Matching Items (96)
Description
A numerical study of wave-induced momentum transport across the tropopause in the presence of a stably stratified thin inversion layer is presented and discussed. This layer consists of a sharp increase in static stability within the tropopause. The wave propagation is modeled by numerically solving the Taylor-Goldstein equation, which governs the dynamics of internal waves in stably stratified shear flows. The waves are forced by a flow over a bell shaped mountain placed at the lower boundary of the domain. A perfectly radiating condition based on the group velocity of mountain waves is imposed at the top to avoid artificial wave reflection. A validation for the numerical method through comparisons with the corresponding analytical solutions will be provided. Then, the method is applied to more realistic profiles of the stability to study the impact of these profiles on wave propagation through the tropopause.
ContributorsCole, Alexandra Shea (Author) / Moustaoui, Mohamed (Thesis director) / Kostelich, Eric (Committee member) / Mahalov, Alex (Committee member) / School of International Letters and Cultures (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
A semi-implicit, fourth-order time-filtered leapfrog numerical scheme is investigated for accuracy and stability, and applied to several test cases, including one-dimensional advection and diffusion, the anelastic equations to simulate the Kelvin-Helmholtz instability, and the global shallow water spectral model to simulate the nonlinear evolution of twin tropical cyclones. The leapfrog scheme leads to computational modes in the solutions to highly nonlinear systems, and time-filters are often used to damp these modes. The proposed filter damps the computational modes without appreciably degrading the physical mode. Its performance in these metrics is superior to the second-order time-filtered leapfrog scheme developed by Robert and Asselin.
ContributorsBurke, Lee Matthew Moore (Author) / Moustaoui, Mohamed (Thesis director) / Kostelich, Eric (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Glioblastoma multiforme (GBM) is a malignant, aggressive and infiltrative cancer of the central nervous system with a median survival of 14.6 months with standard care. Diagnosis of GBM is made using medical imaging such as magnetic resonance imaging (MRI) or computed tomography (CT). Treatment is informed by medical images and includes chemotherapy, radiation therapy, and surgical removal if the tumor is surgically accessible. Treatment seldom results in a significant increase in longevity, partly due to the lack of precise information regarding tumor size and location. This lack of information arises from the physical limitations of MR and CT imaging coupled with the diffusive nature of glioblastoma tumors. GBM tumor cells can migrate far beyond the visible boundaries of the tumor and will result in a recurring tumor if not killed or removed. Since medical images are the only readily available information about the tumor, we aim to improve mathematical models of tumor growth to better estimate the missing information. Particularly, we investigate the effect of random variation in tumor cell behavior (anisotropy) using stochastic parameterizations of an established proliferation-diffusion model of tumor growth. To evaluate the performance of our mathematical model, we use MR images from an animal model consisting of Murine GL261 tumors implanted in immunocompetent mice, which provides consistency in tumor initiation and location, immune response, genetic variation, and treatment. Compared to non-stochastic simulations, stochastic simulations showed improved volume accuracy when proliferation variability was high, but diffusion variability was found to only marginally affect tumor volume estimates. Neither proliferation nor diffusion variability significantly affected the spatial distribution accuracy of the simulations. While certain cases of stochastic parameterizations improved volume accuracy, they failed to significantly improve simulation accuracy overall. Both the non-stochastic and stochastic simulations failed to achieve over 75% spatial distribution accuracy, suggesting that the underlying structure of the model fails to capture one or more biological processes that affect tumor growth. Two biological features that are candidates for further investigation are angiogenesis and anisotropy resulting from differences between white and gray matter. Time-dependent proliferation and diffusion terms could be introduced to model angiogenesis, and diffusion weighed imaging (DTI) could be used to differentiate between white and gray matter, which might allow for improved estimates brain anisotropy.
ContributorsAnderies, Barrett James (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Stepien, Tracy (Committee member) / Harrington Bioengineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
A specific species of the genus Geobacter exhibits useful electrical properties when processing a molecule often found in waste water. A team at ASU including Dr Cèsar Torres and Dr Sudeep Popat used that species to create a special type of solid oxide fuel cell we refer to as a microbial fuel cell. Identification of possible chemical processes and properties of the reactions used by the Geobacter are investigated indirectly by taking measurements using Electrochemical Impedance Spectroscopy of the electrode-electrolyte interface of the microbial fuel cell to obtain the value of the fuel cell's complex impedance at specific frequencies. Investigation of the multiple polarization processes which give rise to measured impedance values is difficult to do directly and so examination of the distribution function of relaxation times (DRT) is considered instead. The DRT is related to the measured complex impedance values using a general, non-physical equivalent circuit model. That model is originally given in terms of a Fredholm integral equation with a non-square integrable kernel which makes the inverse problem of determining the DRT given the impedance measurements an ill-posed problem. The original integral equation is rewritten in terms of new variables into an equation relating the complex impedance to the convolution of a function based upon the original integral kernel and a related but separate distribution function which we call the convolutional distribution function. This new convolutional equation is solved by reducing the convolution to a pointwise product using the Fourier transform and then solving the inverse problem by pointwise division and application of a filter function (equivalent to regularization). The inverse Fourier transform is then taken to get the convolutional distribution function. In the literature the convolutional distribution function is then examined and certain values of a specific, less general equivalent circuit model are calculated from which aspects of the original chemical processes are derived. We attempted to instead directly determine the original DRT from the calculated convolutional distribution function. This method proved to be practically less useful due to certain values determined at the time of experiment which meant the original DRT could only be recovered in a window which would not normally contain the desired information for the original DRT. This limits any attempt to extend the solution for the convolutional distribution function to the original DRT. Further research may determine a method for interpreting the convolutional distribution function without an equivalent circuit model as is done with the regularization method used to solve directly for the original DRT.
ContributorsBaker, Robert Simpson (Author) / Renaut, Rosemary (Thesis director) / Kostelich, Eric (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Chebfun is a collection of algorithms and an open-source software system in object-oriented Matlab that extends familiar powerful methods of numerical computation involving numbers to continuous or piecewise-continuous functions. The success of this strategy is based on the mathematical fact that smooth functions can be represented very efficiently by polynomial interpolation at Chebyshev points or by trigonometric interpolation at equispaced points for periodic functions. More recently, the system has been extended to handle bivariate functions and vector fields. These two new classes of objects are called Chebfun2 and Chebfun2v, respectively. We will show that Chebfun2 and Chebfun2v, and can be used to accurately and efficiently perform various computations on parametric surfaces in two or three dimensions, including path trajectories and mean and Gaussian curvatures. More advanced surface computations such as mean curvature flows are also explored. This is also the first work to use the newly implemented trigonometric representation, namely Trigfun, for computations on surfaces.
ContributorsPage-Bottorff, Courtney Michelle (Author) / Platte, Rodrigo (Thesis director) / Kostelich, Eric (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Coherent vortices are ubiquitous structures in natural flows that affect mixing and transport of substances and momentum/energy. Being able to detect these coherent structures is important for pollutant mitigation, ecological conservation and many other aspects. In recent years, mathematical criteria and algorithms have been developed to extract these coherent structures in turbulent flows. In this study, we will apply these tools to extract important coherent structures and analyze their statistical properties as well as their implications on kinematics and dynamics of the flow. Such information will aide representation of small-scale nonlinear processes that large-scale models of natural processes may not be able to resolve.
ContributorsCass, Brentlee Jerry (Author) / Tang, Wenbo (Thesis director) / Kostelich, Eric (Committee member) / Department of Information Systems (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
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.
ContributorsMancuso, Marina (Author) / Milner, Fabio A (Thesis advisor) / Kuang, Yang (Committee member) / Kostelich, Eric (Committee member) / Eikenberry, Steffen (Committee member) / Manore, Carrie (Committee member) / Arizona State University (Publisher)
Created2023
Description
Over the past 20 years, the fields of synthetic biology and synthetic biosystems engineering have grown into mature disciplines, leading to significant breakthroughs in cancer research, diagnostics, cell-based medicines, biochemical production, etc. Application of mathematical modelling to biological and biochemical systems have not only given great insight into how these systems function, but also have lent enough predictive power to aid in the forward-engineering of synthetic constructs. However, progress has been impeded by several modes of context-dependence unique to biological and biochemical systems that are not seen in traditional engineering disciplines, resulting in the need for lengthy design-build-test cycles before functional prototypes are generated.In this work, two of these universal modes of context dependence – resource competition and growth feedback –their effects on synthetic gene circuits and potential control mechanisms, are studied and characterized. Results demonstrate that a novel competitive control architecture can be utilized to mitigate the effects of winner-take-all resource competition (a form of context dependence where distinct gene modules influence each other by competing over a shared pool of transcriptional/translational resources) in synthetic gene circuits and restore circuits to their intended function. Application of the fluctuation-dissipation theorem and rigorous stochastic simulations demonstrate that realistic resource constraints present in cells at the transcriptional and translational levels influence noise in gene circuits in a nonmonotonic fashion, either increasing or decreasing noise depending on the transcriptional/translational capacity.
Growth feedback on the other hand links circuit function to cellular growth rate via increased protein dilution rate during exponential growth phase. This in turn can result in the collapse of bistable gene circuits as the accelerated dilution rate forces switches in a high stable state to fall to a low stable state. Mathematical modelling and experimental data demonstrate that application of repressive links can insulate sensitive parts of gene circuits against growth-fluctuations and can in turn increase the robustness of multistable circuits in growth contexts.
The results presented in this work aid in the accumulation of understanding of biological and biochemical context dependence, and corresponding control strategies and design principles engineers can utilize to mitigate these effects.
ContributorsStone, Austin (Author) / Tian, Xiao-jun (Thesis advisor) / Wang, Xiao (Committee member) / Smith, Barbara (Committee member) / Kuang, Yang (Committee member) / Cheng, Albert (Committee member) / Arizona State University (Publisher)
Created2023
Description
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.
ContributorsZhang, Fengrui (Author) / Peet, Yulia (Thesis advisor) / Kostelich, Eric (Committee member) / Kim, Jeonglae (Committee member) / Hermann, Marcus (Committee member) / Adrian, Ronald (Committee member) / Arizona State University (Publisher)
Created2022
Description
There is a need in the ecology literature to have a discussion about the fundamental theories from which population dynamics arises. Ad hoc model development is not uncommon in the field often as a result of a need to publish rapidly and frequently. Ecologists and statisticians like Robert J. Steidl and Kenneth P Burnham have called for a more deliberative approach they call "hard thinking". For example, the phenomena of population growth can be captured by almost any sigmoid function. The question of which sigmoid function best explains a data set cannot be answered meaningfully by statistical regression since that can only speak to the validity of the shape. There is a need to revisit enzyme kinetics and ecological stoichiometry to properly justify basal model selection in ecology. This dissertation derives several common population growth models from a generalized equation. The mechanistic validity of these models in different contexts is explored through a kinetic lens. The behavioral kinetic framework is then put to the test by examining a set of biologically plausible growth models against the 1968-1995 elk population count data for northern Yellowstone. Using only this count data, the novel Monod-Holling growth model was able to accurately predict minimum viable population and life expectancy despite both being exogenous to the model and data set. Lastly, the elk/wolf data from Yellowstone was used to compare the validity of the Rosenzweig-MacArthur and Arditi-Ginzburg models. They both were derived from a more general model which included both predator and prey mediated steps. The Arditi-Ginzburg model was able to fit the training data better, but only the Rosenzweig-MacArthur model matched the validation data. Accounting for animal sexual behavior allowed for the creation of the Monod-Holling model which is just as simple as the logistic differential equation but provides greater insights for conservation purposes. Explicitly acknowledging the ethology of wolf predation helps explain the differences in predictive performances by the best fit Rosenzweig-MacArthur and Arditi-Ginzburg models. The behavioral kinetic framework has proven to be a useful tool, and it has the ability to provide even further insights going forward.
ContributorsPringle, Jack Andrew McCracken (Author) / Anderies, John M (Thesis advisor) / Kuang, Yang (Committee member) / Milner, Fabio (Committee member) / Arizona State University (Publisher)
Created2022