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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- Creators: Cooke, Nancy J.
- Creators: Fromme, Petra
Description
There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water and sunlight. As a part of the photosynthetic electron transport chain (PETC) of the green algae Chlamydomonas reinhardtii, water is split via Photosystem II (PSII) and the electrons flow through a series of electron transfer cofactors in cytochrome b6f, plastocyanin and Photosystem I (PSI). The terminal electron acceptor of PSI is ferredoxin, from which electrons may be used to reduce NADP+ for metabolic purposes. Concomitant production of a H+ gradient allows production of energy for the cell. Under certain conditions and using the endogenous hydrogenase, excess protons and electrons from ferredoxin may be converted to molecular hydrogen. In this work it is demonstrated both that certain mutations near the quinone electron transfer cofactor in PSI can speed up electron transfer through the PETC, and also that a native [FeFe]-hydrogenase can be expressed in the C. reinhardtii chloroplast. Taken together, these research findings form the foundation for the design of a PSI-hydrogenase fusion for the direct and continuous photo-production of hydrogen in vivo.
ContributorsReifschneider, Kiera (Author) / Redding, Kevin (Thesis advisor) / Fromme, Petra (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2013
Description
As technology enhances our communication capabilities, the number of distributed teams has risen in both public and private sectors. There is no doubt that these technological advancements have addressed a need for communication and collaboration of distributed teams. However, is all technology useful for effective collaboration? Are some methods (modalities) of communication more conducive than others to effective performance and collaboration of distributed teams? Although previous literature identifies some differences in modalities, there is little research on geographically distributed mobile teams (DMTs) performing a collaborative task. To investigate communication and performance in this context, I developed the GeoCog system. This system is a mobile communications and collaboration platform enabling small, distributed teams of three to participate in a variant of the military-inspired game, "Capture the Flag". Within the task, teams were given one hour to complete as many "captures" as possible while utilizing resources to the advantage of the team. In this experiment, I manipulated the modality of communication across three conditions with text-based messaging only, vocal communication only, and a combination of the two conditions. It was hypothesized that bi-modal communication would yield superior performance compared to either single modality conditions. Results indicated that performance was not affected by modality. Further results, including communication analysis, are discussed within this paper.
ContributorsChampion, Michael (Author) / Cooke, Nancy J. (Thesis advisor) / Shope, Steven (Committee member) / Wu, Bing (Committee member) / Arizona State University (Publisher)
Created2012
Description
The need for a renewable and sustainable light-driven energy source is the motivation for this work, which utilizes a challenging, yet practical and attainable bio-inspired approach to develop an artificial oxygen evolving complex, which builds upon the principles of the natural water splitting mechanism in oxygenic photosynthesis. In this work, a stable framework consisting of a three-dimensional DNA tetrahedron has been used for the design of a bio-mimic of the Oxygen-Evolving Complex (OEC) found in natural Photosystem II (PSII). PSII is a large protein complex that evolves all the oxygen in the atmosphere, but it cannot be used directly in artificial systems, as the light reactions lead to damage of one of Photosystem II's core proteins, D1, which has to be replaced every half hour in the presence of sunlight. The final goal of the project aims to build the catalytic center of the OEC, including the Mn4CaCl metal cluster and its protein environment in the stable DNA framework of a tetrahedron, which can subsequently be connected to a photo-stable artificial reaction center that performs light-induced charge separation. Regions of the peptide sequences containing Mn4CaCl ligation sites are implemented in the design of the aOEC (artificial oxygen-evolving complex) and are attached to sites within the tetrahedron to facilitate assembly. Crystals of the tetrahedron have been obtained, and X-ray crystallography has been used for characterization. As a proof of concept, metal-binding peptides have been coupled to the DNA tetrahedron which allowed metal-containing porphyrins, specifically Fe(III) meso-Tetra(4-sulfonatophenyl) porphyrin chloride, to be encapsulated inside the DNA-tetrahedron. The porphyrins were successfully assembled inside the tetrahedron through coordination of two terminal histidines from the orthogonally oriented peptides covalently attached to the DNA. The assembly has been characterized using Electron Paramagnetic Resonance (EPR), optical spectroscopy, Dynamic Light Scattering (DLS), and x-ray crystallography. The results reveal that the spin state of the metal, iron (III), switches during assembly from the high-spin state to low-spin state.
ContributorsRendek, Kimberly Nicole (Author) / Fromme, Petra (Thesis advisor) / Chen, Julian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Research on priming has shown that exposure to the concept of fast food can have an effect on human behavior by inducing haste and impatience (Zhong & E. DeVoe, 2010). This research suggests that thinking about fast food makes individuals impatient and strengthens their desire to complete tasks such as reading and decision making as quickly and efficiently as possible. Two experiments were conducted in which the effects of fast food priming were examined using a driving simulator. The experiments examined whether fast food primes can induce impatient driving. In experiment 1, 30 adult drivers drove a course in a driving simulator after being exposed to images by rating aesthetics of four different logos. Experiment 1 did not yield faster driving speeds nor an impatient and faster break at the yellow light in the fast food logo prime condition. In experiment 2, 30 adult drivers drove the same course from experiment 1. Participants did not rate logos on their aesthetics prior to the drive, instead billboards were included in the simulation that had either fast food or diner logos. Experiment 2 did not yielded faster driving speeds, however there was a significant effect of faster breaking and a higher number of participants running the yellow light.
ContributorsTaggart, Mistey. L (Author) / Branaghan, Russell (Thesis advisor) / Cooke, Nancy J. (Committee member) / Song, Hyunjin (Committee member) / Arizona State University (Publisher)
Created2014
Description
Photosynthesis is the primary source of energy for most living organisms. Light harvesting complexes (LHC) play a vital role in harvesting sunlight and passing it on to the protein complexes of the electron transfer chain which create the electrochemical potential across the membrane which drives ATP synthesis. phycobilisomes (PBS) are the most important LHCs in cyanobacteria. PBS is a complex of three light harvesting proteins: phycoerythrin (PE), phycocyanin (PC) and allophycocyanin (APC). This work has been done on a newly discovered cyanobacterium called Leptolyngbya Heron Island (L.HI). This study has three important goals: 1) Sequencing, assembly and annotation of the L.HI genome - Since this is a newly discovered cyanobacterium, its genome was not previously elucidated. Illumina sequencing, a type of next generation sequencing (NGS) technology was employed to sequence the genome. Unfortunately, the natural isolate contained other contaminating and potentially symbiotic bacterial populations. A novel bioinformatics strategy for separating DNA from contaminating bacterial populations from that of L.HI was devised which involves a combination of tetranucleotide frequency, %(G+C), BLAST analysis and gene annotation. 2) Structural elucidation of phycoerythrin - Phycoerythrin is the most important protein in the PBS assembly because it is one of the few light harvesting proteins which absorbs green light. The protein was crystallized and its structure solved to a resolution of 2Å. This protein contains two chemically distinct types of chromophores: phycourobilin and phycoerythrobilin. Energy transfer calculations indicate that there is unidirectional flow of energy from phycourobilin to phycoerythrobilin. Energy transfer time constants using Forster energy transfer theory have been found to be consistent with experimental data available in literature. 3) Effect of chromatic acclimation on photosystems - Chromatic acclimation is a phenomenon in which an organism modulates the ratio of PE/PC with change in light conditions. Our investigation in case of L.HI has revealed that the PE is expressed more in green light than PC in red light. This leads to unequal harvesting of light in these two states. Therefore, photosystem II expression is increased in red-light acclimatized cells coupled with an increase in number of PBS.
ContributorsPaul, Robin (Author) / Fromme, Petra (Thesis advisor) / Ros, Alexandra (Committee member) / Roberson, Robert (Committee member) / Arizona State University (Publisher)
Created2014
Description
Membrane proteins are a vital part of cellular structure. They are directly involved in many important cellular functions, such as uptake, signaling, respiration, and photosynthesis, among others. Despite their importance, however, less than 500 unique membrane protein structures have been determined to date. This is due to several difficulties with macromolecular crystallography, primarily the difficulty of growing large, well-ordered protein crystals. Since the first proof of concept for femtosecond nanocrystallography showing that diffraction patterns can be collected on extremely small crystals, thus negating the need to grow larger crystals, there have been many exciting advancements in the field. The technique has been proven to show high spatial resolution, thus making it a viable method for structural biology. However, due to the ultrafast nature of the technique, which allows for a lack of radiation damage in imaging, even more interesting experiments are possible, and the first temporal and spatial images of an undamaged structure could be acquired. This concept was denoted as time-resolved femtosecond nanocrystallography.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
ContributorsKupitz, Christopher (Author) / Fromme, Petra (Thesis advisor) / Spence, John C. (Thesis advisor) / Redding, Kevin (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2014
Description
When discussing human factors and performance, researchers recognize stress as a factor, but overlook mood as contributing factor. To explore the relationship between mood, stress and cognitive performance, a field study was conducted involving fire fighters engaged in a fire response simulation. Firefighter participants completed a stress questionnaire, an emotional state questionnaire, and a cognitive task. Stress and cognitive task performance scores were examined before and after the firefighting simulation for individual cognitive performance depreciation caused by stress or mood. They study revealed that existing stress was a reliable predictor of the pre-simulation cognitive task score, that, as mood becomes more positive, perceived stress scores decrease, and that negative mood and pre-simulation stress are also positively and significantly correlated.
ContributorsGomez-Herbert, Maria Elena (Author) / Cooke, Nancy J. (Thesis advisor) / Becker, Vaughn (Committee member) / Branaghan, Russell (Committee member) / Hyunjin, Song (Committee member) / Arizona State University (Publisher)
Created2014
Description
Preoperative team briefings have been suggested to be important for improving team performance in the operating room. Many high risk environments have accepted team briefings; however healthcare has been slower to follow. While applying briefings in the operating room has shown positive benefits including improved communication and perceptions of teamwork, most research has only focused on feasibility of implementation and not on understanding how the quality of briefings can impact subsequent surgical procedures. Thus, there are no formal protocols or methodologies that have been developed.
The goal of this study was to relate specific characteristics of team briefings back to objective measures of team performance. The study employed cognitive interviews, prospective observations, and principle component regression to characterize and model the relationship between team briefing characteristics and non-routine events (NREs) in gynecological surgery. Interviews were conducted with 13 team members representing each role on the surgical team and data were collected for 24 pre-operative team briefings and 45 subsequent surgical cases. The findings revealed that variations within the team briefing are associated with differences in team-related outcomes, namely NREs, during the subsequent surgical procedures. Synthesis of the data highlighted three important trends which include the need to promote team communication during the briefing, the importance of attendance by all surgical team members, and the value of holding a briefing prior to each surgical procedure. These findings have implications for development of formal briefing protocols.
Pre-operative team briefings are beneficial for team performance in the operating room. Future research will be needed to continue understanding this relationship between how briefings are conducted and team performance to establish more consistent approaches and as well as for the continuing assessment of team briefings and other similar team-related events in the operating room.
The goal of this study was to relate specific characteristics of team briefings back to objective measures of team performance. The study employed cognitive interviews, prospective observations, and principle component regression to characterize and model the relationship between team briefing characteristics and non-routine events (NREs) in gynecological surgery. Interviews were conducted with 13 team members representing each role on the surgical team and data were collected for 24 pre-operative team briefings and 45 subsequent surgical cases. The findings revealed that variations within the team briefing are associated with differences in team-related outcomes, namely NREs, during the subsequent surgical procedures. Synthesis of the data highlighted three important trends which include the need to promote team communication during the briefing, the importance of attendance by all surgical team members, and the value of holding a briefing prior to each surgical procedure. These findings have implications for development of formal briefing protocols.
Pre-operative team briefings are beneficial for team performance in the operating room. Future research will be needed to continue understanding this relationship between how briefings are conducted and team performance to establish more consistent approaches and as well as for the continuing assessment of team briefings and other similar team-related events in the operating room.
ContributorsHildebrand, Emily A (Author) / Branaghan, Russell J (Thesis advisor) / Cooke, Nancy J. (Committee member) / Hallbeck, M. Susan (Committee member) / Bekki, Jennifer M (Committee member) / Blocker, Renaldo C (Committee member) / Arizona State University (Publisher)
Created2014
Description
Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems continues to be a great chal-lenge. Conversely, deoxyribonucleic acid (DNA) engineering is now routinely used to build a wide variety of two dimensional and three dimensional (3D) nanostructures from simple hybridization based rules, and their functional diversity can be significantly ex-panded through site specific incorporation of the appropriate guest molecules. This dis-sertation describes a gentle methodology for using short (8 nucleotide) peptide nucleic acid (PNA) linkers to assemble polypeptides within a 3D DNA nanocage, as a proof of concept for constructing artificial catalytic centers. PNA-polypeptide conjugates were synthesized directly using microwave assisted solid phase synthesis or alternatively PNA linkers were conjugated to biologically expressed proteins using chemical crosslinking. The PNA-polypeptides hybridized to the preassembled DNA nanocage at room tempera-ture or 11 ⁰C and could be assembled in a stepwise fashion. Time resolved fluorescence anisotropy and gel electrophoresis were used to determine that a negatively charged az-urin protein was repelled outside of the negatively charged DNA nanocage, while a posi-tively charged cytochrome c protein was retained inside. Spectroelectrochemistry and an in-gel luminol oxidation assay demonstrated the cytochrome c protein remained active within the DNA nanocage and its redox potential decreased modestly by 10 mV due to the presence of the DNA nanocage. These results demonstrate the benign PNA assembly conditions are ideal for preserving polypeptide structure and function, and will facilitate the polypeptide-based assembly of artificial catalytic centers inside a stable DNA nanocage. A prospective application of assembling multiple cyclic γ-PNA-peptides to mimic the oxygen-evolving complex (OEC) catalytic active site from photosystem II (PSII) is described. In this way, the robust catalytic capacity of PSII could be utilized, without suffering the light-induced damage that occurs by the photoreactions within PSII via triplet state formation, which limits the efficiency of natural photosynthesis. There-fore, this strategy has the potential to revolutionize the process of designing and building robust catalysts by leveraging nature's recipes, and also providing a flexible and con-trolled artificial environment that might even improve them further towards commercial viability.
ContributorsFlory, Justin David (Author) / Fromme, Petra (Thesis advisor) / Yan, Hao (Committee member) / Buttry, Daniel (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
In this research work, a novel control system strategy for the robust control of an unmanned ground vehicle is proposed. This strategy is motivated by efforts to mitigate the problem for scenarios in which the human operator is unable to properly communicate with the vehicle. This novel control system strategy consisted of three major components: I.) Two independent intelligent controllers, II.) An intelligent navigation system, and III.) An intelligent controller tuning unit. The inner workings of the first two components are based off the Brain Emotional Learning (BEL), which is a mathematical model of the Amygdala-Orbitofrontal, a region in mammalians brain known to be responsible for emotional learning. Simulation results demonstrated the implementation of the BEL model to be very robust, efficient, and adaptable to dynamical changes in its application as controller and as a sensor fusion filter for an unmanned ground vehicle. These results were obtained with significantly less computational cost when compared to traditional methods for control and sensor fusion. For the intelligent controller tuning unit, the implementation of a human emotion recognition system was investigated. This system was utilized for the classification of driving behavior. Results from experiments showed that the affective states of the driver are accurately captured. However, the driver's affective state is not a good indicator of the driver's driving behavior. As a result, an alternative method for classifying driving behavior from the driver's brain activity was explored. This method proved to be successful at classifying the driver's behavior. It obtained results comparable to the common approach through vehicle parameters. This alternative approach has the advantage of directly classifying driving behavior from the driver, which is of particular use in UGV domain because the operator's information is readily available. The classified driving mode was used tune the controllers' performance to a desired mode of operation. Such qualities are required for a contingency control system that would allow the vehicle to operate with no operator inputs.
ContributorsVargas-Clara, Alvaro (Author) / Redkar, Sangram (Thesis advisor) / McKenna, Anna (Committee member) / Cooke, Nancy J. (Committee member) / Arizona State University (Publisher)
Created2015