VictorJuiz/thesis huggingface dataset:
Computational insight into catalytic hydrogenation of nitrogen and carbon monoxide [electronic resource]

Computational modeling is becoming an increasingly important tool in the design of heterogeneous catalysts. This thesis explores recent advances in the atomic-scale computational design of catalytic materials. Nitrogen hydrogenation is used to illustrate the core concepts in part I, and these concepts are applied to a wide range of carbon monoxide hydrogenation reactions in part II. Nitrogen hydrogenation, or ammonia synthesis, is one of the most important catalytic processes ever discovered. Industrial-scale ammonia synthesis enabled the mass production of fertilizers which are now used to produce approximately half of the global food supply. Ammonia synthesis is also a well-studied and relatively simple catalytic reaction, and has served as a bellwether reaction for computation in heterogeneous catalysis. Part I of this thesis revisits the ammonia synthesis reaction. Chapter 2 discusses the importance of ammonia synthesis and heterogeneous catalysis in general. Chapter 3 introduces density functional theory (DFT), the workhorse method in quantum-mechanical studies of catalytic materials. Chapter 4 examines how DFT energies can be combined with kinetic modeling in order to gain insight into catalytic trends and design strategies for ammonia synthesis. Chapter 5 applies a novel method for uncertainty quantification and error propagation in order to demonstrate the robustness of the computational catalyst design against uncertainty in the DFT calculations. Hydrogenation of carbon monoxide (CO) is a complex process with many potentially valuable products including methane, methanol, and higher hydrocarbons and alcohols. These reactions will play an increasingly important role in the global economy as fossil resources are exhausted and replaced by more sustainable synthetic fuels. Part II of the thesis applies many of the concepts introduced in part I to CO hydrogenation reactions. Chapter 6 examines the production of ethanol from synthesis gas (CO and H2) and applies the techniques of chapter 4 in order to map the activity and selectivity trends across transition-metal (211) surfaces. Several alloys are identified as promising catalysts for selective ethanol synthesis, including CoCu and CoPt alloys. Chapter 7 combines computational methods and experiments to provide insight into the complex selectivity patterns of CO hydrogenation over rhodium catalysts, indicating that the reaction is structure sensitive and that rhodium catalysts are intrinsically selective toward acetaldehyde rather than ethanol. Chapter 8 and chapter 9 examine CO hydrogenation over non-metallic catalysts (Mo2C and ZnO), revealing the importance of surface termination and the fundamentally different surface reactivity of transition-metal compounds.

Keywords: Chemical Engineering.
Advisor: Nørskov Jens K.
Jaramillo Thomas Francisco advisor. Thesis advisor
Wilcox Jennifer
Computational modeling and evaluation of reverse osmosis and forward osmosis water treatment technologies integrated with CCHP waste heat [electronic resource]

Seawater reverse osmosis (RO), Forward Osmosis (FO) and the FO/RO hybrid process have received increased attention. Providing waste heat of a CCHP plant to these membrane technologies could benefit both energy efficiency and environmental impacts of the hypothetical integrated infrastructure system. In order to evaluate the potential benefits, simulation and modeling need to be performed taking all possible system parameters into consideration. In this study, a simulation approach for RO and FO water treatment processes is presented. The design space of a preheated RO system is explored, using the amount of water produced per unit cost as the optimization objective. The results show that typical optimal designs have 70~90°C operating temperature, 0.3~0.5 recovery goal, 50~60 bar operating pressure and larger design capacity.

Keywords: Civil and Environmental Engineering.
Advisor: Lepech Michael advisor. Thesis advisor
Conceptualizing Critical Thinking in Hong Kong: The Decoupling of Policy and Practice in the New Senior Secondary Curriculum Reform

Critical thinking is a term increasingly incorporated into educational policy around the world as a primary curriculum reform objective. Despite shifts in policy, however, often the mechanisms for ensuring the implementation of policy in practice are decoupled. Hong Kong is among one of the many educational systems that has recently undergone a drastic curriculum reform in which critical thinking has been defined as a key skill. This paper investigates how critical thinking is conceptualized on different levels of curriculum – from intended to resourced to implemented – in the secondary school subject, Liberal Studies, against the backdrop of the New Senior Secondary Curriculum (NSSC) reform. Employing textual analyses and interviews, I investigate whether and why gaps exist in the conceptualization of critical thinking at these three curricular levels in order to understand the process of decoupling from policy to practice. The findings of the study suggest that critical thinking is conceptualized fairly nebulously from policy to practice, leading to decoupling between the two. These findings highlight a need for Hong Kong educational authorities to provide a clearer definition of critical thinking, as well as stronger programmatic support for teachers, in order to best sustain alignment in this curriculum reform.

Keywords: critical thinking education
Liberal Studies
New Senior Secondary Curriculum
curriculum reform
neo-institutionalism
decoupling
Hong Kong
Stanford Graduate School of Education International Education Policy Analysis
Thesis
Conserved regulation of the switch from proliferation to differentiation in the germline [electronic resource]

A defining step in germ cell development is the exit from mitotic proliferation and initiation of meiosis, which enables the generation of haploid gametes. The switch from mitosis to meiosis must be strictly regulated to maintain proper tissue homeostasis and prevent the formation of germ cell tumors. However, the molecular mechanisms that drive the switch from mitotic proliferation to meiosis and differentiation in metazoans are not well understood. It is also not known whether key regulators of the switch are broadly conserved. Here I show that in the Drosophila male germline, the tumor suppressor proteins Benign gonial cell neoplasm (Bgcn) and Bag-of-marbles (Bam) work together to execute the transition from cell proliferation to differentiation through translational repression. Loss-of-function mutations in either bgcn or bam lead to overproliferation of progenitor cells that fail to enter meiosis and differentiate. Bam and Bgcn directly repress the expression of the target mRNA mei-P26 during the mitotic divisions by binding the mei-P26 3′ UTR. Our studies highlight the important role of translational control mechanisms in making the switch from proliferation to differentiation sharp and accurate in the Drosophila germline. I also identified the mammalian homolog of Drosophila bgcn and found that, strikingly, similar to bgcn mutant flies, mBgcn knockout mice are viable but both male and female sterile. mBgcn expression is upregulated at the onset of meiosis in both male and female germ cells. Consistent with the expression pattern of mBgcn, histological analysis of mBgcn mutant adult testes and fetal ovaries revealed that mBgcn-deficient germ cells fail to enter meiotic prophase and instead attempt an additional mitotic division, and then quickly die. My findings indicate that Bgcn has a highly conserved functional role as a gatekeeper to meiotic entry and terminal differentiation in both flies and mice. In addition, my results raise the exciting possibility that, as in Drosophila males, post-transcriptional control mechanisms may drive the switch from mitosis to meiosis in the mammalian germline.

Advisor: Fuller Margaret
Nusse Roel
Oro Anthony
Villeneuve Anne
Constitutional Promises and Environmental Protection

Constitutions detailing the legal obligations of a nation to its peoples have been around for centuries, since England’s Magna Carta. As our conceptions of governance evolved, constitutions became the locus for codifying rights considered worthy of protection from the state or by the state. In the past sixty years, constitutions around the world have begun recognizing people’s rights to a healthy environment. Nearly half a century after the widespread adoption of these constitutional clauses, in a world plagued by issues of cooperation over sustainable development and climate change, it begs the question of how effective these rights have been. This study combines quantitative and qualitative methods to investigate the relationship between the commitments made by advanced economies and their ultimate outcomes.

Keywords:  Program in International Relations
Environmental constitutionalism
environmental performance
Stanford University Program in International Relations
Thesis
Advisor: Lipscy Phillip Y.
Constraining ocean acidification and anoxia during the end-Guadalupian and end-Triassic extinctions with calcium and uranium isotopes [electronic resource]

Many mass extinctions are contemporaneous with emplacement of large igneous provinces (LIPs), suggesting that the environmental effects of LIP volcanism were important kill mechanisms. Of major interest is whether rapid injection of volcanic carbon dioxide into the ocean and atmosphere resulted in seawater acidification and eutrophication. The end-Guadalupian (ca. 260 Ma) and end-Triassic (ca. 201 Ma) extinctions were both associated with LIPs and saw preferential extinction of marine animals sensitive to changes in seawater pH or oxygen content. Carbon isotope fluctuations are consistent with some type of carbon cycle perturbation, and local proxies of acidification and anoxia are widespread. However, we have not yet been able to quantify the severity of acidification or anoxia during these events at a global scale. Calcium and uranium isotopes can be combined with carbon isotope data to constrain these phenomena. This is because the carbon cycle is linked to the calcium cycle via burial of calcium carbonate and chemical weathering of Ca-minerals, and to the uranium cycle via organic carbon production and precipitation of uranium under reducing conditions. For my dissertation, I use these non-traditional isotope systems, along with numerical models of their mass and isotopic fluxes, to constrain the cause of carbon cycle perturbations and the seawater geochemistry during each extinction. Chapter one discusses the end-Guadalupian extinction event. Contrary to claims of large carbon cycle perturbations during the end-Guadalupian extinction, calcium isotope data suggest that acidification was minimal and that carbon isotope excursions were generated or amplified by local conditions. This finding is consistent with much lower revised extinction rates based on new compilations of fossil occurrences. Chapters two and three discuss the end-Triassic extinction event. In contrast to the end-Guadalupian, the end-Triassic calcium isotope record contains a large (0.7‰) negative excursion just above the extinction horizon. Numerical modeling of the carbon and calcium cycles demonstrate that these patterns are consistent with acidification and enhanced calcium isotope fractionation due to higher precipitation rates during recovery from acidification. Uranium isotope data show similarly large perturbations, with a 0.6‰ negative isotope excursion suggesting a 35x increase in the extent of anoxic bottom waters following the end-Triassic extinction. Together, these projects demonstrate the power of combining non-traditional isotope systems with other proxies to constrain the nature of environmental change surrounding mass extinctions in the geologic record.

Keywords: Geological Sciences.
Advisor: Payne Jonathan L. primary advisor. Thesis advisor
Lowe Donald R.
Maher Katharine advisor. Thesis advisor
Contemporary issues in service and operations management [electronic resource]

The essays in this dissertation are motivated by various contemporary issues in the late 2000s and early 2010s related to the environment, healthcare and natural disasters. Chapter 1 explores the issue of environmental and social disclosures on consumer products. Specifically it studies whether consumer reaction to products differ under voluntary and mandatory disclosures, and whether policy makers should mandate disclosure. The results suggest that contrary to basic intuition, mandatory disclosure policies may lead to sub-optimal environmental and social performance by firms. Chapter 2 is motivated by the increasing number of Emergency Departments (EDs) in the US that publish wait times publicly. This work proposes a novel wait time prediction method that combines queuing theory and statistical learning. Implementation results at San Mateo Medical Center (SMMC) show that this method is 30% more accurate than the current industry standard. Furthermore, post-implementation results of the wait time prediction system at SMMC's ED show that publishing accurate wait times led to a decrease in the number of patients who left without being seen by a physician. Chapter 3 is motivated by the events in the aftermath of the Tohoku earthquake, when many supply chains stopped functioning due to upper tier supplier disruptions. This work studies how a manufacturer should optimally source form its suppliers if it knows that disruption risk originates from the upper tiers of its supply chain. The result shows that if there is significant overlap of suppliers in the upper tiers, the manufacturer should pursue an aggressive strategy of inducing its direct suppliers to dual source. On the other hand, if the degree of overlap is low, the manufacturer should focus on its own dual sourcing and inventory mitigation.

Keywords: Business.
Advisor: Bayati Mohsen primary advisor. Thesis advisor
Plambeck Erica L. primary advisor. Thesis advisor
Iancu Dan advisor. Thesis advisor
A continuous adjoint formulation for hypersonic flows in thermochemical nonequilibrium [electronic resource]

This thesis explores the formulation, derivation, and implementation of the continuous adjoint equations for hypersonic, nonequilibrium flow environments. The adjoint method is an efficient means for acquiring sensitivity information that can be used in a gradient-based framework to perform optimal shape design of aerospace systems. A solution to the adjoint system of equations carries a computational cost roughly equal to a single solution of the flow governing equations, regardless of the dimensionality of the design space. When compared to other gradient acquisition methods, where computational costs scale with design space dimensionality, the adjoint method is superior when the dimensionality is high and when solutions to the governing equations are expensive. Such conditions are often representative of most aerospace problems of practical interest. In addition to providing gradient information, solutions to the adjoint equations may be used as 'sensors' or 'weighting factors' to perform error estimation and adaptive mesh refinement. Hypersonic systems operate in unique flow environments that are dominated by chemical and thermodynamic phenomena not observed at lower Mach numbers. Accurate simulations of these environments require sophisticated thermochemical models to resolve atomic-scale physical processes that have first-order effects on integrated vehicle performance metrics, including lift, drag, stability, controllability, and heat transfer. Because of the computational expense demanded by these high-fidelity tools, the conceptual vehicle design process often relies heavily on low- to medium-fidelity, correlation-based tools that are confined to narrow regions of applicability. As a consequence, the hypersonic vehicle design process has remained relatively static for the past several decades. The adjoint method enables the use of high-fidelity tools early in the design cycle of hypersonic systems, and is a transformative technology for the hypersonic community. This work provides the first derivation, implementation, and verification of the continuous adjoint equations for hypersonic flow environments in thermochemical nonequilibrium. Appropriate boundary conditions and surface sensitivities are provided for both projected force and thermal objective functions for continuum, viscous, multi-component gas mixtures. The adjoint system is implemented in a second-order, unstructured, finite-volume-method (FVM) flow solver that is representative of the state-of-the-art in high-fidelity aerothermodynamic analysis for hypersonic entry systems. Gradients from the adjoint-derived surface sensitivities are verified against gradients calculated using a finite-difference methodology for several representative geometries relevant to ballistic and lifting-body entry vehicles.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Jameson Antony
MacCormack R. W. (Robert William)
The contribution of RNA to heterochromatin [electronic resource]

Accurate chromosome segregation is essential for proper cell division and normal organismal development in all eukaryotes. Chromosome segregation errors generate aneuploid cells that cause human genetic disease and characterize most human cancers. Our long term goal is to understand the cellular mechanisms that ensure accurate chromosome segregation. During cell division, pairs of replicated chromosomes must remain linked until anaphase in order to properly segregate to daughter cells. The primary sites for cohesion between sister chromatids exist at the heterochromatic outer regions of the centromere, called pericentric heterochromatin. Disruption of this heterochromatin domain disturbs cohesion, resulting in chromosome segregation errors and aneuploidy. The concept of non-coding RNAs directing chromatin modifications is a growing paradigm in cell biology and substantial evidence implicates non-coding RNAs in the formation of human pericentric heterochromatin. Unraveling the RNA-dependent mechanisms of pericentric heterochromatin formation has clear implications in human disease; dysfunctional regulation of pericentric transcription characterizes numerous cancers in mouse and humans and is thought to contribute to genomic instability. We discovered that RNA remains physically attached to human mitotic chromosomes, and is enriched at pericentric regions. We found that SUV39H1 and SUV39H2, two histone methyltransferases critical for heterochromatin formation, directly bind RNA in vitro and associate with RNA transcribed from pericentric regions in vivo. We found that treatment of mitotic chromosomes with single-stranded ribonuclease decreases SUV39H1 localization to pericentric regions, suggesting an RNA-dependent mechanism for SUV39H1 targeting. To determine to role of direct RNA binding by SUV39H1, we mapped the minimal RNA binding domain of SUV39H1 to its chromodomain, and identified mutants that severely disrupt direct RNA binding in vitro. RNA binding-deficient SUV39H1 mutants display a marked impairment of localization to pericentric regions in vivo, and are generally less stably associated with chromatin. These results suggest a novel role for non-coding RNA in the targeting of SUV39H1 to pericentric heterochromatin. We propose a model in which both direct RNA binding, in addition to histone binding, differentially contribute to the affinity of SUV39H1 for pericentric heterochromatin, ensuring faithful heterochromatic silencing of a chromatin domain that is vital for proper chromosome segregation.

Keywords: Biochemistry.
Advisor: Straight Aaron
Das Rhiju
Gozani Or Pinchas advisor. Thesis advisor
Pfeffer Suzanne advisor. Thesis advisor
Contributions to fault detection and diagnosis with high-dimensional data [electronic resource]

Motivated by applications to root-cause identification of faults in multistage manufacturing processes which involve a large number of tools or equipments at each stage, we consider multiple testing in regression models whose outputs represent the quality characteristics of a multistage manufacturing process. Because of the large number of input variables that correspond to the tools or equipments used, this falls in the framework of regression modeling in the modern era of big data. On the other hand, with quick fault detection and diagnosis followed by tool rectification, sparsity can be assumed in the regression model. We introduce a new approach to address the multiple testing problem and demonstrate its advantages over existing methods. We also illustrate its performance in an application to semiconductor wafer fabrication that motivated this development. The problem of detection and diagnosis of abrupt changes in a stochastic system on the basis of sequential observations has many applications, some of which are discussed in this thesis. In statistical process control (SPC), the past decade witnessed the emergence of a new direction in quality control because of the availability of big data, making use of contemporaneous developments in the statistics literature on high-dimensional data analysis. It has been noticed that in multivariate and high-dimensional applications, only a sparse subset of quality characteristics or other variables of interest undergoes abnormal changes that lead to deviations from the state of statistical control. The past decade also witnessed major developments in surveillance over sensor networks, cyber-security and information systems. We give a general theory for sequential fault detection in these stochastic models and also modify and extend it to the much less developed problem of fault diagnosis. This fault diagnosis, or change isolation problem, is to determine upon detection of change in a system which one in a set of possible changes has actually occurred. In this connection, we also develop a parallel theory of sequential multiple hypothesis testing.

Keywords: Statistics.
Advisor: Lai T. L. primary advisor. Thesis advisor
Siegmund David
Walther Guenther advisor. Thesis advisor