Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / O lanÃamento de efluentes em rios à um grande problema a ser estudado, pois existe a necessidade de que os corpos hÃdricos possuam padrÃes de qualidade correspondentes aos seus respectivos usos. A modelagem da qualidade da Ãgua surge como uma forte ferramenta para auxiliar no gerenciamento dos recursos hÃdricos, pois atravÃs dela à possÃvel determinarmos os inÃmeros parÃmetros de qualidade da Ãgua existentes, sendo de fundamental importÃncia para a concessÃo de outorga e lanÃamento de efluentes nos corpos hÃdricos. Para realizar a modelagem da qualidade da Ãgua em rios, foi desenvolvido um programa computacional baseado na estrutura do software QUAL2E. AlÃm disso, foi realizado um estudo no sentido de analisar o enquadramento dos rios em classes, que visa assegurar Ãs Ãguas qualidade compatÃvel com os usos mais exigentes a que forem destinadas, utilizando-se vÃrios cenÃrios de simulaÃÃes na Bacia do Jaguaribe que à a maior do Estado do CearÃ. TambÃm foi realizada a quantificaÃÃo dos custos de instalaÃÃes das estaÃÃes de tratamento de Ãgua e esgoto, com o objetivo de manter os corpos hÃdricos em padrÃes de qualidade desejados. Esse trabalho visa contribuir no desenvolvimento da modelagem de qualidade da Ãgua em nosso Estado, que ainda se encontra em estÃgio inicial. / The discharge of sewage into rivers is a major problem to be studied, because there is a need for water bodies that have quality standards corresponding to their respective uses. The water quality modeling emerges as a strong tool to help manage water resources, because through it is possible to determine the numerous existing parameters of water quality, being of fundamental importance for the grant award and release of effluents into water bodies. To accomplish the modeling of water quality in rivers, we developed a computer program based on the structure of the software QUAL2E. Furthermore, a study was conducted in order to analyze the framework of the rivers in classes, which aims to ensure water quality compatible with the most demanding uses to which they are intended, using various scenarios of simulations in the Jaguaribe Basin which is the largest in the state of Ceara. It was also performed a quantification of the costs of station facilities for water treatment and sewage, in order to keep the bodies in water quality standards desired. This work aims to contribute to the development of modeling water quality in our state, which is still in its early stages.

A critical step in mounting an immune response is antigen recognition by T cells. This step proceeds by productive interactions between T cell receptors (TCR) on the surface of T cells and foreign antigen, in the form of peptide-major-histocompatibility-complexes (pMHC), on the surface of antigen-presenting-cells (APC). Antigen recognition is exceedingly difficult to understand because the vast majority of pMHC on APCs are derived from self-proteins. Nevertheless, T cells have been shown to be exquisitely sensitive, responding to as few as 10 antigenic pMHC in an ocean of tens of thousands of self pMHC. In addition, T cells are extremely specific and respond only to a small subset of pMHC by virtue of their specific TCR. To explain the sensitivity of T cells to pMHC it has been proposed that a single pMHC may serially bind multiple TCRs. Integrating present knowledge on the spatial-temporal dynamics of TCR/pMHC in the T cell-APC contact interface, we have constructed mathematical models to investigate the degree of TCR serial engagements by pMHC. In addition to reactions within clusters, the models capture the formation and mobility of TCR clusters. We find that a single pMHC serially binds a substantial number of TCRs in a TCR cluster only if the TCR/pMHC bond is stabilized by coreceptors and/or pMHC dimerization. In a separate study we propose that serial engagements can explain T cell specificity. Using Monte Carlo simulations, we show that the stochastic nature of TCR/pMHC interactions means that multiple binding events are needed for accurate detection of foreign pMHC. Critical to our studies are estimates of TCR/pMHC reaction rates and mobilities. In the second half of the thesis, we show that Fluorescence Recovery After Photobleaching (FRAP) experiments can reveal effective diffusion coefficients. We then show, using asymptotic analysis and model fitting, that FRAP experiments can be used to estimate reaction rates between cell surface proteins, like TCR/pMHC. Lastly, we use FRAP experiments to investigate how the actin cytoskeleton modulates TCR mobility and report effective reaction rates between TCR and the cytoskeleton. / Science, Faculty of / Mathematics, Department of / Graduate

Patterns are used as building blocks for design and construction in many fields such as architecture, music, literature, etc. Researchers and practitioners in the information systems area have been exploring patterns and using them in system analysis and design. Patterns found in the analysis stage, when analysts create conceptual models to abstractly represent domain reality, are call business patterns or analysis patterns. Although various business patterns were proposed in previous studies, we found that business semantics were missing in these patterns. These business patterns failed to show functionalities that is essential to patterns in general. Most of these patterns were also not capable of describing business activities, the dynamic aspect of business. This study is conducted to address these issues. In this thesis, we provide a brief literature review on business patterns, and discuss the major problems we found in these studies. Then we introduce our research approach and the major outcomes. We propose a new definition of business patterns with business semantics, which enables us to recover the missing functionality in business patterns. We suggest the key elements to represent business patterns, and propose a two-level template (functional and operational) to describe these elements. Based on theR²M approach, we propose a modeling method with graphical notations to describe the operational level of patterns, where business activities can be modeled. Examples and a case study are provided in this thesis to demonstrate how to use the modeling method and how to use business patterns in practice. / Business, Sauder School of / Management Information Systems, Division of / Graduate

Graduate

Cardiovascular disease is prevalent across the western world and is a major cause of morbidity and mortality, accounting for approximately a third of all fatalities. Investigating the heart by simulating its electrophysiology via the aid of mathematical models has advanced significantly over the past 60 years and is now a well established field. While much of the research focus is placed on the ventricles, the study of the atria is in comparison neglected. Therefore this Thesis is focused on the genesis and maintenance of atrial fibrillation (AF). A series of case studies are performed whereby established biophysically detailed mathematical models are implemented and modified to incorporate electrophysical alterations of atrial cells resulting from a variety of external conditions. The opening section of this Thesis is dedicated to developing a background to the field, including a discussion into the clinical aspect of the diagnosis and management of AF. The suitability of two atrial cell models is discussed and the development of single cell, 1D, 2D, and 3D multi-scale simulation protocols are described in detail. In addition measurements taken to quantify the arrhythmogenic properties of the cells susceptibility to AF are outlined. The second section is focused on the incorporation of conditions thought to enhance atrial tissues ability to initiate and maintain the genesis of AF. Included is a case study into the missence S140G gene mutation, and elevated physiological levels of the hormone Homocystein. The third section investigates the effectiveness of well established and widely used pharmacological treatments such as Beta-Blockers. In addition possible avenues of investigations for the development of atrial specific drugs are explored. These include blocking of the ultra rapid potassium channel and a more novel target for therapy via the targeting of 5HT4 receptors; which is transcribed solely in the atria and alters the electrophysical properties of the L-type Calcium current. The final part of this Thesis is dedicated to the development of a 2D atrial sheet model which includes electrical and spatial heterogeneities via the inclusion of multiple cell types and basic fiber orientation respectively. This allows for an investigation into the role that heterogeneities play in role genesis and maintenance of AF. The main finding of this Thesis is that alterations to the electrophysiology of atrial cells, due to external factors, can be successfully simulated via the implementation of mathematically detailed atrial cell models. It is concluded that simulations of the KENQ1 mutation and elevated levels of Homocystein successfully reproduce conditions which increase the onset of AF. Established treatments such as Beta-Blockers are found to have limited effectiveness. Possible theoretical treatments, such as the blocking of IKur, are found to provide a small amount of therapeutic benefit. In contrast, investigations into the effects of Serotonin were inconclusive. The study into the 2D atria indicated the importance that heterogeneities play in atria. The conclusions show that models provide a powerful tool when investigating how changes to electrophysiology of cells are manifested at a multi-scale level. The models also have their limitations and require further advancement to improve their accuracy.

This study provides a measurable model of the concept of place vulnerability for HIV/AIDS that incorporates both community and structural level effects using data provided at the ZIP code level from the Texas Department of State Health Services. Sociological literature on the effects of place on health has been growing but falls short of providing an operational definition of the effects of place on health. This dissertation looks to the literature in medical/health geography to supplement sociology’s understanding of the effects of place on health, to the end of providing a measurable model. Prior research that has recognized the complexity of the effects of place still have forced data into one scale and emphasized individual-level outcomes. A multilevel model allows for keeping the associated spatial unit data, without aggregating or parsing it out for convenience of model fit. The place vulnerability model proposed examines how exposure, capacity and potentiality variables all influence an area’s HIV/AIDS count. To capture the effects of place vulnerability at multiple levels, this dissertation research uses a multilevel zero-inflated poisson (MLZIP) model to examine how factors measured at the ZIP code and county both affect HIV/AIDS counts per ZIP code as an outcome. Furthermore, empirical Bayes estimates are mapped to display how well the model fits across the state of Texas. Limitations of this research include the need to incorporate time, more specific predictors, and individual level factors. The methodology developed permits a more thorough understanding of place effects on the spatial variation of HIV/AIDS.

The lack of analytical models that can accurately describe large-scale networked systems makes empirical experimentation indispensable for understanding complex behaviors. Research on network testbeds for testing network protocols and distributed services, including physical, emulated, and federated testbeds, has made steady progress. Although the success of these testbeds is undeniable, they fail to provide: 1) scalability, for handling large-scale networks with hundreds or thousands of hosts and routers organized in different scenarios, 2) flexibility, for testing new protocols or applications in diverse settings, and 3) inter-operability, for combining simulated and real network entities in experiments. This dissertation tackles these issues in three different dimensions. First, we present SVEET, a system that enables inter-operability between real and simulated hosts. In order to increase the scalability of networks under study, SVEET enables time-dilated synchronization between real hosts and the discrete-event simulator. Realistic TCP congestion control algorithms are implemented in the simulator to allow seamless interactions between real and simulated hosts. SVEET is validated via extensive experiments and its capabilities are assessed through case studies involving real applications. Second, we present PrimoGENI, a system that allows a distributed discrete-event simulator, running in real-time, to interact with real network entities in a federated environment. PrimoGENI greatly enhances the flexibility of network experiments, through which a great variety of network conditions can be reproduced to examine what-if questions. Furthermore, PrimoGENI performs resource management functions, on behalf of the user, for instantiating network experiments on shared infrastructures. Finally, to further increase the scalability of network testbeds to handle large-scale high-capacity networks, we present a novel symbiotic simulation approach. We present SymbioSim, a testbed for large-scale network experimentation where a high-performance simulation system closely cooperates with an emulation system in a mutually beneficial way. On the one hand, the simulation system benefits from incorporating the traffic metadata from real applications in the emulation system to reproduce the realistic traffic conditions. On the other hand, the emulation system benefits from receiving the continuous updates from the simulation system to calibrate the traffic between real applications. Specific techniques that support the symbiotic approach include: 1) a model downscaling scheme that can significantly reduce the complexity of the large-scale simulation model, resulting in an efficient emulation system for modulating the high-capacity network traffic between real applications; 2) a queuing network model for the downscaled emulation system to accurately represent the network effects of the simulated traffic; and 3) techniques for reducing the synchronization overhead between the simulation and emulation systems.

The similarity between objects is judged in a wide variety of contexts from visual search to categorization to face recognition. There is a correspondingly rich history of similarity research, including empirical work and theoretical models. However, the field lacks an account of the real time neural processing dynamics of different similarity judgment behaviors. Some accounts focus on the lower-level processes that support similarity judgments, but they do not capture a wide range of canonical behaviors, and they do not account for the moment-to-moment stability and interaction of realistic neural object representations. The goal of this dissertation is to address this need and present a broadly applicable and neurally implemented model of object similarity judgments. I accomplished this by adapting and expanding an existing neural process model of change detection to capture a set of canonical, task-general similarity judgment behaviors. Target behaviors to model were chosen by reviewing the similarity judgment literature and identifying prominent and consistent behavioral effects. I tested each behavior for task-generality across three experiments using three diverse similarity judgment tasks. The following behaviors observed across all three tasks served as modeling targets: the effect of feature value comparisons, attentional modulation of feature dimensions, sensitivity to patterns of objects encountered over time, violations of minimality and triangle equality, and a sensitivity to circular feature dimensions like color hue. The model captured each effect. The neural processes implied by capturing these behaviors are discussed, along with the broader theoretical implications of the model and possibilities for its future expansion.

In the present study, methodological approaches to assess the impact of climate change on the thermal and thermo-hydro-mechanical (THM) regimes of the ground in some selected Canadian no-permafrost areas (Ottawa, Sudbury, Toronto) is proposed. A modeling study to evaluate ground temperature variations due to global warming is conducted using TEMP/W software from Geoslope ltd. The effect of future climate change projections, up to 2100, on the ground freeze-thaw cycle frequencies, frost penetration depth, and frost duration is assessed in some selected sites located in the Canadian no-permafrost region. Moreover, three softwares (TEMP/W, SEEP/W and SIGMA/W from Geoslope Ltd) have been used to establish a numerical tool that enable to assess the effect of global warming on THM response of the grounds in the selected Canadian no-permafrost areas. TEMP/W and SEEP/W were coupled in a thermo-hydraulic analysis to assess the impact of global warming on the hydraulic regime of the ground. Afterwards, SEEP/W and SIGMA/W were coupled in a hydraulic-mechanical analysis to study the impact of climate change induced porewater pressures change on the mechanical regime of the ground in some no-permafrost regions. Simulation study to assess the effect ground temperature changes on key geotechnical properties of the soils in the selected sites is conducted by using the aforementioned numerical tool. The change of the porewater pressure changes and distributions in the soil induced by global warming is studied. The effect of climate change on the ground consolidation or settlement in the selected no-permafrost sites is also investigated. Finally, this study provides a simulation of a bridge pile foundation ground to detect the THM changes around the pile structure due to climate warming. The results indicate that climate change will affect the thermal regime of the ground in the selected Canadian no permafrost areas. Ground temperature in the studied no-permafrost regions will likely increase by 2 to 4 C by 2100 due to global warming. Furthermore, the frost penetration depth will be significantly reduced in all study areas. It is also found that the frost duration will experience a gradual reduction with time up to 2100. In addition, the simulation results showed minimal influence of global warming on the porewater pressure distribution and magnitude in the studied grounds. Aligned to this, climate change did not seem to have a significant effect on the consolidation behavior or settlement of the ground in the studied no-permafrost areas. The simulation of the foundation ground confirms the results mentioned above, as temperature changes around the pile structure falls within the same range found in the thermal analysis. Porewater pressure distributions and ground settlement are not significantly affected along the pile perimeter. Overall, the design of pile foundation in the Canadian no-permafrost region will not be significantly affected by climate change up 2100. The tools developed and results obtained will be useful for the geotechnical design of climate-adaptive civil engineering or transportation structures in Canadian no permafrost areas.

Releases of nonaqueous phase liquids (NAPLs) to groundwater systems are a serious and widespread problem throughout the United States. Research was conducted to determine if numerical groundwater flow and transport models could evaluate the effectiveness of alternative remedial strategies to reduce dissolved hydrocarbon contamination in aquifers, and therefore serve as tools to aid environmental managers in the remedial decision making process. A fuel distribution terminal in the Eastern United States was selected as the test site. A release of diesel and jet fuels from the terminal loading rack area contaminated the unconfined aquifer beneath the terminal and migrated off-site, impacting commercial and residential areas. In the analyses, groundwater flow and transport models were calibrated to site data. The calibrated models were applied to simulate four remedial options: (1) natural attenuation, (2) groundwater extraction, (3) groundwater flushing, and (4) microbial fences. Results of the predictive simulations indicated that the groundwater flushing remedial option provided the greatest reduction of benzene and TEX mass from the NAPL source as well as the lowest concentrations of benzene and TEX in the aquifer. The calibrated numerical models were able to predict the effectiveness of various remedial options and provide a basis for comparison. The modeling in conjunction with other factors, such as cost, were utilized to facilitate the decision making process. / Master of Science