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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


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

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

Mitochondria are energy-producing organelles present in eukaryotic cells. Energy as adenosine triphosphate (ATP) is produced at the end of a series of electron transfers called the electron transport chain (ETC). Such a highly coordinated and regulated series of electron transfer reactions give rise to a small percentage of electron leakage which, by the subsequent reduction of molecular oxygen, produce superoxide anions (O2.-). These anions initiate the production of additional highly reactive oxygen-containing radicals commonly known as reactive oxygen species (ROS). Although cells are equipped with endogenous antioxidant systems to minimize ROS accumulation, these endogenous defense systems become inadequate when ROS …

Contributors
Bandyopadhyay, Indrajit, Hecht, Sidney M, Gould, Ian R, et al.
Created Date
2019

Minimally invasive endovascular embolization procedures decrease surgery time, speed up recovery, and provide the possibility for more comprehensive treatment of aneurysms, arteriovenous malformations (AVMs), and hypervascular tumors. Liquid embolic agents (LEAs) are preferred over mechanical embolic agents, such as coils, because they achieve homogeneous filling of aneurysms and more complex angioarchitectures. The gold standard of commercially available LEAs is dissolved in dimethyl sulfoxide (DMSO), which has been associated with vasospasm and angiotoxicity. The aim of this study was to investigate amino acid substitution in an enzyme-degradable side group of an N-isopropylacrylamide (NIPAAm) copolymer for the development of a LEA that …

Contributors
Rosas Gomez, Karime Jocelyn, Vernon, Brent, Weaver, Jessica, et al.
Created Date
2019

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

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

Transient molecules are of great importance having proposed applications in quantum science and technology and tests of fundamental physics. In the present dissertation, the transient molecules studied are SrOH, ThF, ThCl, YbF and YbOH; each having been selected because of their proposed application. Specifically, SrOH is a candidate of constructing a molecular magneto-optical trap (MOT). The simple actinide molecules, ThF and ThCl, were selected as ligand bonding model systems to gain insight into chemical processing of Spent Nuclear Fuel. The lanthanides YbF and YbOH are venues for the determination of electron electric dipole moment (eEDM) and the studies in this …

Contributors
Nguyen, Duc Trung, Steimle, Timothy C, Richert, Ranko, et al.
Created Date
2019

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

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

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

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

Though DNA nanostructures (DNs) have become interesting subjects of drug delivery, in vivo imaging and biosensor research, however, for real biological applications, they should be ‘long circulating’ in blood. One of the crucial requirements for DN stability is high salt concentration (like ~5–20 mM Mg2+) that is unavailable in a cell culture medium or in blood. Hence DNs denature promptly when injected into living systems. Another important factor is the presence of nucleases that cause fast degradation of unprotected DNs. The third factor is ‘opsonization’ which is the immune process by which phagocytes target foreign particles introduced into the bloodstream. …

Contributors
Banerjee, Saswata, Yan, Hao, Angell, Austen, et al.
Created Date
2018

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

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 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

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

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

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

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

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

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

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

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

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

The molecular modification of semiconductors has applications in energy conversion and storage, including artificial photosynthesis. In nature, the active sites of enzymes are typically earth-abundant metal centers and the protein provides a unique three-dimensional environment for effecting catalytic transformations. Inspired by this biological architecture, a synthetic methodology using surface-grafted polymers with discrete chemical recognition sites for assembling human-engineered catalysts in three-dimensional environments is presented. The use of polymeric coatings to interface cobalt-containing catalysts with semiconductors for solar fuel production is introduced in Chapter 1. The following three chapters demonstrate the versatility of this modular approach to interface cobalt-containing catalysts with …

Contributors
Beiler, Anna Mary, Moore, Gary F., Moore, Thomas A., et al.
Created Date
2018

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

Modern semiconductor technologies have been dominated by group-IV materials and III-V analogues. The development of hybrid derivatives combining appropriate members of these systems has been of interest for the purpose of extending the optoelectronic capabilities of the state-of-the-art. Early work on pseudo-binary (III-V)-IV alloys, described with the general formula (III-V)1-x(IV2)x, showed limited progress due to phase segregation, auto-doping and compositional inhomogeneities. Recently, new techniques were introduced for synthesizing new classes of (III-V)-IV hybrid materials using reactions of V(IVH3)3 molecules [V = N, P, As and IV = Si, Ge] with group-III elements (B, Al, Ga, In). The reactions produce (III-V)-IV3 …

Contributors
Sims, Patrick, Kouvetakis, John, Chizmeshya, Andrew V. G., et al.
Created Date
2017

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

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

Banded iron formations (BIFs) are among the earliest possible indicators for oxidation of the Archean biosphere. However, the origin of BIFs remains debated. Proposed formation mechanisms include oxidation of Fe(II) by O2 (Cloud, 1973), photoferrotrophy (Konhauser et al., 2002), and abiotic UV photooxidation (Braterman et al., 1983; Konhauser et al., 2007). Resolving this debate could help determine whether BIFs are really indicators of O2, biological activity, or neither. To examine the viability of abiotic UV photooxidation of Fe, laboratory experiments were conducted in which Fe-bearing solutions were irradiated with different regions of the ultraviolet (UV) spectrum and Fe oxidation and …

Contributors
Castleberry, Parker, Anbar, Ariel D, Herckes, Pierre, et al.
Created Date
2017

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

Since the discovery of graphene, two dimensional materials (2D materials) have become a focus of interest for material research due to their many unique physical properties embedded in their 2D structure. While they host many exciting potential applications, some of these 2D materials are subject to environmental instability issues induced by interaction between material and gas molecules in air, which poses a barrier to further application and manufacture. To overcome this, it is necessary to understand the origin of material instability and interaction with molecules commonly found in air, as well as developing a reproducible and manufacturing compatible method to …

Contributors
Yang, Sijie, Tongay, Sefaattin, Gould, Ian, et al.
Created Date
2017

Microfluidics has shown great potential in rapid isolation, sorting, and concentration of bioparticles upon its discovery. Over the past decades, significant improvements have been made in device fabrication techniques and microfluidic methodologies. As a result, considerable microfluidic-based isolation and concentration techniques have been developed, particularly for rapid pathogen detection. Among all microfluidic techniques, dielectrophoresis (DEP) is one of the most effective and efficient techniques to quickly isolate and separate polarizable particles under inhomogeneous electric field. To date, extensive studies have demonstrated that DEP devices are able to precisely manipulate cells ranging from over 10 μm (mammalian cells) down to about …

Contributors
Ding, Jie, Hayes, Mark A, Ros, Alexandra, et al.
Created Date
2017

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

The energy required in a eukaryotic cell is provided by mitochondria. Mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation generates ATP. During electron transport, electron leakage from the ETC produces reactive oxygen species (ROS). In healthy cells, there are preventive and defense mechanisms in place to manage ROS. Maintaining a steady balance of ROS is very important because overproduction of ROS can lead to several pathological conditions. There are several strategies to prevent ROS production. Addition of external antioxidants is widely used among them. Discussed in the first part of Chapter 1 is the mitochondrial ETC, ROS production and …

Contributors
Roy Chowdhury, Sandipan, Hecht, Sidney, Gould, Ian, et al.
Created Date
2016

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

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

The manipulation of biological targets using synthetic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that act either as probes for studying protein conformational changes or DNA–protein interaction, or as multifunctional radical quenchers. Fluorescent labeling is of paramount importance to biological studies of proteins. For the development of new extrinsic small fluorophores, a series of tryptophan analogues has been designed and synthesized. Their pdCpA derivatives have been synthesized for tRNA activation and in vitro protein synthesis. The photophysical properties of the tryptophan (Trp) analogues have been examined, …

Contributors
TALUKDER, POULAMI, Hecht, Sidney M, Woodbury, Neal, et al.
Created Date
2016

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

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

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

Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states …

Contributors
Jiang, Shuoxing, Yan, Hao, Liu, Yan, et al.
Created Date
2016

Biomolecules can easily recognize its corresponding partner and get bound to it, resulting in controlling various processes (immune system, inter or intracellular signaling) in biology and physiology. Bonding between two partners can be a result of electrostatic, hydrophobic interactions or shape complementarity. It is of great importance to study these kinds of biomolecular interactions to have a detailed knowledge of above mentioned physiological processes. These studies can also open avenues for other aspects of science such as drug development. Discussed in the first part of Chapter 1 are the biotin-streptavidin biomolecular interaction studies by atomic force microscopy (AFM) and surface …

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

The addition of aminoalkyl-substituted 2,6-bis(imino)pyridine (or pyridine diimine, PDI) ligands to [(COD)RhCl]2 (COD = 1,5-cyclooctadiene) resulted in the formation of rhodium monochloride complexes with the general formula (NPDI)RhCl (NPDI = iPr2NEtPDI or Me2NPrPDI). The investigation of (iPr2NEtPDI)RhCl and (Me2NPrPDI)RhCl by single crystal X-ray diffraction verified the absence of amine arm coordination and a pseudo square planar geometry about rhodium. Replacement of the chloride ligand with an outer-sphere anion was achieved by adding AgBF4 directly to (iPr2NEtPDI)RhCl to form [(iPr2NEtPDI)Rh][BF4]. Alternatively, this complex was prepared upon chelate addition following the salt metathesis reaction between AgBF4 and [(COD)RhCl]2. Using the latter method, …

Contributors
Levin, Hagit Ben-Daat, Trovitch, Ryan J, Gould, Ian R, 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

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

Serial crystallography (SX) is a relatively new structural biology technique that collects X-ray diffraction data from microcrystals via femtosecond pulses produced by an X-ray free electron laser (X-FEL) or by synchrotron radiation, allowing for challenging protein structures to be solved from microcrystals at room temperature. Because of the youth of this technique, method development is necessary for it to achieve its full potential. Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. …

Contributors
Conrad, Chelsie Elea, Fromme, Petra, Ros, Alexandra, et al.
Created Date
2016

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

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