VictorJuiz/thesis huggingface dataset:
Quantum Projection Filter Model for the Coherent Ising Machine

A novel optoelectronic system, the coherent Ising machine (CIM), uses networks of optical parametric oscillators (OPOs) in conjunction with a measurement-based feedback scheme to represent and solve fully-connected Ising spin optimization problems. Solutions to these problems have wide-ranging applicability—data set analysis, circuit design, drug discovery and scheduling. Experimentally, the CIM has been demonstrated to successfully find exact or approximate solutions to a variety of hard optimization problems with up to 2,000 all-to-all connected spins. However, whether the CIM offers any computational advantage over conventional computers is an open question that requires understanding the (potentially quantum) dynamics that govern information processing in the CIM.
As a step towards characterizing CIM system dynamics and formally benchmarking any computational advantage afforded by these dynamics, we describe a model reduction approach that can facilitate scalable numerical studies of the CIM via dynamical simulation. Motivated by the low nonlinearity and high optical losses in the system, we consider the CIM dynamics to be described by a series of time evolutions of the system state on a Gaussian manifold of states, using Gaussian maps to represent the operations performed by beam splitters, measurement, and feedback injections. In particular, to ensure that the propagation of the OPO modes through the χ(2) waveguide is computationally tractable, we employ a quantum projection filter technique to differentially project the quantum dynamics induced by the optical nonlinearity onto the Gaussian manifold. In this work, we present the aforementioned model reduction and derive a set of filter-projected differential equations required for integrating the reduced model into numerical simulations of the CIM with nonlinear pump and signal dynamics. This approach may be useful for describing other photonic systems where nonlinear optical effects coexist with sufficiently strong linear losses.
We also provide a brief review of quantum optics and the Gaussian state formalism, along with a description of the measurement-based CIM and a summary of the important experimental results in the sub-field of CIM research.

Keywords:  Department of Physics
quantum optics
Gaussian state dynaimcs
Ising model
optical parametric oscillator
quantum projection filter
coherent Ising machine
Thesis
Advisor: Mabuchi Hideo
Hayden Patrick
Quiver theory, zigzag homology and deep learning

Topological data analysis deals with the study of data using techniques from algebraic topology. It has emerged as a popular and powerful technique in studying data in recent times. In this dissertation, we will introduce a new perspective on algorithms for topological data analysis (TDA). The new framework will allow us to generalize existing algorithms to new problems and also provide novel methods to parallelize the algorithms to compute zigzag persistent homology. We will first introduce how quiver representations can be used to reduce the problem of computing persistent and zigzag homology to that of computing a canonical form similar to the eigenvalue decomposition or the Jordan normal form. Then we will describe an algorithm to compute the canonical form of any type A quiver representation. We will show how the algorithm can be expressed as a sequence of matrix factorizations and matrix passing steps performed on the graph underlying the quiver representation. We will conclude by looking at an example of how TDA can be used along with deep learning, specifically we will show how zigzag homology performs better than persistent homology in the case of the MNIST dataset

Advisor: Carlsson G. (Gunnar)
Gerritsen Margot (Margot G.) 
Guibas Leonidas J.
Racing engines and cracking fuels : laser-based measurement techniques for challenging environments

Although combustion fuels the modern world, much remains unknown about the hydrocarbon chemistry that governs the behavior of fuels and the energy systems used to extract their energy. Many open questions in the field can be traced to the limited diagnostics available to study fuel chemistry and energy-system performance, where relevant processes often occur at millisecond timescales and within inaccessible environments. This work seeks to address the limits of diagnostics in two particularly challenging areas of fuel research and energy-system design: high-temperature fuel pyrolysis and high-performance engines. Part 1 develops new diagnostics for measuring temperature and species in pyrolytic environments, then applies a novel convex-optimization-based technique to the thermal decomposition of ethane and propane to characterize the cracking patterns of these foundational alkane fuels and reveal insights into the governing chemistry. Part 2 shifts gears to present the development of a temperature, pressure, and water-vapor sensor for high-performance-engine applications. The sensor overcomes the challenges of intense vibration, fuel-droplet attenuation, and enclosed geometries to measure intake-runner temperatures, pressures, and water mole fractions with near-crank-angle resolution. Together, these efforts expand the scope of diagnostic capabilities available to kineticists and engine developers to explore new domains, improve predictive modeling capabilities, and ultimately develop more efficient fuels and energy systems for the future

Keywords: Mechanical Engineering.
Advisor: Hanson Ronald
Edwards C. F. (Christopher Francis) 
Wang Hai
Radial estimate of isotropic pseudo-differential operators via FBI transform

This works aims to prove the propagation of singularities and the radial estimates in smooth isotropic symbol settings. The behavior of the Hamilton vector field of pseudo differential operator symbols and the wave front set of the solutions has been well studied. There are classical results in the standard smooth symbols settings, linking the flow of the Hamilton vector field of the symbol with the operator's regularity propagation by Hörmander. Melrose and Vasy then also establish the regularity behavior of solutions around radial points when it forms a sink or source for the Hamilton vector field. This paper extends such results into the setting of isotropic symbols. First setting up the connections between the isotropic and standard symbols, the paper will then utilize the FBI transform mechanisms, similar to the work of Martinez, to achieve results similar to the standard commutator method. Then we shall refine the results in the isotropic setting from Martinez's FBI estimate. Finally a standard regularization process shall be deployed to establish the more precise high regularity threshold

Keywords: Mathematics.
Advisor: Vasy András
Luk Jonathan (Professor)
Mazzeo Rafe
Rapid computational aerodynamic analysis for multi-rotor aircraft

In recent years, multi-rotor aircraft have generated significant interest across the aviation industry, resulting in many new aircraft configurations. These aircraft are typically electric or hybrid-electric and leverage the general scale-invariance of distributed electric propulsion. As a result, hundreds of novel multi-rotor vehicle concepts have arisen. In this work, a medium-fidelity simulation capability is developed for multi-rotor aircraft, which solves the Euler equations on a Cartesian mesh with embedded boundaries. The approach is designed to handle arbitrarily-complex geometry and non-linear aerodynamics while retaining a computational cost that is affordable in the preliminary design process. It leverages the integral velocity sampling (IVS) method for angle of attack prediction, resulting in accurate performance estimates for both isolated rotors and full-vehicle DJI Phantom 3 simulations. In addition, this work also investigates algorithmic robustness throughout the solution process, from mesh generation to unsteady flow simulations

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Jameson Antony
Rapid single-crystalline III-V optoelectronics by pulsed laser crystal splitting

III-V semiconductors are important electronic materials. We split single-crystalline III-V thin films from their single-crystalline growth substrates using standard lattice-matched III-V epitaxy and unfocused Nd:YAG laser pulses. We collaborate with the National Renewable Energy Laboratory and produce high-efficiency III-V photovoltaics in new ways. The devices are the first of their kind and the crystal ejection process offers tremendous opportunities

Keywords: Materials Science and Engineering.
Advisor: Clemens B. M. (Bruce M.)
Lindenberg Aaron Michael
Salleo Alberto
Re-assembling radical indigenous autonomy in the Alta California hinterlands : survivance at Puhú

Conducted in a community-based participatory research (CBPR) framework in partnership with Tongva, Acjachemen, (Blas Adobe Aguliar Museum, Juaneño--Acjachemen Culture Center) and Payómkawichum (Pechanga Band of Luiseno Mission Indians) peoples, this dissertation is an Indigenous Archaeology study of the California Historic Landmark (CHL#217; CA-ORA-132 and CA-ORA-317) Black Star Canyon Puhú Village site in the Santa Ana Mountains of Orange County, California. The landmark memorializes the 1832 CE "Battle in Cañón de los Indios". Indigenous occupants of the Puhú village were accused of stealing horses from local colonial settlers over several months, after which, the village was razed by hired American frontiersmen. I integrate perspectives from descendant collaborators, Indigenous survivance, philosophies of historicity, guerilla resistance, Practice Theory, and Assemblage Theory in the analysis of archaeological and ethnohistorical data collected from five years of interviews, archival research, surveys, excavations, and laboratory research under the Black Star Canyon Archaeology Project (BSCAP). The result of my archaeological and ethnoarchival research reveals how the Puhú occupants exercised economic and political traditions within and beyond the village to exceed a condition of bare survival or micropolitical resistance after colonization. This study facilitates new attention to enduring communal scale Indigenous traditions associated with macropolitical forms of autonomy and prosperity in the Los Angeles Basin proximal colonial hinterlands. In doing so, the archaeological study is envisioned as facilitating a mode of Indigenous survivance-storytelling by challenging the foundations of colonial historiography associated with the landmark

Keywords: Anthropology.
Advisor: Voss Barbara L.
Hodder Ian
Liu Li
Panich Lee M.
Wilcox Michael V. (Michael Vincent)
Reconstructing Indian territory : federal vs. native power and the contested expansion of American sovereignty, 1861 - 1907

Reconstructing Indian Territory is a history of Indian Territory as a critical site of Reconstruction: the multifaceted federal project to rebuild a unified American nation-state committed to free labor, private property ownership, and a homogenous citizenry. Based on U.S. and Native government sources, this project explains how Reconstruction politics and priorities transformed Indian Territory as part of the growth of federal supremacy throughout the continental United States. Federal policymakers sought to reconstruct the Five Tribes of Indian Territory through a variety of legislative and legal reforms, including the Reconstruction Treaties of 1866, the expansion of federal jurisdiction, the allotment of tribal land, and the dissolution of Native governments in favor of single statehood. While piecemeal and often disjointed, this darker side of Reconstruction achieved many more of its aims than its southern sister project, securing the plenary power of the U.S. Congress over Indian affairs at the price of tribal sovereignty. Reconstruction has long been a southern narrative, but this project demonstrates that we cannot fully account for the successes and failures of the multiregional and multinational project of Reconstruction without Indian Territory

Keywords: History.
Advisor: White Richard
Campbell James T.
Hobbs Allyson Vanessa
Reconstructing past events : a study of engineering failure investigations

When a major engineering product failed, a failure investigation is often conducted to prevent similar failures in the future. In this dissertation, I propose an account of the epistemology and methodology of engineering failure investigations, based on a close examination of five major plane crash investigations conducted by the National Transportation Safety Board (NTSB). The dissertation is divided into three parts. The first part consists of the five case studies. In each case study, I summarize the entire investigation process, focusing on articulating the questions that arise and the evidential reasoning that helped resolve each question. The second part examines how the investigators infer causes of failure events. The type of causal inference used in failure investigations typically proceeds from effects to causes, hence it is called reverse causal inference. I identify three types of reverse causal inference in engineering failure investigations: feature dependence, additional outcomes, and process tracing. The third part examines how the investigators construct narratives of failure events and support them with evidence. I argue that both the construction and the justification of a narrative of a failure event depend on the question-and-answer process in the investigation, which I call the question dynamics of the investigation. I examine three main components of the question dynamics: the resolution of questions, the significance of questions, and the arising of questions. I conclude the dissertation with an account of the coherence of narratives, which captures the intuitive idea that the pieces of a coherent narrative "fit together" very well

Keywords: Philosophy.
Advisor: Longino Helen E.
Hills David James
Icard Thomas
Smith George
Regulating the Regulators: Whether User Fees for Prescription Drug Reviews within the FDA Approval Process are a Cause for Concern

This paper studied the potential adverse impact of the Prescription Drug User Fee Act (PDUFA) on the integrity of the U.S. Food and Drug Administration (FDA) drug application review process. The concern was that PDUFA-established user fees could result in agency capture by the pharmaceutical drug industry. To determine the validity of this concern, the paper analyzed public data detailing the submission date of a new drug application and the subsequent date of approval. The data was then used to calculate the average drug review time for each manufacturer and establish whether those with more total user fee contributions experienced quicker review times. External factors were controlled for given a variety of confounding variables. If the firms were found to receive preferential treatment for greater user fee contributions to the FDA, it would be a sign of potential agency capture. Although a great deal more research is needed to verify the results, the analysis suggested that there is little, if any, association between the cumulative fees paid by a sponsor and the review times of its new drug applications. These findings may be good news for the FDA and other agencies who charge, or may want to charge, user fees to supplement their funding.

Keywords: drug reviews
new drug applications
user fees
PDUFA
FDA
agency capture
Thesis
Advisor: Bhattacharya Jayanta
Clerici-Arias Marcelo
Pal-Chee Christine
Otero Sebastian
Regulation of KRAS by SNAREs and noncoding RNAs with therapeutic approaches to treatment

Human malignancies exact a heavy toll on human life expectancy and productive working years even in developed societies with access to leading medical care. Underlying intractable cancers is an innumerable number of inciting factors, all interconnected into an adaptive entity designed to persist and empowered with the tools that enable life itself. Here, we describe work investigating the mechanistic nuances of how a growth factor signaling cascade is regulated by a series of vesicular transport mechanisms modulated by non-coding RNA. These findings lead us to investigate new therapeutic options to treatment and the development of two in-silico methods to accelerate targeted drug discovery in cancer

Advisor: Khavari Paul A.
Oro Anthony
Sage Julien
Stearns Tim
Renewable Energy and American Federalism: The State’s Influence in Tribal Wind and Solar Development

Many tribal lands across the western United States (US) are rich in wind and solar energy resources. Tribal nations’ harnessing of their lands’ wind and solar potential presents opportunities for community and economic development. However, the American Federalist system curbs tribes’ right to self-determination in the context of renewable energy. In the Federalist system, tribal nations are legally subject to the US federal government’s authority but exempt from states’ authority because of tribal sovereignty. As a result, the literature has focused on the federal influence on tribal energy endeavors. This paper spotlights the role of states: I examine how state energy policy influences tribal wind and solar development. Though independent, tribes are affected by state energy policies as each state governs its electricity grid and market. In my thesis, I complete a case study of tribal wind and solar energy development in the context of Montana’s and California’s state energy policies. These two case studies vary greatly in the degree to which each state forwards a clean energy transition through regulation and market incentives, also known as the “aggressiveness” of the state’s energy policy. Through interviews, policy review, and surveying documentation of tribal energy projects, I examine how each state’s renewable portfolio policies, net energy metering, interconnection regulations, tax incentives, and grant and loan programs have impacted tribal wind and solar efforts. As a result, I prove that tribes in states with more aggressive renewable energy policies have greater resources and opportunities to enter the renewable energy market. More critically, I find that tribal circumstances are often neglected in state policies, and consequently many state energy programs and incentives are out of tribal entities’ reach. Moving forward, states must work to consider tribal circumstances and ensure tribal inclusion in all state energy policies to ensure equitable access to the nation’s growing renewable energy market.

Keywords:  Fisher Family Honors Program in Democracy
Civil and Environmental Engineering
Democracy Development and the Rule of Law
Freeman Spogli Institute
tribal lands
renewable energy development
state energy policy
wind
solar
School of Engineering
development
Federalism
Thesis
Advisor: Cain Bruce
Replica wormholes, entanglement wedges and the black hole information paradox

Hawking famously argued, based on semiclassical calculations, that the radiation from evaporating black holes is always perfectly thermal and contains no information about the matter that fell in. Such a result is inconsistent with the unitarity of quantum mechanics. In this thesis, I argue that a more careful replica trick calculation shows that the gravitational path integral becomes dominated at late times by saddles containing spacetime wormholes. These wormholes cause the entropy to decrease after the Page time, consistent with unitarity, and allow information to escape from the interior of the black hole. In very simple toy models, we can evaluate the path integral exactly, and see the information emerge. In more realistic black holes, the full wormhole solutions cannot be found explicitly. However, their existence, and their most important consequences, can be derived by studying the location and properties of a non-trivial `quantum extremal surface' in the original Hawking solution. We can also see how various paradoxes, including the famous rewall paradox, are avoided. A crucial role is played by the framework of universal subspace quantum error correction. This framework is also fundamental to the theory of quantum teleportation and can be used to decompose the process of sending qubits from Alice to Bob into distinct `entanglement' and `communication' pieces. Finally, we see how the complexity of decoding information from Hawking radiation can be explained by the existence of a bulge or `python's lunch' in the spacetime geometry

Keywords: Physics.
Advisor: Hayden Patrick (Patrick M.)
Silverstein Eva
Susskind Leonard
Restoring vision with electronic photoreceptors : from Petri dish to patients and back

Treatments of neurological diseases using electro-neural interfaces are rapidly advancing. Inspired by the deep brain stimulators for Parkinson's patients and by cochlear implants for the deaf, we developed a photovoltaic subretinal prosthesis for restoring vision to patients blinded by retinal degeneration. Our "electronic photoreceptors" replace the function of the natural photoreceptors lost due to age-related macular degeneration. This is an array of photovoltaic pixels that convert incident light into electric current to convey the visual information to the secondary neurons in the retina by electrical stimulation. Images captured by a camera on augmented-reality glasses are projected onto the subretinal photovoltaic implant using pulsed near-infrared light. Patients with such prosthesis can read with acuity closely matching the pixel size of the implant currently used in a clinical trial (100 um), corresponding to 20/460 to 20/550 vision. This work presents the interaction between electronic photoreceptors and the retina, describing the properties of prosthetic vision in preclinical studies and in clinical trials, while informing future prosthesis design. In this thesis, We first explore the characteristics of the retinal response to pulsated electrical stimulation, focusing on the retinal neural code and features of natural retinal signal processing preserved in network-mediated retinal stimulation. We then describe how performance of visual tasks with pixelated images improve with resolution and contrast. Afterwards, we describe the results of behavioral and in vivo electrophysiological studies in rodents demonstrating the contrast sensitivity and visual acuity achievable with various configurations of subretinal implants. Finally, we conclude with the outlook into the ultimate limits of resolution and our progress toward scaling pixel size down to cellular dimensions

Keywords: Physics.
Advisor: Palanker Daniel
Doniach S.
Fisher Daniel S.