VictorJuiz/thesis huggingface dataset:
Design and Automatic Generation of 60Gb/s Wireline Transceivers

The continual expansion of Internet connectivity has raised data traffic substantially, increasing demands on high-bandwidth wireline communication systems. In contrast to the rapid increase in bandwidth that will be necessary, the allowable power consumption of high-speed transceivers remains relatively constant. Specifically, assuming the same total power budget as current designs, transceivers operating in the range of 50-60Gb/s must achieve 3-5pJ/bit efficiency to remain within the current total power window./nTo address these trends and challenges, this thesis first reports a 60Gb/s receiver frontend in a 65nm CMOS process. Current integration combined with a cascode gate-voltage bias technique enables energy-efficient implementation of CTLE, FFE, and DFE circuits while operating near the speed limits of the technology. The addition of interleaved, offset-canceled deserializing samplers addresses the high gain requirement of adaptive error-samplers. The prototype 65nm CMOS receiver operates at 60Gb/s, consuming 173mW from 1.2V and 1.0V supplies./nTo enhance the productivity and quality of the receive equalizer design by capturing the parasitic loading and wiring capacitance promptly and precisely, an automated flow that generates the equalizer schematic and layout from target specifications and technology parameters is developed. Utilizing the Berkeley Analog Generator, the equalizer generation flow is scripted, executed, and iterated automatically to produce an optimal design that meets for a given configuration./nIn addition to presenting the equalizer design, the thesis also introduces a new baud-rate CDR scheme that leverages the current integration frontend and phase dithering. Correlation of the adaptive error sampler output with the phase dithering sequence indicates the direction of phase offset. The resulting baud-rate CDR saves power and complexity compared to an oversampling CDR by not requiring additional clock phases/deserializers. The implemented 65nm CMOS transceiver operates at 60Gb/s with an eye-opening of 30% UI and consumes 288mW while equalizing 21dB of loss at 30GHz over a 0.7m Twinax cable.

Advisor: Alon, Elad
Unmanned Aircraft Systems Flight Planning: System Development and Feasibility Study

Unmanned Aircraft Systems (UAS), commonly known as drones, are becoming increasingly popular in civilian applications. However, the infrastructure to ensure the safe operations are still largely missing. In this dissertation, I addressed two problems related to a flight mission. First, I propose a flight planning system specifically for single multirotor UAS operations. The system generates a 4D trajectory at the pre-flight stage before an actual flight taking place. Safety is achieved by ensuring enough energy to finish a trip under environmental influences such as wind, as well as avoiding static obstacles. Second, I proposed a hybrid controller capable of performing trajectory following as well as single-helicopter collision avoidance. The controller enables a multi-rotor to follow the planned trajectory./nIn the first part of the dissertation, I first divide the flight planning system into two components: energy demand and energy supply. The demand side is determined by the performance of the UAS, the environment, and the flight trajectory, while the energy supply depends on the power source. Then, I focused on two specific problems on the energy demand side. First, I quantify the energy performance of a UAS by developing a theoretical power consumption model for multi-rotor Unmanned Aircraft Systems (UAS). The model is derived from the helicopter literature. The model parameters are identified and validated experimentally by flying an IRIS+ quadrotor UAS. Second, I solved the trajectory generation problem by formulating it as an optimal control problem. The cost to be optimized is the energy consumption or flight duration at the cruise phase of a flight mission, taking into account 3-dimensional wind field and terrain variation. The problem is solved numerically by the Ordered Upwind Method (OUM). By combining the optimized path with timestamps, we can generate 4D trajectories typically used in aviation flight planning, and thus maximize the software compatibility between manned and unmanned aviation. Simulation shows that the generated trajectories are able to avoid obstacles such as high-rise buildings and give energy consumption estimates along the entire trajectory./nIn the second part of the dissertation, I addressed the trajectory following problem with collision avoidance capability given a planned 4D trajectory. I analyzed the tracking performance of an IRIS+ quadrotor for a challenging trajectory. In the scenario, wind played a big role in the cross-track errors. The collision avoidance capability, or a safety controller, is integrated to the trajectory following controller by introducing a hybrid automaton, deciding when to start the avoidance action and what control actions to take. The hybrid controller is examined in a simple straight-line-following scenario to avoid a manned helicopter.

Advisor: Sengupta, Raja
Methods for Optimal Charging of Large Fleets of Electric Vehicles

Today’s electric grid must be transformed to meet modern consumption behaviors and safely integrate renewable energy sources. This has led to major efforts to develop grid-scale energy management solutions and ensure safety and reliability of our modern power network. In particular, large penetrations of Plug-in Electric Vehicles (PEVs) are expected increase energy needs and peak consumption, which would bring new challenges for utilities and grid operators./nIn this work, we develop optimization methods to coordinate the charging of large fleets of PEVs in distribution grids. We show that different methods should be applied, based on the infrastructure requirements and the objective of the controller./nThe first Chapter Optimal Charging of Fleets of Electric Vehicles with Discrete Charging rates: PDE Modeling and Control Techniques presents a continuum modeling framework to coordinate PEV charging with discrete charging rates. We consider PEVs as loads, which diffuse along the State Of Energy (SOE) axis, and can be in three different categories: charging, discharging or idle. We use a discretized form of Partial Differential Equations (PDEs) to model the dynamics of the system and control the transitions between each category. The second Chapter Dual Splitting Framework for Optimal Charging of Fleets of Electric Vehicles with Continuous Charging rates proposes a tailored distributed optimization method to coordinate PEV charging for load shaping. Three iteration methods are presented and their convergence characteristics are detailed. The third Chapter Electric Vehicle Charging in the Smart Grid: Plug-and-Play Model Predictive Control techniques studies a voltage-regulation scenario for PEV charging. Power flow and distribution grid constraints are modeled, and PEV charging is controlled with Plug-and-Play Model Predictive Control. Finally, the final chapter Behavioral study of Demand Response programs studies the impact of non rational choices on energy consumption and on the success of Demand Response programs.

Advisor: Moura, Scott
Bus rapid transit as formalization: Accessibility impacts of transport reform in Cape Town, South Africa

Many cities worldwide are introducing bus rapid transit (BRT) into contexts where informal transport modes serve a substantial part of the public transport market. These BRT initiatives are intended, among other goals, to formalize existing transport systems and to improve accessibility. However, the extent to which BRT reforms actually improve residents' ability to reach activities remains in question. In this dissertation, I contribute to the empirical and theoretical literature on informal transport by investigating how BRT reform has impacted accessibility for residents of Cape Town, South Africa./nHow have Cape Town's transport reforms affected accessibility and its distribution amongst different population groups? Why have reforms had these effects? I address these questions using three methods: (1) an accessibility index computed using a transport network model, (2) a difference-in-difference approach using intercept survey data, and (3) interviews with users and stakeholders./nThe accessibility model suggested that, in this specific case, the BRT reforms slightly improved accessibility to retail, office, and hospital uses for the majority of residents. Because informal modes were only partially removed, only a small fraction of residents experienced reduced accessibility. The survey findings showed BRT was more effective as an upgrade of existing formal modes than as a replacement for informal transport. Survey respondents realized travel time benefits not by switching to BRT from informal transport, but by switching to BRT from existing formal transit -- conventional bus and train. Shifting from conventional bus to BRT was associated with an average commute time savings of 10 minutes. The BRT appears to differentially provide better accessibility to white and high-income residents, although black residents realized the greater travel time savings because they were more likely to switch from conventional bus and train./nEvidence suggests these particular outcome are best explained by changes in the institutional and incentive structures behind transport provision. The shift from informal transport to BRT involved: formalizing multiple dimensions of transport provision in multiple dimensions; expanding the scope of goals for public transport; and changing the relationship between transport providers and users. These changes in transport provision help explain why BRT reforms were more effective as an upgrade for formal transport than as a replacement for informal modes.

Advisor: Chatman, Daniel
A Polyglutamine Domain Enables Transcriptional Reprogramming in Response to pH Change

pH is tightly controlled in the cell as it influences almost all processes. Intracellular pH in Saccharomyces cerevisiae changes according to nutritional state, acidifying as the cell runs out of nutrients. We found that cytosolic acidification plays a role in transcriptional reprograming during carbon starvation. A polyglutamine domain in the SWI/SNF complex senses this pH change, enabling the induction of about 180 glucose-repressed genes. We propose that polyglutamines undergo phase transitions in a pH dependent manner, which allows glutamine transactivation domain proteins to engage and disengage in transcription. This could be a general mechanism for transcriptional reprogramming events within cells.

Advisor: Koshland, Douglas
Holt, Liam
Of Experience and Enterprise: Careers, Organizations and Entrepreneurship

This dissertation examines the antecedents of entrepreneurship through the empirical analysis of over 2 million resumes that constitutes a sample of the high technology start-up ecology in the United States. The first chapter characterizes the latent issues surrounding the study of entrepreneurial entry (Chapter 1). I then resolve these issues through the development of a sociological career framework of entrepreneurship in two parts. The first establishes the framework and distinguishes two types of entrepreneurial activity: high potential ventures and common self-employment (Chapter 2). I show that machine learning models applied to the identity claims of hundreds of thousands of entrepreneurs can successfully classify, characterize and distinguish these types in the tech sector. The two entrepreneur types exhibit diametrically opposing human capital and career based antecedents. In doing so, I demonstrate a necessary de-conflation of entrepreneurial events; the career framework provides a crucial precision in the definition, observation and measurement of the entrepreneurial outcome variable. The second part exemplifies an application of the framework to demonstrate an efficacy in the identification and study of specific sociological mechanisms. Through the introduced apparatus and a prospective sample of the data that represents the graduates of the top 23 science, technology, engineering and mathematics (STEM) colleges in the United States, I study the effect of status gain on entrepreneurial entry and success by examining different forms of entrepreneurial activity of the alumni of companies that experience liquidity events: initial public offerings (IPOs) and large scale acquisitions (Chapter 3). I find that upon vicariously experiencing these liquidity events, the alumni are on average 23% more likely to enter into high potential entrepreneurship and 17% less likely to enter into contract self-employment. However, such forms of status gain confer no significant funding advantages to the nascent venture. I conclude by discussing future directions: this dissertation serves as but an introduction to and an advocate for a larger program of research that seeks to clarify and advance the study of entrepreneurship through sociological career theory.

Advisor: Stuart, Toby E.
Implications for Dark Matter from Supersymmetric Axion Cosmology

With the Higgs boson discovery at the Large Hadron Collider, the Standard Model continues to prove its success in particle physics and cosmology. Despite its remarkable achievements, the Standard Model remains incomplete owing to theoretical difficulties such as the hierarchy problem, the strong charge-parity (CP) problem, and the lack of dark matter candidates. Supersymmetry has been proposed to solve the hierarchy problem by protecting the Higgs mass from radiative quantum corrections. In supersymmetry, the lightest supersymmetric particles are well-motivated candidates for dark matter. When the Peccei-Quinn symmetry is evoked to solve the strong CP problem, the axion becomes another viable candidate./nOne can attempt to simultaneously solve the aforementioned problems with supersymmetric axion theories. Nonetheless, the scalar superpartner of the axion, the saxion, significantly changes the conventional picture of cosmology and dark matter production. During inflation, a potential for saxions is induced and displaces the saxion field value away from the minimum of the potential today. This results in a saxion condensate that dominates the energy density of the Universe -- a non-standard matter-dominated epoch. The saxion subsequently decays to the particles in the thermal bath, generating a large amount of entropy and diluting the dark matter abundance. The saxion hence plays a crucial role in the cosmological evolution of dark matter. We focus on the cases where dark matter is the axion from the misalignment mechanism, or the axino/gravitino lightest supersymmetric particle that is populated from the thermal scattering and freeze-in processes. The former case allows the Peccei-Quinn symmetry and grand unification to be of the same origin, whereas the latter case allows a high reheat temperature after inflation, solving the axino/gravitino problems. We will also discuss interesting phenomenology for this class of theories such as dark radiation and displaced vertices at colliders.

Advisor: Hall, Lawrence J
The Role of Signaling Small Molecules in Clostridial ABE Fermentation

The production of ABE (acetone, butanol, ethanol) by members of the anaerobic bacterial genus Clostridium is a bioprocess capable of converting various renewable substrates into high-value solvents and fuels. While ABE fermentation by clostridia has been performed on an industrial scale since the early 20th Century, several significant technical challenges have prevented this process from being economically competitive with the conventional production of solvents and fuels from petroleum. Here, we discuss the role which signaling small molecules (SSMs) play in controlling industrial traits of solvent-producing species of Clostridium. This includes our discovery and characterization of a family of polyketides from the model ABE-producer Clostridium acetobutylicum ATCC 824, which we demonstrate are important in influencing solvent production and controlling morphological differentiation in this organism. Additionally, we describe the development of genetic tools and techniques for genome editing of another industrial solvent-producing species, Clostridium saccharoperbutylacetonicum strain N1-4 (C. s. N1-4). Applying these methods, we present preliminary results which suggest that SSMs may play critical roles in controlling ABE production in C. s. N1-4. Finally, we present our discovery of the first known non-ribosomal peptide isolated from an anaerobic organism. Through this work, we hope to highlight the significant role of secondary metabolites in clostridial fermentations (as well as anaerobes in general), and provide a relatively unexplored strategy for improving this promising renewable bioprocess.

Advisor: Zhang, Wenjun
Serial Dependence in Visual Working Memory: Time Course and Neural Mechanisms

Visual cognition applies temporal smoothing to its inputs, which creates a serial dependence between successive representations at the focus of attention. This is thought to promote perceptual stability. While the benefits of serial dependence have been assumed, evidence that perception itself is altered has been limited. In the first chapter of this dissertation, I vary the delay between stimulus and response in a spatial delayed response task to investigate whether serial dependence occurs at the time of perception or later in working memory. I find that behavioral responses made immediately after viewing a stimulus are on average veridical. Only as memory demands increase is a blending of past and present information apparent in behavior, reaching its maximum with a memory delay of six seconds./nIn the second chapter, I explore potential neural-circuit mechanisms of serial dependence. I consider two possible substrates of the effect: stable persistent activity during the memory delay and dynamic “activity-silent” synaptic plasticity. I find that networks endowed with both strong reverberation to support persistent activity and dynamic synapses can closely reproduce behavioral serial dependence. Specifically, elevated activity drives synaptic augmentation, which biases activity on the upcoming trial, giving rise to a spatiotemporally tuned shift in the population response. My hybrid neural model is a theoretical advance beyond abstract mathematical characterizations of working memory and demonstrates the power of biological insights to provide a quantitative explanation of human behavior./nThe model developed in Chapter 2 proposes that serial dependence is due in part to synaptic augmentation, which is especially prominent in prefrontal cortex. In the third chapter, I investigate whether the bias in behavior depends on activity in three separate nodes of prefrontal cortex (PFC) – the frontal eye fields, the dorsolateral PFC, and the anterior PFC near the frontal pole. I find that transcranial magnetic stimulation (TMS) to these nodes causes reductions in serial dependence consistent with the model’s predictions. In contrast, TMS to posterior sites – either primary somatosensory cortex or posterior parietal cortex – fails to alter the magnitude of the behavioral effect. This general result holds across TMS protocols (online vs. offline) and tasks with different stimulus and response types.

Advisor: D'Esposito, Mark
Prefrontal Mechanisms Underlying Sequential Tasks

For decades, mechanisms of cognitive behaviors have been studied in a simple form of stimulus- and action-outcome associations. Those seminal studies serve as fundamental frameworks and enable us to explore how neural activities in brain represent the increasingly complex and temporarily-extended associations in sequential tasks. The prefrontal cortex (PFC) has long been suspected to play an important role in cognitive control, in the ability to orchestrate thought and action in accordance with internal representation. In particular, PFC “top-down” processes serve as an internal signal to guide high-level cognitive functions, such as working memory (WM), abstract rules, or goal-directed decision-making. Several models have described how task information, including supra- and super-ordinate information, is organized in prefrontal cortex, but it remains unclear precisely how this cognitive information maps onto neurophysiological functions./nTo explore these issues, we devised primate versions of two tasks that tax sequential behavior: a spatial self-ordered search task and a hierarchical reinforcement learning (HRL) task. These tasks examine how sequential behavior interacts with WM and reinforcement learning (RL), respectively. We examined how prefrontal neurons encoded task-related information across these two cognitive tasks. Our results show that prefrontal neurons are capable of adaptively regulating the precision with which information is encoded. In the spatial self-ordered search task, lateral prefrontal neurons have spatiotemporal mnemonic fields, in that their firing rates are modulated both by the spatial location of future selection behaviors and the temporal organization of that behavior. Furthermore, the precision of this tuning can be dynamically modulated by the demands of the task. In the HRL task, prefrontal neurons are involved in integrating the abstract subject values. Especially, we found that the firing rate of a small population of neurons encoded pseudo-reward prediction errors and these neurons were restricted to anterior cingulate cortex. Taken together, our findings suggest that prefrontal neurons encode not only basic information associated with external stimuli, but also high-level information that is used to organize task relevant behaviors.

Advisor: Wallis, Joni
Behavioral and physiological ecology of mosquito disease vectors (Diptera: Culicidae) as a function of aquatic macrophyte invasions

Abstract/nBehavioral and physiological ecology of mosquito disease vectors (Diptera: Culicidae) as a function of aquatic macrophyte invasions/nby/nRakim Kareem Turnipseed/nDoctor of Philosophy in Environmental Science, Policy, and Management/nUniversity of California, Berkeley/nProfessor George K. Roderick, Chair/nTo investigate the impact of invasive aquatic weeds on mosquito populations in the Sacramento-San Joaquin River Delta, field and laboratory experiments were conducted to test the impact of invasive aquatic plants (water hyacinth, water primrose, and Brazilian waterweed) on the behavioral ecology of Culex pipiens, a primary mosquito vector for West Nile Virus (WNV). In an outdoor caged experiment containing larval mosquitoes and predatory Mosquitofish, mosquito survival was significantly higher among high densities of the three plant species than vegetation-free water. In intermediate plant densities, mosquito survival was higher among water hyacinth than both Brazilian waterweed and water primrose. In low plant densities, mosquito survival was higher among water hyacinth than Brazilian waterweed and vegetation-free water. In another caged experiment containing mesocosms, mosquito larval development time was completed more rapidly in the presence of intermediate densities of water hyacinth than all other treatments. In an outdoor caged choice experiment, mosquitoes laid more eggs in mesocosms containing intermediate densities of water hyacinth than all other treatments. Laboratory choice tests and an olfactometer experiment revealed that mosquitoes were more attracted to water that contained plants or plant infusions than water alone. These results suggest that water hyacinth provides both physical and chemical cues to some species of mosquitoes. Effective management of invasive water hyacinth in waterways may thus reduce mosquito populations and reduce human health risk.

Advisor: Roderick, George K