VictorJuiz/thesis huggingface dataset:
Regulation of cyanobacterial physiology by the stringent response

Signals that communicate a cell’s metabolic state allow organisms to adapt to the suboptimal conditions they often encounter in the environment. If a particular nutrient is lacking, the organism reduces the energy it expends on growth and reproduction, instead redirecting its resources to maintain basic cellular functions./nCyanobacteria were the driving force behind the oxygenation of Earth’s atmosphere, the ancestor of the chloroplast, and remain an important group of primary producers today. These ‘blue-green’ bacteria carry out photosynthesis, capturing solar light energy and converting it into the chemical energy that sustains life. They also perform carbon fixation, reducing carbon dioxide into organic carbon compounds. These processes are both required to sustain cyanobacterial growth, so when the inputs of these pathways – like light – are unavailable, many metabolic changes occur that necessitate physiological adaptations./nHere, I demonstrate a major mechanism by which the cyanobacterium Synechococcus elongatus senses and responds to stresses. I find that the stringent response, a conserved bacterial stress response, is induced in response to darkness, photosynthetic inhibition, and nutrient starvation. The second messengers of this response, the phosphorylated nucleotides ppGpp and pppGpp, reprogram gene expression and induce physiological responses that can be either general or nutrient-specific. I have also begun investigating the roles of polyphosphate, a compound that accumulates in response to stress and may help cells adapt to challenging conditions, in Synechococcus./n/nCyanobacteria like Synechococcus are an interesting subject for study of the stringent response due to their unique metabolism and physiology. While the logic of the stringent response – indeed, many stress responses – is similar across many bacteria, the specific mechanisms behind them often differ. Learning more about how the same stress response mechanism has been adapted by diverse organisms will continue to increase our understanding of how bacteria interact with their environments.

Advisor: Savage, David
Radiation Transport Modeling of Kilonovae and Broad-lined Ic Supernovae

This thesis presents models of the radiative signatures of two unusual electromagnetic transients: radioactive transients ("kilonovae") associated with the merger of a neutron star with a second neutron star or a black hole, and broad-lined Type Ic supernovae. The first portion of the thesis focuses on improving inputs for radiation transport simulations of kilonovae. I first address opacity. I present new calculations of the opacities of elements synthesized in the kilonova ejecta, and carry out radiation transport simulations of kilonovae using these new opacities. Next, I develop detailed models of the radioactive heating of the kilonova ejecta and explore its effects on kilonova light curves. These two projects advanced our understanding of the expected emission from kilonovae, and will inform efforts to find and analyze these elusive transients. The final part of this thesis considers broad-lined Ic supernovae. I use multidimensional hydrodynamical and radiation transport simulations to investigate the validity of the single-engine model for broad-lined superonva Ic/gamma-ray burst systems. I demonstrate that a jet engine injected into a stripped-envelope progenitor star can produce both a supernova with broad spectral features and a long-duration gamma-ray burst.

Advisor: Kasen, Daniel
Acoustically Driven Ferromagnetic Resonance for Device Applications

Magnetic devices have become increasingly integrated into modern technology as they enable technologies as varied as computer hard drives, RF circulators, and medical diagnostic equipment. Electrically controlling magnetism in the small scale, however, has always been difficult due to the inefficiencies of generating the localized nanoscale magnetic fields necessary to precisely control such devices. Traditional macroscale methods (such as simple Oersted fields) fail when scaled to the sizes of modern device components, and even the most efficient established techniques (spin transfer torque, spin hall effect) are current-based and thus dissipate substantial power when used to switch magnetic elements./nRecent work in the field of multiferroic materials has opened the potential for using voltage, rather than current, to manipulate magnetism in these systems, potentially increasing the efficiency of nanoscale magnetic control by several orders of magnitude. In this thesis, we explore the Acoustically Driven Ferromagnetic Resonance effect in composite strain-coupled multiferroic bilayers. This technique allows for a voltage-driven piezoelectric excitation to drive magnetostrictive thin films into resonance with a much greater coupling efficiency than is possible using traditional methods. By leveraging this enhanced coupling, it is possible to develop a number of novel devices based on this interaction that span a number of extremely important commercial fields./nThis thesis experimentally explores the dependence of this effect on a number of factors such as operating frequency, input power, magnetic element size and thickness, and magnetic element composition. We also study three high-potential applications for this technology: magnetic sensing, antenna miniaturization, and room-temperature coupling to quantum systems - specifically diamond nitrogen-vacancy centers. While some of these applications are far from commercial readiness, we are able to demonstrate proof-of-concept examples for each of these concepts that demonstrate that the core concept is valid and is worth further exploration.

Advisor: Salahuddin, Sayeef
Adolescent Evaluation of Marijuana Use: Understanding Teenage Reasoning about Ambiguous Social Issues through a Social Domain Framework

The public’s understandings and attitudes toward marijuana use as well as changes in the legality and acceptability of marijuana use across the United States have undergone substantial changes in the past few decades. These shifts have led to changes in individuals’ informational assumptions (e.g., various considerations or evidence) that come to be associated with the issue, and have made marijuana use a complex social issue that is often comprised of various relevant facets warranting consideration. During adolescence, developments in individuals’ capacities for recognizing and incorporating multiple aspects of an issue enhances the potential for complexity and variation in judgments. In the present investigation, patterns of adolescents’ judgments and justifications regarding marijuana use are explored through a Social Domain Theory framework./nThe sample consisted of 100 high school junior and seniors, ages 16 through 18. Respondents completed a survey with open-ended questions asking about their judgments of marijuana use, as well as judgments of a prototypical moral issue (stealing) and a prototypical personal issue (using one’s allowance money to purchase music). Survey items asked respondents to evaluate and justify each of the three acts generally, as well as under various contingencies. Comparisons of judgment patterns were expected to demonstrate greater homogeneity in evaluations and justifications of the prototypical issues as compared with the marijuana use issue. Informational assumptions about marijuana use were also assessed through questions about the harm (or lack thereof) involved use, and hypothetical conditions regarding the absence or presence of harm./nResults indicated that respondents judged marijuana use across the social domains of reasoning, suggesting that this is an ambiguous social issue; multiple considerations including the prudence of use, individuals’ prerogatives about use, laws prohibiting use, as well as consequences to others if use was prohibited (e.g., medical uses for marijuana) were considered as respondents judged marijuana use. This was in contrast to their judgments of stealing and purchasing music (considered to be prototypical or unambiguous social issues), which were more consistently evaluated within the moral and personal domains, respectively. Moreover, informational assumptions regarding the harm involved in marijuana use suggested an association between respondents’ perceptions of the harm involved in use and their evaluations of the acceptability of marijuana use. Results demonstrated the role of informational assumptions in judgment formation and suggested the complexity in adolescent reasoning about an ambiguous social issue like marijuana use.

Advisor: Turiel, Elliot
Our Fanatics: Figurations of Religious Fanaticism in Ian McEwan, Chimamanda Ngozi Adichie, and Marilynne Robinson

Our Fanatics: Figurations of Religious Fanaticism in Ian McEwan, Chimamanda Ngozi Adichie, and Marilynne Robinson examines how three contemporary novelists complicate oft-repeated accounts that oppose religious fanaticism to reasoned argumentation and secular politics. My dissertation features novels that focus intently on the interiority of protagonists who encounter figures of religious fanaticism, portraying religious fanaticism as something to be negotiated rather than defended against. By analyzing twenty-first century novels that variously figure religious fanaticism in oppositional, paradoxical, and genealogical terms, this project examines how religious fanaticism is constitutive of—rather than external to—the worlds of these novels./nThe first chapter reaches back to Ian McEwan’s Enduring Love (1998), comparing it to his 9/11 novel, Saturday (2005), and, more recently, The Children Act (2014). I argue McEwan’s novels frame religious fanaticism as a form of irrational certainty that generates epistemological uncertainty for the novels’ protagonists. These texts frustrate a simple triumphant narrative whereby secular rationalism prevails over religious fanaticism. More recently, however, McEwan’s fiction resolves such tensions with increasing authority, gradually eliminating the experimental dimensions of McEwan’s early work. Chapter two features Chimamanda Ngozi Adichie’s Purple Hibiscus (2003), which develops an apparently paradoxical religious fanatic— politically admirable but privately violent. I investigate this paradox by analyzing the novel’s cyclical plot, which echoes the Catholic liturgical calendar and which distinguishes it from Chinua Achebe’s Things Fall Apart (1958), a comparison that has dominated Adichie’s critical reception. The third chapter reads Marilynne Robinson’s Gilead trilogy—Gilead (2004), Home (2008), and Lila (2014)—as an extended meditation on the lingering effects of religious fanaticism across the generations of a small mid-Western town. The trilogy’s genealogical figuration of religious fanaticism ties abolitionism to civil rights activism, delivering a resounding critique of “mainline” Protestant disavowals of such fanaticism./nThe religious fanatics that appear across this dissertation cannot be described in any easy sense as “ours.” My title draws attention to the smaller, subtler way that these novels approach religious fanaticism through intimate relationships and private spaces, positioning religious fanaticism as internal to communities, to families, and, particularly in Adichie and Robinson, to Christian traditions.

Advisor: Lye, Collen
Naddaff, Ramona
Alienation in the Andes: Labor and Cultural Disenfranchisement in Colonial Peru, 1570-1640

This dissertation locates a pre-history of modern material alienations in colonial Spanish America. Alienation is often understood as a modern phenomenon, the byproduct of exploitation under industrial labor or the crisis of the individual in the face of the strictures of modern society. Colonial actors, however, sensed, internalized, and expressed an understanding of and frustration with their material marginalization in the face of an ever-intensifying colonial economy that rewarded the landowning benefactor class at the expense of the diverse residents of the colonial world. Focusing on the literature, visual culture, and hagiography of mid-colonial Peru, these alienations appear and reappear in varying discourses of isolation, marginalization, and outsideness (enajenación in early modern Spanish) extending to indigenous, Spanish, and Afroperuvian subjects. In each case, land and labor are at the center of these forms of primitive alienation, causing diverse subjects to feel that the economic climate and conditions of work and worship have led the world around them to become unrecognizable, unfamiliar, and ultimately meaningless. Reading the works of Spanish colonial chroniclers, satirist Mateo Rosas de Oquendo, indigenous chronicler Felipe Guaman Poma de Ayala, and the hagiographers of Afroperuvian saint Martín de Porres as expressions of enajenación that anticipate later theorizations of alienation, I argue that as primitive accumulation anticipates capitalism, diverse colonial primitive alienations (from lands, community, spirituality, and history) arise in anticipation of the alienation of the industrial worker. This pre-history makes patent the modernity of colonial subjectivities to suggest that affective responses to the colonial enterprise mark the onset of the modern individual.

Advisor: Del Valle, Ivonne
Christian Citizenship and the Foreign Work of the YMCA

Beginning in the last decade of the nineteenth century, Christian reformers of the North American Young Men’s Christian Association and related organizations set themselves the task of training the rising leadership of nations around the world in a set of ideals they termed “Christian citizenship.” Motivated by ideas about God’s universal grace, by liberal ideals of personhood, and by fears of moral crisis, the middle class evangelical reformers of the YMCA, the YWCA, the Student Volunteer Movement (SVM), and the World’s Student Christian Federation (WSCF) sought not only to “evangelize the world in this generation,” but to teach good citizenship and encourage fair play among individuals and among nations—to foster ideals of justice, equality, and democracy among their constituencies in China, Japan, India, and beyond, in a millennial project ultimately designed to save the world, politically as well as spiritually. From the 1890s into the 1920s, Christian reformers dedicated themselves to the work of imparting the ideals of “Christian citizenship” through educational, social, and religious programs, as well as through training in sports and sportsmanship. By the 1920s, many of these reformers had come to assume that democratic nationhood should be universal—provided that both the national leaders and a critical mass of citizens had acquired a particular kind of personhood. Ultimately, however, their responses to struggles for national self-determination in the 1920s would show that their universalist commitments were, in most cases, indefinitely deferred, contingent on a pedagogical process that was never complete./nThis dissertation tells the story of the ideals of “Christian citizenship” as developed by these reformers between 1886 and 1925. On the basis of ideas and attitudes expressed by celebrated Association leaders such as Nobel Laureate John Mott, by less known figures such as YMCA Physical Director Harry Kingman, and more generally in institutional histories and surveys, official periodicals, newspaper articles, conference reports, memoirs and personal writings, and visual representations such as logos and architectural drawings, this dissertation argues that the project of fostering “Christian social relations” and instilling the ideals of “Christian citizenship” in the so-called “plastic nations” of the world was at the heart of the North American Associations’ Foreign Work during this period, and it suggests that the history of these ideas contributes to an understanding of the history of the democratic project more broadly.

Advisor: McLennan, Rebecca
Verification and Synthesis of Clock-Gated Circuits

As system complexity and transistor density increase, the power consumed by digital integrated circuits has become a critical constraint for VLSI design and manufacturing./nTo reduce dynamic power dissipation, clock-gating synthesis techniques are applied to circuits to prune register updates by modifying the next-state functions of the registers. Hence to verify this kind of synthesis, sequential equivalence checking (SEC) of clock-gated circuits is required./nIn this thesis, we examine the application of reverse engineering and control logic extraction to assist in the analysis and verification of clock-gated circuits. The proposed methodology also enables sequential clock-gating synthesis to further reduce dynamic power. A secondary focus is on recognizing circuit functionalities with deep learning techniques./nThe first part of the work deals with the use of transparent logic to recognize control and data paths of gated-level circuits. We invent abstraction models (dependencies graphs, DGs) of sequential circuits and then explain how they can be used to formulate sufficient conditions for legal clock-gating. It is then demonstrated how to perform efficient sequential equivalence checking (SEC) between a circuit before and after clock-gating synthesis based on DGs. The proposed formulation is extended to allow sequential clock-gating synthesis to be done systematically and automatically./nThe second part of the thesis introduces the use of neural networks to recognize circuit properties, which can be used to benefit and improve reverse engineering methods. We invent a representation of gate-level circuits to work with neural networks and build a framework for circuit recognition, including function classification and detection. The proposed framework can also be used to locate high-level constructs in the sea of logic gates.

Advisor: Brayton, Robert K
Low-Dimensional Materials at the Nanoscale: Transition Metal Chalcogenides, Carbon Nanomaterials and Organic Semiconductors

The overall theme of this dissertation is the electronic transport and electromechanical study of low dimensional materials at the nanoscale. The dissertation is divided into three parts based on the class of materials: I. collective ground states in ultrathin materials, II. carbon nanomaterials based nanomechanical resonators and III. organic semiconductors./nIn part I, the superconductivity and charge density waves in transition metal chalcogenides are introduced. Crystal synthesis of transition metal chalcogenides by chemical vapor transport is presented. The materials have quasi-low dimensional crystal structure: either quasi-two dimensional (e.g. NbSe2, TaS2, WTe2, FeSe) or quasi-one dimensional (e.g. NbSe3, TaS3, (NbSe4)3I). Monolayer NbSe2, grown by molecular beam epitaxy, shows a superconducting transition at Tc=2K and is studied down to 50mK with magnetic fields. The sliding charge density waves in NbSe3 nanoribbons are studied with narrowband noise, which directly probes the order parameter. A proposal to scale down the contactless conductivity measurement technique for nanoscale samples with lithographically fabricated planar coils is presented./nIn part II, microstructures of suspended carbon nanotubes and graphene are studied as nanomechanical resonators. Carbon nanotubes are clamped on one end and the other end is free to enable field emission. The field emission provides a means of electrical readout. Fabrication of carbon nanotube field emitting mechanical resonators on an integrated platform are explored. The platform is designed to allow the study of the nanomechanical motion across multiple characterization techniques. Graphene nanomechanical resonators are studied as a first step in the development of a microactuator-based platform to control strain fields in graphene. In particular, non-uniaxial strains for large pseudo-magnetic field effects are intended./nIn part III, organic nanowire formation with DPP-TPA molecules for use in photovoltaics is explored. The nanowire’s charge carrier mobility is characterized in a field effect transistor. In addition, the use of rubrene single crystals for the study of photophysics at the interface with novel acceptor molecules is explored.

Advisor: Zettl, Alex
Integration of Lithography and DNA Mediated Self-Assembly for the Synthesis of Responsive Metamaterials

Dynamic materials have always held the interest of scientists because they change their properties in response to some stimulus. Being able to program the desired material properties before and after a stimulus is important to many sensing technologies. One interesting class of materials are termed ‘metamaterials’ because they interact with light in exotic ways that naturally occurring materials do not. These engineered materials are able to interact with light (or other frequencies of electromagnetic waves) in novel ways is due to the low symmetry arrangement of their components. In order to achieve the low symmetry arrangement, lithographic techniques are commonly used to fabricate these materials, because lithography can arrange nanoscale components in arbitrary patterns. However, most lithographed materials are static and do not react to external chemical stimuli. This dissertation lays out a novel approach to rationally assemble dynamic metamaterials by combining lithographic techniques with DNA mediated self-assembly, which imparts a responsive, organic component to the metamaterial./nIntegrating DNA into a metamaterial allows for several advancements over lithographed-only metamaterials. First it allows for sub-nanometer control over the spacing of the constituent components. Second, DNA is responsive to a wide variety of stimuli—such as other DNA strands, salt, proteins, certain organic molecules, and temperature. Depending on the stimuli, one could then program a single metamaterial to respond in divergent ways to different chemical stimuli./nThe model metamaterial examined here is a three nanorod system that exhibits a property known as electromagnetically induced transparency (EIT). Two rods are defined with lithography, and the third is assembled with DNA. This hybrid organic-inorganic structure behaves in accordance to plasmon hybridization theory and finite difference time domain (FDTD) simulations. Finally, external chemical stimuli, such as removing sodium cations or dehydrating the DNA, can cause the components to either decouple or couple more strongly, causing the EIT effect to either disappear or become enhanced, respectively. This assembly method allows for creating of dynamic metamaterials that can be predictably perturbed in order to change their desired optical properties.

Advisor: Alivisatos, Paul