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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.


Subject
Date Range
2010 2019


Processed pyro-gel contains castor oil with solid component of boehmite (Al-OOH). The pyro-gel is synthesized by heat to convert boehmite to gamma-Al2O3 and to a certain extent alpha-Al2O3 nano-particles and castor oil into carbon residue. The effect of heat on pyro-gel is analyzed in a series of experiments using two burning chambers with the initial temperature as the main factor. The obtained temperature distribution profiles are studied and it is observed that the gel behaves very close to the theoretical prediction under heat. The carbon residue with Al2O3 is then processed for twelve hours and then analyzed to obtain the …

Contributors
Sagi, Varun Bangar Raju, Lee, Taewoo, Phelan, Patrick, et al.
Created Date
2010

In eukaryotes, DNA is packed in a highly condensed and hierarchically organized structure called chromatin, in which DNA tightly wraps around the histone octamer consisting of one histone 3-histone 4 (H3-H4) tetramer and two histone 2A- histone 2B (H2A-H2B) dimers with 147 base pairs in an almost two left handed turns. Almost all DNA dependent cellular processes, such as DNA duplication, transcription, DNA repair and recombination, take place in the chromatin form. Based on the critical importance of appropriate chromatin condensation, this thesis focused on the folding behavior of the nucleosome array reconstituted using different templates with various controllable factors …

Contributors
Fu, Qiang, Lindsay, Stuart M, Yan, Hao, et al.
Created Date
2010

A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism …

Contributors
Yan, Qin, Francisco, Wilson A, Allen, James, et al.
Created Date
2010

The electrode-electrolyte interface in electrochemical environments involves the understanding of complex processes relevant for all electrochemical applications. Some of these processes include electronic structure, charge storage, charge transfer, solvent dynamics and structure and surface adsorption. In order to engineer electrochemical systems, no matter the function, requires fundamental intuition of all the processes at the interface. The following work presents different systems in which the electrode-electrolyte interface is highly important. The first is a charge storage electrode utilizing percolation theory to develop an electrode architecture producing high capacities. This is followed by Zn deposition in an ionic liquid in which the …

Contributors
Engstrom, Erika Lyn, Friesen, Cody, Buttry, Daniel, et al.
Created Date
2011

The purpose of this study was to analyze the impact of a context-based teaching approach (STS) versus a more traditional textbook approach on the attitudes and achievement of community college chemistry students. In studying attitudes toward chemistry within this study, I used a 30-item Likert scale in order to study the importance of chemistry in students' lives, the importance of chemistry, the difficulty of chemistry, interest in chemistry, and the usefulness of chemistry for their future career. Though the STS approach students had higher attitude post scores, there was no significant difference between the STS and textbook students' attitude post …

Contributors
Perkins, Gita, Baker, Dale R, Sloane, Finbarr, et al.
Created Date
2011

Mechanisms for oxygen reduction are proposed for three distinct cases covering two ionic liquids of fundamentally different archetypes and almost thirty orders of magnitude of proton activity. Proton activity is treated both extrinsically by varying the concentration and intrinsically by selecting proton donors with a wide range of aqueous pKa values. The mechanism of oxygen reduction in ionic liquids is introduced by way of the protic ionic liquid (pIL) triethylammonium triflate (TEATf) which shares some similarities with aqueous acid solutions. Oxygen reduction in TEATf begins as the one electron rate limited step to form superoxide, O2*-, which is then rapidly …

Contributors
Zeller, Robert August, Friesen, Cody, Sieradzki, Karl, et al.
Created Date
2011

A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences …

Contributors
Zhang, Su, Chaut, John C, Ghirlanda, Giovanna, et al.
Created Date
2011

Bioanalytes such as protein, cells, and viruses provide vital information but are inherently challenging to measure with selective and sensitive detection. Gradient separation technologies can provide solutions to these challenges by enabling the selective isolation and pre-concentration of bioanalytes for improved detection and monitoring. Some fundamental aspects of two of these techniques, isoelectric focusing and dielectrophoresis, are examined and novel developments are presented. A reproducible and automatable method for coupling capillary isoelectric focusing (cIEF) and matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) based on syringe pump mobilization is found. Results show high resolution is maintained during mobilization and &beta-lactoglobulin; protein …

Contributors
Weiss, Noah, Hayes, Mark A, Garcia, Antonio, et al.
Created Date
2011

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 …

Contributors
Nangreave, Jeanette Kim, Yan, Hao, Liu, Yan, et al.
Created Date
2011

The work described in the thesis involves the synthesis of a molecular triad which is designed to undergo proton coupled electron transfer (PCET) upon irradiation with light. Photoinduced PCET is an important process that many organisms use and the elucidation of its mechanism will allow further understanding of this process and its potential applications. The target compound designed for PCET studies consists of a porphyrin chromophore (also a primary electron donor), covalently linked to a phenol-imidazole (secondary electron donor), and a C60 (primary electron acceptor). The phenol-imidazole moiety of this system is modeled after the TyrZ His-190 residues in the …

Contributors
Patterson, Dustin Day, Moore, Ana L, Gust, Devens, et al.
Created Date
2011

A new challenge on the horizon is to utilize the large amounts of protein found in the atmosphere to identify different organisms from which the protein originated. Included here is work investigating the presence of identifiable patterns of different proteins collected from the air and biological samples for the purposes of remote identification. Protein patterns were generated using high performance liquid chromatography (HPLC). Patterns created could identify high-traffic and low-traffic indoor spaces. Samples were collected from the air using air pumps to draw air through a filter paper trapping particulates, including large amounts of shed protein matter. In complimentary research …

Contributors
Staton, Sarah J. R., Hayes, Mark A, Hayes, Mark A, et al.
Created Date
2011

The challenging search for clean, reliable and environmentally friendly energy sources has fueled increased research in thermoelectric materials, which are capable of recovering waste heat. Among the state-of-the-art thermoelectric materials β-Zn4Sb3 is outstanding because of its ultra-low glass-like thermal conductivity. Attempts to explore ternary phases in the Zn-Sb-In system resulted in the discovery of the new intermetallic compounds, stable Zn5Sb4In2-δ (δ=0.15) and metastable Zn9Sb6In2. Millimeter-sized crystals were grown from molten metal fluxes, where indium metal was employed as a reactive flux medium.Zn5Sb4In2-δ and Zn9Sb6In2 crystallize in new structure types featuring complex framework and the presence of structural disorder (defects and …

Contributors
Wu, Yang, Haussermann, Ulrich, Seo, Dong, et al.
Created Date
2011

Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to …

Contributors
Gurunathan, Kaushik, Levitus, Marcia, Lindsay, Stuart, et al.
Created Date
2011

This work investigates in-situ stress evolution of interfacial and bulk processes in electrochemical systems, and is divided into two projects. The first project examines the electrocapillarity of clean and CO-covered electrodes. It also investigates surface stress evolution during electro-oxidation of CO at Pt{111}, Ru/Pt{111} and Ru{0001} electrodes. The second project explores the evolution of bulk stress that occurs during intercalation (extraction) of lithium (Li) and formation of a solid electrolyte interphase during electrochemical reduction (oxidation) of Li at graphitic electrodes. Electrocapillarity measurements have shown that hydrogen and hydroxide adsorption are compressive on Pt{111}, Ru/Pt{111}, and Ru{0001}. The adsorption-induced surface stresses …

Contributors
Mickelson, Lawrence L, Friesen, Cody, Sieradzki, Karl, et al.
Created Date
2011

The Santa Gertrudis Mining District of Sonora, Mexico contains more than a dozen purported Carlin-like, sedimentary-hosted, disseminated-gold deposits. A series of near-surface, mostly oxidized gold deposits were open-pit mined from the calcareous and clastic units of the Cretaceous Bisbee Group. Gold occurs as finely disseminated, sub-micron coatings on sulfides, associated with argillization and silicification of calcareous, carbonaceous, and siliciclastic sedimentary rocks in structural settings. Gold occurs with elevated levels of As, Hg, Sb, Pb, and Zn. Downhole drill data within distal disseminated gold zones reveal a 5:1 ratio of Ag:Au and strong correlations of Au to Pb and Zn. This …

Contributors
Geier, John Jeffrey, Reynolds, Stephen J, Burt, Donald, et al.
Created Date
2011

Atmospheric particulate matter has a substantial impact on global climate due to its ability to absorb/scatter solar radiation and act as cloud condensation nuclei (CCN). Yet, little is known about marine aerosol, in particular, the carbonaceous fraction. In the present work, particulate matter was collected, using High Volume (HiVol) samplers, onto quartz fiber substrates during a series of research cruises on the Atlantic Ocean. Samples were collected on board the R/V Endeavor on West–East (March–April, 2006) and East–West (June–July, 2006) transects in the North Atlantic, as well as on the R/V Polarstern during a North–South (October–November, 2005) transect along the …

Contributors
Hill, Hansina Rae, Herckes, Pierre, Westerhoff, Paul, et al.
Created Date
2011

A potential new class of cancer chemotherapeutic agents has been synthesized by varying the 2 position of a benzimidazole based extended amidine. Compounds 6-amino-2-chloromethyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1A) and 6-amino-2-hydroxypropyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1B) were assayed at the National Cancer Institute's (NCI) Developmental Therapeutic Program (DTP) and found to be cytotoxic at sub-micromolar concentrations, and have shown between a 100 and a 1000-fold increase in specificity towards lung, colon, CNS, and melanoma cell lines. These ATP mimics have been found to correlate with sequestosome 1 (SQSTM1), a protein implicated in drug resistance and cell survival in various cancer cell lines. Using the DTP COMPARE algorithm, compounds …

Contributors
Darzi, Evan Rashied, Skibo, Edward, Gould, Ian, et al.
Created Date
2011

Applications of non-traditional stable isotope variations are moving beyond geosciences to biomedicine, made possible by advances in multiple collector inductively coupled plasma mass spectrometry (MC-ICP-MS) technology. Mass-dependent isotope variation can provide information about the sources of elements and the chemical reactions that they undergo. Iron and calcium isotope systematics in biomedicine are relatively unexplored but have great potential scientific interest due to their essential nature in metabolism. Iron, a crucial element in biology, fractionates during biochemically relevant reactions. To test the extent of this fractionation in an important reaction process, equilibrium iron isotope fractionation during organic ligand exchange was determined. …

Contributors
Morgan, Jennifer Lynn Louden, Anbar, Ariel D., Wasylenki, Laura E., et al.
Created Date
2011

Combretastatin A-4 (CA-4) represents one of the most promising antineoplastic and cancer vascular targeting stilbenes that have been isolated from the South African bush willow, Combretum Caffrum Kuntze. In order to further explore the bioactivity of this molecule, a diiodo derivative of CA-4, as well as its phosphate prodrug, was synthesized and analyzed for its biological activity; although only a scale up synthesis of this compound was performed herein for ongoing analysis. In general, no increased specificity was noted for the human cancer cell lines. Antiangiogenic properties were similar to the untreated control. The diiodocombstatin was active against M. luteus, …

Contributors
Trickey-Platt, Brindi, Pettit, George R, Moore, Ana, et al.
Created Date
2011

Natural photosynthesis features a complex biophysical/chemical process that requires sunlight to produce energy rich products. It is one of the most important processes responsible for the appearance and sustainability of life on earth. The first part of the thesis focuses on understanding the mechanisms involved in regulation of light harvesting, which is necessary to balance the absorption and utilization of light energy and in that way reduce the effect caused by photooxidative damage. In photosynthesis, carotenoids are responsible not only for collection of light, but also play a major role in protecting the photosynthetic system. To investigate the role of …

Contributors
Pillai, Smitha Thulasi, Moore, Ana, Moore, Thomas, et al.
Created Date
2011

Cellular redox phenomena are essential for the life of organisms. Described here is a summary of the synthesis of a number of redox-cycling therapeutic agents. The work centers on the synthesis of antitumor antibiotic bleomycin congeners. In addition, the synthesis of pyridinol analogues of alpha-tocopherol is also described. The bleomycins (BLMs) are a group of glycopeptide antibiotics that have been used clinically to treat several types of cancers. The antitumor activity of BLM is thought to be related to its degradation of DNA, and possibly RNA. Previous studies have indicated that the methylvalerate subunit of bleomycin plays an important role …

Contributors
Cai, Xiaoqing, Hecht, Sidney M, Gould, Ian R, et al.
Created Date
2011

Bioparticles comprise a diverse amount of materials ubiquitously present in nature. From proteins to aerosolized biological debris, bioparticles have important roles spanning from regulating cellular functions to possibly influencing global climate. Understanding their structures, functions, and properties provides the necessary tools to expand our fundamental knowledge of biological systems and exploit them for useful applications. In order to contribute to this efforts, the work presented in this dissertation focuses on the study of electrokinetic properties of liposomes and novel applications of bioaerosol analysis. Using immobilized lipid vesicles under the influence of modest (less than 100 V/cm) electric fields, a novel …

Contributors
Castillo Gutierrez, Josemar Andreina, Hayes, Mark A, Herckes, Pierre, et al.
Created Date
2011

Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are …

Contributors
Pal, Suchetan, Liu, Yan, Yan, Hao, et al.
Created Date
2012

As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA …

Contributors
Han, Dongran, Yan, Hao, Liu, Yan, et al.
Created Date
2012

Mitochondria produce most of the ATP needed for the cell as an energy source. It is well known that cellular respiration results in oxidative damage to the cell due to the production of reactive oxygen species (ROS). Mitochondrial dysfunction is believed to contribute to a number of degenerative diseases; because of this the mitochondrial respiratory chain is considered as potential drug target. A few series of idebenone analogues with quinone, pyridinol and pyrimidinol redox cores have been synthesized and evaluated as antioxidants able to protect cellular integrity and, more specifically, mitochondrial function. The compounds exhibited a range of activities. The …

Contributors
Arce Amezquita, Pablo Misael, Hecht, Sidney M, Moore, Ana, et al.
Created Date
2012

Group IV alloy films exhibit the ability to tune both band structure and lattice parameters and have recently attracted attention for their potential applications in Si-photonics and photovoltaics. In this work, several new approaches to produce these alloys directly on Si(100) and Ge(100) wafers are developed. For photovoltaics, use of Ge-buffered Si(100) wafers as a low cost platform for epitaxy of In1-xGaxAs layers was explored. The results indicate that this approach has promise for transitioning from bulk Ge platforms to virtual substrates for a significant cost reduction. The electrical and optical properties of Ge and Ge1-ySny layers produced using several …

Contributors
Beeler, Richard Todd, Kouvetakis, John, Menéndez, José, et al.
Created Date
2012

Complex samples, such as those from biological sources, contain valuable information indicative of the state of human health. These samples, though incredibly valuable, are difficult to analyze. Separation science is often used as the first step when studying these samples. Electrophoretic exclusion is a novel separations technique that differentiates species in bulk solution. Due to its ability to isolate species in bulk solution, it is uniquely suited to array-based separations for complex sample analysis. This work provides proof of principle experimental results and resolving capabilities of the novel technique. Electrophoretic exclusion is demonstrated at a single interface on both benchtop …

Contributors
Kenyon, Stacy Marie, Hayes, Mark A., Ros, Alexandra, et al.
Created Date
2012

Understanding the mechanisms of metalloproteins at the level necessary to engineer new functionalities is complicated by the need to parse the complex overlapping functions played by each amino acid without negatively impacting the host organism. Artificial or designed metallopeptides offer a convenient and simpler platform to explore metal-ligand interactions in an aqueous, biologically relevant coordination context. In this dissertation, the peptide SODA (ACDLPCG), a synthetic derivative of the nickel-binding pocket of nickel superoxide dismutase, is used as a scaffold to construct a variety of novel metallopeptides and explore their reactivity. In Chapter 2, I show that SODA binds Co(II) and …

Contributors
Dutta, Arnab, Jones, Anne K, Moore, Ana L, et al.
Created Date
2012

It has been well established that mitochondria play a critical role in the pathology of Friedreich's Ataxia. This disease is believed to be caused by a deficiency of frataxin, which research suggests is responsible for iron sulfur cluster assembly. This incomplete assembly of iron sulfur clusters is believed to be linked with dysfunctional complexes in the mitochondrial respiratory chain, increased oxidative stress, and potential cell death. Increased understanding of the pathophysiology of this disease has enabled the development of various therapeutic strategies aimed at restoring mitochondrial respiration. This thesis contains an analysis of the biological activity of several classes of …

Contributors
Jaruvangsanti, Jennifer, Hecht, Sidney, Woodbury, Neal, et al.
Created Date
2012

The disordered nature of glass-forming melts results in two features for its dynamics i.e. non-Arrhenius and non-exponential behavior. Their macroscopic properties are studied through observing spatial heterogeneity of the molecular relaxation. Experiments performed in a low-frequency range tracks the flow of energy in time on slow degrees of freedom and transfer to the vibrational heat bath of the liquid, as is the case for microwave heating. High field measurements on supercooled liquids result in generation of fictive temperatures of the absorbing modes which eventually result in elevated true bath temperatures. The absorbed energy allows us to quantify the changes in …

Contributors
Pathak, Ullas, Richert, Ranko, Dai, Lenore, et al.
Created Date
2012

Carbon lacks an extended polyanionic chemistry which appears restricted to carbides with C4-, C22-, and C34- moieties. The most common dimeric anion of carbon atoms is C22- with a triple bond between the two carbon atoms. Compounds containing the dicarbide anion can be regarded as salts of acetylene C2H2 (ethyne) and hence are also called acetylides or ethynides. Inspired by the fact that molecular acetylene undergoes pressure induced polymerization to polyacetylene above 3.5 GPa, it is of particular interest to study the effect of pressure on the crystal structures of acetylides as well. In this work, pressure induced polymerization was …

Contributors
Konar, Sumit, Häussermann, Ulrich, Seo, Dong, et al.
Created Date
2012

Mass spectrometric analysis requires that atoms from the sample be ionized in the gas phase. Secondary ion mass spectrometry achieves this by sputtering samples with an energetic primary ion beam. Several investigations of the sputtering and ionization process have been conducted. Oxygen is commonly used in secondary ion mass spectrometry (SIMS) to increase ion yields, but also can complicate the interpretation of SIMS analyses. An 18O implant in silicon has been used to quantify the oxygen concentration at the surface of sputtered silicon in order to study the dependence on oxygen of several sputtering and depth profile phenomena. The ion …

Contributors
Sobers Jr., Richard Carlisle, Williams, Peter, Hayes, Mark, et al.
Created Date
2012

Nanoporous crystalline oxides with high porosity and large surface areas are promising in catalysis, clean energy technologies and environmental applications all which require efficient chemical reactions at solid-solid, solid-liquid, and/or solid-gas interfaces. Achieving the balance between open porosity and structural stability is an ongoing challenge when synthesizing such porous materials. Increasing porosity while maintaining an open porous network usually comes at the cost of fragility, as seen for example in ultra low density, highly random porous aerogels. It has become increasingly important to develop synthetic techniques that produce materials with these desired properties while utilizing low cost precursors and increasing …

Contributors
Ladd, Danielle Marie, Seo, Don, Haussermann, Ulrich, et al.
Created Date
2012

Nanoporous electrically conducting materials can be prepared with high specific pore volumes and surface areas which make them well-suited for a wide variety of technologies including separation, catalysis and owing to their conductivity, energy related applications like solar cells, batteries and capacitors. General synthetic methods for nanoporous conducting materials that exhibit fine property control as well as facility and efficiency in their implementation continue to be highly sought after. Here, general methods for the synthesis of nanoporous conducting materials and their characterization are presented. Antimony-doped tin oxide (ATO), a transparent conducting oxide (TCO), and nanoporous conducting carbon can be prepared …

Contributors
Volosin, Alex, Seo, Dong-Kyun, Buttry, Daniel, et al.
Created Date
2012

The purpose of this study was to construct an instructional systems design model for chemistry teaching laboratories at the undergraduate level to accurately depict the current practices of design experts. This required identifying the variables considered during design, prioritizing and ordering these variables, and constructing a model. Experts were identified by multiple publications in the Journal of Chemical Education on undergraduate laboratories. Twelve of these individuals participated in three rounds of Delphi surveys. An initial literature review was used to construct the first survey, which established the variables of design. The second and third surveys were constructed based on the …

Contributors
Bunag, Tara Francis, Savenye, Wilhelmina C, Springer, Joseph W, et al.
Created Date
2012

Alkali treated aluminosilicate (geopolymer) was functionalized by surfactant to increase the hydrophobicity for making Pickering emulsion for the first part of this work. In the first part of this study, alkali treated metakaolin was functionalized with cetyltrimethylammonium bromide ((C16H33)N(CH3)3Br, CTAB). The electrostatic interaction between this quaternary ammonium and the surface of the aluminosilicate which has negative charge has taken place. The particles then were used to prepare Pickering emulsion. The resulting stable dispersions, obtained very fast at very simple conditions with low ratio of aluminosilicate to liquid phase. In the second part, the interaction between geopolymer and glycerol was studied …

Contributors
Mesgar, Milad, Seo, Dong-Kuyn, Petuskey, William, et al.
Created Date
2012

Hydrogenases, the enzymes that reversibly convert protons and electrons to hydrogen, are used in all three domains of life. [NiFe]-hydrogenases are considered best suited for biotechnological applications because of their reversible inactivation with oxygen. Phylogenetically, there are four groups of [NiFe]-hydrogenases. The best characterized group, "uptake" hydrogenases, are membrane-bound and catalyze hydrogen oxidation in vivo. In contrast, the group 3 [NiFe]-hydrogenases are heteromultimeric, bifunctional enzymes that fulfill various cellular roles. In this dissertation, protein film electrochemistry (PFE) is used to characterize the catalytic properties of two group 3 [NiFe]-hydrogenases: HoxEFUYH from Synechocystsis sp. PCC 6803 and SHI from Pyrococcus furiosus. …

Contributors
Mcintosh, Chelsea Lee, Jones, Anne K, Ghirlanda, Giovanna, et al.
Created Date
2012

Polydimethyl siloxane is a commonly used fabrication material for microfluidic devices. However, its hydrophobic nature and protein adsorption on the surface restricts its use for microfluidic applications. Also, it is critical to control the electroosmotic flow for electrophoretic and dielectrophoretic manipulations. Therefore, surface modification of PDMS is essential to make it well suited for bioanalytical applications. In this project, the role of polyethylene oxide copolymers F108 and PLL-PEG has been investigated to modify the surface properties of PDMS using physisorption method. Measuring electroosmotic flow and adsorption studies tested the quality and the long-term stability of the modified PDMS surface. Static …

Contributors
Manchanda, Shikha, Ros, Alexandra, Hayes, Mark, et al.
Created Date
2012

With a recent shift to a more environmentally conscious society, low-carbon and non-carbon producing energy production methods are being investigated and applied all over the world. Of these methods, fuel cells show great potential for clean energy production. A fuel cell is an electrochemical energy conversion device which directly converts chemical energy into electrical energy. Proton exchange membrane fuel cells (PEMFCs) are a highly researched energy source for automotive and stationary power applications. In order to produce the power required to meet Department of Energy requirements, platinum (Pt) must be used as a catalyst material in PEMFCs. Platinum, however, is …

Contributors
Adame, Anthony, Madakannan, Arunachalanadar, Peng, Xihong, et al.
Created Date
2012

Low temperature fuel cells are very attractive energy conversion technology for automotive applications due to their qualities of being clean, quiet, efficient and good peak power densities. However, due to high cost and limited durability and reliability, commercialization of this technology has not been possible as yet. The high fuel cell cost is mostly due to the expensive noble catalyst Pt. Alkaline fuel cell (AFC) systems, have potential to make use of non-noble catalysts and thus, provides with a solution of overall lower cost. Therefore, this issue has been addressed in this thesis work. Hydrogen-oxygen fuel cells using an alkaline …

Contributors
Shah, Quratulain Jawed, Madakannan, Arunachalanadar, Tamizhmani, Govindasamy, et al.
Created Date
2012

Most of the sunlight powering natural photosynthesis is absorbed by antenna arrays that transfer, and regulate the delivery of excitation energy to reaction centers in the chloroplast where photosynthesis takes place. Under intense sunlight the plants and certain organisms cannot fully utilize all of the sunlight received by antennas and excess redox species are formed which could potentially harm them. To prevent this, excess energy is dissipated by antennas before it reaches to the reaction centers to initiate electron transfer needed in the next steps of photosynthesis. This phenomenon is called non-photochemical quenching (NPQ). The mechanism of NPQ is not …

Contributors
Bhushan, Kul, Gust, Devens, Moore, Ana, et al.
Created Date
2012

The green fluorescent protein (GFP)-like fluorescent proteins play an important role for the color of reef-building corals. Different colors of extant coral fluorescent proteins (FPs) have evolved from a green ancestral protein. Interestingly, green-to-red photoconversion FPs (Kaede-type Red FPs) are only found in clade D from Scleractinia (Faviina suborder). Therefore, I focus on the evolution of Kaede-type FPs from Faviina suborder ancestral FP. A total of 13 mutations have been identified previously that recapitulate the evolution of Kaede-type red FPs from the ancestral green FP. To examine the effect of each mutation, total ten reconstructed FPs were analyzed and six …

Contributors
Kim, Hanseong, Wachter, Rebekka M, Fromme, Petra, et al.
Created Date
2012

The sun provides Earth with a virtually limitless source of energy capable of sustaining all of humanity's needs. Photosynthetic organisms have exploited this energy for eons. However, efficiently converting solar radiation into a readily available and easily transportable form is complex. New materials with optimized physical, electrochemical, and photophysical properties are at the forefront of organic solar energy conversion research. In the work presented herein, porphyrin and organometallic dyes with widely-varied properties were studied for solar energy applications. In one project, porphyrins and porphyrin-fullerene dyads with aniline-like features were polymerized via electrochemical methods into semiconductive thin films. These were shown …

Contributors
Brennan, Bradley, Gust, Devens, Moore, Thomas A, et al.
Created Date
2012

Studying charge transport through single molecules tethered between two metal electrodes is of fundamental importance in molecular electronics. Over the years, a variety of methods have been developed in attempts of performing such measurements. However, the limitation of these techniques is still one of the factors that prohibit one from gaining a thorough understanding of single molecule junctions. Firstly, the time resolution of experiments is typically limited to milli to microseconds, while molecular dynamics simulations are carried out on the time scale of pico to nanoseconds. A huge gap therefore persists between the theory and the experiments. This thesis demonstrates …

Contributors
Guo, Shaoyin, Tao, Nongjian, Bennett, Peter, et al.
Created Date
2012

The behaviors of various amorphous materials are characterized at high pressures to deduce phase transitions, coordination changes, densification, and other structural or electronic alterations in the system. Alongside, improvements on high pressure techniques are presented to measure equations of state of glassy materials and probe liquids using in-situ high resolution nuclear magnetic resonance (NMR) spectroscopy. 27Al NMR is used to quantify coordination changes in CaAl2O4 glass pressure cycled to 16 GPa. The structure and coordination environments remain unchanged up to 8 GPa at which 93% of the recovered glass exists as 4-fold Al, whereas the remaining population exists as [5,6]Al. …

Contributors
Amin, Samrat Ashokkumar, Yarger, Jeffery L, Wolf, George, et al.
Created Date
2012

Pedagogical content knowledge (PCK) has been described as the knowledge teachers' use in the process of designing and implementing lessons to a particular group of students. This includes the most effective representations that make the content understandable to students, together with the preconceptions and misconceptions that students hold. For chemistry, students have been found to have difficulty with the discipline due to its reliance upon three levels of representation called the triplet: the macro, the submicro, and the symbolic. This study examines eight beginning chemistry teachers' depiction of the chemistry content through the triplet relationship and modifications as a result …

Contributors
Adams, Krista Lynn, Luft, Julie A., Baker, Dale, et al.
Created Date
2012

Hydrogenases catalyze the interconversion of protons, electrons, and hydrogen according to the reaction: 2H+ + 2e- <-> H2 while using only earth abundant metals, namely nickel and iron for catalysis. The enzymatic turnover of Clostridium acetobutylicum [FeFe]-hydrogenase has been investigated through the use of electrochemical and scanning probe techniques. Scanning tunneling microscopy (STM) imaging revealed sub-monolayer surface coverage. Cyclic voltammetry yielded a catalytic, cathodic hydrogen production signal similar to that observed for a platinum electrode. From the direct observation of single enzymes and the macroscopic electrochemical measurements obtained from the same electrode, the apparent turnover frequency (TOF) per single enzyme …

Contributors
Madden, Christopher, Moore, Thomas A, Jones, Anne, et al.
Created Date
2012

In today's world there is a great need for sensing methods as tools to provide critical information to solve today's problems in security applications. Real time detection of trace chemicals, such as explosives, in a complex environment containing various interferents using a portable device that can be reliably deployed in a field has been a difficult challenge. A hybrid nanosensor based on the electrochemical reduction of trinitrotoluene (TNT) and the interaction of the reduction products with conducting polymer nanojunctions in an ionic liquid was fabricated. The sensor simultaneously measures the electrochemical current from the reduction of TNT and the conductance …

Contributors
Diaz Aguilar, Alvaro, Tao, Nongjian, Tsui, Raymond, et al.
Created Date
2012

[FeFe]-hydrogenases are enzymes for the reduction of protons to hydrogen. They rely on only the earth abundant first-row transition metal iron at their active site (H cluster). In recent years, a multitude of diiron mimics of hydrogenases have been synthesized, but none of them catalyzes hydrogen production with the same exquisite combination of high turnover frequency and low activation energy as the enzymes. Generally, model complexes fail to include one or both of two features essential to the natural enzyme: an intricate array of outer coordination sphere contacts that constrain the coordination geometry to attain a catalytically optimal conformation, and …

Contributors
Roy, Souvik, Jones, Anne K, Moore, Thomas, et al.
Created Date
2013

Human breath is a concoction of thousands of compounds having in it a breath-print of physiological processes in the body. Though breath provides a non-invasive and easy to handle biological fluid, its analysis for clinical diagnosis is not very common. Partly the reason for this absence is unavailability of cost effective and convenient tools for such analysis. Scientific literature is full of novel sensor ideas but it is challenging to develop a working device, which are few. These challenges include trace level detection, presence of hundreds of interfering compounds, excessive humidity, different sampling regulations and personal variability. To meet these …

Contributors
Prabhakar, Amlendu, Tao, Nongjian, Forzani, Erica, et al.
Created Date
2013

Developing a system capable of using solar energy to drive the conversion of an abundant and available precursor to fuel would profoundly impact humanity's energy use and thereby the condition of the global ecosystem. Such is the goal of artificial photosynthesis: to convert water to hydrogen using solar radiation as the sole energy input and ideally do so with the use of low cost, abundant materials. Constructing photoelectrochemical cells incorporating photoanodes structurally reminiscent of those used in dye sensitized photovoltaic solar cells presents one approach to establishing an artificial photosynthetic system. The work presented herein describes the production, integration, and …

Contributors
Sherman, Benjamin, Moore, Thomas, Moore, Ana, et al.
Created Date
2013

Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of …

Contributors
Bergkamp, Jesse J, Moore, Ana L, Mariño-Ochoa, Ernesto, et al.
Created Date
2013

The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino …

Contributors
Maini, Rumit, Hecht, Sidney M, Gould, Ian, et al.
Created Date
2013

Chemistry as a subject is difficult to learn and understand, due in part to the specific language used by practitioners in their professional and scientific communications. The language and ways of representing chemical interactions have been grouped into three modes of representation used by chemistry instructors, and ultimately by students in understanding the discipline. The first of these three modes of representation is the symbolic mode, which uses a standard set of rules for chemical nomenclature set out by the IUPAC. The second mode of representation is that of microscopic, which depicts chemical compounds as discrete units made up of …

Contributors
Wood, Lorelei Louise, Baker, Dale, Ganesh, Tirupalavanam, et al.
Created Date
2013

Metal hydride materials have been intensively studied for hydrogen storage applications. In addition to potential hydrogen economy applications, metal hydrides offer a wide variety of other interesting properties. For example, hydrogen-dominant materials, which are hydrides with the highest hydrogen content for a particular metal/semimetal composition, are predicted to display high-temperature superconductivity. On the other side of the spectrum are hydrides with small amounts of hydrogen (0.1 - 1 at.%) that are investigated as viable magnetic, thermoelectric or semiconducting materials. Research of metal hydride materials is generally important to gain fundamental understanding of metal-hydrogen interactions in materials. Hydrogenation of Zintl phases, …

Contributors
Puhakainen, Kati, Häussermann, Ulrich, Seo, Dong, et al.
Created Date
2013

This work demonstrated a novel microfluidic device based on direct current (DC) insulator based dielectrophoresis (iDEP) for trapping individual mammalian cells in a microfluidic device. The novel device is also applicable for selective trapping of weakly metastatic mammalian breast cancer cells (MCF-7) from mixtures with mammalian Peripheral Blood Mononuclear Cells (PBMC) and highly metastatic mammalian breast cancer cells, MDA-MB-231. The advantage of this approach is the ease of integration of iDEP structures in microfliudic channels using soft lithography, the use of DC electric fields, the addressability of the single cell traps for downstream analysis and the straightforward multiplexing for single …

Contributors
Bhattacharya, Sanchari, Ros, Alexandra, Ros, Alexandra, et al.
Created Date
2013

Thiol functionalization is one potentially useful way to tailor physical and chemical properties of graphene oxides (GOs) and reduced graphene oxides (RGOs). Despite the ubiquitous presence of thiol functional groups in diverse chemical systems, efficient thiol functionalization has been challenging for GOs and RGOs, or for carbonaceous materials in general. In this work, thionation of GOs has been achieved in high yield through two new methods that also allow concomitant chemical reduction/thermal reduction of GOs; a solid-gas metathetical reaction method with boron sulfides (BxSy) gases and a solvothermal reaction method employing phosphorus decasulfide (P4S10). The thionation products, called "mercapto reduced …

Contributors
Jeon, Kiwan, Seo, Dong-Kyun, Jones, Anne K, et al.
Created Date
2013

The bleomycins are a family of glycopeptide-derived antibiotics isolated from various Streptomyces species and have been the subject of much attention from the scientific community as a consequence of their antitumor activity. Bleomycin clinically and is an integral part of a number of combination chemotherapy regimens. It has previously been shown that bleomycin has the ability to selectively target tumor cells over their non-malignant counterparts. Pyrimidoblamic acid, the N-terminal metal ion binding domain of bleomycin is known to be the moiety that is responsible for O2 activation and the subsequent chemistry leading to DNA strand scission and overall antitumor activity. …

Contributors
Bozeman, Trevor, Hecht, Sidney M, Chaput, John, et al.
Created Date
2013

Water-soluble, adenosine triphosphate (ATP)-stabilized palladium nanoparticles have been synthesized by reduction of palladium salt in the presence of excess ATP. They have been characterized by electron microscopy, energy dispersive X-ray spectroscopy, ultraviolet-visible (UV-Vis) spectroscopy, and X-ray diffraction in order to determine particle size, shape, composition and crystal structure. The particles were then subsequently attached to a glassy carbon electrode (GCE) in order to explore their electrochemical properties with regard to hydrogen insertion in 1 M sodium hydroxide. The particles were found to be in the size range 2.5 to 4 nm with good size dispersion. The ATP capping ligand allowed …

Contributors
Lamb, Timothy, Buttry, Daniel A, Yarger, Jeffery, et al.
Created Date
2013

This thesis describes the fabrication of several new classes of Ge1-x-ySixSny materials with the required compositions and crystal quality to engineer the band gaps above and below that of elemental Ge (0.8 eV) in the near IR. The work initially focused on Ge1-x-ySixSny (1-5% Sn, 4-20% Si) materials grown on Ge(100) via gas-source epitaxy of Ge4H10, Si4H10 and SnD4. Both intrinsic and doped layers were produced with defect-free microstructure and viable thickness, allowing the fabrication of high-performance photodetectors. These exhibited low ideality factors, state-of-the-art dark current densities and adjustable absorption edges between 0.87 and 1.03 eV, indicating that the band …

Contributors
Xu, Chi, Kouvetakis, John, Menendez, Jose, et al.
Created Date
2013

Black carbon (BC) is the product of incomplete combustion of biomass and fossil fuels. It is found ubiquitously in nature and is relevant to studies in atmospheric science, soil science, oceanography, and anthropology. Black carbon is best described using a combustion continuum that sub-classifies BC into slightly charred biomass, char, charcoal and soot. These sub-classifications range in particle size, formation temperature, and relative reactivity. Interest in BC has increased because of its role in the long-term storage of organic matter and the biogeochemistry of urban areas. The global BC budget is unbalanced. Production of BC greatly outweighs decomposition of BC. …

Contributors
Hamilton, George A., Hartnett, Hilairy E, Herckes, Pierre, et al.
Created Date
2013

Natural photosynthesis dedicates specific proteins to achieve the modular division of the essential roles of solar energy harvesting, charge separation and carrier transport within natural photosynthesis. The modern understanding of the fundamental photochemistry by which natural photosynthesis operates is well advanced and solution state mimics of the key photochemical processes have been reported previously. All of the early events in natural photosynthesis responsible for the conversion of solar energy to electric potential energy occur within proteins and phospholipid membranes that act as scaffolds for arranging the active chromophores. Accordingly, for creating artificial photovoltaic (PV) systems, scaffolds are required to imbue …

Contributors
Watson, Brian Lyndon, Gust, Devens, Gould, Ian, et al.
Created Date
2013

The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated …

Contributors
Nangreave, Ryan Christopher, Hecht, Sidney M, Yan, Hao, et al.
Created Date
2013

ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips respectively. In this work, peptide microarray fabrication based on the abovementioned techniques were optimized. In addition, MALDI mass spectrometry based peptide synthesis characterization on semiconductor microchips was developed and novel applications of a CombiMatrix (CBMX) platform for electrochemically controlled synthesis were explored. We have investigated performance of 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) derivatives as photo-labile protecting group. Specifically, influence of substituents on 4 …

Contributors
Kumar, Pallav, Woodbury, Neal, Allen, James, et al.
Created Date
2013

This thesis studies three different types of anhydrous proton conducting electrolytes for use in fuel cells. The proton energy level scheme is used to make the first electrolyte which is a rubbery polymer in which the conductivity reaches values typical of activated Nafion, even though it is completely anhydrous. The protons are introduced into a cross-linked polyphospazene rubber by the superacid HOTf, which is absorbed by partial protonation of the backbone nitrogens. The decoupling of conductivity from segmental relaxation times assessed by comparison with conductivity relaxation times amounts to some 10 orders of magnitude, but it cannot be concluded whether …

Contributors
Ansari, Younes, Angell, Charles A, Richert, Ranko, et al.
Created Date
2013

The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk Ge, dominated by indirect gap emission, and the PL spectrum of Ge-on-Si films, dominated by direct gap emission. It was found that the difference is due to the supression of self-absorption effects in Ge films, combined with a deviation from quasi-equilibrium conditions in the conduction band of undoped films. The latter is confirmed by a model suggesting that the deviation …

Contributors
Grzybowski, Gordon J., Kouvetakis, John, Chizmeshya, Andrew, et al.
Created Date
2013

The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional …

Contributors
Zhao, Zhao, Yan, Hao, Liu, Yan, et al.
Created Date
2013

ABSTRACT Manipulation of biological targets using synthetic or naturally occurring organic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that are targeted either to cell surface receptors, to the ribosomal catalytic center or to human immunodeficiency virus reverse transcriptase. Bleomycins (BLMs) are a family of naturally occurring glycopeptidic antitumor agents with an inherent selectivity towards cancer cells. DeglycoBLM, which lacks the sugar moiety of bleomycin, has much lower cytotoxicity in cellular assays. A recent study using microbbuble conjugates of BLM and deglycoBLM showed that BLM was able …

Contributors
Paul, Rakesh, Hecht, Sidney M, Moore, Ana L, et al.
Created Date
2013

Healthy mitochondria are essential for cell survival. Described herein is the synthesis of a family of novel aminoquinone antioxidants designed to alleviate oxidative stress and prevent the impairment of cellular function. In addition, a library of bleomycin disaccharide analogues has also been synthesized to better probe the tumor targeting properties of bleomycin. The first study involves the synthesis of a benzoquinone natural product and analogues that closely resemble the redox core of the natural product geldanamycin. The synthesized 5-amino-3-tridecyl-1,4-benzoquinone antioxidants were tested for their ability to protect Friedreich's ataxia (FRDA) lymphocytes from induced oxidative stress. Some of the analogues synthesized …

Contributors
Mathilakathu Madathil, Manikandadas, Hecht, Sidney M, Rose, Seth, et al.
Created Date
2013

Small molecules have proven to be very important tools for exploration of biological systems including diagnosis and treatment of lethal diseases like cancer. Fluorescent probes have been extensively used to further amplify the utilization of small molecules. The manipulation of naturally occurring biological targets with the help of synthetic compounds is the focus of the work described in this thesis. Bleomycins (BLMs) are a class of water soluble, glycopeptide-derived antitumor antibiotics consisting of a structurally complicated unnatural hexapeptide and a disaccharide, clinically used as an anticancer chemotherapeutic agent at an exceptionally low therapeutic dose. The efficiency of BLM is likely …

Contributors
Bhattacharya, Chandrabali, Hecht, Sidney M, Moore, Ana, et al.
Created Date
2014

Americans spend upwards of 90% of their time indoors, hence indoor air quality (IAQ) and the impact of IAQ on human health is a major public health concern. IAQ can be negatively impacted by outdoor pollution infiltrating indoors, the emission of indoor pollutants, indoor atmospheric chemistry and poor ventilation. Energy saving measures like retrofits to seal the building envelope to prevent the leakage of heated or cooled air will impact IAQ. However, existing studies have been inconclusive as to whether increased energy efficiency is leading to detrimental IAQ. In this work, field campaigns were conducted in apartment homes in Phoenix, …

Contributors
Frey, Sarah Elizabeth, Herckes, Pierre, Fraser, Matthew P, et al.
Created Date
2014

Photosystem I (PSI) is a multi-subunit, pigment-protein complex that catalyzes light-driven electron transfer (ET) in its bi-branched reaction center (RC). Recently it was suggested that the initial charge separation (CS) event can take place independently within each ec2/ec3 chlorophyll pair. In order to improve our understanding of this phenomenon, we have generated new mutations in the PsaA and PsaB subunits near the electron transfer cofactor 2 (ec2 chlorophyll). PsaA-Asn604 accepts a hydrogen bond from the water molecule that is the axial ligand of ec2B and the case is similar for PsaB-Asn591 and ec2A. The second set of targeted sites was …

Contributors
BADSHAH, SYED LAL, REDDING, KEVIN E, FROMME, PETRA, et al.
Created Date
2014

Carbonaceous chondrites (CCs) present a unique opportunity for learning about the earliest organic chemistry that took place in our Solar System. The complex and diverse suite of meteoritic organic material is the result of multiple settings and physicochemical processes, including aqueous and thermal alteration. Though meteorites often inform origin-of-life discussions because they could have seeded early Earth with significant amounts of water and pre-biotic, organic material, their record of abiotic, aqueous, and organic geochemistry is of interest as well. CC materials previously resided on asteroidal parent bodies, relic planetesimals of Solar System formation which never accreted enough material to develop …

Contributors
Monroe, Adam Alexander, Pizzarello, Sandra, Williams, Peter, et al.
Created Date
2014

Chloroform (CHCl3) is an important atmospheric pollutant by its direct health effects as well as by its contribution to photochemical smog formation. Chloroform outgassing from swimming pools is not typically considered a source of atmospheric CHCl3 because swimming pools are scarce compared to other sources. However, large urban areas in hot climates such as Phoenix, AZ contain a substantial amount of swimming pools, potentially resulting in significant atmospheric fluxes. In this study, CHCl3 formation potential (FP) from disinfection of swimming pools in Phoenix was investigated through laboratory experiments and annual CHCl3 emission fluxes from swimming pools were estimated based on …

Contributors
Rose, Christy Joyce, Herckes, Pierre, Fraser, Matthew, et al.
Created Date
2014

The AAA+ ATPase Rubisco activase (Rca) regulates the activity of Rubisco, the photosynthetic enzyme responsible for catalyzing biological carbon fixation. However, the detailed mechanism by which Rca self-association controls Rubisco reactivation activity remains poorly understood. In this work, we are using fluorescence correlation spectroscopy (FCS) to better characterize the thermodynamics of the assembly process of cotton Rca. We present FCS data for Rca in the presence of Mg*ATPgS and Mg*ADP and for the D173N Walker B motif mutant in the presence of Mg*ATP. Our data are consistent with promotion and stabilization of hexamers by Mg*ATPgS and Mg*ATP, whereas Mg*ADP facilitates …

Contributors
Kuriata, Agnieszka Magdalena, Wachter, Rebekka, Redding, Kevin, et al.
Created Date
2014

Scientists around the world have been striving to develop artificial light-harvesting antenna model systems for energy and other light-driven biochemical applications. Among the various approaches to achieve this goal, one of the most promising is the assembly of structurally well-defined artificial light-harvesting antennas based on the principles of structural DNA nanotechnology. DNA has recently emerged as an extremely efficient material to organize molecules such as fluorophores and proteins on the nanoscale. It is desirable to develop a hybrid smart material by combining artificial antenna systems based on DNA with natural reaction center components, so that the material can be engineered …

Contributors
Dutta, Palash Kanti, Liu, Yan, Yan, Hao, et al.
Created Date
2014

A vast amount of energy emanates from the sun, and at the distance of Earth, approximately 172,500 TW reaches the atmosphere. Of that, 80,600 TW reaches the surface with 15,600 TW falling on land. Photosynthesis converts 156 TW in the form of biomass, which represents all food/fuel for the biosphere with about 20 TW of the total product used by humans. Additionally, our society uses approximately 20 more TW of energy from ancient photosynthetic products i.e. fossil fuels. In order to mitigate climate problems, the carbon dioxide must be removed from the human energy usage by replacement or recycling as …

Contributors
Vaughn, Michael David, Moore, Thomas, Fromme, Petra, et al.
Created Date
2014

Monitoring of air pollutants is critical for many applications and studies. In order to access air pollutants with high spatial and temporal resolutions, it is necessary to develop an affordable, small size and weight, low power, high sensitivity and selectivity, and wireless enable device that can provide real time monitoring of air pollutants. Three different kind of such devices are presented, they are targeting environmental pollutants such as volatile organic components (VOCs), nitrogen dioxide (NO2) and ozone. These devices employ innovative detection methods, such as quartz crystal tuning fork coated with molecularly imprinted polymer and chemical reaction induced color change …

Contributors
Chen, Cheng, Tao, Nongjian, Kiaei, Sayfe, et al.
Created Date
2014

The utilization of solar energy requires an efficient means of its storage as fuel. In bio-inspired artificial photosynthesis, light energy can be used to drive water oxidation, but catalysts that produce molecular oxygen from water are required. This dissertation demonstrates a novel complex utilizing earth-abundant Ni in combination with glycine as an efficient catalyst with a modest overpotential of 0.475 ± 0.005 V for a current density of 1 mA/cm<super>2</super> at pH 11. The production of molecular oxygen at a high potential was verified by measurement of the change in oxygen concentration, yielding a Faradaic efficiency of 60 ± 5%. …

Contributors
Wang, Dong, Allen, James P, Ghirlanda, Giovanna, et al.
Created Date
2014

The first chapter reviews three decades of artificial photosynthetic research conducted by the A. Moore, T. Moore, and D. Gust research group. Several carotenoid (Car) and tetrapyrrole containing molecules were synthesized and investigated for excitation energy transfer (EET), photoregulation, and photoprotective functions. These artificial photosynthetic compounds mimicked known processes and investigated proposed mechanisms in natural systems. This research leads to a greater understanding of photosynthesis and design concepts for organic based solar energy conversion devices. The second and third chapters analyze the triplet energy transfer in carotenoid containing dyads. Transient absorption, time-resolved FTIR and resonance Raman spectra revealed that in …

Contributors
Wongcarter, Katherine, Moore, Ana L, Gust, Devens, et al.
Created Date
2014

Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal of the tightly bound sugar phosphates from the active sites of RuBisCO. In this work, we investigated the ATP/ADP dependent oligomerization equilibrium of fluorescently tagged Rca for a wide range of concentrations using fluorescence correlation spectroscopy. Results show that in the presence of ADP-Mg2+, the oligomerization state of Rca gradually …

Contributors
Chakraborty, Manas, Levitus, Marcia, Angell, Charles, et al.
Created Date
2014

Natural hydrogenases catalyze the reduction of protons to molecular hydrogen reversibly under mild conditions; these enzymes have an unusual active site architecture, in which a diiron site is connected to a cubane type [4Fe-4S] cluster. Due to the relevance of this reaction to energy production, and in particular to sustainable fuel production, there have been substantial amount of research focused on developing biomimetic organometallic models. However, most of these organometallic complexes cannot revisit the structural and functional fine-tuning provided by the protein matrix as seen in the natural enzyme. The goal of this thesis is to build a protein based …

Contributors
Roy, Anindya, Ghirlanda, Giovanna, Yan, Hao, et al.
Created Date
2014

Colloidal quantum dots (QDs) or semiconductor nanocrystals are often used to describe 2 to 20 nm solution processed nanoparticles of various semiconductor materials that display quantum confinement effects. Compared to traditional fluorescent organic dyes, QDs provide many advantages. For biological applications it is necessary to develop reliable methods to functionalize QDs with hydrophilic biomolecules so that they may maintain their stability and functionality in physiological conditions. DNA, a molecule that encodes genetic information, is arguably the smartest molecule that nature has ever produced and one of the most explored bio-macromolecules. DNA directed self-assembly can potentially organize QDs that are functionalized …

Contributors
Samanta, Anirban, Yan, Hao, Liu, Yan, et al.
Created Date
2014

Arsenic (As) and chromium (Cr) occur naturally in AZ surface and groundwaters, pose different health impacts, and exhibit different treatment efficacies. Hexavalent chromium (Cr(VI)) has newly recognized human health concerns, and State and Federal agencies are evaluating a low Cr(VI)-specific maximum contaminant level (MCL) for drinking water. Occurrence of Cr and As in municipal drinking waters and industrial cooling tower waters was quantified by grab samples and compared with sampling results obtained from a new passive sampler developed specifically for Cr(VI). Cr(VI) and As concentrations in groundwater used for cooling tower make-up water concentrations were ~3 ppb and ~4 ppb, …

Contributors
Bowen, Alexandra Brynn, Paul, Westerhoff K., Hristovski, Kiril, et al.
Created Date
2014

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 …

Contributors
Wei, Xixi, Liu, Yan, Yan, Hao, et al.
Created Date
2014

Solar energy is a promising alternative for addressing the world's current and future energy requirements in a sustainable way. Because solar irradiation is intermittent, it is necessary to store this energy in the form of a fuel so it can be used when required. The light-driven splitting of water into oxygen and hydrogen (a useful chemical fuel) is a fascinating theoretical and experimental challenge that is worth pursuing because the advance of the knowledge that it implies and the availability of water and sunlight. Inspired by natural photosynthesis and building on previous work from our laboratory, this dissertation focuses on …

Contributors
Mendez-Hernandez, Dalvin D., Moore, Ana L, Mujica, Vladimiro, et al.
Created Date
2014

Rapid and reliable separation and analysis of proteins require powerful analytical methods. The analysis of proteins becomes especially challenging when only small sample volumes are available, concomitantly with low concentrations of proteins. Time critical situations pose additional challenges. Due to these challenges, conventional macro-scale separation techniques reach their limitations. While microfluidic devices require only pL-nL sample volumes, they offer several advantages such as speed, efficiency, and high throughput. This work elucidates the capability to manipulate proteins in a rapid and reliable manner with a novel migration technique, namely dielectrophoresis (DEP). Since protein analysis can often be achieved through a combination …

Contributors
Nakano, Asuka, Ros, Alexandra, Hayes, Mark, et al.
Created Date
2014

A clean and sustainable alternative to fossil fuels is solar energy. For efficient use of solar energy to be realized, artificial systems that can effectively capture and convert sunlight into a usable form of energy have to be developed. In natural photosynthesis, antenna chlorophylls and carotenoids capture sunlight and transfer the resulting excitation energy to the photosynthetic reaction center (PRC). Small reorganization energy, &#955; and well-balanced electronic coupling between donors and acceptors in the PRC favor formation of a highly efficient charge-separated (CS) state. By covalently linking electron/energy donors to acceptors, organic molecular dyads and triads that mimic natural photosynthesis …

Contributors
Arero, Jaro, Gust, Devens, Moore, Ana, et al.
Created Date
2014

DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on …

Contributors
Li, Wei, Yan, Hao, Liu, Yan, et al.
Created Date
2014

Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified across all gold:silver ratios by a linear shift in the plasmon band maxima against alloy composition. The molar absorptivities of the NPs decreased non-linearly with increasing gold content from 2.0 x 108 M-1 cm-1 (fÉmax = 404 nm) for pure silver to 4.1 x 107 M-1 cm-1 (fÉmax = 511 …

Contributors
Starr, Christopher Allen, Buttry, Daniel A, Petuskey, William, et al.
Created Date
2014

We studied the relationship between the polarizability and the molecular conductance that arises in the response of a molecule to an external electric field. To illustrate the plausibility of the idea, we used Simmons' tunneling model, which describes image charge and dielectric effects on electron transport through a barrier. In such a model, the barrier height depends on the dielectric constant of the electrode-molecule-electrode junction, which in turn can be approximately expressed in terms of the molecular polarizability via the classical Clausius-Mossotti relation. In addition to using the tunneling model, the validity of the relationships between the molecular polarizability and …

Contributors
Vatan Meidanshahi, Reza, Mujica, Vladimiro, Chizmeshya, Andrew, et al.
Created Date
2014

Mitochondria are crucial intracellular organelles which play a pivotal role in providing energy to living organisms in the form of adenosine triphosphate (ATP). The mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation (OX-PHOS) transforms the chemical energy of amino acids, fatty acids and sugars to ATP. The mitochondrial electron transport system consumes nearly 90% of the oxygen used by the cell. Reactive oxygen species (ROS) in the form of superoxide anions (O2*-) are generated as byproduct of cellular metabolism due to leakage of electrons from complex I and complex III to oxygen. Under normal conditions, the effects of ROS …

Contributors
Alam, Mohammad Parvez, Hecht, Sidney M, Gould, Ian R, et al.
Created Date
2014

The transmembrane subunit (gp41) of the envelope glycoprotein of HIV-1 associates noncovalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR, residues 649-683) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain (residues 684-705) of gp41 not only anchors the envelope glycoprotein complex in the viral membrane but also dynamically affects the interactions of the MPR with the membrane. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the …

Contributors
Gong, Zhen, Fromme, Petra, Mor, Tsafrir, et al.
Created Date
2014

The communication of genetic material with biomolecules has been a major interest in cancer biology research for decades. Among its different levels of involvement, DNA is known to be a target of several antitumor agents. Additionally, tissue specific interaction between macromolecules such as proteins and structurally important regions of DNA has been reported to define the onset of certain types of cancers. Illustrated in Chapter 1 is the general history of research on the interaction of DNA and anticancer drugs, most importantly different congener of bleomycin (BLM). Additionally, several synthetic analogues of bleomycin, including the structural components and functionalities, are …

Contributors
Roy, Basab, Hecht, Sidney M, Jones, Anne, et al.
Created Date
2014

Redox reactions are crucial to energy transduction in biology. Protein film electrochemistry (PFE) is a technique for studying redox proteins in which the protein is immobilized at an electrode surface so as to allow direct exchange of electrons. Establishing a direct electronic connection eliminates the need for redox­active mediators, thus allowing for interrogation of the redox protein of interest. PFE has proven a versatile tool that has been used to elucidate the properties of many technologically relevant redox proteins including hydrogenases, laccases, and glucose oxidase. This dissertation is comprised of two parts: extension of PFE to a novel electrode material …

Contributors
Kwan, Patrick, Jones, Anne K, Francisco, Wilson, et al.
Created Date
2014

This thesis develops molecular models for electron transport in molecular junctions and intra-molecular electron transfer. The goal is to identify molecular descriptors that afford a substantial simplification of these electronic processes. First, the connection between static molecular polarizability and the molecular conductance is examined. A correlation emerges whereby the measured conductance of a tunneling junction decreases as a function of the calculated molecular polarizability for several systems, a result consistent with the idea of a molecule as a polarizable dielectric. A model based on a macroscopic extension of the Clausius-Mossotti equation to the molecular domain and Simmon’s tunneling model is …

Contributors
Khezr Seddigh Mazinani, Shobeir, Mujica, Vladimiro, Pilarisetty, Tarakeshwar, et al.
Created Date
2015

Humanity’s demand for energy is increasing exponentially and the dependence on fossil fuels is both unsustainable and detrimental to the environment. To provide a solution to the impending energy crisis, it is reasonable to look toward utilizing solar energy, which is abundant and renewable. One approach to harvesting solar irradiation for fuel purposes is through mimicking the processes of natural photosynthesis in an artificial design to use sunlight and water to store energy in chemical bonds for later use. Thus, in order to design an efficient energy conversion device, the underlying processes of the natural system must be understood. An …

Contributors
Brown, Chelsea Lynn, Moore, Ana L, Gust, Devens, et al.
Created Date
2015

Efficient separation techniques for organelles and bacteria in the micron- and sub-micron range are required for various analytical challenges. Mitochondria have a wide size range resulting from the sub-populations, some of which may be associated with diseases or aging. However, traditional methods can often not resolve within-species size variations. Strategies to separate mitochondrial sub-populations by size are thus needed to study the importance of this organelle in cellular functions. Additionally, challenges also exist in distinguishing the sub-populations of bio-species which differ in the surface charge while possessing similar size, such as Salmonella typhimurium (Salmonella). The surface charge of Salmonella wild-type …

Contributors
Luo, Jinghui, Ros, Alexandra, Hayes, Mark, et al.
Created Date
2015

Photovoltaic (PV) module degradation is a well-known issue, however understanding the mechanistic pathways in which modules degrade is still a major task for the PV industry. In order to study the mechanisms responsible for PV module degradation, the effects of these degradation mechanisms must be quantitatively measured to determine the severity of each degradation mode. In this thesis multiple modules from three climate zones (Arizona, California and Colorado) were investigated for a single module glass/polymer construction (Siemens M55) to determine the degree to which they had degraded, and the main factors that contributed to that degradation. To explain the loss …

Contributors
Chicca, Matthew, Tamizhmani, Govindasamy, Rogers, Bradley, et al.
Created Date
2015

Massive glycerol cluster ions with many charges (~ 106 Da, ~ ±100 charges) have been generated by electrospray to bombard biomolecules and biological sample surfaces. The low impact energy per nucleon facilitates intact sputtering and ionization of biomolecules which can be subsequently imaged. Various lipids, peptides and proteins have been studied. The primary cluster ion source has been coupled with an ion-microscope imaging mass spectrometer (TRIFT-1, Physical Electronics). A lateral resolution of ~3µm has been demonstrated, which is acceptable for sub-cellular imaging of animal cells (e.g. single cancer cell imaging in early diagnosis). Since the available amount of target molecules …

Contributors
Zhang, Jitao, Williams, Peter, Hayes, Mark, et al.
Created Date
2015