In order to simulate cellular blood, a coarse-grained spectrin-link (SL) red blood cell (RBC) membrane model is coupled with a lattice-Boltzmann (LB) based suspension solver. The LB method resolves the hydrodynamics governed by the Navier--Stokes equations while the SL method accurately models the deformation of RBCs under numerous configurations. This method has been parallelized using Message Passing Interface (MPI) protocols for the simulation of dense suspensions of RBCs characteristic of whole blood on world-class computing resources. Simulations were performed to study rheological effects in unbounded shear using the Lees-Edwards boundary condition with good agreement with rotational viscometer results from literature. The particle-phase normal-stress tensor was analyzed and demonstrated a change in sign of the particle-phase pressure from low to high shear rates due to RBCs transitioning from a compressive state to a tensile state in the flow direction. Non-Newtonian effects such as viscosity shear thinning were observed for shear rates ranging from 14-440 inverse seconds as well as the strong dependence on hematocrit at low shear rates. An increase in membrane bending energy was shown to be an important factor for determining the average orientation of RBCs, which ultimately affects the suspension viscosity. The shear stress on platelets was observed to be higher than the average shear stress in blood, which emphasizes the importance of modeling platelets as finite particles. Hagen-Poiseuille flow simulations were performed in rigid vessels for investigating the change in cell-depleted layer thickness with shear rate, the Fåhraeus-Linqvist effect, and the process of platelet margination. The process of platelet margination was shown to be sensitive to platelet shape. Specifically, it is shown that lower aspect ratio particles migrate more rapidly than thin disks. Margination rate is shown to increase with hematocrit, due to the larger number of RBC-platelet interactions, and with the increase in suspending fluid viscosity.

An understanding of the motion of soft capsules in microchannels is useful for a number applications. This knowledge can be used to develop devices to sort biological cells based on their size and stiffness. For example, cancer cells have a different stiffness from healthy cells and thus can be readily identified. Additionally, devices can be developed to detect flaws in synthetic particles. Using a 3D hybrid lattice Boltzmann and lattice spring method, the motion of rigid and soft capsules in a pressure-driven microfluidic flow was probed. The effect of inertial drift is evaluated in channels different Reynolds numbers. Other system parameters such as capsule elasticity and channel size are also varied to determine their effect. The equilibrium position of capsules in the channel is also obtained. The equilibrium position of rigid and soft capsules depends on the relative particle size. If the capsule is small, the equilibrium position is found to be closer to the channel wall. Conversely, for larger capsules, the equilibrium position is closer to the channel centerline. The capsule stiffness affects the magnitude of the cross-stream drift velocity. For a given Reynolds number, the equilibrium position of softer capsules is closer to the channel centerline. However, It is found that the equilibrium position of soft capsules is insensitive to the magnitude of the Reynolds number.

Les études présentées dans ce mémoire portent sur la simulation numérique et l'analyse physique des milieux granulaires immergés dans un fluide. Des développements numériques ont été réalisés pour coupler la méthode Lattice Boltzmann pour la dynamique du fluide avec la méthode Contact Dynamics en 2D et avec la méthode Molecular Dynamics en 3D pour la dynamique des grains. Ces outils numériques ont été utilisés pour étudier l'initiation des avalanches sur un plan incliné en fonction de la compacité initiale et de l'angle d'inclinaison en 3D. Les résultats sont en bon accord quantitatif avec les expériences et ont permis de mettre en évidence la stabilisation de la pente granulaire par une pression négative du fluide interstitielle induite par la dilatance, et l'évolution spatiotemporelle des grandeurs telles que la compacité et la déformation de cisaillement. Ces évolutions dans la phase de fluage qui précède la rupture de pente ont pu être mises à l'échelle par un modèle théorique incorporant la loi de Darcy et l'effet de la dilatance sur l'angle de frottement interne. L'analyse de la texture granulaire a révélé la distortion du réseau des contacts pendant le fluage et la saturation de l'anisotropie comme un critère de rupture. La propagation des avalanches granulaires a été étudiée dans une configuration 2D pour deux géométries différentes : 1) l'effondrement et l'étalement d'une colonne sous son propre poids, 2) l'étalement d'une pente sous l'effet d'une énergie cinétique injectée. Nous avons en particulier montré que la distance et la durée d'étalement obéissent à des lois de puissance en fonction du rapport d'aspect initial ou de l'énergie injectée. Le fluide exerce deux effets contradictoires : réduire les temps de relaxation et lubrifier les contacts. Ces effets ont été analysés dans le régime visqueux en fonction des conditions initiales et la viscosité du fluide.

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Modeling of flow in porous and fractured media is a very important problem in reservoir engineering. As for numerical simulations conventional Navier-Stokes codes are applied to flow in both porous and fractured media. But they have long computation times, poor convergence and problems of numerical instabilities. Therefore, it is desired to develop another computational method that is more efficient and use simple rules to represent the flow in fractured media rather than partial differential equations. In this thesis Lattice Boltzmann Automaton Model will be used to represent the single phase fluid flow in two dimensional synthetic fractures and the simulation results obtained from this model are used to train Artificial Neural Networks. It has been found that as the mean aperture-fractal dimension ratio increases permeability increases. Moreover as the anisotropy factor increases permeability decreases with a second order polynomial relationship.

Many industrial processes use biological agents as catalysts. In this context, the study of the cellular metabolism becomes relevant for planning the best strategies (environmental and/or genetic modifications) to manipulate the cell in order to maximise the production of a metabolite of interest and minimise the by-products one. This increases the yield of the fermentation and reduces the cost of product recovery; thereby the profitability of the process is improved. The intracellular reactions are carried out in a complex, crowded and heterogeneous medium composed by solid components (macromolecules, ions, enzymes, small solutes, etc.) in a fluid phase called cytoplasm, all of them enclosed within the cellular membrane. The interactions among the intracellular components (as well as with the extracellular environment) determine the behaviour of the organism. The modelling and simulations of these interactions help the understanding of the metabolism. The aim of this thesis is to provide generic tools for the analysis and simulation of metabolic systems under the intracellular environmental conditions. In particular, this research focuses on the estimation of metabolic fluxes and the simulation of the diffusion process. The stoichiometric models have been widely used for the calculation of unmeasured fluxes in a metabolic network, assuming the system is at steady state. The addition of thermodynamic constraints allows only the prediction of fluxes that go in the direction of the Gibbs free energy drop. The Gibbs free energy change ( ) depends on the (intracellular) environmental conditions and determine the direction, feasibility and reversibility of the reactions involved in the pathways. The thermodynamically constrained stoichiometric model proposed here allows the estimation of the range of fluxes of a metabolic network, where the information about the presence of the enzymes that catalyse the reactions can be incorporated (if available). The effect of considering a zero flux reaction as blocked or at equilibrium on the flux predictions was investigated, as well as the environmental conditions ionic strength, temperature and pH. Additionally, since the solid components within the cell occupy about 40% of its total volume, these crowding conditions could alter the thermodynamic feasibility of the pathways. For this reason, the thermodynamically constrained stoichiometric model is extended to incorporate the crowding effect. The case study used in this work is the central carbon metabolic network of Actinobacillus succinogenes for the production of succinic acid from glycerol, a by-product in the biodiesel manufacture. Moreover, the crowding conditions also affect the diffusion of the molecules. The prokaryotic cells have been widely used in fermentation processes for the production of metabolites of interest. In this type of cells the diffusion is the primary mean of the particles’ motion, so that the diffusion reduction due to the crowding conditions could affect the possibility of encounter among the reactants, decreasing the reactions’ rate and therefore the yield of the process. A methodology based on the Lattice Boltzmann Method (LBM) and the Scaled Particle Theory (SPT) is presented in this thesis for fast simulations of the diffusion of hard-disk molecules in 2D crowded systems, which also allows evaluating the effect of the molecules’ size on their diffusion.

The permeability of rocks has a critical influence on their fluid transport response in critical geo-environmental applications, such as pollutant transport or underground storage of hazardous nuclear waste. In such processes, the materials microstructure may be altered as a result of various stimuli, thereby impacting the fluid transfer properties. Stress or strain state modifications are one of the main causes for such evolutions. To numerically address this concern, an integrated and automated numerical tool was developed and illustrated on subsets of microCT scans of a Vosges sandstone (i) to explore the links between the pore space properties and the corresponding macroscopic transfer properties, with (ii) an incorporation of the microstructural alterations associated with stress state variations by using a realistic image-based representation of the microstructural morphology. The ductile mechanical deformation behavior under high confining pressures at the scale of the microstructure, inducing pore closures by local plastifications, was modelled using finite elements simulations with a non-linear elastoplastic law, allowing to take into account the redistribution of local stresses. These simulations require robust discretization tools to capture the complex geometry of the porous network and the corresponding solid boundaries of the heterogeneous microstructural geometries. To achieve this, an integrated approach for the conformal discretization of complex implicit geometries based on signed distance fields was developed, producing high quality meshes from both imaging techniques and computational RVE generation methodologies. This conforming discretization approach was compared with an incompatible mode-based framework using a non conforming approach. This comparison highlighted the complementarity of both methods, the former capturing the effect of more detailed geometrical features, while the latter is more flexible as it allows using the same (non conforming) mesh for potentially variable geometries.The evolution of permeability was evaluated at different confining pressure levels using the Lattice-Bolzmann method. This uncoupled solid-fluid interaction made it possible to study the combined influence on the permeability, porosity and the pores size distribution of the pore space morphology and the solid skeleton constitutive law parameters during loading and unloading conditions. The results highlight the need to consider elastoplastic laws and heterogeneities in the rock model to simulate the ductile behavior of rocks at high confining pressures leading to significant permeability alterations under loading, and irreversible alterations under loading/unloading cycles induced by progressive pore closures.The proposed methodology is designed to be flexible thanks to the interfacing with 'classical' discretization approaches and can be easily readapted to other contexts given the block approach. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

<div>The thesis includes two application studies of computational fluid dynamics. The first is new and efficient drug delivery to the posterior part of the eye, a growing health necessity worldwide. Current treatment of eye diseases, such as age related macular degeneration (AMD), relies on repeated intravitreal injections of drug-containing solutions. Such a drug delivery has significant drawbacks, including short drug life, vital medical service, and high medical costs. In this study, we explore a new approach of controlled drug delivery by introducing unique porous implants. Computational</div><div>modeling contains physiological and anatomical traits. We simulate the IgG1 Fab drug delivery to the posterior eye to evaluate the effectiveness of the porous implants to control the drug delivery. The computational model was validated by established computation results from independent studies and experimental data. Overall, the results indicate that therapeutic drug levels in the posterior eye are sustained for</div><div>eight weeks, similar to those performed with intravitreal injection of the same drug. We evaluate the effects of the porous implant on the time evaluation of the drug concentrations in the sclera, choroid, and retina layers of the eye. Subsequent simulations were carried out with varying porosity values of a porous episcleral implant.</div><div>Our computational results reveal that the time evolution of drug concentration is distinctively correlated to drug source location and pore size. The response of this porous implant for controlled drug delivery applications was examined. A correlation between porosity and fluid properties for the porous implants was revealed in this study. The second application lays in the computational modeling of the oscillating flow in rectangular ducts. This computational study has further applications in investigating the fluid flow motion in bodily organs. It can be useful in studying the</div><div>response of bone cells to the wall shear stress in the human body. </div>

[pt] Esta pesquisa aborda o processo de fraturamento hidráulico ou processo de propagação de fraturas em rocha através da injeção de um fluido sob pressão, o que gera fissuras no material que se propagam de acordo com a quantidade de fluido injetado. Esta técnica leva a um incremento da transmissividade hidráulica da rocha e, como consequência, ocorre um incremento da produção de óleo. Diversos trabalhos analíticos e numéricos têm sido propostos para estudar o mecanismo de fratura, geralmente baseados em meios contínuos ou através da utilização de elementos de interface em uma trajetória de propagação conhecida. Neste trabalho, a propagação de uma fratura é simulada utilizando o modelo potencial PPR[72] através da sua implementação extrínseca. Assim, os elementos coesivos de interface são inseridos na malha de elementos finitos de forma adapativa para capturar o processo de fraturamento. A pressão do fluido é simulada utilizando o modelo de lattice-Boltzmann[84]. Através de um processo interativo, os contornos da fratura, computados utilizando o método dos elementos finitos, são transferidos para o modelo de lattice-Boltzmann como uma condição de contorno. Assim, a força que o fluido exerce nestes contornos, gerada pela injeção do fluido, pode ser calculada. Estas forças são utilizadas no modelo de elementos finitos como uma força externa aplicada nas faces da fratura. A nova posição das faces da fratura é calculada e transferida novamente para o modelo de lattice-Boltzmann como condição de contorno. Este processo interativo fluido-estrutura permite modelar o processo de fraturamento hidráulico em trajetórias de propagação irregulares. / [en] This research addresses hydraulic fracturing or hydro-fracking, i.e. fracture propagation process in rocks through the injection of a fluid under pressure, which generates cracks in the rock that propagate according to the amount of fluid injected. This technique leads to an increase of the hydraulic transmissivity of the rock mass and, consequently, improves oil production. Several analytical and numerical models have been proposed to study this fracture mechanism, generally based in continuum mechanics or using interface elements through a known propagation path. In this work, the crack propagation is simulated using the PPR potential-based cohesive zone model[72] by means of an extrinsic implementation. Thus, interface cohesive elements are adaptively inserted in the mesh to capture the softening fracture process. The fluid pressure is simulated using the lattice Boltzmann model[84] through an iterative procedure. The boundaries of the crack, computed using the finite element method, are transferred to the lattice Bolztmann model as boundary conditions, where the fluid pressure (or fluid forces) applied on these boundaries, caused by the fluid injected, can be calculated. These forces are then used in the finite element model as external forces applied on the faces of the crack. The new position of the crack faces is then calculated and transferred to the lattice-Boltzmann model to update the boundary conditions. This feedback-loop for fluid-structure interaction allows modeling of hydraulic fracturing processes for irregular path propagation.

Analyses of heat and mass transfer between different materials and phases are essential in numerous fundamental scientific problems and practical engineering applications, such as thermal and chemical transport in porous media, design of heat exchangers, dendritic growth during solidification, and thermal/mechanical analysis of additive manufacturing processes. In the numerical simulation, interface treatment can be further divided into sharp interface schemes and diffuse interface schemes according to the morphological features of the interface. This work focuses on the following subjects through computational studies: (1) critical evaluation of the various sharp interface schemes in the literature for conjugate heat and mass transfer modeling with the lattice Boltzmann method (LBM), (2) development of a novel sharp interface scheme in the LBM for conjugate heat and mass transfer between materials/phases with very high transport property ratios, and (3) development of a new diffuse-interface phase-field-lattice Boltzmann method (PFM/LBM) for dendritic growth and solidification modeling. For comparison of the previous sharp interface schemes in the LBM, the numerical accuracy and convergence orders are scrutinized with representative test cases involving both straight and curved geometries. The proposed novel sharp interface scheme in the LBM is validated with both published results in the literature as well as in-house experimental measurements for the effective thermal conductivity (ETC) of porous lattice structures. Furthermore, analytical correlations for the normalized ETC are proposed for various material pairs and over the entire range of porosity based on the detailed LBM simulations. In addition, we provide a modified correlation based on the SS420-air and SS316L-air metal pairs and the high porosity range for specific application. The present PFM/LBM model has several improved features compared to those in the literature and is capable of modeling dendritic growth with fully coupled melt flow and thermosolutal convection-diffusion. The applicability and accuracy of the PFM/LBM model is verified with numerical tests including isothermal, iso-solutal and thermosolutal convection-diffusion problems in both 2D and 3D. Furthermore, the effects of natural convection on the growth of multiple crystals are numerically investigated.