VictorJuiz/thesis huggingface dataset:
To co-opt or to coerce? How the adversaries of great power proteges respond to retrenchment
Keywords: Political Science.

When great powers withdraw security from weaker proteges, how will the territorial adversaries of those proteges respond? While existing scholarship in international relations implies that adversaries will respond by coercing territorial concessions from the former proteges, the historical record shows that many adversaries actually make territorial concessions to former great power proteges in the wake of retrenchment. Scholars had not previously identified - much less explained - this puzzle. To do so, I argue that retrenchment offers adversaries a few strategic opportunities. While the loss of great power assistance weakens the protege's defenses, it also leaves the protege's foreign policy alignment ``up for grabs." Thus, the adversaries of former great power proteges have the opportunity to coerce territorial gains or to attempt to bring the protege into their sphere of influence. Because offering territorial concessions is a powerful way for the adversary to co-opt the protege's foreign policy alignment, however, pursuing both strategies simultaneously is challenging. Thus, the adversaries of the former proteges face a trade-off between gaining territory and gaining influence. I offer several predictions about the conditions under which adversaries are likely to pursue territorial coercion vs. foreign policy co-option and test my theory in two cases: (1) Britain's withdrawal of security from proteges in the Middle East after World War II and (2) the Soviet Union's withdrawal of security assistance from client states in the late 1980s. The results support my hypotheses. My theory and findings contribute to existing scholarship on alliances, alignments, territorial disputes, and retrenchment and also have important implications for current policy debates about the potential consequences of American retrenchment
To Trust or Not to Trust: Exploring Legal Control in the Context of Youth Homelessness in Portland, Oregon
Keywords: Homeless teenagers
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Thesis

Alisha Zhao’s capstone project combines ethnographic research with her interest in art as a medium to explore and bring awareness to youth homelessness in the US. She interviewed youth experiencing homelessness in her hometown, Portland, OR, in order to better understand youth experiencing homelessness and their perceptions on authority, which may affect their willingness or ability to seek institutional support and resources. Alisha's capstone includes a series of oil paintings that depict different forms of homelessness, such as family homelessness, in addition to her ethnographic research. Alisha hopes that this art series can serve as an accessible way of engaging in dialogue about pressing social and human rights issues.
Too Big to Fail?: Evaluating the association between large-scale irrigation schemes and civil violence in sub-Saharan Africa, in the context of the climate crisis
Keywords: Center for International Security and Cooperation
Irrigation
Violence
Security, International
Peace-building
Nigeria
Dams > Social aspects
Dams > Evaluation
Dams
Sub-Saharan Africa
Food security > Climatic factors
National security > Climatic factors
World Bank
International Development
USAID
Civil conflict
African Development Bank
Crops and climate
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Thesis

A “code red for humanity;” the “number one threat to mankind;” as lethal as “guns and bombs.” Climate change represents an existential threat to humanity. The coming decades will see a surge of funding for climate adaptation aid in response to this threat – led by US President Joe Biden’s pledge of $11 billion in climate aid annually by 2024. This expansion of funding for climate development interventions, in particular, suggests a need to evaluate how past infrastructure interventions have impacted communities, and lessons for the future. This thesis thus explores the relationship between large-scale irrigation projects in sub-Saharan Africa and communal violence. Recognizing the wide-ranging variation in use and effectiveness of irrigation schemes, it asks: To what extent does violence influence the location and effectiveness of large-scale irrigation projects? Essentially, is there a violence effect – does violence prior to or during the construction of projects influence projects influence their utility, and, conversely, in what circumstances do these projects amplify or reduce the risks of communal violence? Using a mixed methods approach, the paper does not find a strong relationship between violence and the relative success of irrigation projects. However, it finds that irrigation projects are more likely to be placed in locations with greater exposure to violence. The reason for this increased exposure to violence appears two-fold: first, there is an intentional decision to use irrigation projects as a mechanism to promote regional stability and socioeconomic development. This relationship is also, in part, unintentional, reflecting multilateral funding bodies’ historically limited efforts to mitigate risk. A case study of Nigeria is used to delve further into these findings, identifying several instances in which projects have exacerbated community grievances against the state –– and where violence has ensued. These findings suggest that stakeholders in the climate change, development, and peacebuilding spheres should prioritize mechanisms for greater environmental and social risk assessments; increase opportunities for community-based development and governance; and strive to better integrate conflict-sensitivity into climate adaptation interventions.
Topological photonics in non-Hermitian and scattering systems
Keywords: Electrical Engineering.

In photonics, topological effects can be used to design systems with robust and novel behavior. These topological effects are traditionally studied in closed systems without gain, described by Hermitian Hamiltonians. However, many systems in photonics do have gain or loss and can be described by non-Hermitian Hamiltonians. Systems with inputs and outputs are also widespread in photonics and are usually described by a scattering matrix. In this Thesis, we study topological features in non-Hermitian and scattering systems in photonics. First, we give a characterization of the space of all gapped non-Hermitian Hamiltonians using the mathematical framework of homotopy theory. We do this pedagogically in two-band systems, starting with the familiar Hermitian case before generalizing to the non-Hermitian setting, and then giving several physical interpretations of the results. Next, we study the topology of many-band non-Hermitian systems, and we see the importance of braid-group eigenvalue topology emerge. We provide a complete description of eigenvalue topology in gapped and gapless systems, again using the mathematics of homotopy theory. Finally, we move to scattering systems, where we study a topological feature in the spectrum of the scattering matrix known as a scattering threshold. Here, the scattering matrix has a square-root branch point, and we show that this singularity leads to a universal behavior in a wide variety of physical systems
Topology and disorder in quantum condensed matter systems
Keywords: Physics.

This thesis covers a number of topics related to condensed matter systems in which degrees of freedom are strongly interacting with each other, subject to strong randomness from impurities and dirt, or both. The first part of the thesis presents the lattice constructions of the recently proposed web of dualities between quantum field theories in (2+1) dimensions. These dualities and the lattice constructions shed light on non-perturbative aspects of strongly interacting systems in two spatial dimensions. The second part of the thesis covers exactly solvable 2D Hamiltonians for topologically ordered states with chiral edge states and quantum spin Hall insulators. These models, obtained upon decorating previously-well-known physical models with fermions and parafermions, provide analytically tractable ways of studying 2D topological phases of matter in presence of strong interaction, disorder, or both. The final part of the thesis shows how the phase transitions involving dirty three-dimensional topological insulators can be understood in terms of the semiclassical percolation picture of electrons in the 3D network
Toward the rational design of fluorescent proteins : elucidating the photodynamics of the GFP chromophore in various environments
Keywords: Chemistry.

The green fluorescent protein (GFP) has revolutionized the fields of chemistry and biology. Due to their ability to highlight protein dynamics in living organisms, GFP and GFP-like proteins have emerged as ubiquitous tools in biological imaging. The versatility of GFP has inspired a rainbow-like palette of fluorescent reporters; however, the creation of novel GFP variants is often imprecise and inefficient. Using molecular dynamics simulations, I unravel the intricate steric and electronic factors responsible for the performance of these fluorescent proteins. Across many systems (i.e., gas phase, water, and GFP/Dronpa2 scaffolds), I study the photodynamics of the GFP chromophore. Changes to the chromophore's intrinsic properties (e.g. fluorescence propensity, photoisomerization quantum yield, etc.) are monitored as the molecule occupies various condensed phase systems. Applying this knowledge, I have developed a computational workflow that can (1) generate structures for tens of thousands of GFP mutants and (2) characterize these mutants using steric and electronic features. This structural data is coupled with machine learning models to identify important interactions within the system and inspire the creation of novel GFP reporters
Towards a human-like understanding of the physical world
Keywords: Electrical Engineering.

Humans have a rich understanding of the physical world, which enables us to effectively interact with and navigate in our environment. A core component of this understanding is the ability to decompose the visual environment into objects, and reason effectively about the dynamic interactions between these objects. We introduce an end-to-end differentiable graph neural network that learns to predict the physical dynamics of a wide variety of three-dimensional objects using a hierarchical particle-based object representation. Additionally, we present a physical prediction benchmark that compares a broad suite of state-of-the-art models to humans on a diverse set of physical phenomena. We show that graph neural networks with access to the physical state best capture human behavior, whereas models that receive only visual input fall far short of human accuracy. This suggests that endowing models with more physically explicit state representations is a promising path towards human-like physical understanding
Towards a Multiple-Systems Understanding of Race-Related Biases in Human Memory
Keywords: Wagner, Anthony
Bias
Memory
Episodic memory
Psychology
Neurosciences
Behavioral neuroscience
Perception
Attention
Race
Racism
Cognitive science
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Thesis

Human memory is biased. In memory research, bias is often studied as a monolith, operationalized in a single behavioral measurement. However, memory behaviors are supported by a concert of interacting systems, and understanding our biases requires disentangling the unique contributions of each system and how each one is shaped by social dynamics around us. Here, we begin to isolate the contributions of perceptual and mnemonic race-related bias to episodic memory retrieval. To do so, we construct a novel stimulus set of face images capturing both naturalistic variation (including across subjectively classified racial categories) and low-level control and implement a multi-task behavioral experiment. Participants performed a 3-way concurrent face discrimination task, and subsequently a 2-alternative-forced-choice recognition memory test. Moreover, to test for race-related bias in the generalizability of memory representations, we tested participants on previously seen faces from both studied and unstudied viewpoints. We find evidence for canonical ingroup perceptual biases but (reverse-canonical) outgroup-favoring memory bias, with preliminary evidence that viewing time at encoding may explain some of this memory bias. Furthermore, we find no evidence for bias in participants’ memory generalizability to decisions on novel viewpoints. This work offers a more fine-grained understanding of how social biases (here, racial biases) shape different systems of human cognition and models new approaches to studying race-related biases with attention to the subjectivity of race perceptions, the social ramifications of race and racism, and the complexity of human cognition and behavior.
Towards a regional and urban air mobility future : the development of computational approaches for quantifying trade-offs in electric aircraft design
Keywords: Aeronautics and Astronautics.

Air travel is rapidly changing before our very eyes. From the multitude of ways in which we perceive sustainability to our evolving perspectives on connectivity, transportation by air has once again become a topic of earnest discussion. Once theorized and in some cases attempted modes of air travel that have long been considered impractical or unachievable have again resurfaced to garner substantial attention within industry, government and academia. The focus of this work is one of these modes of air travel - the movement of people, goods and services between confined spaces in densely populated areas. Coined regional and urban air mobility (RUAM), this mode of transportation has reignited the idea of using both short and vertical takeoff and landing aircraft that offer advantages in both speed and range compared to personal automobiles, rideshare services and other forms of public ground transportation. Furthermore, these aircraft can potentially facilitate other niche applications such as air ambulances, search and rescue missions, surveillance and commercial cargo delivery. However, despite recent technological advances providing the impetus for realizing RUAM, several questions pertaining to vehicle design, electrification, infrastructure, regulations, and societal constraints remain unanswered. Making inroads into some of these impeding challenges, this dissertation seeks to streamline the understanding of critical aspects of the design process for these aircraft via three key milestones. The first of which is the adoption of computational techniques capable of providing fast and accurate predictions of both physical components as well as the whole aircraft. The second is the representation of realistic flight dynamics for these non-conventional aircraft. Lastly, the third is the use of flight profiles that symbolize realistic routes through urban canyons. Specifically, within this work, the two critical aspects of aircraft noise and propulsive efficiency are positioned under the microscope whereby the nuances of their relationship that manifest at the system-level are identified and explored
Towards accessible quantum chemistry and automated photochemical design via machine learning and nonadiabatic dynamics simulation
Keywords: Chemistry.

The ability to reliably design molecular systems for targeted applications has the potential to revolutionize drug and material discovery. Quantum chemistry can now accurately predict useful chemical properties for a wide range of molecules and continues to enhance its predictive power as new algorithms and hardware come online. However, several major hurdles remain. In this work, I focus on two outstanding challenges: building accessible tools for the wider chemistry community to interact with quantum chemistry, and designing photochemical systems with nonadiabatic dynamics simulations. I develop ChemPix, a hand-drawn hydrocarbon structure recognition software to provide an almost barrierless molecule input method for computational chemistry software. ChemPix and other accessible molecular input tools are combined with cloud-based GPU- accelerated quantum chemistry and extended reality visualization to build a series of interactive quantum chemistry tools. These tools can compute quantum mechanical properties in real-time from hand-drawn structures or voice input. Photochemical systems can be modeled with nonadiabatic dynamics simulations. However, the complex multi-reference electronic structure calculations required for these simulations means that modelling even simple photochemical processes demands domain expertise and substantial human effort. Here, I employ cis-stilbene, a prototypical photo- switch, to explore the path towards automated photochemical design. First, nonadiabatic dynamics simulations of cis-stilbene are performed and analyzed to uncover the cis-trans photoisomerization and photocyclization mechanisms. Next, I propose the use of ensembled simulations to build stronger mechanistic predictors and link the predictions to the experimental ultrafast electron diffraction signal. Finally, a highly symmetric light- induced molecular motor is designed based on the simulations by photo-exciting cis- stilbene with circularly polarized light
Towards an Equitable Development of the Regional Earthquake Resilience of the Greater Metro Manila Area, Philippines
Keywords: Public Policy Program
Baker, Jack
Earthquake Risk
Regional Resilience
Metro Manila
Philippines
Stanford University
Humanities and Sciences
Public Policy Program
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Thesis

The Philippines with its densely populated Greater Metro Manila Area faces serious threats to the security of its people, livelihood, and infrastructure from unpredictable earthquakes due to its proximity to the Pacific Ring of Fire. For the past decades, the country’s earthquake resilience has been centered solely on the structural health of a single building without any extensive reference to the socio-economic capacity of its community. Previous large-scale earthquake risk studies also focused only on the well-known “Big One” magnitude-7.2 earthquake scenario for post-earthquake response planning purposes and neglected the probabilistic behavior of earthquake occurrence that can be a basis for policies that could mitigate the risk to the communities. Using the recently released probabilistic earthquake hazard maps in 2020, this study performed the first metropolitan-scale estimation of average annualized earthquake economic losses and ratios of 23 municipalities and cities in the Greater Metro Manila Area and compared the findings with the current socio-economic productivity parameter called the 2021 Cities and Municipalities Competitive Index developed by the national government. Our findings revealed a prevailing disconnect between the socio-economic capacity of different local jurisdictions and their degree of earthquake risk of economic losses, casualties, and damaged floor areas. Our study presents different policy recommendations that can be implemented at the regional and local levels toward an equitable development of earthquake resilience in the region.
Towards characterizing the distinct contributions of genetically defined neuron populations in value-based decision making
Keywords: Bioengineering
Choice (Psychology)
Neurosciences
Calcium imaging
Neural circuitry
Choice (Psychology) > Economic aspects
Reward (Psychology)
Substance abuse
Drug addiction
Decision making > Psychological aspects
Bioengineering
Orbitofrontal Cortex
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Thesis

Animals must constantly engage in economic choice behaviors, evaluating the available options in their environments and deciding which to pursue. However, how these decisions are computed in the brain remains poorly understood. One reason for this is because most studies of this form of decision-making have been performed in primates, for which we currently lack tools for recording and manipulating the activity of defined cell types. Here, in preliminary work I analyze single cell activity data from mice and reveal differential responses to cue and reward in excitatory and inhibitory populations of neurons. This highlights the need for the development of economic choice paradigms that can be integrated with animal models and tools for the manipulation of genetically defined cell types. To meet this need, my honors thesis implements a head-fixed, value-based decision-making paradigm in mice. Using the behavioral apparatus and training protocol designed, mice learned to choose between two olfactory cues that predicted the delivery of one of the two reward types (sugar water or water). Analysis of choice data reveals that mice make appropriate decisions based on reward type and amount, suggesting they integrate information about both reward quality and quantity to guide behavior. With this paradigm in mice, we will be able to exploit the genetic accessibility of the mouse to probe neural circuits that mediate economic decisions.
Towards controlling active matter : from light control to topological traps
Keywords: Applied Physics.

Activity can organize matter in unique configurations inaccessible to equilibrium systems. The potential to harness principles of self-organization by studying active matter has immense implications in engineering and design. In the first part of this dissertation, I propose a self-driven microfluidic device propelled by a suspension of active, light-controllable molecular motors. Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. We model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed solely on the boundary. Specifically, we simulate light-controlled surface-driven flows, probing the emergent properties of a suspension of active colloids that can bind and unbind from surfaces of a closed microchamber, together creating an active carpet. The attached colloids generate large scale flows that in turn can advect detached particles towards the walls. Switching the particle velocities with light, we program the active suspension and demonstrate a rich design space of flow patterns characterised by topological defects. We derive the possible mode structures and use this theory to optimize different microfluidic functions including hydrodynamic compartmentalisation and chaotic mixing. Our results pave the way towards designing and controlling surface-driven active fluids. In the second part of this disseration, I shift gears and discuss a structure formed by the collective motion of a species of gliding, filamentous cyanobacteria we term the "active spiral". How persistent yet dynamic patterns can form in motile active systems remains an open question. We leverage the ability to segment and track each filament individually to gain insight into this question, giving us single-particle resolution into the spiral dynamics. Due to the reversible gliding motility of individual filaments in the spiral, the filaments shear past each other with no coherent system-level vorticity, forming highly dynamic structures exhibiting radial material flux. These rearrangements are primarily driven by rules of interaction between motile tips. We enumerate these rules of interaction on a polar coordinate lattice, and show we can predict material flux within the system as a result. We also present the discovery of a new topological trap in active spirals, which creates un-crossable boundaries in an otherwise dynamic structure capable of material movement. Interestingly, these topological traps arise purely from the geometry of long filaments with winding number greater than zero. Understanding the dynamics of an active system with single filament resolution enables the detailed understanding of particle interactions, a necessary step toward controlling active matter