VictorJuiz/thesis huggingface dataset:
Novel materials and nanofabrication methods for the Dielectric Laser Accelerator (DLA)

Dielectric laser accelerators (DLA), laser-driven photonic structures whose evanescent fields can synchronously accelerate charged particles, have recently demonstrated acceleration gradients far exceeding those possible with conventional radio frequency (RF) sources, opening the possibility of shrinking both the size and cost of linear accelerators by orders of magnitude. The acceleration gradient of the DLA is ultimately limited by the laser-induced damage threshold (LIDT) of the constituent materials. A material with high LIDT which can be shaped precisely into sub-wavelength nano-structures is an ideal candidate for DLA. My contributions can be roughly categorized into two sections: improvements to single-stage DLA and proof-of-concept demonstrations of essential elements to realize a multi-stage implementation of DLA. My improvements to single-stage acceleration are as follows: I report the first successful DLA demonstration using novel materials with high LIDT. I present the nanofabrication methods that I have developed to shape these novel metal oxide materials (Al2O3 and Ga2O3) precisely into sub-wavelength nanostructures. I demonstrate the first successful metal oxide-based laser-driven electron acceleration in the sub-relativistic regime, with devices made of both Al2O3 and Ga2O3. I propose and simulate the performance of metal oxide-based DLA for the relativistic regime, which can achieve higher acceleration gradients when compared to current SiO2 DLA structures. Finally, I show that thin-layer coatings of these metal oxide materials act as a field reduction layer, which improves accelerator performance. My contributions to future multi-stage DLA are essential elements for a practical on-chip accelerator. I have fabricated Ga2O3-core/SiO2-clad waveguide on Si substrate and Al2O3-core/SiO2-clad waveguide on Si substrate for laser power delivery, which is crucial for future on-chip integrated DLA. I, along with Professor Peter Hommelhoff's Group, present work on realizing sustained acceleration. These include a chirped DLA grating to counteract dephasing effects, a laser-driven electron lens, and the first demonstration of a two-stage DLA. I show co-propagation-based DLA, including a ring resonator-based DLA and total internal reflection-based DLA. These results constitute an important step towards enabling an "Accelerator On A Chip.".

Keywords: Electrical Engineering.
Advisor: Harris J. S. (James Stewart)
Byer R. L. (Robert L.)
Solgaard Olav
Novel methods and applications for kinetic plasma simulation

Understanding the behavior of plasma is important for a broad range of applications, such as understanding the production of energetic particles in astrophysics, developing predictive models for space weather, and harnessing the potential of nuclear fusion power. Due to limitations such as noise from numerical collisions and the large number of simulation particles required to capture the development of nonthermal tails in the particle distribution, multiscale plasma simulations are extremely challenging. In this thesis the simplex-in-cell algorithm is presented, which holds promise for overcoming these difficulties by interpreting the simulation particles as the vertices of a mesh that traces the evolution of the distribution function in phase space. This enables a discretization using deformable phase space volume elements rather than fixed-shape clouds of charge. Using test problems including Landau damping and the Weibel instability it is shown how this new view retains fine-scale structure in the distribution function and can drastically reduce the number of simulation particles required to reach a given noise level. Magnetic reconnection is a promising candidate mechanism for accelerating the nonthermal particles associated with explosive phenomena in astrophysics. Laboratory experiments with high-power lasers can play an important role in the study of the detailed microphysics of reconnection and the dominant particle acceleration mechanisms. In this thesis the results of particle-in-cell simulations used to explore particle acceleration in conditions relevant for current and future laser-driven reconnection experiments are presented. These simulations indicate that laser-driven plasmas offer a promising platform for studying particle acceleration from reconnection, with the potential to reach multi-plasmoid regimes of strong astrophysical interest. These results provide new insight into the physics of reconnection and particle acceleration and are now helping to guide experimental campaigns.

Keywords: Physics.
Advisor: Abel Tom G.
Fiuza Frederico 
Glenzer S. H.
Novel pharmacological modulators of mitochondrial function in cell physiology and pathology

Within a single cell, thousands of mitochondria form a beautiful dynamic network. Beyond their canonical adenosine triphosphate (ATP) generating role, mitochondria more recently gained recognition as the hub of numerous signaling pathways that mediate cell life and death. Mitochondria are ubiquitous organelles that play a pivotal role in many organs. It is not therefore not surprising that dysfunctional mitochondria, and the excessive reactive oxygen species (ROS) they produce, have been implicated as the culprits of a variety of disorders spanning multiple body systems. This dissertation describes the development of novel pharmacological tools that target mitochondrial function in cell physiology and pathology. Chapters 1 and 2 introduce mitochondria as attractive therapeutic targets for cardiovascular and neurodegenerative diseases, respectively. Each chapter includes a review of relevant clinical trials and outcomes of therapeutics that either generally target ROS versus ones that specifically target mitochondrial dysfunction. In addition, they highlight the advantages and the challenges of therapeutic avenues involving mitochondria. Chapter 3 summarizes the use of peptides as specific protein-protein interaction (PPI) inhibitors for ameliorating the ischemia-reperfusion (IR) damage associated with myocardial infarction. These novel pharmacological tools target protein kinase C delta ( PKC), which translocates to the mitochondria in response to stress induced by IR and phosphorylates numerous mitochondrial substrates. These PPI peptide inhibitors each specifically inhibit the phosphorylation of one protein substrate. Chapters 4 and 5 focus on the characterization of activators and inhibitors of mitochondrial fission and fusion, the core processes of mitochondrial dynamics. Mitochondrial dynamics govern mitochondrial shape and size, which are tightly linked to function. Dysregulation of these processes is a hallmark of neurodegeneration, in particular Huntington's disease and Charcot Marie Tooth Type IIa, both of which serve as the backdrop model for these newly-identified peptide modulators.

Keywords: Chemical and Systems Biology.
Advisor: Mochly-Rosen Daria 
Bernstein Daniel
Jarosz Daniel 
Meyer Tobias
Novel roles for the EP2 receptor in Alzheimer's disease

Microglia, the primary immune cells of the central nervous system, are critical to the inflammatory homeostasis of the brain. These cells halt toxic inflammation and clear debris, degrading misfolded proteins and clearing plaques. In cases of severe inflammation, aging, or neurodegenerative disease, however, microglia become overwhelmed, and their beneficial functions are replaced by dysfunctional, pro-inflammatory responses, further catalyzing the brain's loss of synapses and neurons. In an effort to bolster microglial clearance and halt this feed-forward pathology, the prostaglandin EP2 receptor was recently established as a key regulator of myeloid dysfunction in mouse models of Alzheimer's disease. My current findings indicate that this EP2 receptor deletion improves myeloid cell function by orchestrating lysosomal and mitochondrial activity. Specifically, deletion of EP2 mobilizes the CLEAR network, a canonical regulator of lysosomal clearance and recently-established regulator of mitochondrial biogenesis and function that I find is broadly implicated in microglial affected by neurological disease. Suppressing EP2 signaling in microglia and macrophages stimulates lysosomal gene expression, biogenesis, and function, rescuing degradative capacity that is otherwise suppressed by amyloid beta (Aβ), a misfolded protein implicated in Alzheimer's disease. Concurrently, EP2 deletion stimulates mitochondrial biogenesis, simultaneously rescuing oxidative phosphorylation and metabolite production, both impaired by Aβ. Together, these findings demonstrate that myeloid EP2 signaling coordinates and orchestrates immunometabolism and lysosomal degradation and, in this way, may serve as a critical target to restore healthy microglial function, prevent neuroinflammation, and stall progression of Alzheimer's disease.

Advisor: Andreasson Katrin
Ricci Anthony 
Palmer Theo 
Reimer Richard J. 
Wang Xinnan
Nuclear Propaganda in Select Regional Newspapers in Japan: A Snapshot Analysis of 1986 and 2010

Given the devastation of suffering two nuclear attacks in its history, how has Japan become so comfortable and invested at a social level with nuclear energy? How has this manifested at a local level, outside of the urban center of such a centralized nation? Historically, the media and private energy industry have a long history of interconnectivity and, throughout the latter half of the 20th century, efforts were made to leverage nuclear energy as a nation-building socio-technological tool. Working within the framework of scholarship in Science, Technology and Society (STS) studies and Japanese scholarship, this thesis investigates pro-nuclear advertisements in regional newspapers in Japan in order to understand how public opinion towards nuclear energy was influenced at a local level. By accessing a unique data set of regional newspapers in 1986 and 2010, the qualitative analysis explores how advertising strategy and local characteristics shifted and evolved over the course of the years. This kind of investigation can shed light on the historical strategies used by the private energy industry in local regions, so that these tactics can be recognized in the future as Japan’s energy policy continues to evolve.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Japan
Nuclear Energy
STS
Media and Industry
Thesis
Advisor: Sato Kyoko
Numerical artifacts in the generalized porous medium equation and solutions

The degenerate parabolic Generalized Porous Medium Equation (GPME) poses numerical challenges due to self-sharpening and its sharp corner solutions. Spurious temporal oscillations, and nonphysical locking and lagging have been reported in the literature for averaged-based second order finite volume discretizations. In these works, the numerical artifacts have been attributed to harmonic averaging of the coefficient k(p) for small p, and arithmetic averaging has been suggested as an alternative in the continuous coefficient case. In addition to the degeneracy and self-sharpening of the GPME with continuous coefficients, increased numerical challenges occur in the discontinuous coefficient case. These numerical challenges manifest themselves in spurious temporal oscillations in second order finite volume discretizations with both arithmetic and harmonic averaging. The integral average, developed in van der Meer et al. 2016, leads to improved solutions with monotone and reduced amplitude temporal oscillations. We aim to understand the cause of these artifacts, and to use that understanding to propose solutions. In the first part of this dissertation, we investigate the causes of the numerical artifacts using modified equation analysis for the continuous coefficient case. The provided modified equation framework can be used for any type of discretization. We show results for the second order finite volume method. We find that the observed problems with harmonic averaging can be traced to two leading error terms in its modified equation. This is also illustrated numerically in one and two dimensions through our newly developed Modified Harmonic Method (MHM) that can locally modify the critical terms to remove the aforementioned numerical artifacts. For the continuous coefficient case, we show results for two subclasses of the GPME with differentiable k(p) with respect to p, namely the Porous Medium Equation (PME) and the superslow diffusion equation. In the second part of this dissertation, we propose a new method called the Shock-Based Averaging Method (SAM) that incorporates the shock position into the numerical scheme. The shock position is numerically calculated by discretizing the theoretical speed of the front from the GPME theory. The speed satisfies the jump condition for integral conservation laws. SAM results in a non-oscillatory temporal profile, producing physically valid numerical results. We use SAM to demonstrate that the choice of averaging alone is not the cause of the oscillations, and that the shock position must be a part of the numerical scheme to avoid the artifacts. For the discontinuous coefficient case, we show results for a subclass of the discontinuous GPME, known as the Stefan problem.

Advisor: Gerritsen Margot (Margot G.) 
Sampaio Luiz Augusto
Suckale Jenny
Numerical experiments in thermal convection with and without mean shear

The specific problem of thermal convection with and without mean shear is studied. By leveraging advances in flow visualization, numerical algorithms, and large-scale computing, both laboratory and numerical experiments are just beginning to outline a picture of turbulent convection in wide fluid layers and clarify the effects of buoyancy and related analogies on shear-flow turbulence in many industrial and environmental fluid flows. Herein, mean shear is established by mechanical means and density fluctuations induced by heating a horizontal fluid layer sandwiched between hot and cold walls. Even without mean shear, vigorous convection currents develop under the influence of such heating by the direct action of buoyant body forces. It is of some importance to predict how heat transport by both big and small eddies is affected by the action of buoyancy and mean shear in wall-bounded channel flows as well as in other more complex configurations. One of the most striking features of unstable buoyant shear layers is the appearance of unsteady longitudinal vortices, which are characterized by an organized helical circulation of individual buoyant thermals stirred into alignment by mean shear near the walls. These are in marked contrast to the polygonal convection cells and heat transport associated with Rayleigh-Benard convection without strong mean shear. This report provides a unique physical picture of wall turbulence in these flows and discusses the significance of the present results for predicting and modeling subgrid-scale phenomena.

Keywords: Mechanical Engineering.
Advisor: Moin Parviz 
Lele Sanjiva K. (Sanjiva Keshava)
Mani Ali (Professor of mechanical engineering) 
Urzay Lobo Javier
Numerical simulations of turbulent reacting flows with finite-rate chemistry and combustion-model adaptation [electronic resource]

The utilization of finite-rate chemistry with realistic chemical kinetics in large-eddy simulations (LES) of turbulent reacting flows has attracted increasing interest in recent years. It enables further improvement in the prediction of emissions in the combustion process and helps eliminate the restriction often imposed by regime-specific combustion models. However, the cost of such approaches remains a great concern despite the continuing growth of computational capacity, as they are often orders-of-magnitude more expensive than the regime-specific flamelet-type models. In this study, the framework of Pareto-efficient combustion (PEC) modeling is developed, which allows the adaptive utilization of multiple combustion models under consideration of cost-fidelity characteristics for efficient simulations of complex turbulent flames. This adaptive approach provides a general combustion modeling capability with an adjustable level of fidelity and complexity. Based on the user-specific inputs on quantities of interest, desired simulation accuracy and computational cost, the PEC framework makes adaptive model assignments restricting the application of sub-models within their intended use. For complex problems, the proposed framework allows the usage of detailed description of the combustion chemistry in limited regions where it is necessary, while avoiding the concomitant overhead in regions where flamelet-type models are deemed sufficient. Efficient computational strategies are developed to accelerate large-scale parallel simulations with stiff finite-rate chemistry, including time stepping methods and load rebalancing techniques. The combined approach is applied to LES of turbulent flames, demonstrating its capability in improving the predictability and cost-effectiveness of turbulent combustion simulations.

Keywords: Mechanical Engineering.
Advisor: Ihme Matthias
Moin Parviz advisor. Thesis advisor
Wang Hai
Oil and Gas Development and Risk of Preterm Birth: Evidence from San Joaquin Valley, California

Background. Prior studies report an association between adverse birth outcomes, including preterm birth, and proximity to oil and gas wells. Most attention has focused on unconventional natural gas developments, with little attention to conventional oil and gas extraction. Both conventional and unconventional oil and gas development have high levels of air pollution emissions.
Objective. Our objective was to determine whether maternal residence proximity to conventional oil and gas wells in active development increases the risk of preterm birth. Methods. We obtained health data from birth certificates linked to hospital discharge data from the Office of Statewide Health Planning and Development. Data on oil and gas wells came from the California Department of Conservation. After exclusion, the births dataset had 27,913 preterm cases and 197,461 term controls, with a total of 225,374 births, and the wells dataset included 11,972 oil and gas wells in active development. For each birth, we computed an exposure index by taking the sum of the inverse distance to all wells in active development within a 15 km radius of the maternal residence. We defined four preterm birth categories based on gestational length (in weeks): 20-23, 24-27, 28-31, and 32-36. We estimate crude and adjusted odds ratios for preterm birth using logistic regression. To test the robustness of our results, we used different radii and formulas to generate the exposure index and determined whether this changed the findings. To assess the effect of distance to wells, we generated an indicator for maternal residences with at least one well within a radius of 1 km, 3 km, 5 5 km, 7 km, or 10 km.
Results. Exposure to oil and gas wells in active development was associated with a small but significant increase in the risk of preterm birth. The risk was highest for the 32 to 36-week preterm birth category, with exposure throughout gestation associated with increased risk for this group. Several sensitivity analyses testing the assumptions of our exposure assessment method found similar results. In addition, the significant effects persisted for births that had at least one well within 1 km, 3 km, or 10 km for early preterm birth, and within 5 km or 7 km for late preterm birth.
Conclusions. Exposure to oil and gas wells in active development was associated with higher risk of preterm birth. More work is needed to infer whether a causal link exists between the exposure and adverse birth outcomes.

Keywords: Epidemiology and Clinical Research
Health Research and Policy
School of Medicine
preterm birth
environmental epidemiology
perinatal health
Thesis
On fast preconditioners for time-harmonic high-frequency wave equations [electronic resource]

Solving time-harmonic wave equations in high frequency regime is an important yet numerically challenging problem. This dissertation presents three fast preconditioners for time-harmonic high frequency wave equations under different problem settings. The first preconditioner adopts a recursive approach from the moving PML sweeping preconditioner for the 3D Helmholtz equation, which reduces both the setup and the application costs to linear while maintaining the iteration number to be frequency insensitive. The second one is an enhancement of the sparsifying preconditioner for periodic structures by taking the local potential information into account, which improves the accuracy of the preconditioner and reduces the iteration number to be essentially independent of the problem size. The third one assembles the key ideas from the first two works, which results in a highly efficient preconditioner for the Lippmann-Schwinger equation, where both the setup and the application costs are linear. Moreover, numerical results show that the iteration number grows only logarithmically as the frequency increases. To the best of our knowledge, this is the first method that achieves near-linear cost to solve the Lippmann-Schwinger equation in 3D high frequency regime.

Advisor: Ying Lexing primary advisor. Thesis advisor
Papanicolaou George advisor. Thesis advisor
Ryzhik Leonid advisor. Thesis advisor
On Payday, and on Principle: Mick Mulvaney and the Bounds of Reasonable Debate in Consumer Financial Protection

In the first half of 2018, amid a flurry of deregulatory action across financial markets, Consumer Financial Protection Bureau (CFPB) Acting Director Mick Mulvaney announced the reconsideration of newly adopted restrictions on payday loans alongside the sudden end of both lawsuits against and investigations into some of America’s largest payday lenders. The following paper evaluates the motivation, economic rationale, and context of Mulvaney’s actions. Payday loans are high-interest loans usually collateralized by a forward-dated check due on the borrower’s next payday. Academic sentiment concerning these loans is divided, with some positing that the product can be narrowly welfare promoting for the financially desperate, others maintaining that payday loans are simply a predatory debt trap, and both sides acknowledging a paucity of alternatives for those in financial despair. However, as I will argue, Mulvaney’s actions as Acting Director- especially those related to the enforcement of existing law pertaining to payday loans- fall outside the scope of what might be defended by those on either side of debate concerning the economics and policy choices surrounding payday lending. Instead, his actions make sense almost exclusively when viewed through the lens of Mulvaney’s stated distain for CFPB, his opposition to federal intervention in financial markets, and a desire to defend the payday industry at large. As I will discuss, this exists both aside from and in direct opposition to conservative ideals regarding regulation.

Keywords:  Public Policy Program
Stanford University
Humanities and Sciences
Public Policy Program
CFPB
payday lending
Mick Mulvaney
consumer finance
Thesis
Advisor: Admati Anat