Glioblastoma Multiforme is a prevalent and aggressive brain tumor. It has an average 5-year survival rate of 6% and average survival time of 14 months. Using patient-specific MRI data from the Barrow Neurological Institute, this thesis investigates the impact of…
Glioblastoma Multiforme is a prevalent and aggressive brain tumor. It has an average 5-year survival rate of 6% and average survival time of 14 months. Using patient-specific MRI data from the Barrow Neurological Institute, this thesis investigates the impact of parameter manipulation on reaction-diffusion models for predicting and simulating glioblastoma growth. The study aims to explore key factors influencing tumor morphology and to contribute to enhancing prediction techniques for treatment.
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Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector…
Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector and host demography as well as MBD transmission. This dissertation addresses the questions of how vector and host demography impact WNV dynamics, and how expected and likely climate change scenarios will affect demographic and epidemiological processes of WNV transmission. First, a data fusion method is developed that connects non-autonomous logistic model parameters to mosquito time series data. This method captures the inter-annual and intra-seasonal variation of mosquito populations within a geographical location. Next, a three-population WNV model between mosquito vectors, bird hosts, and human hosts with infection-age structure for the vector and bird host populations is introduced. A sensitivity analysis uncovers which parameters have the most influence on WNV outbreaks. Finally, the WNV model is extended to include the non-autonomous population model and temperature-dependent processes. Model parameterization using historical temperature and human WNV case data from the Greater Toronto Area (GTA) is conducted. Parameter fitting results are then used to analyze possible future WNV dynamics under two climate change scenarios. These results suggest that WNV risk for the GTA will substantially increase as temperature increases from climate change, even under the most conservative assumptions. This demonstrates the importance of ensuring that the warming of the planet is limited as much as possible.
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Advancements to a dual scale Large Eddy Simulation (LES) modeling approach for immiscible turbulent phase interfaces are presented. In the dual scale LES approach, a high resolution auxiliary grid, used to capture a fully resolved interface geometry realization, is linked…
Advancements to a dual scale Large Eddy Simulation (LES) modeling approach for immiscible turbulent phase interfaces are presented. In the dual scale LES approach, a high resolution auxiliary grid, used to capture a fully resolved interface geometry realization, is linked to an LES grid that solves the filtered Navier-Stokes equations. Exact closure of the sub-filter interface terms is provided by explicitly filtering the fully resolved quantities from the auxiliary grid. Reconstructing a fully resolved velocity field to advance the phase interface requires modeling several sub-filter effects, including shear and accelerational instabilities and phase change. Two sub-filter models were developed to generate these sub-filter hydrodynamic instabilities: an Orr-Sommerfeld model and a Volume-of-Fluid (VoF) vortex sheet method. The Orr-Sommerfeld sub-filter model was found to be incompatible with the dual scale approach, since it is unable to generate interface rollup and a process to separate filtered and sub-filter scales could not be established. A novel VoF vortex sheet method was therefore proposed, since prior vortex methods have demonstrated interface rollup and following the LES methodology, the vortex sheet strength could be decomposed into its filtered and sub-filter components. In the development of the VoF vortex sheet method, it was tested with a variety of classical hydrodynamic instability problems, compared against prior work and linear theory, and verified using Direct Numerical Simulations (DNS). An LES consistent approach to coupling the VoF vortex sheet with the LES filtered equations is presented and compared against DNS. Finally, a sub-filter phase change model is proposed and assessed in the dual scale LES framework with an evaporating interface subjected to decaying homogeneous isotropic turbulence. Results are compared against DNS and the interplay between surface tension forces and evaporation are discussed.
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A pneumonia-like illness emerged late in 2019 (coined COVID-19), caused by SARSCoV-2, causing a devastating global pandemic on a scale never before seen sincethe 1918/1919 influenza pandemic. This dissertation contributes in providing deeper
qualitative insights into the transmission dynamics and control…
A pneumonia-like illness emerged late in 2019 (coined COVID-19), caused by SARSCoV-2, causing a devastating global pandemic on a scale never before seen sincethe 1918/1919 influenza pandemic. This dissertation contributes in providing deeper
qualitative insights into the transmission dynamics and control of the disease in the
United States. A basic mathematical model, which incorporates the key pertinent
epidemiological features of SARS-CoV-2 and fitted using observed COVID-19 data,
was designed and used to assess the population-level impacts of vaccination and face
mask usage in mitigating the burden of the pandemic in the United States. Conditions
for the existence and asymptotic stability of the various equilibria of the model were
derived. The model was shown to undergo a vaccine-induced backward bifurcation
when the associated reproduction number is less than one. Conditions for achieving
vaccine-derived herd immunity were derived for three of the four FDA-approved vaccines (namely Pfizer, Moderna and Johnson & Johnson vaccine), and the vaccination
coverage level needed to achieve it decreases with increasing coverage of moderately and highly-effective face masks. It was also shown that using face masks as a singular
intervention strategy could lead to the elimination of the pandemic if moderate or
highly-effective masks are prioritized and pandemic elimination prospects are greatly
enhanced if the vaccination program is combined with a face mask use strategy that
emphasizes the use of moderate to highly-effective masks with at least moderate coverage. The model was extended in Chapter 3 to allow for the assessment of the
impacts of waning and boosting of vaccine-derived and natural immunity against
the BA.1 Omicron variant of SARS-CoV-2. It was shown that vaccine-derived herd
immunity can be achieved in the United States via a vaccination-boosting strategy
which entails fully vaccinating at least 72% of the susceptible populace. Boosting
of vaccine-derived immunity was shown to be more beneficial than boosting of natural immunity. Overall, this study showed that the prospects of the elimination of
the pandemic in the United States were highly promising using the two intervention
measures.
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The main purpose of this project is to create a method for determining the absolute position of an accelerometer. Acceleration and angular speed were obtained from an accelerometer attached to a vehicle as it moves around. As the vehicle moves…
The main purpose of this project is to create a method for determining the absolute position of an accelerometer. Acceleration and angular speed were obtained from an accelerometer attached to a vehicle as it moves around. As the vehicle moves to collect information the orientation of the accelerometer changes, so a rotation matrix is applied to the data based on the angular change at each time. The angular change and distance are obtained by using the trapezoidal approximation of the integrals. This method was first validated by using simple sets of "true" data which are explicitly known sets of data to compare the results to. Then, an analysis of how different time steps and levels of noise affect the error of the results was performed to determine the optimal time step of 0.1 sec that was then used for the actual tests. The tests that were performed were: a stationary test for uses of calibration, a straight line test to verify a simple test, and a closed loop test to test the accuracy. The graphs for these tests give no indication of the actual paths, so the final results can only show that the data from the accelerometer is too noisy and inaccurate for this method to be used by this sensor. The future work would be to test different ways to get more accurate data and then use it to verify this methods. These ways could include using more sensors to interpolate the data, reducing noise by using a different sensor, or adding a filter. Then, if this method is considered accurate enough, it could be implemented into control systems.
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In the last two decades, fantasy sports have grown massively in popularity. Fantasy football in particular is the most popular fantasy sport in the United States. People spend hours upon hours every year building, researching, and perfecting their teams to…
In the last two decades, fantasy sports have grown massively in popularity. Fantasy football in particular is the most popular fantasy sport in the United States. People spend hours upon hours every year building, researching, and perfecting their teams to compete with others for money or bragging rights. One problem, however, is that National Football League (NFL) players are human and will not perform the same as they did last week or last season. Because of this, there is a need to create a machine learning model to help predict when players will have a tough game or when they can perform above average. This report discusses the history and science of fantasy football, gathering large amounts of player data, manipulating the information to create more insightful data points, creating a machine learning model, and how to use this tool in a real-world situation. The initial model created significantly accurate predictions for quarterbacks and running backs but not receivers and tight ends. Improvements significantly increased the accuracy by reducing the mean average error to below one for all positions, resulting in a successful model for all four positions.
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This thesis focuses on the turbulent bluff body wakes in incompressible and compressible flows. An incompressible wake flow past an axisymmetric body of revolution at a diameter-based Reynolds number Re=5000 is investigated via a direct numerical simulation. It is followed…
This thesis focuses on the turbulent bluff body wakes in incompressible and compressible flows. An incompressible wake flow past an axisymmetric body of revolution at a diameter-based Reynolds number Re=5000 is investigated via a direct numerical simulation. It is followed by the development of a compressible solver using a split-form discontinuous Galerkin spectral element method framework with shock capturing. In the study on incompressible wake flows, three dominant coherent vortical motions are identified in the wake: the vortex shedding motion with the frequency of St=0.27, the bubble pumping motion with St=0.02, and the very-low-frequency (VLF) motion originated in the very near wake of the body with the frequencies St=0.002 and 0.005. The very-low-frequency motion is associated with a slow precession of the wake barycenter. The vortex shedding pattern is demonstrated to follow a reflectional symmetry breaking mode, with the detachment location rotating continuously and making a full circle over one vortex shedding period. The VLF radial motion with St=0.005 originates as m = 1 mode, but later transitions into m = 2 mode in the intermediate wake. Proper orthogonaldecomposition (POD) and dynamic mode decomposition (DMD) are further performed to analyze the spatial structure associated with the dominant coherent motions. Results of the POD and DMD analysis are consistent with the results of the azimuthal Fourier analysis. To extend the current incompressible code to be able to solve compressible flows, a computational methodology is developed using a high-order approximation for the compressible Navier-Stokes equations with discontinuities. The methodology is based on a split discretization framework with a summation-by-part operator. An entropy viscosity method and a subcell finite volume method are implemented to capture discontinuities. The developed high-order split-form with shock-capturing methodology is subject to a series of evaluation on cases from subsonic to hypersonic, from one-dimensional to three dimensional. The Taylor-Green vortex case and the supersonic sphere wake case show the capability to handle three-dimensional turbulent flows without and with the presence of shocks. It is also shown that higher-order approximations yield smaller errors than lower-order approximations, for the same number of total degrees of freedom.
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High-dimensional systems are difficult to model and predict. The underlying mechanisms of such systems are too complex to be fully understood with limited theoretical knowledge and/or physical measurements. Nevertheless, redcued-order models have been widely used to study high-dimensional systems, because…
High-dimensional systems are difficult to model and predict. The underlying mechanisms of such systems are too complex to be fully understood with limited theoretical knowledge and/or physical measurements. Nevertheless, redcued-order models have been widely used to study high-dimensional systems, because they are practical and efficient to develop and implement. Although model errors (biases) are inevitable for reduced-order models, these models can still be proven useful to develop real-world applications. Evaluation and validation for idealized models are indispensable to serve the mission of developing useful applications. Data assimilation and uncertainty quantification can provide a way to assess the performance of a reduced-order model. Real data and a dynamical model are combined together in a data assimilation framework to generate corrected model forecasts of a system. Uncertainties in model forecasts and observations are also quantified in a data assimilation cycle to provide optimal updates that are representative of the real dynamics. In this research, data assimilation is applied to assess the performance of two reduced-order models. The first model is developed for predicting prostate cancer treatment response under intermittent androgen suppression therapy. A sequential data assimilation scheme, the ensemble Kalman filter (EnKF), is used to quantify uncertainties in model predictions using clinical data of individual patients provided by Vancouver Prostate Center. The second model is developed to study what causes the changes of the state of stratospheric polar vortex. Two data assimilation schemes: EnKF and ES-MDA (ensemble smoother with multiple data assimilation), are used to validate the qualitative properties of the model using ECMWF (European Center for Medium-Range Weather Forecasts) reanalysis data. In both studies, the reduced-order model is able to reproduce the data patterns and provide insights to understand the underlying mechanism. However, significant model errors are also diagnosed for both models from the results of data assimilation schemes, which suggests specific improvements of the reduced-order models.
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Synthetic biology (SB) has become an important field of science focusing on designing and engineering new biological parts and systems, or re-designing existing biological systems for useful purposes. The dramatic growth of SB throughout the past two decades has not…
Synthetic biology (SB) has become an important field of science focusing on designing and engineering new biological parts and systems, or re-designing existing biological systems for useful purposes. The dramatic growth of SB throughout the past two decades has not only provided us numerous achievements, but also brought us more timely and underexplored problems. In SB's entire history, mathematical modeling has always been an indispensable approach to predict the experimental outcomes, improve experimental design and obtain mechanism-understanding of the biological systems. \textit{Escherichia coli} (\textit{E. coli}) is one of the most important experimental platforms, its growth dynamics is the major research objective in this dissertation. Chapter 2 employs a reaction-diffusion model to predict the \textit{E. coli} colony growth on a semi-solid agar plate under multiple controls. In that chapter, a density-dependent diffusion model with non-monotonic growth to capture the colony's non-linear growth profile is introduced. Findings of the new model to experimental data are compared and contrasted with those from other proposed models. In addition, the cross-sectional profile of the colony are computed and compared with experimental data. \textit{E. coli} colony is also used to perform spatial patterns driven by designed gene circuits. In Chapter 3, a gene circuit (MINPAC) and its corresponding pattern formation results are presented. Specifically, a series of partial differential equation (PDE) models are developed to describe the pattern formation driven by the MINPAC circuit. Model simulations of the patterns based on different experimental conditions and numerical analysis of the models to obtain a deeper understanding of the mechanisms are performed and discussed. Mathematical analysis of the simplified models, including traveling wave analysis and local stability analysis, is also presented and used to explore the control strategies of the pattern formation. The interaction between the gene circuit and the host \textit{E. coli} may be crucial and even greatly affect the experimental outcomes. Chapter 4 focuses on the growth feedback between the circuit and the host cell under different nutrient conditions. Two ordinary differential equation (ODE) models are developed to describe such feedback with nutrient variation. Preliminary results on data fitting using both two models and the model dynamical analysis are included.
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Large amplitude westward propagating long waves in midlatitudes of Northern Hemisphere occasionally sustain coherent phase propagation over multiple weeks. Owing to the large amplitude and the life cycle of these waves previous studies have speculated their influence on extended-range weather…
Large amplitude westward propagating long waves in midlatitudes of Northern Hemisphere occasionally sustain coherent phase propagation over multiple weeks. Owing to the large amplitude and the life cycle of these waves previous studies have speculated their influence on extended-range weather forecasts but have not quantified them. The primary aim of this study is to establish an updated long-term catalog of Retrograde events which can then be used to investigate the statistics and structure of these waves. Guided by the newly created catalog the dynamics of these waves are further explored. A preliminary look into the dynamics of these waves reveal a sequence of poleward extrusion, westward migration and vortex shedding occurring frequently during certain strong Retrograde wave events. A strong connection between the westward moving low PV structures and the East Asian cold air outbreak is uncovered. Also, the initiation of the sequence of low PV extrusion and vortex shedding is found to be linked with the phase of propagating Wave-1 zonal component. Enhanced predictability of global midlatitude Geopotential Height at 500mb is noted during active period of strong Retrograde wave activity in comparison to inactive period. Skilled forecasts were produced almost (on an average) 12 days in advance during the active period of one of the winters (1995/96) as compared to 9 days during the inactive period of the season.
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