Matching Items (40)
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DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing

DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.
ContributorsWei, Xixi (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
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Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle:

Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands.

Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
ContributorsChapman, Eric (Author) / Childers, Daniel L. (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Hall, Sharon J (Committee member) / Turetsky, Merritt (Committee member) / Arizona State University (Publisher)
Created2015
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This thesis focuses on the theoretical work done to determine thermodynamic properties of a chalcopyrite thin-film material for use as a photovoltaic material in a tandem device. The material of main focus here is ZnGeAs2, which was chosen for the relative abundance of constituents, favorable photovoltaic properties, and good lattice

This thesis focuses on the theoretical work done to determine thermodynamic properties of a chalcopyrite thin-film material for use as a photovoltaic material in a tandem device. The material of main focus here is ZnGeAs2, which was chosen for the relative abundance of constituents, favorable photovoltaic properties, and good lattice matching with ZnSnP2, the other component in this tandem device. This work is divided into two main chapters, which will cover: calculations and method to determine the formation energy and abundance of native point defects, and a model to calculate the vapor pressure over a ternary material from first-principles. The purpose of this work is to guide experimental work being done in tandem to synthesize ZnGeAs2 in thin-film form with high enough quality such that it can be used as a photovoltaic. Since properties of photovoltaic depend greatly on defect concentrations and film quality, a theoretical understanding of how laboratory conditions affect these properties is very valuable. The work done here is from first-principles and utilizes density functional theory using the local density approximation. Results from the native point defect study show that the zinc vacancy (VZn) and the germanium antisite (GeZn) are the more prominent defects; which most likely produce non-stoichiometric films. The vapor pressure model for a ternary system is validated using known vapor pressure for monatomic and binary test systems. With a valid ternary system vapor pressure model, results show there is a kinetic barrier to decomposition for ZnGeAs2.
ContributorsTucker, Jon R (Author) / Van Schilfgaarde, Mark (Thesis advisor) / Newman, Nathan (Committee member) / Adams, James (Committee member) / Arizona State University (Publisher)
Created2011
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ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a

ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a variety of DNA nanostructures, which can be organized into both discrete and periodic structures. This dissertation focuses on studying the dynamic behavior of DNA nanostructure recognition processes. The thermodynamics and kinetics of nanostructure binding are evaluated, with the intention of improving our ability to understand and control their assembly. Presented here are a series of studies toward this goal. First, multi-helical DNA nanostructures were used to investigate how the valency and arrangement of the connections between DNA nanostructures affect super-structure formation. The study revealed that both the number and the relative position of connections play a significant role in the stability of the final assembly. Next, several DNA nanostructures were designed to gain insight into how small changes to the nanostructure scaffolds, intended to vary their conformational flexibility, would affect their association equilibrium. This approach yielded quantitative information about the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. Finally, a multi-helical DNA nanostructure was used as a model `chip' for the detection of a single stranded DNA target. The results revealed that the rate constant of hybridization is strongly dominated by a rate-limiting nucleation step.
ContributorsNangreave, Jeanette (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian J.-L. (Committee member) / Seo, Dong Kyun (Committee member) / Arizona State University (Publisher)
Created2011
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III-nitride alloys are wide band gap semiconductors with a broad range of applications in optoelectronic devices such as light emitting diodes and laser diodes. Indium gallium nitride light emitting diodes have been successfully produced over the past decade. But the progress of green emission light emitting devices has been limited

III-nitride alloys are wide band gap semiconductors with a broad range of applications in optoelectronic devices such as light emitting diodes and laser diodes. Indium gallium nitride light emitting diodes have been successfully produced over the past decade. But the progress of green emission light emitting devices has been limited by the incorporation of indium in the alloy, mainly due to phase separation. This difficulty could be addressed by studying the growth and thermodynamics of these alloys. Knowledge of thermodynamic phase stabilities and of pressure - temperature - composition phase diagrams is important for an understanding of the boundary conditions of a variety of growth techniques. In this dissertation a study of the phase separation of indium gallium nitride is conducted using a regular solution model of the ternary alloy system. Graphs of Gibbs free energy of mixing were produced for a range of temperatures. Binodal and spinodal decomposition curves show the stable and unstable regions of the alloy in equilibrium. The growth of gallium nitride and indium gallium nitride was attempted by the reaction of molten gallium - indium alloy with ammonia at atmospheric pressure. Characterization by X-ray diffraction, photoluminescence, and secondary electron microscopy show that the samples produced by this method contain only gallium nitride in the hexagonal phase. The instability of indium nitride at the temperatures required for activation of ammonia accounts for these results. The photoluminescence spectra show a correlation between the intensity of a broad green emission, related to native defects, and indium composition used in the molten alloy. A different growth method was used to grow two columnar-structured gallium nitride films using ammonium chloride and gallium as reactants and nitrogen and ammonia as carrier gasses. Investigation by X-ray diffraction and spatially-resolved cathodoluminescence shows the film grown at higher temperature to be primarily hexagonal with small quantities of cubic crystallites, while the one grown at lower temperature to be pure hexagonal. This was also confirmed by low temperature photoluminescence measurements. The results presented here show that cubic and hexagonal crystallites can coexist, with the cubic phase having a much sharper and stronger luminescence. Controlled growth of the cubic phase GaN crystallites can be of use for high efficiency light detecting and emitting devices. The ammonolysis of a precursor was used to grow InGaN powders with different indium composition. High purity hexagonal GaN and InN were obtained. XRD spectra showed complete phase separation for samples with x < 30%, with ~ 9% indium incorporation in the 30% sample. The presence of InGaN in this sample was confirmed by PL measurements, where luminescence from both GaN and InGaN band edge are observed. The growth of higher indium compositions samples proved to be difficult, with only the presence of InN in the sample. Nonetheless, by controlling parameters like temperature and time may lead to successful growth of this III-nitride alloy by this method.
ContributorsHill, Arlinda (Author) / Ponce, Fernando A. (Thesis advisor) / Chamberlin, Ralph V (Committee member) / Sankey, Otto F (Committee member) / Smith, David J. (Committee member) / Tsen, Kong-Thon (Committee member) / Arizona State University (Publisher)
Created2011
Description
Cooperativity can be used to manipulate binding affinities of DNA biosensors – improving specificity without sacrificing sensitivity; examples include tentacle probes (TPs) and cooperative primers (CPs). This thesis body of work: (1) used TPs to develop a rapid, low-cost diagnostic for detecting the point mutation leading to Navajo Neurohepatopathy (NNH)

Cooperativity can be used to manipulate binding affinities of DNA biosensors – improving specificity without sacrificing sensitivity; examples include tentacle probes (TPs) and cooperative primers (CPs). This thesis body of work: (1) used TPs to develop a rapid, low-cost diagnostic for detecting the point mutation leading to Navajo Neurohepatopathy (NNH) and (2) used CPs to amplify a symmetric bowtie-barcoded origami with captured t-cell receptor (TCR) α and β mRNA of a single cell.

NNH (affecting 1-in-1600 Navajo babies) is a fatal genetic disorder often caused by 149G>A mutation and is characterized by brain damage and liver disease/failure. Phoenix Children’s Hospital currently uses gene sequencing to identify the 149G>A mutation. While this process is conclusive, there are limitations, as it requires both time (3-4 weeks) and money (>$700). Ultimately, these factors create barriers that can directly impact a patient’s quality of life. Assessment of the developed TP diagnostic, using genomic DNA derived from FFPE patient liver samples, suggests nearly 100% specificity and sensitivity while reducing cost to ~$250 (including cost of labor) and providing a diagnosis within 48 hours.

TCR specificity is dependent on V(D)J recombination as well as pairing of the αβ chains. Drs. Schoettle and Blattman have developed a solution in which a bowtie-barcoded origami strand nanostructure is transfected into individual cells of a heterogeneous cell population to capture and protect αβ mRNA. When PCR of the origami template is performed with Vα, X, Vβ, and Y primers, the α and β gene segments cannot be tied back to a barcode – and paired. Assessment of the developed CPs for PCR suggests correct individual amplification using (1) Va + Xcp and (2) Vβ + Ycp primers, whereas combination of all the primers (Va, Xcp, Vb, and Ycp) suggests hybridization of the Vα + Xcp and Vβ + Ycp products due to the origami target symmetry.
ContributorsDubois, Courtney Michelle (Author) / Caplan, Michael R (Thesis advisor) / Vernon, Brent (Committee member) / Carpentieri, David (Committee member) / Arizona State University (Publisher)
Created2018
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Planetary surface studies across a range of spatial scales are key to interpreting modern and ancient operative processes and to meeting strategic mission objectives for robotic planetary science exploration. At the meter-scale and below, planetary regolith conducts heat at a rate that depends on the physical properties of the regolith

Planetary surface studies across a range of spatial scales are key to interpreting modern and ancient operative processes and to meeting strategic mission objectives for robotic planetary science exploration. At the meter-scale and below, planetary regolith conducts heat at a rate that depends on the physical properties of the regolith particles, such as particle size, sorting, composition, and shape. Radiometric temperature measurements thus provide the means to determine regolith properties and rock abundance from afar. However, heat conduction through a matrix of irregular particles is a complicated physical system that is strongly influenced by temperature and atmospheric gas pressure. A series of new regolith thermal conductivity experiments were conducted under realistic planetary surface pressure and temperature conditions. A new model is put forth to describe the radiative, solid, and gaseous conduction terms of regolith on Earth, Mars, and airless bodies. These results will be used to infer particle size distribution from temperature measurements of the primitive asteroid Bennu to aid in OSIRIS-REx sampling site selection. Moving up in scale, fluvial processes are extremely influential in shaping Earth's surface and likely played an influential role on ancient Mars. Amphitheater-headed canyons are found on both planets, but conditions necessary for their development have been debated for many years. A spatial analysis of canyon form distribution with respect to local stratigraphy at the Escalante River and on Tarantula Mesa, Utah, indicates that canyon distribution is most closely related to variations in local rock strata, rather than groundwater spring intensity or climate variations. This implies that amphitheater-headed canyons are not simple markers of groundwater seepage erosion or megaflooding. Finally, at the largest scale, volcanism has significantly altered the surface characteristics of Earth and Mars. A field campaign was conducted in Hawaii to investigate the December 1974 Kilauea lava flow, where it was found that lava coils formed in an analogous manner to those found in Athabasca Valles, Mars. The location and size of the coils may be used as indicators of local effusion rate, viscosity, and crustal thickness.
ContributorsRyan, Andrew J (Author) / Christensen, Philip R. (Thesis advisor) / Bell, James F. (Committee member) / Whipple, Kelin X (Committee member) / Ruff, Steven W (Committee member) / Asphaug, Erik I (Committee member) / Arizona State University (Publisher)
Created2018
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The seasonal deposition of CO2 on the polar caps is one of the most dynamic processes on Mars and is a dominant driver of the global climate. Remote sensing temperature and albedo data were used to estimate the subliming mass of CO2 ice on south polar gullies near Sisyphi Cavi.

The seasonal deposition of CO2 on the polar caps is one of the most dynamic processes on Mars and is a dominant driver of the global climate. Remote sensing temperature and albedo data were used to estimate the subliming mass of CO2 ice on south polar gullies near Sisyphi Cavi. Results showed that column mass abundances range from 400 - 1000 kg.m2 in an area less than 60 km2 in late winter. Complete sublimation of the seasonal caps may occur later than estimated by large-scale studies and is geographically dependent. Seasonal ice depth estimates suggested variations of up to 1.5 m in depth or 75% in porosity at any one time. Interannual variations in these data appeared to correlate with dust activity in the southern hemisphere. Correlation coefficients were used to investigate the relationship between frost-free surface properties and the evolution of the seasonal ice in this region. Ice on high thermal inertia units was found to disappear before any other ice, likely caused by inhibited deposition during fall. Seasonal ice springtime albedo appeared to be predominantly controlled by orientation, with north-facing slopes undergoing brightening initially in spring, then subliming before south-facing slopes. Overall, the state of seasonal ice is far more complex than globally and regionally averaged studies can identify.

The discovery of cryovolcanic features on Charon and the presence of ammonia hydrates on the surfaces of other medium-sized Kuiper Belt Objects suggests that cryovolcanism may be important to their evolution. A two-dimensional, center-point finite difference, thermal hydraulic model was developed to explore the behavior of cryovolcanic conduits on midsized KBOs. Conduits on a Charon-surrogate were shown to maintain flow through over 200 km of crust and mantle down to radii of R = 0.20 m. Radii higher than this became turbulent due to high viscous dissipation and low thermal conductivity. This model was adapted to explore the emplacement of Kubrik Mons. Steady state flow was achieved with a conduit of radius R = 0.02 m for a source chamber at 2.3 km depth. Effusion rates computed from this estimated a 122 - 163 Myr upper limit formation timescale.
ContributorsMount, Christopher (Author) / Christensen, Philip R. (Thesis advisor) / Desch, Steven J (Committee member) / Bell, James F. (Committee member) / Clarke, Amanda B (Committee member) / Whipple, Kelin X (Committee member) / Arizona State University (Publisher)
Created2019
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In these times of increasing industrialization, there arises a need for effective and energy efficient heat transfer/heat exchange devices. The focus nowadays is on identifying various methods and techniques which can aid the process of developing energy efficient devices. One of the most common heat transfer devices is a heat

In these times of increasing industrialization, there arises a need for effective and energy efficient heat transfer/heat exchange devices. The focus nowadays is on identifying various methods and techniques which can aid the process of developing energy efficient devices. One of the most common heat transfer devices is a heat exchanger. Heat exchangers are an essential commodity to any industry and their efficiency can play an important role in making industries energy efficient and reduce the energy losses in the devices, in turn decreasing energy inputs to run the industry.

One of the ways in which we can improve the efficiency of heat exchangers is by applying ultrasonic energy to a heat exchanger. This research explores the possibility of introducing the external input of ultrasonic energy to increase the efficiency of the heat exchanger. This increase in efficiency can be estimated by calculating the parameters important for the characterization of a heat exchanger, which are effectiveness (ε) and overall heat transfer coefficient (U). These parameters are calculated for both the non-ultrasound and ultrasound conditions in the heat exchanger.

This a preliminary study of ultrasound and its effect on a conventional shell-and-coil heat exchanger. From the data obtained it can be inferred that the increase in effectiveness and overall heat transfer coefficient upon the application of ultrasound is 1% and 6.22% respectively.
ContributorsAnnam, Roshan Sameer (Author) / Phelan, Patrick (Thesis advisor) / Rykaczewski, Konrad (Committee member) / Milcarek, Ryan (Committee member) / Arizona State University (Publisher)
Created2019
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Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this

Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this diversity, there are numerous models of $1/f$ noise. In this dissertation, I summarize my research into models based on linking the characteristic times of fluctuations of a quantity to its multiplicity of states. With this condition satisfied, I show that a quantity will undergo $1/f$ fluctuations and exhibit associated properties, such as slow dynamics, divergence of time scales, and ergodicity breaking. I propose that multiplicity-dependent characteristic times come about when a system shares a constant, maximized amount of entropy with a finite bath. This may be the case when systems are imperfectly coupled to their thermal environment and the exchange of conserved quantities is mediated through their local environment. To demonstrate the effects of multiplicity-dependent characteristic times, I present numerical simulations of two models. The first consists of non-interacting spins in $0$-field coupled to an explicit finite bath. This model has the advantage of being degenerate, so that its multiplicity alone determines the dynamics. Fluctuations of the alignment of this model will be compared to voltage fluctuations across a mesoscopic metal-insulator-metal junction. The second model consists of classical, interacting Heisenberg spins with a dynamic constraint that slows fluctuations according to the multiplicity of the system's alignment. Fluctuations in one component of the alignment will be compared to the flux noise in superconducting quantum interference devices (SQUIDs). Finally, I will compare both of these models to each other and some of the most popular models of $1/f$ noise, including those based on a superposition of exponential relaxation processes and those based on power law renewal processes.
ContributorsDavis, Bryce F (Author) / Chamberlin, Ralph V (Thesis advisor) / Mauskopf, Philip (Committee member) / Wolf, George (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2018