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Organic compounds are influenced by hydrothermal conditions in both marine and terrestrial environments. Sedimentary organic reservoirs make up the largest share of organic carbon in the carbon cycle, leading to petroleum generation and to chemoautotrophic microbial communities. There have been numerous studies on the reactivity of organic compounds in water

Organic compounds are influenced by hydrothermal conditions in both marine and terrestrial environments. Sedimentary organic reservoirs make up the largest share of organic carbon in the carbon cycle, leading to petroleum generation and to chemoautotrophic microbial communities. There have been numerous studies on the reactivity of organic compounds in water at elevated temperatures, but these studies rarely explore the consequences of inorganic solutes in hydrothermal fluids. The experiments in this thesis explore new reaction pathways of organic compounds mediated by aqueous and solid phase metals, mainly Earth-abundant copper. These experiments show that copper species have the potential to oxidize benzene and toluene, which are typically viewed as unreactive. These pathways add to the growing list of known organic transformations that are possible in natural hydrothermal systems. In addition to the characterization of reactions in natural systems, there has been recent interest in using hydrothermal conditions to facilitate organic transformations that would be useful in an applied, industrial or synthetic setting. This thesis identifies two sets of conditions that may serve as alternatives to commonplace industrial processes. The first process is the oxidation of benzene with copper to form phenol and chlorobenzene. The second is the copper mediated dehalogenation of aryl halides. Both of these processes apply the concepts of geomimicry by carrying out organic reactions under Earth-like conditions. Only water and copper are needed to implement these processes and there is no need for exotic catalysts or toxic reagents.
ContributorsLoescher, Grant (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2020
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Description
Mixed-ionic electronic conducting (MIEC) oxides have drawn much attention from researchers because of their potential in high temperature separation processes. Among many materials available, perovskite type and fluorite type oxides are the most studied for their excellent oxygen ion transport property. These oxides not only can be oxygen adsorbent or

Mixed-ionic electronic conducting (MIEC) oxides have drawn much attention from researchers because of their potential in high temperature separation processes. Among many materials available, perovskite type and fluorite type oxides are the most studied for their excellent oxygen ion transport property. These oxides not only can be oxygen adsorbent or O2-permeable membranes themselves, but also can be incorporated with molten carbonate to form dual-phase membranes for CO2 separation.

Oxygen sorption/desorption properties of perovskite oxides with and without oxygen vacancy were investigated first by thermogravimetric analysis (TGA) and fixed-bed experiments. The oxide with unique disorder-order phase transition during desorption exhibited an enhanced oxygen desorption rate during the TGA measurement but not in fixed-bed demonstrations. The difference in oxygen desorption rate is due to much higher oxygen partial pressure surrounding the sorbent during the fixed-bed oxygen desorption process, as revealed by X-ray diffraction (XRD) patterns of rapidly quenched samples.

Research on using perovskite oxides as CO2-permeable dual-phase membranes was subsequently conducted. Two CO2-resistant MIEC perovskite ceramics, Pr0.6Sr0.4Co0.2Fe0.8 O3-δ (PSCF) and SrFe0.9Ta0.1O3-δ (SFT) were chosen as support materials for membrane synthesis. PSCF-molten carbonate (MC) and SFT-MC membranes were prepared for CO2-O2 counter-permeation. The geometric factors for the carbonate phase and ceramic phase were used to calculate the effective carbonate and oxygen ionic conductivity in the carbonate and ceramic phase. When tested in CO2-O2 counter-permeation set-up, CO2 flux showed negligible change, but O2 flux decreased by 10-32% compared with single-component permeation. With CO2 counter-permeation, the total oxygen permeation flux is higher than that without counter-permeation.

A new concept of CO2-permselective membrane reactor for hydrogen production via steam reforming of methane (SRM) was demonstrated. The results of SRM in the membrane reactor confirm that in-situ CO2 removal effectively promotes water-gas shift conversion and thus enhances hydrogen yield. A modeling study was also conducted to assess the performance of the membrane reactor in high-pressure feed/vacuum sweep conditions, which were not carried out due to limitations in current membrane testing set-up. When 5 atm feed pressure and 10-3 atm sweep pressure were applied, the membrane reactor can produce over 99% hydrogen stream in simulation.
ContributorsWu, Han-Chun (Author) / Lin, Jerry Y.S. (Thesis advisor) / Deng, Shuguang (Committee member) / Jiao, Yang (Committee member) / Emady, Heather (Committee member) / Muhich, Christopherq (Committee member) / Arizona State University (Publisher)
Created2020
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Description
This dissertation focuses on the structure-function relationships of nanomaterials (NMs) and some of their applications in environmental engineering. The aim is to investigate NMs of different surface chemistries and assess their interactions with biological models, evaluate the weathering impact and degradation parameters to improve polymer coatings, test their efficiency for

This dissertation focuses on the structure-function relationships of nanomaterials (NMs) and some of their applications in environmental engineering. The aim is to investigate NMs of different surface chemistries and assess their interactions with biological models, evaluate the weathering impact and degradation parameters to improve polymer coatings, test their efficiency for contaminant removal and provide further understanding in the safe design of nanomaterials. Nanoecotoxicological risk assessment currently suffers from a lack of testing procedures adapted to nanomaterials. Graphene oxide (GO) is a carbon nanomaterial (CNM) that consists of a single layer of carbon atoms arranged in a hexagonal network. It is decorated with a high density of oxygen functional groups including epoxide and hydroxyl moieties on the basal planes and carboxylic and carbonyl groups at the edges. The changes in surface chemistry give GO unique properties that can be tailored for a function. Additionally, because of its simple synthesis and flexible chemistry, GO has been a popular building block of many composite CNMs. In environmental engineering, specifically, water treatment, GO has been studied by itself or as a composite for pollutant removal, biofouling reduction, and as an antimicrobial agent, just to name a few. Like GO, silver (Ag) is another NM widely used in water treatment for its biocidal properties. Despite the recent growth in this field, a fundamental understanding of the function-structure relationships in NMs is still progressing. Through a systematic set of experiments, the structure-properties-function and structure-properties-hazard relationships were investigated. These relationships can be used to establish guidelines to engineer “safe-by-design” functional nanomaterials, where materials are tailored to enhance their function while minimizing their inherent biological or environmental hazard.
ContributorsBarrios, Ana Cecilia (Author) / Perreault, Francois (Thesis advisor) / Abbaszadegan, Morteza (Committee member) / Conroy-Ben, Otakuye (Committee member) / Hua-Wang, Qing (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Since the inception of DNA nanotechnology, DNA has found itself poised as one of the most robust self-assembling building blocks due to its well understood double helix structure formed by two anti-parallel strands of DNA held together by hydrogen bond from nucleobases which also provides the material programmability due to

Since the inception of DNA nanotechnology, DNA has found itself poised as one of the most robust self-assembling building blocks due to its well understood double helix structure formed by two anti-parallel strands of DNA held together by hydrogen bond from nucleobases which also provides the material programmability due to the well-understood Watson Crick base pairing rules. These capabilities have led to the exponential increase in publications showing off intricate and remarkable designs alongside ever-expanding applications. However, as the field expands there is an apparent lack of chemical diversity and functionality. To combat this my research focused on creating hybrid peptide oligonucleotide conjugates (POC) where the conjugated peptide could add chemical and structural diversity using the 20 canonical amino acids and various peptide secondary structures. In this work, I conjugate DNA to the self-assembling peptide building block the coiled coil. The coiled coil motif is formed from the self-assembly of two or more α-helical peptides and, like DNA, the coiled coil has well understood programmability. Together as a conjugate, the DNA and coiled coil, create a new self-assembling building block capable of two orthogonal self-assembling modes that can work in tandem. In this work, I used DNA coiled coil conjugates to show the capability to create first of their kind hybrid DNA/coiled coil one-dimensional fibers (chapter 2), integrate proteins (chapter 3), and to create hybrid cage structures (chapter 4). Finally, a POC hydrogel is created using the polypeptide gelatin with DNA crosslinks to create a reversible stiffening gel using toe-hold mediated strand displacement (chapter 5).
ContributorsBuchberger, Alex Richard (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Mills, Jeremy (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Fluorescence spectroscopy has been a vital technique in biophysics due to its high sensitivity and specificity. While the recent development of single-molecule (SM) techniques has furthered the molecular-level understanding of complicated biological systems, the full potential of these techniques hinges on the development and selection of fluorescent probes with customized

Fluorescence spectroscopy has been a vital technique in biophysics due to its high sensitivity and specificity. While the recent development of single-molecule (SM) techniques has furthered the molecular-level understanding of complicated biological systems, the full potential of these techniques hinges on the development and selection of fluorescent probes with customized photophysical properties. Red region probes are inherently desirable as background noise from typical biological systems tends to be at its minimum in this spectral region. The first part of this work studies the photophysical properties of red cyanine dyes to access their usefulness for particular SM applications.Protein-induced fluorescence enhancement (PIFE) based approaches are increasingly being used to investigate DNA-protein interactions at the SM level. However, a key limitation remains the absence of good red PIFE probes. This work investigates the photophysical properties of a red hemicyanine dye (Dy-630) as a potential PIFE probe. Results shed light on optimal design principles for ideal probes for PIFE applications, opening new avenues for the technique’s broad applicability in biophysical studies. Further, the photophysical behavior of two novel cyanine fluorophores in the far-red (rigidized pentacyanine) and near-Infrared (IR) (rigidized heptacyanine) region are studied. Both probes are designed to eliminate a photoisomerization caused non-radiative pathway by rigidization of the cyanine backbone. The rigidized pentacyanine was found to have desired photophysical properties and improved quantum yield, vital for application in super-resolution imaging. For rigidized heptacyanine, in contrast to the prior project, it was found that photoisomerization does not contribute significantly to the deactivation pathway. Thus, this work clarifies the role of photoisomerization on heptamethine cyanine scaffold and will enable future efforts to optimize NIR dyes for diverse applications. The second part of this work aims to answer the fundamental question of how the physics of DNA can impact its biology. To this end, interlinkage between the flexibility of local sequence context and the efficiency of uracil removal by Uracil-DNA glycosylase (UDG) protein is investigated using fluorescent base analogue, 2-Aminopurine (2-AP). In summary, this work focuses on photophysical investigations, the understanding of which is vital for the selection and development of fluorescent probes for biophysical studies.
ContributorsKumari, Nikita (Author) / Levitus, Marcia (Thesis advisor) / Gould, Ian (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two

Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two facets of the field: (1) introducing functionality through the incorporation of peptides to create DNA-peptide hybrid materials, and (2) the development of self-assembling DNA crystal lattices for scaffolding biomolecules. DNA nanostructures have long been proposed as drug delivery vehicles; however, they are not biocompatible because of their low stability in low salt environments and entrapment within the endosome. To address these issues, a functionalized peptide coating was designed to act as a counterion to a six-helix bundle, while simultaneously displaying numerous copies of an endosomal escape peptide to enable cytosolic delivery. This functionalized peptide coating creates a DNA-peptide hybrid material, but does not allow specific positioning or orientation of the peptides. The ability to control those aspects required the synthesis of DNA-peptide or DNA-peptide-DNA conjugates that can be incorporated into the nanostructure. The approach was utilized to produce a synbody where three peptides that bind transferrin with micromolar affinity, which were presented for multivalent binding to optimize affinity. Additionally, two DNA handle was attached to an enzymatically cleavable peptide to link two unique nanostructures. The second DNA handle was also used to constrain the peptide in a cyclic fashion to mimic the cell-adhesive conformations of RGD and PHSRN in fibronectin. The original goal of DNA nanotechnology was to use a crystalline lattice made of DNA to host proteins for their structural determination using X-ray crystallography. The work presented here takes significant steps towards achieving this goal, including elucidating design rules to control cavity size within the scaffold for accommodating guest molecules of unique sizes, approaches to improve the atomic detail of the scaffold, and strategies to modulate the symmetry of each unique lattice. Finally, this work surveys methodologies towards the incorporation of several guest molecules, with promising preliminary results that constitute a significant advancement towards the ultimate goal of the field.
ContributorsMacCulloch, Tara Lynn (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Over the past four decades, DNA nanotechnology has grown exponentially from a field focused on simple structures to one capable of synthesizing complex nano-machines capable of drug delivery, nano-robotics, digital data storage, logic gated circuitry, nano-photonics, and other applications. The construction of these nanostructures is possible because of the predictable

Over the past four decades, DNA nanotechnology has grown exponentially from a field focused on simple structures to one capable of synthesizing complex nano-machines capable of drug delivery, nano-robotics, digital data storage, logic gated circuitry, nano-photonics, and other applications. The construction of these nanostructures is possible because of the predictable and programmable Watson-Crick base pairing of DNA. However, there is an increasing need for the incorporation of chemical diversity and functionality into these nanostructures. To overcome this challenge, this work explored creating hybrid DNA nanostructures by making self-assembling small molecule/protein-DNA conjugates.In one direction, well studied host-guest interactions (i.e. cucurbituril[7]-adamantane) were used as the choice of self-assembling species. Binding studies using these small molecule-DNA conjugates were performed and thereafter they were used to assemble larger DNA origami nanostructures. Finally, a stimulus responsive DNA nano-box that opens and closes based on these interactions was also demonstrated. In another direction, a trimeric KDPG aldolase protein-DNA conjugate was probed as a structural building block by assembling it into a DNA origami tetrahedron with four cavities. This hybrid building block was thereafter characterized by single particle cryo-EM and the resulting electron density map was best fit by simulating origami cages with varying number of proteins (ranging from 0 to 4). Next, to increase access and for larger democratization of the field, an automation designer software tool capable of making DNA nanostructures was made. In this work, the focus was on making curved 3D DNA nanostructures. The last direction probed in this work was to make optical metamaterials based on complex 3D DNA architectures. Realization of a self-assembled 3D tetrastack geometry is still an unachieved dream in the field of DNA self-assembly. Thus, this direction was probed using DNA origami icosahedrons. Finally, the work covered in my thesis probes multiple directions for advancing DNA nanotechnology, both fundamentally and for potential applications.
ContributorsNarayanan Pradeep, Raghu (Author) / Yan, Hao HY (Thesis advisor) / Stephanopoulos, Nicholas NS (Thesis advisor) / Liu, Yan YL (Committee member) / Mills, Jeremy JHM (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Interactions between proteins form the basis of almost all biological mechanisms. The majority of proteins perform their functions as a part of an assembled complex, rather than as an isolated species. Understanding the functional pathways of these protein complexes helps in uncovering the molecular mechanisms involved in the interactions. In

Interactions between proteins form the basis of almost all biological mechanisms. The majority of proteins perform their functions as a part of an assembled complex, rather than as an isolated species. Understanding the functional pathways of these protein complexes helps in uncovering the molecular mechanisms involved in the interactions. In this thesis, this has been explored in two fundamental ways. First, a biohybrid complex was assembled using the photosystem I (PSI) protein complex to translate the biochemical pathways into a non-cellular environment. This involved incorporating PSI on a porous antimony-doped tin oxide electrode using cytochrome c. Photocurrent was generated upon illumination of the PSI/electrode system alone at microamp/cm2 levels, with reduced oxygen apparently as the primary carrier. When the PSI/electrode system was coupled with ferredoxin, ferredoxin-NADP+ reductase (FNR), and NADP+, the resulting light-powered NADPH production was coupled to a dehydrogenase system for enzymatic carbon reduction. The results demonstrated that light-dependent reduction readily takes place. However, the pathways do not always match the biological pathways of PSI in nature. To create a complex self-assembled system such as the one involving PSI that is structurally well defined, there is a need to develop ways to guide the molecular interactions. In the second part of the thesis, this problem was approached by studying a well-defined system involving monoclonal antibodies (mAbs) binding their cognate epitope sequences to understand the molecular recognition properties associated with protein-protein interactions. This approach used a neural network model to derive a comprehensive and quantitative relationship between an amino acid sequence and its function by using sparse measurements of mAb binding to peptides on a high density peptide microarray. The resulting model can be used to predict the function of any peptide in the possible combinatorial sequence space. The results demonstrated that by training the model on just ~105 peptides out of the total combinatorial space of ~1010, the target sequences of the mAbs (cognate epitopes) can be predicted with high statistical accuracy. Furthermore, the biological relevance of the algorithm’s predictive ability has also been demonstrated.
ContributorsSingh, Akanksha (Author) / Woodbury, Neal (Thesis advisor) / Liu, Yan (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021
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Description
The severe resistance of bacteria and fungi towards common antibiotic drugs has led to the increasing prevalence of infections due to multi-drug resistant microbes, which is one of the most serious issue faced by the healthcare system worldwide. These drug-resistant bacteria have led to significant health problems and fatalities whereas

The severe resistance of bacteria and fungi towards common antibiotic drugs has led to the increasing prevalence of infections due to multi-drug resistant microbes, which is one of the most serious issue faced by the healthcare system worldwide. These drug-resistant bacteria have led to significant health problems and fatalities whereas drug-resistance fungi possess significant threat to humans, livestock, and crops globally. Furthermore, this drug resistance leads to the formation of biofilms, which are thick layers of microbes embedded in extracellular polymeric matrix. They adhere to both living and nonliving surfaces, making it harder to contain or eradicate these pathogens. The conventional strategy for combating these pathogenic bacteria and fungi has its limitations and new antimicrobials are constantly required to fight the growing resistant mechanisms. Hence, there is an immediate need for an alternative strategy to combat these drug-resistant isolates. Herein, this dissertation reports the development of novel potent antimicrobial agent based on tow-dimensional layered nanomaterials dispersed in biocompatible oligonucleotide, biomolecules, polymers, and surfactant. These synthesized novel nanomaterials successfully eliminated multidrug-resistant microbes with synergistic efforts of physical interaction, membrane disintegration, depolarization and intrinsic antimicrobial properties leading to cell death. These systems were highly effective against a broad spectrum of microbes including drug-resistant gram-positive, gram-negative bacteria and fungal isolates. Furthermore, they were successful in eradication of mature biofilm as well as inhibition of biofilms on several medically relevant surfaces. Overall, these novel systems have exceptional potential as a promising alternative solution in solving current problems faced by the healthcare system sue to these pathogenic microbes. For the next direction, a different avenue was explored where a novel system based on two-dimensional layered material with antibacterial properties was analyzed for enzyme-like activity. These nanomaterials with intrinsic enzyme-like properties are commonly known as nanozymes have many advantages over natural enzymes such as low cost, scalability and high stability. A class of ultra-high temperature ceramics known as metal diborides were synthesized in biocompatible surfactant followed by analysis of their enzymatic activity and antibacterial activity. Results demonstrate this novel system possesses a unique combination of exceptionally high affinity towards hydrogen peroxide and high activity per cost. Furthermore, it is extremely potent against pathogenic bacteria and has a high degree of biocompatibility. Hence, this new system opens the door for future possible applications in biomedicine with further research.
ContributorsSaha, Sanchari (Author) / Green, Alexander A. (Thesis advisor) / Wang, Qing Hua (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2021
Description
Membrane proteins act as sensors, gatekeepers and information carriers in the cell membranes. Functional engineering of these proteins is important for the development of molecular tools for biosensing, therapeutics and as components of artificial cells. However, using protein engineering to modify existing protein structures is challenging due to the limitations

Membrane proteins act as sensors, gatekeepers and information carriers in the cell membranes. Functional engineering of these proteins is important for the development of molecular tools for biosensing, therapeutics and as components of artificial cells. However, using protein engineering to modify existing protein structures is challenging due to the limitations of structural changes and difficulty in folding polypeptides into defined protein structures. Recent studies have shown that nanoscale architectures created by DNA nanotechnology can be used to mimic various protein functions, including some membrane proteins. However, mimicking the highly sophisticated structural dynamics of membrane proteins by DNA nanostructures is still in its infancy, mainly due to lack of transmembrane DNA nanostructures that can mimic the dynamic behavior, ubiquitous to membrane proteins. Here, I demonstrate design of dynamic DNA nanostructures to mimic two important class of membrane proteins. First, I describe a DNA nanostructure that inserts through lipid membrane and dynamically reconfigures upon sensing a membrane-enclosed DNA or RNA target, thereby transducing biomolecular information across the lipid membrane similar to G-protein coupled receptors (GPCR’s). I use the non-destructive sensing property of our GPCR-mimetic nanodevice to sense cancer associated micro-RNA biomarkers inside exosomes without the need of RNA extraction and amplification. Second, I demonstrate a fully reversibly gated DNA nanopore that mimics the ligand mediated gating of ion channel proteins. The 20.4 X 20.4 nm-wide channel of the DNA nanopore allows timed delivery of folded proteins across synthetic and biological membranes. These studies represent early examples of dynamic DNA nanostructures in mimicking membrane protein functions. I envision that they will be used in synthetic biology to create artificial cells containing GPCR-like and ion channel-like receptors, in site-specific drug or vaccine delivery and highly sensitive biosensing applications.
ContributorsDey, Swarup (Author) / Yan, Hao (Thesis advisor) / Hariadi, Rizal F (Thesis advisor) / Liu, Yan (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2021