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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.


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  • English
Subject
Date Range
2010 2019


Plastic crystals as a class are of much interest in applications as solid state electrolytes for electrochemical energy conversion devices. A subclass exhibit very high protonic conductivity and its members have been investigated as possible fuel cell electrolytes, as first demonstrated by Haile’s group in 2001 with CsHSO4. To date these have been inorganic compounds with tetrahedral oxyanions carrying one or more protons, charge-balanced by large alkali cations. Above the rotator phase transition, the HXO4- anions re-orient at a rate dependent on temperature while the centers of mass remain ordered. The transition is accompanied by a conductivity "jump" (as much …

Contributors
Klein, Iolanda Santana, Angell, Charles A, Buttry, Daniel A, et al.
Created Date
2016

This work describes the development of a device for measuring CO2 in breath, which has applications in monitoring a variety of health issues, such as Chronic Obstructive Pulmonary Disease (COPD), asthma, and cardiovascular disease. The device takes advantage of colorimetric sensing technology in order to maintain a low cost and high user-friendliness. The sensor consists of a pH dye, reactive element, and base coated on a highly porous Teflon membrane. The transmittance of the sensor is measured in the device via a simple LED/photodiode system, along with the flow rate, ambient relative humidity, and barometric pressure. The flow is measured …

Contributors
Bridgeman, Devon, Forzani, Erica S, Nikkhah, Mehdi, et al.
Created Date
2017

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

In this thesis, a breadboard Integrated Microarray Printing and Detection System (IMPDS) was proposed to address key limitations of traditional microarrays. IMPDS integrated two core components of a high-resolution surface plasmon resonance imaging (SPRi) system and a piezoelectric dispensing system that can print ultra-low volume droplets. To avoid evaporation of droplets in the microarray, a 100 μm thick oil layer (dodecane) was used to cover the chip surface. The interaction between BSA (Bovine serum albumin) and Anti-BSA was used to evaluate the capability of IMPDS. The alignment variability of printing, stability of droplets array and quantification of protein-protein interactions based …

Contributors
Xiao, Feng, Tao, Nongjian, Borges, Chad, et al.
Created Date
2017

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

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

The ability to manipulate the interaction between small molecules and biological macromolecules towards the study of disease pathogenesis has become a very important part of research towards treatment options for various diseases. The work described here shows both the use of DNA oligonucleotides as carriers for a nicotine hapten small molecule, and the use of microsomes to study the stability of compounds derived to treat mitochondrial diseases. Nicotine addiction is a worldwide epidemic because nicotine is one of the most widely used addictive substances. It is linked to early death, typically in the form of heart or lung disease. A …

Contributors
Schmierer, Margaret Louise, Hecht, Sidney M, Allen, James, et al.
Created Date
2016

Dielectrophoresis (DEP) is a technique that influences the motion of polarizable particles in an electric field gradient. DEP can be combined with other effects that influence the motion of a particle in a microchannel, such as electrophoresis and electroosmosis. Together, these three can be used to probe properties of an analyte, including charge, conductivity, and zeta potential. DEP shows promise as a high-resolution differentiation and separation method, with the ability to distinguish between subtly-different populations. This, combined with the fast (on the order of minutes) analysis times offered by the technique, lend it many of the features necessary to be …

Contributors
Hilton, Shannon, Hayes, Mark A, Borges, Chad, et al.
Created Date
2019

The field of Ionic Liquid (IL) research has received considerable attention during the past decade. Unique physicochemical properties of these low melting salts have made them very promising for applications in a many areas of science and technology such as electrolyte research, green chemistry and electrodeposition. One of the most important parameters dictating their physicochemical behavior is the basicity of their anion. Using four sets of Protic Ionic Liquids (PILs) and spectroscopic characterization of them, a qualitative order for anion basicity of ILs is obtained. Protic Ionic Liquids are made by proton transfer form a Brønsted acid to a base. …

Contributors
Hasani, Mohammad, Angell, C. Austen, Yarger, Jeffrey L, et al.
Created Date
2016

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

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

Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications. Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to …

Contributors
Manna, Saikat, Lindsay, Stuart, Zhang, Peiming, et al.
Created Date
2016

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

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

[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

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

This work demonstrates a capable reverse pulse deposition methodology to influence gap fill behavior inside microvia along with a uniform deposit in the fine line patterned regions for substrate packaging applications. Interconnect circuitry in IC substrate packages comprises of stacked microvia that varies in depth from 20µm to 100µm with an aspect ratio of 0.5 to 1.5 and fine line patterns defined by photolithography. Photolithography defined pattern regions incorporate a wide variety of feature sizes including large circular pad structures with diameter of 20µm - 200µm, fine traces with varying widths of 3µm - 30µm and additional planar regions to …

Contributors
Ganesan, Kousik, Tasooji, Amaneh, Manepalli, Rahul, et al.
Created Date
2018

The US National Academy of Sciences and The Royal Society have recently released a detailed report on the causes and effects of global climate change.1 This report states that the Earth’s climate is rapidly changing due to human activity. Specifically, the burning of fossil fuels to satisfy the energy demands of rising global population has resulted in unprecedented levels of greenhouse gasses in the atmosphere. These high levels of greenhouse gasses are serving to warm the surface of the planet resulting in extreme weather events. Thus, controlling the atmospheric CO2 level is motivating a great deal of scientific research in …

Contributors
Rheinhardt, Joseph, Buttry, Daniel A., Angell, Charles A., et al.
Created Date
2018

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

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 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 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

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

Optoelectronic and microelectronic applications of germanium-based materials have received considerable research interest in recent years. A novel method for Ge on Si heteroepitaxy required for such applications was developed via molecular epitaxy of Ge5H12. Next, As(GeH3)3, As(SiH3)3, SbD3, S(GeH3)2 and S(SiH3)2 molecular sources were utilized in degenerate n-type doping of Ge. The epitaxial Ge films produced in this work incorporate donor atoms at concentrations above the thermodynamic equilibrium limits. The donors are nearly fully activated, and led to films with lowest resistivity values thus far reported. Band engineering of Ge was achieved by alloying with Sn. Epitaxy of the alloy …

Contributors
Senaratne, Charutha Lasitha, Kouvetakis, John, Chizmeshya, Andrew, et al.
Created Date
2016

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 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

In the past, the photovoltaic (PV) modules were typically constructed with glass superstrate containing cerium oxide and EVA (ethylene vinyl acetate) encapsulant containing UV absorbing additives. However, in the current industry, the PV modules are generally constructed without cerium oxide in the glass and UV absorbing additives in EVA to increase quantum efficiency of crystalline silicon solar cells in the UV regions. This new approach is expected to boost the initial power output of the modules and reduce the long-term encapsulant browning issues. However, this new approach could lead to other durability and reliability issues such as delamination of encapsulant …

Contributors
Arularasu, Pooja, Tamizhmani, Govindasamy, Mu, Bin, et al.
Created Date
2019

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

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

DNA and RNA are generally regarded as one of the central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology witnessed the success of usage of DNA/RNA as programmable molecules to construct nano-objects with predefined shapes and dynamic molecular machines for various functions. From the perspective of structural design with nucleic acid, there are basically two types of assembly method, DNA tile based assembly and DNA origami based assembly, used to construct infinite-sized crystal structures and finite-sized molecular structures. The assembled structure can be used for arrangement of other molecules or nanoparticles with the resolution of nanometers …

Contributors
Hong, Fan, Yan, Hao, Liu, Yan, et al.
Created Date
2019

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

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

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

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

For reading DNA bases more accurately, a series of nitrogen-containing aromatic heterocycles have been designed and synthesized as candidates of universal reader to interact with all naturally occurring DNA nucleobases by hydrogen bonding interaction and eventually is used to read DNA by recognition tunneling. These recognition molecules include 6-mercapto-1H-benzo[d]imidazole-2-carboxamide, 5-(2-mercaptoethyl)-1H-imidazole-2-carboxamide, 5-(2-mercaptoethyl)-4H-1,2,4-traizole-3-carboxamide and 1-(2-mercaptoethyl)-1H-pyrrole-3-carboxamide. Their formation of hydrogen bonding complexes with nucleobases was studied and association constants were measured by proton NMR titration experiments in deuterated chloroform at room temperature. To do so, the mercaptoethyl chain or thiol group of these reading molecules was replaced or protected with the more lipophilic …

Contributors
Biswas, Sovan, Lindsay, Stuart, Zhang, Peiming, et al.
Created Date
2016

Engineered nanoparticles (NPs) pose risk potentials, if they exist in water systems at significant concentrations and if they remain reactive to cause toxicity. Three goals guided this study: (1) establishing NP detecting methods with high sensitivity to tackle low concentration and small sizes, (2) achieving assays capable of measuring NP surface reactivity and identifying surface reaction mechanisms, and (3) understanding the impact of surface adsorption of ions on surface reactivity of NPs in water. The size detection limit of single particle inductively coupled plasma spectrometry (spICP-MS) was determined for 40 elements, demonstrating the feasibility of spICP-MS to different NP species …

Contributors
Bi, Xiangyu, Westerhoff, Paul K, Rittmann, Bruce E, et al.
Created Date
2018

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

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

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

Over the last few decades, homogeneous molybdenum catalysis has been a center of interest to inorganic, organic, and organometallic chemists. Interestingly, most of the important advancements in molybdenum chemistry such as non-classical dihydrogen coordination, dinitrogen reduction, olefin metathesis, and water reduction utilize diverse oxidation states of the metal. However, employment of redox non-innocent ligands to tune the stability and reactivity of such catalysts have been overlooked. With this in mind, the Trovitch group has developed a series of novel bis(imino)pyridine (or pyridine diimine, PDI) and diimine (DI) ligands that have coordinating phosphine or amine arms to exert coordination flexibility to …

Contributors
Pal, Raja, Trovitch, Ryan J, Buttry, Daniel, et al.
Created Date
2016

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

Glycans are monosaccharide-based heteropolymers that are found covalently attached to many different proteins and lipids and are ubiquitously displayed on the exterior surfaces of cells. Serum glycan composition and structure are well known to be altered in many different types of cancer. In fact, glycans represent a promising but only marginally accessed source of cancer markers. The approach used in this dissertation, which is referred to as “glycan node analysis”, is a molecularly bottom-up approach to plasma/serum (P/S) glycomics based on glycan linkage analysis that captures features such as α2-6 sialylation, β1-6 branching, and core fucosylation as single analytical signals. …

Contributors
Roshdiferdosi, Shadi, Borges, Chad R, Woodbury, Neal, et al.
Created Date
2018

Broadband dielectric spectroscopy is a powerful technique for understanding the dynamics in supercooled liquids. It generates information about the timescale of the orientational motions of molecular dipoles within the liquid. However, dynamics of liquids measured in the non-linear response regime has recently become an area of significant interest, because additional information can be obtained compared with linear response measurements. The first part of this thesis describes nonlinear dielectric relaxation experiments performed on various molecular glass forming-liquids, with an emphasis on the response at high frequencies (excess wing). A significant nonlinear dielectric effect (NDE) was found to persist in these modes, …

Contributors
Samanta, Subarna, Richert, Ranko, Steimle, Timothy, et al.
Created Date
2016

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

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

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

Nature is a master at organizing biomolecules in all intracellular processes, and researchers have conducted extensive research to understand the way enzymes interact with each other through spatial and orientation positioning, substrate channeling, compartmentalization, and more. DNA nanostructures of high programmability and complexity provide excellent scaffolds to arrange multiple molecular/macromolecular components at nanometer scale to construct interactive biomolecular complexes and networks. Due to the sequence specificity at different positions of the DNA origami nanostructures, spatially addressable molecular pegboard with a resolution of several nm (less than 10 nm) can be achieved. So far, DNA nanostructures can be used to build …

Contributors
Yang, Yuhe Renee, Yan, Hao, Liu, Yan, et al.
Created Date
2016

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

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

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

Metalloporphyrins represent a class of molecular electrocatalysts for driving energy relevant half-reactions, including hydrogen evolution and carbon dioxide reduction. As electrocatalysts, they provide a strategy, and potential structural component, for linking renewable energy sources with the production of fuels and other value-added chemicals. In this work, porphyrins are used as structural motifs for exploring structure-function relationships in electrocatalysis and as molecular building blocks for assembling photoelectrochemical assemblies leveraging the light capture and conversion properties of a gallium phosphide (GaP) semiconductor. These concepts are further covered in Chapter 1. A direct one-step method to chemically graft metalloporphyrins to GaP surfaces is …

Contributors
Khusnutdinova, Diana, Moore, Gary F., Moore, Ana L., et al.
Created Date
2019

Biological systems have long been known to utilize two processes for energy conservation: substrate-level phosphorylation and electron transport phosphorylation. Recently, a new bioenergetic process was discovered that increases ATP yields: flavin-based electron bifurcation (FBEB). This process couples an energetically favorable reaction with an energetically unfavorable one to conserve energy in the organism. Currently, the mechanisms of enzymes that perform FBEB are unknown. In this work, NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn), a FBEB enzyme, is used as a model system to study this phenomenon. Nfn is a heterodimeric enzyme that reversibly couples the exergonic reduction of NADP+ by reduced ferredoxin with …

Contributors
Jennings, David, Jones, Anne K, Redding, Kevin E, et al.
Created Date
2018

Palladium metal in its various forms has been heavily studied for many catalytic, hydrogen storage and sensing applications and as an electrocatalyst in fuel cells. A short review on various applications of palladium and the mechanism of Pd nanoparticles synthesis will be discussed in chapter 1. Size dependent properties of various metal nanoparticles and a thermodynamic theory proposed by Plieth to predict size dependent redox properties of metal nanoparticles will also be discussed in chapter 1. To evaluate size dependent stability of metal nanoparticles using electrochemical techniques in aqueous media, a synthetic route was designed to produce water soluble Pd …

Contributors
Kumar, Ashok, Buttry, Daniel A., Gould, Ian R., et al.
Created Date
2016

Spider dragline silk is an outstanding biopolymer with a strength that exceeds steel by weight and a toughness greater than high-performance fibers like Kevlar. For this reason, structural and dynamic studies on the spider silk are of great importance for developing future biomaterials. The spider dragline silk comprises two silk proteins, Major ampullate Spidroin 1 and 2 (MaSp1 and 2), which are synthesized and stored in the major ampullate (MA) gland of spiders. The initial state of the silk proteins within Black Widow MA glands was probed with solution-state NMR spectroscopy. The conformation dependent chemical shifts information indicates that the …

Contributors
Xu, Dian, Yarger, Jeffery L, Holland, Gregory P, et al.
Created Date
2015

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

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

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

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 work described in this thesis explores the synthesis of new semiconductors in the Si-Ge-Sn system for application in Si-photonics. Direct gap Ge1-ySny (y=0.12-0.16) alloys with enhanced light emission and absorption are pursued. Monocrystalline layers are grown on Si platforms via epitaxy-driven reactions between Sn- and Ge-hydrides using compositionally graded buffer layers that mitigate lattice mismatch between the epilayer and Si platforms. Prototype p-i-n structures are fabricated and are found to exhibit direct gap electroluminescence and tunable absorption edges between 2200 and 2700 nm indicating applications in LEDs and detectors. Additionally, a low pressure technique is described producing pseudomorphic Ge1-ySny …

Contributors
Wallace, Patrick Michael, Kouvetakis, John, Menendez, Jose, et al.
Created Date
2018

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

Atmospheric deposition of iron (Fe) can limit primary productivity and carbon dioxide uptake in some marine ecosystems. Recent modeling studies suggest that biomass burning aerosols may contribute a significant amount of soluble Fe to the surface ocean. Existing studies of burn-induced trace element mobilization have often collected both entrained soil particles along with material from biomass burning, making it difficult to determine the actual source of aerosolized trace metals. In order to better constrain the importance of biomass versus entrained soil as a source of trace metals in burn aerosols, small-scale burn experiments were conducted using soil-free foliage representative of …

Contributors
Sherry, Alyssa Meredith, Anbar, Ariel D, Herckes, Pierre, et al.
Created Date
2019

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

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

Guided by cognitive, socio-cognitive, and socio-cultural learning theories, large-scale studies over multiple semesters, multiple instructors and at two different institutions have been performed in order to understand the factors that contribute to student performance in general organic chemistry. Students’ cognitive abilities were assessed in a new way based on a categorization of problem types in a standard organic chemistry curriculum. Problem types that required higher cognitive load were found to be more predictive of overall course performance. However, student performance on high cognitive load problems was different when compared in terms of non-cognitive factors, e.g. whether they were pre-health students …

Contributors
Austin, Ara, Gould, Ian R., Atkinson, Robert K., et al.
Created Date
2018

In anthropological models of social organization, kinship is perceived to be fundamental to social structure. This project aimed to understand how individuals buried in neighborhoods or patio groups were affiliated, by considering multiple possibilities of fictive and biological kinship, short or long-term co-residence, and long-distance kin affiliation. The social organization of the ancient Maya urban center of Copan, Honduras during the Late Classic (AD 600-822) period was evaluated through analysis of the human skeletal remains drawn from the largest collection yet recovered in Mesoamerica (n=1200). The research question was: What are the roles that kinship (biological or fictive) and co-residence …

Contributors
Miller, Katherine Anne, Buikstra, Jane E, Bell, Ellen E, et al.
Created Date
2015

Disease prevention and personalized treatment will be impacted by the continued integration of protein biomarkers into medical practice. While there are already numerous biomarkers used clinically, the detection of protein biomarkers among complex matrices remains a challenging problem. One very important strategy for improvements in clinical application of biomarkers is separation/preconcentration, impacting the reliability, efficiency and early detection. Electrophoretic exclusion can be used to separate, purify, and concentrate biomarkers. This counterflow gradient technique exploits hydrodynamic flow and electrophoretic forces to exclude, enrich, and separate analytes. The development of this technique has evolved onto an array-based microfluidic platform which offers a …

Contributors
Zhu, Fanyi, Hayes, Mark, Ros, Alexandra, et al.
Created Date
2019

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

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

The larger tolerance to lattice mismatch in growth of semiconductor nanowires (NWs) offers much more flexibility for achieving a wide range of compositions and bandgaps via alloying within a single substrate. The bandgap of III-V InGaAsP alloy NWs can be tuned to cover a wide range of (0.4, 2.25) eV, appealing for various optoelectronic applications such as photodetectors, solar cells, Light Emitting Diodes (LEDs), lasers, etc., given the existing rich knowledge in device fabrication based on these materials. This dissertation explores the growth of InGaAsP alloys using a low-cost method that could be potentially important especially for III-V NW-based solar …

Contributors
Hashemi Amiri, Seyed Ebrahim, Ning, Cun-Zheng, Petuskey, William, et al.
Created Date
2018

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

Microfluidic systems have gained popularity in the last two decades for their potential applications in manipulating micro- and nano- particulates of interest. Several different microfluidics devices have been built capable of rapidly probing, sorting, and trapping analytes of interest. Microfluidics can be combined with separation science to address challenges of obtaining a concentrated and pure distinct analyte from mixtures of increasingly similar entities. Many of these techniques have been developed to assess biological analytes of interest; one of which is dielectrophoresis (DEP), a force which acts on polarizable analytes in the presence of a non-uniform electric fields. This method can …

Contributors
Crowther, Claire Victoria, Hayes, Mark A, Gile, Gillian H, et al.
Created Date
2018

Measurements of different molecular species from single cells have the potential to reveal cell-to-cell variations, which are precluded by population-based measurements. An increasing percentage of researches have been focused on proteins, for its central roles in biological processes. Immunofluorescence (IF) has been a well-established protein analysis platform. To gain comprehensive insights into cell biology and diagnostic pathology, a crucial direction would be to increase the multiplexity of current single cell protein analysis technologies. An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of …

Contributors
Liao, Renjie, Guo, Jia, Borges, Chad, et al.
Created Date
2019

Carboxylic acids are an abundant and reactive species present throughout our solar system. The reactions of carboxylic acids can shape the organic abundances within oil field brines, carbonaceous chondrites, and different ranks of coal. I have performed hydrothermal experiments with model aromatic carboxylic acids in the presences of different oxide minerals to investigate the reactions available to carboxylic acids in the presence of mineral surfaces. By performing experiments containing one organic compound and one mineral surface, I can begin to unravel the different reactions that can occur in the presence of different minerals. I performed experiments with phenylacetic acid (PAA), …

Contributors
Johnson, Kristin Nicole, Shock, Everett, Hartnett, Hilairy, et al.
Created Date
2017

Cell heterogeneity is widely present in the biological world and exists even in an isogenic population. Resolving the protein heterogeneity at the single cell level is of enormous biological and clinical relevance. However, single cell protein analysis has proven to be challenging due to extremely low amount of protein in a single cell and the huge complexity of proteome. This requires appropriate sampling and sensitive detection techniques. Here, a new approach, microfluidics combined with MALDI-TOF mass spectrometry was brought forward, for the analysis of proteins in single cells. The detection sensitivity of peptides as low as 300 molecules and of …

Contributors
Yang, Mian, Ros, Alexandra, Hayes, Mark, et al.
Created Date
2016

DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with …

Contributors
SEN, SUMAN, Lindsay, Stuart, Zhang, Peiming, et al.
Created Date
2016

Glycosaminoglycans (GAGs) are a class of complex biomolecules comprised of linear, sulfated polysaccharides whose presence on cell surfaces and in the extracellular matrix involve them in many physiological phenomena as well as in interactions with pathogenic microbes. Decorin binding protein A (DBPA), a Borrelia surface lipoprotein involved in the infectivity of Lyme disease, is responsible for binding GAGs found on decorin, a small proteoglycan present in the extracellular matrix. Different DBPA strains have notable sequence heterogeneity that results in varying levels of GAG-binding affinity. In this dissertation, the structures and GAG-binding mechanisms for three strains of DBPA (B31 and N40 …

Contributors
Morgan, Ashli, Wang, Xu, Allen, James, 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

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

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

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

DNA and DNA nanoassemblies such as DNA origamis have large potential in biosensing, drug delivery, nanoelectronic circuits, and biological computing requiring suitable methods for migration and precise positioning. Insulator-based dielectrophoresis (iDEP) provides an efficient and matrix-free approach for manipulation of micro-and nanometer-sized objects. In order to exploit iDEP for naturally formed DNA and DNA nanoassemblies, a detailed understanding of the underlying polarization and dielectrophoretic migration is essential. The shape and the counterion distribution are considered two essential factors in the polarization mechanism. Here, the dielectrophoretic behavior of 6-helix bundle (6HxB) and triangle DNA origamis with identical sequences but substantial topological …

Contributors
Gan, Lin, Ros, Alexandra, Buttry, Daniel, et al.
Created Date
2015

The fundamental photophysics of fluorescent probes must be understood when the probes are used in biological applications. The photophysics of BODIPY dyes inside polymeric micelles and rhodamine dyes covalently linked to proteins were studied. Hydrophobic boron-dipyrromethene (BODIPY) dyes were noncovalently encapsulated inside polymeric micelles. Absorbance and fluorescence measurements were employed to study the photophysics of these BODIPY dyes in the micellar environments. Amphiphilic polymers with a hydrophobic character and low Critical Micelle Concentration (CMC) protected BODIPYS from the aqueous environment. Moderate dye loading conditions did not result in ground-state dimerization, and only fluorescence lifetimes and brightnesses were affected. However, amphiphilic …

Contributors
Donaphon, Bryan Matthew, Levitus, Marcia, Van Horn, Wade, et al.
Created Date
2018

The inexorable upsurge in world’s energy demand has steered the search for newer renewable energy sources and photovoltaics seemed to be one of the best alternatives for energy production. Among the various photovoltaic technologies that emerged, organic/polymer photovoltaics based on solution processed bulk-heterojunctions (BHJ) of semiconducting polymers has gained serious attention owing to the use of inexpensive light-weight materials, exhibiting high mechanical flexibility and compatibility with low temperature roll-to-roll manufacturing techniques on flexible substrates. The most widely studied material to date is the blend of regioregular P3HT and PC61BM used as donor and acceptor materials. The object of this study …

Contributors
Das, Sayantan, Alford, Terry L, Petuskey, William, et al.
Created Date
2015

Biophysical techniques have been increasingly applied toward answering biological questions with more precision. Here, three different biological systems were studied with the goal of understanding their dynamic differences, either conformational dynamics within the system or oligomerization dynamics between monomers. With Cy3 on the 5' end of DNA, the effects of changing the terminal base pair were explored using temperature-dependent quantum yields. It was discovered, in combination with simulations, that a terminal thymine base has the weakest stacking interactions with the Cy3 dye compared to the other three bases. With ME1 heterodimers, the goal was to see if engineering a salt …

Contributors
Binder, Jennifer K., Levitus, Marcia, Wachter, Rebekka, et al.
Created Date
2015

The physiological phenomenon of sensing temperature is detected by transient receptor (TRP) ion channels, which are pore forming proteins that reside in the membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8 respectively, can be modulated by diverse stimuli and are finely tuned by proteins and lipids. PIRT (phosphoinositide interacting regulator of TRP channels) is a small membrane protein that modifies TRPV1 responses to heat and TRPM8 responses to cold. In this dissertation, the first direct measurements between PIRT and TRPM8 are quantified with nuclear magnetic resonance and microscale thermophoresis. Using Rosetta computational biology, TRPM8 is …

Contributors
Sisco, Nicholas John, Van Horn, Wade D, Mills, Jeremy H, et al.
Created Date
2018

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

Ionic liquids (ILs), or low-temperature liquid salts, are a class of materials with unique and useful properties. Made up entirely of ions, ILs are remarkably tunable and diverse as cations and anions can be mixed and matched to yield desired properties. Because of this, IL/water systems range widely—from homogeneous mixtures to multiphasic systems featuring ionic liquid/liquid interfaces. Even more diversity is added when particles are introduced to these systems, as hard particles or soft-matter microgels interact with both ILs and water in complex ways. This work examines both miscible ionic liquid/water mixture and two-phase, immiscible ionic liquid/water systems. Extensive molecular …

Contributors
Nickerson, Stella Day, Dai, Lenore L, Yu, Hongyu, et al.
Created Date
2016

Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR) was detected in numerous systems with a pH < 4. Rates of DIR are influenced by the availability of ferric minerals and organic carbon. Microbial iron oxidation (MIO) was detected from pH 2 – 5.5. In systems with abundant Fe (II), dissolved oxygen controls the presence of MIO. Rates generally increase with increased Fe(II) concentrations, but rate constants are not significantly altered by additions of Fe(II). MIRC was detected in …

Contributors
St Clair, Brian, Shock, Everett L, Anbar, Ariel, et al.
Created Date
2017

Time-resolved serial femtosecond crystallography is an emerging method that allows for structural discovery to be performed on biomacromolecules during their dynamic trajectory through a reaction pathway after activation. This is performed by triggering a reaction on an ensemble of molecules in nano- or microcrystals and then using femtosecond X-ray laser pulses produced by an X-ray free electron laser to collect near-instantaneous data on the crystal. A full data set can be collected by merging a sufficient number of these patterns together and multiple data sets can be collected at different points along the reaction pathway by manipulating the delay time …

Contributors
Coe, Jesse, Fromme, Petra, Sayres, Scott, et al.
Created Date
2018

Ultrasonication-mediated liquid-phase exfoliation has emerged as an efficient method for producing large quantities of two-dimensional materials such as graphene, boron nitride, and transition metal dichalcogenides. This thesis explores the use of this process to produce a new class of boron-rich, two-dimensional materials, namely metal diborides, and investigate their properties using bulk and nanoscale characterization methods. Metal diborides are a class of structurally related materials that contain hexagonal sheets of boron separated by metal atoms with applications in superconductivity, composites, ultra-high temperature ceramics and catalysis. To demonstrate the utility of these materials, chromium diboride was incorporated in polyvinyl alcohol as a …

Contributors
Yousaf, Ahmed, Green, Alexander A, Wang, Qing Hua, et al.
Created Date
2018

A lack of adequate energy storage technologies is arguably the greatest hindrance to a modern sustainable energy infrastructure. Chemical energy storage, in the form of batteries, is an obvious solution to the problem. Unfortunately, today’s state of the art battery technologies fail to meet the desired metrics for full scale electric grid and/or electric vehicle role out. Considerable effort from scientists and engineers has gone into the pursuit of battery chemistries theoretically capable of far outperforming leading technologies like Li-ion cells. For instance, an anode of the relatively abundant and cheap metal, magnesium, would boost the specific energy by over …

Contributors
Watkins, Tylan Strike, Buttry, Daniel A, Wolf, George, et al.
Created Date
2016

Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base. First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a …

Contributors
Xiang, Limin, Tao, Nongjian, Lindsay, Stuart, et al.
Created Date
2016

Increasing concentrations of carbon dioxide in the atmosphere will inevitably lead to long-term changes in climate that can have serious consequences. Controlling anthropogenic emission of carbon dioxide into the atmosphere, however, represents a significant technological challenge. Various chemical approaches have been suggested, perhaps the most promising of these is based on electrochemical trapping of carbon dioxide using pyridine and derivatives. Optimization of this process requires a detailed understanding of the mechanisms of the reactions of reduced pyridines with carbon dioxide, which are not currently well known. This thesis describes a detailed mechanistic study of the nucleophilic and Bronsted basic properties …

Contributors
Ranjan, Rajeev, Gould, Ian R, Buttry, Daniel A, et al.
Created Date
2015

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

X-ray crystallography is the most widely used method to determine the structure of proteins, providing an understanding of their functions in all aspects of life to advance applications in fields such as drug development and renewable energy. New techniques, namely serial femtosecond crystallography (SFX), have unlocked the ability to unravel the structures of complex proteins with vital biological functions. A key step and major bottleneck of structure determination is protein crystallization, which is very arduous due to the complexity of proteins and their natural environments. Furthermore, crystal characteristics govern data quality, thus need to be optimized to attain the most …

Contributors
Abdallah, Bahige Gary, Ros, Alexandra, Buttry, Daniel, et al.
Created Date
2016

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

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

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