VictorJuiz/thesis huggingface dataset:
van der Waals Corrected Density Functional Theory Calculations on Zeolitic Imidazolate Frameworks

The van der Waals force is ubiquitous in nature, however, first principles calculations of this interaction for large systems, i.e., around 1000 atoms, have been performed only recently. In the following are presented results on the application of the van der Waals density functional (vdW-DF) to gas adsorption and transport in zeolitic imidazolate frameworks (ZIFs)./nCarbon dioxide and methane binding energies and positions are calculated with the vdW-DF in three distinct binding sites in a series of five rho topology ZIFs. The isostructural set of ZIFs was selected in order to isolate the effect of framework functionalization. Gas molecules are found to bind in locations with high coordination to framework atoms at distances of around 3 A. Contributions to the binding energy from induced polarization and dispersion are quantified in order to elucidate the origins of strong CO2 adsorption and selectivity over CH4. The dispersion energy is found to dominate the interactions, however, CO2 adsorption is also enhanced by electrostatic interactions with asymmetrically functionalized linkers. Steric constraints for methane molecules, that do not impede carbon dioxide binding, further contribute to selectivity./nBinding energy landscapes for CO2 and CH4 are calculated using classical force fields for the same set of rho ZIFs and several other ZIFs that differ in functionalization and topology. Quantities extracted from these landscapes are used to explain the effect of framework topology on gas adsorption at low and high pressure as well as how the positions of adsorbed gas molecules evolve as a function of pressure. Materials with large surface areas have greater gas uptake at high pressure, while smaller pores, which are associated with stronger binding, adsorb more gas at low pressure./nFinally, the effect of framework flexibility on CO2 transport through the double 8-ring channel of ZIF-97 is investigated with computationally intensive climbing-nudged elastic band calculations utilizing two versions of the vdW-DF. The results are largely consistent between the two versions and show a small decrease (12-33 meV) in the transport barrier with flexibility./nIn addition, several versions of the vdW-DF are applied to the Kr dimer, graphite, and H2, Al, and Li on graphene. For these systems experimental binding energies and separations are available, such that they provide useful benchmarks for the accuracy of the vdW-DF type methods. The vdW-DF2 and vdW-optB88 methods are found to both produce accurate results for dispersion dominated binding. Analyses of mixed ionic-dispersion binding highlight the importance of further study of these functionals at short-range.

Advisor: Asta, Mark
Louie, Steven G.
Using FPGAs to Simulate Novel Datacenter Network Architectures At Scale

The tremendous success of Internet services has led to the rapid growth of Warehouse-Scale/nComputers (WSCs). The networking infrastructure has become one of the most vital components/nin a datacenter. With the rapid evolving set of workloads and software, evaluating/nnetwork designs really requires simulating a computer system with three key features: scale,/nperformance, and accuracy. To avoid the high capital cost of hardware prototyping, many/ndesigns have only been evaluated with a very small testbed built with off-the-shelf devices,/noften running unrealistic microbenchmarks or traces collected from an old cluster. Many/nevaluations assume the workload is static and that computations are only loosely coupled/nwith the very adaptive networking stack. We argue the research community is facing a/nhardware-software co-evaluation crisis./nIn this dissertation, we propose a novel cost-efficient evaluation methodology, called/nDatacenter-in-a-Box at Low cost (DIABLO), which uses Field-Programmable Gate Arrays/n(FPGAs) and treats datacenters as whole computers with tightly integrated hardware and/nsoftware. Instead of prototyping everything in FPGAs, we build realistic reconfigurable abstracted/nperformance models at scales of O(10,000) servers. Our server model runs the full/nLinux operating system and open-source datacenter software stack, including production/nsoftware such as memcached. It achieves two orders of magnitude simulation speedup over/nsoftware-based simulators. This speedup enables us to run the full datacenter software stack/nfor O(100) seconds of simulated time. We have built a DIABLO prototype of a 2,000-node/nsimulated cluster with runtime-configurable 10 Gbps interconnect using 6 multi-FPGA BEE3/nboards.

Advisor: Patterson, David A
Asanovic, Krste
A Mechanism for Behavioral Cross-Inhibition in Drosophila

How animals generate stable, appropriate decisions in a noisy sensory environment is a fundamental question in neuroscience. Animals must correctly appraise the sensory world, taking into account their internal state and previous experiences. Feeding behavior in the fruit fly, Drosophila melanogaster, is an ideal model system to investigate the neural basis of decision-making. While feeding initiation in Drosophila is mostly described as the simple product of the palatability of a given substance, this behavioral decision is actually quite complex and is influenced by sensory stimuli, internal states, prior encounters, and other factors./nAs with other animals, feeding behavior in the fruit fly is likely influenced by the commitment to other behaviors, as the engagement in one behavior typically suppresses the initiation of others. The first part of this thesis describes the interaction between two mutually exclusive behaviors in the fly, feeding and locomotion. This study characterizes a single pair of interneurons in the nerve cord of the fly that mediates the suppression of feeding initiation by locomotion. These neurons are activated by mechanosensory input from the legs of the fly and suppress feeding initiation through the inhibition of the proboscis extension response. This work shows that these behaviors are indeed mutually exclusive and identifies a single pair of neurons that mediates part of this interaction./nThe second part of this thesis attempts to place these proboscis extension-inhibiting neurons in the larger context of the feeding circuit. Anatomical, functional, and behavioral experiments identify potential synaptic partners with these neurons as well as other, as of yet unidentified, neurons that modulate feeding initiation in the fly. This work identifies candidate neurons that influence feeding decisions in Drosophila, and provides a starting point for the characterization of neurons in the Drosophila feeding circuit.

Advisor: Scott, Kristin
Instruction sets for walks and the quantile path transformation

This thesis examines two objects: the stacked-instructions representation of a walk on a general state space, and the novel quantile path transformation for real-valued walks./nInstead of representing a walk by a chronological sequence of states visited, we may represent the walk by a collection of lists of instructions located at each state. On successive visits to a state, the walker reads and follows successive instructions from the list. However, there are some collections of finite lists for which there is no walk that follows all listed instructions; given such instructions, a walker would eventually arrive at some state at which it had already exhausted all instructions, and become stuck, prior to having read all instructions at other states. This thesis characterizes the instruction sets that can be exhausted by the walker before they become stuck./nThe quantile transform is a novel path transformation on real-valued walks and Brownian motions of finite duration. This transformation relates to identities in fluctuation theory due to Wendel, Port, Dassios and others, and to discrete and Brownian versions of Tanaka's formula. For an n-step random walk, the quantile transform reorders increments according to the value of the walk at the start of each increment. We describe the distribution of the quantile transform of a simple random walk of n steps, using a bijection to characterize the number of pre-images of each possible transformed path. We deduce, both for simple random walks and for Brownian motion, that the quantile transform has the same distribution as Vervaat's transform. For Brownian motion, the quantile transforms of the embedded simple random walks converge to a time change of the local time profile. We characterize the distribution of the local time profile, giving rise to an identity that generalizes Jeulin's description of the local time profile of a Brownian bridge or excursion.

Advisor: Pitman, Jim
Organizing International Society: The French Peace Movement and the Origins of Reformist Internationalism, 1821-1853

This dissertation seeks to contribute to the history of internationalism through an examination of the early nineteenth century French peace movement. It argues that the French movement contributed to the international peace movement both in theory and practice, by drawing on the intellectual heritage of the Enlightenment to make peace the subject of organized activism./nThe early nineteenth century international peace movement is seen as the work of Dissenting sects in Britain and America, with the assistance of Free Traders like Richard Cobden. The French peace advocates' ideological roots, in contrast, can be found in the Enlightenment - in the peace thinking of the philosophes, but also in debates on economy, culture, religion, politics, etc. They drew upon the work of particular authors like Jean-Baptiste Say, Adam Smith and Immanuel Kant, but above all continued general Enlightenment notions like historical progress and human perfectability. This intellectual heritage helped French peace advocates to imagine a distinct model of international cooperation, one in which political, cultural and economic borders remained in flux. It also gave them the tools to denounce colonialism - all while attempting to maintain forms of soft power for French `civilization'./nFrench peace advocates were more restricted than American and British pacifists in their forms of activism, but they also published a wide range of materials on peace, developed arguments for peace within associations, and participated in and promoted the international congresses. Through these practices, French peace advocates contributed to the development of civil society, nationally and internationally. A study of their movement shows how and why this transition from philosophy to organized action became possible./nOften dismissed as utopian, the history of the early peace movement can help us to better understand the development of French, European and international history. Like many groups in the early nineteenth century, French peace advocates were deeply optimistic about their program and their potential agency. However, this seemingly utopian program continues to have considerable resonance today, in contemporary international institutions as well as in ongoing debates about democracy and political change.

Advisor: Hesse, Carla A
Controller Synthesis and Vibration Suppression Techniques for Industrial Robotic Manipulators with Joint Flexibilities

This dissertation focuses on the design of feedback and feedforward controllers for direct application to industrial manipulators. In this dissertation, an iterative online controller tuning algorithm based on nonlinear programming concepts and extremum seeking control is introduced and applied to a 6 degree of freedom FANUC M16$i$B industrial robot. Details regarding stepsize selection and gradient estimation for the proposed controller tuning is also discussed. Experimental results show that the proposed controller tuning method is able to improve robot performance by successively reducing a cost function. Additionally, a controller tuning framework based off the disturbance observer is also introduced for stable controller tuning. The framework is shown to be robustly stable under most practical tuning applications. The assumptions and constraints of the proposed framework is also detailed. The framework is experimentally verified by sweeping through a variety of controller gains that satisfy the framework conditions. Finally, an input shaping technique for application to industrial robots with elastic joints is also proposed in this dissertation. The approach is simple to apply and can be easily integrated to existing trajectory generation techniques for industrial robots. Experimental results show substantial joint vibration suppression during transient motions.

Advisor: Tomizuka, Masayoshi
Investigating Gas Migration in Enzymes: Dioxygen Channels inside of Soybean Lipoxygenase 1

Enzymes are complex systems that contain a variety of pockets, clefts, and channels throughout the protein matrix. These gaps and tunnels represent potential transport pathways for gases, ions, and other small molecules, and can play a critical role in tuning enzyme function. In this work, the functional role of gas migration pathways was examined in soybean lipoxygenase 1 (SLO-1), a prototypical lipoxygenase that catalyzes the regio- and stereospecific peroxidation of linoleic acid to 13S hydroperoxyoctadecadienoic acid (13S HPOD). Two computational techniques--implicit ligand sampling and CAVER--were employed to evaluate pathways for oxygen migration in the enzyme. Both approaches converged on a single channel deemed most competent for oxygen delivery. Interestingly, this channel is consistent with a cavity originally detected in the crystal structure of SLO-1 and previously proposed as a pathway for oxygen. Site-directed mutagenesis was used to assess the impact of introducing bulk at the channel's bottleneck residues. Introducing tryptophan into the pathway at positions 553 and 496 resulted in increased Michaelis constants for oxygen and disrupted reaction regio- and stereospecificity, supporting a functional role for the tunnel in oxygen trafficking. Intriguingly, mutations at Ile553 and Leu496 appear to influence oxygen migration in distinct ways. Introducing tryptophan at 553 dramatically reduces O2 access to the active site, as evidenced by a markedly increased KM(O2)--744 uM O2 compared to 38 uM O2 for wild-type--together with an increase in the proportion of 13R, 9S, and 9R HPOD isomers generated. Introducing bulk at 496, by contrast, appears to ungate an alternate pathway for O2 access, as evidenced by an increased proportion of 9S and 9R HPOD isomers generated. The divergent behavior of the Ile553Trp and Leu496Trp mutants provides striking evidence for the plasticity of oxygen pathways, which can be manipulated via single site mutations. Taken together, our computational and mutagenesis studies point to a single delivery channel that shuttles oxygen to the active site of SLO-1 and tunes the regio- and stereospecificity of oxygen insertion into linoleic acid. Our results speak to the vital role that the protein matrix plays in regulating catalysis and lay the framework for future protein engineering efforts in oxygen-dependent enzymes.

Advisor: Klinman, Judith P
The Vietnamese Bauxite Mining Controversy: the Emergence of a New Oppositional Politics

In the first half of 2009, a highly controversial public debate emerged in Vietnam over government plans to mine bauxite in the remote upland regions of the Central Highlands. Many and diverse persons and organizations spoke out vociferously against these plans. They included, among others, government scientists, artist–intellectuals, domestic reporters, activist bloggers, religious leaders, overseas Vietnamese, and retired high level state officials, including no less than the iconic military leader of the anti-colonial revolution and “wars of independence”, General Võ Nguyên Giáp. Their means for engaging state authorities on bauxite mining were also many and diverse. They included organizing workshops and seminars, publishing articles in the domestic press, writing open letters and petitions, posting information and commentaries online, and, in a few exceptional cases, demonstrating publicly, distributing “no bauxite” T–shirts, and filing a lawsuit against the Prime Minister. The critiques raised against bauxite mining were also wide–ranging. While early discussions emphasized a wide range of social and environmental impacts of bauxite mining, these discussions quickly became embroiled with such divisive issues as national security, Sino–Viet relations and, not least of all, the relations of the communist party to the Vietnamese people./nThis widespread opposition to bauxite mining generated one of the most significant domestic confrontations with the party–state since at least the Vietnam War. This dissertation provides a detailed ethnographic examination into this controversy and the different groups, people and processes that made it happen. It argues that the bauxite mining controversy signaled the emergence of strong “political cultures of opposition” in contemporary Vietnam. Political cultures of opposition are significant for their capacity to bring many and diverse groups and processes together and translate their diverse grievances into a common opposition to the ruling regime. As such, they can also signal a potentially pivotal moment in processes of broad socio–political transformation. The research for this dissertation is based on two years of ethnographic fieldwork, while I was living in Hanoi, Vietnam, from 2009 to 2011. It comprised in–depth and semi–structured interviews with sixty different informants, whom I interviewed on nearly one hundred distinct occasions; the collection of hundreds of different types of texts that were generated from the bauxite mining controversy; and participant observation in various settings.

Advisor: Romm, Jeff
Peluso, Nancy
German Missionaries, Chinese Christians, and the Globalization of Christianity, 1860-1950

This dissertation makes two broad claims about the enduing imprint of the European missionary enterprise on the modern world. The first is self-evident: European missionaries made Christianity a global religion. By pushing and spreading Christianity beyond the boundaries of Europe into every single corner of the globe, missionaries laid the foundation for the transformation of Christianity from a predominantly European religion in the nineteenth century to one that is largely non-European in the twenty-first century. Drawing on previously unopened and unused archives in Germany, Italy, Taiwan, and China, I argue that globalization and indigenization were two sides of the same coin: from the stand-point of German missionaries, their religion became more global, while for Chinese Christians, this already global religion became particularly "Chinese."/nThe second argument flows from the first: European missionaries helped to usher in a new secular age; they laid the seeds for the Christianity's own secularization. Through their encounters with the world, I argue, the European missionary enterprise self-secularized. The missionary experience in China pushed German missionaries and theologians to re-think, and in some cases, renounce, the religious convictions that they once held. As a result of this re-thinking, they devolved and gave up the religious control and authority that they once wielded./nFinally, my dissertation revises the view of the German missionary enterprise in China as a "debacle," which has long dominated the historical narrative of Christianity in China. I uncover the history of their work, and locate some its successes, showing how the German model laid the foundation for much of the current religious revival in China. The German Protestant and Catholic models of missionary work, considered "conservative" in their stress on individual conversion and evasion of politics, proved remarkably sturdy in the face of a hostile regime, providing the model that drives Christian conversion in China today.

Advisor: Anderson, Margaret L
Economics and Computation: Ad Auctions and Other Stories

There is a growing research tradition in the interface between Economics and Computer Science: Economic insights and questions about incentives inform the design of systems, while concepts from the theory of computation help illuminate classical Economics problems. This dissertation presents results in both directions of the intellectual exchange./nOriginally designed by industry engineers, the sponsored search auction has raised many interesting questions and spurred much research in auction design. For example, early auctions were based on a first-price payment model and proved to be highly unstable --- this dissertation explores how improvements in the bidding language could restore stability. We also show that a first-price auction offers substantially better performance guarantees when a single advertiser may benefit from multiple ads. Another interesting problem arises because sponsored search auctions must operate with limited information about a user's behavior --- we show how sampling can maintain incentive compatibility even when the auctioneer incorrectly predicts the user's behavior./nComputational tools also offer novel ways to understand the limits of complex economic systems. For example, a fundamental observation in this intellectual exchange is that people cannot be expected to solve computationally intractable problems. We show that this insight engenders a new form of stability we call complexity equilibria: when production has economies of scale, markets may be stable because finding a good deviation is computationally intractable. We also use techniques from communication complexity to show that equilibrium prices, even when they exist, may need to encode an impractical amount of information to guarantee that a market clears.

Advisor: Papadimitriou, Christos H
The Value of Green in Transportation Decisions

To address issues of climate change, information about greenhouse gas emissions is more and more often being presented to people. For example, labels and signs displaying pounds and kilograms of CO2 are showing up in trip planners, in car advertisements, and even in restaurant menus. This is being done under the assumption that the information about the environmental impacts of different alternatives will encourage more sustainable behavior. However, little is known about whether or not this strategy affects the choices people make. In order for people to change their behavior for the benefit of reduced emissions, they first need to place positive value on those reductions. This research aims to answer three questions regarding the efficacy of presenting people with this information: first, do people place significant value on reducing their greenhouse gas emissions, second, can people consistently value a pound of CO2, and third, how does this value of green vary across the population? To answer these questions, five experiments were designed and conducted using discrete choice experiments, a framework typically used to investigate how people value reducing their travel time. UC Berkeley students and residents of the San Francisco Bay Area made stated and revealed preference transportation choices from a set of alternatives. With knowledge of the attributes of their chosen alternative as well as those of their available alternates, their choices were analyzed using logit, mixed logit, and hybrid choice models. The findings include that not only can people consistently interpret and place value on the pounds of CO2 associated with their transportation alternatives, but also that there exists a discrete distribution in the value of green. For all except one experiment, the best models indicate that while a majority of the population does not act as though they care about reducing their greenhouse gas emissions, there is a small group with a willingness to pay of $2.68 per pound of CO2.

Advisor: Walker, Joan L