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.

The last decade has seen substantial advances in single-molecule tracking methods with nano-metre level precision. A powerful tool in single-molecule tracking is fluorescence imaging. One particular application, total internal reflection microscopy, can capture biological processes at high contrast video rate imaging at the single-particle level. This thesis presents methodologically novel methods in analysing single particle tracking data. Presented here is an application of a Bayesian statistical approach that can discriminate between the different diffusive modes that appear with the presence of membrane architecture. This algorithm is denoted BARD; a Bayesian Analysis to Ranking Diffusion. These algorithms are applied to a total internal fluorescence microscopy based experimental data of a novel membrane probe in Escherichia coli. This probe is a plasmid expressed, non-native membrane integrating trans-membrane helix and thus acts as an ideal protein based probe under no specific native control. Two experiments were performed using a combination of varying helix probe size and growth temperature experiments effectively altering the transition temperature of the membrane. These data are suggestive of a passive partitioning of the helix protein into mobile and immobile domains that emerge from the underlying phase behaviour of the membrane.

The extended Kalman lter (EKF) has a long history in the field of non-linear tracking. More recently, statistically-based estimators have emerged that avoid the need for a deterministic linearisation process. The Unscented Kalman filter (UKF) is one such technique that has been shown to perform favourably for some non-linear systems when compared to an EKF implementation, both in terms of accuracy and robustness. In this Thesis, the UKF is applied to a high energy physics particle tracking problem where currently the EKF is being implemented. The effects of measurement redundancy are investigated to determine improvements in accuracy of particle track reconstruction. The relationship between measurement redundancy and relative observability is also investigated through an experimental and theoretical analysis. Smoothing (backward filtering), in the high energy physics experiments, is implementedusing the Rauch Tung Striebel (RTS) smoother with the EKF , however, in Unscented Kalman filter algorithms, the Jacobian matrices required by the RTS method, are not available. The Unscented Rauch Tung Striebel (URTS) smoother addresses this problem by avoiding the use of Jacobian matrices but is not effi cient for large dimensional systems such as high energy physics experiments. A technique is implemented in the RTS smoother to make it suitable for the UKF. The method is given the name the Jacobian Equivalent Rauch Tung Striebel (JE-RTS) smoother. The implementation of this method is quite straight forward when the UKF is used as an estimator.

A methodology for the thermodynamic-kinetic evaluation of circulating systems as TSA carbon capture processes is developed and used in the assessment of a novel CFB configuration against a benchmark (co-current riser). The novel CFB features a counter-current adsorber, a counter-current regenerator and a riser, the latter element playing a double role of solids conveyer and co-current adsorber. The advantages sought by using a counter-current adsorber are not only the more efficient gas-solid contact mode with respect co-current, but also a low pressure drop derived from operation at lower gas velocities and hydrostatic head partially supported on the contactor internals. Knowledge of the adsorption equilibrium alone is sufficient to realise the much higher sorbent circulation rates required by co-current configurations –compared to counter-current– to meet the stringent carbon capture specifications of 90% recovery and 95% purity. Higher solids circulation rates imply higher energy requirements for regeneration, and therefore research and development of co-current gas-solid contactors cannot be justified in terms of searching for energy-efficient post-combustion carbon capture processes. Parallel experimental investigation in the operation and fluid dynamics of cold model CFB rigs is carried out with the purposes of: 1) providing information that may impact the process performance and can be fed into the mathematical model used in the theoretical assessment for more realistic evaluation, and 2) determine gas and solids residence time distributions (RTDs), which are used for the estimation of axial dispersion and comparison with published results in similar systems. Gas RTD data is generated using a tracer pulse injection-detection technique, whereas RTD for the solid phase is studied using positron emission particle tracking (PEPT). The PEPT technique proved to be adequate for the identification of flow regimes in the novel design of the counter-current adsorber, featuring inclined orifice trays. At low gas velocities the particles flow straight down through the tray holes, whereas at higher velocities the particles flow down in zig-zag, increasing the residence time of the particles and reducing the particle axial dispersion, both beneficial in terms of separation efficiency.

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.