No description available.

Cord-forming fungi form extensive networks that continuously adapt to maintain an efficient transport system, and we can photograph their growth, digitize the network structure, and measure the movement of radio-tracers. Mycelial networks are more accessible than the transport networks of other multicellular organisms, but there are many open questions concerning the coordination of growth and transport within fungal networks. As osmotically driven water uptake is often distal from the growing margin, and aqueous fluids are effectively incompressible, we propose that growth induces mass flows across the mycelium, towards the growing regions. We imaged the temporal evolution of networks formed by Phanerochaete velutina, and at each stage calculated the unique set of currents that account for the observed changes in cord volume, while minimizing the work required to overcome viscous drag. Predicted speeds were in reasonable agreement with experimental data, and cords that were predicted to carry large currents were significantly more likely to increase in size than cords with small currents. We have also developed an efficient method for calculating the exact quantity of resource in each part of an arbitrary network, where the resource is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. This method enabled us to model the spatial distribution of resource that emerges as a fungal network grows over time, and we found good empirical agreement between our model and experimental data gathered using radio-labelled tracers. Our results suggest that in well insulated fungal networks, growth-induced mass flow is sufficient to account for long distance transport. We conclude that active transport mechanisms may only be required at the very end of the transport pathway, near the growing tips. We also developed a simple model of glucose delivery through vascular networks, which indicates that increasing the number of blood vessels in a region can actually decrease the total rate of glucose delivery.

Yes / Traditional Lattice-Boltzmann modelling of advection–diffusion flow is affected by numerical instability if the advective term becomes dominant over the diffusive (i.e., high-Péclet flow). To overcome the problem, two 3D one-way coupled models are proposed. In a traditional model, a Lattice-Boltzmann Navier–Stokes solver is coupled to a Lattice-Boltzmann advection–diffusion model. In a novel model, the Lattice-Boltzmann Navier–Stokes solver is coupled to an explicit finite-difference algorithm for advection–diffusion. The finite-difference algorithm also includes a novel approach to mitigate the numerical diffusivity connected with the upwind differentiation scheme.

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No description available.

This dissertation aims to use theory and numerical simulations to quantify the propagation of fronts, which consist of autocatalytic reaction fronts, fronts with feedback and pattern forming fronts in Rayleigh-Bénard convection. The velocity and geometry of fronts are quantified for fronts traveling through straight parallel convection rolls, spatiotemporally chaotic rolls, and weakly turbulent rolls. The front velocity is found to be dependent on the competing influence of the orientation of the convection rolls and the geometry of the wrinkled front interface which is quantified as a fractal having a non-integer box-counting dimension. Front induced solutal and thermal feedback to the convective flow field is then studied by solving an exothermic autocatalytic reaction where the products and the reactants can vary in density. A single self-organized fluid roll propagating with the front is created by the solutal feedback while a pair of propagating counterrotating convection rolls are formed due to heat release from the reaction. Depending on the relative change in density induced by the solutal and thermal feedback, cooperative and antagonistic feedback scenarios are quantified. It is found that front induced feedback enhances the front velocity and reactive mixing length and induces spatiotemporal oscillations in the front and fluid dynamics. Using perturbation expansions, a transition in symmetry and scaling behavior of the front and fluid dynamics for larger values of feedback is studied. The front velocity, flow structure, front geometry and reactive mixing length scales for a range of solutal and thermal feedback are quantified. Lastly, pattern forming fronts of convection rolls are studied and the wavelength and velocity selected by the front near the onset of convective instability are investigated. This research was partially supported by DARPA Grant No. HR0011-16-2-0033. The numerical computations were done using the resources of the Advanced Research Computing center at Virginia Tech. / Doctor of Philosophy / Quantification of transport of reacting species in the presence of a flow field is important in many problems of engineering and science. A front is described as a moving interface between two different states of a system such as between the products and reactants in a chemical reaction. An example is a line of wildfire which separates burnt and fresh vegetation and propagates until all the fresh vegetation is consumed. In this dissertation the propagation of reacting fronts in the presence of convective flow fields of varying complexity is studied. It is found that the spatial variations in a convective flow field affects the burning and propagation of fronts by reorienting the geometry of the front interface. The velocity of the propagating fronts and its dependence on the spatial variation of the flow field is quantified. In certain scenarios the propagating front feeds back to the flow by inducing a local flow that interacts with the background convection. The rich and emergent dynamics resulting from this front induced feedback is quantified and it is found that feedback enhances the burning and propagation of fronts. Finally, the properties of pattern forming fronts are studied for fronts which leave a trail of spatial structures behind as they propagate for example in dendritic solidification and crystal growth. Pattern forming fronts of convection rolls are studied and the velocity of the front and spatial distribution of the patterns left behind by the front is quantified. This research was partially supported by DARPA Grant No. HR0011-16-2-0033. The numerical computations were done using the resources of the Advanced Research Computing center at Virginia Tech.

.Dans cette thèse, il a été étudié la structure des milieux poreux, en particulier sur des sols sableux et un paquet virtuel de sphères; Sur la base de références bibliographiques, nos propres outils ont été créés pour calculer la porosité, la surface spécifique et la distribution de la taille des pores. Nous avons construit un algorithme pour résoudre l'équation de diffusion de l'advection directement sur la structure du milieu poreux (en utilisant un résultat d'image 3D du scan $ mu $ CT du support poreux). Nous avons utilisé l'opérateur de division pour calculer la partie advective avec une méthode de volume fini (FV), mettant en œuvre un schéma de réduction de la variation totale (TVD). La partie diffusion a été calculée en utilisant une méthode de FV et avec l’aide du logiciel MUMPS pour résoudre le système linéaire résultant. A partir du champ de concentration obtenu avec l’algorithme et suivant une méthode de moyenne volumique, nous avons calculé les propriétés macroscopiques de: dispersivité et coefficient de dispersion à Pe = 223,23,2.3,0,23 pour un échantillon de sable de Fontainbleau NE34. Nous avons observé que ces résultats dépendent de la qualité de l'image 3D. Les propriétés structurelles et de transport ont été étudiées à l'aide d'images 3D à différentes résolutions. Les images à différentes résolutions ont été appelées images redimensionnées, elles ont été générées numériquement et prises directement à partir du micro CT scan. Comme premier résultat, nous avons proposé un critère basé sur la distribution de la taille des pores pour déterminer si une résolution d'image 3D convient ou non au calcul de la perméabilité d'un matériau granulaire avec une méthode de volume fini (FV). Dans un deuxième résultat, nous avons montré comment les propriétés des macros de transport de soluté sont moins affectées par une détérioration de la résolution que la propriété d’écoulement de la perméabilité (les deux cas sont calculés par une méthode FV). Et comme troisième résultat, nous avons montré qu'une image numérique redimensionnée préserve davantage le comportement des propriétés macroscopiques qu'une image réelle redimensionnée. / In this thesis it was studied the structure of the porous media, particularly on a sandy soils and a virtual pack of spheres; based on bibliographic references here were generated our own tools to compute the porosity, specific surface and pore size distribution. We built an algorithm to solve advection diffusion equation directly on the porous media structure (using a 3D image result of the $mu $ CT scan of the porous media). We used the splitting operator to compute the advective part with a Finite Volume (FV) method, implementing a Total Variation Diminishing (TVD) scheme. The diffusion part was computed using with a FV method with the assistance of the MUMPS software to solve the resulting linear system. From the concentration field obtained with the algorithm and following a volume averaging method, we computed the macroscopic properties of: dispersivity and dispersion coefficient at Pe=223,23,2.3,0.23 for a sample of Fontainbleau NE34 sand. We observing that these results depend on the quality of the 3D image, structural and transport properties were studied using 3D images at different resolutions. The images at different resolutions were called rescaled images, and they were generated numerically and taken directly from the micro CT scan. As a first result we proposed a criterion based on the pore size distribution to assess if a 3D image resolution is suitable or not for permeability computation of a granular material with a finite volume (FV) method. As a second result we showed how the solute transport macro properties are less affected by a deterioration of the resolution than the flow property of permeability (both cases computed through a FV method). And as a third result we showed that a numerical rescaled image preserve the behavior of the macroscopic properties more than a real rescaled image

Ce mémoire aborde la question de la production d’observables intrinsèques au comportement thermomécanique des matériaux pour mieux en formuler les lois d’états. Ces observables sont les sources de chaleur thermomécaniques, activées par sollicitation mécanique. Ces sources peuvent être reconstruites dans l’espace et le temps par inversion de mesures de champs de température obtenus par thermographie IR. Nous présentons essentiellement deux méthodes développées lors de ce travail de thèse qui reposent sur des approches spectrales réduites (dont la décomposition sur Modes de Branche) et des inversions séquentielles (méthode de Beck) ou itératives (Gradient Conjugué). Concernant cette dernière, nous proposons d’y adjoindre une régularisation efficace en s’inspirant de techniques de filtrage par TSVD. S’agissant de matériaux sujets aux instabilités plastiques (PolyEthylène Haute Densité) pour lesquels les vitesses locales peuvent être non négligeables, l’inversion des mesures en température nécessite que l’on considère un opérateur d’advection-diffusion, qui impose alors l’apport d’une connaissance supplémentaire : le champ de vitesses locales. Celui-ci est mesuré par corrélation d’images 3D et nous détaillons le travail expérimental mené ainsi que les résultats obtenus sur des essais de traction pilotés par vidéo-extensométrie. Nous montrons que pour des essais quasi-statiques à vitesses relativement élevées, les effets d’advection sont généralement négligeables. Nous montrons également en quoi la richesse des informations thermomécaniques (Sources) et cinématiques (Taux de déformation, vitesses) permet de mieux comprendre la dynamique de l’instabilité plastique. Enfin nous critiquons les résultats obtenus sur la reconstruction de source par confrontation des deux algorithmes développés et par une analyse physique des phénomènes observés / This work concerns the way intrinsic observables can be produced, which are related to the thermomechanical behavior of materials and necessary for better formulation of state laws. These observables are Thermomechanical Heat Sources (THS) which are activated through mechanical excitation. These sources can be reconstructed both in space and time by the inversion of measured temperature fields obtained through IR thermography. We develop two main methods in this work which rely on spectral reduced approaches (one of them being the decomposition on Branch Modes) and both on a sequential inversion (Beck’s method) and an iterative one (Conjugated Gradient). Regarding the latter, we suggest to combine the standard approach with an efficient regularization method which comes from the filtering techniques based on TSVD. As we are concerned with materials which can be subjected to plastic instabilities (High Density PolyEthylene) for which local velocities of matter displacement can be non negligible, the inversion of the measurements must be performed with the advection-diffusion operator of heat transfer. It is then necessary to obtained additional knowledge: the velocity field. This one is measured by 3D Digital Image Correlation and we detail the experimental work we have carried out, which are based on tensile tests monitored with video-extensometry. We show that for quasi-static tests at relatively high strain rates, the advective effects are generally negligible. We also show the richness of the information brought by this dual thermomechanical (heat sources) and kinematical (strain-rates, velocities) information. It allows for a better understanding of the plastic instability (necking) dynamics. Lastly, we criticize the obtained results on THS reconstruction by the confrontation between the two algorithms and by a physical analysis of the observed phenomena

Cette thèse porte sur l’étude des interactions entre les globules rouges (GRs)et l’endothélium, la couche des cellules qui délimite les vaisseaux sanguins.Il a été démontré que l’endothélium et les GRs jouent des rôles actifs dans divers processus du système vasculaire, et leurs interactions produisent un signal bio chimique grâce à des moyens à la fois chimiques (molécules de signalisation) et mécaniques (taux de cisaillement sur les parois). D’abord,nous étudions le rôle des GRs, y compris dans des conditions pathologiques, dans la création de contraintes de cisaillement spatialement et temporellement dynamiques sur l’endothélium. Il a été montré que les contraintes de cisaillement constituaient un élément critique dans le déclenchement d’un signal bio mécanique depuis l’endothélium. Par ailleurs, étant donné qu’il a été montré que les parois des vaisseaux sanguins ondulent en raison des cellules endothéliales individuelles qui le composent, nous avons intégré à notre modélisation cette géométrie. On trouve que cette ondulation affecte la dynamique des GRs dans l’écoulement ainsi que le taux de cisaillement sur les parois. Nous étudions rapidement dans quelle mesure la déformabilité d’un GR affecte sa trajectoire dans un vaisseau ondulé. Pour cela, nous nous inspirons du processus de fonctionnement un appareil de déplacement latéral déterministe (DLD) qui utilise les variations de trajectoires des particules en fonction de leur taille pour les séparer dans l’écoulement. Nous étudions par ailleurs l’effet des suspensions de GRs sur les caractéristiques rhéologiques et les contraintes de cisaillement sur la paroi du vaisseau.Finalement, nous nous adressons à les interaction chimiques en développons un modèle numérique avec la méthode de Boltzmann sur réseaux-limite immergée (LB-IBM) pour résoudre la diffusion et l’advectiond’un soluté libéré par un particule en mouvement et déformable. L’oxygène et l’adénosine triphosphate (ATP) sont toutes les deux libérées par les GRs,se diffusent dans l'écoulement, et sont absorbées par l’endothélium. Ils représentent des facteurs de signalisation critiques pour les processus de l’inflammation et vasodilatation. Nous montrons que la morphologie des GRs affectera le temps de résidence et la dilution des espèces chimiques lorsqu’elles rentreront en contact avec la paroi du vaisseau. Ensemble, ces éléments nous conduisent vers la développement d’un modèle capable de simuler des processus vitaux du système vasculaire qui résultent d’événements locaux de composants individuels. / This thesis is devoted to the study of the interactions between red blood cells (RBCs) and the endothelium, the monolayer of cells lining blood vessels. The endothelium and RBCs have been shown to be active participants in various processes in the vascular system, and their interactions trigger biochemical signalling by mechanical (wall shear stress) and chemical (signalling molecules) means. We first investigate the role of RBCs, including pathological conditions, in creating time- and space-varying shear stress on the endothelium. Shear stress has been shown to be a critical element in biochemical signalling from the endothelium. In addition, as it has been shown that the endothelium is undulating due to the individual endothelial cells comprising it, we take this into account in our model of the geometry of the vessel wall. We find that this undulation affects the dynamics of the RBCs in the flow and the wall shear stress. We briefly explore how the deformability of a single RBC affects its trajectory in undulating channels, inspired by the idea behind deterministic lateral displacement devices (DLDs) which exploit the differing trajectories of particles based upon their sizes to separate them in flow. We also investigate the effect of suspensions of RBCs in undulating channels on rheological properties and wall shear stress. Finally, we address the chemical interactions by building a numerical model with the lattice Boltzmann-immersed boundary method (LB-IBM) to solve advection-diffusion of solute released from moving, deformable particles. Oxygen and adenosine triphosphate (ATP) are both released by RBCs and are advected and diffused in the flow and uptaken by the endothelium and serve as critical signalling factors in inflammation and vasodilation. We find that the morphology of RBCs will affect the residence time and dilution of the chemical species upon contact with the wall. Together, these elements lead us towards the development of a model capable of simulating vital processes in the vascular system which result from local interactions of individual components.

Questões ambientais estão no centro das discussões nas últimas décadas. A poluição atmosférica, causada pela expansão pós-revolução industrial fez surgir a necessidade de aprender a descrever, usando modelos matemáticos, esse fenômeno. Com esse conhecimento pode-se propor soluções que mitiguem a poluição e os danos colaterais causados ao ambiente. A dispersão de poluentes modelada por soluções analíticas, a partir das equações de advecção-difusão oferecem um conhecimento sobre cada componente que constrói a equação, característica inexistente em outras abordagens, como a numérica. Entretanto ela era incapaz de descrever propriedades que se referem à turbulência, as estruturas coerentes, causadas por componentes não-lineares suprimidas por construção das equações governantes do modelo. Este trabalho estudou uma forma de recuperar características associadas à turbulência através de uma componente fundamental em estruturas coerentes, a fase. Essa é incluída no modelo que passa a descrever manifestações da turbulência em processos de dispersão através de flutuações de pequena escala na concentração da solução do modelo sesquilinear, que é determinístico-estocástico. No decorrer do trabalho há um estudo através de variações de parâmetros para compreender os efeitos da fase no modelo. Ele também foi aplicado ao experimento de Copenhagen e a dois cenários reais com a intenção de compreender o modelo frente à variáveis micrometeorológicas assim como aprimorá-lo para simular a dispersão de poluentes oriundos de fontes de forma realística. / Environmental issues have been at the center of discussions in the last few decades. Atmospheric pollution, caused by post-industrial revolution, has increased the necessity to describe, using mathematical models, this phenomenon. With this knowledge is possible to propose solutions mitigating the pollution and collateral damages caused in the environment. The pollutant dispersion modeled by analytical solutions, from advection-diffusion equations, offers a knowledge about each component that constructs the equation, a characteristic that does not exist in other approaches, such as numerical. However it was unable to describe properties that refer to turbulence, coherent structures, caused by nonlinear components suppressed by constructing the model governing equations. This work studied a way to recover characteristics associated with turbulence through a fundamental component in coherent structures, the phase. This is included in the model which describes manifestations of turbulence in the dispersion process through the presence of small-scale concentration fluctuations in the sesquilinear model, which is deterministicstochastic. In the course of this work there is a study through variations of parameters to understand the phase effects in the model. It was also applied to Copenhagen experiment and to two real scenarios with the intention of understanding the model regarding micrometeorological variables as well as improving it to simulate the pollutant dispersion from sources in a realistic way.