VictorJuiz/thesis huggingface dataset:
Automated qubit design for superconducting circuit topologies via autodifferentiation
Keywords: Physics
Superconducting
Quantum computing
Optimization
Josephson junctions
Autodifferentiation
Back propagation (Artificial intelligence)
Machine learning
Electronic circuits
Quantum electronics
Decoherence
Quantum hardware
Text
Thesis

In this thesis, we explore the possibility of optimizing general superconducting circuits via autodifferentiation. Following a summary of the essential components of superconducting circuits leading to a generalized expression for their Hamiltonian, we use an analytical solution for the gradient of the eigenvalues and eigenvectors to fill in a missing gradient step and form a general computational graph for arbitrary smooth loss functions that depend on circuit parameter values and its eigenvalues or eigenvectors.
After verifying numerically that the resultant gradients predicted match a first-order approximation to high precision, we leverage knowledge of the gradient to perform optimization over key metrics including the fundamental resonant frequency of the circuit, its anharmonicity, charge and flux sensitivities, and both its longitudinal and dephasing coherence times. We demonstrate by comparison of these key metrics before and after that the minimization of our objective loss functions corresponds to the intended improvement in circuit characteristics. We demonstrate concurrent optimization of each of these objectives in the flux-tunable transmon and fluxonium circuit topologies, then show that randomly sampling parameter values within some fixed range can lead to optimization on-par with SOTA experimental devices.
Finally, we assess how to address the problem of allocating truncation numbers for fixed computational resources, to maximize the convergence of the circuit eigenspectrum. Using this means of truncation number allocation, we undertake a preliminary investigation of a circuit with N = 3 inductive (Josephson junction) elements, showing that its overall performance for a small set of random samples can outperform that of both kinds of circuits with only N = 2 single-loop inductive elements. We conclude with an outlook on further applications of the tools and methodologies developed here, particularly with regards to designing better qubits for design and experimentation in-lab.
Bacteriophage as diagnostic and pathogenic factors in human disease
Keywords: Medicine.
Microbiology and Immunology.

The human microbiome plays an important role in human health and disease. Study of the human microbiome typically focuses on bacteria, fungi, and viruses which infect mammalian cells. An often-ignored facet of these communities are bacteriophage. These are viruses which infect bacteria with a specificity to the species or strain level. Though bacteriophage do not infect mammalian tissues, they are important in human health and disease. In this dissertation, I will describe our work in exploring the role of bacteriophage in the human body -- from their utility as diagnostic targets in bacterial infections, to their direct and indirect influence on mammalian cells and health outcomes. Collectively, these studies demonstrate that bacteriophage are a critical facet of the human microbiome, in particular in contexts of bacterial infection, and provide new avenues for both diagnostic and prognostic targets in human health and disease.
Balance and coordination between cell growth and DNA replication in distantly related bacteria
Keywords: Humanities and Sciences.
Biology.

Cell growth and DNA replication are ubiquitous processes of all cellular life. Model bacteria, being genetically tractable and relatively simple to work with, provide excellent systems to investigate cellular growth. Yet, bacterial life is also highly diverse, allowing us to examine a wide variety of questions about how cells grow and proliferate. In this work, we leverage this natural variability to ask two very different questions about cell growth and its relationship to DNA replication. Chapter 2 addresses the question, what are the origins of the fundamental limits of cell growth? We employ the popular model organism Escherichia coli to interrogate the assumption that ribosomes serve as the sole bottleneck of growth rate in bacteria. Using timelapse microscopy of filamenting strains, as well as single molecule tracking of the molecular machines RNA polymerase (RNAP) and ribosomes, this project shows that when genome concentration is diluted by cell growth, growth quickly exits the exponential regime and reaches a plateau. As the genome is diluted, the fraction of active RNAPs and ribosomes decreases, presumably as a result of decreased mRNA concentration. Thus, this project demonstrates that DNA concentration quickly becomes limiting for the attainable cell growth rate, and does so within the physiologic cell size range. This work proposes that bacteria live at the cusp of DNA limitation, a bottleneck of cell growth not previously appreciated. Our findings highlight the economical nature of bacteria and emphasize the importance of initiating DNA replication at a particular mass per origin of replication. Chapter 3 poses the question, how does a bacterium with an unusually complex life cycle grow? Using modified timelapse microscopy techniques, this work shows that the functionally different daughter cells that result from the asymmetric division of the ɑ-proteobacterium Caulobacter crescentus grow at different rates that are associated with the amount of time cells spend in the pre-DNA replication (G1) phase. By following the cell cycle localization of the well-described DNA replication-associated protein MipZ, this project identifies a connection between growth rate and DNA replication not previously appreciated in this bacterium: a requisite increase in cell size that must be added between cell birth and DNA replication initiation, referred to here as the "G1 adder". We speculate on the utility of the G1 adder as a means to integrate growth rate, cell size, and cell cycle progression with the functionality of the G1 phase specific to this bacterium. Finally, this project begins probing the source of the cell cycle correlated growth rate change and proposes areas of future study. Together, these studies represent the questions, from the broad and universal to the fascinatingly specific, that can be examined using bacteria as models of cell growth.
Beatrix Potter and The Art of Topophilia
Keywords: Beatrix Potter, Topophilia, preservation, art
Text
Thesis

Beatrix Potter and The Art of Topophilia

Beatrix Potter, the children’s author, and illustrator of over thirty books, including The Tale of Peter Rabbit, is known for her elegantly dressed anthropomorphic animals and charming stories set in the British countryside. Discovering Potter’s obsession with place, we find she looks with dismay at industrialization’s erosion of British landscapes and rural life and uses her books not only to represent natural spaces in their most idealized form but also to engender a profound emotional attachment to those spaces--a kind of topophilia--in her readership. Her storybook renderings of the English countryside and way of life, challenge monolithic Victorian narratives of progress and development by inviting readers to inhabit a natural world defined by diurnal rhythms. Reading Potter's writings and artwork through a topophilic lens, we see that her goal is not merely to provide an escape from the constant encroachment of industrialized modernity on nature, but rather to send her readers back into the real world with a heightened sensitivity to the intrinsic value of natural spaces and an increased commitment to preserving them.
Before the red pill : the men's rights movement and American politics, 1960-2005
Keywords: Humanities and Sciences.
History.

"Before the Red Pill" traces the American men's rights movement (MRM) from its roots in the early 1960s to its growing influence in mainstream national politics by the early 2000s. Examining both MRM leadership efforts and grassroots organizing across the United States, this dissertation utilizes organizational papers, activist correspondence, oral histories, movement newsletters, advice literature and memoirs, and mainstream press coverage. The dissertation reveals the complex dynamics of gender, race, and politics in the growth of the MRM. The experience of divorce radicalized men's rights activists, who began organizing in the 1960s to reform family law. Rather than a mere backlash against feminism, men's rights thinkers adapted some of their most important insights and strategies from second-wave feminists throughout the 1970s, before becoming militantly misogynistic by the 1990s. Both conservative women intellectuals and second wives of divorced men's rights activists played critical roles during this era, softening the movement's public image and aiding in the development of a fathers' rights sub-movement devoted to child custody and support reforms. Overwhelmingly white themselves, men's rights thinkers made selective allusions to race to compare their politics to the Black freedom struggle, yet they distanced themselves from potential Black members amid the racialized politics of the 1980s and 1990s. By the turn of the twenty-first century, men's rights activists devoted themselves to undermining feminist organizing against rape, domestic violence, and sexual harassment while claiming that men, rather than women, were the true victims of gendered violence. The simultaneous intensification of antifeminist and anti-state sentiments among activists pushed the movement further rightward into conservative partisan politics. Understanding the men's rights movement helps explain the emotive roles of masculinity, grievance, and entitlement in mobilizing the far Right base and maintaining persistent inequalities in the contemporary United States
Belonging at work : the role of organizational factors and interpersonal interactions in maintaining workplace inequality
Keywords: Humanities and Sciences.
Sociology.

This dissertation, comprised of three papers, explores mechanisms operating within engineering and technology work environments at the organizational and interactional levels that help perpetuate societal-level gender and race inequalities. The first paper provides support for the hypothesis that in the absence of intentional action to counteract stereotypes, organizations promote employees into jobs aligned with racialized gendered stereotypes, net of performance and experience. This paper highlights the importance of taking an intersectional approach to the study of gender inequality by demonstrating how analyzing data by gender alone can mask important trends by race, gender, and job and their intersection. The second paper demonstrates that undesirable and inequitable working conditions for women in occupations filled mostly with men contribute to lower retention of women, especially racial minority women, in traditionally masculine, higher paying jobs, contributing to occupational gender segregation, the biggest contributor to the gender pay gap. The third paper describes one way to create more equitable conditions for minority groups, including women, at work. This paper documents the results of a field experiment showing that improving interpersonal interactions in a tech company has an especially positive effect among workers who feel least like they belong at work, a group of workers who are disproportionately women and racial minorities. This paper provides an experimentally validated template for improving interactions, pointing a way toward creating more inclusive organizations that support a sense of belonging for all workers, an important step toward reducing societal gender and racial inequality. Together, these papers contribute new knowledge to our understanding of how gender and race inequalities persist within technical work organizations and suggest ways of mitigating those inequalities. More broadly, this research sheds light on the continual creation and maintenance of inequalities that occur in many settings throughout society through interpersonal interactions and organizational structures and policies
The best laid plans : assessing urban space on Hadrian's wall
Keywords: Humanities and Sciences.
Classics.

Rarely are sites on Rome's northern frontiers, especially Hadrian's Wall, described as 'urban'. Their smaller spaces and military origins lack many features of Mediterranean cities. Yet in modern planning theory, the definition of urban can be far more expansive; it can include frontier sites, offering a broader perspective on their military architecture. The theory emphasizes the role of multiple communities, the cyclical patterns in space, and the long-term and adaptive reuse of structures. The close study of structural patterns and spatial themes draws out the complexity of the socio-spatial interactions at frontier sites. This dissertation adapts Everyday Urbanism, a postmodern planning framework, to interpret Vindolanda and Corbridge as urban spaces on the Hadrian's Wall frontier. Combining structural analysis with an intensive study of archival material, it explores the changing dynamics of community and place over multiple centuries. The Vindolanda case study evaluates the area within the fort's walls from the third century CE into the post-Roman period. Tracing structural continuity and change across buildings and infrastructure, it demonstrates how the physical fabric of the fort both accommodated and reflected the needs of the larger community. The Corbridge case study explores the negotiations between design, intended used, and lived reality along the main street and its structures both monumental and ordinary. Research on Corbridge has focused predominantly on its early military role; this work centers its longer history and larger community in an urban context. Reconsidering Vindolanda and Corbridge as urban spaces emphasizes their architectural dynamism and reflects the inhabitants' influence on the place. The urban framework offers a new approach to interpreting spatial organization and structural use on the frontier. Evaluating the archaeological details within a larger theoretical frame, this dissertation affords insights into how the community made urban space and the lived experience of the frontier
Beyond the Laughter: Exploring Notions of Gender, Race, and Empathy in the Landscape of Reaction Memes
Keywords: Social media
Technology
Memes
Twitter
Gender identity
Performance
Text
Thesis

This project explores the significance of viewing social media and technology through the lens of cultural and knowledge production, particularly within the context of Black studies. It emphasizes the role of social media as a platform for communication and the production of cultural knowledge, which influences and integrates into real-world experiences. The project specifically focuses on the interaction between memes, reaction culture, and the representation of Black Gender-Marginalized individuals on Twitter. Drawing on the works of scholars like Sylvia Wynter, Saidiya Hartman, Nicole Fleetwood, Sarah Haley, Zakiyyah Iman Jackson, Toni Morrison, Katherine McKittrick, and Christina Sharpe, the research seeks to understand the implications of memes and reaction culture in shaping identities and examining how they are constituted, ascribed, and organized. The project also aims to uncover what is gained or lost in the viral nature of these reaction videos and how it impacts individuals who encounter these tweets. This research holds significance due to the unique nature of technology as both a liberating and violent sphere of social communication. It recognizes that violence can manifest in visible and shocking ways, but also in practices that obscure the harm inflicted. By examining the nuanced forms of violence that occur on social media platforms, the study seeks to bring attention to these issues in the hope of minimizing and eliminating such violence.
Bidirectional relationships between sleep and affect in daily life
Keywords: Humanities and Sciences.
Psychology.

Sleep and affect often are said to have a bidirectional relationship that can lead to either negative or positive results. On this view, when we feel bad before bed, we sleep poorly that night, and when we sleep poorly, we feel worse the next day. In contrast, when we feel good before bed, we sleep well that night, and when we sleep well, we feel better the next day. Despite the widespread currency of this bidirectional view, the empirical literature on bidirectional sleep-affect links in healthy adults is mixed. The aims of this dissertation were to bring conceptual clarity to the question of whether bidirectional links exist between sleep and affect and to test whether observational evidence exists for temporally directional links between specific granular dimensions of sleep and affect. Three projects were conducted to address these aims. The first project proposes a conceptual framework that characterizes associations between sleep and affect by granular, dimensional categories. That framework is then used to organize a systematic review of relevant PubMed articles and identify gaps as well as patterns of converging associations in the literature. The second and third projects address gaps or inconclusive patterns identified by the systematic review. Specifically, the second project examines how naturalistic pre-sleep affect in three different domains -- positive, negative, and arousal -- relates to sleep macro- and micro-architecture during a subsequent night of sleep at home. The third project examines associations from the same three domains of affect before bed to sleep quality and duration that night, and from sleep quality and duration to affect the next morning. Testing for the presence of bidirectional associations in a single model makes it possible to determine whether each temporal direction accounts for independent variance. Taken together, these projects provide a new framework for describing existing findings and testing new hypotheses about sleep-affect links. Finally, the dissertation concludes with a discussion of several factors that could explain the gap between lay intuitions and empirical results as described in the present work and offers promising future research directions to further investigate links between sleep and affect
Biofidelic colloidal interactions : advanced computational representation and impacts on cellular biology
Keywords: Engineering.
Chemical Engineering.

The interior of biological cells is a dynamic milieu of interacting molecules that work together to carry out life-essential functions. Mechanistic understanding of cellular behavior thus requires integration of physics and chemistry across multiple length- and timescales, from molecular self-assembly to whole-cell processes. The established modeling paradigms of structural and systems biology excel at interrogating the extremes of these scales. In the past few decades, emergent computational efforts have closed this divide, aiming to predict whole-cell behaviors based solely on knowledge of microscopic biomolecular details. This 'mesoscale' is the domain of colloidal physics, suspension mechanics, and fluid dynamics. In this dissertation, I describe our work developing colloidal-scale computational models of biological systems, with explicit representation of molecular size, interactions, reaction chemistry, and first-principles diffusive transport. Across three specific applications in cell biology, I demonstrate how such physico-chemical phenomena underpin emergent molecular behaviors essential to predicting cell function. My work enables interrogation of dynamics below experimental resolution limits, illustrated by our model of ultra-weak protein-protein interactions (PPIs) in minimal cells. I then expand our group's previous model of bacterial protein synthesis, which identified that physical transport of translation molecules was rate limiting. I demonstrate a 'pre-loading' mechanism by which PPIs between translation molecules further shorten transport times, thus speeding protein synthesis and supporting faster cellular growth rates. Finally, I present our whole-cell colloidal model of E. coli, developed alongside in vivo particle tracking experiments, which demonstrates how molecular interactions and cell-scale characteristics organize the cellular interior. Overall, these results support a broader colloidal basis for cell fitness and lay a foundation for prediction and engineering of whole-cell behaviors by tuning molecular and mesoscale physical features
Biomaterials-based models of adult and pediatric brain cancer elucidate the role of cell-matrix interactions
Keywords: Engineering.
Bioengineering.

Adult and pediatric brain cancers reside in complex 3D microenvironments and are constantly subjected to a spectrum of mechanical and biochemical cues from the surrounding extracellular matrix (ECM). Cells sense and respond to these niche cues, and this interplay plays a critical role in regulating tumor progression. For instance, despite being mechanically confined by the 3D microenvironment, cancer cells are notoriously invasive and can rapidly overcome physical barriers. This requires cancer cells to engage mechanotransductive pathways to adapt, generate, and transmit biophysical forces to overcome the surrounding mechanical constraints. Moreover, these ECM niche properties have also been found to influence aggressive cancer cell phenotype and response to standard-of-care therapy regiments. While recent advancements have revealed the importance of niche cues in driving tumor progression, this field is still in its infancy especially for these aggressive brain cancers. My thesis work aims to investigate how mechanical properties of the tumor niche such as matrix viscoelasticity and stiffness regulate adult Glioblastoma Multiforme (GBM) invasive behavior and chemoradiotherapy response. Specifically, through the development of an engineered and tunable 3D biomaterials-based hydrogel model, I show that adult derived GBM cells are sensitive to matrix viscoelasticity and stiffness cues present within the tumor niche. Moreover, I identify and validate biophysical mechanisms mediating aggressive behavior via both cytoskeletal and nuclear mechanotransduction pathways in response to brain-mimicking mechanical cues. Additionally, I have worked to uncover the role of ECM ligands and their associated integrin receptors on invasion and treatment response for a rare but devasting pediatric brain cancer known as Diffuse Intrinsic Pontine Glioma (DIPG). By leveraging human induced pluripotent stem cell-derived neural organoids as a model system, I demonstrate that laminin associated integrin knockdown dampens DIPG invasion and improves therapy response. Ultimately, this thesis work elucidates novel biophysical mechanisms driving key brain cancer processes and identifies potential strategies to improve current treatment regimens.