VictorJuiz/thesis huggingface dataset:
Modeling the Observational Signatures and Feeding of Super-massive Black Holes using Monte Carlo Radiative Transfer

This thesis presents numerical calculations designed to understand aspects of the feeding of, and feedback from, super-massive black holes at the centers of galaxies. The first portion of the thesis describes the development of radiative transfer tools used to address these problems. I present a description of how the Monte Carlo technique can be used to solve the radiative transfer equation, and I demonstrate a coupling of the transfer solution with the equations of hydrodynamics and statistical equilibrium. I next present two major applications of these ideas. The first is to quantify the effects of radiative feedback in active galactic nuclei in the form of radiation pressure on dust at the center of a gas-rich galaxy. The second is a calculation of the spectral energy distributions and optical spectral line strengths emitted during the tidal disruption of a star by a massive black hole. In so doing, I help to answer a number of puzzling questions relating to such disruptions, such as whether the lack of hydrogen emission in their spectra can be the result of radiative transfer effects rather than a lack of hydrogen in the disrupted star.

Advisor: Kasen, Daniel
Understanding Memory Configurations for In-Memory Analytics

A proliferation of frameworks have emerged to handle the challenges of making distributed computations reliable and scalable. These enable users to easily perform analysis of large datasets on commodity clusters. As users have demanded better response times for these computations, newer versions of these frameworks have focused on efficiently keeping computation in memory. A major challenge in deploying such frameworks is understanding application memory requirements. Just as the layers of abstraction of frameworks assist in writing efficient and robust applications, they hide the true memory requirements./nIn this dissertation, I describe and evaluate SLAMR, a tool I have developed for providing users with memory recommendations for programs written for the Apache Spark analytics stack. These recommendations practically address the lack of visibility users have into memory requirements even as they are asked to assign resources to deploy their analytics programs. My tool records activity from an example execution, both from the framework and the garbage collector of its underlying language runtime. Given this instrumentation, it estimates a memory configuration that effectively keeps the entire computation in memory, such that allocating more memory would have minimal benefit on performance. Because in-memory analytics frameworks are built to take advantage of the memory available to them, simply observing actual memory usage is not an effective way to produce such estimates. A challenge, then, is to produce these estimates without performing effort similar to trying configurations around the ultimate recommendation./nSLAMR provides these recommendations without requiring many example executions or detailed analysis of the semantics of the program. What I instrument allows it to predict the effect of different memory configurations rather than simply reflecting the available memory. It collects information corresponding to the abstractions provided by frameworks, so it can distinguish which memory usage is useful and account for when alternate storage was used. To understand the requirements of the underlying language runtime in this analytics stack, it also collects statistics about the program execution that can replayed into a dramatically simplified model of a garbage collector. Both of these models are built around the goal of providing a conservative bound, allowing users to use the resulting memory recommendations in confidence rather than inflate them to avoid the risk of memory exhaustion from errors in the estimates. I show through evaluation that SLAMR provides effective, consistently safe recommendations for a variety of analytics programs and does so with minimal measurement overhead.

Advisor: Katz, Randy H
Courteous Capitalism: Customer Relations, Public Opinion, and the Defense of Monopoly Utilities

Abstract/nCourteous Capitalism: Customer Relations, Public Opinion, and the Defense of Utility Monopolies/nby/nDaniel Martin Robert/nDoctor of Philosophy in History/nUniversity of California, Berkeley/nProfessor Robin Einhorn, Chair/nIn the beginning of the twentieth century, as Americans erupted in righteous indignation over the flagrant abuses of monopolies, utility executives responded by launching four major public relations strategies. First, in a strategy I call courteous capitalism, executives compelled their clerks to exude “courtesy,” “sunshine,” and “patience” whenever these workers interacted with customers. By the late-1920s, public opinion toward corporate utilities had improved, but the cost to low level workers was high. Their plastered smiles and scripted pleasantries represented a great loss of emotional autonomy and a new level of managerial control./nUtility officers also sought to dissipate antimonopoly sentiment by remodeling the customer-service centers where most courteous interactions took place. To do this, executives tore down the bars, high counters, and frosted glass, which utilities had inherited from bank designs, and replaced these “closed offices” with new “open offices,” as managers called them. In doing so, executives hoped to architecturally communicate to customers the supposedly open and above-board operating practices for which utilities now wanted to be known./nStreetcar, electricity, and telephone executives also tried to improve public opinion and thwart government ownership by introducing “customer ownership.” To do this, managers required their employees to sell stock directly to customers. Since these customers were also likely voters, the dividends customers received were likely to pay dividends of their own, back to the company, whenever measures regarding utilities came up at the ballot box. By the crash of 1929, utility employees had directly sold stock to twenty percent of the total number of shareholding Americans./nFinally, utility officers produced immense amounts of publicity, including print matter, speeches, and movies. Yet executives never believed that publicity, or the other strategies of open architecture and customer stock ownership could replace courteous capitalism in terms of its public relations effectiveness. While historians have credited print and finance with everything from forming nations to fashioning consumers, in the case of forming enduring corporate monopolies, courtesy mattered most.

Advisor: Einhorn, Robin
Site-Specific Surface Immobilization of Proteins and Development of Synthetic Fluorescent Sensors for Studying the Cell Biology of Metals

As the major building block of life, proteins have an extraordinary range of structures and functions, which can be harnessed through their controlled immobilization. The covalent attachment of proteins onto surfaces has broad applications in biotechnology and materials science, but current strategies rely on nonspecific conjugation reactions. These reactions often affect protein properties and function. To address this problem, we have developed two site-specific immobilization strategies that target only the N-termini of proteins: one for the functionalization of hydrogels and one for the photopatterning of proteins on glass substrates. We have successfully applied the novel hydrogel material for studying substrate stiffness-dependent cell behavior. We envision that this site-specific immobilization strategy will be applicable to other hydrogel substrates and widely adopted in the field of mechanobiology./nMetal homeostasis is vital for the survival and health of all living organisms. Monitoring metal ion accumulation, efflux, trafficking and organelle distribution is essential for the understanding of roles of sodium and copper ions in cell biology. Synthetic fluorescent sensors have been used to investigate such molecular processes in high spatial and temporal resolution. We have developed novel sodium sensors, which show significant improvements over the commerically-available sensors in their sensitivities and affinities. They are able to reliably report sodium ion levels in live cells. We have also expanded the molecular imaging tool box with a series of photostable copper(I) sensors, which are able to report cellular copper(I) levels in real time.

Advisor: Francis, Matthew B
Kumar, Sanjay
Contextual Visual Recognition from Images and Videos

Object recognition from images and videos has been a topic of great interest in the computer vision community. Its success directly impacts a wide variety of real-world applications; from surveillance and health care to self-driving cars and online shopping./nObjects exhibit organizational structure in their real-world setting (Biederman et al., 1982). Contextual reasoning is part of human's visual understanding and has been modeled by various efforts in computer vision in the past (Torralba, 2001). Recently, object recognition has reached a new peak with the help of deep learning. State-of-the-art object recognition systems use convolutional neural networks (CNNs) to classify regions of interest in an image. The visual cues extracted for each region are limited to the content of the region and ignore the contextual information from the scene. So the question remains, how can we enhance convolutional neural networks with contextual reasoning to improve recognition?/nWork presented in this manuscript shows how contextual cues conditioned on the scene and the object can improve CNNs' ability to recognize difficult, highly contextual objects from images. Turning to the most interesting object of all, people, contextual reasoning is a key for the fine-grained tasks of action and attribute recognition. Here, we demonstrate the importance of extracting cues in an instance-specific and category-specific manner tied to the task in question. Finally, we study motion which captures the change in shape and appearance in time and is a way to extract dynamic contextual cues. We show that coupling motion with the complementary signal of static visual appearance leads to a very effective representation for action recognition from videos.

Advisor: Malik, Jitendra
Transcriptional and Epigenetic Regulation of Embryonic Stem Cell Pluripotency and Reprogramming

Embryonic stem cells (ESCs), like all tissues, largely rely on precise transcriptional and epigenetic regulation for proper cell specification and differentiation. General transcription factors, transcriptional regulators, coactivators, and chromatin remodelers are often coordinated and expressed in a cell-type specific manner to ensure the integrity of this gene expression network. However, how ESCs are able to tightly regulate gene expression and remain highly malleable to external developmental cues is still an open biological question. The XPC DNA repair complex was recently identified as one of a set of critical stem cell coactivators (SCC) involved in driving robust OCT4/SOX2-dependent expression of pluripotent genes in ESCs. This dissertation will focus on the molecular mechanisms of the XPC complex and other SCCs in controlling cell identity and fate in pluripotent stem cells./nChapter 1 will provide an introduction to the transcriptional and epigenetic regulation in pluripotent stem cells. Specifically, it will highlight the core transcriptional network, the mechanisms of reprogramming, and barriers to gene expression (e.g. DNA methylation). Chapter 2 will describe a novel role of the XPC DNA repair complex in regulating DNA methylation in both somatic and pluripotent cells, in part through regulating the activity of thymine DNA glycosylase, a major player in active DNA demethylation. Chapter 3 will describe the identification and characterization of two additional stem cell coactivators: the DKC1 ribonucleoprotein and ABCF1. As it is with the case of the XPC DNA repair complex, DKC1 and ABCF1 are multifunctional proteins with unanticipated roles in pluripotent gene transcription./nIn summary, this dissertation will highlight the role of versatile proteins in pluripotent stem cells and their involvement in transcriptional regulation and beyond. By strengthening our understanding of the fundamental molecular mechanisms employed by pluripotent stem cells, we may gain a better insight into how cell identity is specified.

Advisor: Tjian, Robert
Engineering the electronic structure of atomically-precise graphene nanoribbons

Graphene nanoribbons (GNRs) have recently attracted great interest because of their novel electronic and magnetic properties, as well as their significant potential for device applications. Although several top-down techniques exist for fabricating GNRs, only bottom-up synthesis of GNRs from molecular precursors yields nanoribbons with atomic-scale structural control. Furthermore, precise incorporation of dopant species into GNRs, which is possible with bottom-up synthesis, is a potentially powerful way to control the electronic structure of GNRs. However, it is not well understood how these dopants affect the electronic structure of GNRs. Are these effects dependent on the dopant site? Can the band gap be tuned by doping? This dissertation helps to answer these questions through studying the electronic structure of bottom-up grown GNRs with controlled atomic dopants. The effects of edge and interior doping with different atomic species such as sulfur, boron and ketone were investigated and showed significant site dependence. Topographic and local electronic structure characterization was performed via scanning tunneling microscopy & spectroscopy (STM & STS) and compared to first-principle calculations. The chemical structure of GNRs and GNR heterojunctions was characterized by CO-tip-functionalized non-contact atomic force microscopy (nc-AFM) as well as by a newly developed technique of bond-resolved STM (BRSTM)./nIn an effort to develop a new method for directly synthesizing GNRs on an insulating substrate, we also studied light-induced photo-isomerization of azobenzene molecules adsorbed on an insulating surface of CVD-grown monolayer boron nitride (BN) on Cu(111). This study provides important insights into molecular behavior on an insulating surface, how to couple light to an STM system, and how to utilize local field enhancement effects due to surface plasmon resonance.

Advisor: Crommie, Michael F
Limit Shapes in the Six Vertex Model

The purpose of this thesis is to present some new results about the six-vertex model and dimer model, andi in particular some aspects of the limit shapes that form in the thermodynamic limit and the partial differential equations that arise in their study. Chapter 1 provides a detailed introduction to limit shape phenomena and its mathematics. Chapter 2 reviews basic facts about the six-vertex model and dimer model and their properties in the thermodynamic limit./nChapter 3 investigates the role of integrability of the six vertex model in the formation of limit shapes. By integrability we mean, on one hand the discrete integrability of the six-vertex model in the sense of commutative families of transfer matrices, and on the other hand the integrability in the continuum limit in the Liouville sense of Poisson commutative families of functions (integrals of motion) on the phase space. The main result is to show that the partial differential equations describing the limit shape have an infinite number of conserved quantities./nChapter 4 explains the results of the previous chapter in a more general setting. The main result is a straightforward theorem in Hamiltonian mechanics, which gives conditions for the Poisson commutativity of two Hamiltonian functions in terms of their principal action functions. It suggests a generalization of our previous results to other integrable lattice models, for example, the generalizations of the six-vertex model related to other Lie algebras./nChapter 5 studies the six-vertex model for a special class of weights called the stochastic six-vertex model. for which the six vertex model is closely related to interacting particle models. The main result of this chapter is the derivation for the partial differential equations for the height function of the stochastic 6-vertex model on the cylinder./nChapter 6 studies models at the intersection of discrete geometry and statistical mechanics. The main result is the asymptotic expansion of the discrete Laplacian that approximate Laplace operators induced by a Riemannian metric. They arise as a discretization of the of the Gaussian free field and are closely related to Dimer models that can be regarded as a discretization of Dirac operators in a background metric.

Advisor: Nomura, Yasunori
Reshetikhin, Nicolai Y
The Statistical Mechanics of Biodiversity

Since at least the time of Darwin biologists have searched for a simple set of universal governing mechanisms that dictate the dynamics of biodiversity. While much progress has been made in understanding system-specific processes and in documenting the context-dependent roles of such mechanisms as competition and facilitation, we still lack a universal governing rule set. The goal of understanding and predicting biodiversity dynamics comes at a critical moment when human systems are disrupting those very dynamics. In this thesis I approach this long-standing problem with the hypothesis that general patterns in biodiversity emerge from a combination of the statistical mechanics of large systems and the unique non-equilibrium dynamics imparted to biological systems by their evolutionary history. Statistical mechanics provides the key analytical approaches to abstracting the complex details of biodiversity into general macroscopic predictions that I show receive support from empirical data. However, key deviations from the simplest statistical mechanics of biodiversity reveal the key role of biological evolution in driving systems away from the idealized steady state predicted by statistical mechanics./nIn Chapter 1 I expand a branch of non-equilibrial statistical mechanics, known as super statistics, to explain previously unaccounted for wild fluctuations in the richness of taxa through the Phanerozoic marine invertebrate fossil record and show how this non-equilibrium is driven by clades' punctuated exploration of their adaptive landscapes. This theory provides a novel explanation for deep time diversity dynamics invoking emergence of lineage-level traits as the drivers of complexity via the same mechanisms by which complexity emerges in large physical and social systems. In the context of fossil diversity I show how this complexity arises naturally from the uniquely biological mechanisms of punctuated adaptive radiation followed by long durations of niche conservatism, and thus identify these mechanisms as sufficient and necessary to produce observed patterns in the fossil record. I test this theory using two seminal fossil datasets./nIn Chapter 2 I use the chronosequence afforded by the Hawaiian Islands to capture evolutionary snapshots of arthropod communities at different ages and stages of assembly to understand how the history underlying an assemblage determine its contemporary biodiversity patterns. I apply static ecological theory of trophic networks based on statistical mechanics to these rapidly evolving ecosystems to highlight what about the evolutionary process drives communities away from statistical idealizations. This study indicates that rapid assembly from immigration and speciation in young ecosystems and extinction in old ecosystems could drive observed patterns./nIn Chapter 3 I highlight and explain the computational requirements to testing one statistical theory of biodiversity--the Maximum Entropy Theory of Ecology--with real data and make those test available in a stream-lined framework via the R package meteR that I authored.

Advisor: Harte, John
Gillespie, Rosemary G.
The Effects of Hoja loca on Maize Organogenesis

Plant organs initiate from meristems and grow into diverse forms. Initiation is followed by a morphological phase where organ shape is elaborated, and finally tissues differentiate into their mature state. This process involves a variety of mechanisms, including complex gene regulatory networks, intricate patterning of plant hormones, and dynamic tissue growth. Hoja loca is a maize mutant that has defects in initiating and forming leaves and other lateral organs. I aim to use the Hoja loca mutation to investigate processes involved in transitioning tissue from undifferentiated meristem to lateral organs. Its unique phenotype suggests that it can greatly aid the understanding of plant organogenesis due to the specificity of mutant defects to organ initiation./nIn this dissertation, I investigate the effects of the Hoja loca mutation on shoot organogenesis in Zea mays. In Chapter 1, I describe the mutant phenotype. In Chapter 2, I identify the mutant locus. I use RNA-seq differential gene expression to look at global changes and identify genes that are likely to mediate the Hoja loca defect. In Chapter 3, I investigate the localization of genes and metabolites that are important in organogenesis, namely the patterning of auxin. Together, these results suggest that Hoja loca causes an auxin-insensitivity in part of the auxin signaling response, likely at the site of organ initiation. This change is signaling leads to the misexpression of a beta glucosidase capable of activating cytokinin glucoside conjugates, and potentially the degradation of flavonols. The balance of cytokinin and auxin is a critical regulator of tissue differentiation, and flavonols affect auxin transport. Disrupting the localization of either of these compounds in the shoot could plausibly lead to the mutant phenotypes of skipped leaf initiation and altered leaf morphology.

Advisor: Hake, Sarah C
Measurement of jets produced in top quark events using the emu final state with 2 b-tagged jets in pp collisions at 8 TeV with the ATLAS detector

The transverse momentum and multiplicity of jets produced in top quark events are measured using 20.3 inverse fb of pp collision data at a center-of-mass energy of 8 tev. Jets are selected from top events requiring an opposite-charge $e\mu$ pair and two b-tagged jets in the final state./nThe data are corrected to obtain the particle-level fiducial cross section for additional jets with rank 1-4, where rank=1 is the leading additional jet. These distributions are used to obtain the extra jet multiplicity as a function of minimum jet pt threshold. The results are compared with several next to leading order Monte Carlo generators. The resulting measurements can be used to tune Monte Carlo QCD modelling and may also reduce associated modelling uncertainties for LHC top quark physics measurements.

Advisor: Shapiro, Marjorie