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Nucleic acid nanotechnology is a field of nanoscale engineering where the sequences of deoxyribonucleicacid (DNA) and ribonucleic acid (RNA) molecules are carefully designed to create self–assembled nanostructures with higher spatial resolution than is available to top–down fabrication methods. In the 40 year history of the field, the structures created have scaled

Nucleic acid nanotechnology is a field of nanoscale engineering where the sequences of deoxyribonucleicacid (DNA) and ribonucleic acid (RNA) molecules are carefully designed to create self–assembled nanostructures with higher spatial resolution than is available to top–down fabrication methods. In the 40 year history of the field, the structures created have scaled from small tile–like structures constructed from a few hundred individual nucleotides to micron–scale structures assembled from millions of nucleotides using the technique of “DNA origami”. One of the key drivers of advancement in any modern engineering field is the parallel development of software which facilitates the design of components and performs in silico simulation of the target structure to determine its structural properties, dynamic behavior, and identify defects. For nucleic acid nanotechnology, the design software CaDNAno and simulation software oxDNA are the most popular choices for design and simulation, respectively. In this dissertation I will present my work on the oxDNA software ecosystem, including an analysis toolkit, a web–based graphical interface, and a new molecular visualization tool which doubles as a free–form design editor that covers some of the weaknesses of CaDNAno’s lattice–based design paradigm. Finally, as a demonstration of the utility of these new tools I show oxDNA simulation and subsequent analysis of a nanoscale leaf–spring engine capable of converting chemical energy into dynamic motion. OxDNA simulations were used to investigate the effects of design choices on the behavior of the system and rationalize experimental results.
ContributorsPoppleton, Erik (Author) / Sulc, Petr (Thesis advisor) / Yan, Hao (Committee member) / Forrest, Stephanie (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Understanding solvent-mediated interactions in biomolecular systems at the molecular level is important for the development of predictive models for processes such as protein folding and ligand binding to a host biomolecule. Solvent-mediated interactions can be quantified as changes in the solvation free energy of solvated molecules. Theoretical models of solvent-mediated

Understanding solvent-mediated interactions in biomolecular systems at the molecular level is important for the development of predictive models for processes such as protein folding and ligand binding to a host biomolecule. Solvent-mediated interactions can be quantified as changes in the solvation free energy of solvated molecules. Theoretical models of solvent-mediated interactions thus need to include ensemble-averaged solute-solvent interactions. In this thesis, molecular dynamics simulations were coupled with the 3D-2PT method to decompose solvation free energies into spatially resolved local contributions. In the first project, this approach was applied to benzene derivatives to guide the development of efficient and predictive models of solvent-mediated interactions in the context of computational drug design. Specifically, the effects of carboxyl and nitro groups on solvation were studied due to their similar sterical requirements but distinct interactions with water. A system of solvation free energy arithmetics was developed and showed that non-additive contributions to the solvation free energy originate in electrostatic solute-solvent interactions, which are qualitatively reproduced by computationally efficient continuum models. In the second project, a simple model system was used to analyze hydrophilic water-mediated interactions (water-mediated hydrogen bonds), which have been previously suggested to play a key role in protein folding. Using the spatially resolved analysis of solvation free energies, the sites of bridging water molecules were identified as the primary origin of solvent-mediated forces and showed that changes in hydration shell structure can be neglected. In the third project, the analysis of solvation free energy contributions is applied to proteins in inhomogeneous electric fields to explore water-mediated contributions to protein dielectrophoresis. The results provide a potential explanation for negative dielectrophoretic forces on proteins, which have been observed experimentally but cannot be explained with previous theoretical models.
ContributorsLazaric, Aleksandar (Author) / Heyden, Matthias (Thesis advisor) / Ozkan, Banu S (Committee member) / Sulc, Petr (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Geographical visualizations are critical for multi-criteria analysis, optimization, and decision making, where the translation of spatial data into a visual form allows analysts to quickly see patterns, explore summaries and relate domain knowledge about underlying geographical phenomena. However, several critical challenges arise when visualizing large spatiotemporal datasets. While, the underlying

Geographical visualizations are critical for multi-criteria analysis, optimization, and decision making, where the translation of spatial data into a visual form allows analysts to quickly see patterns, explore summaries and relate domain knowledge about underlying geographical phenomena. However, several critical challenges arise when visualizing large spatiotemporal datasets. While, the underlying geographical component of the data lends itself well to univariate visualization in the form of traditional cartographic representations (e.g., choropleth, isopleth, dasymetric maps), as the data becomes multivariate, cartographic representations become more complex, requiring new approaches for multiclass map visualization and exploration. In this thesis, novel visual analytics methods and frameworks are proposed to support multiclass map analysis. An interactive conservation portfolio development system that combines visualization, multicriteria analysis, optimization, and decision making is developed that showcases a novel visualization and interaction design to compare different purchasing profiles under various optimization constraints. Such multiclass map analysis is then extended using concepts from scalar field topology for hotspot analysis including the introduction of a novel visualization construct combining Merge Trees and Streamgraphs.
ContributorsZhang, Rui (Author) / Maciejewski, Ross RM (Thesis advisor) / Sefair, Jorge JS (Committee member) / Bryan, Chris CB (Committee member) / Hsiao, Sharon SH (Committee member) / Arizona State University (Publisher)
Created2022
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Description
In recent years, privately owned and operated residential programs for troubled youth have been at the forefront of national discussion on institutional child abuse in state-sanctioned carceral facilities. Survivors and their advocates have argued that these programs should be regulated by state agencies and closed because they are harmful to

In recent years, privately owned and operated residential programs for troubled youth have been at the forefront of national discussion on institutional child abuse in state-sanctioned carceral facilities. Survivors and their advocates have argued that these programs should be regulated by state agencies and closed because they are harmful to residents and divert resources from effective treatment options. In opposition to the survivor movement stand owners, practitioners, and “tough on crime” politicians, who claim that that state intervention in the Troubled Teen Industry (TTI) would curtail effective treatment options for families, and in the case of faith-based programs, violate their constitutionally protected religious freedoms. Guided by the fields of Mad Studies and Critical Prison Studies, this research offers a political history of the TTI, focused on the faith-based residential facilities of Lester Roloff and Herman Fountain. It also draws on first-person interviews with three survivors of a faith-based bootcamp called Bethel Boys Academy, of the World Wide Association of Specialty Programs to delineate how these survivors make sense of their experiences before, during, and after being held captive. I conclude by arguing that the TTI survivor movement and prison abolitionists should cooperate to dismantle white supremacist political structures and improve access to meaningful treatment options for vulnerable youth.
ContributorsBrown, Andrew Gordon (Author) / Quan, H.L.T. (Thesis advisor) / Gomez, Alan E. (Committee member) / Talebi, Shahla (Committee member) / Arizona State University (Publisher)
Created2022
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Description
The focus of this study was to explore the socialization process of aerial acrobats to pain and how these workers (re)produce traditional Circus d/Discourses through occupational identity enactment. The two research questions posed in this study were answered through semi-structured interviews with 27 professional acrobats and the arts-based elicitation method

The focus of this study was to explore the socialization process of aerial acrobats to pain and how these workers (re)produce traditional Circus d/Discourses through occupational identity enactment. The two research questions posed in this study were answered through semi-structured interviews with 27 professional acrobats and the arts-based elicitation method of Photovoice. A phronetic iterative analysis revealed a subcategory of body work—pain work. Pain workers are those employees who are required to sustain, endure, and manage embodied pain to enact their occupational role. This study introduced a four-phase cyclical socialization process model through which pain work is enacted: (a) experience, (b) tolerate, (c) embrace, and (d) proselytize. Using a dramaturgical analysis framework, the findings of this study revealed aerial acrobats engage three front stage and three backstage identity enactment strategies that (re)produce institutional d/Discourses: (a) masking pain, (b) performing-despite-risk, (c) artistic sacrifice, (d) body-work double bind, (e) complicit anonymity, and (f) self-deprecation. The findings of this study carry theoretical and methodological implications for organizational communication literature in the areas of socialization, identification, and body work, as well as embodiment in qualitative research. Importantly, this study demonstrates how discourse simultaneously changes collective embodied experiences and social realities by portraying the vivid, tangible consequences on members. Limitations of the study and future directions of research are discussed.
ContributorsMartinez, Laura Victoria (Author) / Tracy, Sara J (Thesis advisor) / Zanin, Alaina C (Thesis advisor) / Brummans, Boris HJM (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Climate change poses a serious challenge humankind. Society’s reliance on fossil fuels raises atmospheric CO2 concentrations causing global warming. Already, the planet has warmed by 1.1 °C making it nearly impossible to heed the advice of the IPCC (2022) and prevent warming in excess of 1.5 °C by 2050. Even

Climate change poses a serious challenge humankind. Society’s reliance on fossil fuels raises atmospheric CO2 concentrations causing global warming. Already, the planet has warmed by 1.1 °C making it nearly impossible to heed the advice of the IPCC (2022) and prevent warming in excess of 1.5 °C by 2050. Even the current excess of CO2 in the atmosphere poses significant risks. Direct air capture (DAC) of CO2 offers one of the most scalable options to the drawdown of carbon. DAC can collect CO2 that is already diluted into the atmosphere for disposal or utilization. Central to most DAC are sorbents, i.e., materials that bind and release CO2 in a capture and release cycle. There are sorbents that cycle through a temperature swing. Others use a moisture swing, or a pressure swing or combinations of all of them. Since DAC is still a nascent technology, advancement of sorbents is an important part of DAC development. There is a nearly infinite combination of possible sorbents and form factors of sorbents that can be deployed in many different variations of DAC. Our goal is to develop a methodology for characterizing sorbents to facilitate rational choices among different options. Good sorbent characteristics include high capacity, fast sorption and desorption kinetics, low energy need for unloading, and longevity. This work presents the development of a systematic approach to evaluate sorbents from the milligram to tonne scale focusing on the important characteristics mentioned above. The work identified a good temperature swing sorbent whose characterization moved from the mg to kg scale without loss in performance. This work represents a first step in systematizing sorbent characterization for rational sorbent development programs.
ContributorsStangherlin Barbosa, Thiago (Author) / Lackner, Klaus (Thesis advisor) / Cirucci, John (Committee member) / Dirks, Gary (Committee member) / Arizona State University (Publisher)
Created2022
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Description
DNA methylation (DNAm) is an epigenetic mark with a critical role in regulating gene expression. Altered clinical states, including toxin exposure and viral infections, can cause aberrant DNA methylation in cells, which may persist during cell division. Current methods to study genome-wide methylome profiles of the cells require a long

DNA methylation (DNAm) is an epigenetic mark with a critical role in regulating gene expression. Altered clinical states, including toxin exposure and viral infections, can cause aberrant DNA methylation in cells, which may persist during cell division. Current methods to study genome-wide methylome profiles of the cells require a long processing time and are expensive. Here, a novel technique called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), which is amenable to automation. Up to 15 different samples can be combined into the same run of Mx-MeDIP-Seq, using only 25 ng of DNA per sample. Mx-MeDIP-Seq was used to study DNAm profiles of peripheral blood mononuclear cells (PBMCs) in two biologically distinct RNA viral infections with different modes of transmission, symptoms, and interaction with the host immune system: human immunodeficiency virus1 (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Analysis of 90 hospitalized patients with SARS-CoV-2 and 57 healthy controls revealed that SARS-CoV-2 infection led to alterations in 920 methylated regions in PBMCs, resulting in a change in transcription that affects host immune response and cell survival. Analysis of publicly available RNA-Sequencing data in COVID-19 correlated with DNAm in several key pathways. These findings provide a mechanistic view toward further understanding of viral infections. Genome-wide DNAm changes post HIV-1-infection from 37 chronically ill patients compared to 17 controls revealed dysregulation of the actin cytoskeleton, which could contribute to the establishment of latency in HIV-1 infections. Longitudinal DNAm analysis identified several potentially protective and harmful genes that could contribute to disease suppression or progression.
ContributorsRidha, Inam (Author) / LaBaer, Joshua (Thesis advisor) / Murugan, Vel (Thesis advisor) / Plaisier, Christopher (Committee member) / Nikkhah, Mehdi (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)
Created2022
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Description
The developing world has witnessed a rapid growth in crop production since the green revolution in the 1960s. Even though the population has almost doubled since then, food production has tripled; most of this growth can be attributed to crop research, fertilizers, infrastructure, and market development. Although the green revolution

The developing world has witnessed a rapid growth in crop production since the green revolution in the 1960s. Even though the population has almost doubled since then, food production has tripled; most of this growth can be attributed to crop research, fertilizers, infrastructure, and market development. Although the green revolution came with benefits, it has been widely criticized for its negative impact on the environment. The excessive and inappropriate use of fertilizers has led to human and livestock diseases, polluted waterways, loss of soil fertility, and soil acidity. Even though the green revolution was started to ensure food security, it has unintended consequences on human health and the surrounding environment. This dissertation focuses on the surface characteristics of graphene nanomaterials (GNMs) and their application in agriculture. Among the nutrients needed for crops, some can be easily obtained from the environment (e.g., carbon, hydrogen, oxygen, etc.), while others, like nitrogen (N), phosphorus (P), and potassium (K), often requires supplementation by fertilizers. However, conventional fertilizers have caused problems associated with soil pH changes, stunted plant growth, and disrupted beneficial microbial processes. Implementing nano-fertilizers, which can act as controlled-release fertilizers, is important. GNMs have shown some promising characteristics for the controlled release of drugs and other chemicals. Therefore, in the first part of this study, the loading capacity of the three macronutrients (N, P, and K) over GNMs of different surface chemistry was characterized. In the second part of this thesis, the effect of graphene oxide (GO) addition on wheat germination was evaluated. Rapid germination is essential for crop establishment to ensure low-cost and high-quality products and keep in check the sustainable use of resources in commercial agriculture. The results of this thesis indicated that the application of GO significantly enhanced the seed germination potential of the wheat crops. It not only increases the root weight but also improves its volume. Future work should focus on the impact of surface chemistry of GNMs on germination, which, when combined with the materials’ ability to bind nutrients, could help better guide the use of GNMs in agriculture.
ContributorsKumar, Abhishek (Author) / Perreault, Francois (Thesis advisor) / Fox, Peter (Committee member) / Oukarroum, Abdallah (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Writing speculative fiction is a valuable method for exploring the potential societal transformations elicited by advances in science and technology. The aim of this project is to use speculative fiction to explore the potential consequences of precision medicine for individuals’ daily lives. Precision medicine is a vision of the future

Writing speculative fiction is a valuable method for exploring the potential societal transformations elicited by advances in science and technology. The aim of this project is to use speculative fiction to explore the potential consequences of precision medicine for individuals’ daily lives. Precision medicine is a vision of the future in which medicine is about predicting, and ultimately preventing disease before symptoms arise. The idea is that identification of all the factors that influence health and contribute to disease development will translate to better and less expensive healthcare and empower individuals to take responsibility for maintaining their own health and wellness. That future, as envisioned by the leaders of the Human Genome Project, the Institute for Systems Biology, and the Obama administration’s Precision Medicine Initiative, is assumed to be a shared future, one that everyone desires and that is self-evidently “better” than the present. The aim of writing speculative fiction about a “precision medicine” future is to challenge that assumption, to make clear the values underpinning that vision of precision medicine, and to leave open the question of what other possible futures could be imagined instead.
ContributorsVenkatraman, Richa (Author) / Brian, Jennifer (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Hurlbut, James (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Protein-nucleic acid interactions are ubiquitous in biological systems playing a pivotal role in fundamental processes such as replication, transcription and translation. These interactions have been extensively used to develop biosensors, imaging techniques and diagnostic tools.This dissertation focuses on design of a small molecule responsive biosensor that employs transcription factor/deoxyribonucleic acid

Protein-nucleic acid interactions are ubiquitous in biological systems playing a pivotal role in fundamental processes such as replication, transcription and translation. These interactions have been extensively used to develop biosensors, imaging techniques and diagnostic tools.This dissertation focuses on design of a small molecule responsive biosensor that employs transcription factor/deoxyribonucleic acid (DNA) interactions to detect 10 different analytes including antibiotics such as tetracyclines and erythromycin. The biosensor harnesses the multi-turnover collateral cleavage activity of Cas12a to provide signal amplification in less than an hour that can be monitored using fluorescence as well as on paper based diagnostic devices. In addition, the functionality of this assay was preserved when testing tap water and wastewater spiked with doxycycline. Overall, this biosensor has potential to expand the range of small molecule detection and can be used to identify environmental contaminants. In second part of the dissertation, interactions between nonribosomal peptide synthetases (NRPS) and ribonucleic acid (RNA) were utilized for programming the synthesis of nonribosomal peptides. RNA scaffolds harboring peptide binding aptamers and interconnected using kissing loops to guide the assembly of NRPS modules modified with corresponding aptamer-binding peptides were built. A successful chimeric assembly of Ent synthetase modules was shown that was characterized by the production of Enterobactin siderophore. It was found that the programmed RNA/NRPS assembly could achieve up to 60% of the yield of wild-type biosynthetic pathway of the iron-chelator enterobactin. Finally, a cas12a-based detection method for discriminating short tandem repeats where a toehold exchange mechanism was designed to distinguish different numbers of repeats found in Huntington’s disease, Spinocerebellar ataxia type 10 and type 36. It was observed that the system discriminates well when lesser number of repeats are present and provides weaker resolution as the size of DNA strands increases. Additionally, the system can identify Kelch13 mutations such as P553L, N458Y and F446I from the wildtype sequence for Artemisinin resistance detection. This dissertation demonstrates the great utility of harnessing protein-nucleic acid interactions to construct biomolecular devices for detecting clinically relevant nucleic acid mutations, a variety of small molecule analyte and programming the production of useful molecules.
ContributorsChaudhary, Soma (Author) / Green, Alexander (Thesis advisor) / Stephanopoulos, Nicholas (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2022