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Diseases have been part of human life for generations and evolve within the population, sometimes dying out while other times becoming endemic or the cause of recurrent outbreaks. The long term influence of a disease stems from different dynamics within or between pathogen-host, that have been analyzed and studied by many researchers using mathematical models. Co-infection with different pathogens is common, yet little is known about how infection with one pathogen affects the host's immunological response to another. Moreover, no work has been found in the literature that considers the variability of the host immune health or that examines a disease at the population level and its corresponding interconnectedness with the host immune system. Knowing that the spread of the disease in the population starts at the individual level, this thesis explores how variability in immune system response within an endemic environment affects an individual's vulnerability, and how prone it is to co-infections. Immunology-based models of Malaria and Tuberculosis (TB) are constructed by extending and modifying existing mathematical models in the literature. The two are then combined to give a single nine-variable model of co-infection with Malaria and TB. Because these models are difficult to gain any insight analytically due to the large number of parameters, a phenomenological model of co-infection is proposed with subsystems corresponding to the individual immunology-based model of a single infection. Within this phenomenological model, the variability of the host immune health is also incorporated through three different pathogen response curves using nonlinear bounded Michaelis-Menten functions that describe the level or state of immune system (healthy, moderate and severely compromised). The immunology-based models of Malaria and TB give numerical results that agree with the biological observations. The Malaria--TB co-infection model gives reasonable results and these suggest that the order in which the two diseases are introduced have an impact on the behavior of both. The subsystems of the phenomenological models that correspond to a single infection (either of Malaria or TB) mimic much of the observed behavior of the immunology-based counterpart and can demonstrate different behavior depending on the chosen pathogen response curve. In addition, varying some of the parameters and initial conditions in the phenomenological model yields a range of topologically different mathematical behaviors, which suggests that this behavior may be able to be observed in the immunology-based models as well. The phenomenological models clearly replicate the qualitative behavior of primary and secondary infection as well as co-infection. The mathematical solutions of the models correspond to the fundamental states described by immunologists: virgin state, immune state and tolerance state. The phenomenological model of co-infection also demonstrates a range of parameter values and initial conditions in which the introduction of a second disease causes both diseases to grow without bound even though those same parameters and initial conditions did not yield unbounded growth in the corresponding subsystems. This results applies to all three states of the host immune system. In terms of the immunology-based system, this would suggest the following: there may be parameter values and initial conditions in which a person can clear Malaria or TB (separately) from their system but in which the presence of both can result in the person dying of one of the diseases. Finally, this thesis studies links between epidemiology (population level) and immunology in an effort to assess the impact of pathogen's spread within the population on the immune response of individuals. Models of Malaria and TB are proposed that incorporate the immune system of the host into a mathematical model of an epidemic at the population level.
ContributorsSoho, Edmé L (Author) / Wirkus, Stephen (Thesis advisor) / Castillo-Chavez, Carlos (Thesis advisor) / Chowell-Puente, Gerardo (Committee member) / Arizona State University (Publisher)
Created2011
Description
In an effort to address the lack of literature in on-campus active travel, this study aims to investigate the following primary questions:<br/>• What are the modes that students use to travel on campus?<br/>• What are the motivations that underlie the mode choice of students on campus?<br/>My first stage of research involved a series of qualitative investigations. I held one-on-one virtual interviews with students in which I asked them questions about the mode they use and why they feel that their chosen mode works best for them. These interviews served two functions. First, they provided me with insight into the various motivations underlying student mode choice. Second, they provided me with an indication of what explanatory variables should be included in a model of mode choice on campus.<br/>The first half of the research project informed a quantitative survey that was released via the Honors Digest to attract student respondents. Data was gathered on travel behavior as well as relevant explanatory variables.<br/>My analysis involved developing a logit model to predict student mode choice on campus and presenting the model estimation in conjunction with a discussion of student travel motivations based on the qualitative interviews. I use this information to make a recommendation on how campus infrastructure could be modified to better support the needs of the student population.
ContributorsMirtich, Laura Christine (Author) / Salon, Deborah (Thesis director) / Fang, Kevin (Committee member) / School of Public Affairs (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
ABSTRACT Group III-nitride semiconductor materials have been commercially used in fabrication of light-emitting diodes (LEDs) and laser diodes (LDs) covering the spectral range from UV to visible and infrared, and exhibit unique properties suitable for modern optoelectronic applications. Great advances have recently happened in the research and development in high-power and high-efficiency blue-green-white LEDs, blue LDs and other optoelectronic applications. However, there are still many unsolved challenges with these materials. In this dissertation, several issues concerning structural, electronic and optical properties of III-nitrides have been investigated using a combination of transmission electron microscopy (TEM), electron holography (EH) and cathodoluminescence (CL) techniques. First, a trend of indium chemical inhomogeneity has been found as the indium composition increases for the InGaN epitaxial layers grown by hydride vapor phase epitaxy. Second, different mechanisms contributing to the strain relaxation have been studied for non-polar InGaN epitaxial layers grown on zinc oxide (ZnO) substrate. Third, various structural morphologies of non-polar InGaN epitaxial layers grown on free-standing GaN substrate have been investigated. Fourth, the effect of the growth temperature on the performance of GaN lattice-matched InAlN electron blocking layers has been studied. Finally, the electronic and optical properties of GaN nanowires containing a AlN/GaN superlattice structure have been investigated showing relatively small internal electric field and superlattice- and defect-related emissions along the nanowires.
ContributorsSun, Kewei (Author) / Ponce, Fernando (Thesis advisor) / Smith, David (Committee member) / Treacy, Michael (Committee member) / Drucker, Jeffery (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2011
Description
In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human samples. As this takes place, a serendipitous opportunity has become evident. By the virtue that as one narrows the focus towards "single" protein targets (instead of entire proteomes) using pan-antibody-based enrichment techniques, a discovery science has emerged, so to speak. This is due to the largely unknown context in which "single" proteins exist in blood (i.e. polymorphisms, transcript variants, and posttranslational modifications) and hence, targeted proteomics has applications for established biomarkers. Furthermore, besides protein heterogeneity accounting for interferences with conventional immunometric platforms, it is becoming evident that this formerly hidden dimension of structural information also contains rich-pathobiological information. Consequently, targeted proteomics studies that aim to ascertain a protein's genuine presentation within disease- stratified populations and serve as a stepping-stone within a biomarker translational pipeline are of clinical interest. Roughly 128 million Americans are pre-diabetic, diabetic, and/or have kidney disease and public and private spending for treating these diseases is in the hundreds of billions of dollars. In an effort to create new solutions for the early detection and management of these conditions, described herein is the design, development, and translation of mass spectrometric immunoassays targeted towards diabetes and kidney disease. Population proteomics experiments were performed for the following clinically relevant proteins: insulin, C-peptide, RANTES, and parathyroid hormone. At least thirty-eight protein isoforms were detected. Besides the numerous disease correlations confronted within the disease-stratified cohorts, certain isoforms also appeared to be causally related to the underlying pathophysiology and/or have therapeutic implications. Technical advancements include multiplexed isoform quantification as well a "dual- extraction" methodology for eliminating non-specific proteins while simultaneously validating isoforms. Industrial efforts towards widespread clinical adoption are also described. Consequently, this work lays a foundation for the translation of mass spectrometric immunoassays into the clinical arena and simultaneously presents the most recent advancements concerning the mass spectrometric immunoassay approach.
ContributorsOran, Paul (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Ros, Alexandra (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
Defines the concept of the arcology as conceived by architect Paolo Soleri. Arcology combines "architecture" and "ecology" and explores a visionary notion of a self-contained urban community that has agricultural, commercial, and residential facilities under one roof. Two real-world examples of these projects are explored: Arcosanti, AZ and Masdar City, Abu Dhabi, UAE. Key aspects of the arcology that could be applied to an existing urban fabric are identified, such as urban design fostering social interaction, reduction of automobile dependency, and a development pattern that combats sprawl. Through interviews with local representatives, a holistic approach to applying arcology concepts to the Phoenix Metro Area is devised.
ContributorsSpencer, Sarah Anne (Author) / Manuel-Navarrete, David (Thesis director) / Salon, Deborah (Committee member) / Barrett, The Honors College (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / School of Sustainability (Contributor)
Created2015-05
Description
In this dissertation, remote plasma interactions with the surfaces of low-k interlayer dielectric (ILD), Cu and Cu adhesion layers are investigated. The first part of the study focuses on the simultaneous plasma treatment of ILD and chemical mechanical polishing (CMP) Cu surfaces using N2/H2 plasma processes. H atoms and radicals in the plasma react with the carbon groups leading to carbon removal for the ILD films. Results indicate that an N2 plasma forms an amide-like layer on the surface which apparently leads to reduced carbon abstraction from an H2 plasma process. In addition, FTIR spectra indicate the formation of hydroxyl (Si-OH) groups following the plasma exposure. Increased temperature (380 °C) processing leads to a reduction of the hydroxyl group formation compared to ambient temperature processes, resulting in reduced changes of the dielectric constant. For CMP Cu surfaces, the carbonate contamination was removed by an H2 plasma process at elevated temperature while the C-C and C-H contamination was removed by an N2 plasma process at elevated temperature. The second part of this study examined oxide stability and cleaning of Ru surfaces as well as consequent Cu film thermal stability with the Ru layers. The ~2 monolayer native Ru oxide was reduced after H-plasma processing. The thermal stability or islanding of the Cu film on the Ru substrate was characterized by in-situ XPS. After plasma cleaning of the Ru adhesion layer, the deposited Cu exhibited full coverage. In contrast, for Cu deposition on the Ru native oxide substrate, Cu islanding was detected and was described in terms of grain boundary grooving and surface and interface energies. The thermal stability of 7 nm Ti, Pt and Ru ii interfacial adhesion layers between a Cu film (10 nm) and a Ta barrier layer (4 nm) have been investigated in the third part. The barrier properties and interfacial stability have been evaluated by Rutherford backscattering spectrometry (RBS). Atomic force microscopy (AFM) was used to measure the surfaces before and after annealing, and all the surfaces are relatively smooth excluding islanding or de-wetting phenomena as a cause of the instability. The RBS showed no discernible diffusion across the adhesion layer/Ta and Ta/Si interfaces which provides a stable underlying layer. For a Ti interfacial layer RBS indicates that during 400 °C annealing Ti interdiffuses through the Cu film and accumulates at the surface. For the Pt/Cu system Pt interdiffuion is detected which is less evident than Ti. Among the three adhesion layer candidates, Ru shows negligible diffusion into the Cu film indicating thermal stability at 400 °C.
ContributorsLiu, Xin (Author) / Nemanich, Robert (Thesis advisor) / Chamberlin, Ralph (Committee member) / Chen, Tingyong (Committee member) / Smith, David (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2012
Description
The energy band gap of a semiconductor material critically influences the operating wavelength of an optoelectronic device. Realization of any desired band gap, or even spatially graded band gaps, is important for applications such as lasers, light-emitting diodes (LEDs), solar cells, and detectors. Compared to thin films, nanowires offer greater flexibility for achieving a variety of alloy compositions. Furthermore, the nanowire geometry permits simultaneous incorporation of a wide range of compositions on a single substrate. Such controllable alloy composition variation can be realized either within an individual nanowire or between distinct nanowires across a substrate. This dissertation explores the control of spatial composition variation in ternary alloy nanowires. Nanowires were grown by the vapor-liquid-solid (VLS) mechanism using chemical vapor deposition (CVD). The gas-phase supersaturation was considered in order to optimize the deposition morphology. Composition and structure were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive x-ray spectroscopy (EDS), and x-ray diffraction (XRD). Optical properties were investigated through photoluminescence (PL) measurements. The chalcogenides selected as alloy endpoints were lead sulfide (PbS), cadmium sulfide (CdS), and cadmium selenide (CdSe). Three growth modes of PbS were identified, which included contributions from spontaneously generated catalyst. The resulting wires were found capable of lasing with wavelengths over 4000 nm, representing the longest known wavelength from a sub-wavelength wire. For CdxPb1-xS nanowires, it was established that the cooling process significantly affects the alloy composition and structure. Quenching was critical to retain metastable alloys with x up to 0.14, representing a new composition in nanowire form. Alternatively, gradual cooling caused phase segregation, which created heterostructures with light emission in both the visible and mid-infrared regimes. The CdSSe alloy system was fully explored for spatial composition variation. CdSxSe1-x nanowires were grown with composition variation across the substrate. Subsequent contact printing preserved the designed composition gradient and led to the demonstration of a variable wavelength photodetector device. CdSSe axial heterostructure nanowires were also achieved. The growth process involved many variables, including a deliberate and controllable change in substrate temperature. As a result, both red and green light emission was detected from single nanowires.
ContributorsNichols, Patricia (Author) / Ning, Cun-Zheng (Thesis advisor) / Carpenter, Ray (Committee member) / Bennett, Peter (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Solution methods for certain linear and nonlinear evolution equations are presented in this dissertation. Emphasis is placed mainly on the analytical treatment of nonautonomous differential equations, which are challenging to solve despite the existent numerical and symbolic computational software programs available. Ideas from the transformation theory are adopted allowing one to solve the problems under consideration from a non-traditional perspective. First, the Cauchy initial value problem is considered for a class of nonautonomous and inhomogeneous linear diffusion-type equation on the entire real line. Explicit transformations are used to reduce the equations under study to their corresponding standard forms emphasizing on natural relations with certain Riccati(and/or Ermakov)-type systems. These relations give solvability results for the Cauchy problem of the parabolic equation considered. The superposition principle allows to solve formally this problem from an unconventional point of view. An eigenfunction expansion approach is also considered for this general evolution equation. Examples considered to corroborate the efficacy of the proposed solution methods include the Fokker-Planck equation, the Black-Scholes model and the one-factor Gaussian Hull-White model. The results obtained in the first part are used to solve the Cauchy initial value problem for certain inhomogeneous Burgers-type equation. The connection between linear (the Diffusion-type) and nonlinear (Burgers-type) parabolic equations is stress in order to establish a strong commutative relation. Traveling wave solutions of a nonautonomous Burgers equation are also investigated. Finally, it is constructed explicitly the minimum-uncertainty squeezed states for quantum harmonic oscillators. They are derived by the action of corresponding maximal kinematical invariance group on the standard ground state solution. It is shown that the product of the variances attains the required minimum value only at the instances that one variance is a minimum and the other is a maximum, when the squeezing of one of the variances occurs. Such explicit construction is possible due to the relation between the diffusion-type equation studied in the first part and the time-dependent Schrodinger equation. A modication of the radiation field operators for squeezed photons in a perfect cavity is also suggested with the help of a nonstandard solution of Heisenberg's equation of motion.
ContributorsVega-Guzmán, José Manuel, 1982- (Author) / Sulov, Sergei K (Thesis advisor) / Castillo-Chavez, Carlos (Thesis advisor) / Platte, Rodrigo (Committee member) / Chowell-Puente, Gerardo (Committee member) / Arizona State University (Publisher)
Created2013
Description
The contemporary architectural pedagogy is far removed from its ancestry: the classical Beaux-Arts and polytechnic schools of the 19th century and the Bauhaus and Vkhutemas models of the modern period. Today, the "digital" has invaded the academy and shapes pedagogical practices, epistemologies, and ontologies within it, and this invasion is reflected in teaching practices, principles, and tools. Much of this digital integration goes unremarked and may not even be explicitly taught. In this qualitative research project, interviews with 18 leading architecture lecturers, professors, and deans from programs across the United States were conducted. These interviews focused on advanced practices of digital architecture, such as the use of digital tools, and how these practices are viewed. These interviews yielded a wealth of information about the uses (and abuses) of advanced digital technologies within the architectural academy, and the results were analyzed using the methods of phenomenology and grounded theory. Most schools use digital technologies to some extent, although this extent varies greatly. While some schools have abandoned hand-drawing and other hand-based craft almost entirely, others have retained traditional techniques and use digital technologies sparingly. Reasons for using digital design processes include industry pressure as well as the increased ability to solve problems and the speed with which they could be solved. Despite the prevalence of digital design, most programs did not teach related design software explicitly, if at all, instead requiring students (especially graduate students) to learn to use them outside the design studio. Some of the problems with digital design identified in the interviews include social problems such as alienation as well as issues like understanding scale and embodiment of skill.
ContributorsAlqabandy, Hamad (Author) / Brandt, Beverly (Thesis advisor) / Mesch, Claudia (Committee member) / Newton, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier.
ContributorsBuddi, Sai (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Nelson, Randall (Committee member) / Duman, Tolga (Committee member) / Arizona State University (Publisher)
Created2012