VictorJuiz/thesis huggingface dataset:
Optical Study on WS2/WSe2 Moir ́e Superlattices

Two-dimensional (2D) materials have drawn tremendous research interest ever since the isolation of graphene in 2004. Due to weak Van der Waals bonding between layers, 2D ma- terials can be stacked together to form synthetic heterostructures with emergent electronic and excitonic properties. Recently, there has been great research interest in controlling the twisting angle between different layers to further control the material properties. One inter- esting case is when the system forms moir ́e superlattices. In this thesis, I focus on optical studies on one of the model moir ́e superlattices—transition metal dichalcogenides (TMD) based WS2/WSe2 moir ́e superlattices. With their strong light-matter interactions and large spin-orbital splitting, this system provides a unique opportunity to optically detect and ma- nipulate the correlated quantum states of matter. Our studies show important influence from the moir ́e potential on TMD’s optical properties and illustrate how we can utilize TMD’s unique properties to study interesting phases in moir ́e superlattices.In the first chapter, I will give a brief introduction to moir ́e superlattices and exciton states in WS2/WSe2 and their heterostrcutures. Following chapters consist of a series of studies we conducted on the system. Chapter 2 focuses on interlayer exciton states in WS2/WSe2 moir ́e superlattcies and their novel selection rules. Combining senstive measurements of pump probe spectroscopy and photoluminescence excitation, we identified different components in their selection rule and uniquely determine their quasi-angular momentum. Chapter 3 shows how we can utilize the intralayer exciton states in TMDs to detect strongly correlated insulating states in moir ́e superlattcies. We observed generalized Wigner crystal states that confirms the very strong correlation in WS2/WSe2 moir ́e superlattcies. In Chapter 4, I discuss our study on intralayer exciton states near correlated phases. With doping dependent aborption spectrum, we observed sharpening of the exciton states near correlated states. This indicates the changing of dielectric environments for these exciton states and other potentially interesting interactions between the insulating states and exciton states. In Chapter 5, I describe the spin-valley current in WS2/WSe2 moir ́e superlattices. We used spatially-resolved pump probe spectroscopy to create and detect pure spin-valley current. We observed much smaller mobility in the moir ́e superlattcies than large twist angle heterostructures, indicating strong moir ́e potential might impede the motion of spin. Since the mobility stays flat near correlated insulating phases while the electron conductivity dramatically changes, the system shows spin charge separation.

Advisor: Wang, Feng
Holistic Study of Bacterial Signaling System Evolution

Bacterial signaling systems regulate vast physiological functions, from general stress responses to consumption of nutrients. Their study is often limited to the interrogation of single systems within model bacterial species, such as Escherichia coli. This framework is limiting, because it does not consider evolutionary relationships between the hundreds of systems on a single chromosome and omits the context of other extant non-model bacterial species. In this thesis, I make a case for a holistic approach to interrogate the functions of bacterial signaling systems. I develop a suite of high-throughput experimental and computational methods that when implemented elucidate the functional and evolutionary relationships between bacterial two-component systems. A holistic view of bacterial signaling systems might one day be utilized as a general tool for functional annotation and has the potential to unlock networks of regulation for non-model bacterial species.

Advisor: Keasling, Jay D
Mukhopadhyay, Aindrila
Searching for 0νββ Decay with CUORE and CUPID

Since they were first postulated, neutrinos have been one of the most mysterious fundamental particles known to us. The discovery of neutrino oscillation has shown that contrary to our original assumptions, neutrinos are not all massless. This has renewed interest in the idea of Majorana neutrinos as an explanation for the small but nonzero neutrino masses, and the search for neutrinoless double-beta ($0\nu\beta\beta$) decay is currently the most sensitive way to probe this possibility. An observation of this process would constitute the first example of violation of lepton number conservation, demonstrate that neutrinos have a Majorana nature, and help set the scale of their absolute masses. CUORE (Cryogenic Underground Observatory for Rare Events) is one of the leading experiments in the current international program looking for evidence of $0\nu\beta\beta$ decay./nIn part I of this dissertation I present a $0\nu\beta\beta$ search based on analysis of CUORE data from its first tonne-year of $^{\textrm{nat}}$TeO$_2$ exposure, corresponding to 288.8 kg$\cdot$yr of $^{130}$Te exposure. We observe no evidence of $0\nu\beta\beta$ decay of $^{130}$Te and set a Bayesian 90\% C.I. lower limit on the corresponding half-life of $T^{0\nu}_{1/2} > 2.2\times10^{25}$ years, as well as a Frequentist 90\% C.L. lower limit of $T^{0\nu}_{1/2} > 2.6\times10^{25}$ years./nAs CUORE continues to take data, efforts are already underway to build towards its eventual successor CUPID (CUORE Upgrade with Particle ID). In part II of this dissertation I present the work I have contributed towards the realization of CUPID, including light yield characterization and simulation for TeO$_2$, analysis efforts for the CUPID-Mo demonstrator, and the development of cryogenic front-end electronics for CUPID.

Advisor: Kolomensky, Yury G
Assessing Vectors of Xylella fastidiosa in California: From Ecology to Transmission Dynamics

Although spittlebugs were first confirmed as vectors of Xylella fastidiosa in the 1950s, their role in epidemics of Pierce’s disease of grapevine in the California North Coast remains unknown. The goal of this dissertation was to assess the biology and ecology of spittlebug vectors, Philaenus spumarius and Aphrophora nr. permutata, in California North Coast vineyards in relation to Pierce’s disease and to characterize differences in X. fastidiosa transmission following acquisition by spittlebug and sharpshooter leafhopper vectors.In chapter 1, I provide a brief background on the plant pathogenic bacterium, X. fastidiosa, its associated diseases, and its relationship with plant hosts and insect vectors. I also contextualize and summarize the subsequent chapters of my dissertation. Chapter 2 explores the seasonal abundance and infectivity of P. spumarius in California North Coast vineyards. Analysis of sweep and trap data revealed significant effects of survey month, vineyard site, and year on adult abundance in sweep and trap surveys. Analysis of X. fastidiosa natural infectivity in groups of field-collected spittlebug adults showed significant difference in transmission rates among months. I propose hypotheses on how to contextualize P. spumarius infectivity within the established framework of Pierce’s disease winter recovery. In chapter 3, I present results from a four-year field study analyzing the effects of site characteristics and host plant community on the abundance and development of A. nr. permutata nymphs. Woodland and riparian sites hosted larger nymphal populations than sites surrounded by vineyards. Among plant cover taxa surveyed in 2020, A. nr. permutata nymph abundance was positively associated with Helminthotheca echoides, Vicia sativa, and Daucus carota cover and negatively associated with Taraxacum officinale cover. Analysis of the development surveys found a significant effect of site, year, and plant taxa on first detection of nymphs as well as a significant effect of site and year on the estimated development time between 1st and 5th instars. In chapter 4, I assess differences in X. fastidiosa transmission efficiency over time between P. spumarius and the blue green sharpshooter, Graphocephala atropunctata. There was a significant effect of days post-acquisition on the proportion of plants infected by P. spumarius but the effect of days post-acquisition on G. atropunctata transmission efficiency was not significant. I consider species specific feeding behaviors and mouthpart fluid dynamics to explain the observed transmission patterns.

Advisor: Almeida, Rodrigo P. P.
Social Hierarchy as Moral Question: Male Reasoning about Gender in Rural Lebanon

To a greater or lesser extent, human societies are organized around systems of social hierarchy, structures which place individuals in relations of inequality, of social dominance and subordination. The differentiation of various groups of humanity has often been conceptualized as natural or ordained, acting to produce superordinate and subordinate social statuses which maintain the privilege and advantage of those in higher positions. Psychological research, however, shows that understandings of equality and fairness are universally held and that individuals, including very young children, assess events involving unfairness and inequality as wrong, even when authority, rules, or custom deem otherwise. Systemic social inequality may be seen, thus, to contradict values of fairness, rights, and equality, and the psychological question arises, how do those in positions of higher social status reason about and justify their advantage? How do members of superordinate social groups accept and justify social privilege? While it has been suggested that the perspectives of such individuals may be based on self-interest alone, this question has remained open from a cognitive perspective and requires further investigation. In this study, the social system under investigation is gender hierarchy, with a focus on male evaluation of and justification for equality or inequality between females and males. The study was conducted with adult males in rural Lebanon, a site with demographic and sociological evidence of continuing traditions of gender hierarchy, particularly in rural areas. The participants (N = 60; mean age 43.6 years) were presented with five everyday situations in family and work life and asked to evaluate and reason about decision-making power and opportunities between females and males. A sixth situation involving two males was also posed in order to assess similarities and differences in assessments of relations between two males. Results from the study show a tenuous form of gender equality in family contexts—as assessed by Lebanese men—an asserted parity but mutable rights for females (not males), justified with a mix of moral, relationship, and pragmatic reasoning. In work contexts, results show evidence of both gender equality and inequality—equality justified with moral reasoning and inequality justified with male/female social role difference and/or biological difference reasoning. Results further show robust equality between two males, justified with moral reasoning. Overall, there is evidence of emerging norms of greater equity between males and females in Lebanon, but male status continues to be elevated in many contexts due to conceptions of prescriptive male roles and traits and expectations of female deference to family needs.

Advisor: Turiel, Elliot
The impact of correlated variability on models of neural coding

Variability is a prominent feature of neural systems: neural responses to repeated presentations of the same external stimulus will typically vary from trial to trial. Furthermore, neural variability exhibits pairwise correlations, commonly referred to as correlated variability. Correlated variability is a pervasive neural phenomenon that arises due to a variety of sources including shared input, biological noise, global fluctuations, and neural activity unobserved by experimental apparatuses. It is of theoretical interest because of its importance for models of neural coding: the existence of correlated variability can improve or harm neural coding depending on its structure. In this work, we examine how correlated variability impacts neural coding for both analyses on decoding efficacy and parametric models of neural activity. First, we demonstrate that correlated variability induced by noise sources common to a neural population can be manipulated by heterogeneous synaptic weighting to improve neural coding, even at the cost of amplifying the noise. Second, we demonstrate that correlated variability in neural data exhibits worse than chance decoding fidelity, and identify biological constraints in achieving optimal neural representations. Third, we examine how an improved inference algorithm for common parametric models can shape the scientific interpretation of common systems neuroscience models, despite the presence of correlated variability in the data. Lastly, we identify how omitting correlated variability arising from unobserved activity in parametric models of tuning and functional coupling can bias parametric estimates, and propose a new model and inference procedure to mitigate these biases. Together, our results highlight the importance of correlated variability on a wide range neural coding models.

Advisor: DeWeese, Michael R
Bouchard, Kristofer E
Delivery of Therapeutically Relevant Cargo to Mammalian Cells Using Cell-Permeant Miniature Proteins

Despite the growing interest in protein-based therapeutics, one of the major limitations towards their development is the fact that proteins cannot simply diffuse into the cell interior. Instead, most proteinaceous cargo must be taken up via the biological process of endocytosis. Proteins become engulfed by the endocytic vesicle that travels into the cell and many of these protein cargoes remained trapped within endosomes. While some protein therapeutics, such as Cerezyme and Fabrazyme, take advantage of this entrapment to exhibit their functions within the endocytic pathway, the inability to access the cytosol and other organelles within the cell prevents development of intracellular-targeting proteins. A number of delivery vehicles have been proposed, including liposomes, nanoparticles, polymers, and cell-penetrating peptides (CPPs). Unfortunately, each of these techniques must be optimized for their respective cargo and target and may still suffer from overall low cytosolic delivery. Cell-permeant miniature proteins (CPMPs) provide a promising solution as they reach the cytosol intact at high concentrations, have a defined mechanism, and can deliver protein cargo./nHere, I describe progress from the evaluation of CPMPs alone to delivery of therapeutically relevant proteins and enzymes in both mammalian cells and mice. First, I present a summary of CPMP development, from designing miniature proteins that installed structural elements of traditionally flexible CPPs, to describing mechanistic details of endosomal uptake and escape, to delivering enzymatic cargo to the liver of mice. Next, I describe fluorescence correlation spectroscopy (FCS) in conjunction with flow cytometry experiments for monitoring proteins in live cells and evaluating endosomal escape. This methodology is followed by FCS studies that establish diffusion properties of free dye and CPMPs to assess whether intact CPMPs reach the cytosol of Saos-2 cells. The following chapter illustrates that among a panel of CPPs and CPMPs, the CPMP ZF5.3 is a superior delivery vehicle for a model cargo in multiple cell lines. Next, I describe the development and use of ZF5.3 conjugated to argininosuccinate synthetase (ZF-AS), an enzyme involved in an inborn error of metabolism. ZF-AS was the first ZF5.3-containing molecule to participate in animal studies to evaluate clinical utility of CPMPs. To continue improving cellular delivery of therapeutically relevant proteins, I describe functional and cellular uptake studies in which ZF5.3 is appended to the well-studied endonuclease Cas9 and initial development towards ZF5.3 conjugates of NS1, a monobody that binds Ras proteins with high affinity. Finally, I conclude with remarks on CPMP-mediated delivery. Together, these projects demonstrate that the CPMP ZF5.3 is a superior delivery vehicle compared to canonical and cyclic CPPs, illustrate ZF5.3-mediated delivery of three protein cargos, and support further ZF5.3 clinical development as a tool for protein-based therapeutics.

Advisor: Schepartz, Alanna
Design and Theory of Diverse Forms of Participation in Mathematics through Geometris, a Collaborative, Body-scale Game

Mathematics education, especially in school settings, is too often a disempowering experience for learners, who come away with the educationally and economically limiting impression that mathematics is not for them. I seek to broaden participation in mathematical practices by exploring the theoretical implications and design heuristics that can be gleaned from contextualizing geometric and spatial reasoning within play in the form of a collaborative, body-scale game./nMy work is informed by theories of learning as materially and socially situated and of cognition as inextricably rooted in embodied, physical experience. The analyses presented herein use both close case analysis and qualitative coding techniques to identify and characterize interaction behaviors./nThis dissertation contains three papers. The first paper focuses on the interpersonal dynamics of parent-child player groups and characterizes participatory facilitation, a pattern of flexible adoption, adaptation, casting-off, and redeployment of scaffolding behaviors by adults toward alternating pedagogical and performance goals. The second paper zooms out to examine the learning opportunities available through observation of gameplay. I identify range of participation roles – from player to spectator and some in between – that constitute a rich learning ecology and document the ways participants fluidly within it. Finally, my third paper zooms out again to consider how the social relationships that players bring to the body-scale game shape their collaborative movement patterns and resultant learning opportunities./nThroughout, I propose theoretical constructs about the role of material and social forces in informal learning and re-assert the role of these forces in mathematics learning. I also inform the design of other embodied mathematics learning activities by implicating particular design decisions as enabling or constraining the documented interactions.

Advisor: Abrahamson, Dor
Jitney-lite: a low-cost strategy for informal flexible feeder service with minimal technology

Efforts to provide informal, low-cost, flexible feeder services have occurred in many parts of the world. However, these services are often inefficient because informal operators cannot afford technologies for matching users and operators and efficiently routing vehicles. Transit riders are also concerned with the prices of technologies. This study develops a low-cost strategy for collective flexible feeder service, called the Jitney-lite service, that requires minimal technology. Our Jitney-lite bus operations offer door-to-door service to patrons who egress from a trunk-line transit system and fixed-route feeder service to those accessing the trunk-line system. This research formulated analytical models for this strategy, and the other two strategies exist in developing countries: (i) fixed-route bus and (ii) stand-based motorcycle taxi services. The cost evaluation starts from a level of a single trunk-line transit station by choosing the most cost-effective mode, and these costs are combined together for representing an entire city. The Bangkok Metropolitan Region (BMR) is used as a case study. The cost comparisons indicate that users who travel from a trunk-line transit station gain much benefits from the proposed strategy. The comparisons also indicate that Jitney-lite service is the most cost-effective in suburbs where zone size is large and trip density is low. The Jitney-lite is more favorable where residents earn low-to-middle incomes and/or where the quality of walking infrastructure is underdeveloped.

Advisor: Cassidy, Michael J.
Daganzo, Carlos F.
Machine Learning and Corporate Fraud Detection

The purpose of this dissertation was to study why corporate fraud detection models are often met with skepticism by industry practitioners despite a vast literature supporting their use. This dissertation examined the parsimonious standards in the academic literature for corporate fraud detection and included the latest studies that introduced ideas from Benford’s Law and machine learning algorithms. The study of corporate fraud detection models is important because academic literature is relied upon by industry practitioners and government regulators including the Securities and Exchange Commission. This paper starts with a critique that was recently published in Econ Journal Watch. This critique examined the results of a paper recently published in the Journal of Accounting Research applying machine learning to the detection of accounting fraud. Afterwards, I applied the most popular ensemble boosting algorithm in machine learning known as XGBoost to a comprehensive sample of financial ratios and variables. In addition to this model, I ran a horserace with the other models from the extant literature. Results showed that the F-Score (Dechow, et al. 2011) stood up quite well against the machine learning models. Interestingly, a univariate screen on sales growth performed about as well as more complicated methodologies at the top of the probability distribution. Finally, I provided a discussion based on a Bayesian analysis that illustrated why practitioners find fraud detection difficult.

Advisor: Patatoukas, Panos
Sylphs, Serpents and Acrobats: Dance and the Body in the Poetics of Gautier, Baudelaire and Mallarmé

By bringing to light the importance of the body and feminine expressive agency in the writing of Théophile Gautier, Charles Baudelaire and Stéphane Mallarmé, this dissertation makes a case for dance as a key locus of modernity in nineteenth century French literary history. Each of these poets was challenged by the question of how to represent the dancer as an embodied being. My study works through the entanglement of images, figures of speech and fantasies centering on dance in these poets’ works, through which each of these writers confronts and responds to changing aspects of the modern world. In particular, I am interested in moments in which the dancer is neither idealized nor denigrated, but rather a powerful symbol of movement, agency and embodiment. How does the autonomy and resistance of the female dancing body inspire the poetics of these writers? In addition, how can a critical emphasis on feminine artistry and agency through the figure of the dancer help us better understand these male authors’ relationship to gender and femininity? I will propose that these authors’ writings were not purely misogynistic and dismissive of the feminine; rather, each was forced to grapple with the dancer’s autonomy and individuality. Finally, this study seeks to reaffirm the importance of each author’s interest in the body and bodily experience, challenging a literary history that has often characterized the poetics of these writers as disembodied and disengaged.

Advisor: Sanyal, Debarati