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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
141

Towards Lattice-Boltzmann modelling of unconfined gas mixing in anaerobic digestion

Dapelo, Davide, Trunk, R., Krause, M.J., Bridgeman, John 18 December 2018 (has links)
Yes / A novel Lattice-Boltzmann model to simulate gas mixing in anaerobic digestion is developed and described. For the first time, Euler–Lagrange multiphase, non-Newtonian and turbulence modelling are applied jontly with a novel hybrid boundary condition. The model is validated in a laboratory-scale framework and flow patterns are assessed through Particle Imaging Velocimetry (PIV) and innovative Positron-Emission Particle Tracking (PEPT). The model is shown to reproduce the experimental flow patterns with fidelity in both qualitative and quantitative terms. The model opens up a new approach to computational modelling of the complex multiphase flow in anaerobic digesters and offers specific advantages, such as computational efficiency, over an analogous Euler-Lagrange finite-volume computational fluid dynamics approach. / UK EPSRC Grant (EP/R01485X/1, Computational Methods for Anaerobic Digestion Optimization, “CoMAnDO”). The numerical work was performed in the HPC Cirrus EPSRC Tier-2 National HPC Facility, Edinburgh, UK, under a UK EPSRC Tier-2 Research Allocation Panel (RAP) award.
142

Investigation of open channel flow with unsubmerged rigid vegetation by the lattice Boltzmann method

Jing, H., Cai, Y., Wang, W., Guo, Yakun, Li, C., Bai, Y. 10 September 2019 (has links)
Yes / Aquatic vegetation can significantly affect flow structure, sediment transport, bed scour and water quality in rivers, lakes, reservoirs and open channels. In this study, the lattice Boltzmann method is applied for performing the two dimensional numerical simulation of the flow structure in a flume with rigid vegetation. A multi-relaxation time model is applied to improve the stability of the numerical scheme for flow with high Reynolds number. The vegetation induced drag force is added in lattice Boltzmann equation model with the algorithm of multi-relaxation time in order to improve the simulation accuracy,. Numerical simulations are performed for a wide range of flow and vegetation conditions and are validated by comparing with the laboratory experiments. Analysis of the simulated and experimentally measured flow field shows that the numerical simulation can satisfactorily reproduce the laboratory experiments, indicating that the proposed lattice Boltzmann model has high accuracy for simulating flow-vegetation interaction in open channel. / National Natural Science Foundation of China (grant number: 11861003 and 11761005)
143

OpenLB-Open source lattice Boltzmann code

Krause, M.J., Kummerländer, A., Avis, S.J., Kusumaatmaja, H., Dapelo, Davide, Klemens, F., Gaedtke, M., Hafen, N., Mink, A., Marquardt, J.E., Maier, M.-L., Haussmann, M., Simonis, S. 25 November 2020 (has links)
Yes / We present the OpenLB package, a C++ library providing a flexible framework for lattice Boltzmann simulations. The code is publicly available and published under GNU GPLv2, which allows for adaption and implementation of additional models. The extensibility benefits from a modular code structure achieved e.g. by utilizing template meta-programming. The package covers various methodical approaches and is applicable to a wide range of transport problems (e.g. fluid, particulate and thermal flows). The built-in processing of the STL file format furthermore allows for the simple setup of simulations in complex geometries. The utilization of MPI as well as OpenMP parallelism enables the user to perform those simulations on large-scale computing clusters. It requires a minimal amount of dependencies and includes several benchmark cases and examples. The package presented here aims at providing an open access platform for both, applicants and developers, from academia as well as industry, which facilitates the extension of previous implementations and results to novel fields of application for lattice Boltzmann methods. OpenLB was tested and validated over several code reviews and publications. This paper summarizes the findings and gives a brief introduction to the underlying concepts as well as the design of the parallel data structure.
144

The Quantized Velocity Finite Element Method

Cook, Charles 23 April 2024 (has links)
The Euler and Navier-Stokes-Fourier equations will be directly expressed as distribution evolution equations, where a new and proper continuum prescription will be derived. These equations of motion will be numerically solved with the development of a new and unique finite element formulation. Out of this framework, the 7D phasetime element has been born. To provide optimal stability, a new quantization procedure is established based on the principles of quantum theory. The entirety of this framework has been coined the "quantized velocity finite element method" (QVFEM). The work performed herein lays the foundational development of what is hoped to become a new paradigm shift in computational fluid dynamics. / Doctor of Philosophy / To model any of the four fundamental states of matter, for practical engineering applications, we must first recognize the complexity of such states. In consequence, a new and novel approach is presented on how to numerically simulate the dynamics of a gas using both the Euler and Navier-Stokes-Fourier equations of continuum mechanics and thermodynamics. In contrast to direct numerical simulation, a statistical mechanical prescription will be given where the equations of motion will be quantized using methods taken from the study of quantum mechanics. This newly developed discretization of the phase space and time, or phasetime, provides optimal stability for compressible flow simulations. From the newly proposed framework, the 7D phasetime element has been born.
145

Pore-scale Study of Flow and Transport in Energy Georeservoirs

Fan, Ming 22 July 2019 (has links)
Optimizing proppant pack conductivity and proppant-transport and -deposition patterns in a hydraulic fracture is of critical importance to sustain effective and economical production of petroleum hydrocarbons. In this research, a numerical modeling approach, combining the discrete element method (DEM) with the lattice Boltzmann (LB) simulation, was developed to provide fundamental insights into the factors regulating the interactions between reservoir depletion, proppant-particle compaction and movement, single-/multiphase flows and non-Darcy flows in a hydraulic fracture, and fracture conductivity evolution from a partial-monolayer proppant concentration to a multilayer proppant concentration. The potential effects of mixed proppants of different sizes and types on the fracture conductivity were also investigated. The simulation results demonstrate that a proppant pack with a smaller diameter coefficient of variation (COV), defined as the ratio of standard deviation of diameter to mean diameter, provides better support to the fracture; the relative permeability of oil was more sensitive to changes in geometry and stress; when effective stress increased continuously, oil relative permeability increased nonmonotonically; the combination of high diameter COV and high effective stress leads to a larger pressure drop and consequently a stronger non-Darcy flow effect. The study of proppant mixtures shows that mixing of similar proppant sizes (mesh-size-20/40) has less influence on the overall fracture conductivity than mixing a very fine mesh size (mesh-size-100); selection of proppant type is more important than proppant size selection when a proppant mixture is used. Increasing larger-size proppant composition in the proppant mixture helps maintain fracture conductivity when the mixture contains lower-strength proppants. These findings have important implications to the optimization of proppant placement, completion design, and well production. In the hydraulic-mechanical rock-proppant system, a fundamental understanding of multiphase flow in the formation rock is critical in achieving sustainable long-term productivity within a reservoir. Specifically, the interactions between the critical dimensionless numbers associated with multiphase flow, including contact angle, viscosity ratio, and capillary number (Ca), were investigated using X-ray micro computed tomography (micro-CT) scanning and LB modeling. The primary novel finding of this study is that the viscosity ratio affects the rate of change of the relative permeability curves for both phases when the contact angle changes continuously. Simulation results also indicate that the change in non-wetting fluid relative permeability was larger when the flow direction was switched from vertical to horizontal, which indicated that there was stronger anisotropy in larger pore networks that were primarily occupied by the non-wetting fluid. This study advances the fundamental understanding of the multiphysics processes associated with multiphase flow in geologic materials and provides insight into upscaling methodologies that account for the influence of pore-scale processes in core- and larger-scale modeling frameworks. During reservoir depletion processes, reservoir formation damage is an issue that will affect the reservoir productivity and various phases in fluid recovery. Invasion of formation fine particles into the proppant pack can affect the proppant pack permeability, leading to potential conductivity loss. The combined DEM-LB numerical framework was used to evaluate the role of proppant particle size heterogeneity (variation in proppant particle diameter) and effective stress on the migration of detached fine particles in a proppant supported fracture. Simulation results demonstrate that a critical fine particle size exists: when a particle diameter is larger or smaller than this size, the deposition rate increases; the transport of smaller fines is dominated by Brownian motion, whereas the migration of larger fines is dominated by interception and gravitational settling; this study also indicates that proppant packs with a more heterogeneous particle-diameter distribution provide better fines control. The findings of this study shed lights on the relationship between changing pore geometries, fluid flow, and fine particle migration through a propped hydraulic fracture during the reservoir depletion process. / Doctor of Philosophy / Hydraulic fracturing stimulation design is required for unconventional hydrocarbon energy (e.g., shale oil and gas) extraction due to the low permeability and complex petrophysical properties of unconventional reservoirs. During hydrocarbon production, fractures close after pumping due to the reduced fluid pressure and increased effective stress in rock formations. In the oil and gas industry, proppant particles, which are granular materials, typically sand, treated sand, or man-made ceramic materials, are pumped along with fracturing fluids to prevent hydraulic fractures from closing during hydrocarbon extraction. In order to relate the geomechanical (effective stress), geometric (pore structure and connectivity), and transport (absolute permeability, relative permeability, and conductivity) properties of a proppant assembly sandwiched in a rock fracture, a geomechanics-fluid mechanics framework using both experiment and simulation methods, was developed to study the interaction and coupling between them. The outcome of this research will advance the fundamental understanding of the coupled, multiphysics processes with respect to hydraulic fracturing and benefit the optimization of proppant placement, completion design, and well production.
146

Discovering the Complex Aerodynamics of Flapping Flight with Bio-kinematics Using Boltzmann and Eulerian Methods

Feaster, Jeffrey Oden 31 August 2017 (has links)
The cross-sectional geometry of an insect wing has historically been simplified to a rectangular, elliptic, or having a streamlined airfoil shape. Up until this point, no analysis has utilized a morphologically accurate insect wing. As such, there remains significant questions as to whether or not there are aerodynamic benefits to the wing vein structure accompanying the already known structural improvements. The present study uses a bumblebee specimen (Bombus pensylvanicus) acquired by the author, scanned using a skyscan microCT scanner, and post-processed for computational analysis. The resulting geometry captures the naturally occurring vein structures present in the bee wing and is used to better understand aerodynamic effects of biological corrugation. The aerodynamics associated with a morphologically accurate bee wing geometry are explored in two and three dimensions for the first time. Multiple methodologies are validated with experimental results presented in the literature to capture the fluid dynamics in two dimensions including the Lattice-Boltzmann method and unstructured dynamic remeshing using a Navier-Stokes approach. The effects of wing cross-section are compared first with common geometries used in the literature in two dimensions and then between cross-sections extracted at different locations along the wing span. A three-dimensional methodology is validated and used to compare the true bee wing with one using a rectangular cross-section in symmetric hovering. The influence of spanwise cross-section is revisited in three dimensions and compared to the results found in two-dimensions for the same kinematics in forward flight. The final focus of the dissertation is the first simulation of a morphologically accurate wing using kinematics described in the literature. / PHD
147

Méthodes numériques hybrides basées sur une approche Boltzmann sur réseau en vue de l'application aux maillages non-uniformes / Hybrid numerical methods based on the lattice Boltzmann approach with application to non-uniform grids

Horstmann, Tobias 12 October 2018 (has links)
Malgré l'efficacité informatique et la faible dissipation numérique de la méthode de Boltzmann sur réseau (LBM) classique reposant sur un algorithme de propagation-collision, cette méthode est limitée aux maillages cartésiens uniformes. L'adaptation de l'étape de discrétisation à différentes échelles de la mécanique des fluides est généralement réalisée par des schémas LBM à échelles multiples, dans lesquels le domaine de calcul est décomposé en plusieurs sous-domaines uniformes avec différentes résolutions spatiales et temporelles. Pour des raisons de connectivité, le facteur de résolution des sous-domaines adjacents doit être un multiple de deux, introduisant un changement abrupt des échelles spatio-temporelles aux interfaces. Cette spécificité peut déclencher des instabilités numériques et produire des sources de bruit parasite rendant l'exploitation de simulations à finalités aéroacoustiques impossible. Dans la présente thèse, nous avons d'abord élucidé le sujet du raffinement de maillage dans la LBM classique en soulignant les défis et les sources potentielles d'erreur. Par la suite, une méthode de Boltzmann sur réseau hybride (HLBM) est proposée, combinant l'algorithme de propagation-collision avec un algorithme de flux au sens eulérien obtenu à partir d'une discrétisation en volumes finis des équations de Boltzmann à vitesse discrète. La HLBM combine à la fois les avantages de la LBM classique et une flexibilité géométrique accrue. La HLBM permet d'utiliser des maillages cartésiens non-uniformes. La validation de la méthode hybride sur des cas tests 2D à finalité aéroacoustique montre qu'une telle approche constitue une alternative viable aux schémas Boltzmann sur réseau à échelles multiples, permettant de réaliser des raffinements locaux en H. Enfin, un couplage original, basé sur l'algorithme de propagation-collision et une formulation isotherme des équations de Navier-Stokes en volumes finis, est proposé. Une telle tentative présente l'avantage de réduire le nombre d'équations du solveur volumes finis tout en augmentant la stabilité numérique de celui-ci, en raison d'une condition CFL plus favorable. Les deux solveurs sont couplés dans l'espace des moments, où la solution macroscopique du solveur Navier-Stokes est injectée dans l'algorithme de propagation-collision à l'aide de la collision des moments centrés. La faisabilité d'un tel couplage est démontrée sur des cas tests 2D, et les résultas obtenus sont comparés avec la HLBM. / Despite the inherent efficiency and low dissipative behaviour of the standard lattice Boltzmann method (LBM) relying on a two step stream and collide algorithm, a major drawback of this approach is the restriction to uniform Cartesian grids. The adaptation of the discretization step to varying fluid dynamic scales is usually achieved by multi-scale lattice Boltzmann schemes, in which the computational domain is decomposed into multiple uniform subdomains with different spatial resolutions. For the sake of connectivity, the resolution factor of adjacent subdomains has to be a multiple of two, introducing an abrupt change of the space-time discretization step at the interface that is prone to trigger instabilites and generate spurious noise sources that contaminate the expected physical pressure signal. In the present PhD thesis, we first elucidate the subject of mesh refinement in the standard lattice Boltzmann method and point out challenges and potential sources of error. Subsequently, we propose a novel hybrid lattice Boltzmann method (HLBM) that combines the stream and collide algorithm with an Eulerian flux-balance algorithm that is obtained from a finite-volume discretization of the discrete velocity Boltzmann equations. The interest of a hybrid lattice Boltzmann method is the pairing of efficiency and low numerical dissipation with an increase in geometrical flexibility. The HLBM allows for non-uniform grids. In the scope of 2D periodic test cases, it is shown that such an approach constitutes a valuable alternative to multi-scale lattice Boltzmann schemes by allowing local mesh refinement of type H. The HLBM properly resolves aerodynamics and aeroacoustics in the interface regions. A further part of the presented work examines the coupling of the stream and collide algorithm with a finite-volume formulation of the isothermal Navier-Stokes equations. Such an attempt bears the advantages that the number of equations of the finite-volume solver is reduced. In addition, the stability is increased due to a more favorable CFL condition. A major difference to the pairing of two kinetic schemes is the coupling in moment space. Here, a novel technique is presented to inject the macroscopic solution of the Navier-Stokes solver into the stream and collide algorithm using a central moment collision. First results on 2D tests cases show that such an algorithm is stable and feasible. Numerical results are compared with those of the previous HLBM.
148

Extension et analyse des schémas de Boltzmann sur réseau : les schémas à vitesse relative / Extension and analysis of the lattice Boltzmann schemes : the relative velocity schemes

Février, Tony 05 December 2014 (has links)
Cette thèse introduit et étudie une nouvelle classe de schémas de Boltzmann sur réseau appelés schémas à vitesse relative. Les schémas de Boltzmann sur réseau visent à approcher des problèmes de nature macroscopique en mimant la dynamique microscopique d’équations cinétiques du type Boltzmann. L’algorithme calcule des distributions de particules évoluant au travers de deux phases de transport et de relaxation, les particules se déplaçant en les noeuds d’un réseau cartésien en espace. Les schémas de Boltzmann à plusieurs temps de relaxation (ou schéma MRT de d’Humières), dont la relaxation im- plique un ensemble de moments combinaison linéaire polynomiale des distributions, constituent le cadre initial de la thèse. Les schémas à vitesse relative sont une extension de ces schémas de d’Humières. Ils sont inspirés du schéma cascade de Geier apportant davantage de stabilité que les schémas de d’Hu- mières pour des régimes peu visqueux des équations de Navier-Stokes. La différence avec ces schémas se situe au niveau de la relaxation : elle utilise un ensemble de moments relatifs à un paramètre champ de vitesse fonction du temps et de l’espace. Cette différence se matérialise par une matrice de tran- sition des moments fixes (les schémas de d’Humières correspondent à un paramètre champ de vitesse nul) aux moments mobiles. La structure algébrique de cette matrice est étudiée. Le schéma cascade est ensuite traduit comme un schéma à vitesse relative pour un nouvel ensemble de polynômes définissant les moments. L’étude de la consistance des schémas à vitesse relative par la méthode des équations équivalentes est un point central de la thèse. Les équations limites pour un nombre arbitraire de dimen- sions et de vitesses sont dérivées et illustrées sur des exemples tels que le D2Q9 pour les équations de Navier-Stokes. Ces équations équivalentes sont également un outil pour prédire la stabilité des schémas grâce à l’analyse des termes de diffusion et dispersion. La dernière partie traite de la stabilité suivant le choix du paramètre champ de vitesse. Nous sommes particulièrement intéressés en les deux choix de paramètre nul (d’Humières) et la vitesse du fluide (cascade). Le schéma D2Q9 pour les équations de Navier-Stokes est étudié numériquement par une méthode de Von Neumann puis appuyé sur des cas tests non linéaires. La stabilité des schémas relatifs à la vitesse du fluide est dépendante du choix des polynômes définissant les moments. L’amélioration la plus notable se produit si les polynômes du schéma cascade sont choisis. Nous étudions enfin les stabilités théorique et numérique d’un schéma bidimensionnel minimal. Le contexte physique est la simulation d’une équation d’advection diffusion linéaire. Le choix de la vitesse d’advection comme paramètre champ de vitesse annule certains termes de dispersion des équations équivalentes contrairement aux schémas de d’Humières. Ceci se traduit par un meilleur comportement en termes de stabilité pour de grandes vitesses, appuyé théoriquement à l’aide d’une notion de stabilité à poids. / In this PhD thesis, a new class of lattice Boltzmann schemes called relative velocity schemes is introduced and studied. The purpose of lattice Boltzmann schemes is to approximate problems of macroscopic nature using the microscopic dynamic of Boltzmann type kinetic equations. They compute particle distributions through two phases of transport and relaxation, the particles moving on the nodes of a cartesian lattice. The multiple relaxation times schemes---MRT of d'Humières---, whose relaxation uses a set of moments, linear combinations of the particle distributions, constitutes the initial framework of the thesis. The relative velocity schemes extend the MRT d'Humières schemes. They originate from the cascaded automaton of Geier which provides more stability for the low viscosity regime of the Navier-Stokes equations. Their difference with the d'Humières schemes is carried by the relaxation : a set of moments relative to a velocity field parameter function of space and time is used. This difference is represented by a shifting matrix sending the fixed moments---The d'Humières schemes are associated with a zero velocity field parameter---On the relative moments. The algebraic structure of this matrix is studied. The cascaded automaton is then interpreted as a relative velocity scheme for a new set of polynomials defining the moments. The consistency study of the relative velocity schemes with the equivalent equations method is a keypoint of the thesis. These equations are derived for an arbitrary number of dimensions and velocities. They are then illustrated on examples like the D2Q9 scheme for the Navier-Stokes equations. These equivalent equations are also a tool to predict the stability behaviour of the schemes by analysing their diffusion and dispersion terms. In a last part, the stability according to the velocity field parameter is studied. Two cases especially interest us : a parameter equal to zero---D'Humières schemes---And equal to the fluid velocity---Cascaded automaton. The D2Q9 scheme for the Navier-Stokes equations is numerically studied with a linear Von Neumann analysis and some non linear test cases. The stability of the relative velocity schemes depends on the choice of the polynomials defining the moments. The most important improvement occurs if the polynomials of the cascaded automaton are chosen. We finally study the theoretical and numerical stability of a minimal bidimensional scheme for a linear advection diffusion equation. If the velocity field parameter is chosen equal to the advection velocity, some dispersion terms of the equivalent equations vanish unlike the d'Humières scheme. This implies a better stability behaviour for high velocities, characterized thanks to theoretical weighted stability notion.
149

Calcul parallèle pour la modélisation d'images de résonance magnétique nucléaire / Parallel computing in modeling of magnetic resonance imaging / Obliczenia równoległe w modelowaniu obrazowania technika rezonansu magnetycznego

Jurczuk, Krzysztof 28 August 2013 (has links)
L'objet de cette thèse est la modélisation computationnelle de l'Imagerie par Résonance Magnétique (IRM), appliquée à l'imagerie des réseaux vasculaires. Les images sont influencées par la géométrie des vaisseaux mais aussi par le flux sanguin. Par ailleurs, outre la qualité des modèles développés, il est important que les calculs soient performants. C'est pourquoi, le calcul parallèle est utilisé pour gérer ce type de problèmes complexes. Dans cette thèse, trois solutions sont proposées. La première concerne les algorithmes parallèles pour la modélisation des réseaux vasculaires. Des algorithmes dédiés à différentes architectures sont proposés. Le premier est basé sur le modèle de « passage de messages » pour les machines à mémoires distribuées. La parallélisation concerne l'irrigation de nouvelles zones de tissu par les vaisseaux existants. Le deuxième algorithme est dédié aux machines à mémoire partagée. Il parallélise également le processus de perfusion mais des processeurs différents se chargent de gérer les différents arbres vasculaires. Le troisième algorithme est une combinaison des approches précédentes offrant une solution pour les architectures parallèles hybrides. Les algorithmes proposés permettent d'accélérer considérablement la croissance des réseaux vasculaires complexes, ce qui rend possible la simulation de structures vasculaires plus précises, en un temps raisonnable et aide à améliorer le modèle vasculaire et à tester plus facilement différents jeux de paramètres. Une nouvelle approche de modélisation computationnelle des flux en IRM est également proposée. Elle combine le calcul de flux par la méthode de Lattice Boltzmann, la simulation IRM par le suivi temporel de magnétisations locales, ainsi qu'un nouvel algorithme de transport des magnétisations. Les résultats montrent qu'une telle approche intègre naturellement l'influence du flux dans la modélisation IRM. Contrairement aux travaux de la littérature, aucun mécanisme additionnel n'est nécessaire pour considérer les artéfacts de flux, ce qui offre une grande facilité d'extension du modèle. Les principaux avantages de cette méthode est sa faible complexité computationnelle, son implémentation efficace, qui facilitent le lancement des simulations en utilisant différents paramètres physiologiques ou paramètres d'acquisition des images. La troisième partie du travail de thèse a consisté à appliquer le modèle d'imagerie de flux à des réseaux vasculaires complexes en combinant les modèles de vaisseaux, de flux et d'acquisition IRM. Les algorithmes sont optimisés à tous les niveaux afin d'être performants sur des architectures parallèles. Les possibilités du modèle sont illustrées sur différents cas. Cette démarche de modélisation peut aider à mieux interpréter les images IRM grâce à l'intégration, dans les modèles, de connaissances variées allant de la vascularisation des organes jusqu'à la formation de l'image en passant par les propriétés des flux sanguins. / This PhD thesis concerns computer modeling of magnetic resonance imaging (MRI). The main attention is centered on imaging of vascular structures. Such imaging is influenced not only by vascular geometries but also by blood flow which has to been taken into account in modeling. Next to the question about the quality of developed models, the challenge lies also in the demand for high performance computing. Thus, in order to manage computationally complex problems, parallel computing is in use. In the thesis three solutions are proposed. The first one concerns parallel algorithms of vascular network modeling. Algorithms for different architectures are proposed. The first algorithm is based on the message passing model and thus, it is suited for distributed memory architectures. It parallelizes the process of connecting new parts of tissue to existing vascular structures. The second algorithm is designed for shared memory machines. It also parallelizes the perfusion process, but individual processors perform calculations concerning different vascular trees. The third algorithm combines message passing and shared memory approaches providing solutions for hybrid parallel architectures. Developed algorithms are able to substantially speed up the time-demanded simulations of growth of complex vascular networks. As a result, more elaborate and precise vascular structures can be simulated in a reasonable period of time. It can also help to extend the vascular model and to test multiple sets of parameters. Secondly, a new approach in computational modeling of magnetic resonance (MR) flow imaging is proposed. The approach combines the flow computation by lattice Boltzmann method, MRI simulation by following discrete local magnetizations in time and a new magnetization transport algorithm together. Results demonstrate that such an approach is able to naturally incorporate the flow influence in MRI modeling. As a result, in the proposed model, no additional mechanism (unlike in prior works) is needed to consider flow artifacts, what implies its easy extensibility. In combination with its low computational complexity and efficient implementation, the solution is a user-friendly and manageable at different levels tool which facilitates running series of simulations with different physiological and imaging parameters. The goal of the third solution is to apply the proposed MR flow imaging model on complex vascular networks. To this aim, models of vascular networks, flow behavior and MRI are combined together. In all the model components, computations are adapted to be performed at various parallel architectures. The model potential and possibilities of simulations of flow and MRI in complex vascular structures are shown. The model aims at explaining and exploring MR image formation and appearance by the combined knowledge from many processes and systems, starting from vascular geometry, through flow patterns and ending on imaging technology.
150

Lattice-gas cellular automata for the analysis of cancer invasion / Zelluläre Gitter-Gas Automaten Modelle für die Analyse von Tumorinvasion

Hatzikirou, Haralambos 16 July 2009 (has links) (PDF)
Cancer cells display characteristic traits acquired in a step-wise manner during carcinogenesis. Some of these traits are autonomous growth, induction of angiogenesis, invasion and metastasis. In this thesis, the focus is on one of the latest stages of tumor progression, tumor invasion. Tumor invasion emerges from the combined effect of tumor cell-cell and cell-microenvironment interactions, which can be studied with the help of mathematical analysis. Cellular automata (CA) can be viewed as simple models of self-organizing complex systems in which collective behavior can emerge out of an ensemble of many interacting "simple" components. In particular, we focus on an important class of CA, the so-called lattice-gas cellular automata (LGCA). In contrast to traditional CA, LGCA provide a straightforward and intuitive implementation of particle transport and interactions. Additionally, the structure of LGCA facilitates the mathematical analysis of their behavior. Here, the principal tools of mathematical analysis of LGCA are the mean-field approximation and the corresponding Lattice Boltzmann equation. The main objective of this thesis is to investigate important aspects of tumor invasion, under the microscope of mathematical modeling and analysis: Impact of the tumor environment: We introduce a LGCA as a microscopic model of tumor cell migration together with a mathematical description of different tumor environments. We study the impact of the various tumor environments (such as extracellular matrix) on tumor cell migration by estimating the tumor cell dispersion speed for a given environment. Effect of tumor cell proliferation and migration: We study the effect of tumor cell proliferation and migration on the tumor’s invasive behavior by developing a simplified LGCA model of tumor growth. In particular, we derive the corresponding macroscopic dynamics and we calculate the tumor’s invasion speed in terms of tumor cell proliferation and migration rates. Moreover, we calculate the width of the invasive zone, where the majority of mitotic activity is concentrated, and it is found to be proportional to the invasion speed. Mechanisms of tumor invasion emergence: We investigate the mechanisms for the emergence of tumor invasion in the course of cancer progression. We conclude that the response of a microscopic intracellular mechanism (migration/proliferation dichotomy) to oxygen shortage, i.e. hypoxia, maybe responsible for the transition from a benign (proliferative) to a malignant (invasive) tumor. Computing in vivo tumor invasion: Finally, we propose an evolutionary algorithm that estimates the parameters of a tumor growth LGCA model based on time-series of patient medical data (in particular Magnetic Resonance and Diffusion Tensor Imaging data). These parameters may allow to reproduce clinically relevant tumor growth scenarios for a specific patient, providing a prediction of the tumor growth at a later time stage. / Krebszellen zeigen charakteristische Merkmale, die sie in einem schrittweisen Vorgang während der Karzinogenese erworben haben. Einige dieser Merkmale sind autonomes Wachstum, die Induktion von Angiogenese, Invasion und Metastasis. Der Schwerpunkt dieser Arbeit liegt auf der Tumorinvasion, einer der letzten Phasen der Tumorprogression. Die Tumorinvasion ensteht aus der kombinierten Wirkung von den Wechselwirkungen Tumorzelle-Zelle und Zelle-Mikroumgebung, die mit die Hilfe von mathematischer Analyse untersucht werden können. Zelluläre Automaten (CA) können als einfache Modelle von selbst-organisierenden komplexen Systemen betrachtet werden, in denen kollektives Verhalten aus einer Kombination von vielen interagierenden "einfachen" Komponenten entstehen kann. Insbesondere konzentrieren wir uns auf eine wichtige CA-Klasse, die sogenannten Zelluläre Gitter-Gas Automaten (LGCA). Im Gegensatz zu traditionellen CA bieten LGCA eine einfache und intuitive Umsetzung der Teilchen und Wechselwirkungen. Zusätzlich erleichtert die Struktur der LGCA die mathematische Analyse ihres Verhaltens. Die wichtigsten Werkzeuge der mathematischen Analyse der LGCA sind hier die Mean-field Approximation und die entsprechende Lattice - Boltzmann - Gleichung. Das wichtigste Ziel dieser Arbeit ist es, wichtige Aspekte der Tumorinvasion unter dem Mikroskop der mathematischen Modellierung und Analyse zu erforschen: Auswirkungen der Tumorumgebung: Wir stellen einen LGCA als mikroskopisches Modell der Tumorzellen-Migration in Verbindung mit einer mathematischen Beschreibung der verschiedenen Tumorumgebungen vor. Wir untersuchen die Auswirkungen der verschiedenen Tumorumgebungen (z. B. extrazellulären Matrix) auf die Migration von Tumorzellen dürch Schätzung der Tumorzellen-Dispersionsgeschwindigkeit in einem gegebenen Umfeld. Wirkung von Tumor-Zellenproliferation und Migration: Wir untersuchen die Wirkung von Tumorzellenproliferation und Migration auf das invasive Verhalten der Tumorzellen durch die Entwicklung eines vereinfachten LGCA Tumorwachstumsmodells. Wir leiten die entsprechende makroskopische Dynamik und berechnen die Tumorinvasionsgeschwindigkeit im Hinblick auf die Tumorzellenproliferation- und Migrationswerte. Darüber hinaus berechnen wir die Breite der invasiven Zone, wo die Mehrheit der mitotischer Aktivität konzentriert ist, und es wird festgestellt, dass diese proportional zu den Invasionsgeschwindigkeit ist. Mechanismen der Tumorinvasion Entstehung: Wir untersuchen Mechanismen, die für die Entstehung von Tumorinvasion im Verlauf des Krebs zuständig sind. Wir kommen zu dem Schluss, dass die Reaktion eines mikroskopischen intrazellulären Mechanismus (Migration/Proliferation Dichotomie) zu Sauerstoffmangel, d.h. Hypoxie, möglicheweise für den Übergang von einem gutartigen (proliferative) zu einer bösartigen (invasive) Tumor verantwortlich ist. Berechnung der in-vivo Tumorinvasion: Schließlich schlagen wir einen evolutionären Algorithmus vor, der die Parameter eines LGCA Modells von Tumorwachstum auf der Grundlage von medizinischen Daten des Patienten für mehrere Zeitpunkte (insbesondere die Magnet-Resonanz-und Diffusion Tensor Imaging Daten) ermöglicht. Diese Parameter erlauben Szenarien für einen klinisch relevanten Tumorwachstum für einen bestimmten Patienten zu reproduzieren, die eine Vorhersage des Tumorwachstums zu einem späteren Zeitpunkt möglich machen.

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