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Description
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.
ContributorsHe, Changhan (Author) / Kuang, Yang (Thesis advisor) / Wang, Xiao (Committee member) / Kostelich, Eric (Committee member) / Tian, Xiaojun (Committee member) / Gumel, Abba (Committee member) / Arizona State University (Publisher)
Created2021
Description
Transorbital surgery has gained recent notoriety due to its incorporation into endoscopic skull base surgery. The body of published literature on the field is cadaveric and observation. The pre-clinical studies are focused on the use of the endoscope only. Furthermore the methodology utilised in the published literature is inconsistent and does not embody the optimal principles of scientific experimentation. This body of work evaluates a minimally invasive novel surgical corridor - the transorbital approach - its validity in neurosurgical practice, as well as both qualitatively and quantitatively assessing available technological advances in a robust experimental fashion. While the endoscope is an established means of visualisation used in clinical transorbital surgery, the microscope has never been assessed with respect to the transorbital approach. This question is investigated here and the anatomical and surgical benefits and limitations of microscopic visualisation demonstrated. The comparative studies provide increased knowledge on specifics pertinent to neurosurgeons and other skull base specialists when planning pre-operatively, such as pathology location, involved anatomical structures, instrument maneuvrability and the advantages and disadvantages of the distinct visualisation technologies. This is all with the intention of selecting the most suitable surgical approach and technology, specific to the patient, pathology and anatomy, so as to perform the best surgical procedure. The research findings illustrated in this body of work are diverse, reproducible and applicable. The transorbital surgical corridor has substantive potential for access to the anterior cranial fossa and specific surgical target structures. The neuroquantitative metrics investigated confirm the utility and benefits specific to the respective visualisation technologies i.e. the endoscope and microscope. The most appropriate setting wherein the approach should be used is also discussed. The transorbital corridor has impressive potential, can utilise all available technological advances, promotes multi-disciplinary co-operation and learning amongst clinicians and ultimately, is a means of improving operative patient care.
ContributorsHoulihan, Lena Mary (Author) / Preul, Mark C. (Thesis advisor) / Vernon, Brent (Thesis advisor) / O' Sullivan, Michael G.J. (Committee member) / Lawton, Michael T. (Committee member) / Santarelli, Griffin (Committee member) / Smith, Brian (Committee member) / Arizona State University (Publisher)
Created2021
Description
The fast pace of global urbanization makes cities the hotspots of population density and anthropogenic activities, leading to intensive emissions of heat and carbon dioxide (CO2), a primary greenhouse gas. Urban climate scientists have been actively seeking effective mitigation strategies over the past decades, aiming to improve the environmental quality for urban dwellers. Prior studies have identified the role of urban green spaces in the relief of urban heat stress. Yet little effort was devoted to quantify their contribution to local and regional CO2 budget. In fact, urban biogenic CO2 fluxes from photosynthesis and respiration are influenced by the microclimate in the built environment and are sensitive to anthropogenic disturbance. The high complexity of the urban ecosystem leads to an outstanding challenge for numerical urban models to disentangling and quantifying the interplay between heat and carbon dynamics.This dissertation aims to advance the simulation of thermal and carbon dynamics in urban land surface models, and to investigate the role of urban greening practices and urban system design in mitigating heat and CO2 emissions. The biogenic CO2 exchange in cities is parameterized by incorporating plant physiological functions into an advanced single-layer urban canopy model in the built environment. The simulation result replicates the microclimate and CO2 flux patterns measured from an eddy covariance system over a residential neighborhood in Phoenix, Arizona with satisfactory accuracy. Moreover, the model decomposes the total CO2 flux from observation and identifies the significant CO2 efflux from soil respiration. The model is then applied to quantify the impact of urban greening practices on heat and biogenic CO2 exchange over designed scenarios. The result shows the use of urban greenery is effective in mitigating both urban heat and carbon emissions, providing environmental co-benefit in cities. Furthermore, to seek the optimal urban system design in terms of thermal comfort and CO2 reduction, a multi-objective optimization algorithm is applied to the machine learning surrogates of the physical urban land surface model. There are manifest trade-offs among ameliorating diverse urban environmental indicators despite the co-benefit from urban greening. The findings of this dissertation, along with its implications on urban planning and landscaping management, would promote sustainable urban development strategies for achieving optimal environmental quality for policy makers, urban residents, and practitioners.
ContributorsLi, Peiyuan (Author) / Wang, Zhihua (Thesis advisor) / Vivoni, Enrique (Committee member) / Huang, Huei-Ping (Committee member) / Myint, Soe (Committee member) / Xu, Tianfang (Committee member) / Arizona State University (Publisher)
Created2021
Description
This dissertation describes a series of four studies on cognitive aging, working memory, and cognitive flexibility in dogs (Canis lupus familiaris) and their wild relatives. In Chapters 2 and 3, I designed assessments for age-related cognitive deficits in pet dogs which can be deployed rapidly using inexpensive and accessible materials. These novel tests can be easily implemented by owners, veterinarians, and clinicians and therefore, may improve care for elderly dogs by aiding in the diagnosis of dementia. In addition, these widely deployable tests may facilitate the use of dementia in pet dogs as a naturally occurring model of Alzheimer’s Disease in humans.In Chapters 4 and 5, I modified one of these tests to demonstrate for the first time that coyotes (Canis latrans) and wolves (Canis lupus lupus) develop age-related deficits in cognitive flexibility. This was an important first step towards differentiating between the genetic and environmental components of dementia in dogs and in turn, humans. Unexpectedly, I also detected cognitive deficits in young, adult dogs and wolves but not coyotes. These finding add to a recent shift in understanding cognitive development in dogs which may improve cognitive aging tests as well as training, care, and use of working and pet dogs. These findings also suggest that the ecology of coyotes may select for flexibility earlier in development.
In Chapter 5, I piloted the use of the same cognitive flexibility test for red and gray foxes so that future studies may test for lifespan changes in the cognition of small-bodied captive canids. More broadly, this paradigm may accommodate physical and behavioral differences between diverse pet and captive animals. In Chapters 4 and 5, I examined which ecological traits drive the evolution of behavioral flexibility and in turn, species resilience. I found that wolves displayed less flexibility than dogs and coyotes suggesting that species which do not rely heavily on unstable resources may be ill-equipped to cope with human habitat modification. Ultimately, this comparative work may help conservation practitioners to identify and protect species that cannot cope with rapid and unnatural environmental change.
ContributorsVan Bourg, Joshua (Author) / Wynne, Clive D (Thesis advisor) / Aktipis, C. Athena (Committee member) / Gilby, Ian C (Committee member) / Young, Julie K (Committee member) / Arizona State University (Publisher)
Created2022
Description
Concerns, such as global warming, greenhouse gas emissions, and changes in hydrological regimes, have been raised in response to the global ecosystem changes caused by humans. Understanding the ecosystem functions is crucial for assisting stakeholders in formulating viable plans to address the issues for a healthier planet. However, a systematic evaluation of recent environmental changes and current ecosystem status, focusing on terrestrial ecosystem carbon-water trade-off, in the Lower Mekong Basin (LMB) is lacking. This dissertation involves: (1) examining the long-term spatiotemporal patterns of ecosystem conditions in response to gains and losses of the forest; (2) evaluating the current consumptive water use variation across all biome and land use types with remotely sensed evapotranspiration (ET) products; (3) analyzing the trade-off between terrestrial carbon and water stress condition during the photosynthesis process in response to different climatic/ecosystem conditions, and (4) developing a spatial optimization model to effectively determine possible reforestation/afforestation options considering the balance between water conservation and carbon fluxes. These studies were conducted with many recently developed algorithms and satellite imagery. This dissertation makes significant contributions and expands the knowledge of the variation in water consumption and carbon assimilation within the ecosystem when different conditions are present. In addition, the spatial optimization model was applied to the entire region to formulate possible reforestation plans under different water-carbon tradeoff scenarios for the first time. The findings and results of this research can be used to provide constructive suggestions to policymakers, managers, planners, government officials, and any other stakeholders in LMB to formulate policies and guidelines for the environmentally responsible and sustainable development of LMB.
ContributorsLi, Yubin (Author) / Myint, Soe (Thesis advisor) / Tong, Daoqin (Thesis advisor) / Muenich, Rebecca (Committee member) / Schaffer-Smith, Danica (Committee member) / Arizona State University (Publisher)
Created2023
Description
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.
ContributorsGoodrich, Austin Chase (Author) / Herrmann, Marcus (Thesis advisor) / Dahm, Werner (Committee member) / Kim, Jeonglae (Committee member) / Huang, Huei-Ping (Committee member) / Kostelich, Eric (Committee member) / Arizona State University (Publisher)
Created2023
Description
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.
ContributorsSafdar, Salman (Author) / Gumel, Abba (Thesis advisor) / Kostelich, Eric (Committee member) / Kang, Yun (Committee member) / Fricks, John (Committee member) / Espanol, Malena (Committee member) / Arizona State University (Publisher)
Created2023
Description
A description of numerical and analytical work pertaining to models that describe the growth and progression of glioblastoma multiforme (GBM), an aggressive form of primary brain cancer. Two reaction-diffusion models are used: the Fisher-Kolmogorov-Petrovsky-Piskunov equation and a 2-population model that divides the tumor into actively proliferating and quiescent (or necrotic) cells. The numerical portion of this work (chapter 2) focuses on simulating GBM expansion in patients undergoing treatment for recurrence of tumor following initial surgery. The models are simulated on 3-dimensional brain geometries derived from magnetic resonance imaging (MRI) scans provided by the Barrow Neurological Institute. The study consists of 17 clinical time intervals across 10 patients that have been followed in detail, each of whom shows significant progression of tumor over a period of 1 to 3 months on sequential follow up scans. A Taguchi sampling design is implemented to estimate the variability of the predicted tumors to using 144 different choices of model parameters. In 9 cases, model parameters can be identified such that the simulated tumor contains at least 40 percent of the volume of the observed tumor. In the analytical portion of the paper (chapters 3 and 4), a positively invariant region for our 2-population model is identified. Then, a rigorous derivation of the critical patch size associated with the model is performed. The critical patch (KISS) size is the minimum habitat size needed for a population to survive in a region. Habitats larger than the critical patch size allow a population to persist, while smaller habitats lead to extinction. The critical patch size of the 2-population model is consistent with that of the Fisher-Kolmogorov-Petrovsky-Piskunov equation, one of the first reaction-diffusion models proposed for GBM. The critical patch size may indicate that GBM tumors have a minimum size depending on the location in the brain. A theoretical relationship between the size of a GBM tumor at steady-state and its maximum cell density is also derived, which has potential applications for patient-specific parameter estimation based on magnetic resonance imaging data.
ContributorsHarris, Duane C. (Author) / Kuang, Yang (Thesis advisor) / Kostelich, Eric J. (Thesis advisor) / Preul, Mark C. (Committee member) / Crook, Sharon (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2023
Description
Safe, readily available, and reliable sources of water are an essential component of any municipality’s infrastructure. Phoenix, Arizona, a southwestern city, has among the highest per capita water use in the United States, making it essential to carefully manage its reservoirs. Generally, municipal water bodies are monitored through field sampling. However, this approach is limited spatially and temporally in addition to being costly. In this study, the application of remotely sensed reflectance data from Landsat 7’s Enhanced Thematic Mapper Plus (ETM+) and Landsat 8’s Operational Land Imager (OLI) along with data generated through field-sampling is used to gain a better understanding of the seasonal development of algal communities and levels of suspended particulates in the three main terminal reservoirs supplying water to the Phoenix metro area: Bartlett Lake, Lake Pleasant, and Saguaro Lake. Algal abundances, particularly the abundance of filamentous cyanobacteria, increased with warmer temperatures in all three reservoirs and reached the highest comparative abundance in Bartlett Lake. Prymnesiophytes (the class of algae to which the toxin-producing golden algae belong) tended to peak between June and August, with one notable peak occurring in Saguaro Lake in August 2017 during which time a fish-kill was observed. In the cooler months algal abundance was comparatively lower in all three lakes, with a more even distribution of abundance across algae classes. In-situ data from March 2017 to March 2018 were compared with algal communities sampled approximately ten years ago in each reservoir to understand any possible long-term changes. The findings show that the algal communities in the reservoirs are relatively stable, particularly those of the filamentous cyanobacteria, chlorophytes, and prymnesiophytes with some notable exceptions, such as the abundance of diatoms, which increased in Bartlett Lake and Lake Pleasant. When in-situ data were compared with Landsat-derived reflectance data, two-band combinations were found to be the best-estimators of chlorophyll-a concentration (as a proxy for algal biomass) and total suspended sediment concentration. The ratio of the reflectance value of the red band and the blue band produced reasonable estimates for the in-situ parameters in Bartlett Lake. The ratio of the reflectance value of the green band and the blue band produced reasonable estimates for the in-situ parameters in Saguaro Lake. However, even the best performing two-band algorithm did not produce any significant correlation between reflectance and in-situ data in Lake Pleasant. Overall, remotely-sensed observations can significantly improve our understanding of the water quality as measured by algae abundance and particulate loading in Arizona Reservoirs, especially when applied over long timescales.
ContributorsRussell, Jazmine Barkley (Author) / Neuer, Susanne (Thesis advisor) / Fox, Peter (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2018
Description
This dissertation develops a second order accurate approximation to the magnetic resonance (MR) signal model used in the PARSE (Parameter Assessment by Retrieval from Single Encoding) method to recover information about the reciprocal of the spin-spin relaxation time function (R2*) and frequency offset function (w) in addition to the typical steady-state transverse magnetization (M) from single-shot magnetic resonance imaging (MRI) scans. Sparse regularization on an approximation to the edge map is used to solve the associated inverse problem. Several studies are carried out for both one- and two-dimensional test problems, including comparisons to the first order approximation method, as well as the first order approximation method with joint sparsity across multiple time windows enforced. The second order accurate model provides increased accuracy while reducing the amount of data required to reconstruct an image when compared to piecewise constant in time models. A key component of the proposed technique is the use of fast transforms for the forward evaluation. It is determined that the second order model is capable of providing accurate single-shot MRI reconstructions, but requires an adequate coverage of k-space to do so. Alternative data sampling schemes are investigated in an attempt to improve reconstruction with single-shot data, as current trajectories do not provide ideal k-space coverage for the proposed method.
ContributorsJesse, Aaron Mitchel (Author) / Platte, Rodrigo (Thesis advisor) / Gelb, Anne (Committee member) / Kostelich, Eric (Committee member) / Mittelmann, Hans (Committee member) / Moustaoui, Mohamed (Committee member) / Arizona State University (Publisher)
Created2019