VictorJuiz/thesis huggingface dataset:
The surprising persistence of symmetry protected topology

Symmetry protected topological (SPT) systems are important both from a theoretical perspective, where they can provide new insight into order, symmetry, and topology, and from an applied standpoint, where they could form the basis for novel technologies. Yet for the most part, SPT systems are understood only in idealized settings. This thesis opens the door to the study of SPT systems under more realistic conditions. By theoretically and computationally investigating three physically motivated scenarios involving strong interaction, strong disorder, and quench dynamics, we demonstrate that signatures of topology can persist, in some form or another, when conditions are far from ideal. While these investigations focus on one class of model systems, we argue that the observed persistence of topological signatures should be characteristic of SPT systems, regardless of spatial dimension or protecting symmetries

Keywords: Physics.
Advisor: Devereaux Thomas Peter
Qi Xiaoliang
Khemani Vedika
Ying Lexing
Synchronous sound : strategies for collective sound generation and dispersion

Synchronization plays a critical role in the way in which we perceive sound in the natural world. In many scenarios, the auditory environment is constructed from an aggregation of coordinative and interactive behaviors that give rise to emergent sonic phenomena such as the self-organizing stridulations from a field of crickets, the urban noise surrounding a city metro stop, or the dense sonic timbres from crowd applause at the concert hall. Different models of synchronization can be utilized to analyze, recreate, and perceptually evaluate the collective dynamics of these types of phenomena. I first provide an overview of novel generative and perceptual approaches for synthesis and design applications using "coupled-oscillator" models and then propose methods for applying them to sound generation techniques more broadly. I discuss several mathematical models that simulate dynamics associated with self-synchronizing phenomena and examine different analysis techniques from relevant literature. The second part of my work concerns the "Collective Rhythms Toolbox", an open-source software toolkit for sound generation that allows users to interact with these synchronous systems. Different sonification paradigms and real-time parameterization encourage flexibility, experimentation, and cross-platform accessibility. The third part of the dissertation is a series of behavioral studies that attempt to characterize how humans extract beat when listening to swarms of sounds containing various levels of synchrony. More specifically these sensorimotor synchronization studies (SMS) concern how entrainment arises when subjects are asked to tap to stimuli synthesized from an ensemble of coupled metronome sounds with different coupling strengths. While participants were better able to extract beat when tapping to sounds containing more coupling, results also suggested that they depart from more regular beat extraction routines to accommodate stimuli with less coupling; when stimuli coupling was decreased, more participants began to tap at a faster rate and subjects were categorized into one of three tap strategy groups accordingly. In a second SMS study, I consider the effects of timbre by allowing individual metronomes to take on slight timbral variation. In this "metronome cocktail party", fewer participants resorted to frequent tapping during tap trials which suggests that differences in metronome timbres facilitated more regular beat extraction. Given that coupled systems model both musical interaction in a group setting and the production of sound in the environment, these studies provide a first glimpse into how beat is extracted in rhythmic swarms comprised of phase-locked sound onsets. Lastly, I detail the ways one can design for collective synchrony as a compositional paradigm to create immersive soundscapes. My own artistic work employing such approaches to sound design is presented alongside this research as a form of applied practice

Keywords: Music.
Advisor: Chafe Chris
DeMarinis Paul
Fujioka Takako
Synthesis and characterization of two dimensional materials for electronic and thermoelectric applications

The family of two-dimensional (2D) materials has been demonstrated to possess unique characteristics that make them appealing for scaled electronic applications. However, this versatile class of materials comes with its own unique challenges for fabrication and integration into widespread adoption. Therefore, in this work, we investigate the synthesis and properties of selected 2D materials, working to understand how their unique characteristics may impact their utility. First, we develop and refine processes for large-area chemical vapor deposition (CVD) of hexagonal boron nitride (h-BN) onto carbon nanotube (CNT) and metal substrates. We report one of the first demonstrations of direct deposition of multilayer h-BN on CNTs, resulting in a thin capping layer on the CNTs without the use of a transfer process. Additionally, we elucidate some effects of substrate crystallinity on the resultant h-BN film by characterizing films deposited on both polycrystalline and single crystal Pt substrates. Finally, we demonstrate the use of monolayer h-BN as an ultra-thin protective barrier layer, protecting monolayer MoS2 from degradation at elevated temperatures, and we discuss additional applications for this material. In addition, we investigate fundamental thermoelectric properties of thin WSe2, fabricating on-chip heater and thermometer structures and quantifiably demonstrating the benefits of using a low-thermal conductivity substrate to maintain a larger temperature gradient along the channel. Using our measurement platform, we measure the highest Seebeck coefficients for thin WSe2 reported in literature to date, demonstrating its promise for temperature sensing and energy harvesting applications. We conduct measurements on multiple WSe2 samples, studying the effect of film thickness on the thermoelectric properties, and electrostatically gate the channels using an ion gel, which enables us to sweep over a wide range of electron and hole carrier densities. Finally, we explore the effects of edge contributions to narrow MoS2 and WSe2 channels, fabricating back-gated devices on exfoliated nanoribbons. The exfoliation process to deposit these nanoribbons is promising for maintaining "pristine" edges, which are ideally in the armchair or zigzag configuration. This can allow for the impact of these edges on the electronic transport properties to be studied, and we measure numerous transistors with parallel nanoribbon channels to consider these effects. We observe some trends with the maximum and minimum currents vs. the average ribbon width of these channels, and outline the next steps for this project to further understand the edge contributions. This work explores the deposition as well as fundamental electronic and thermoelectric properties of 2D materials, aiming to incrementally advance this family of materials towards viability in larger-scale applications

Keywords: Electrical Engineering.
Advisor: Pop Eric
Asheghi Mehdi
Saraswat Krishna
Synthesis of danicalipin a precursors and cycloaddition chemistry towards the production of strained and energetic materials

This dissertation comprises two projects centered around cycloaddition chemistry towards the production of strained rings and other energy-rich compounds. The first is aimed towards developing methods for simple and scalable syntheses of useful pre-energetic materials. This research is conducted in collaboration with the Naval Air Weapons Station China Lake, the Army Research Lab at Aberdeen Proving Ground, and the Defense Advanced Research Projects Agency (DARPA). High energy materials are of significant interest for their ability to store and release energy, and are utilized in explosives, propellants, and pyrotechnics. Energetic materials for military applications must meet rigorous requirements regarding toxicity, volatility, density, and stability to storage. We aim to identify novel, low-cost materials or small molecules which could serve as energetic materials for military use. Moreover, we seek to identify energetic materials that can be accessed via simple and scalable synthetic methods. Specifically, this work focuses on the synthesis of novel isoxazole nitroxyethyl-nitramines (NENAs) and less precedented, highly strained fluoroladderenes. The second project involves the development of a novel cyclobutadiene equivalent. Cyclobutadiene has been used in Diels--Alder reactions to form strained intermediates en route to synthetic target molecules such as cubane and (+)-asteriscanolide. Due to the anti-aromatic character and intrinsic instability of cyclobutadiene itself, several cyclobutadiene metal complexes have been developed. Cyclobutadieneiron tricarbonyl is the most commonly used metal complex, but its use requires a low-yielding multistep synthesis, toxic metal-carbonyl reagents, and harsh conditions to liberate the cyclobutadiene. Our goal is to develop a bench-stable cyclobutadiene equivalent for use in Diels--Alder reactions that can be accessed in a high-yielding and scalable manner, as well as a straightforward synthesis of analogs to make substituted cyclobutadienes

Keywords: Chemistry.
Advisor: Burns Noah
Wandless Thomas
Wender Paul A.
Systematic discovery of transcriptional effectors and integrases in human cells

To understand how thousands of DNA and protein factors interact to govern the expression of the human genome and to learn how to manipulate these functions to encourage cells towards healthy states, we need scalable quantitative methods to study these factors inside human cells. In this dissertation, I describe how high-throughput synthetic biology uncovers the functions of transcription factors, non-coding regulatory elements, and recombinases, which together advance our capacity to manipulate and understand the human genome and its regulation. First, I describe how CRISPRa/i perturbation tools can exhibit off-target toxicities when applied to test the function of non-coding sequences in the human genome, and how those toxicities can be mitigated. I then discuss a high-throughput protein function screen, HT-recruit, that enabled the systematic discovery of transcriptional effector protein domains. Lastly, I describe a computational approach that identified microbial recombinases for efficient large-payload genome editing. Together, these projects demonstrate how high-throughput synthetic biology can help identify functions of protein and DNA factors in human cells and improve technologies to precisely manipulate the genome and gene regulation

Keywords: Genetics.
Advisor: Bassik Michael
Bintu Lacramioara
Greenleaf William James
Porteus Matthew H.
Ting Alice Y.
Systemic tumor immunity across tumor development and metastatic progression

The study of tumor immunology has led to great successes in the advancement of effective cancer treatments. Despite these advances, there are still tumor types and patient populations that remain unresponsive to current immunotherapies. My studies are intended to better understand the mechanisms and consequences of tumor-immune cell interactions. The studies in Chapter 1 demonstrate that effective immune responses maintain activation and proliferation of lymphocytes in the periphery rather than the tumor microenvironment. This work provides insight into the mechanisms of effective immunotherapy responses in solid tumors while also demonstrating the importance of taking a system-wide approach to such studies. We then use a mouse model of lymph node metastasis developed in our lab to investigate the factors that enable primary tumor cells to survive immune attack as they traffic to the draining lymph nodes. Based on this work we introduce our "Metastatic Tolerance" model which describes that lymph node colonization induces systemic tumor-immune tolerance and thus enables distant metastasis. In chapter two I expand on our model of metastatic tolerance by identifying B cells as an important cell type in both melanoma lymph node metastasis and tolerance induction. In chapter three I once again take a system-wide approach to demonstrate how specific genotypes, specifically Kras mutation and Trp53 deletion, alter immune responses in pancreatitis prior to the development of pancreatic ductile adenocarcinoma

Advisor: Engleman Edgar G.
Attardi Laura
Bendall Sean
Winslow Monte
Taking Data Hostage: Exploring the Feasibility of Using Ransomware for Interstate Coercion

Ransomware, a type of malware that prevents targets from accessing their own data unless a ransom is paid, has become an irresistibly lucrative tool for cyber criminals. In recent years, high-profile ransomware attacks have successfully demanded hefty ransoms from organizations worldwide, with some attacks even targeting nationally critical infrastructure. Ransomware is highly effective for extracting money, but could this technology be used by other actors, such as states, to demand things other than money? This thesis seeks to answer whether and how ransomware can be used between states to directly coerce behavioral change. To answer this question, this thesis first presents a game-theoretical model of ransomware that offers a means of logically theorizing how ransomware against states might play out. The thesis then turns to case studies of two notable criminal ransomware incidents, examining them through the lens of theories of interstate coercion. This study finds that ransomware offers some upsides as a coercive weapon between states, including the ability to improve the attack's credibility. However, ransomware is still limited by the need to assure the target that compliance will allow them to recover their data. Although it is difficult to conclusively predict the future of ransomware based on available evidence, these limitations suggest that ransomware will be bounded to narrow use cases. Nonetheless, by examining this hypothetical cyber tactic, this thesis offers some precautionary insights and reinforces the importance of strengthening the cybersecurity of critical infrastructure.

Keywords: Center for International Security and Cooperation
ransomware
Coercion
cyber warfare
Computer security
Game theory
Malware (Computer software)
Cyberinfrastructure
Computer crimes
International relations
Text
Thesis
Advisor: Lin Herbert
Ullman Jeffrey
A tale of two Americas : how rich and poor navigate the digital landscape

While social and economic inequalities in the digital landscape are a growing topic of research, there are large gaps in our knowledge of how low-income individuals engage with information online and how their digital experiences can translate into cognitive and emotional consequences. The present investigation fills these pressing gaps by combining economic principles with novel interdisciplinary research methods called Screenomics. Using Screenomics, we developed a unique dataset of more than 13 million screenshots (N = 13,498,584) taken every five seconds from the smartphones of low-income individuals and high-income individuals (N = 65) in U.S. metropolitan areas over a two-month period in 2019. This rich digital repository provides new insights into how economically disadvantaged individuals' information needs are (un)met in daily life, compared to more affluent peers. Topics include how individuals across income classes engaged with information in their roles as consumers, workers, audience members of entertainment, and voters (Study 1), how they encountered and reacted to targeted advertisements, such as payday loan ads (Study 2) and for-profit college ads (Study 3), and how individuals with low incomes faced obstacles to interacting with government websites and applications when they searched for social safety net assistance, including the Supplemental Nutrition Assistance Program (SNAP, formerly known as food stamps) and unemployment benefits (Study 4). The results show that various information demand and supply factors shaped individuals' online information lives. Consistent with the Downsian theory of rational ignorance about politics and policy, news consumption constituted only a small part of individuals' smartphone use in both income groups although low-income individuals spent significantly less time on news applications than their high-income counterparts. Digital content was generally supported by advertising for both income groups, while individuals with low incomes engaged in self-expression substantially more than individuals with high incomes. Another set of important findings highlights how encounters with content that can vex low-income individuals generate a scarcity mindset and what their smartphone use can reveal about their psychological stress. Negative digital experiences, such as exposures to payday loan ads and frustrating interactions with the government, taxed low-income individuals' cognitive and emotional resources, as evidenced by subsequent changes in consumption of future-oriented words and negative emotional words and in application switching. This dissertation enhances our understanding of how the current online information marketplace works for different income communities and the psychological consequences of disparate digital experiences, shifting the nature of the debates about digital infrastructure gaps into a new debate about content-level barriers and inequities

Keywords: Communication.
Advisor: Hamilton James
Hancock Jeff
Reeves Byron
Robinson Thomas (Thomas N.)
A tale of two minerals : using isotopes and trace elements of tourmaline and zircon to constrain fluid and magma sources in diverse settings

Accessory minerals such as tourmaline and zircon typically comprise a small fraction of a given rock, yet they offer powerful insights into its history that far outweigh their size and abundance. These insights stem from their ability to incorporate a suite of elements and their isotopes that have remarkable petrogenetic utility and retain such information across a range of geologic environments. In this dissertation, I use isotopic and trace element analysis of tourmaline and zircon to constrain the sources of fluids and magmas and understand their evolution in diverse settings. Chapter 1 of this dissertation investigates the probable sources of boron-bearing fluids that gave rise to the presence of hydrothermal tourmaline within a granitic intrusion, its metamorphosed aureole, and its unaltered wallrocks. By examining tourmaline recovered from each locality, I demonstrate via boron isotopic constraints that the ultimate source of boron is the subduction-accretionary rocks of the Franciscan Complex, although its incorporation into the intrusive-metamorphic system is accomplished in various ways. Chapters 2 and 3 of this dissertation involve two related studies that utilize zircon both as a geochronometer and as a geochemical proxy to determine magmatic crystallization ages and to infer the tectonic environments within which a magma system evolved. In Chapter 2, I demonstrate that metamorphosed plutonic and volcaniclastic sedimentary "exotic" blocks within the Yuli Belt mélange of Taiwan represent accreted and deeply-buried fragments of an early--middle Miocene magmatic arc that is a likely precursor to the modern Luzon Arc. This contrasts markedly with the current paradigm that these exotic blocks represent fragments of the South China Sea oceanic crust. In Chapter 3, I analyzed zircons from the late Miocene-- Pleistocene Luzon Arc accreted onto the Taiwan orogen to assess the arc magmatic response to the transition from intra-oceanic subduction to arc-continent collisional regime

Keywords: Geology.
Advisor: Grove Marty
Bird Dennis K.
Dorsey Rebecca J.
Pamukcu Ayla Susan
Talk is Cheap: Democracy Promotion, Human Rights Rhetoric, and the US International Military Education and Training Program

The US International Military Education and Training (IMET) Program plays a small but mighty role in fostering security cooperation with foreign military partners. IMET funding has been justified on the grounds of promoting human rights and democratic norms among foreign officer corps. IMET's track record, however, is mixed. Does the US really attempt to promote democracy through the IMET program? What relationship exists between official democracy promotion rhetoric and actual IMET aid? What kinds of regime tend to receive more IMET aid? To answer these questions,
an original sentiment analysis of nearly 4,000 US Human Rights Reports is combined with publicly available foreign aid data to reveal several key findings. US rhetoric of democracy promotion tends to call out autocrats and praise democracies. IMET aid goes primarily to middling autocracies or near-democracies. These findings suggest a pragmatic liberal internationalism may undergird IMET aid distribution. They also suggest a possible disconnect between democracy promotion and foreign military aid efforts that may cheapen American rhetoric and undermine both projects in the long run.

Keywords: Democracy
Military relations > Foreign countries
Military education > International cooperation
Civil-military relations
Text
Thesis
Advisor: Schultz Kenneth
Targeting an allosteric site in dynamin-related protein 1 to inhibit Fis1-mediated mitochondrial dysfunction

Dynamin-related protein 1 (Drp1) is a large cytosolic GTPase that orchestrates mitochondrial fission, the process by which mitochondria divide. This process is important for a variety of cellular functions including removal of damaged mitochondria, and regulation of oxidative metabolism and apoptosis. A variety of signals can activate Drp1, stimulating its translocation to the mitochondria and oligomerization into a constricting loop. Drp1 binds to and is regulated by at least four mitochondrial adaptors, Fis1, Mff, MiD49, and MiD51. Binding to mitochondrial Fis1 is linked to the cellular stress response and seems to be dispensable for normal physiological function, since inhibitors are not toxic in many cell types and in vivo. In contrast, inhibiting Drp1 binding to Mff results in mitochondrial dysfunction. When cell stress is high, Fis1-mediated mitochondrial fission increases dramatically resulting in excessive fission and a fragmented mitochondrial network. These small spherical mitochondria have a lower mitochondrial membrane potential resulting in high ROS production, metabolic collapse, release of cytochrome c, and cell death. Consequently, Drp1 has been identified as an attractive drug target offering the potential to block cell stress in diseases such as neurodegeneration, cardiac ischemia, and sepsis. However, since Drp1-Mff interaction is needed for mitochondrial quality control, general inhibition of Drp1 function may lead to on-target toxicity. Inhibition of Drp1-Fis1 interaction without blocking Drp1-Mff function could offer a way of selectively inhibiting stress-induced mitochondrial fission while maintaining mitochondrial quality. P110, a peptide-inhibitor of Drp1-Fis1 interaction, reduces pathology in numerous models of neurodegeneration, ischemia, and sepsis, without blocking physiological functions of Drp1. However, as a peptide, P110 has pharmacokinetic limitations. We therefore sought to better understand the molecular basis of P110's regulation of Drp1, and using this information, develop a small molecule that mimics P110's benefit. Ultimately, we hope to translate our findings into treatments for chronic diseases associated with excessive mitochondrial fission

Keywords: Chemical and Systems Biology.
Advisor: Mochly-Rosen Daria
Chistol Gheorghe 
Ferrell James Ellsworth