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Description
A general continuum model for simulating the flow of ions in the salt baths that surround and fill excitable neurons is developed and presented. The ion densities and electric potential are computed using the drift-diffusion equations. In addition, a detailed model is given for handling the electrical dynamics on interior

A general continuum model for simulating the flow of ions in the salt baths that surround and fill excitable neurons is developed and presented. The ion densities and electric potential are computed using the drift-diffusion equations. In addition, a detailed model is given for handling the electrical dynamics on interior membrane boundaries, including a model for ion channels in the membranes that facilitate the transfer of ions in and out of cells. The model is applied to the triad synapse found in the outer plexiform layer of the retina in most species. Experimental evidence suggests the existence of a negative feedback pathway between horizontal cells and cone photoreceptors that modulates the flow of calcium ions into the synaptic terminals of cones. However, the underlying mechanism for this feedback is controversial and there are currently three competing hypotheses: the ephaptic hypothesis, the pH hypothesis and the GABA hypothesis. The goal of this work is to test some features of the ephaptic hypothesis using detailed simulations that employ rigorous numerical methods. The model is first applied in a simple rectangular geometry to demonstrate the effects of feedback for different extracellular gap widths. The model is then applied to a more complex and realistic geometry to demonstrate the existence of strictly electrical feedback, as predicted by the ephaptic hypothesis. Lastly, the effects of electrical feedback in regards to the behavior of the bipolar cell membrane potential is explored. Figures for the ion densities and electric potential are presented to verify key features of the model. The computed steady state IV curves for several cases are presented, which can be compared to experimental data. The results provide convincing evidence in favor of the ephaptic hypothesis since the existence of feedback that is strictly electrical in nature is shown, without any dependence on pH effects or chemical transmitters.
ContributorsJones, Jeremiah (Author) / Gardner, Carl (Committee member) / Baer, Steven (Committee member) / Crook, Sharon (Committee member) / Kostelich, Eric (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2013
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Description
The retina is the lining in the back of the eye responsible for vision. When light photons hits the retina, the photoreceptors within the retina respond by sending impulses to the optic nerve, which connects to the brain. If there is injury to the eye or heredity retinal problems, this

The retina is the lining in the back of the eye responsible for vision. When light photons hits the retina, the photoreceptors within the retina respond by sending impulses to the optic nerve, which connects to the brain. If there is injury to the eye or heredity retinal problems, this part can become detached. Detachment leads to loss of nutrients, such as oxygen and glucose, to the cells in the eye and causes cell death. Sometimes the retina is able to be surgically reattached. If the photoreceptor cells have not died and the reattachment is successful, then these cells are able to regenerate their outer segments (OS) which are essential for their functionality and vitality. In this work we will explore how the regrowth of the photoreceptor cells in a healthy eye after retinal detachment can lead to a deeper understanding of how eye cells take up nutrients and regenerate. This work uses a mathematical model for a healthy eye in conjunction with data for photoreceptors' regrowth and decay. The parameters for the healthy eye model are estimated from the data and the ranges of these parameter values are centered +/- 10\% away from these values are used for sensitivity analysis. Using parameter estimation and sensitivity analysis we can better understand how certain processes represented by these parameters change within the model as a result of retinal detachment. Having a deeper understanding for any sort of photoreceptor death and growth can be used by the greater scientific community to help with these currently irreversible conditions that lead to blindness, such as retinal detachment. The analysis in this work shows that maximizing the carrying capacity of the trophic pool and the rate of RDCVF, as well as minimizing nutrient withdrawal of the rods and the cones from the trophic pool results in both the most regrowth and least cell death in retinal detachment.
ContributorsGoldman, Miriam Ayla (Author) / Camacho, Erikia (Thesis director) / Wirkus, Stephen (Committee member) / School of Mathematical and Natural Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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Description
Recent experimental and mathematical work has shown the interdependence of the rod and cone photoreceptors with the retinal pigment epithelium in maintaining sight. Accelerated intake of glucose into the cones via the theoredoxin-like rod-derived cone viability factor (RdCVF) is needed as aerobic glycolysis is the primary source of energy

Recent experimental and mathematical work has shown the interdependence of the rod and cone photoreceptors with the retinal pigment epithelium in maintaining sight. Accelerated intake of glucose into the cones via the theoredoxin-like rod-derived cone viability factor (RdCVF) is needed as aerobic glycolysis is the primary source of energy production. Reactive oxidative species (ROS) result from the rod and cone metabolism and recent experimental work has shown that the long form of RdCVF (RdCVFL) helps mitigate the negative effects of ROS. In this work I investigate the role of RdCVFL in maintaining the health of the photoreceptors. The results of this mathematical model show the necessity of RdCVFL and also demonstrate additional stable modes that are present in this system. The sensitivity analysis shows the importance of glucose uptake, nutrient levels, and ROS mitigation in maintaining rod and cone health in light-damaged mouse models. Together, these suggest areas on which to focus treatment in order to prolong the photoreceptors, especially in situations where ROS is a contributing factor to their death such as retinitis pigmentosa (RP). A potential treatment with RdCVFL and its effects has never been studied in mathematical models. In this work, I examine an optimal control with the treatment of RdCVFL and mathematically illustrate the potential that this treatment might have for treating degenerative retinal diseases such as RP. Further, I examine optimal controls with the treatment of both RdCVF and RdCVFL in order to mathematically understand the potential that a dual treatment might have for treating degenerative retinal diseases such as RP. The RdCVFL control terms are nonlinear for biological accuracy but this results in the standard general theorems for existence of optimal controls failing to apply. I then linearize these models to have proof of existence of an optimal control. Both nonlinear and linearized control results are compared and reveal similarly substantial savings rates for rods and cones.
ContributorsWifvat, Kathryn (Author) / Camacho, Erika (Thesis advisor) / Wirkus, Stephen (Thesis advisor) / Gardner, Carl (Committee member) / Fricks, John (Committee member) / Kawski, Matthias (Committee member) / Arizona State University (Publisher)
Created2022
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Description
\begin{abstract}The human immunodeficiency virus (HIV) pandemic, which causes the syndrome of opportunistic infections that characterize the late stage HIV disease, known as the acquired immunodeficiency syndrome (AIDS), remains a major public health challenge to many parts of the world. This dissertation contributes in providing deeper qualitative insights into the transmission

\begin{abstract}The human immunodeficiency virus (HIV) pandemic, which causes the syndrome of opportunistic infections that characterize the late stage HIV disease, known as the acquired immunodeficiency syndrome (AIDS), remains a major public health challenge to many parts of the world. This dissertation contributes in providing deeper qualitative insights into the transmission dynamics and control of the HIV/AIDS disease in Men who have Sex with Men (MSM) community. A new mathematical model (which is relatively basic), which incorporates some of the pertinent aspects of HIV epidemiology and immunology and fitted using the yearly new case data of the MSM population from the State of Arizona, was designed and used to assess the population-level impact of awareness of HIV infection status and condom-based intervention, on the transmission dynamics and control of HIV/AIDS in an MSM community. Conditions for the existence and asymptotic stability of the various equilibria ofthe model were derived. The numerical simulations showed that the prospects for the effective control and/or elimination of HIV/AIDS in the MSM community in the United States are very promising using a condom-based intervention, provided the condom efficacy is high and the compliance is moderate enough. The model was extended in Chapter 3 to account for the effect of risk-structure, staged-progression property of HIV disease, and the use of pre-exposure prophylaxis (PrEP) on the spread and control of the disease. The model was shown to undergo a PrEP-induced \textit{backward bifurcation} when the associated control reproduction number is less than one. It was shown that when the compliance in PrEP usage is $50%(80%)$ then about $19.1%(34.2%)$ of the yearly new HIV/AIDS cases recorded at the peak will have been prevented, in comparison to the worst-case scenario where PrEP-based intervention is not implemented in the MSM community. It was also shown that the HIV pandemic elimination is possible from the MSM community even for the scenario when the effective contact rate is increased by 5-fold from its baseline value, if low-risk individuals take at least 15 years before they change their risky behavior and transition to the high-risk group (regardless of the value of the transition rate from high-risk to low-risk susceptible population).
ContributorsTollett, Queen Wiggs (Author) / Gumel, Abba (Thesis advisor) / Crook, Sharon (Committee member) / Fricks, John (Committee member) / Gardner, Carl (Committee member) / Nagy, John (Committee member) / Arizona State University (Publisher)
Created2023
Description

This project aims to propose a novel approach for visualizing 4D geometry through the utilization of augmented reality (AR). While previous work has explored virtual reality (VR) as a means to bring 4D objects into a 3D environment, as well as 2D projections to display 4D geometry on screens, this

This project aims to propose a novel approach for visualizing 4D geometry through the utilization of augmented reality (AR). While previous work has explored virtual reality (VR) as a means to bring 4D objects into a 3D environment, as well as 2D projections to display 4D geometry on screens, this project seeks to extend the possibilities by leveraging the immersive nature of AR technology. By overlaying virtual 4D objects onto the real world, users can experience a more tangible representation and gain a deeper understanding of the complex structures present in higher dimensions.

ContributorsHum, Aaron (Author) / Nishimura, Joel (Thesis director) / Wang, Haiyan (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-05
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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)

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
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Description
Earth-system models describe the interacting components of the climate system and

technological systems that affect society, such as communication infrastructures. Data

assimilation addresses the challenge of state specification by incorporating system

observations into the model estimates. In this research, a particular data

assimilation technique called the Local Ensemble Transform Kalman Filter (LETKF) is

applied

Earth-system models describe the interacting components of the climate system and

technological systems that affect society, such as communication infrastructures. Data

assimilation addresses the challenge of state specification by incorporating system

observations into the model estimates. In this research, a particular data

assimilation technique called the Local Ensemble Transform Kalman Filter (LETKF) is

applied to the ionosphere, which is a domain of practical interest due to its effects

on infrastructures that depend on satellite communication and remote sensing. This

dissertation consists of three main studies that propose strategies to improve space-

weather specification during ionospheric extreme events, but are generally applicable

to Earth-system models:

Topic I applies the LETKF to estimate ion density with an idealized model of

the ionosphere, given noisy synthetic observations of varying sparsity. Results show

that the LETKF yields accurate estimates of the ion density field and unobserved

components of neutral winds even when the observation density is spatially sparse

(2% of grid points) and there is large levels (40%) of Gaussian observation noise.

Topic II proposes a targeted observing strategy for data assimilation, which uses

the influence matrix diagnostic to target errors in chosen state variables. This

strategy is applied in observing system experiments, in which synthetic electron density

observations are assimilated with the LETKF into the Thermosphere-Ionosphere-

Electrodynamics Global Circulation Model (TIEGCM) during a geomagnetic storm.

Results show that assimilating targeted electron density observations yields on

average about 60%–80% reduction in electron density error within a 600 km radius of

the observed location, compared to 15% reduction obtained with randomly placed

vertical profiles.

Topic III proposes a methodology to account for systematic model bias arising

ifrom errors in parametrized solar and magnetospheric inputs. This strategy is ap-

plied with the TIEGCM during a geomagnetic storm, and is used to estimate the

spatiotemporal variations of bias in electron density predictions during the

transitionary phases of the geomagnetic storm. Results show that this strategy reduces

error in 1-hour predictions of electron density by about 35% and 30% in polar regions

during the main and relaxation phases of the geomagnetic storm, respectively.
ContributorsDurazo, Juan, Ph.D (Author) / Kostelich, Eric J. (Thesis advisor) / Mahalov, Alex (Thesis advisor) / Tang, Wenbo (Committee member) / Moustaoui, Mohamed (Committee member) / Platte, Rodrigo (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The most advanced social insects, the eusocial insects, form often large societies in which there is reproductive division of labor, queens and workers, have overlapping generations, and cooperative brood care where daughter workers remain in the nest with their queen mother and care for their siblings. The eusocial insects

The most advanced social insects, the eusocial insects, form often large societies in which there is reproductive division of labor, queens and workers, have overlapping generations, and cooperative brood care where daughter workers remain in the nest with their queen mother and care for their siblings. The eusocial insects are composed of representative species of bees and wasps, and all species of ants and termites. Much is known about their organizational structure, but remains to be discovered.

The success of social insects is dependent upon cooperative behavior and adaptive strategies shaped by natural selection that respond to internal or external conditions. The objective of my research was to investigate specific mechanisms that have helped shaped the structure of division of labor observed in social insect colonies, including age polyethism and nutrition, and phenomena known to increase colony survival such as egg cannibalism. I developed various Ordinary Differential Equation (ODE) models in which I applied dynamical, bifurcation, and sensitivity analysis to carefully study and visualize biological outcomes in social organisms to answer questions regarding the conditions under which a colony can survive. First, I investigated how the population and evolutionary dynamics of egg cannibalism and division of labor can promote colony survival. I then introduced a model of social conflict behavior to study the inclusion of different response functions that explore the benefits of cannibalistic behavior and how it contributes to age polyethism, the change in behavior of workers as they age, and its biological relevance. Finally, I introduced a model to investigate the importance of pollen nutritional status in a honeybee colony, how it affects population growth and influences division of labor within the worker caste. My results first reveal that both cannibalism and division of labor are adaptive strategies that increase the size of the worker population, and therefore, the persistence of the colony. I show the importance of food collection, consumption, and processing rates to promote good colony nutrition leading to the coexistence of brood and adult workers. Lastly, I show how taking into account seasonality for pollen collection improves the prediction of long term consequences.
ContributorsRodríguez Messan, Marisabel (Author) / Kang, Yun (Thesis advisor) / Castillo-Chavez, Carlos (Thesis advisor) / Kuang, Yang (Committee member) / Page Jr., Robert E (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2018
Description
A continuously and stably stratified fluid contained in a square cavity subjected to harmonic body forcing is studied numerically by solving the Navier-Stokes equations under the Boussinesq approximation. Complex dynamics are observed near the onset of instability of the basic state, which is a flow configuration that is always an

A continuously and stably stratified fluid contained in a square cavity subjected to harmonic body forcing is studied numerically by solving the Navier-Stokes equations under the Boussinesq approximation. Complex dynamics are observed near the onset of instability of the basic state, which is a flow configuration that is always an exact analytical solution of the governing equations. The instability of the basic state to perturbations is first studied with linear stability analysis (Floquet analysis), revealing a multitude of intersecting synchronous and subharmonic resonance tongues in parameter space. A modal reduction method for determining the locus of basic state instability is also shown, greatly simplifying the computational overhead normally required by a Floquet study. Then, a study of the nonlinear governing equations determines the criticality of the basic state's instability, and ultimately characterizes the dynamics of the lowest order spatial mode by the three discovered codimension-two bifurcation points within the resonance tongue. The rich dynamics include a homoclinic doubling cascade that resembles the logistic map and a multitude of gluing bifurcations.

The numerical techniques and methodologies are first demonstrated on a homogeneous fluid contained within a three-dimensional lid-driven cavity. The edge state technique and linear stability analysis through Arnoldi iteration are used to resolve the complex dynamics of the canonical shear-driven benchmark problem. The techniques here lead to a dynamical description of an instability mechanism, and the work serves as a basis for the remainder of the dissertation.
ContributorsYalim, Jason (Author) / Welfert, Bruno D. (Thesis advisor) / Lopez, Juan M. (Thesis advisor) / Jones, Donald (Committee member) / Tang, Wenbo (Committee member) / Platte, Rodrigo (Committee member) / Arizona State University (Publisher)
Created2019
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Description
The dynamics of a fluid flow inside 2D square and 3D cubic cavities

under various configurations were simulated and analyzed using a

spectral code I developed.

This code was validated against known studies in the 3D lid-driven

cavity. It was then used to explore the various dynamical behaviors

close to the onset

The dynamics of a fluid flow inside 2D square and 3D cubic cavities

under various configurations were simulated and analyzed using a

spectral code I developed.

This code was validated against known studies in the 3D lid-driven

cavity. It was then used to explore the various dynamical behaviors

close to the onset of instability of the steady-state flow, and explain

in the process the mechanism underlying an intermittent bursting

previously observed. A fairly complete bifurcation picture emerged,

using a combination of computational tools such as selective

frequency damping, edge-state tracking and subspace restriction.

The code was then used to investigate the flow in a 2D square cavity

under stable temperature stratification, an idealized version of a lake

with warmer water at the surface compared to the bottom. The governing

equations are the Navier-Stokes equations under the Boussinesq approximation.

Simulations were done over a wide range of parameters of the problem quantifying

the driving velocity at the top (e.g. wind) and the strength of the stratification.

Particular attention was paid to the mechanisms associated with the onset of

instability of the base steady state, and the complex nontrivial dynamics

occurring beyond onset, where the presence of multiple states leads to a

rich spectrum of states, including homoclinic and heteroclinic chaos.

A third configuration investigates the flow dynamics of a fluid in a rapidly

rotating cube subjected to small amplitude modulations. The responses were

quantified by the global helicity and energy measures, and various peak

responses associated to resonances with intrinsic eigenmodes of the cavity

and/or internal retracing beams were clearly identified for the first time.

A novel approach to compute the eigenmodes is also described, making accessible

a whole catalog of these with various properties and dynamics. When the small

amplitude modulation does not align with the rotation axis (precession) we show

that a new set of eigenmodes are primarily excited as the angular velocity

increases, while triadic resonances may occur once the nonlinear regime kicks in.
ContributorsWu, Ke (Author) / Lopez, Juan (Thesis advisor) / Welfert, Bruno (Thesis advisor) / Tang, Wenbo (Committee member) / Platte, Rodrigo (Committee member) / Herrmann, Marcus (Committee member) / Arizona State University (Publisher)
Created2019