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Description
DNA nanotechnology uses the reliability of Watson-Crick base pairing to program and generate two-dimensional and three-dimensional nanostructures using single-stranded DNA as the structural material. DNA nanostructures show great promise for the future of bioengineering, as there are a myriad of potential applications that utilize DNA’s chemical interactivity and ability to

DNA nanotechnology uses the reliability of Watson-Crick base pairing to program and generate two-dimensional and three-dimensional nanostructures using single-stranded DNA as the structural material. DNA nanostructures show great promise for the future of bioengineering, as there are a myriad of potential applications that utilize DNA’s chemical interactivity and ability to bind other macromolecules and metals. DNA origami is a method of constructing nanostructures, which consists of a long “scaffold” strand folded into a shape by shorter “staple” oligonucleotides. Due to the negative charge of DNA molecules, divalent cations, most commonly magnesium, are required for origami to form and maintain structural integrity. The experiments in this paper address the discrepancy between salt concentrations required for origami stability and the salt concentrations present in living systems. The stability of three structures, a two-dimensional triangle, a three-dimensional solid cuboid and a three-dimensional wireframe icosahedron were examined in buffer solutions containing various concentrations of salts. In these experiments, DNA origami structures remained intact in low-magnesium conditions that emulate living cells, supporting their potential for widespread biological application in the future.
ContributorsSeverson, Grant William (Author) / Stephanopoulos, Nicholas (Thesis director) / Mills, Jeremy (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Carbon allotropes are the basis for many exciting advancements in technology. While sp² and sp³ hybridizations are well understood, the sp¹ hybridized carbon has been elusive. However, with recent advances made using a pulsed laser ablation in liquid technique, sp¹ hybridized carbon allotropes have been created. The fabricated carbon chain

Carbon allotropes are the basis for many exciting advancements in technology. While sp² and sp³ hybridizations are well understood, the sp¹ hybridized carbon has been elusive. However, with recent advances made using a pulsed laser ablation in liquid technique, sp¹ hybridized carbon allotropes have been created. The fabricated carbon chain is composed of sp¹ and sp³ hybridized bonds, but it also incorporates nanoparticles such as gold or possibly silver to stabilize the chain. The polyyne generated in this process is called pseudocarbyne due to its striking resemblance to the theoretical carbyne. The formation of these carbon chains is yet to be fully understood, but significant progress has been made in determining the temperature of the plasma in which the pseudocarbyne is formed. When a 532 nm pulsed laser with a pulsed energy of 250 mJ and pulse length of 10ns is used to ablate a gold target, a peak temperature of 13400 K is measured. When measured using Laser-Induced Breakdown spectroscopy (LIBS) the average temperature of the neutral carbon plasma over one second was 4590±172 K. This temperature strongly suggests that the current theoretical model used to describe the temperature at which pseudocarbyne generates is accurate.
ContributorsWala, Ryland Gerald (Co-author) / Wala, Ryland (Co-author) / Sayres, Scott (Thesis director) / Steimle, Timothy (Committee member) / Drucker, Jeffery (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Department of Physics (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Tempe Town Lake is the site of fifteen years’ worth of chemical data collection by ASU researchers. In 2018 the dataSONDE, an instrument capable of measuring different water quality parameters every thirty minutes for a month at a time was installed in the lake. The SONDE has the potential to

Tempe Town Lake is the site of fifteen years’ worth of chemical data collection by ASU researchers. In 2018 the dataSONDE, an instrument capable of measuring different water quality parameters every thirty minutes for a month at a time was installed in the lake. The SONDE has the potential to completely reduce the need for sampling by hand. Before the SONDE becomes the sole means of gathering data, it is important to verify its accuracy. In this study, the measurements gathered by the SONDE (pH, dissolved oxygen, temperature, conductivity and colored dissolved organic matter) were compared to measurements gathered using the verified methods from the past fifteen years.
ContributorsSauer, Elinor Rayne (Author) / Hartnett, Hilairy (Thesis director) / Glaser, Donald (Committee member) / Shock, Everett (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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Description

Augmented Reality (AR) especially when used with mobile devices enables the creation of applications that can help students in chemistry learn anything from basic to more advanced concepts. In Chemistry specifically, the 3D representation of molecules and chemical structures is of vital importance to students and yet when printed in

Augmented Reality (AR) especially when used with mobile devices enables the creation of applications that can help students in chemistry learn anything from basic to more advanced concepts. In Chemistry specifically, the 3D representation of molecules and chemical structures is of vital importance to students and yet when printed in 2D as on textbooks and lecture notes it can be quite hard to understand those vital 3D concepts. ARsome Chemistry is an app that aims to utilize AR to display complex and simple molecules in 3D to actively teach students these concepts through quizzes and other features. The ARsome chemistry app uses image target recognition to allow students to hand-draw or print line angle structures or chemical formulas of molecules and then scan those targets to get 3D representation of molecules. Students can use their fingers and the touch screen to zoom, rotate, and highlight different portions of the molecule to gain a better understanding of the molecule's 3D structure. The ARsome chemistry app also features the ability to utilize image recognition to allow students to quiz themselves on drawing line-angle structures and show it to the camera for the app to check their work. The ARsome chemistry app is an accessible and cost-effective study aid platform for students for on demand, interactive, 3D representations of complex molecules.

ContributorsEvans, Brandon (Author) / LiKamWa, Robert (Thesis director) / Johnson, Mina (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05
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Description

Non-canonical amino acids (NCAAs) can be used in protein chemistry to determine their structures. A common method for imaging proteins is cryo-electron microscopy (cryo-EM) which is ideal for imaging proteins that cannot be obtained in large quantities. Proteins with indistinguishable features are difficult to image using this method due to

Non-canonical amino acids (NCAAs) can be used in protein chemistry to determine their structures. A common method for imaging proteins is cryo-electron microscopy (cryo-EM) which is ideal for imaging proteins that cannot be obtained in large quantities. Proteins with indistinguishable features are difficult to image using this method due to the large size requirements, therefore antibodies designed specifically for binding these proteins have been utilized to better identify the proteins. By using an existing antibody that binds to stilbene, NCAAs containing this molecule can be used as a linker between proteins and an antibody. Stilbene containing amino acids can be integrated into proteins to make this process more access able. In this paper, synthesis methods for various NCAAs containing stilbene were proposed. The resulting successfully synthesized NCAAs were E)-N6-(5-oxo-5-((4-styrylphenyl) amino) pentanoyl) lysine, (R,E)-2-amino-3-(5-oxo-5-((4-styrylphenyl)amino)pentanamido)propanoic acid, (E)-2-amino-5-(5-oxo-5-((4-styrylphenyl) amino) pentanamido) pentanoic acid. A synthesis for three more shorter amino acids, (R,E)-2-amino-3-(3-oxo-3-((4-styrylphenyl) amino) propanamido) propanoic acid, (E)-2-amino-5-(3-oxo-3-((4-styrylphenyl) amino) propanamido) pentanoic acid, and (E)-N6-(3-oxo-3-((4-styrylphenyl) amino) propanoyl) lysine, is also proposed.

ContributorsJenkins, Bryll (Author) / Mills, Jeremy (Thesis director) / Ghirlanda, Giovanna (Committee member) / Nannenga, Brent (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2022-05
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Description
Ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (Rubisco) is responsible for the majority of carbon fixation and is also the least efficient enzyme on Earth. Rubisco assists 1,5-ribulose bisphosphate (RuBP) in binding CO2, however CO2 and oxygen have similar binding affinities to Rubisco, resulting in a low enzymatic efficiency. Rubisco activase (Rca) is an

Ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (Rubisco) is responsible for the majority of carbon fixation and is also the least efficient enzyme on Earth. Rubisco assists 1,5-ribulose bisphosphate (RuBP) in binding CO2, however CO2 and oxygen have similar binding affinities to Rubisco, resulting in a low enzymatic efficiency. Rubisco activase (Rca) is an enzyme that removes inhibiting molecules from Rubisco’s active sites, promoting the Rubisco activity. The binding of Rubisco and Rca stimulates a high-rate of carbon fixation and lowers the overall CO2 concentration in the atmosphere. To study the interaction between the two complexes, Rubisco was extracted from baby spinach (Spinacia oleracea) and purified using anion-exchange chromatography and size-exclusion chromatography. Rca was designed to use a recombinant gene and overexpressed in Escherichia coli (E. coli). The purified proteins were verified using SDS-PAGE. The two proteins were assembled in vitro and the interaction of the protein complex was stabilized using glutaraldehyde cross-linking. The samples were then deposited on a carbon-coated electron microscopy (EM) grid, stained with uranyl formate, and observed under a transmission electron microscope (TEM). The ultimate goal is to image the specimen and reconstruct the structure of the protein complex at high resolution.
ContributorsHart, Hayden (Author) / Chiu, Po-Lin (Thesis director) / Redding, Kevin (Committee member) / Van Horn, Wade (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / Department of Military Science (Contributor)
Created2022-05
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Description
Diabetes is the 7th leading cause of death globally. In 2018, 34.2 million Americans had type 2 diabetes. Many symptoms of diabetes are similar to those of scurvy or vitamin C deficiency. Vitamin C marginality and inadequacy are more prevalent in Type 2 Diabetes/prediabetes than with normal glucose tolerance. Intracellular

Diabetes is the 7th leading cause of death globally. In 2018, 34.2 million Americans had type 2 diabetes. Many symptoms of diabetes are similar to those of scurvy or vitamin C deficiency. Vitamin C marginality and inadequacy are more prevalent in Type 2 Diabetes/prediabetes than with normal glucose tolerance. Intracellular vitamin C inadequacy is suspected due to competition between dehydroascorbic acid and glucose at GLUT 1 and 3 cellular receptors. Erythrocyte osmotic fragility is noted in Gulo -/- knockout mice unable to synthesize endogenous vitamin C. The ascorbate deficient red blood cells presented with low cytoskeletal B-spectrin, spherocyte appearance, and impaired deformability. This cross-sectional study investigated the relationships between diabetes status, erythrocyte osmotic fragility, and serum vitamin C status. Participants were aged 18-65, non-smoking, reported no unresolved health complications, and denied prior vitamin C supplementation. Those with T2D indicated diagnosis of >1 year. All participants provided written informed consent and the study was approved by the local Institutional Review Board in January 2021. Participants provided one fasted blood sample. Erythrocyte osmotic fragility was measured via UV/Vis spectrophotometry with various concentrations of sodium chloride (0.85% - 0.10%) to induce osmotic stress. In addition, plasma was extracted and mixed 1:1 with 10% (w/v) metaphosphoric acid in 2 mmol/L disodium EDTA and centrifuged. The supernatant was stored at -80°C until analysis with isocratic reverse-phase UV-HPLC separation. Participant characteristics did not differ significantly between groups apart from age (p< 0.01) and HbA1c (p=0.002). Data are presented for adults with T2D (n=14; 36% female; 55.5±8.2 y; 31.5±9.0 kg/m2; HbA1c: 7.4±1.9%; plasma vitamin C: 36.0±12.2 uM) and without T2D (n=16; 69% female; 38.7±13.5 y; 26.8±6.6 kg/m2; A1c: 5.4±0.3%; plasma vitamin C: 34.8±10.9uM). Erythrocyte osmotic fragility was significantly elevated (+4.4% hemolysis) in adults without T2D at 0.35% saline (p=0.039). Greater VC status (>30 uM) was associated with lower hemolysis at 0.35% NaCl (p=0.031). Erythrocyte osmotic stability was linked to greater vitamin C intake at 0.20% saline in those without T2D (p =0.019). In this pilot study, vitamin C status did not differ significantly by diabetes status. Vitamin C status was directly linked to erythrocyte osmotic stability in adults without T2D.
ContributorsLundy, Ciara Cheyanne (Author) / Johnston, Carol (Thesis advisor) / Sweazea, Karen (Committee member) / Alexon, Christy (Committee member) / Arizona State University (Publisher)
Created2022
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Description
This work comprises a cumulative effort to provide analysis of proteins relevant to understanding and treating human disease. This dissertation focuses on two main protein complexes: the structure of the Chimp adenovirus Y25 capsid assembly, as used in the SARS-CoV-2 vaccine, Vaxzveria, and the Dbl family RhoGEF (guanosine exchange factor)

This work comprises a cumulative effort to provide analysis of proteins relevant to understanding and treating human disease. This dissertation focuses on two main protein complexes: the structure of the Chimp adenovirus Y25 capsid assembly, as used in the SARS-CoV-2 vaccine, Vaxzveria, and the Dbl family RhoGEF (guanosine exchange factor) Syx and its associated small G protein, RhoA. The course of research was influenced heavily by the onset of the Covid-19 pandemic and associated lockdown, which pushed anyone with the means to do meaningful research to shift priorities towards addressing the greatest public health crisis since the 1918 flu pandemic. Analysis of the Syx-RhoA complex for the purposes of structurally guided drug design was initially the focus of heavy optimization efforts to overcome the numerous challenges associated with expression, purification, and handling of this protein. By analyzing E. Coli derived protein new important knowledge was gained about this protein’s biophysical characteristics which contribute to its behavior and may inform drug design efforts. Expression in SF9 insect cells resulted in promising conditions for production of homogeneous and monodispersed protein. Homology modeling and molecular dynamics simulation of this protein support hypotheses about its interactions with both RhoA as well as regions of the cytoplasmic leaflet of the cell membrane. Structural characterization of ChAdOx1, the adenoviral vector used in the AstraZeneca Covid-19 vaccine, Vaxzveria resulted in the highest resolution adenovirus structure ever solved (3.07Å). Subsequent biochemical analysis and computational simulations of PF4 with the ChAdOx1 capsid reveal interactions with important implications for vaccine induced thrombocytic throbocytopenia syndrome, a disorder observed in approximately 0.000024% of patients who receive Vaxzveria.
ContributorsBoyd, Ryan J (Author) / Fromme, Petra (Thesis advisor) / Chiu, Po-Lin (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2021
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Description
MAX phases are an intriguing class of materials with exotic combinations of properties, essentially turning them into metallic ceramics. Despite this unique feature, no commercialization has been accomplished yet. Looking at the state of the art within the MAX phase community, almost all published studies can be summarized using the

MAX phases are an intriguing class of materials with exotic combinations of properties, essentially turning them into metallic ceramics. Despite this unique feature, no commercialization has been accomplished yet. Looking at the state of the art within the MAX phase community, almost all published studies can be summarized using the term “traditional high temperature synthesis”. Contrasting the scientific interest that has been on the rise especially since the discovery of MXenes, the synthetic spectrum has been largely the same as it has been over the past decades.Herein, the newly-emerging sol-gel chemistry is being explored as an alternative non-conventional synthetic approach. Building on the successful sol-gel synthesis of Cr2GaC, this study focuses around the expansion of sol-gel chemistry for MAX phases. Starting with a thorough mechanistic investigation into the reaction pathway of sol-gel synthesized Cr2GaC, the chemical understanding of this system is drastically deepened. It is shown how the preliminary nano-structured metal-oxide species develop into bulk oxides, before the amorphous and disordered graphite partakes in the reaction and reduces the metals into the MAX phase. Furthermore, the technique is extended to the two Ge- based MAX phases V2GeC and Cr2GeC, a critical step needed to prove the viability and applicability of the newly developed technique. Additionally, by introducing Mn into the Cr-Ga-C system, a Mn-doping was achieved, and for the first time for (Cr1–xMnx)2GaC, a unit cell increase could be recorded. Based on magnetometry measurements, the currently widely accepted assumption of statistically distributed Mn in the M-layer is challenged. The versatility of wet chemistry is explored using the model system Cr2GaC. Firstly, the MAX phase can be obtained in a microwire shape leveraging the branched biopolymer dextran, eliminating the need for any post-synthesis machining. Via halide intercalation, the electrical transport properties could be purposefully engineered. Secondly, leveraging the unique and linear biopolymer chitosan, Cr2GaC was obtained as thick films and dense microspheres, drastically opening potential areas of application for MAX phases. Lastly, hollow microspheres with diameters of tens of μm were synthesized via carboxymethylated dextran. This shape once more opens the door to very specific applications requiring sophisticated structures.
ContributorsSiebert, Jan (Author) / Birkel, Christina (Thesis advisor) / Gould, Ian (Committee member) / Kouvetakis, John (Committee member) / Arizona State University (Publisher)
Created2022
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Description

There has been a recent push to examine the materials that nature is able to synthesize and consider whether the materials that humans have invented are geomimetic in nature, and whether designing nature-inspired materials is economically and environmentally beneficial. Mesoporous silica represents a class of materials with pore sizes of

There has been a recent push to examine the materials that nature is able to synthesize and consider whether the materials that humans have invented are geomimetic in nature, and whether designing nature-inspired materials is economically and environmentally beneficial. Mesoporous silica represents a class of materials with pore sizes of 2-50 nm and has been studied in catalysis, separations, and drug delivery. It has generally been made using organosilicon precursors, but in this work, we demonstrate for the first time the successful synthesis of mesoporous silica with uniform mesoporosity of 10 nm using the mineral forsterite (Mg2SiO4) as a silica source, providing a potentially cheaper and more Earth-friendly route to making this technologically important material. Forsterite was synthesized by a solid-state chemistry route and underwent dissolution-reprecipitation in an aqueous acid solution containing the soft template surfactant, Pluronic P123. The formation of forsterite was confirmed with X-ray diffraction (XRD), the successful templating of surfactant was demonstrated with thermogravimetric analysis (TGA) and Fourier-transform infrared spectroscopy (FTIR), the surface area was determined through Brunauer-Emmett-Teller (BET) analysis, and pore size and distribution were demonstrated with Barrett-Joyner-Halenda (BJH) analysis. The synthesized mesoporous silica at optimal conditions has surface area of 740 m2/g and pore volume of 1.4 mL/g.

Created2022-05