VictorJuiz/thesis huggingface dataset:
From compartments to networks : model complexity and infectious disease policy
Keywords: Management Science and Engineering.

The opioid abuse epidemic in the United States calls for new and cost-effective policies to address the rise of morbidity and mortality associated with drug injection. This dissertation explores how, and the extent to which, mathematical modeling can inform policy interventions surrounding HIV for people who inject drugs (PWID). First, we develop a dynamic compartmental model empirically calibrated to the US HIV epidemic to assess the cost-effectiveness of HIV preexposure chemoprophylaxis (PrEP) for PWID. We identify the optimal delivery scenario for PrEP but nonetheless find that it is not likely to be cost-effective. Next, we consider PrEP within a context of other HIV interventions. We find that an optimal portfolio of opioid agonist therapy (OAT), needle syringe exchange programs, and test and treat programs can deliver greater health benefit for less cost than PrEP. Although PrEP averts more infection than OAT, OAT provides more value because of its immediate quality of life improvements for an individual with high competing mortality risks. Finally, to explore how structural modeling assumptions influence policy conclusions, we perform a case study of a potential HIV vaccination across a family of linked models. We find that aggregating individuals into compartments biases us towards intervention, an effect most pronounced when targeting to smaller populations. Parameter complexity, although it has little effect on network models in this context, can mitigate overestimation effects in compartmental models.
From nation-building to nation-branding : literature and cultural diplomacy in twentieth century Mexico
Keywords: Iberian and Latin American Cultures.

My dissertation explores the vital intersection between literature and cultural diplomacy in twentieth-century Mexico. As part of a strategy of nation-building abroad, carried out mainly by state-sponsored foreign-language publications promoting Mexican culture, and by the overwhelming number of writer/diplomats incorporated into the Mexican diplomatic service, I argue that the post-revolutionary governments, facing international threats and a legitimacy crisis, made use of literature as a means for engaging with foreign publics. Focusing on the dynamics and exchange of symbolic capital in the relationship between the writer and the Mexican government, my dissertation explores the hybrid nature of the writer/diplomat. Specifically, I focus on the roles of writer/diplomats: Amado Nervo, Alfonso Reyes, the Contemporáneos, José Juan Tablada, Octavio Paz, Carlos Fuentes, Fernando Benitez, Hugo Gutierrez Vega, Victor Sandoval, and Fernando del Paso in the development of Mexican cultural diplomacy. Furthermore, I suggest that during the last decade of the century, within the context of the negotiation and implementation of the North American Free Trade Agreement (NAFTA), Mexican cultural diplomacy transitioned towards a nation-branding approach, evidenced by Mexico's participation as Guest of Honor at the 1992 Frankfurt Book Fair. Ultimately, my dissertation shows that Mexican literature of the twentieth century is intrinsically tied to the political process of post-revolutionary cultural diplomacy.
Full-chip synthesis and transport characterization of monolayer semiconducting transition metal dichalcogenides [electronic resource]
Keywords: Electrical Engineering.

In recent years, monolayer (1L) semiconducting transition metal dichalcogenides (TMDs) have attracted significant attention for use in a plethora of electronic applications, including logic and memory. However, few studies have examined important metrics for scaling device numbers up and dimensions down for eventual system-level applications. Among the many problems that have been waiting to be solved are demonstration of large area synthesis, description of device-to-device variation, and characterization of velocity saturation. In this work, I will explore these issues principally for 1L MoS2. First, I highlight the recent advancements in solid-source chemical vapor deposition of 1L two-dimensional (2D) semiconductors. I begin by reviewing the theory and conditions necessary for van der Waals epitaxy of large, highly crystalline films of 1L materials. Using this understanding, I establish growth of MoS2, WS2, MoSe2, and WSe2 crystals on SiO2, and perform extensive spectroscopic characterization verifying the quality and integrity of the materials. For MoS2, I also demonstrate an optimized process that yields films large enough (~cm^2) to fabricate thousands of devices simultaneously by optical lithography. Next, I discuss the low-field electrical transport of devices fabricated from these large MoS2 films. In additional to careful measurements revealing the highest mobility (30 to 50 cm^2/V/s) and lowest contact resistance (~1 kΩ∙μm) in any undoped 1L semiconductor, I employ statistical data for devices fabricated on a single, die-sized film to show exceptionally low values for hysteresis (< 5 mV per nm of equivalent SiO2 thickness), and low variation in intrinsic carrier density (~10^11 cm^-2) and drift mobility (~3 cm^2/V/s). I also demonstrate remarkable reliability through bias temperature instability measurements, which constitute an improvement by two orders of magnitude compared to other 2D devices. Finally, I focus on measuring the high-field saturation velocity of electrons in 1L MoS2. A detailed thermal model is used to account for device self-heating, and reveals that devices in high-field operation self-heat by ~200 °C, severely limiting drift velocity. Temperature-dependent measurements subsequently reveal a velocity of 4.3×10^6 cm/s at 295 K, high enough to allow for saturation currents to easily exceed 1.5 mA/μm for digital electronics. This work represents the first evaluation of its kind carried out for 2D electronics, and addresses critical issues to consider for scaling 1L semiconductors for larger applications.
Fully-coupled simulations of subduction zone earthquakes and tsunamis
Keywords: Geophysics.

Tsunamis from subduction zone earthquakes are fairly rare but extremely devastating. In order to prepare our coastlines and develop effective early warning systems for tsunamis, we must have a sufficiently full understanding of the physics of tsunami generation. We develop a model that fully couples dynamic earthquake rupture to the response of the ocean, capturing the full seismic, ocean acoustic, and tsunami wavefield. We first use this model to determine self-consistent initial conditions for tsunami problems, finding that horizontal momentum imparted to the ocean by the earth goes largely into ocean acoustic waves rather than the tsunami. The standard approach of setting initial horizontal velocity in the ocean to zero is correct. We also study the question of how the compliant materials in sedimentary prisms affect earthquake slip and tsunamigenesis, finding that friction, material properties, and prism size all play a role in determining the efficiency of tsunami generation, sometimes in nonintuitive ways. We then use data from seismic surveys, drilling expeditions, and laboratory experiments to construct complex numerical models of real subduction zones. The Japan Trench's small sedimentary prism enhances shallow slip but has only a small effect on tsunami height. In Nankai where there is a prominent splay fault, frictional parameters and off-fault material properties both influence the choice of rupture pathway in complex ways. The splay generates tsunami waves more efficiently than the decollement. Rupture in Cascadia is buried beneath the seafloor but causes a tsunami that is highly complex due to the rough seafloor bathymetry. We demonstrate the effects of using realistic material properties and show how horizontal seafloor motion impacts tsunami generation in realistic subduction zone geometries.
Game of Drones: An Investigation into American Public Opinion on the Use of Unmanned Aerial Vehicles to Combat Terrorism
Keywords:  Center for International Security and Cooperation
Center for International Security and Cooperation
Terrorism
Drones
Unmanned aerial vehicles
Public opinion
Collateral damage
Proportionality
Thesis

The United States first employed unmanned aerial vehicles, or drones, as a means to combat terrorism in 2001. Their use proliferated steadily in the succeeding decade and dramatically increased under the Obama administration. This surge in use has been met with an increased level of attention from academia. There remains, however, a gap in the understanding of American public opinion on the application of this technology in warfare. This thesis contributes to this body of scholarly knowledge by studying public attitudes on collateral damage and proportionality as they relate to the use of drones to combat terrorism. It substantiates previous findings indicating that Americans are more likely to express favorable opinions of the use of drones to eliminate terrorists when the victims of collateral damage are members of particularly ostracized out-groups, such as Muslims. However, in contrast to previous literature that demonstrates Americans’ unique valuing of their fellow citizens, this thesis finds that Americans express more favorable opinions of the use of drones when the victims of collateral damage are compatriots compared to when the victims are European civilians, with many indicating they believe it is ‘unjust’ to sacrifice European civilians to save their fellow citizens. Further, this thesis finds that many Americans exhibit an expansive versus narrow definition of proportionality, not only taking into consideration the collateral damage presented within a given scenario but also the collateral damage that may come as a result of their decision to support or not support the use of a drone strike.
Gaseous plasmonic resonators for metamaterial applications
Keywords: Mechanical Engineering.

In this dissertation, we explore the potential to generate metamaterials out of thin air using high-energy lasers. The artificial atom or meta-atom studied is a laser-induced plasma generated by focusing a high-energy laser pulse through a lens and into a gas. The resulting plasma spheroid behaves similar to a metallic spheroid, but with the additional properties of both tunability and stealth. The research into these gaseous plasmonic resonators was divided into two main parts. The first dealt with the scattering properties of a single subwavelength laser-induced plasma. In this part of the investigation a simple analytical model is used to describe the scattering resonance of these near-ellipsoidal plasmas and its dependence on their eccentricity and intrinsic plasma properties. This dependence is investigated through Ku band transmission experiments of a waveguide with an embedded single plasma element and optical diagnostics of the laser-induced plasma. Once the resonant properties of the single laser-induced plasma were confirmed, we moved onto the second part of our investigation, which focused on studying the scattering properties of a two-dimensional array of these subwavelength plasmas. Similar to the single-particle investigation, a simple analytical model is used to describe the scattering properties of a laser-induced plasma metasurface. Results from this model are compared to those of electromagnetic simulations to confirm its validity. The model and simulations were then used to determine that a reflection/absorption band would result from an electromagnetic wave incident on an array of these resonators. The reflection band was a result of destructive and constructive interferences between wavelets scattered from the resonators, which redistribute energy from lateral to backward scattering, i.e., reflection. The existence of the described reflection/absorption band was verified experimentally confirming the potential to achieve an all-plasma metamaterial effect in the microwave regime of the electromagnetic spectrum.
Gaza Stripped: Palestinian Refugees within an International and State Context
Keywords:  Program in International Relations
International Relations
Program in International Relations
Palestinian
refugee
regime
international refugee regime
UNHCR
UNRWA
Lebanon
Jordan
Syria
Gaza
West Bank
regional refugee regime
state interests
Thesis

The ongoing Israeli-Palestinian conflict has created one of the longest standing refugee populations in the world, Palestinian refugees. The issue of Palestinian refugees poses a complicated problem within the larger context of refugees due to the fact that Palestinian refugees fall under the protection of the United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA). This excludes Palestinian refugees from the 1951 Refugee Convention, which is responsible for outlining the legal protections that refugees are able to access. Why are there two separate entities for managing international refugees and Palestinian refugees? Is there a larger international umbrella that protects Palestinian refugee interests, and if not, does the treatment of Palestinian refugees vary based on geographic location? This thesis aims to understand the Palestinian refugee issue within an international context through the UN Refugee Agency (UNHCR) and UNRWA, as well as within a geopolitical state context through an examination of Jordan and its political history and policy.
Generalized Donaldson-Thomas invariants via kirwan blowups
Keywords: Mathematics.

In this thesis, we develop a virtual cycle approach towards generalized Donaldson-Thomas theory of Calabi-Yau threefolds. Starting with an Artin moduli stack parametrizing semistable sheaves or perfect complexes, we construct an associated Deligne-Mumford stack, called its Kirwan partial desingularization, with an induced semi-perfect obstruction theory of virtual dimension zero, and define the generalized Donaldson-Thomas invariant via Kirwan blowups as the degree of the corresponding virtual cycle. The key ingredients are a generalization of Kirwan's partial desingularization procedure and recent results from derived symplectic geometry regarding the local structure of stacks of sheaves and perfect complexes on Calabi-Yau threefolds. Examples of applications include Gieseker stability of coherent sheaves and Bridgeland and polynomial stability of perfect complexes. In the case of Gieseker semistable sheaves, this new Donaldson-Thomas invariant is invariant under deformations of the complex structure of the Calabi-Yau threefold. More generally, deformation invariance is true under appropriate assumptions which are expected to hold in all cases.
Generating structures by editing prototypes
Keywords: Statistics.

Methods for structured prediction underlie many successful applications of machine learning, including machine translation, speech synthesis, image generation, protein structure prediction and many other problems. However, producing high-quality structures is challenging because the individual components of a structure (e.g., the words in a sentence or the pixels in an image) constrain and depend on each other in complex ways. A wide variety of approaches have been proposed to tackle this problem. At one extreme, retrieval-based methods sidestep the difficulty of modeling the internal consistency of structures by simply selecting from a pre-populated repository of ``good'' structures. However, this may sacrifice flexibility and coverage, as the repository could fail to contain every possible structure that might be required. At the other extreme, generation-based methods synthesize structures from scratch, often building them up one unit at a time. This offers extreme flexibility, but faces the difficult problem of modeling the complex dependencies that exist between units, as well as the challenge of searching over all possible structures for good configurations. We aim to combine the best of both worlds using a new approach called retrieve-then-edit: first, a structure is retrieved from a repository of high quality candidates (as in retrieval-based methods), and then it is edited into a new structure using a synthesis-based editor. The retrieval step ensures that we start in the neighborhood of an already high quality structure, while the editing step gives us the flexibility to customize the structure in a fine-grained way. We demonstrate that this approach can be successfully applied across diverse structured prediction problems spanning text generation, executable code generation, and reinforcement learning to interact with a web browser (where an agent's sequence of actions is treated as a structure).
Generation of pulsed quantum light
Keywords: Electrical Engineering.

At the nanoscale, light can be made to strongly interact with matter, where quantum mechanical effects govern its behavior and the concept of a photon emerges—the branch of physics describing these phenomena is called quantum optics. Throughout the history of quantum optics, experiments and theory focused primarily on understanding the internal dynamics of the matter when interacting with the light field. For instance, in an ion trap quantum computer the motional states of the ions are of interest while the state of the light field is secondary. However, a new paradigm for information processing is becoming experimentally accessible where many quantum-optical devices are integrated in nanophotonic circuits. Then, the relevant information is encoded in the quantum states of the photon wavepackets as they fly around the nanophotonic chip. Hence, the converse problem is now important: the way the state of the photon field changes after interacting with the piece of matter. The effect of an individual device on a photon can now be formally described in a so-called scattering experiment. First, a photon wavepacket is prepared far away from the device. It travels freely towards the device and as it hits the interaction region forms a strongly entangled state of light and matter. Afterwards, the character of the interaction is imprinted on the outgoing wavepacket. This concept of a scattering experiment was originally envisioned in high-energy field theories with static Hamiltonians, and this thesis shows the concept adapted to nanophotonic devices driven by pulses of laser light (corresponding to time-dependent or energy nonconserving Hamiltonians). The formalism developed here will thus be of relevance to design and analysis of quantum information processing systems in which the information is encoded in the state of the photonic field, with the piece of matter implementing either a source of photons or implementing a unitary operation on the photonic state. In summary, for this dissertation I show experiments and theory that fully describe how the quantum state of a laser pulse changes when interacting with nano-sized pieces of matter. In particular, this work covers both a general formalism for photon scattering as well as two standard physical systems as experimental examples that generate quantum light: the quantum two-level system and the Jaynes--Cummings system.
Genetic and molecular insights into diatom nanopatterning and cell shape
Keywords: Biology.

Among cell biologists, diatoms are best known for their extraordinary and beautifully nano-patterned cell walls, made of hydrated silicon dioxide—that is, glass. Many of us first encountered diatoms in the form of isolated silica cell walls, known as frustules, mounted on slides used as a measure of resolving power, for dark field alignment of microscopes, or in scanning electron micrographs invoking alien-like architecture. Their exquisite complexity is reminiscent of high-magnification images of snowflakes; however, the diatom frustules are created by genetically encoded developmental programs, and as such are highly reproducible and characteristic for many of the 10,000 to 100,000 estimated species. How do these cells design and build their glass houses? Why do we know so little about the cell biological mechanisms of these exquisite organisms? Classical biochemical methods have identified several important classes of silica-interacting peptides that are tightly associated within biosilica. However, advanced genetic methods have only recently been developed for diatoms, and remain largely inefficient, limiting their use in genome-wide screens. Nevertheless, critical genetic techniques have rapidly improved for key model diatoms in recent years. Improvements to the efficiency of genetic techniques will be key toward our understanding of these mysterious organisms. This work presents molecular genetic data regarding genes and mechanisms by which diatoms control cell shape and metabolism.
Genetic interaction mapping identifies the INO80 chromatin remodeling complex as a key metabolic regulator in the yeast Saccharomyces cerevisiae [electronic resource]
Keywords: Biology.

Eukaryotic genomes function in a chromatin environment. Chromatin modifying enzymes are critical for imparting epigenetic regulation to maintain a dynamic and responsive chromatin state, allowing cells to carry out chromatin templated processes such as transcription, DNA replication and chromosome segregation. In this work, we further our understanding of the function and mechanism of chromatin remodelers. We investigate the INO80 chromatin remodeler in the budding yeast Saccharomyces cerevisiae using genetic, biochemical, and molecular approaches. In Chapter 1, we report an expansive genetic screen with chromatin remodelers and metabolic regulators. We find that the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We demonstrate that the INO80 complex is a central component of metabolic homeostasis, including mitochondrial maintenance and TORC1 signaling, that influences histone acetylation and may contribute to disease when disrupted. In Chapter 2, we identify functional roles of the Arp5 and Ies6 subunits of INO80 in maintaining metabolic stability. We find Arp5-Ies6 form a distinct subcomplex, the relative occupancy of which correlates with nucleosome positioning and expression levels of over 1000 genes which are significantly enriched in energy metabolism pathways. In Chapter 3, we delineate a hierarchical assembly of Arp5-Ies6 into INO80. We identify conserved domains of Arp5 that are needed to couple ATP hydrolysis with productive nucleosome remodeling by INO80. Our results illustrate the dynamic nature of the INO80 complex, and demonstrate for the first time that a chromatin-remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability.
Germline-Targeting HIV-1 Immunogen Design
Keywords:  Department of Bioengineering
HIV
Immunogen
Vaccine
gp120
Rational Design
Stanford School of Engineering
Department of Bioengineering
Thesis

Human immunodeficiency virus type 1 (HIV-1) has caused one of the worst pandemics in human history. Although treatments can slow the progression of HIV-1, no cure exists and infected patients must live with the virus for life. Moreover, HIV-1 continues to spread rapidly in certain regions of the world, making vaccine development a global health priority. Because of HIV-1's high antigenic diversity, an effective vaccine must be able to elicit broadly-neutralizing antibodies (bnAbs). BnAbs against the CD4 binding site of the HIV envelope glycoprotein 120 (gp120) have been isolated from rare HIV-infected individuals, but attempts to elicit such bnAbs through vaccination have failed. This lack of bnAb induction is largely due to viral features that obstruct germline (gl) antibody binding and thereby prevent maturation into high-affinity bnAbs. Guided by computational modeling, we engineered a germline-targeting immunogen based on gp120's outer domain. This construct is able to bind multiple mature bnAbs with high affinity in addition to a predicted germline precursor, making it a strong vaccine candidate.