VictorJuiz/thesis huggingface dataset:
Fluctuations in Supercooled Fluids and Ionic Solutions

An overview of five studies is presented in two parts. The first part presents two studies/nof supercooled fluids. The second part presents three studies of water and aqueous solutions./nEach study seeks a minimal model of a condensed matter system. In the first study,/nkinetically constrained models (KCM’s) are compared to alternative theories of the glass/ntransition in high dimensions. Dimensionality is used as a parameter to tune the connectivity/nof a lattice, where a higher dimensional model has more interactions between neighboring/nsites. This study finds that KCM’s outperform alternative theories in high dimensions. The/nsecond study explores the possibility that bacteria have evolved to exploit the glass transition/nto enter a dormant state when environmental conditions are unfavorable. Although the/navailable evidence shows that the bacterial cytoplasm does not meet the strict definition of a/nfragile glass former, much of its behavior is similar to and can be described using close analogies/nwith the glass transition. In the second part, the third study describes the molecular/nmechanisms that gives rise to large electric field fluctuations, which in turn cause autoionization/nand ion dissociation. The fourth study analyzes several candidate order parameters/nas the basis for a Gaussian field theory of ion solvation. Finally, the fifth study discusses the/nmost popular current explanation for observed charge asymmetry at liquid-vapor interfaces./nThis explanation, based on linear response of the surface polarization to the presence of an/nion, is incorrect. Instead, the surface polarization responds non-linearly to the presence of an/nion. Incorporating these non-linear fluctuations is essential to predict solvation free energies.

Advisor: Geissler, Phillip
Computational Considerations for Targeted Learning

Targeted Learning represents a principled methodology that has the potential to leverage the availability of big datasets and large scale computing facilities. However, many of the methods are computationally demanding, and therefore require careful consideration as to their implementation. This thesis comprises three cases studies at the intersection between Targeted Learning and computation. Chapter 1 describes the Targeted Bootstrap, a novel bootstrap technique that samples from a TMLE distribution and therefore has asymptotic performance guarantees, while avoiding issues related to cross-validation on bootstrap samples. Chapter 2 considers the problem of estimating both a target parameter and nuisance parameter on which it depends, when ideally both would be estimated with cross-validation. By carefully considering what parts of the sample are used for what estimation tasks, nested cross-validation can be avoided at great computational savings. This is achieved using the novel SplitSequential cross-validation approach. Chapter 3 describes the opttx package for learning optimal treatment rules. This package contains an implementation of SplitSequential Super Learner, and also contains a novel approach to learning an optimal rule for a categorical treatment variable. Further, performance-based variable importance measures are used to evaluate which of the covariates are most useful for making treatment decisions.

Advisor: Hubbard, Alan E
Spatial and Temporal Variability in Benthic Invertebrate Assemblages and Population Genetics in a Lake and Stream System

An understanding of the spatial and temporal diversity of benthic invertebrates is necessary to understand, manage, and protect freshwater habitats. Benthic invertebrates are important components of aquatic ecosystems and are frequently used in bioassessment and biomonitoring programs. Benthic invertebrates can also play a role in nutrient cycling in lentic environments through bioturbation activities. This dissertation uses a range of techniques and analyses to understand the arrangement of benthic invertebrate diversity in Upper Klamath Lake, Oregon, and several watersheds in northern southern California./nUpper Klamath Lake (UKL) is a large, shallow, naturally eutrophic lake that has experienced declines in water quality, which has led to annual cyanobacterial blooms of Aphanizomenon flos-aquae. Benthic invertebrates can increase autochthonous nutrient cycling through benthic bioturbation activities. In order to better understand the role that benthic invertebrates play in UKL, I studied the density, taxonomic richness, and species composition of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. I also characterized sediment composition and water quality at each collection site and determined which environmental variables correlated with differences in benthic invertebrate composition. This research is located in Chapters 1 and 3 of this dissertation./nLike benthic invertebrates in UKL, the mayfly Baetis tricaudatus is an abundant and ecologically important organism of freshwater ecosystems. Despite its widespread distribution, B. tricaudatus cannot be consistently and accurately identified and belongs to a species group known to have cryptic species diversity. While previous studies have examined the spatial distribution of this diversity, none have studied the temporal distribution. To better understand the temporal arrangement of diversity at the cytochrome oxidase subunit 1 (CO1) mitochondrial gene region, I collected B. tricaudatus specimens from 3 sites over 4 years and used haplotype networks to visualize diversity. Because my results were different than those from other studies on the same taxon, for my final chapter I analyzed Baetis rhodani group COI sequences from northern and southern California using Bayesian phylogenetic analyses and haplotype networks. This research contributes to our understanding of genetic diversity, which is an important component to biodiversity.

Advisor: Resh, Vincent Resh H
Applications of Magnetic Particle Imaging to Brain Imaging

Magnetic Particle Imaging is a novel imaging modality with many applications in the preclinical, and soon, clinical space. In particular, MPI/nshows promise for imaging of various brain related pathologies, such as stroke, hemmorhage, and traumatic brain injury. In this thesis, we/ndemonstrate a series of first-in-animal proof-of-concept experiments that MPI could soon be superior to our conventional imaging technologies, including X-ray CT, MRI, ultrasounds and nuclear medicine for particular neuroimaging applications. In the process, we will develop algorithmic enhancements to the image reconstruction of MPI signals in order to achieve real time interventional imaging, much like X-ray fluoroscopic imaging, but without ionizing radiation and significant risksof catheter and iodinated contrast media.

Advisor: Conolly, Steven
The Body in Space: In Search of a Sensuous Dwelling in the Space of Accumulation

This dissertation asks after the possibility of an unalienated relationship to the aesthetic dimension within the confines of the capitalist space of accumulation, and makes the argument for a conceptual foundation from which to consider living well under conditions of subjection. It does this by considering how aspects of 20th century French phenomenology – conceptualizations of the body, of the aesthetic, and of space – might be brought to bear on questions that pertain to the dialectics of captivity and freedom under market capitalism. These questions are further opened by the works of bell hooks and Herman Wallace, whose contemporary projects take on a more explicit political urgency. In this way, the dissertation seeks to bring to the fore ways of reimagining the aesthetic through the question of dwelling in ways that are not free from the forms of subjection inherent in capitalism, but that nonetheless remain unassimilable to market logics./nThe first and second chapters of this work trace the conceptual foundations through which the aesthetic might be approached as a structuring force of lived experience. The first chapter turns to Henri Lefebvre’s The Production of Space and draws forth a Nietzschean account of the body in space. Reading the image of a tightrope walker that appears early in Lefebvre’s critique, the chapter attends to the conditions under which the body in space is capable of recuperating an aesthetic knowledge from the logics of abstract space. The subsequent chapter turns from Lefebvre’s account of the space of capitalist accumulation to Merleau-Ponty’s concept of flesh in order to foreground the structuring poetics of the body in space. I then turn to Bachelard’s Poetics of Space, opening onto a critical notion of “aesthetic dwelling.” Aesthetic dwelling is the fulcrum of the dissertation project, offering an account of life structured by felicitous experience of aesthetic dialectics. I read his prioritizing of the felicitous as an ontological move towards a space in which living can be taken up as a poetic and free experience; here, being does not find its dwelling in experiences of oppression. The final chapter addresses the question of accessing this lived experience of the aesthetic under the negative pressures of market capitalism. I focus on the aesthetic subject of capitalism as it emerges in rhetorics of ethical consumption and on the notion of luxury as it evokes and distorts the aesthetic’s non-utilitarian function. The dissertation concludes with an engagement of the “dream home,” first as the spatiality of the aesthetic subject, and then as it emerges as a collaborative artwork between Herman Wallace and Jackie Sumell. There, I read Wallace’s dream home as a critical site of disidentification with luxury that opens onto a different, lived sense of the aesthetic.

Advisor: Butler, Judith
Talkin' About a Revolution: The Dynamics of the Rotary Motor of Bacterial Flagella

The bacterial flagellar motor (BFM) is an ion-powered nanomachine that drives swimming in many bacteria. Its central role in processes like chemotaxis and biofilm formation has made obtaining a mechanistic understanding of its function a central challenge in biophysics. This protein complex is comprised of several transmembrane rings connected to a long flagellar filament by a flexible hook. Rotation is known to occur via an interaction between one or more membrane-embedded "stator" units and protein spokes on the periphery of the "rotor" ring. Further modeling has been stymied by the lack of atomic-level structures, which are hard to obtain because the BFM is large and traverses the membrane./nThe work in this thesis attempts to clear this hurdle by combining partial crystal structures, mutation and crosslinking experiments, and biophysical measurements to propose a mechanically-specific, experimentally-testable model of how the motor generates torque. Predictions are validated against biophysical measurements on single-stator motors, which isolate the properties of the motor's fundamental mechanochemical cycle by removing the effects of interactions between individual stator units./nThis base model is also extended to consider the behavior of multi-stator motors. Recent experiments have shown that stator units dynamically bind and leave the motor, influenced by several factors, including the ion gradient, external load, and motor speed. This has brought into question past results, one of which is the long-held conviction that the maximum speed of the motor is independent of stator number; that is, that at near-zero load, one engaged stator unit can push the motor at its maximum speed. The model proposed in this thesis predicts that such a "limiting" zero-torque speed in fact does not exist: Recruitment of additional stator units, even at very low external load, results in an increase in motor speed. This assertion is supported by experimental results in chimeric sodium-driven motors./nFinally, validation experiments for this model are described. The mechanism presented is unique in that it suggests motor rotation is loosely coupled to ion flux; that is, an ion passage may not always constitute a fully efficient power stroke. Thus, motor steps are likely to be unequal in size, and the number of ions required for a full revolution of the motor may vary with external conditions. This notion is tested using single-cell fluorescent measurements to compare ion flux in motors at different speeds.

Advisor: Oster, George
Native American Embodiment in Educational and Carceral Contexts: Fixing, Eclipsing, and Liberating

Today Native American youth are overrepresented in detention centers and receive some of the harshest treatment from state and federal carceral institutions. To intervene in this crisis, U.S. and tribal governments have partnered to create tribal juvenile halls, located on Indian reservations, which seek to educate and rehabilitate Native youth through culturally relevant curricula. Little has been written about tribal juvenile halls, their relationship to 19th and 20th century boarding schools designed to assimilate Native youth, and the experiences of Native peoples in these spaces./nScholars have also yet to address the link between education and incarceration historically and contemporarily in the Native context. I investigate Native youth’s experiences with educational and embodied programming at two institutions located on the Rosebud Reservation in South Dakota: St. Francis Mission School, a former on-reservation boarding school (1886-1972), and Wanbli Wiconi Tipi (Eagle Life Home), the tribal juvenile detention center founded in 2005. Examining Native American basketball, dance, and theater reveals that St. Francis officials largely omitted ideas about “Indianness” except for in athletics and the arts. I center my research on the Rosebud Reservation because U.S. policies regarding education and incarceration have frequently targeted the Sicangu Lakota./nDrawing on close readings of newspaper articles, photographs, performances, short films, and in-depth interviews with educators, students, and incarcerated youth, I demonstrate how the mission school and the detention center have articulated almost identical goals but with very different cultural bases: to produce loyal, productive citizens of high character through educational and embodied programming. I uncover how educators and students at St. Francis created and contested ideas about the assimilative processes intended to fix and eclipse Lakota bodies. In the context of human rights violations related to various methods of confinement, Wanbli Wiconi Tipi employees adopt what I describe as decolonial tactics within the restrictions imposed by the current system to counter and refute colonial logics of Native dehumanization and displacement and assert Native peoples and nations’ interests. I offer the term carceral liberation to describe the U.S. government’s ongoing limitations on tribal sovereignty, Native peoples’ negotiation of these restrictions, and the paradoxical opportunities that Native peoples may experience while incarcerated. My interviews with Lakota and other Native youth held in detention at Wanbli Wiconi Tipi illuminate that settler colonialism has shifted their perceptions of force and oppression, so that they exert their own fixing of the facility’s mission.

Advisor: Biolsi, Thomas
Meta Learning for Control

In this thesis, we discuss meta learning for control:/npolicy learning algorithms that can themselves generate algorithms that are highly customized towards a certain domain of tasks./nThe generated algorithms can be orders of magnitudes faster than human-designed, general purpose algorithms./nWe begin with a thorough review of existing policy learning algorithms for control, which motivates the need for better algorithms that can solve complicated tasks with affordable sample complexity./nThen, we discuss two formulations of meta learning./nThe first formulation is meta learning for reinforcement learning, where the task is specified through a reward function, and the agent needs to improve its performance by acting in the environment, receiving scalar reward signals, and adjusting its strategy according to the information it receives./nThe second formulation is meta learning for imitation learning, where the task is specified through an expert demonstration of the task, and the agent needs to mimic the behavior of the expert to achieve good performance under new situations of the same task, as measured by the underlying objective of the expert (which is not directly given to the agent)./nWe present practical algorithms for both formulations, and show that these algorithms can acquire sophisticated learning behaviors on par with learning algorithms designed by human experts, and can scale to complex, high-dimensional tasks./nWe also analyze their current limitations, including challenges associated with long horizons and imperfect demonstrations, which suggest important venues for future work./nFinally, we conclude with several promising future directions of meta learning for control.

Advisor: Abbeel, Pieter
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution

Key evolutionary transitions have shaped the tree of life by driving the processes of speciation and extinction. This dissertation aims to advance statistical and computational approaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model-based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the missing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. The models reveal the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, these models permit estimation of the location and timing of possible chromosome speciation events over the phylogeny. Finally, Chapter 3 demonstrates a new method of stochastic character mapping for state-dependent speciation and extinction models and applies it to test the impact of plant mating systems on the extinction of lineages. This approach estimates the timing of both character state transitions and shifts in diversification rates over the phylogeny. Confirming long standing theory, I found that self-compatible lineages have higher extinction rates and lower net diversification rates compared to self-incompatible lineages. Additionally, the method shows that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in evolutionary decline.

Advisor: Baldwin, Bruce G
Molecular Mechanisms of Autophagy and its Cellular Functions

Autophagy is an essential process in cells whereby, paradoxically, destruction of cellular components is necessary for cellular renewal, homeostasis, and survival under stresses ranging from starvation to infection. Substrates of autophagy, either bulk cytoplasmic contents or selectively targeted proteins and organelles, are engulfed in a growing double-membraned structure known as the phagophore. The phagophore matures and closes to form into the autophagosome, whose contents are degraded upon fusion of the autophagosome with the vacuole or lysosome. Autophagy occurs in all eukaryotes and many components of the autophagic machinery are conserved among yeast, animals, and plants. Many open questions remain as to how these individual components mechanistically work together to orchestrate autophagy, as well as how autophagy then functions in specific cellular contexts. Here, I study two protein complexes that are necessary for autophagy initiation, the Atg1 kinase complex and the phosphatidylinositol 3-kinase complex. In the first study, I use super-resolution, quantitative imaging of live cells coupled with structure-based mutational analysis to show that the Atg1 C-terminal domain has an essential function in autophagosome expansion that is downstream and separate from its Atg13-dependent role in autophagy initiation. The Atg1 C terminus is strikingly dynamic in the absence of Atg13, a phenomenon of unknown significance given that Atg1 and Atg13 have been thought to function in complex. The identification of an Atg13-independent role for the Atg1 suggests that these dynamics may be important for Atg1 function, particularly in autophagosome maturation. The second study examines the remarkable dynamics of the VPS34 kinase domain in context of the autophagic phosphatidylinositol 3-kinase complex. Using electron microscopy and both in vitro and in vivo assays of autophagy activity, we show that the dynamic dislodging of the VPS34 kinase domain is essential for autophagy initiation and that this movement is sterically inhibited by the VPS15 scaffold. Taking a step back from mechanistic intricacies and examining the ever-growing functions of autophagy in cellular context, in the last chapter I show that autophagy functions in organelle biogenesis. Specifically, autophagy degrades the protein OFD1 at centriolar satellites and promotes growth of the primary cilia, a sensory organelle. We identify a previously unknown substrate of autophagy and show that autophagic degradation of OFD1 can induce the formation of primary cilia in cancer cells, setting the stage for further investigations of the function of primary cilia and autophagy in cancer and other ciliopathies. Thus, this work spans studies of the molecular mechanisms of autophagy as well as its cellular functions.

Advisor: Hurley, James H