Computational Fluid Dynamics in a Terminal Alveolated Bronchiole Duct with Expanding Walls: Proof-of-Concept in OpenFOAM

Mathematical Biology has found recent success applying Computational Fluid Dynamics (CFD) to model airflow in the human lung. Detailed modeling of flow patterns in the alveoli, where the oxygen-carbon dioxide gas exchange occurs, has provided data that is useful in treating illnesses and designing drug-delivery systems. Unfortunately, many CFD software packages have high licensing fees that are out of reach for independent researchers. This thesis uses three open-source software packages, Gmsh, OpenFOAM, and ParaView, to design a mesh, create a simulation, and visualize the results of an idealized terminal alveolar sac model. This model successfully demonstrates that OpenFOAM can be used to model airflow in the acinar region of the lung under biologically relevant conditions

Finite Volume Discrete Boltzmann Method on a Cell-Centered Triangular Unstructured Mesh

Due to its basis in kinetics, the lattice Boltzmann method (LBM) has been shown to be superior to conventional computational fluid dynamic (CFD) tools that solve the Navier-Stokes (NS) equation for complex flow problems, such as multiphase and/or multicomponent flows. However, after development for decades, the LBM still has not gained prominence over other CFD tools for a number of reasons, one of which is its unsatisfactory ability to handle complex boundary geometries. The goal of the current work is to overcome this difficulty. In order to fully integrate the unstructured mesh for treating complex boundary geometries, the discrete Boltzmann equation (DBE), which is the Eulerian counterpart of the lattice Boltzmann equation (LBE), is chosen for the study. The finite volume (FV) method is selected to solve the governing equation due to its outstanding performance in handling an unstructured mesh and its built-in conservation. Therefore, the method in the current work is called the finite volume discrete Boltzmann method (FVDBM). A FVDBM platform, both for isothermal and thermal models, is developed in the current work, which consists of three parts: the cell-centered (CC) triangular unstructured mesh, the FVDBM solver, and the boundary treatment, among which the latter two are the main areas of contribution. In the FVDBM solver, there are three components: the time marching scheme, the flux scheme, and the collision calculator. The flux schemes are the major area of study because of their significance in the overall FVDBM model (they control the spatial order of accuracy) and their complexity (they calculate the spatial gradient term) on the unstructured mesh. A universal stencil is developed on the arbitrary CC triangular unstructured mesh, with which two categories of flux schemes are developed systematically: the Godunov type and the non-Godunov type. As a result, a total of five schemes (three Godunov schemes and two non-Godunov schemes) with different orders of accuracy are formulated, numerically validated and analyzed. Two major conclusions can be drawn. First, for any flux scheme, Godunov or non-Godunov, its actual order is roughly one order lower than its theoretical order for velocity solutions, due to the diffusion error introduced by the unstructured mesh and the Eulerian nature of the solver. Second, a Godunov scheme is less diffusive and more stable than a non-Godunov one if they are of the same order of accuracy. Furthermore, a unique three-step boundary treatment is developed in detail for the current model. With the proposed boundary treatment, a variety of physical boundary conditions (velocity, density, and temperature, etc.) can be realized on the complex boundaries with the triangular unstructured mesh in a unified way. It can also incorporate different lattice models indiscriminately. With sufficient numerical testing, it is found that the boundary treatment is at least second-order accurate in space, and it can accurately preserve Dirichlet boundary conditions up to machine accuracy under different scenarios

Multiscale aeroelastic modelling in porous composite structures

Driven by economic, environmental and ergonomic concerns, porous composites are increasingly being adopted by the aeronautical and structural engineering communities for their improved physical and mechanical properties. Such materials often possess highly heterogeneous material descriptions and tessellated/complex geometries. Deploying commercially viable porous composite structures necessitates numerical methods that are capable of accurately and efficiently handling these complexities within the prescribed design iterations. Classical numerical methods, such as the Finite Element Method (FEM), while extremely versatile, incur large computational costs when accounting for heterogeneous inclusions and high frequency waves. This often renders the problem prohibitively expensive, even with the advent of modern high performance computing facilities. Multiscale Finite Element Methods (MsFEM) is an order reduction strategy specifically developed to address such issues. This is done by introducing meshes at different scales. All underlying physics and material descriptions are explicitly resolved at the fine scale. This information is then mapped onto the coarse scale through a set of numerically evaluated multiscale basis functions. The problems are then solved at the coarse scale at a significantly reduced cost and mapped back to the fine scale using the same multiscale shape functions. To this point, the MsFEM has been developed exclusively with quadrilateral/hexahedral coarse and fine elements. This proves highly inefficient when encountering complex coarse scale geometries and fine scale inclusions. A more flexible meshing scheme at all scales is essential for ensuring optimal simulation runtimes. The Virtual Element Method (VEM) is a relatively recent development within the computational mechanics community aimed at handling arbitrary polygonal (potentially non-convex) elements. In this thesis, novel VEM formulations for poromechanical problems (consolidation and vibroacoustics) are developed. This is then integrated at the fine scale into the multiscale procedure to enable versatile meshing possibilities. Further, this enhanced capability is also extended to the coarse scale to allow for efficient macroscale discretizations of complex structures. The resulting Multiscale Virtual Element Method (MsVEM) is originally applied to problems in elastostatics, consolidation and vibroacoustics in porous media to successfully drive down computational run times without significantly affecting accuracy. Following this, a parametric Model Order Reduction scheme for coupled problems is introduced for the first time at the fine scale to obtain a Reduced Basis Multiscale Virtual Element Method. This is used to augment the rate of multiscale basis function evaluation in spectral acoustics problems. The accuracy of all the above novel contributions are investigated in relation to standard numerical methods, i.e., the FEM and MsFEM, analytical solutions and experimental data. The associated efficiency is quantified in terms of computational run-times, complexity analyses and speed-up metrics. Several extended applications of the VEM and the MsVEM are briefly visited, e.g., VEM phase field Methods for brittle fracture, structural and acoustical topology optimization, random vibrations and stochastic dynamics, and structural vibroacoustics

Numerical Investigation of Particles Breakage and Growth in Gas-Solid Processes: Spiral Jet Milling and Polyolefin Polymerization in Fluidized Bed Reactors

L'abstract è presente nell'allegato / the abstract is in the attachmen

Failure processes in soft and quasi-brittle materials with nonhomogeneous microstructures

Material failure pervades the fields of materials science and engineering; it occurs at various scales and in various contexts. Understanding the mechanisms by which a material fails can lead to advancements in the way we design and build the world around us. For example, in structural engineering, understanding the fracture of concrete and steel can lead to improved structural systems and safer designs; in geological engineering, understanding the fracture of rock can lead to increased efficiency in oil and gas extraction; and in biological engineering, understanding the fracture of bone can lead to improvements in the design of bio-composites and medical implants. In this thesis, we numerically investigate a wide spectrum of failure behavior; in soft and quasi-brittle materials with nonhomogeneous microstructures considering a statistical distribution of material properties. The first topic we investigate considers the influence of interfacial interactions on the macroscopic constitutive response of particle reinforced elastomers. When a particle is embedded into an elastomer, the polymer chains in the elastomer tend to adsorb (or anchor) onto the surface of the particle; creating a region in the vicinity of each particle (often referred to as an interphase) with distinct properties from those in the bulk elastomer. This interphasial region has been known to exist for many decades, but is primarily omitted in computational investigations of such composites. In this thesis, we present an investigation into the influence of interphases on the macroscopic constitutive response of particle filled elastomers undergoing large deformations. In addition, at large deformations, a localized region of failure tends to accumulate around inclusions. To capture this localized region of failure (often referred to as interfacial debonding), we use cohesive zone elements which follow the Park-Paulino-Roesler traction-separation relation. To account for friction, we present a new, coupled cohesive-friction relation and detail its formulation and implementation. In the process of this investigation, we developed a small library of cohesive elements for use with a commercially available finite element analysis software package. Additionally, in this thesis, we present a series of methods for reducing mesh dependency in two-dimensional dynamic cohesive fracture simulations of quasi-brittle materials. In this setting, cracks are only permitted to propagate along element facets, thus a poorly designed discretization of the problem domain can introduce artifacts into the fracture behavior. To reduce mesh induced artifacts, we consider unstructured polygonal finite elements. A randomly-seeded polygonal mesh leads to an isotropic discretization of the problem domain, which does not bias the direction of crack propagation. However, polygonal meshes tend to limit the possible directions a crack may travel at each node, making this discretization a poor candidate for dynamic cohesive fracture simulations. To alleviate this problem, we propose two new topological operators. The first operator we propose is adaptive element-splitting, and the second is adaptive mesh refinement. Both operators are designed to improve the ability of unstructured polygonal meshes to capture crack patterns in dynamic cohesive fracture simulations. However, we demonstrate that element-splitting is more suited to pervasive fracture problems, whereas, adaptive refinement is more suited to problems exhibiting a dominant crack. Finally, we investigate the use of geometric and constitutive design features to regularize pervasive fragmentation behavior in three-dimensions. Throughout pervasive fracture simulations, many cracks initiate, propagate, branch and coalesce simultaneously. Because of the cohesive element method's unique framework, this behavior can be captured in a regularized manner. In this investigation, unstructuring techniques are used to introduce randomness into a numerical model. The behavior of quasi-brittle materials undergoing pervasive fracture and fragmentation is then examined using three examples. The examples are selected to investigate some of the significant factors influencing pervasive fracture and fragmentation behavior; including, geometric features, loading conditions, and material gradation

Computational modelling of reactive processes in lithium-metal batteries

This Thesis presents a computational phase-field model to describe the electrodeposition process that forms dendrites within lithium-metal batteries. We describe the evolution of a phase field, the lithium-ion concentration, and electric potential during a battery charge cycle. We simulate three-dimensional spike-like lithium structures in agreement with experimentally-observed dendrite growth rates and morphologies reported in the literature. This work constitutes a relevant step towards physical-based, quantitative models needed to achieve the commercial realisation of lithium-metal batteries

GeomInt–Mechanical Integrity of Host Rocks

This open access book summarizes the results of the collaborative project “GeomInt: Geomechanical integrity of host and barrier rocks - experiment, modeling and analysis of discontinuities” within the Program: Geo Research for Sustainability (GEO: N) of the Federal Ministry of Education and Research (BMBF). The use of geosystems as a source of resources, a storage space, for installing underground municipal or traffic infrastructure has become much more intensive and diverse in recent years. Increasing utilization of the geological environment requires careful analyses of the rock–fluid systems as well as assessments of the feasibility, efficiency and environmental impacts of the technologies under consideration. The establishment of safe, economic and ecological operation of underground geosystems requires a comprehensive understanding of the physical, (geo)chemical and microbiological processes on all relevant time and length scales. This understanding can only be deepened on the basis of intensive laboratory and in-situ experiments in conjunction with reliable studies on the modeling and simulation (numerical experiments) of the corresponding multi-physical/chemical processes. The present work provides a unique handbook for experimentalists, modelers, analysts and even decision makers concerning the characterization of various types of host rocks (salt, clay, crystalline formations) for various geotechnical applications

Fluid-electro-mechanical model of the human heart for supercomputers

The heart is a complex system. From the transmembrane cell activity to the spatial organization in helicoidal fibers, it includes several spatial and temporal scales. The heart muscle is surrounded by two main tissues that modulate how it deforms: the pericardium and the blood. The former constrains the epicardial surface and the latter exerts a force in the endocardium. The main function of this peculiar muscle is to pump blood to the pulmonary and systemic circulations. In this way, solid dynamics of the heart is as important as the induced fluid dynamics. Despite the work done in computational research of multiphysics heart modelling, there is no reference of a tightly-coupled scheme that includes electrophysiology, solid and fluid mechanics in a whole human heart. In this work, we propose, develop and test a fluid-electro-mechanical model of the human heart. To start, the heartbeat phenomenon is disassembled in the different composing problems. The first building block is the electrical activity of the myocytes, that induces the mechanical deformation of the myocardium. The contraction of the muscle reduces the intracavitary space, that pushes out the contained blood. At the same time, the inertia, pressure and viscous stresses in this fluid exerts a force on the solid wall. In this way, we can understand the heart as a fluid-electro-mechanical problem. All the models are implemented in Alya, the Barcelona Supercomputing Center simulation software. A multi-code approach is used, splitting the problem in a solid and a fluid domain. In the former, electrophysiology coupled with solid mechanics are solved. In the later, fluid dynamics in an arbitrary Lagrangian-Eulerian domain are computed. The equations are spatially discretized using the finite element method and temporally discretized using finite differences. Facilitated by the multi-code approach, a novel high performance quasi-Newton method is developed to deal with the intrinsic issues of fluid-structure interaction problems in iomechanics. All the schemes are optimized to run in massively parallel computers. A wide range of experiments are shown to validate, test and tune the numerical model. The different hypothesis proposed — as the critical effect of the atrium or the presence of pericardium — are also tested in these experiments. Finally, a normal heartbeat is simulated and deeply analyzed. This healthy computational heart is first diseased with a left bundle branch block. After this, its function is restored simulating a cardiac resynchronization therapy. Then, a third grade atrioventricular block is simulated in the healthy heart. In this case, the pathologic model is treated with a minimally invasive leadless intracardiac pacemaker. This requires to include the device in the geometrical description of the problem, solve the structural problem with the tissue, and the fluid-structure interaction problem with the blood. As final experiment, we test the parallel performance of the coupled solver. In the cases mentioned above, the results are qualitatively compared against experimental measurements, when possible. Finally, a first glance in a coupled fluid-electro-mechanical cardiovascular system is shown. This model is build adding a one dimensional model of the arterial network created by the Laboratório Nacional de Computação Científica in Petropolis, Brasil. Despite the artificial geometries used, the outflow curves are comparable with physiological observations. The model presented in this thesis is a step towards the virtual human heart. In a near future computational models like the presented in this thesis will change how pathologies are understood and treated, and the way biomedical devices are designed.El corazón es un sistema complejo. Desde la actividad celular hasta la organización espacial en fibras helicoidales, incluye gran cantidad de escalas espaciales y temporales. El corazón está rodeado principalmente por dos tejidos que modulan su deformación: el pericardio y la sangre. El primero restringe el movimiento del epicardio, mientras el segundo ejerce fuerza sobre el endocardio. La función principal de este músculo es bombear sangre a la circulación sistémica y a la pulmonar. Así, la deformación del miocardio es tan importante como la fluidodinámica inducida. Al día de hoy, solo se han propuesto modelos parciales del corazón. Ninguno de los modelos publicados resuelve electrofisiología, mecánica del sólido, y dinámica de fluidos en una geometría completa del corazón. En esta tesis, proponemos, desarrollamos y probamos un modelo fluido -electro -mecánico del corazón. Primero, el problema del latido cardíaco es descompuesto en los distintos subproblemas. El primer bloque componente es la actividad eléctrica de los miocitos, que inducen la deformación mecánica del miocardio. La contratación de este músculo, reduce el espacio intracavitario, que empuja la sangre contenida. Al mismo tiempo, la inercia, presión y fuerzas viscosas del fluido inducen una presión sobre la pared del sólido. De esta manera, podemos entender el latido cardíaco como un problema fluido-electro-mecánico. Los modelos son implementados en Alya, el software de simulación del Barcelona Supercomputing Center. Se utiliza un diseño multi-código, separando el problema según el dominio en sólido y fluido. En el primero, se resuelve electrofisiología acoplado con mecánica del sólido. En el segundo, fluido dinámica en un dominio arbitrario Lagrangiano-Euleriano. Las ecuaciones son discretizadas espacial y temporalmente utilizando elementos finitos y diferencias finitas respectivamente. Facilitado por el diseño multi-codigo, se desarrolló un novedoso método quasi-Newton de alta performance, pensado específicamente para lidiar con los problemas intrínsecos de interacción fluido-estructura en biomecánica. Todos los esquemas fueron optimizados para correr en ordenadores masivamente paralelos.Se presenta un amplio espectro de experimentos con el fin de validar, probar y ajustar el modelo numérico. Las diferentes hipótesis propuestas tales como el efecto producido por la presencia de las aurículas o el pericardio son también demostradas en estos experimentos. Finalmente un latido normal es simulado y sus resultados son analizados con profundidad. El corazón computacional sano es, primeramente enfermado de un bloqueo de rama izquierda. Posteriormente se restaura la función normal mediante la terapia de resincronización cardíaca. Luego se afecta al corazón de un bloqueo atrioventricular de tercer grado. Esta patología es tratada mediante la implantación de un marcapasos intracardíaco. Para esto, se requiere incluir el dispositivo en la descripción geométrica, resolver el problema estructural con el tejido y la interacción fluido-estructura con la sangre. Como experimento numérico final, se prueba el desempeño paralelo del modelo acoplado.Finalmente, se muestran resultados preliminares para un modelo fluido-electro-mecánico del sistema cardiovascular. Este modelo se construye agregando un modelo unidimensional del árbol arterial. A pesar de las geometrías artificiales usadas, la curva de flujo en la raíz aórtica es comparable con observaciones experimentales. El modelo presentado aquí representa un avance hacia el humano virtual. En un futuro, modelos similares, cambiarán la forma en la que se entienden y tratan las enfermedades y la forma en la que los dispositivos biomédicos son diseñados.Postprint (published version