ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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Description
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
ContributorsHunter, Mark (Author) / Fromme, Petra (Thesis advisor) / Wolf, George (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.
ContributorsBarr, Daniel Alan (Author) / van der Vaart, Arjan (Thesis advisor) / Matyushov, Dmitry (Committee member) / Wolf, George (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
The increasing isolation and segregation of children in American cities and suburbs is of special significance. This has meant a loss of freedom for children to explore their neighborhood and city as they get older, their exclusion from varied contacts with diverse adults in a variety of settings, and their consequent inability to learn from personal experience and observation, so essential to social and emotional development. The purpose of this study is to measure the differences in child-friendliness between neighborhoods with different income levels by developing an indicator framework that can be used by planning departments and other local authorities based on available data. The research also focus on what other factor (besides income) influences child-friendliness in a city at the neighborhood level. If a relationship does exist, how big is the difference in terms of child-friendliness between low-income and high-income neighborhoods, and what indicators play the most important role in creating the difference? Neighborhoods in the city of Glendale, Arizona serve as case studies to aid in refining the assessment method, and show the potential for how cities can become more child-friendly. The neighborhoods were selected based on income, same size and different location.
ContributorsRakhimova, Nelya (Author) / Stein, Jay (Thesis advisor) / Pijawka, David (Committee member) / Crewe, Katherine (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation examines the conditions that foster or hinder success of university-based community design centers (CDCs) in the United States. Little is known about the normative underpinnings of CDCs, how successful these centers have been, which factors have contributed to or impeded their success, and how they have responded to the changes in social, political, professional and economic contexts. Adopting Giddens' theory of structuration as a research framework, this study examined CDCs via a mixed-methods sequential research design: a cross-sectional survey of CDCs on current definitions of success and metrics in use; and in-depth interviews to document the centers' histories of change or stasis, and how these changes influenced their successes. The findings of the first phase were utilized to develop a comprehensive success model for current CDCs that comprise measures related to organizational impacts, activities, and capacities. In the multiple case study analysis, four major rationales were identified: universities for public service, pragmatist learning theories, civic professionalism, and social change. These four rationales were evident in all of the studied cases at varying degrees. Using the concept of permeability, the study also exemplified how the processes of CDCs had transformative impacts in institutional, societal, and personal contexts. Multidisciplinarity has also emerged as a theme for the current organizational transformations of CDCs. The main argument that emerged from these findings is that it is not possible to identify a singular model or best practice for CDCs. The strengths and unique potentials of CDCs depend on the alternative rationales, involved agencies, and their social, political and spatial contexts. However, capitalizing on the distinctive attributes of the institutional context (i.e. the university), I consider some possibilities for university-based CDCs with an interdisciplinary structure, pushing the professional, curricular, and institutional boundaries, and striving for systemic change and social justice. In addition to contributing to the theoretical knowledge base, the findings provide useful information to various CDCs across the country, particularly today as they struggle with financial constraints while the community needs they provide are increasingly in demand. Since CDCs have a long history of community service and engagement, the findings can inform other university-community partnerships.
ContributorsTural, Elif (Author) / Ahrentzen, Sherry (Thesis advisor) / Meunier, John (Committee member) / Yabes, Ruth (Committee member) / Arizona State University (Publisher)
Created2011
Description
The United States has a long history of providing public parks and amenities, especially for children. Unfortunately, children today are spending less time in public parks, less time getting physical activity and more time being indoors and sedentary. While multiple factors may be responsible for this lack of activity, multiple researchers have found the availability of parks is a significant influence on the physical activity levels of children as well as on the occurrence of obesity related illness. Public parks are ideal locations for children to get physical activity, however they are not always equitably distributed within communities. Income and race/ethnicity especially are common variables found to impact availability of parks. Such socioeconomic variables typically have an impact on the availability of public parks within a community. Such variables may also impact the quality of the parks provided. A case study of Scottsdale, Arizona was conducted analyzing the availability of public parks within the City between the years of 1990 and 2000 and the current quality of the parks. Statistical analysis and observation were utilized to assess the amount of park space available (in acres) and the quality of the parks in comparison to selected socioeconomic variables including ethnicity, income and total percent housing type (single family or multi-family). All analysis was conducted using U.S. Census data from the years 1990 and 2000 and was at the tract level. The results of the analysis indicate that in contrast to the initial hypothesis and past research, within the City of Scottsdale, lower income neighborhoods actually have more public park space available to them than higher income neighborhoods. Between 1990 and 2000 the difference in park space between the lowest and highest income quartiles increased considerably, approximately 230% over the ten years. The quality analysis results indicate that the overall quality of parks is slightly higher in the highest income neighborhoods, which also have no parks that could be considered of poor quality. Given the atypical results of this analysis, further research is necessary to better understand the impacts of socioeconomic characteristics on park, especially regarding children.
ContributorsSamples, Samantha (Author) / Crewe, Katherine (Thesis advisor) / Booze, Randy (Committee member) / Pijawka, David (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several approaches to next generation DNA sequencing via tunneling current method based on a Scanning Tunneling Microscope system. In chapters 5 and 6, preliminary results have shown that DNA bases could be identified by their characteristic tunneling signals. Measurements taken in aqueous buffered solution showed that single base resolution could be achieved with economic setups. In chapter 7, it is illustrated that some ongoing measurements are indicating the sequence readout by making linear scan on a piece of short DNA oligomer. However, to overcome the difficulties of controlling DNA especially ssDNA movement, it is much better to have the tunneling measurement incorporated onto a robust nanopore device to realize sequential reading of the DNA sequence while it is being translocated.
ContributorsHuang, Shuo (Author) / Lindsay, Stuart (Thesis advisor) / Sankey, Otto (Committee member) / Tao, Nongjian (Committee member) / Drucker, Jeff (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
The uncertainty of change inherent in issues such as climate change and regional growth has created a significant challenge for public decision makers trying to decide what adaptation actions are needed to respond to these possible changes. This challenge threatens the resiliency and thus the long term sustainability of our social-ecological systems. Using an empirical embedded case study approach to explore the application of advanced scenario analysis methods to regional growth visioning projects in two regions, this dissertation provides empirical evidence that for issues with high uncertainty, advanced scenario planning (ASP) methods are effective tools for helping decision makers to anticipate and prepare to adapt to change.
ContributorsQuay, Ray (Author) / Pijawka, David (Thesis advisor) / Shangraw, Ralph (Committee member) / Holway, James (Committee member) / Arizona State University (Publisher)
Created2011
Description
Interior design continues to re-define itself as a discipline that presents designers with new problems that require innovative solutions. This is particularly true in the case in office design. The transformation of the office environment from the standard bullpen configuration to today's dynamic, flexible, and open floor plans has required new design methodologies that incorporate tools and technologies that are readily available to interior designers. Today, increased use of teams in the workplace challenges interior designers to create environments that accommodate both group and individual tasks (Brill, Weidermann & BOSTI associates, 2001). Collaboration has received considerable attention as organizations focus on productivity and reducing costs to compete in a global economy (Hassanain, 2006). Designers and architects should learn to create environments that respond to dynamic, moveable, and flexible work methods. This web-based research study explores the use of pattern language as a new tool for designing collaborative work environments. In 1977, Christopher Alexander and his associates developed `Pattern language' (Alexander, Ishikawa & Silverstein, 1977) as a design formulation methodology. It consists of a series of interrelated physical elements combined to create a framework for design solutions. This pattern language tool for collaborative work environments was created based on research by Lori Anthony (2001). This study further builds upon current trends and research in collaborative work environments. The researcher conducted a pilot test by sending the web-based tool and an online questionnaire to all graduate students and faculty members in the fields of interior design and healthcare and healing environment (HHE). After testing its validity in The Design School at Arizona State University, the same tool and questionnaire was sent to the employees of one of the leading architecture and interior design firms in Phoenix, AZ. The results showed that among those design professionals surveyed, the majority believe pattern language could be a valuable design tool. The insights obtained from this study will provide designers, architects, and facility managers with a new design tool to aid in creating effective collaborative spaces in a work environment.
ContributorsSangoi, Deepika (Author) / Bender, Diane (Thesis advisor) / Brandt, Beverly (Committee member) / Heywood, William (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.
ContributorsCao, Zhai (Author) / Lindsay, Stuart (Thesis advisor) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Marzke, Robert (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
Biological membranes are critical to cell sustainability by selectively permeating polar molecules into the intracellular space and providing protection to the interior organelles. Biomimetic membranes (model cell membranes) are often used to fundamentally study the lipid bilayer backbone structure of the biological membrane. Lipid bilayer membranes are often supported using inorganic materials in an effort to improve membrane stability and for application to novel biosensing platforms. Published literature has shown that a variety of dense inorganic materials with various surface properties have been investigated for the study of biomimetic membranes. However, literature does not adequately address the effect of porous materials or supports with varying macroscopic geometries on lipid bilayer membrane behavior. The objective of this dissertation is to present a fundamental study on the synthesis of lipid bilayer membranes supported by novel inorganic supports in an effort to expand the number of available supports for biosensing technology. There are two fundamental areas covered including: (1) synthesis of lipid bilayer membranes on porous inorganic materials and (2) synthesis and characterization of cylindrically supported lipid bilayer membranes. The lipid bilayer membrane formation behavior on various porous supports was studied via direct mass adsorption using a quartz crystal microbalance. Experimental results demonstrate significantly different membrane formation behaviors on the porous inorganic supports. A lipid bilayer membrane structure was formed only on SiO2 based surfaces (dense SiO2 and silicalite, basic conditions) and gamma-alumina (acidic conditions). Vesicle monolayer adsorption was observed on gamma-alumina (basic conditions), and yttria stabilized zirconia (YSZ) of varying roughness. Parameters such as buffer pH, surface chemistry and surface roughness were found to have a significant impact on the vesicle adsorption kinetics. Experimental and modeling work was conducted to study formation and characterization of cylindrically supported lipid bilayer membranes. A novel sensing technique (long-period fiber grating refractometry) was utilized to measure the formation mechanism of lipid bilayer membranes on an optical fiber. It was found that the membrane formation kinetics on the fiber was similar to its planar SiO2 counterpart. Fluorescence measurements verified membrane transport behavior and found that characterization artifacts affected the measured transport behavior.
ContributorsEggen, Carrie (Author) / Lin, Jerry Y.S. (Thesis advisor) / Dai, Lenore (Committee member) / Rege, Kaushal (Committee member) / Thornton, Trevor (Committee member) / Vogt, Bryan (Committee member) / Arizona State University (Publisher)
Created2011