VictorJuiz/thesis huggingface dataset:
Mechanics of Confined Microbial Populations

Living systems offer a richness of behaviors that are of broad interest to many fields of science. For instance, cells that are dwelling in their natural environment are mostly subject not only to the scarcity of energy resources, but also the space in which they can grow and live. This space limitation eventually leads to the emergence of contact forces (mechanical stress) between neighboring cells or the cells and their confining environment. These emergent forces may further have a crucial impact on the cells' biology, the dynamics of the whole population, or even the integrity of confinement (resulting in the remodeling of the environment). Even though the general importance of these forces has been widely recognized, technical difficulties and the complexity of the emergent phenomena prevented much progress in this direction. In this thesis, using mostly computer simulations, I make steps towards overcoming these barriers. In the first part of this thesis, I describe, on the coarse level, how the geometric properties of micro-confinement entails clogging of the microbial populations of Saccharomyces cerevisiae. These clogged populations are found to be quite disordered, with intermittent growth dynamics and heterogeneous mechanical stresses - properties much more like those of granular materials than a continuum. Thus, granular materials are an appealing framework to describe dense microbial populations. However, using a simple 2D model, I numerically show that the coupling between cellular growth rate and mechanical stress gives rise to deviation from the expected behavior of inanimate granular materials, and it increases the complexity of the emergent phenomena. The simple and coarse model used in the first part of the thesis is sufficient for relatively low density systems, but it is not adequate for strongly compacted systems. Thus, in the second part of this thesis, I employ the Finite Element Method to study in detail the structure and mechanics of the disordered packings of elastic shells - our proxy model for dense cellular packings. Therein, I discuss how deformations resulting from large compressive forces couple the structural and mechanical properties of the compact packings. Finally, using Lattice-Boltzmann simulations, I investigate the fluid transport in such compacted packings of deformable shells. I show that a relatively simple model proposed by Kozeny & Carman, combined with a percolation theory, can capture the fluid transport in porous materials. This result is of interest not only in dense biological systems, but also in a broader class of granular porous materials.

Advisor: Hallatschek, Oskar
Asymptotics of the Tate-Shafarevich Group

For any elliptic curve $E$ with everywhere good or split multiplicative reduction over a finite extension of $\mathbb{F}_q(t)$ with $q=p^e$, $p\ne 2$, we consider the family of elliptic curves $\{E^{(p^n)}\}_{n\in \mathbb{Z}_+}$ consisting of $p^n$-power frobenius automorphism twists of $E$. Assuming BSD for function fields, we compute the asymptotics of the order of the Tate-Shafarevich group of $E^{(p^n)}$ as $n$ approaches infinity. We prove that there is a twist $E^{(p^k)}$ such that for any $n$ greater than $k$, we can explicitly compute the order of the Tate-Shafarevich group of $E^{(p^n)}$ as a power of $p$ (given in terms of $n$) times the order of the Tate-Shafarevich group of $E^{(p^k)}$. In particular, as $n$ approaches infinity, the size of the Tate-Shafarevich group of $E^{(p^n)}$ grows on the order of $\mathcal{O}(q^{\delta p^n})$ for some constant $\delta$ determined by $E^{(p^k)}$. More precisely, the size of the Tate-Shafarevich group of $E^{(p^n)}$ grows as $\mathcal{\theta}(p^{e\delta p^n-n(m+r)})$ where $r$ is the rank of $E^{(p^k)}$ and $m$ is the number of places of bad reduction of $E^{(p^k)}$.

Advisor: Yuan, Xinyi
Learning Single-view 3D Reconstruction of Objects and Scenes

We address the task of inferring the 3D structure underlying an image, in particular focusing on two questions -- how we can plausibly obtain supervisory signal for this task, and what forms of representation should we pursue. We first show that we can leverage image-based supervision to learn single-view 3D prediction, by using geometry as a bridge between the learning systems and the available indirect supervision. We demonstrate that this approach enables learning 3D structure across diverse setups e.g. learning deformable models, predctive models for volumetric 3D, or inferring textured meshes. We then advocate the case for inferring interpretable and compositional 3D representations. We present a method that discovers the coherent compositional structure across objects in a unsupervised manner by attempting to assemble shapes using volumetric primitives, and then demonstrate the advantages of predicting similar factored 3D representations for complex scenes.

Advisor: Malik, Jitendra
An improved all-speed projection algorithm for low Mach number flows

The objective of this work is to design and implement a high fidelity method for simulating/nlow Mach number compressible flows ranging from inviscid gas dynamics to compressible/nNavier-Stokes with reactions. In order to achieve this objective, we introduce three goals./nThe first is that ∆t only be constrained by the advective CFL condition. The seconds goal/nis that we attain accurate treatment of compressible effects such as bulk compression and/nexpansion due to thermo-chemical processes and long wavelength acoustics. In particular,/nwe want to capture well-known low Mach number limiting behavior. The third and final/ngoal is that we want to use easy solvers.

Advisor: Colella, Phillip
Papadopoulos, Panayiotis
B(l)ack Like It Never Left: Race, Resonance, and Reruns

This audience research study explores how 1990s Black sitcoms such as Martin, A Different/nWorld, Living Single, Moesha, and The Fresh Prince of Bel-Air serve as a form of heritage for/nBlack millennials. To better understand this phenomenon, I conducted semi-structured, in-depth/ninterviews and focus groups with 26 Black undergraduate students at a large, public, research/nuniversity in the western part of the United States. In addition to interviews and focus groups, I/nperformed textual analyses of sitcom episodes as well as the various popular texts produced in/nresponse to the shows. My analysis reveals how Black millennials sample ideas about race,/ngender, and class from 1990s Black sitcoms as well as how they critique the continued/ncirculation of the texts in Black popular culture. Identifying social mobility as a central theme in/nmost 1990s Black sitcoms, participants used the shows to help shape their professional, social,/nand educational aspirations. Specifically, participants stated that the shows helped them imagine/nthemselves as college students who would go on to pursue careers with high-earning potential,/nwhile also framing their expectations of the romantic and platonic relationships necessary to/nachieve upward mobility. Participants described watching reruns of 1990s Black sitcoms as a/nnormative part of their childhood and thus imagined most Black millennials as having a/nknowledge of and affinity for the shows. For many participants, their 1990s Black sitcom/nfandom was understood as a form of familial inheritance as they credited their parents and older/nsiblings with introducing them to the shows. Participants drew on their affinities for 1990s Black/nsitcoms as points of connection between them and other Black students. Despite participants/nfinding great utility in the sitcoms, they also described vexed relationships with the programs./nThis was particularly true related to Martin, which was the most popular sitcom among/nparticipants. Participants attributed their ambivalent relationship with Martin to what they/ndescribed as the show’s penchant for affirming and advancing negative stereotypes about Black/nwomen and the show’s troubling depictions of Black heterosexual romantic relationships.

Advisor: Leonardo, Zeus
A Hodge-theoretic study of augmentation varieties associated to Legendrian knots/tangles

In this article, we give a tangle approach in the study of Legendrian knots in the standard/ncontact three-space. On the one hand, we define and construct Legenrian isotopy invariants/nincluding ruling polynomials and Legendrian contact homology differential graded algebras/n(LCH DGAs) for Legendrian tangles, generalizing those of Legendrian knots. Ruling polynomials/nare the Legendrian analogues of Jones polynomials in topological knot theory, in the/nsense that they satisfy the composition axiom./nOn the other hand, we study certain aspects of the Hodge theory of the “representation/nvarieties (of rank 1)” of the LCH DGAs, called augmentation varieties, associated to Legendrian/ntangles. The augmentation variety (with fixed boundary conditions), hence its mixed/nHodge structure on the compactly supported cohomology, is a Legendrian isotopy invariant/nup to a normalization. This gives a generalization of ruling polynomials in the following/nsense: the point-counting/weight (or E-) polynomial of the variety, up to a normalized factor,/nis the ruling polynomial. This tangle approach in particular provides a generalization/nand a more natural proof to the previous known results of M.Henry and D.Rutherford. It/nalso leads naturally to a ruling decomposition of this variety, which then induces a spectral/nsequence converging to the MHS. As some applications, we show that the variety is of Hodge-Tate/ntype, show a vanishing result on its cohomology, and provide an example-computation/nof the MHSs.

Advisor: Shende, Vivek
Borcherds, Richard
Immobilization of Enzymes to Create Heterogeneous-Enzyme Hybrid Catalysts

Enzymes are highly selective and active biocatalysts that can catalyze reactions at much milder conditions than heterogeneous catalysts. However, in solution enzymes are not reusable, can not be used in a flow cell, and can be difficult to separate from the products. By immobilizing enzymes onto a solid support, it is possible to create a catalytic system that combines the activity and selectivity of enzymes with the reusability and ease of separation of heterogeneous catalysis. This immobilization process also allows for enzymes to be studied with surface-specific techniques./nOne method to immobilize enzymes is through DNA directed immobilization (DDI). This method uses the selective binding of complementary DNA strands to immobilize enzymes in an ordered and selective manner. The activity of aldolase—an enzyme in the glycolysis pathway that catalyzes the C-C bond breaking step—was found to be significant after conjugation to DNA and subsequent immobilization onto functionalized glass surfaces. These immobilized enzyme surfaces were found to be reusable for multiple reaction cycles and regeneratable by dehybridizing the DNA strands./nThese DNA and enzyme modified surfaces were studied by using sum frequency generation (SFG) vibrational spectroscopy. This showed that quartz modified with double-stranded DNA has an ordered structure, while single-stranded DNA surfaces are more disordered due to the lack of rigidity./nAlcohol dehydrogenase, which catalyzes the conversion of a primary or secondary alcohol into an aldehyde or ketone, can be immobilized onto the mesoporous silica material SBA-15 through non-specific physical adsorption. These immobilized enzymes are active upon adsorption but are prone to significant leaching. The specificity of immobilized alcohol dehydrogenase towards longer alcohols was found to be slightly diminished./nThis dissertation builds on existing knowledge of enzyme immobilization methods and surface science characterization techniques. This research shows that immobilized enzymes are a promising method for creating novel catalytic systems. The results show the importance of limiting the leaching of enzymes off of the support for potential catalytic applications.

Advisor: Somorjai, Gabor A
Configurations of Community and Collaboration in Online Learning: An Assemblage Approach

Delivering engaging and rigorous learning experiences in online environments has become a key priority for higher education institutions, driving prolific innovation in tools, pedagogy, and research over the last 20 years. The design and research of collaborative, networked learning experiences in particular has been fueled both by socially-turned theories of learning as well as the meteoric rise of social media and digital networks, which have introduced radical new forms of connectivity and sharing in daily life. In this dissertation, I offer three articles that each focus on one tool in the SuiteC collaborative learning system, a set of interconnected software applications designed to foster peer-to-peer sharing and collaborative, remix composing in a gamified environment. Looking across four semesters of student usage of the SuiteC tools in an online/hybrid undergraduate education course, I employ a mixed-methods approach grounded in “assemblage theory” that leverages learning analytics mined from the SuiteC database, content analysis of student artifacts, and student feedback to explore the kinds of social interactions and collaborations that emerged in the course. Findings suggest best practices and curricular strategies for the design of peer-centered online learning courses, recommendations for software tools, and the utility of assemblage concepts in studying complex sociotechnical systems.

Advisor: Hull, Glynda A
Essays in Financial Economics

This dissertation is comprised of two essays in a topic at the intersection of Financial Economics and Industrial Organization. Both analyze the effect of common ownership in the U.S. corporate loan market. In recent years, firms and banks increasingly have institutional investors as shareholders in common. These shareholders receive profits from the interest rates set by the bank, and they also benefit from the firm's profits. I study how such common ownership affects loans, particularly as measured by size and price./nIn my first chapter, I illustrate through a simple model the implications of firm and bank common ownership on loans. I then provide new evidence on the rise and extent of common ownership between firms and banks. I outline three trends in institutional investors' holdings of public companies, and I describe how these trends drive firm and bank common ownership. First, the overall holdings of institutional investors have grown ten-fold in the past 20 years in terms of market value. The average fraction of a public company owned by these investors nearly doubled (to almost 60 percent) over the same time period. The second trend is the increasing fraction of firms and banks that are owned by common owners and also have a loan relationship. The percentage of firm shares held by institutional investors that also hold bank shares at the time of loan origination has doubled to nearly 40 percent between 1990 and 2012. Similarly, the percentage of bank shares held by institutional investors that also hold firm shares doubled to nearly 30 percent over the same time span. Third, I find that common owners are persistent in their holdings. Around 90 percent of investors the drive common ownership between firms and banks remain as investors in the subsequent year, both in terms of the number of investors and in terms of the percentage of shares held by these recurring investors./nIn my second chapter, I empirically show that when a firm and a bank have common ownership, the firm obtains larger loans from the bank at a lower interest rate. I use the growth of index funds as a source of exogenous variation to estimate a plausibly causal link between common ownership and loan terms not confounded by unobserved factors such as strategic investments by active institutional investors. I find that a one standard deviation increase in common ownership leads to a five basis point interest rate decrease and a three percent loan size increase. I show that these loan terms do not go to underperforming firms but to firms that are less likely to receive a credit rating downgrade. I also find that this improvement in loan terms is more pronounced for smaller and unrated firms. This suggests that the benefits of common ownership may result from decreased information frictions and decreased monitoring frictions for the lender if the lender's shareholders also have access to firm returns and firm information.

Advisor: Malmendier, Ulrike
Enduring Inequality: How Social Class Shapes Where High-Achieving Students Apply to College

Higher education destinations continue to be a significant source of stratification in the United States (Ayalon, Grodsky, Gamoran, and Yogev 2008; Gladieux 2004). Among high-achieving students, research studies consistently point to the significance of social class in shaping where they attend college: students from socioeconomically disadvantaged backgrounds are more likely to end up at less selective institutions compared to their higher income counterparts with similar academic qualifications (McPherson and Schapiro 2006; Hoxby and Avery 2012; Hill and Winston 2006). A key reason for social class differences in access to selective colleges is that few highly able, socioeconomically disadvantaged students actually apply to such institutions in the first place (Radford 2013; Hoxby and Avery 2012; Lopez Turley, Santos, and Ceja 2007). Yet, the process through which social class shapes college application choices among such students is not well understood./nThis dissertation draws upon in-depth interviews with 46 high-achieving students from the San Francisco Bay Area to examine how social class shapes where students apply to college. It reveals how inequality is maintained when students from lower-class backgrounds (lower-SES) limit their choices of colleges to selective and nonselective institutions close to home in California whereas their middle and upper-middle class (higher-SES) counterparts apply to the top selective colleges across the U.S. More specifically, this research identifies two mechanisms of social stratification by showing how institutions and families of the middle- and upper-middle class work to procure advantages by cultivating dispositions among their children for specific types of higher education opportunities, specifically leading colleges and universities in the form of mostly private selective colleges across the U.S. First, I show that higher-SES students attend schools in which they are exposed to a college-going culture that expects them to only apply to the top colleges across the country. In contrast, most lower-SES students attend high schools and participate in programs in which college is one of multiple paths after high school. Lower-SES students are encouraged to attend a four-year college in California, regardless of academic quality. Second, I demonstrate that family upbringing and experiences foster an understanding of college among higher-SES students as an opportunity to leave their families and immerse themselves in a different part of the country. In contrast, most lower-SES students understand college as a continuation of family interdependence that requires them to take into account the real and perceived needs and wishes of the family, which places geographic limitations on where they can apply and attend college

Advisor: Harding, David J
Interactions of Microbes in Communities

Groups of microorganisms sharing an environment (microbial communities) are ubiquitous in nature. Microbial communities provide essential ecosystem services to other life on Earth by e.g., participating in global biogeochemical processes or interacting with a host’s immune system. Such microbes compete for scarce resources, modify an environment for their own purposes, actively war, and occasionally cooperate. Though numerous studies have surveyed the diversity of microbial life in different environments, few have determined the ways in which members of microbial communities interact with one another. Understanding the ways and means by which microbes interact is essential if we are to understand how microbial communities form, persist, and change over time. Knowledge of these processes will allow us to rationally design microbial communities to perform useful functions and predict how our actions might shift the balance of microbes in a community, and thus affect its function. In this work, we develop and apply novel methods for understanding microbial interactions.

Advisor: Arkin, Adam P
Understanding and Assessing the Impact of Data Visualization On Stakeholder Access to Data, Sensemaking and Decision Making in the context of the Local Control Funding Formula

Implemented in 2013, the Local Control Funding Formula (LCFF) requires Local Education Agencies (LEA’s) to engage in a continuous improvement process that identifies actions that extend and improve services for targeted student groups. The vision of the LCFF is that all stakeholder groups including Staff (certificated, classified, management and community members) are consulted and have the opportunity to provide feedback on the LCAP./nHowever, stakeholders have varying degrees of access, levels of technical knowledge and understanding of the fiscal, adult behavioral data and student achievement and outcome data./nThese differences set the stage for some stakeholders to unwittingly included or exclude different information based on personal biases and local accountability demands./nThis design study is intended to provide stakeholders with a tool that supports their access and use of data as they engage LCFF continuous improvement process. A focused group was convened to review the data dashboards. Early feedback from stakeholders characterized the dashboards as a good starting point. They also provided feedback about integrating additional data elements into the dashboards which would make them more useful in their work of reviewing programs in the LCAP. Also, stakeholders requested that more systems be built to support access to data as well as increase opportunities for collaborative data driven decision making.

Advisor: Gifford, Bernard