram analisados a série temporal do desvio padrão médio, da dispersão relativa e dos saltos dentro do mapa de Poincar´e e também foram confeccionados histogramas com a distribuição desses saltos. Foi encontrado que, com duas ondas de deriva e para uma determinada combinação de parâmetros, surgem correntes de jato, que persistem por longos períodos, imersas na região caótica. Verificamos que, assim como nas ilhas, a região interna às correntes de jato são inacessíveis às ELCs. Também foi encontrado que, quando existe uma corrente de jato, o transporte observado na região caótica não é simétrico com uma pequena deriva na direção contraria ao jato. Esse fenômeno observado ocorre em contrapartida ao caso típico de sistemas com mistura em que as ELCs tem acesso a todo o plano de fase e o transporte é difusivo. / In this thesis we studied the particle transport in the edge of magnetically confined plasma in tokamaks using a model of drift waves due to electrostatic fluctuations generated by the non-uniformity of the plasma. To investigate this issue, we consider the model with two drift waves, which has a complex nonlinear dynamics where we can find both anomalous and diffusive transport. To find the Lagrangian Coherent Structures (LCSs) and the jets, we used Poincaré maps, Finite time Lyapunov exponent diagrams, quadratic displacement diagrams, autocorrelation velocity diagrams and return displacement diagram. To evaluate the impact of LCSs in the transport of particles, we analyzed the time series of both average standard deviation and relative dispertion and also histograms of the distribution of these jumps. It was found that, with two drift waves and for a given combination of parameters, a jet streams appear in the phase space and persist for long periods of time immersed in the chaotic region. We found that, as well as on the islands, the inner region of the jet streams are inaccessible to LCSs. It was also found that when there is a jet stream, the transport observed in the chaotic region is not symmetrical and have a small drift in the opposite direction to the jet. This phenomenon is observed in contrast to the typical case of systems with mixing in wich the LCSs have access to all the phase space and the trasnport is diffusive.

Reactive transport models are essential tools for predicting contaminant fate and transport in the subsurface and for designing effective remediation strategies. Sound understanding of subsurface mixing in heterogeneous porous media is the key for the realistic modeling of reactive transport. This dissertation aims to investigate the extent of mixing and improve upscaling effective macroscopic models for mixing-controlled reactive transport in connected heterogeneous formations, which usually exhibit strongly anomalous transport behavior. In this research, a novel approach is developed for an accurate geostatistical characterization of connected heterogeneous formations transformed from Gaussian random fields. Numerical experiments are conducted in such heterogeneous fields with different connectivity to investigate the performance of macroscopic mean transport models for simulating mixing-controlled reactive transport. Results show that good characterization of anomalous transport of a conservative tracer does not necessarily mean that the models may characterize mixing well and that, consequently, it is questionable that the models capable of characterizing anomalous transport behavior of a conservative tracer are appropriate for simulating mixing-controlled reactive transport. In connected heterogeneous fields with large hydraulic conductivity variances, macroscopic mean models ignoring concentration variations yield good prediction, while in fields with intermediate conductivity variances, the models must consider both the mean concentration and concentration variations, which are very difficult to evaluate both theoretically and experimentally. An innovative and practical approach is developed by combining mean conservative and reactive breakthrough curves for estimating concentration variations, which can be subsequently used by variance transport models for prediction. Furthermore, a new macroscopic framework based on the dual-permeability conceptualization is developed for describing both mean and concentration variation for mixing-controlled reactive transport. The developed approach and models are validated by numerical and laboratory visualization experiments. In particular, the new dual-permeability model demonstrates significant improvement for simulating mixing-controlled reactive transport in heterogeneous media with intermediate conductivity variances. Overall, results, approaches and models from this dissertation advance the understanding of subsurface mixing in anomalous transport and significantly improve the predictive ability for modeling mixing-controlled reactive transport in connected heterogeneous media.

Nesta tese foi estudado o transporte de partículas na borda do plasma confinado magneticamente em tokamaks a partir de um modelo para ondas de deriva proveniente de flutuaçõoes eletrostáticas geradas pela não uniformidade do plasma. Para investigar esse problema, consideramos o modelo com duas ondas de deriva, que possui uma complexa dinâmica não linear onde podemos encontrar tanto transporte anômalo quanto transporte difusivo. Para a encontras no plano de fases as Estruturas Lagrangianas Coerentes (ELCs) e os jatos, foram confeccionados mapas de Poincaré, diagramas de expoente de Lyapunov a tempo finito, diagramas de deslocamento quadrático, diagramas de autocorrelação da velocidade e o diagrama de retorno. Para avaliar o impacto dessas ELCs no transporte de partículas foram analisados a série temporal do desvio padrão médio, da dispersão relativa e dos saltos dentro do mapa de Poincar´e e também foram confeccionados histogramas com a distribuição desses saltos. Foi encontrado que, com duas ondas de deriva e para uma determinada combinação de parâmetros, surgem correntes de jato, que persistem por longos períodos, imersas na região caótica. Verificamos que, assim como nas ilhas, a região interna às correntes de jato são inacessíveis às ELCs. Também foi encontrado que, quando existe uma corrente de jato, o transporte observado na região caótica não é simétrico com uma pequena deriva na direção contraria ao jato. Esse fenômeno observado ocorre em contrapartida ao caso típico de sistemas com mistura em que as ELCs tem acesso a todo o plano de fase e o transporte é difusivo. / In this thesis we studied the particle transport in the edge of magnetically confined plasma in tokamaks using a model of drift waves due to electrostatic fluctuations generated by the non-uniformity of the plasma. To investigate this issue, we consider the model with two drift waves, which has a complex nonlinear dynamics where we can find both anomalous and diffusive transport. To find the Lagrangian Coherent Structures (LCSs) and the jets, we used Poincaré maps, Finite time Lyapunov exponent diagrams, quadratic displacement diagrams, autocorrelation velocity diagrams and return displacement diagram. To evaluate the impact of LCSs in the transport of particles, we analyzed the time series of both average standard deviation and relative dispertion and also histograms of the distribution of these jumps. It was found that, with two drift waves and for a given combination of parameters, a jet streams appear in the phase space and persist for long periods of time immersed in the chaotic region. We found that, as well as on the islands, the inner region of the jet streams are inaccessible to LCSs. It was also found that when there is a jet stream, the transport observed in the chaotic region is not symmetrical and have a small drift in the opposite direction to the jet. This phenomenon is observed in contrast to the typical case of systems with mixing in wich the LCSs have access to all the phase space and the trasnport is diffusive.

Die vorliegende Arbeit befasst sich mit der Verallgemeinerung von Reaktions-Diffusions-Systemen auf Subdiffusion. Die subdiffusive Dynamik auf mesoskopischer Skala wurde mittels Continuous-Time Random Walks mit breiten Wartezeitverteilungen modelliert. Die Reaktion findet auf mikroskopischer Skala, d.h. während der Wartezeiten, statt und unterliegt dem Massenwirkungsgesetz. Die resultierenden Integro-Differentialgleichungen weisen im Integralkern des Transportterms eine Abhängigkeit von der Reaktion auf. Im Falle der Degradation A->0 wurde ein allgemeiner Ausdruck für die Lösungen beliebiger Dirichlet-Randwertprobleme hergeleitet. Die Annahme, dass die Reaktion dem Massenwirkungsgesetz unterliegt, ist eine entscheidende Voraussetzung für die Existenz stationärer Profile unter Subdiffusion. Eine nichtlineare Reaktion stellt die irreversible autokatalytische Reaktion A+B->2A unter Subdiffusion dar. Es wurde ein Analogon zur Fisher-Kolmogorov-Petrovskii-Piscounov-Gleichung (FKPP) aufgestellt und die resultierenden propagierenden Fronten untersucht. Numerische Simulationen legten die Existenz zweier Regimes nahe, die sowohl mittels eines Crossover-Argumentes als auch durch analytische Berechnungen untersucht wurden. Das erste Regime ist charakterisiert durch eine Front, deren Breite und Geschwindigkeit sich mit der Zeit verringert. Das zweite, fluktuationsdominierte Regime liegt nicht im Geltungsbereich der kontinuierlichen Gleichung und weist eine stärkere Abnahme der Frontgeschwindigkeit sowie eine atomar scharf definierte Front auf. Ein anderes Szenario, bei dem eine Spezies A in ein mit immobilen B-Partikeln besetztes Medium hineindiffundiert und gemäß dem Schema A+B->(inert) reagiert, wurde ebenfalls betrachtet. Diese Anordnung wurde näherungsweise als ein Randwertproblem mit einem beweglichen Rand (Stefan-Problem) formuliert. Die analytisch gewonnenen Ergebnisse bzgl. der Position des beweglichen Randes wurden durch numerische Simulationen untermauert. / The present work studies the generalization of reaction-diffusion schemes to subdiffusion. The subdiffusive dynamics was modelled by means of continuous-time random walks on a mesoscopic scale with a heavy-tailed waiting time pdf lacking the first moment. The reaction was assumed to take place on a microscopic scale, i.e. during the waiting times, obeying the mass action law. The resultant equations are of integro-differential form, and the reaction explicitly affects the transport term. The long ranged memory of the subdiffusion kernel is modified by a factor accounting for the reaction of particles during the waiting times. The degradation A->0 was considered and a general expression for the solution to arbitrary Dirichlet Boundary Value Problems was derived. For stationary solutions to exist in reaction-subdiffusion, the assumption of reactions according to classical rate kinetics is essential. As an example for a nonlinear reaction-subdiffusion system, the irreversible autocatalytic reaction A+B->2A under subdiffusion is considered. A subdiffusive analogue of the classical Fisher-Kolmogorov-Petrovskii-Piscounov (FKPP) equation was derived and the resultant propagating fronts were studied. Two different regimes were detected in numerical simulations, and were discussed using both crossover arguments and analytic calculations. The first regime is characterized by a decaying front velocity and width. The fluctuation dominated regime is not within the scope of the continuous description. The velocity of the front decays faster in time than in the continuous regime, and the front is atomically sharp. Another setup where reactants A penetrate a medium initially filled with immobile reactants B and react according to the scheme A+B->(inert) was also considered. This problem was approximately described in terms of a moving boundary problem (Stefan-problem). The theoretical predictions concerning the moving boundary were corroborated by numerical simulations.

Nous étudions les propriétés des états stationnaires et de dynamiques hors-équilibre, d’un point de vue théorique et numérique. Ces dynamiques sont obtenues en perturbant la dynamique d’équilibre par forçage mécanique et/ou thermique. Dans l’approche théorique, le système considéré évolue selon une dynamique de Langevin à laquelle on ajoute une force extérieure. Nous étudions la convergence de la loi de la dynamique vers la mesure stationnaire, en donnant des estimations quantitatives du taux, dans les régimes Hamiltonien et sur amorties. Dans l’approche numérique, nous considérons une chaîne de rotateurs soumise aux deux forçages et une chaîne d’oscillateurs de Toda soumise à un forçage thermique et à une perturbation stochastique. Nous étudions les caractéristiques de l’état stationnaire et les propriétés de transport. Dans le cas de la chaîne de rotateurs nous observons en particulier que le courant d’énergie moyen est dans certains cas accru par un gradient de température opposé. / We study the properties of stationary states associated with nonequilibrium dynamics from a theoretical and a numerical point of view. These dynamics are obtained by perturbing equilibrium dynamics with mechanical and / or thermal forcings. In the theoretical approach, the system considered evolves according to a Langevin dynamics perturbed by a torque. In this framework, we study the convergence of the law of dynamics to the stationary measure, giving quantitative estimates of the exponential rate, both in the Hamiltonian and `` overdamped '' regimes.By a numerical approach, we consider a chain of rotors subjected to both forcings and a chain of Toda oscillators subject to a thermal forcing and a stochastic perturbation. We study the features of the stationary state and analyze its transport properties. In particular, in the case of the rotor chain, contrary to what is naively expected, we observe that the average energy current is in some cases increased by an opposite temperature gradient.