VictorJuiz/thesis huggingface dataset:
Implicit hybrid upwinding and advanced nonlinear solver for multiphase flow and transport in porous media [electronic resource]
Keywords: Energy Resources Engineering.

The partial differential equations governing multiphase flow and transport in heterogeneous porous media are highly nonlinear. Therefore, in the fully implicit finite-volume method, solving the algebraic systems at each time step is challenging and accounts for the majority of the simulation cost. We present numerical schemes and solution strategies applicable to general-purpose simulation that reduce the computational cost by drastically improving the nonlinear convergence. In the discretized transport problem, the interfacial approximation of the functions of saturation -- i.e., phase relative permeability and capillary pressure -- has a strong impact on the strength of the nonlinearities. We generalize and analyze an approximation method tailored to the underlying three-phase flow physics and based on Implicit Hybrid Upwinding (IHU) that results in fast nonlinear convergence. This is achieved with a differentiable and monotone numerical flux for two- and three-phase transport obtained from separate evaluations of the viscous, buoyancy, and capillary fluxes. Then, using IHU, we construct an efficient physically based discretization scheme for the mixed elliptic-parabolic problem in which the flow is coupled to the transport of species. The resulting IHU scheme is more general and more efficient than the saturation damping methods previously used to improve the nonlinear convergence. In addition, to correctly represent the trapping mechanisms associated with capillary heterogeneity, the proposed finite-volume scheme accounts for spatially discontinuous relative permeabilities and capillary pressure at the boundary between different rock types. Specifically, we design a robust numerical method that combines IHU with discrete transmission conditions between rock regions to improve the accuracy of the flux approximation compared to the standard Phase-Potential Upwinding (PPU) scheme. Importantly, we present a mathematical analysis that places this new fully implicit finite-volume scheme on a strong theoretical foundation. The mathematical study is supported by challenging heterogeneous two- and three-phase numerical tests. These computational examples demonstrate that the IHU scheme results in significant reductions in the number of nonlinear iterations compared to the commonly used PPU scheme for viscous-, buoyancy-, and capillary-dominated flow. Finally, we extend a nonlinear solution strategy in which the flow variables (pressure) and the transport variables (saturation and composition) are updated sequentially. The saturation and composition update relies on a reordering of the control volumes exploiting the directionality of the transport problem and is done locally in decreasing order of potential. We show that this procedure leads to a drastic improvement in the nonlinear convergence properties compared to Newton's method with damping for immiscible, Black-Oil, and compositional problems with strong buoyancy.
Improving functions of redox proteins for hydrogen production [electronic resource]
Keywords: Bioengineering.

The usage of hydrogen as an alternative energy carrier has become increasingly important to support environmental sustainability. A portion of this hydrogen could be produced from renewable biomass sources, particularly from the sugar components of cellulosic feedstocks. The electrons extracted from the sugars would be delivered to one of the best hydrogen producing catalysts available in nature, an [FeFe] hydrogenase from Clostridium pasteurianum, through a synthetic pathway involving NADPH and two other proteins: Ferredoxin-NADP+ Reductase (FNR) and the Clostridium pasteurianum ferredoxin (CpFd) as an electron carrier protein. This electron transfer pathway enables in vitro hydrogen production and, when coupled with unpurified cell extracts containing native E. coli metabolic pathway enzymes, will provide an economical advantage. We sought to improve the electron transfer efficiency between the proteins for more efficient hydrogen generation from biomass sugars. We focused on improving the electron transfer rate of the downstream NADPH to hydrogen pathway, because it has been shown to limit the overall productivity. We initially hypothesized that the rate-limiting step in the pathway lies in the FNR-catalyzed electron transfer, but also evaluated the CpFd-mediated electron transfer from FNR. Several mutagenesis strategies were employed to change the inherent properties of the two redox proteins, FNR and CpFd, to increase their electron transfer rates. First, two different FNR mutant libraries from Anabaena PCC 7119 and rice root were mutated and evaluated. Subsequently, a mutant library of CpFd was explored. Mutagenesis of both redox proteins has enabled a final ~2.3-fold improvement in hydrogen productivity compared to the wild-type proteins, with an FNR turnover rate of 0.9 s-1. Beneficial mutations consist of S154H in rice root FNR and S17V in CpFd, and significantly lower the KM of the rice root FNR mutant and the CpFd mutant. Electron transfer from NADPH to the FAD cofactor of FNR occurs by a hydride transfer, but the CpFd can only accept two electrons. The improved ability of the new histidine (in S154H mutant) to accept the un-transferred proton may be improving FNR functionality in our pathway. Since the interaction between rice root FNR and CpFd has been improved, future work will employ similar mutagenesis strategies to search for an [FeFe] hydrogenase variant that can improve the hydrogen production rate even further. Ultimately, the electron transfer between proteins is a complex process that needs to be optimized for hydrogen production. This study provides further understanding of how redox protein interactions influence electron transfer.
Improving heterologous expression in yeast through a selective assay [electronic resource]
Keywords: Biology.

Heterologous expression of valuable proteins and biosynthetic pathways is a worthwhile endeavor of modern biotechnology, with pharmaceutical, industrial, and agricultural applications. But the process of expressing heterologous protein often requires significant optimization. Here, I have sought to express several proteins of bacterial, fungal, and human origin. In Chapter 2, I demonstrate the successful expression of two genes from the disorazole biosynthetic pathway from Sorangium cellulosum ce12: the first module (dszM1) and the trans-acting acyltransferase (dszD). I developed a growth-based reporter for protein expression by fusing the yeast URA3 gene to the C-terminus of dszM1 and explored the role of codon optimization in improving protein expression. In Chapter 3, I describe an assay for host improvement by screening the yeast homozygous deletion collection for strains that improve the heterologous expression of proteins fused to selectable markers. I performed this screen for three genes: dszM1; the core enzyme of the cytochalasin biosynthetic cluster (ccsA); and an isoform of human fibrinogen (FGA). I identified two (Δtif2 and Δecm25) strains that improve the heterologous expression of a fungal (ccsA) and a bacterial (dszM1) biosynthetic gene and proceeded to test these strains under alternate promoters. These results demonstrate the utility of unbiased screens coupled to selectable reporters and may be useful for researchers seeking to express large, complex pathways in yeast.
Improving lanthanide-based upconversion by overcoming the parity selection rule [electronic resource]
Keywords: Materials Science and Engineering.

Upconverting materials generate high-energy photons from two or more lower-energy photons. By virtue of this ability, they have the potential to allow solar cells to utilize sub-band gap photons and to enable inherently background-free biological imaging. Lanthanide-based upconverters, which convert near-infrared light to visible light, are particularly well-suited to these applications but remain hindered by poor efficiencies, typically below 1% in nanoparticles. Primarily responsible are their low radiative rates, which stem from the parity-forbidden nature of the constituent transitions. Here, I demonstrate three successful methods of overcoming the parity selection rule, thereby enhancing radiative rates and increasing performance in lanthanide-based upconverting nanoparticles. First, I show how we use mechanical strain to increase orbital mixing and relax the parity selection rule in NaYF4 nanoparticles doped with Yb and Er. Upconversion emission spectra and lifetimes are monitored as the NaYF4:Yb, Er nanoparticles are compressed hydrostatically with a diamond anvil cell. A 1% compressive strain diminishes upconversion emission in the hexagonal-phase nanoparticles but yields nearly a twofold emission enhancement in the cubic-phase particles. I then describe how we use synthetic strain to induce local symmetry distortions. Hexagonal-phase NaYF4:Yb, Er nanoparticles are codoped with Gd and Lu, which have slightly larger and smaller ionic radii than does Y, respectively. Using this approach, a 1.6x upconversion quantum yield enhancement as well as a record efficiency value are achieved. A broad suite of characterization techniques is used to confirm that the particle morphology, global structure, and Yb/Er concentrations are constant throughout the sample series, confirming symmetry distortion to be the source of the quantum yield improvement. Finally, I discuss a method we demonstrate in which energy is shuttled to a fluorescent dye rather than being emitted directly from the upconverter. Here, NaYF4:Yb, Er nanoparticles are decorated with a dye capable of achieving radiative efficiencies above 90%. This sensitization yields size-dependent upconversion quantum yield enhancements as high as 10x. These three broadly implementable approaches for improving upconversion are among the first to successfully overcome the parity selection rule in lanthanides. In conjunction with alternative methods of efficiency enhancement, this work provides a clear path toward realizing the transformative potential of upconversion for photovoltaic and bioimaging applications.
In Vivo Characterization of Murine Inner Ear Hair Cell Progenitors
Keywords:  Department of Biology
Atoh1
Gfi1
Ki67
proliferation
differentiation
regeneration
Thesis

The most common cause of hearing loss and balance disorders is loss of inner ear sensory hair cells. While sensory organs from non-mammalian species robustly regenerate, previous studies have found no regeneration in the mature mammalian cochlea and only limited regeneration in the mammalian vestibular system. It has recently been found that a subset of non-sensory supporting cells, marked by the protein Lgr5 (leucine rich repeat containing G protein-coupled receptor 5), is capable of spontaneously regenerating lost hair cells in the neonatal mouse cochlea and utricle. However, knowledge of the time-course of cell fate change, differentiation, and proliferation by these hair cell progenitors is lacking. Here we probed the genetic signature of hair cell progenitors to understand the molecular mechanisms that guide hair cell regeneration after damage. A mouse model that allowed for selective ablation of hair cells was used, and immunohistochemical staining of early hair cell markers (Gfi1, Atoh1) and a proliferation marker (Ki67) allowed us to map the transition of supporting cells into hair cells in the neonatal mouse cochlea and utricle after damage. The findings demonstrated that the neonatal utricle and cochlea have an upregulation of early hair cell markers before proliferative markers. These data suggested that regenerating cells in the neonatal mouse inner ear sensory organs follow a similar temporal pattern of regeneration to the inner ear organs from non-mammalian species.
Income Segregation and Intergenerational Mobility: Evidence from U.S. Highways
Keywords: Department of Economics
Stanford University
Undergraduate Honors Thesis Program
Thesis

In recent decades, racial segregation has declined while income segregation has increased and continues to intensify, but past studies have failed to estimate the effects of income segregation through causal methods. I measure the intergenerational mobility gap between children with low income and high income parents by gender in response to higher levels of income segregation at the county-level. A causal estimate is approached through an original instrumental variables strategy that uses income sorting of census tracts following the construction of the interstate highway system. Neighborhoods in close proximity to a highway experience a negative disamenity effect from the noise and pollution generated from the highway but also receive access benefits from using the faster transportation network. I find that income segregation leads to less upward mobility for children from both low income and high income backgrounds, and in particular exacerbates income disparity among boys. These results show that the correlational estimates of previous studies have underestimated the effects of income segregation and shed light on the impacts of transportation infrastructure on the shape of the income distribution.
Inferring nonlinear computation in multilayered neural circuits [electronic resource]
Keywords: Neurosciences.

The brain performs of a remarkable variety of computations. These computations arise in circuits comprised of interconnected neurons and mediated by a rich diversity of biophysical mechanisms. Neuroscientists are tasked with characterizing and understanding this complexity using a combination of experimental and theoretical tools. In particular, we typically have to infer computations and mechanisms underlying neural processing given limited experimental recordings. In this thesis, I describe my work on developing and applying computational tools to study these issues in multilayered neural circuits in the retina. Speciﬁcally, I am interested in the following fundamental questions: What computations do early sensory neurons perform on their inputs? How do biophysical mechanisms mediate these computations? And finally, what can we infer about these computations and mechanisms given partial experimental observation of a multilayered circuit? Chapter 1 introduces these questions in more detail, and Chapter 2 covers relevant background material. Chapter 3 discusses quantitatively the relationship between these encoding models and commonly used descriptive statistics of the neural code. Chapter 4 explores a particular encoding model, a two layer linear-nonlinear cascade (LN-LN). Chapter 5 uses encoding models to better understand the retinal response to natural scenes. Finally, Chapter 6 discusses implications of this work and touches on future directions.
The influence of a robot's mere presence on human communication [electronic resource]
Keywords: Communication.

Does the mere presence of a robot change the way that a patient thinks about and behaves toward her medical provider? We investigated this question using a commercially-available robot that millions of people will soon encounter. Fifty-one participants interacted with a nutritionist in the presence of either a tablet (control), a robot with unmoving eyes that stared toward the participant (nonsocial implicit cue), or a robot with eyes that tracked the participant's face (social implicit cue). Participants in the social robot condition looked at the nutritionist more than those in the nonsocial condition, and perceived her less warmly than those in the control condition. Those in the presence of either robot also contributed less to their conversations with the nutritionist than those in the presence of a tablet. Discussion focuses on causal mechanisms; the validity of concepts like sociality; the ambiguous meaning of eye movements; and implications for design, doctor-patient rapport, and human culture.
The influence of school-related factors on educational outcomes in Brazil [electronic resource]
Keywords: Education.

Across three papers, I examine the influence of school-related factors on student outcomes in Brazil. In the first and second papers, I investigate the effects of teachers' contractual ties with the school on different outcomes. Two aspects of contractual ties were considered: 1) whether teachers hold a permanent or temporary contract, and 2) whether they work at a single or multiple schools during the week. In Brazil, a large proportion of teachers work on temporary contracts and at multiple schools. However, little is known about the educational implications of these contractual arrangements. My dissertation work aims to address this gap. The first paper makes causal inferences about the impact of permanent and single-school teachers on teacher-student relationships and student performance. Analyses use unique administrative and test data from Sao Paulo, Brazil. To account for nonrandom sorting of students and teachers across schools and classrooms, I use a cross-subject analysis with student-fixed effects. Results show that single-school and permanent teachers have a positive and significant impact on teachers' provision of support and academic feedback. Permanent teachers also have a positive effect on student achievement. However, findings indicate that the effects of teachers' contractual ties are smaller for students at higher risk of school failure. The second paper builds on these findings and explores whether teachers' contractual ties affect school dropout. This study uses extensive data from Brazil's Census of Basic Education over four academic years (2011-2014) and employs two classes of fixed effects models based on school-grade-year variation. Results are mixed. School dropout rates are 0.5 to 1 percent lower when students are taught exclusively by single-school teachers; however, dropout rates are 0.4 to 0.8 percent higher when students are taught by permanent teachers. The third paper extends the research on socioeconomic achievement gaps by looking at the extent to which inequality in test scores explains attainment gaps in Brazil. This study draws on Boudon's (1974) theoretical model of inequality in educational opportunity to estimate the primary effects of social background on high school graduation: that is, the proportion of the overall inequality in high school completion associated with the socioeconomic test score gap between students from low and high social backgrounds. Analyses are based on administrative and test data from Sao Paulo and use a decomposition technique for non-linear probably models. Results indicate that the test score gap in middle school is associated with half of the overall socioeconomic inequality in high school graduation. These primary effects are similar to those estimated for the U.S. This is a contribution to previous studies of primary effects, which are based primarily on data from European countries and the United States.
Influences of Evaporite Minerals on the Vertical Distribution, Storage, and Mobility of Uranium in Response to Hydrological Conditions
Keywords:  Earth Systems Program
School of Earth Energy &amp; Environmental Sciences
uranium
evaporite
Thesis

Uranium-contaminated groundwater in Riverton, Wyoming persists despite anticipated natural attenuation outside of a former uranium ore processing facility. The inability of natural flushing to dilute the uranium below the regulatory threshold indicates that sediments act as secondary sources likely (re)supplying uranium to groundwater. Throughout the contaminated floodplain, uranium rich-evaporites are readily abundant in the upper 2 m of sediments and are spatially coincident with the location of the plume, which suggests a likely link between evaporites and increased uranium levels. Systematic sampling before and after a flooding event and sequential chemical extractions were used to decipher the concentration, hosted phase, and relative vertical mobility of uranium in the sediments/soil. The sum of these analyses provides a model for the effect of seasonal hydrologic changes on uranium incorporation within evaporite sediments. These findings hold implications for the fate of uranium throughout contaminated sites across the Colorado River Basin.
Information-theoretic limits of distributed randomness generation [electronic resource]
Keywords: Electrical Engineering.

Randomness generation has numerous important applications, for example, in statistical sampling, randomized algorithms and cryptography. In this dissertation, we study randomness generation from an information-theoretic point of view. Extending the seminal work of Knuth and Yao on generating random variables from coin flips, we investigate several multi-terminal randomness generation settings. First we consider the distributed generation setting in which Alice and Bob share a common random source, and each of them would like to generate a random variable such that the two random variables follow a prescribed joint distribution. The goal is to minimize the amount of common randomness needed. We show that for log-concave distributions, the amount of common randomness is within a constant gap of the mutual information. The proof uses a novel construction called dyadic decomposition. We then consider the remote generation setting in which Alice, who knows the chosen distribution, wishes to send a message to Bob to enable him to generate a random variable distributed according to this distribution. We design a scheme that applies to any continuous distribution and establish an upper bound on its expected codeword length using dyadic decomposition. Finally, we consider the one-shot channel simulation setting with unlimited common randomness. We strengthen the result by Harsha et al. using a new strong functional representation lemma, and show that it can be applied in designing schemes for one-shot lossy source coding, and providing a simple proof of the Gelfand-Pinsker theorem for channels with state.
Inhomogeneity in complex oxides [electronic resource] : probing superconductivity and magnetism with scanning SQUID
Keywords: Applied Physics.

Complex oxides, materials consisting of two or more metals and oxygen, are studied widely in condensed matter physics. Heterostructures made of complex oxides are highly tunable platforms for realizing novel electronic and magnetic states. I used a local mangetic imaging technique, scanning superconducting quantum interference device (SQUID) microscopy, to investigate the role of inhomogeneity in two complex oxide heterostructures. By mapping the diamagnetic susceptibility of superconducting delta-doped SrTiO3 and LaAlO3/SrTiO3 as a function of temperature, I showed that an intrinsic source of inhomogeneity—domains of different orientations of the crystallographic unit cell formed at a structural phase transition—causes the superconducting transition temperature to spatially vary in both materials. Previous scanning SQUID measurements as well as other techniques found magnetism in LaAlO3/SrTiO3. Oxygen vacancies were proposed as a possible source. I measured a series of samples with different levels of oxygen vacancies and, finding no magnetism, set limits that are comparable to or are more stringent than signal sizes previously reported in the literature, placing strong constraints on the role of oxygen vacancies in producing magnetism in LaAlO3/SrTiO3 heterostructures. Both heterostructures that I studied exhibit two-dimensional superconductivity. Pointlike defects have the simplest possible geometry for a defect in two dimensions. I compared susceptibility images of several two-dimensional, complex-oxide-based superconductors to a model for the way in which our scanning SQUID susceptometers image defects in two-dimensional superconductors that are much smaller than the length scales of our sensor and found good agreement.