VictorJuiz/thesis huggingface dataset:
Synthesis of low-valent lanthanide organometallics for photocatalysis and electronic structure studies

Chapter 1. To date, the exploration of ligands that can support cerium, or any other lanthanide (Ln), in photocatalysis has been limited to halides, pseudohalides, and simple nitrogen donors. No organometallic photocatalyst has yet been reported that combines the photoexcitable cerium cation with strongly binding, multifunctional, tunable ligands. This chapter conveys the synthesis and characterization of a range of cerium photocatalysts, alongside a new family of photoactive Ln(III) compounds (Ln = La, Nd, Sm) supported by a light-absorbing tunable aryloxide-tethered N-heterocyclic carbene (NHC), tetramethylcyclopentadienyl (CpMe4), and pseudohalide ligands. The synthesis and characterization of the trivalent uranium analogue of these species is also presented, alongside investigation into the photophysical properties of select complexes./nChapter 2. The complexes described in Chapter 1 are capable of the rare, selective,photocatalytic C–F bond functionalization of sp3 hybridized C–F bonds, when used in conjunction with magnesium alkyl reagents. The work described in this chapter is, to the best of our knowledge, the first example of catalytic C–F bond activation and functionalization mediated by a rare-earth metal complex. Ligand light-absorption and redox non-innocence allows for the photocatalysis to be accessed even by typically photo- and redox-inactive metals including lanthanum and magnesium. Through a combination of experiment and theory, this work provides unique insight into the cooperativity between metal and ligand in photocatalysis, and the significance of ligand redox-non innocence in radical mechanisms./nChapter 3. The studies described in Chapter 2 of this thesis conclude that specialized, light- absorbing aryloxide ligands are required for the efficient photocatalytic cleavage of strong C– F bonds by Ln complexes. In this chapter, trivalent Ln tetramethylcyclopentadienyl complexes (Ln = La, Ce, Pr, Nd, Sm) are shown to photochemically activate the weaker sp3 carbon– chlorine bond of chlorinated hydrocarbons via a reactive lanthanide alkyl species. Becauselight absorption by the CpMe4 ligand is efficient, photocatalytic reactivity is enhanced for cerium and possible for neighboring, normally photoinactive, Ln congeners. Calculations are utilized to further understand the mechanism of this process, and preliminary results in the catalytic dechlorination of polyvinyl chloride (PVC) are presented.

Advisor: Arnold, Polly L
Structures and Mechanisms of Protein Channels

Proteins are biological machines composed of a single or multiple threads of amino acids which fold into three-dimensional shapes. These shapes and surfaces directly participate in many of the molecular interactions essential to life. Some proteins exist in lipid membranes and thus have been termed membrane proteins. Membranes serve as sites of import, export, and signaling and allow for compartmentalization; all critical functions for living organisms. After decades of research throughout the 20th century, many families of membrane proteins were revealed to form transport proteins that facilitate movement of substrates across membranes. The general group of transport proteins can be further divided into two groups: active and passive transporters. Passive transport proteins have been called channels, given their observed activity of opening to allow substrate diffusion down an electrochemical gradient. Channels are diverse both in their architecture and substrates, which include ions, small molecules, and other proteins. Despite the broad importance of channels in a vast array of biology many aspects of how these machines operate at a molecular level are yet to be revealed. Determining the structures of channels, which in many cases was not technically feasible until recently, has provided key insights into the form and function of these intricate machines. Presented here are studies of two different channels: the Translocase of the Outer Mitochondrial Membrane (TOM complex) and the light-gated ion channel, ChRmine./nThe first study in this thesis examines the long-awaited architecture and transport mechanisms of the major protein gate of the outer mitochondrial membrane. The high-resolution structure of the TOM complex revealed its overall organization-- including all its core subunits, multiple assemblies of the complex, and a glimpse at the pore which provides insights into mechanisms of protein transport. The subsequent study examines the first ever structures of a light-gated ion channel in a native-like membrane environment, using lipid nanodiscs and cryogenic electron-microscopy(cryo-EM). Determining cryo-EM structures of ChRmine was a technical achievement and revealed its surprising trimeric assembly, ion conduction path, and retinal binding pocket. Through analysis of the structure, we were able to tune the kinetics of ChRmine using a rational engineering approach. Lastly, the latest work on ChRmine paves the path for the determination of structures previously too dynamic to capture. These elusive structures are attractive targets because they could lay the foundation for building the next generation of tools for studying the brain.

Advisor: Brohawn, Stephen
Grounded critical digital literacies: Youth countering algorithmic and platform power in school and everyday life

With recent advances in generative artificial intelligence, it may come as no surprise that AI influences our society in profound ways. This dissertation project examines how educational and social media platforms and their algorithms shape educational practices and the identity, digital literacies and views of middle school youth participants. Through a digital ethnography (Pink et al., 2016) rooted in sociotechnical and discursive theories of agency and power (Foucault, 1994; Latour, 2005), the study is one of few to empirically explore how participants shape and are shaped by these technologies. The study focuses on the experiences, development and views of 6th grade participants in a California Bay Area K-8 school as they 1) attended virtual schooling during the pandemic and used the educational platform Google Classroom and 2) as they participated in an online afterschool club and developed critical digital literacies (CDL) to counter algorithmic processes./nOne key finding of the study is the lively presence of youth agency in the face of the seemingly overwhelming power of algorithms and platforms to shape and control our lives. Youth participants crafted and enacted identities and digital literacies in ways that disrupted algorithms through literacies that, for example, crossed platforms or hacked algorithmic processes. Teachers and students “made-do” with Google Classroom in ways that subverted, transgressed or denied the technically-embedded business model. Youth participants developed critical digital literacies rooted in a sociotechnical discourse about algorithms that enabled them to unearth patterns in social media algorithms and begin to understand how platforms tracked and profiled them. The actor-networks in which participants, platforms and algorithms were embedded provided opportunities for youth agency to manifest. At the same time, the study empirically documents how participants were reciprocally shaped by these technologies in ways that oriented teaching and learning toward narrow academic goals and that aligned participant identities with the algorithmic identity on their favorite platforms./nThis study contributes to a range of scholarship critically examining the impact of technology and artificial intelligence on education and society. Specifically, it shows the importance of studying agency in relation to algorithmic and platform power and the importance of conducting empirical research to document how such technologies actually shape education and society. The study also identifies a new concept for CDL researchers and theorists: grounded critical digital literacies. A key implication of the afterschool program is that CDL programs should be rooted in youth participants’ existing algorithmic imaginaries (Bucher, 2017). A grounded CDL sharpens youths’ existing critical competencies with technology and suggests that CDL programs should fold sociotechnical orientations to technology into their budding critical digital literacy practices

Advisor: Hull, Glynda A
Essay on Innovation and Finance

Do patents facilitate market entry and job creation? Using a 2014 Supreme Court decision that limited patent eligibility and natural language processing methods to identify invalid patents, I find that large treated firms reduce job creation and create fewer new establishments in response, with no effect on new firm entry. Moreover, companies shift toward innovation aimed at improving existing products consistent with the view that patents incentivize creative destruction.

Advisor: Manso, Gustavo
McQuade, Timothy
Deterministic and stochastic fluid-structure interaction

This thesis will study fluid-structure interaction (FSI), which describes the coupled multiphysical dynamical interaction between fluids and deformable structures. From modeling the flow of blood in compliant elastic arteries to modeling biomedical prostheses and large-scale structures such as wings, bridges, and dams, FSI is prevalent in science, making the rigorous analysis of such coupled fluid-structure systems important for continued technological development and progress in engineering. While prototypical models of FSI involving incompressible, viscous, Newtonian fluids interacting with elastic structures have been well-studied in the literature, the types of FSI models found in present-day real-life applications have unique and interesting features that require new mathematical methods for their analysis. The goal of this thesis will be to develop new tools for studying new complex FSI models of practical importance that extend past work on prototypical models of FSI. Motivated by real-life applications, we will study stochastic FSI systems involving coupled FSI dynamics under the additional influence of random noise in time, and fluid-poroelastic structure interaction (FPSI) which describes FSI systems in which the structure is poroelastic and hence admits fluid flow through its pores. In the study of stochastic FSI, we establish well-posedness for two models: (1) a reduced model where the full stochastic fluid-structure dynamics can be reduced to a single stochastic equation known as the stochastic viscous wave equation and (2) a fully coupled stochastic FSI system involving linear coupling between a Stokes flow through a channel and the stochastically forced elastic walls of the channel, where the full system is described by a stochastic system of PDEs. Next, we study deterministic nonlinearly coupled FPSI and consider a model in which a multilayered poroelastic structure consisting of a thin plate and a thick poroelastic medium, modeled by the Biot equations, interacts with an incompressible fluid modeled by the Navier-Stokes equation. We study well-posedness and consistency of this nonlinearly coupled FPSI model, which is especially challenging since the fluid and poroelastic structure domains are time-dependent and a priori unknown. To the best of our knowledge, the results in this thesis represent the first well-posedness results for stochastic fluid-structure systems and nonlinearly coupled FPSI with moving domains.

Advisor: Canic, Suncica
Nonlinear Optical Spectroscopy of Ions at Aqueous Interfaces

That selected ions have an energetic preference to reside at the air-water interface, rather than in the bulk, is a relatively new development in our understanding of aqueous interfaces. While significant experimental and theoretical advances have been made in this field in recent years, the underlying physics, which existing models of ion solvation and ion partitioning are based upon, is still not completely understood. The benefits of a rich understanding of interfacial phenomena are many-fold, including enhancing our knowledge of atmospheric aerosol chemistry, accelerated reactions in “on-water” catalysis, and many biological interactions. The contents of this thesis describe efforts to deepen the detailed understanding of ion adsorption to air-water and water-hydrophobe interfaces through the use of nonlinear spectroscopy tools, which exclusively probe ions and water molecules at liquid interfaces.

Advisor: Saykally, Richard J
Robust Machine Learning for the Control of Real-world Robotic Systems

Optimal control is a powerful paradigm for controller design as it can be used to implicitly encode complex stabilizing behaviors using cost functions which are relatively simple to specify. On the other hand, the curse of dimensionality and the presence of non-convex optimization landscapes can make it challenging to reliably obtain stabilizing controllers for complex high-dimensional systems. Recently, sampling-based reinforcement learning approaches have enabled roboticists to obtain approximately optimal feedback controllers for high-dimensional systems even when the dynamics are unknown. However, these methods remain too unreliable for practical deployment in many application domains./nThis dissertation argues that the key to reliable optimization-based controller synthesis is obtaining a deeper understanding of how the cost functions we write down and the algorithms we design interact with the underlying feedback geometry of the control system. First, we next investigate how to accelerate model-free reinforcement learning by embedding control Lyapunov functions — which are energy like functions for the system— into the objective. Next we will introduce a novel data-driven policy optimization framework which embeds structural information from an approximate dynamics model and family of low-level feedback controllers into the update scheme. We then turn to a dynamic programming perspective, and investigate how the geometric structure of the system places fundamental limitations on how much computation is required to compute or learn a stabilizing controller. Finally, we investigate derivative-based search algorithms and investigate how to design `good’ cost functions for model predictive control schemes, which ensure these methods stabilize the system even when gradient-based methods are used to search over a non-convex objective. Throughout an emphasis will be placed on how structural insights gleaned from a simple analytical model can guide our design decisions, and we will discuss applications to dynamic walking, flight control, and autonomous driving.

Advisor: Sastry, Shankar
Modeling Contact and Spatial Heterogeneity in the Transmission of SARS-CoV-2 and Chagas Disease

The study of infectious disease is more than how pathogens transmit between hosts and cause illness and death. Infectious diseases are social, political, environmental, and infrastructural phenomena that humans have limited but equal power to eradicate or to exacerbate. Using modern disease modeling methods, researchers have the ability to test our assumptions about disease dynamics and to explore ways in which our behavior may help or hurt, and to imagine a better world with effective interventions. In this dissertation I focus on three applications of such models to two diseases: an evaluation of vaccine distribution and long-term seasonality of SARS-CoV-2, the pathogen causing the COVID-19 pandemic, and Chagas Disease, a parasitic infection in Brazil that despite its relative infrequency, has the potential to cause debilitating and fatal complications. In all studies, I focus on the heterogeneous risk of transmission and infection present in the population with an eye towards disease-averting interventions.In Chapter 1, I find that distributing vaccines for COVID-19 in decreasing priority by age is a more effective strategy to limit deaths than prioritizing by high-contact employment status, consistent with the CDC’s recommendations in early 2021. In the second chapter, I continue the analysis of SARS-CoV-2 using an Agent-Based Network Simulation, finding that recurrent outbreaks of the disease are likely to persist but, depending on the epidemiology of the pathogen, may be mitigated by annual booster doses distributed at certain times of year. Finally, I conclude in chapter 3 by finding that cases of Acute Chagas Disease may be expected to increase over the ensuing decade, driven by an increasing population in affected areas and changing climate.

Advisor: Mahmud, Ayesha
Choanoflagellate transcriptional regulation and the origin of animal cell types

Animal bodies develop through complex developmental pathways in which cells are programmed for particular fates and functions. Transcriptional regulation has been shown to be central to this process, but we know little about how transcriptional regulatory programs evolved along the animal stem lineage. Can we trace animal developmental programs to their unicellular, pre-animal roots? Which mechanistic aspects of transcriptional regulation are unique to animals and which are more deeply conserved? My doctoral research explored these questions through bioinformatic and genetic approaches in choanoflagellates, the closest living relatives of animals. Through a better understanding of transcription factors and cell type specification in these organisms, I strove to help us triangulate the transcriptional regulatory capacity of the common ancestor of animals and choanoflagellates, which lived hundreds of millions of years in the past./nChapter 1 reviews how transcriptional regulation has evolved along the animal stem lineage. It has been frequently proposed that animal origins required the evolution of increasingly “complex” transcriptional regulation. I break this idea of complexity into specific mechanisms and trace what is known about the evolution of these mechanisms in animals and their closest living relatives./nIn Chapter 2, I present an example of how functional interrogation of choanoflagellate transcriptional networks can help us better understand the ancient roles of specific transcription factors as well as the regulatory architecture of cell differentiation. I explored the function of the RFX family of transcription factors in choanoflagellates, identifying a particular sub-family (cRFXa) that has a functionally conserved role in regulating dozens of genes required for ciliogenesis. By generating genome-edited mutant strains, I show that cRFXa is essential for proper ciliogenesis in the model choanoflagellate Salpingoeca rosetta, and that this defect is coupled with the loss of full expression of dozens of highly conserved ciliary genes. Coupled with existing data from animals, this work shows that the RFX/ciliogenesis regulatory module dates before the divergence of animals and choanoflagellates. It also helps us to understand the regulatory changes that might have been required for the differentiation of ciliated and non-ciliated cells early in animal evolution./nFinally, in the Appendix I present work from early in my dissertation on a novel virus I helped to discover in Entomophthora muscae, a behavior-manipulating fungal pathogen of dipteran flies, including Drosophila melanogaster. We identified this virus through sequence analysis, including small RNA sequencing signatures generated by host Dicer processing, as well as through electron microscopy to directly visualize viral capsids in both cell-free extract and within fungal cells themselves.

Advisor: King, Nicole
Feelin’ Diasporic: Embodied Memory in Sri Lankan America

This study explores the role of embodied memory on identity formation in U.S.-born and/or raised Sinhala Sri Lankan Americans through the frame of temporal diasporic embodiment. At the intersection of the body, diaspora, and time, a temporal diasporic embodiment engages with a diasporic experience of the body that exists in multiple locations, times, and racializations simultaneously, and is subject to various forms of power. A temporal diasporic embodiment reveals the impermanent and non-teleological nature of the body, ideologies of home, racializations, trauma, and generational understandings race, place, and time. The tensions between time, memory, and diaspora take on contradictory meanings that affect Sri Lankan Americans’ experiences and identities. As they grapple with their temporal misalignment, U.S. born and/or raised Sri Lankan Americans use different methods to redefine what it means to be Sri Lankan in the U.S./nUsing an interdisciplinary and queer diasporic methodology, this study analyzes how diaspora is affectively experienced, how diasporic identities are formed and negotiated, and how intimacy influences diasporic imaginings of past and future. Specifically, this study examines how the tattooed diasporic body serves as an archive for embodied storytelling, how Nayomi Munaweera’s Island of a Thousand Mirrors depicts the visceral and the failure of the heteronational, how the solo play To T, or not to T? by D’Lo, a Sri Lankan Tamil American transmasculine performance artist, reveals how the diasporic body is regulated, how Sri Lankan Americans respond to antiblackness within their coethnic community and in U.S. society with a transnational social justice orientation, and how a politics of care manifests through rethinking auntiehood. In doing so, we see how Sri Lankan American bodies formed in diaspora create new epistemologies as they contend with the complexities of living as racialized diasporic subjects.

Advisor: Siu, Lok
Um, Khatharya
Higher Accuracy, Lower Cost: Developments in Molecular and Periodic Electronic Structure Theory

Proper applications of electronic structure theory use the most accurate computational method that is feasible for the system size of interest. Modern electronic structure theory methods therefore seek to maximize the ratio of accuracy to computation time. To improve upon an existing method, one must therefore either increase the accuracy or lower the computational cost. In this work, we present techniques for both. In Chapter 2, we present a study of regularized orbital optimized second order M{\o}ller-Plesset theory (OOMP2) and provide an analysis of appropriate empirical parameters across a broad spectrum of chemical systems - yielding a factor of 9 reduction in error over unregularized OOMP2 for certain classes of problems! In Chapter 3, we present a new algorithm utilizing tensor hypercontraction to compute exact exchange for periodic systems including $\bm{k}$-point sampling; this approach significantly reduces the computation time and memory usage for hybrid density functional theory (DFT) when large $\bm{k}$-point meshes are used. In Chapter 4, we analyze the effect of orbitals in third order M{\o}ller-Plesset theory (MP3), showing that DFT orbitals can yield a factor of 3 reduction in error over the more traditional Hartree-Fock orbitals for many applications at no extra computational cost. Finally, in Chapter 5 we utilize MP3 with DFT orbitals to compute reaction energies and reaction rate constants for an experimentally observed reaction and use these to predict the product, which the experiment could only characterize by molecular weight.

Advisor: Head-Gordon, Martin