VictorJuiz/thesis huggingface dataset:
Efficient Data-Driven Simulations of Subsurface Phenomena
Keywords:  Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Probabilistic Support Vector Machine
Convolution Neural Network
Numerical Analysis
Thesis

Delineation of geological features from limited hard and/or soft data is crucial to predicting subsurface phenomena. Ubiquitous sparsity of available data implies that the reliability of any delineation effort is inherently uncertain. We present probabilistic support vector machines (pSVM) as a viable method for both lithofacies delineation from sparse data and quantification of the corresponding predictive uncertainty. Our numerical experiments demonstrate an agreement between the probability of a pixel classifier predicted with pSVM and indicator Kriging. While the latter requires manual inference of a variogram (two-point correlation function) from spatial observations, pSVM are highly automated and less data intensive. We also investigate the robustness of pSVM with respect to its hyper-parameters and the number of measurements. The deep learning methodology is also considered to solve a similar problem. Convolutional Neural Network (CNN) is applied to obtain an accurate geobodies segmentation from underground data given sparse labeling of geobodies in a 3D seismic volume. Augmenting the CNN model with the semi-supervised learning approach allows us to leverage the limited training dataset in this niche field while improving upon naive, baseline results.
After the geological structure is understood, reservoir simulation is performed to determine the productivity of the field. This portion of the thesis concerns the numerical solution of the underground fluid flow system, which is inherently stiff. Applying an explicit numerical scheme on a stiff system is proven to be challenging as the required time step could be so small that it is infeasible to compute. Even though stiff systems are common in several engineering and science fields, particularly when complex physics is modeled, it remained difficult to solve until recently. This paper discusses one of the best performance schemes called exponential time differencing. Such a scheme takes advantage of the natural separation of the problem as a linear stiff term and non-linear non-stiff term by solving the first portion analytically and solve the second part numerically. Such natural separation, however, is not found in multiphase flow in oil and gas reservoir simulation. This thesis demonstrates the way to reformulate the problem to a simple stiff equation so exponential time differencing can be applied. Numerical experiments demonstrate that the best scheme considering time step size is the combination of exponential time differencing and fourth-order Rung-Kutta scheme.
Efficient exploration in bandit and reinforcement learning
Keywords: Electrical Engineering.

Sequential decision making problems appear is the core problem in many real world applications. In such problems, an agent is aiming at achieving a certain goal by optimally taking a sequence of actions based on noisy observations. Bandit and reinforcement learning are fundamental frameworks for modeling decision making under uncertainty. Efficient exploration in such problems significantly increases data efficiency by speeding up the learning process and requiring less data for making decisions. As such, it is of utmost importance to design sophisticated exploration schemes based on the special characteristics of each practical problem. In this dissertation, we first consider a safe exploration problem in linear bandits and proposes an algorithm that satisfies safety constraints while minimizing the regret. We provide theoretical analysis and simulation results to demonstrate the efficiency of the proposed algorithm. Then, we consider best arm identification problem in generalized linear bandits and provide a gap-based exploration strategy that achieves desirable accuracy. We also provide an upper bound on the sample complexity of the proposed algorithm and offer numerical studies to evaluate its performance.
Election Cybersecurity: Assessing the Roles of Federalism and Partisanship
Keywords: elections
cybersecurity
Center for International Security and Cooperation
Thesis

State and local governments administer elections in the United States—not the national government. In response to Russian interference in the 2016 U.S. presidential election, the U.S. national government has offered funding and other assistance to help state election officials bolster election cybersecurity. The conventional wisdom in political science is that proposals that purport to benefit national security or would distribute resources will be popular. Yet while some state election officials welcomed national government assistance, others initially opposed it. Given that national assistance for election cybersecurity is in the U.S. national security interest and would permit members of Congress to distribute resources to their districts, why is there opposition to it? To answer this question, I analyze three case studies: Obama’s move to expand national aid for elections, the failure of an election cybersecurity bill in the Senate, and a Trump effort to improve intelligence sharing between national and state officials. In each case study, I analyze the impact of two variables on state election officials’ policy preferences: (1) partisanship and (2) the institutional culture of federalism, which I operationalize as skepticism about national government involvement. Existing research suggests that partisanship is increasingly influencing state politics; however, I find that election cybersecurity is not a party-line issue at the state level. I suggest that skepticism about national government involvement drives state election officials’ views on election cybersecurity reform. These findings suggest that national officials will be most effective in assisting state election officials if they address fears about losing local control.
Electrically tunable metamaterials with high-aspect-ratio nanostructures
Keywords: Electrical Engineering.

Metamaterials are engineered optical media composed of subwavelength structures. With different physical arrangements and dimensions of such elements as well as a wide range of possible constituent materials, metamaterials can possess novel optical properties and enable many interesting applications. Dynamic control of light is also possible in semiconductor-based metamaterials by tuning the carrier density with field-effect modulation. However, most papers in the literature on electrically tunable infrared metamaterials use essentially flat designs or so-called "metasurfaces" with ultrathin semiconductor layers and resonant metal antennas, which suffer from exceptionally small interaction lengths with light. This thesis will demonstrate two projects that follow an alternative approach with three-dimensional, high-aspect-ratio nanostructures to increase the optical interaction length within a thicker metamaterial, thus allowing for large modulation of the amplitude and phase of light by varying the applied voltage. For both sets of devices, the fabrication process with electron-beam lithography, experimental measurements of reflectance modulation, and simulation results from effective medium models will be discussed. One potential future application of this work could be a completely solid-state beam steering solution with a phased array of electrically tunable metamaterials to replace the bulky mechanical lidar scanning systems in self-driving cars.
Electrocatalysis by surface immobilized discrete molecular complexes
Keywords: Chemistry.

Direct methanol fuel cells are a promising means of generating electricity from methanol and dioxygen. However, state of the art catalysts for the oxidation of methanol and reduction of dioxygen must operate at significant overpotentials to obtain reasonable reaction rates. Finding alternative catalysts operative at lesser overpotentials would make direct methanol fuel cells more attractive. Among the many alternative catalyst designs that have been explored, the use of discrete molecular complexes is particularly appealing as molecular structure may be methodically modified to provide mechanistic insight. Such surface immobilized metal complexes have shown activity towards alcohol and water oxidation as well as dioxygen reduction. Described herein, are advances made in the development of discrete molecular complexes for methanol oxidation and dioxygen reduction. A ruthenium polypyridyl complex covalently attached to a carbon electrode shows methanol oxidation. Benzyl alcohol oxidation is used as a benchmark to compare with related complexes. This complex shows a 240 mV decrease in overpotential for benzyl alcohol oxidation compared to the best surface immobilized ruthenium polypyridyl complexes, an order of magnitude larger turnover frequency, and a 15% improvement in faradaic efficiency. Pourbaix and mechanistic analysis suggests that the active oxidant is a RuIV=O complex. Formation of this active catalyst is strongly dependent on surface immobilization under dry, inert atmosphere conditions. Methanol oxidation is not observed from carbon electrodes under aqueous surface immobilization conditions. Nor is methanol oxidation observed from metal oxide electrodes under nonaqueous immobilization treatment. Thus, the surface, the tether bonding the discrete molecule to the surface, and the solution, contribute to forming this active electrocatalyst. The organized distribution of binuclear copper complexes on a carbon electrode significantly enhances dioxygen reduction compared to a random distribution of mononuclear copper complexes. Nafion coatings enhance the stability of the surface immobilized molecular complex. Surface immobilized discrete metal complexes are significantly more robust than complexes prepared from metalation of surface immobilized ligands. These results highlight the value of surface immobilized discrete metal complexes as electrocatalysts.
Electrochemical barriers : kinetic modeling of charge transfer reactions for energy applications
Keywords: Chemical Engineering.

Computational modeling using density functional theory has been a very important tool for finding design criteria and explaining activity trends in heterogeneous catalysts. Recently, these tools have been applied to electrochemical reactions. Current challenges for computational electrochemical catalysis involve extending thermodynamic - or limiting potential - analyses to microkinetic models. These kinetic models can be used to predict turnover frequencies that can be compared to experimentally measured current densities. Additionally, kinetic models allow us to explore other relevant phenonmena such as coverage under reaction conditions and selectivity. This works seeks to refine methods for quantifying electrochemical activation energies and their dependence on applied potential. We further apply these energetics to microkinetic models for electrochemical reactions such as oxygen reduction, water splitting, and CO reduction.
Electrolyte biasing of the proximate kitaev spin liquid α-Ruthenium (III) chloride
Keywords: Applied Physics.

A quantum spin liquid (QSL) is an exotic phase of matter identified by interacting spins that do not develop long-range magnetic order down to T = 0 K. QSLs have topological order and are therefore relevant to storing and processing quantum information. Additionally, doped QSLs may be related to high temperature-superconductivity, making the study of this phase relevant to a broad section of condensed matter physics. I use electronic transport measurements and Raman spectroscopy under electrolyte bias to show that, upon doping, the proximate Kitaev QSL alpha-ruthenium (III) chloride (RuCl3) undergoes a first order phase transition with only small changes in conductivity. X-ray diffraction of electrolyte-biased RuCl3 rules out intercalation being the cause of this phase transition, and confirms the assumption that electrochemical reactions are negligible. I suggest that this phase transition prevents RuCl3 from being used to study doped spin liquid physics and suggest further measurements to characterize the newly identified phase.
Electron correlation effects in attosecond photoionization of carbon dioxide
Keywords: Physics.

State-resolved measurements of the attosecond scale photoionization time delays are presented for carbon dioxide. Calculations are performed and compared to the experimental data. The comparison of theory to experiment demonstrates the effect of multi-electron dynamics on the attosecond time scale. Electron correlations are shown to affect the photoionization time delays through two unique physical phenomena: Autoionizing Rydberg states and shape resonances.
Electronic structure in strontium titanate probed by planar tunneling spectroscopy
Keywords: Applied Physics.

SrTiO3 superconductivity has been studied for decades and still attracts much attention due to its uniqueness. The properties of superconductivity in SrTiO3 are two-sided; some aspects are conventional and others are not. Its carrier density is extremely low and outside of the adiabatic condition in the conventional BCS (Bardeen-Copper-Schrie er) theory for superconductivity in metals. Despite longstanding query, probing its electronic structure has been a challenge because of the large surface depletion layer, especially for the low carrier density regime. In this work, we examine the electronic structure of SrTiO3 for the entire superconducting dome probed by planar tunneling spectroscopy. The suppression of the problematic depletion layer was achieved by using a polar oxide (LaAlO3) as a tunnel barrier. The atomically precise band engineering enabled the construction of a high-quality tunnel junction in electron-doped SrTiO3, which produced the high-resolution tunneling spectra. The evolution of tunneling spectra demonstrates that superconducting electrons are weakly coupled to pairing bosons while normal state electrons are strongly coupled to the longitudinal phonons. The transverse optic soft phonon is suggested as a possible candidate for pairing to explain this discrepancy in the adiabatic condition. How the transverse mode can couple to electrons in this inversion symmetric system still remains unclear, and this can be a unique feature in this incipient ferroelectric system. Furthermore, the physics of SrTiO3 tunneling devices are discussed in this thesis. First, the origins and control of the depletion width in electron-doped SrTiO3 were studied. In addition, LaAlO3, which is used to suppress the depletion width, can accumulate electrons at the interface with electron-doped SrTiO3. The detection and control of electron accumulation are presented, and these are essential to obtain high-quality tunnel junctions to probe the low-density SrTiO3 of interest.
Elegant Offering: a Glimpse of Later Bronze Culture Through Chen Hongshou's Art
Keywords:  Stanford Global Studies
Stanford
East Asian Studies
Ming dynasty
Chen Hongshou
later bronze
Chinese art history
Thesis

The role of bronzes gradually changed throughout Chinese history from the period of the Xia, Shang and Zhou of three thousand years ago, collectively known as the Three Dynasties, through the Song dynasty of the Chinese culture renaissance to the Ming dynasty, which was a period of social openness, thriving culture and widespread commercialization. The diverse aspects of Chinese bronze at various historical stages explicitly convey that the cultural context of each time period is distinct from others. Bronzes were variously ritual vessels to be worshiped and buried underground for ancestral blessings; great monuments to document past glories of heroes and sage kings; carriers of significant historical records awaiting to be deciphered by the descendants of the Central Plains; symbols of widespread Confucian moral teaching and embodiments of the mandate of Heaven; iconographies of popular culture that appeared in paintings, printing manuals, porcelain designs, architectural ornaments and even garment patterns; as well as purely luxury consumption goods. My curiosity about bronze culture was aroused by the late Ming literati and professional artist Chen Honghou (1598-1652) and his captivating works that depict the rich coloration of metalworks in various interior spaces. I intend to explore and to understand the story behind these bronze objects, trying to answer a series of questions: why did artists such as Chen Hongshou choose to depict bronze antiquities, for what reasons and purposes? Why are they so visually attractive? Was Chen the first artist to pay attention to them? What subtle message did these bronze objects convey within the late Ming material culture milieu?
The elements of counterfactuality in Mandarin Chinese
Keywords: East Asian Languages and Cultures.

Natural languages vary in their strategies for communicating information about states or events which are contrary to facts. Most languages do not have a dedicated category of counterfactual markers. Instead, languages commonly employ a combination of grammatical materials which have functions independent of counterfactual meaning to mark counterfactuality. Without formal markings of the common grammatical ingredients for counterfactuality, including tense, aspect, or subjunctive morphemes, Mandarin Chinese uses functional and lexical expressions with meanings unrelated to counterfactuality but which in certain grammatical environments and context can give rise to counterfactual inferences. This study provides an analysis of how counterfactuality arises in Mandarin Chinese by investigating two classes of counterfactual expressions: modals for the past and the so-called counterfactual conditionals. The work reveals that the expressions of counterfactuality in Mandarin Chinese involve interactions between elements of temporal modification, modality, conditionals, causal reasoning, negation, and discourse felicity conditions. In addition to exploring issues related to the language-specific composition of counterfactuality in Mandarin Chinese, this study sheds light on the general contextual and logical assumptions that might be behind the strategies used cross-linguistically to convey counterfactuality.
Elucidating and empowering stem cell-chondrocyte interactions for cartilage tissue regeneration
Keywords: Bioengineering.

Cells are social, and dynamic interactions among cells play an important role in tissue development. While stem cells are widely known for their potential to differentiate directly into a variety of cell types, stem cells can also support tissue regeneration by secreting trophic factors to stimulate other cells. Using a 3D hydrogel co-culture model, our lab has previously reported that adipose-derived stem cells (ADSCs) can substantially enhance cartilage tissue regeneration by juvenile chondrocytes, making them become "super chondrocytes", through cell-cell communications. This finding is significant, as it aids in overcoming donor scarcity associated with chondrocytes by mixing them with ADSCs, an abundantly available autologous cell source. However, the molecular mechanisms through which chondrocytes become "super chondrocytes" remain unknown. Furthermore, while using a mixed cell population overcomes the cell source problem, the resulting cartilage remains mechanically weak, with a compressive modulus an order of magnitude lower than that of native cartilage. My thesis seeks to overcome the above two key challenges by: (1) Identifying the key molecular signal changes that drive the "super chondrocyte" phenotype during co-culture, and (2) Improving the mechanical properties of engineered cartilage during co-culture by developing novel 3D scaffolds. Using RNA microarray technology, I compared the gene expression changes during co-culture vs. mono-culture and identified top candidate genes (up-regulation and down-regulation) associated with the "super chondrocyte" phenotype. These targets offer potential new ways to produce "super chondrocytes" via genetic modification, thereby removing the need for co-culture. To further enhance the mechanical properties of tissue engineered cartilage, I developed a new composite scaffold made of macroporous gelatin-based microribbon (µRB)s as well as a rapidly degradable hydrogel. The scaffold was optimized to support initial retention of paracrine signals required for synergistic ADSC-chondrocyte co-culture, but also provide macroporosity to facilitate new tissue formation. When implanted in vivo using a mouse model, the composite scaffold led to a rapid increase in mechanical properties of cartilage produced by mixed ADSCs and chondrocytes, yet minimal increase was observed using conventional hydrogels. Together, the findings from this thesis fill the gap of knowledge of how stem cells catalyze cartilage formation by chondrocytes during co-culture, and will accelerate the translation of using mixed cell populations for cartilage regeneration with enhanced mechanical functions.
Elucidating the role of the PRC2 sub-unit Ezh2 during early xenopus development and investigating human placentation and pregnancy using first trimester chorionic villi
Keywords: genetics) degree supervisor.
Developmental Biology.

The Polycomb Repressive Complex 2 (PRC2) is of central importance to the establishment and maintenance of transcriptional silencing during development. Limited research on the role of PRC2 during early vertebrate development has produced very different, species-specific results, and recent studies have uncovered roles for the catalytic subunit, Ezh2, independent of its ability to tri-methylate lysine 27 of histone 3 (H3K27me3). In Chapter 1, I review recent findings on the role and regulation of Ezh2 in vertebrate models. In Chapter 2, I present my findings on the role of the Xenopus laevis ezh2 homolog during early development. Embryos deficient for ezh2 failed to specify the mesoderm and were unable to proceed successfully through gastrulation. The effects of ezh2 knockdown seemed to occur prior to the deposition of H3K27me3 in the Xenopus embryo, suggesting a non-canonical role of ezh2 during germ layer specification. Furthermore, deposition of H3K27me3 by the neurula stage was unaffected by depletion of ezh2. In Chapter 3, I present the findings from a collaboration between our laboratory and the Lucille Packard Children's Hospital studying placentation during the first trimester of human pregnancy. Chorionic villus sampling (CVS) is routinely used for prenatal diagnosis of cytogenetic disorders, but the potential of these samples to provide insights into the etiology of pregnancy complications like pre-eclampsia remains largely unexplored. After examining the morphology and transcriptomes of first trimester chorionic villi, we found that pre-eclampsia markers were associated with villi with low morphological complexity and identified the gene SVEP1 as a possible biomarker for determining gestational age.