Dans le cadre du design des assemblages combustibles, les écoulements turbulents induits par les grilles de maintien provoquent de fortes fluctuations de pression dues aux niveaux de vitesses du fluide induisant la vibration des crayons combustibles. Or ces vibrations sont une source de vieillissement accéléré et d’usure prématurée des assemblages combustibles dont l’origine convient d’être mieux analysée.Dans cette l'optique, des simulations numériques ont été utilisées pour prédire les niveaux de vitesses transverses ainsi que le niveau de turbulence en aval de la grille. Cependant, les codes CFD doivent être validés avec des mesures expérimentales conduisant ainsi à une meilleure compréhension des structures mis en jeu dans le processus de mélange. Or la caractéristique de ce type d'écoulement repose sur son caractère tridimensionnel entre les faisceaux de crayons où l'accès optique est limité et à l'heure actuelle, aucune mesure de vitesse 3D n'a été réalisée. C'est pourquoi nous nous proposons de présenter dans cette étude l'application d'une technique de mesure 3D résolue en temps dans une boucle hydraulique transparente. L’approche consiste à utiliser une stratégie de suivi, dans lequel des particules traceuses individuelles sont d'abord détectées dans l’écoulement et ensuite suivies dans le temps – PTV 3D.Cette thèse présente les résultats obtenus dans une veine d’essais hydraulique en utilisant une approche de suivi à l’aide de deux caméras. Dans un premier temps, une nouvelle extension de la technique de défocalisation permettant de récupérer les positions des particules dans le temps avec une caméra est présentée et la méthodologie pour récupérer les déplacements individuels est décrite. Des cas d’application et de validation de la technique sont présentés afin de mieux quantifier les erreurs de mesures. Ensuite, la boucle hydraulique est introduite et son écoulement caractérisé par des techniques établies de mesure de vitesse. Finalement, les mesures 3D à deux caméras sont réalisées et discutées. / In order to validate the numerical simulation of the mixing phenomena downstream a spacer grid in the reactor core, reaching the 3rd velocity component through experimental studies is of major importance since mechanical structures responses are linked to transverse velocities. Nevertheless the main difficulty relies on applying a non-intrusive velocimetry technique around obstacles composed of a vertical set of rods. So far only 1D and 2D temporal studies have been performed.Hence, numerical methods have been widely used to predict correctly those transverse velocities and the turbulence level downstream the grid. However, CFD codes are to be validated with experimental measurements leading to a better understanding of the detailed flow structure in the mixing process. Therefore we propose to present in this study the application of a 3D time resolved velocity measurement technique to a hydraulic test facility. The approach is to use a tracking strategy, in which individual particles are first detected then followed in time - 3D time resolved Particle Tracking Velocimetry.This PhD Thesis presents results obtained in a hydraulic test section using a tracking based approach with two cameras. At first, a new extension of the defocussing technique to recover particles location in time with one camera is presented and the methodology o get individual velocity vector is then described. Applications and validations of the technique in dedicated flows allow to determinate and quantify measurement uncertainties. Then the hydraulic test section is introduced together with preliminary flow characterization using Laser Doppler Velocimetry or 2D time resolved PIV analysis. Finally, two cameras measurements are reported and post-processing techniques are discussed.

Hydraulic structures such as dykes and groynes are commonly used to help control river flows and reduce flood risk. The present research aims to develop an idealized model of the hydrodynamics in the vicinity of a large river bend, and the advection and mixing processes where groynes are located. In this study a curvilinear model of shallow water equations is applied to investigate chaotic advection of particles in a river bend similar in dimensions to a typical bend in the River Danube, Hungary. First, a curvilinear grid generator is developed based on Poisson-type elliptic partial differential equations. The grid generator is verified for benchmark tests concerning a circular domain and for distorted grids in a rectangular domain. It is found that multi-grid (MG) and conjugate gradient (CG) methods performed better computationally than successive over-relaxation (SOR) in generating the curvilinear grids. The open channel hydrodynamics are modelled using the shallow water equations (SWEs) derived by depth-averaging the continuity and Navier-Stokes momentum equations. Both Cartesian and curvilinear forms of the shallow water equations are presented. Both sets of equations are discretized spatially using finite differences and the solution marched forward in time using fourth-order Runge-Kutta scheme. The shallow water solvers are verified and validated for uniform flow in the rectangular channel, wind-induced set up in rectangular and circular basins, flow past a sidewall expansion, and Shallow flow in a rectangular channel with single groyne. A Lagrangian particle tracking model is used to predict the trajectories of tracer particles, and bilinear interpolation is used to provide a representation of the continuous flow field from discrete results. The particle tracking model is verified for trajectories in the flow field of a single free vortex and in the alternating flow field of a pair of blinking vortices. Excellent agreement is obtained with analytical solutions, previously published results in the literature. The combined shallow flow and Lagrangian particle tracking model is then used to simulate particle advection in the flow past a side-wall cavity containing a groyne and reasonable agreement is obtained with published experimental and alternative numerical data. Finally, the combined model is applied to simulate the shallow flow hydrodynamics, advection and mixing processes in the vicinity of groynes in river bend, the dimensions representative of a typical bend in the Danube River, Hungary.

Title: Live-cell tracking in time-lapse sequences Author: Tomáš Zámečník Department: Department of Software and Computer Science Education Supervisor: RNDr. Michal Šorel Ph.D., Oddělení zpracování obrazu ÚTIA AV ČR Abstract: This diploma thesis deals with methods of tracking particles in image sequences. It's goal is to design and implement a complete system for tracking of live cells, their motion and division. The thesis uses conclusions of published scientific papers, studies their application and analyzes possibilities for their mo- difications or improvement. As a result, there are two applications. First of them is a demonstrational pro- gram, provided as an attachment of this thesis. Second implementation is a mo- dule of commercial software NIS-Elements, by Laboratory Imaging, Ltd., which is used by both scientific and commercial institutions in the whole world. Keywords: cell tracking, particle tracking, cell division 1

Graphics Processing Units (GPUs) have grown in popularity beyond the original video game enthusiast audience. They have been embraced by the high-performance computing community due to their high computational throughput, low cost, low energy demands, wide availability, and ability to dramatically improve application performance. In addition, as hybrid computing continues into mainstream applications, the use of GPUs will continue to grow. However, due to architectural difference between the CPU and GPU, adapting CPU-based scientific computing applications to fully exploit the potential speedup that GPUs offer is a non-trivial task. Algorithms must be designed with the architecture benefits and limitations in mind in order to unlock the full performance gains afforded by the use GPU. In this work, we develop fast GPU methods to improve the performance of two important components in computational lung modeling - image registration and particle tracking. We first propose a novel method for multi-level mass-preserving deformable image registration. The strength of this method is that it allows for flexibility of choice for the similarity criteria to be used by the registration method, making possible the implementation of simple and complex similarity measures on the GPU with excellent performance results. The method is tested using three similarity criteria for registering two CT lung datasets - the commonly used sum of squared intensity differences (SSD), the sum of squared tissue value differences (SSTVD), and a symmetric version of SSTVD currently being developed by our research group. The GPU method is validated against a previously validated single-threaded CPU counterpart using six healthy human subjects, and demonstrated strong agreement of results. Separately, three GPU methods were developed for tracking particle trajectories and deposition efficiencies in the human airway tree, including a multiple-GPU method. Though parallelization was straightforward, the complex geometry of the lungs and use of an unstructured mesh provided challenges that were addressed by the GPU methods. The results of the GPU methods were tested for various numbers of particles and compared to a previously validated single-threaded CPU version and demonstrated dramatic speedup over the single-threaded CPU version and 12-threaded CPU versions.

Neurons are polarized cells with dendrites and an axon projecting from their cell body. Due to this polarized structure a major challenge for neurons is the transport of material to and from the cell body. The transport that occurs between the cell body and axons is called Axonal transport. Axonal transport has three major components: molecular motors which act as vehicles, microtubules which serve as tracks on which these motors move and microtubule associated proteins which regulate the transport of material. Axonal transport maintains the integrity of a neuron and its dysfunction is linked to neurodegenerative diseases such as, Alzheimer’s disease, Frontotemporal dementia linked to chromosome 17 and Pick’s disease. Therefore, understanding the process of axonal transport is extremely important. Single particle tracking is one method in which axonal transport is studied. This involves fluorescent labelling of molecular motors and microtubule associated proteins and tracking their position in time. Single particle tracking has shown that both, molecular motors and microtubule associated proteins exhibit motion with multiple components. These components are directed, where motion is in one direction, diffusive, where motion is random, and static, where there is no motion. Moreover, molecular motors and microtubule associated proteins also switch between these different components in a single instance of motion. We have developed a MATLAB program, called MixMAs, which specializes in analyzing the data provided by single particle tracking. MixMAs uses a sliding window approach to analyze trajectories of motion. It is capable of distinguishing between different components of motion that are exhibited by molecular motors and microtubule associated proteins. It also identifies transitions that take place between different components of motion. Most importantly, it is not limited by the number of transitions and the number of components present in a single trajectory. The analysis results provided by MixMAs include all the necessary parameters required for a complete characterization of a particle’s motion. These parameters are the number of different transitions that take place between different components of motion, the dwell times of different components of motion, velocity for directed component of motion and diffusion coefficient for diffusive component of motion. We have validated the working of MixMAs by simulating motion of particles which show all three components of motion with all the possible transitions that can take place between them. The simulations are performed for different values of error in localizing the position of a particle. The simulations confirm that MixMAs accurately calculates parameters of motion for a range of localization errors. Finally, we show an application of MixMAs on experimentally obtained single particle data of Kinesin-3 motor.

is a major polysaccharide of the plant cell wall which is known to play a role in many mechanical functionalities, especially when a gel is formed in the presence of calcium. Understanding the gelling abilities of pectin is of great interest to the food industry also, since pectin is a widely used as a gelling agent and thickener. The aim of this study was to apply two complementary microrheological techniques to these systems, multiple particle tracking (MPT) and a light scattering technique called diffusing wave spectroscopy (DWS). While the first one provides fundamental information about the homogeneity of the studied gel, the second gives access to the high frequency behaviour, related to the nature of the basic strands of the network. Firstly, after verifying the validity of the experimental apparati and analysis approaches in a series of careful control experiments on archetypal systems, a regime where pectin gels exhibit the signatures of semi-flexible networks was identified in experiments carried out on gels made of pectin chains pre-engineered by enzymatic deesterification and subsequently assembled with the release of Ca2+. These results were the first showing that polysaccharides networks could be accommodated within the framework of semi-flexible networks, which have become a paradigm for biological gels, such as the well-known F-actin solutions present in the cell cytoskeleton. However, in the plant cell wall, where calcium is already present, the assembly mechanism could be controlled in a different manner, and a more biologically relevant system was studied where the action of the plant enzyme pectinmethylesterase was used to liberate ion-binding groups in the presence of Ca2+. Gels formed according to this alternative methodology were found to behave as punctually cross-linked flexible networks, strikingly different from the first results. This would be explained by the presence of short blocks of charged residues. Finally, experiments on pectins carried out with controlled blocky structures showed that a pectin made of short blocks can exhibit both sorts of network, depending on the polymer and Ca2+ concentrations. This lead naturally to the construction of a state diagram for the regimes of assembly, with proposed control parameters being the polymer concentration and the ratio of the amount of Ca2+ to the quantity of pectic residues which can effectively bind the calcium into cross-links, christened Reff.

The Region of Waterloo relies mainly (75 %) on local groundwater resources for its drinking water supply. The water demand is increasing with the growth of the population and there is a need to enhance the present water supplies. The Regional Municipality of Waterloo (RMOW), which is the governing body in charge of providing the drinking water supply, is conducting an extensive program to protect the groundwater resources of the Waterloo Moraine aquifer. The focus of that work is defining the wellhead protection areas of the existing production wells as well as the investigation of potential further water supply. The main goal of the work presented here is to delineate the capture zones for the major well fields of the Region. To achieve that goal, the flow for the expected pumping conditions is simulated using a fully 3D finite element model (WATFLOW) which has been proven to be highly flexible to represent the natural boundaries and the highly irregular stratigraphy by previous researchers and scholars. The modified version of this model which includes a pseudo-unsaturated module is used for the solution of flow equation. For the delineation of capture zones, a new particle tracking code (WATRAC) as well as two advective-dispersive transport models are used by using a probabilistic approach presented by Neupauer and Wilson [1999]. For the probabilistic approach (Wilson's method), two transport models, a conventional time-marching code (WTC) and a time-continuous code (LTG) are usedand their results are compared. The LTG is computationally more efficient than the WTC, but it gives oscillatory results close to the steady state condition. A combined used of LTG and WTC istherefore recommended to obtain the steady state capture zones. The 0. 25 probability contour agrees very well with the particle tracks, except for somewhat greater transverse spreading due tothe dispersion which is not considered by the particle tracking algorithm. Both methods, backward particle tracking and probabilistic advective-dispersive modelling are clearly more informative and give better insight when considered together than each by itself.

This study was concerned with the most common reverse flow type of cyclones where the flow enters the cyclone through a tangential inlet and leaves via an axial outlet pipe at the top of the cyclone. Numerical computations of two different cyclones were based on the so-called Stairmand cyclone. The difference in geometry between these two cyclones was basically characterized by the geometrical swirl number Sg of 3.5 and 4. Turbulent secondary flows inside a straight square channel have been studied numerically by using Large Eddy Simulation (LES) in order to verify the implementation process. Prandtl’s secondary motion calculated by LES shows satisfying agreement with both, Direct Numerical Simulation (DNS) and experimental results. Numerical calculations were carried out at various axial positions and at the apex cone of a gas cyclone separator. Two different NS-solvers (a commercial one, and a research code), based on a pressure correction algorithm of the SIMPLE method have been applied to predict the flow behavior. The flow was assumed as unsteady, incompressible and isothermal. A k − epsilon turbulence model has been applied first using the commercial code to investigate the gas flow. Due to the nature of cyclone flows, which exhibit highly curved streamlines and anisotropic turbulence, advanced turbulence models such as RSM (Reynolds Stress Model) and LES (Large Eddy Simulation) have been used as well. The RSM simulation was performed using the commercial package CFX4.4, while for the LES calculations the research code MISTRAL/PartFlow-3D code developed in our multiphase research group has been applied utilizing the Smagorinsky model. It was found that the k − epsilon model cannot predict flow phenomena inside the cyclone properly due to the strong curvature of the streamlines. The RSM results are comparable with LES results in the area of the apex cone plane. However, the application of the LES reveals qualitative agreement with the experimental data, but requires higher computer capacity and longer running times than RSM. These calculations of the continuous phase flow were the basis for modeling the behavior of the solid particles in the cyclone separator. Particle trajectories, pressure drop and the cyclone separation efficiency have been studied in some detail. This thesis is organized into five chapters. After an introduction and overview, chapter 2 deals with continuous phase flow turbulence modeling including the governing equations. The emphasis will be based on LES modelling. Furthermore, the disperse phase motion is treated in chapter 3. In chapter 4, the validation process of LES implementation with channel flow is presented. Moreover, prediction profiles of the gas flow are presented and discussed. In addition, disperse phase flow results are presented and discussed such as particle trajectories; pressure drop and cyclone separation efficiency are also discussed. Chapter 5 summarizes and concludes the thesis.

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