VictorJuiz/thesis huggingface dataset:
Atomistic Simulations of Screw Dislocations in Titanium

This dissertation contains a variety of atomistic calculations concerning screw dislocations in pure or nearly-pure titanium alloys. Many aspects of these dislocations are considered. First, the core structures of -type screw dislocations in pure titanium at zero temperature and no applied stress are calculated. The parameters required to converge calculations of the cores structures are identified. The energy differences between core structures were found to be small, which suggests that at practical temperatures there will be occupation of more than one core structure configuration. Next, the effects of applied stresses with zero resolved shear stress on these dislocations are considered. The results suggest that non-Schmid stresses alter the critical resolved shear stress by inducing changes in the equilibrium core structure. This corroborates earlier conjecture that the non-Schmid slip behavior of screw dislocations in α-titanium alloys is due to non-planar core structure. Chapter 5 describes a new parameter based on elasticity theory for dislocation core identification and classification. This parameter is applied to the study of dislocation core structures in an empirical potential, examining the dependence of the core orientation on temperature and applied non-Schmid stresses. It is found that increasing the temperature leads to a larger variation in the core orientations. It is also found that applied stress on the [11̄00] axis normal to the dislocation line direction leads to a transition from the prismatic core structure to the pyramidal core structure. This transition appears to shift to lower pressure at higher temperature, suggesting that entropy of the core structures is important. It is demonstrated that temperature/non-Schmid stress conditions that permit easier access to the prismatic core orientation lead to higher strain rates for the same applied shear stress. In Chapter 6 I introduce a novel interstitial shuffling mechanism to explain how dilute concentrations of interstitial impurities can promote increased planarity of dislocation slip. This invites design of titanium alloys with increased tolerance to variations in interstitial impurity content. Finally, in Chapter 7 nucleation of the β to α phase transition in pure titanium is examined through a combination of elasticity theory and molecular dynamics simulation. Screw dislocations in the β phase act as heterogeneous nucleation sites and increase the α phase growth rate, but also restrict the orientation of the α nuclei to certain directions along which the strain field of the dislocation aligns with the strain required to complete the Burgers transformation path.

Advisor: Chrzan, Daryl C
Asta, Mark D
Physiology and Biotechnological Applications of Microbial (Per)chlorate Reduction

Respiration is a set of metabolic reactions and processes that release chemical energy to fuel cellular activity. While humans can only breathe oxygen, microorganisms are able to respire other terminal electron acceptors such as chlorate and perchlorate [collectively (per)chlorate]. My graduate thesis aims to elucidate the molecular mechanisms and physiology of (per)chlorate respiration in the model (per)chlorate reducing bacteria, Azospira suillum PS; and to transform our fundamental knowledge of perchlorate reduction into applied technologies to solve practical industrial problems./nThe first chapter of this dissertation is a published review article. This chapter represents an overview of my thesis and summarizes the potential biotechnological applications of (per)chlorate reduction, including enzymatic perchlorate detection; enhanced xenobiotic bioremediation; oil reservoir biosouring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and biogenic oxygen production for planetary exploration./nThe second chapter of this dissertation is a published research article. This chapter aims to identify the redundancy between perchlorate and nitrate reduction pathways. Our results demonstrate two genes (pcrQ and pcrO) that encode electron transfer cytochromes are essential for perchlorate respiration; but completely redundant and fully replaceable with their respective homologous genes napC and napO in the denitrification pathway. While (per)chlorate reducers are known to preferentially reduce nitrate in the presence of both nitrate and perchlorate, by rewiring the terminal electron transport pathways in PS we were able to engineer strains that preferentially reduce perchlorate or concurrently reduce both nitrate and perchlorate./nThe third chapter of this dissertation is a transcriptomic analysis of PS under different growth conditions. These data establish the expression profiles of proteins involved in the nitrate, chlorate, perchlorate, and aerobic respiration pathways. This information also serves as a hypothesis-generating foundation for future investigations in microbial (per)chlorate reduction./nThe fourth chapter of this dissertation describes a biocide/biocide-resistant system for bacteriophage and microbial contamination prevention and treatment during biomanufacturing. This technology is based on the biocide chlorite(ClO2-), a toxic intermediate generated during perchlorate respiration, and the corresponding detoxifying enzyme, chlorite dismutase (Cld)./nThe fifth chapter of this dissertation discusses the implications of this research for future investigations regarding the biology and the biotechnology of microbial (per)chlorate reduction./nThe sixth chapter is the conclusion of this dissertation.

Advisor: Coates, John D
Method of Local Corrections Solver for Manycore Architectures

Microprocessor designs are now changing to reflect the ending of Dennard Scaling. This leads to a reconsideration of design tradeoffs for designing discretization methods for PDEs based on simplified performance models like Roofline./nIn this work we carry out an end-to-end analysis and implementation study on a Cray XC40 with Intel⃝R XeonTM E5-2698 v3 processors for the Method of Local Corrections (MLC). MLC is a non-iterative method for solving Poisson’s Equation on locally rectangular meshes. The Roofline model predicts that MLC should have faster time to solution than traditional iterative methods such as Geometric Multigrid. We find that Roofline is a useful guide for performance engineering and obtain perfor- mance within a factor of 3 the Roofline performance upper bound. We determine that the algorithm is limited by identified architectural features that are not captured in the Roofline model, are quantifiable, and can be addressed in future implementations.

Advisor: Colella, Phil
Four Statistical Explorations of Genetic Variation

Genetic variation is the result of DNA sequence differences between individuals or populations. Our understanding of genetic variation has benefited greatly from advances in DNA sequencing, computational power, and statistical tools. I will present four statistical analyses of genetic variation related to genetic mapping, genome editing, evolutionary biology, and de novo genome assembly and annotation. First, I will present a novel methodology for genotype imputation and composite genetic marker construction. This technique, minimum spanning tree imputation, is designed to improve linkage maps in outbred F1 crosses, particularly from genetic markers derived from low confidence sequencing. I then use minimum spanning tree imputation to construct sex-specific genetic maps for Xenopus laevis, Branchiostoma floridae, and Miscanthus sinensis. Second, I will present a case of three mouse lines edited with the CRISPR/Cas9 system in order to delete an enhancer locus in the IL2RA gene. All three lines were confirmed to have the intended deletion. Curiously, one line displayed a severe immune deficient phenotype that persistently bred true. By resequencing mice from these lines, I was able to identify the occurrence of a tandem duplication as an off-target consequence of the editing in the immune compromised individuals that was absent in the other lines. The tandem duplication was then confirmed experimentally. I close by proposing a repair mechanism mediated by microhomology that might have caused the tandem duplication to form. Third, I will compare the chromosomal position of orthologous genes between lancelet amphioxus, Branchiostoma floridae (an early-branching living chordate) and five vertebrates. These comparisons will offer support for the “2R hypothesis,” that early vertebrate organisms underwent two rounds of whole genome duplication. This analysis takes advantage of a novel way of computing and visualizing mutual best hits between previously identified chordate linkage groups (CLGs) and segments of vertebrate chromosomes. Finally, I will present my contributions to the assembly and annotation of the genome of a regenerative model organism, Hofstenia miamia.

Advisor: Rokhsar, Daniel
Wemmer, David
Inhibitory pathways in the neocortical microcircuit

Understanding how the canonical circuit implements computations requires that we characterize the components of the circuit and determine how they interact. Cortical components are often equated to the various classes of excitatory and inhibitory neuronal cell-types that occupy the six cortical layers. Excitatory cortical neurons are known to exhibit stereotyped, cell-type specific patterns of connectivity; these excitatory synaptic pathways are a central feature of cortical organization. It has been less clear whether inhibitory neurons are organized according to a similar logic. In this thesis I describe my efforts to map the inhibitory pathways of the neocortex, using the mouse primary somatosensory barrel cortex as a model./nIn Chapter 1, I will give an introduction to theories of cortical function and general overview of the organization of cortical circuits. I will also provide a focused review of the inhibitory circuitry in layer 5 of the cortex. This chapter is presented, in part, in the form of reproductions of material from two reviews (one published and one in preparation) that I co-authored with my advisor. In Chapter 2, I describe the discovery of a novel disynaptic inhibitory pathway between layer 4 and layer 5 of the somatosensory cortex, and present evidence that this pathway contributes to selective sensory representations in layer 5. This work is presented as a published manuscript, which I co-authored with Dr. Scott Pluta. In Chapter 3, I describe a series of experiments probing the organization of two subnetworks of dendrite-targeting interneurons. These subnetworks exhibit complementary patterns of connectivity which enable them to differentially modulate the dynamics of cortical activity in a layer-specific manner. This work is presented as a first author manuscript (currently in review). Finally, in Chapter 4 I offer closing thoughts and directions for future work.

Advisor: Adesnik, Hillel A
Expansions of Executive Authority: Government Leaders’ Near-Term Pressures and Long-Term Fates

In many developing countries, even those that now have democratically elected governments, there remain widespread concerns about strong leaders exercising unchecked power and imposing important decisions through executive orders or decrees. Concentrated executive authority seems most popular during times of crisis or political gridlock, but can backfire in the long run. Many developing democracies have also had presidents removed early and/or prosecuted for abuses of power. Yet it remains unclear whether these forms of accountability actually work, when prosecutions are often politicized and may drive incumbents to cling to power to protect themselves./nIn this dissertation, I study how the fates of former Latin American presidents influence successors’ efforts to consolidate power, through their use of executive decrees. I use computational methods to parse decrees and identify those that not only enact external policies, but that make changes to internal government institutions. I also introduce measures of the consistency or predictability of former leaders’ punishments and rewards, and test whether that predictability influences subsequent leaders’ decisions about how to use their own power while in office. This dissertation contributes to our understanding of how strong political leaders make important decisions – even restructuring powerful components of the governing apparatus – and what signals about their future punishment or reward encourage them to seek more power for themselves or to exercise restraint.

Advisor: Anzia, Sarah
Towards a More Stable Network Infrastructure

There have been many recent proposals to change the network infrastructure in order to meet different performance objectives. These changes are often difficult to deploy, either requiring specialized network switching hardware or greatly complicating network management. Rather than continuing to add new features to the network in an adhoc manner, we advocate a more principled approach for meeting different performance objectives, that leads to a more stable network infrastructure. This approach is based on the following two questions:/n(1) Can we avoid making changes to the network infrastructure by finding solutions that only change the end-points? Here, we focus on congestion control for both wide-area and datacenter networks, showing how the end-points can be updated to achieve near-optimal performance using commodity switches, and on redesigning RDMA NICs to eliminate their reliance on the in-network mechanism for loss avoidance./n(2) When infrastructure changes are needed, can we make them universal in nature? Here, we focus on packet scheduling, examining whether we can have a universal packet scheduling algorithm that can mimic all others. We show, both theoretically and practically, that we can have an almost-universal packet scheduling algorithm that can closely mimic other scheduling algorithms and can achieve a variety of network-wide performance objectives.

Advisor: Shenker, Scott
Ratnasamy, Sylvia
War and Peace in the Political Thought of Francis Bacon

This dissertation examines war and peace in the political thought of Francis Bacon, moving from internal warfare (civil war) outward via wars of expansion, attrition, and empire to Bacon’s conception of peace. The first chapter considers Bacon’s views of the causes of civil war and strife within the body politic in relation to the contemporary and near-contemporary views held by Machiavelli, Montaigne, Bodin, and Edward Forset, concluding that for Bacon civil wars are caused by poverty and discontentment, both of which are themselves caused by excess population. Excess population may, in Bacon’s assessment, best be reduced by being spread outward in wars for colonies, expansion, and empire and by wars of attrition in which a state engages in wars of aggression for the purposes of killing its own population. The second chapter of the dissertation examines Bacon’s views of empire based upon the title of conquest and Bacon’s preference for the government of colonies under martial law. Wars for colonies, expansion, and empire, do not, in Bacon’s assessment, justify themselves, but had to be legitimized in terms of the justifications of war that then predominated. Chapters three and four of the dissertation thus examine Bacon’s deployments of and innovations within the just war tradition and within the tradition of justifying war on religious grounds. Here, Bacon’s views are contrasted with those of his contemporaries Justus Lipsius and Alberico Gentili. The final chapter of the dissertation examines Bacon’s views of peace and his understanding of true peace as the incapacity of rival states and opponents to do harm. The chapter argues that this view of peace is in concord with Bacon’s views of empire and amounts to an understanding of peace as hegemony. The final chapter further examines Bacon’s distaste for the 1604 Treaty of London and offers a reading of Bacon’s classic fable, The New Atlantis, in light of Bacon’s views on peace. The dissertation concludes with a summation of its findings alongside a consideration of avenues for future research.

Advisor: Hoekstra, Kinch SJ
Design and Application of Photoinduced-Electron Transfer-Based Voltage-Sensitive Dyes to Biological Imaging

Voltage-sensitive dyes have provided recent promise for affording new methods to interrogate the electrical activity of biological circuits. In particular, small-molecule based approaches have proven useful for designing sensitive molecules that can observe neuronal activity in a noninvasive, highly-parallel manner. However, currently-available voltage-sensitive dyes are marred by low sensitivity, brightness, and/or poor solubility. In order to overcome these challenges, we designed and synthesized voltage-sensitive dyes based on a new family of photoinduced-electron transfer-based voltage sensors, or VoltageFluors. Using the VoltageFluor scaffold, we designed two new families of rhodol- and rhodamine-based voltage-sensitive dyes optimized for two-photon voltage imaging in thick biological tissues, such as brain slices and intact brains. Using these dyes, we characterized the neuronal phenotype associated with the epileptic disorder tuberous sclerosis and monitored spiking activity in awake, behaving mice. We then developed a synergistic computational and experimental approach to guide the rational design of new VoltageFluor dyes. Through this approach, we design and test the most voltage-sensitive VoltageFluor dye to date and also the brightest, highest signal-to-noise fluorescein-based VoltageFluor dye. This work lays the foundation for the diverse array of biological applications of VoltageFluor dyes and develops the guiding principles for future dye design.

Advisor: Miller, Evan W
Morphogenesis and Specification of the Muscle Lineage During Xenopus laevis Embryo Development

Development consists of complex morphogenetic movements that shape individual tissues as well as the embryo. Tissues must interact both physically and through signaling molecules to coordinate the formation of various organs and the entire body plan. My thesis work sought to characterize tissue interactions that govern muscle formation during vertebrate embryo development using the African clawed frog Xenopus laevis as a model system./nChapter 1 of this dissertation provides a general introduction to the morphogenetic events and molecular regulation leading to muscle formation. Chapter 2 presents two previously-undiscovered morphogenetic phenomena involving the muscle tissue as well as individual muscle fibers. My experiments confirmed the function and mechanisms of muscle tissue unfolding as well as the cell rearrangements that ultimately place muscle fibers into organized arrays for proper functioning. Chapter 3 summarizes my work to further analyze a previously-unreported reciprocal relationship between the neural tissue and the prospective muscle tissue. My work shows that the neural plate influences the size of the underlying muscle. Enlarging the neural plate results in a corresponding increase in the size of the muscle tissue. Here, I dissect the source and fate of ectopic muscle tissue and determine the effect of tissue size on muscle morphogenesis. As a whole, this work summarizes my research to characterize the molecular and morphological events necessary for proper muscle formation during embryo development.

Advisor: Harland, Richard
Design and Evaluation of a Shoulder Supporting Exoskeleton for Occupational Use

Overexertion is a common cause of work related musculoskeletal disorder (WMSD) in the modern industry. The shoulder is one of the most susceptible joints to injury and requires the longest amount of recovery time to heal, currently accounting for about one fifth of the total cost associated with WMSD’s. Exoskeleton technology has the potential to provide beneficial augmentation to workers in many industrial fields. A strategic application of support reduces the forces exerted by the operator, potentially decreasing risk of injury and increasing productivity though the added capability. Their mobility allows for application in environments where a static aid is not feasible due to constantly changing surroundings, such as in construction or shipbuilding, or due to high costs of modifying an established manufacturing line for ergonomic benefit. As the field of shoulder supporting exoskeletons begins to emerge, little is known about the effects these devices have on operator’s effort and productivity./nThis work introduces a novel design for a shoulder supporting exoskeleton as well as a preliminary evaluation of the device’s effects during common workplace tasks. The exoskeleton builds off of the success of a trunk and a leg supporting exoskeleton developed at the UC Berkeley Human Engineering and Robotics Laboratory. A passive actuation strategy is presented to augment the torques about the shoulder due to the gravitational forces on the arm and a handheld tool for a variety of workplace tasks and individual preference. A modified iso-elastic base profile divides support into a working and non-working range of motion and can be modified in its amplitude, on/off state, and gravitational offset. A biomimetic frame design provides the support and motion necessary to apply the supporting torques across the shoulder joint for a majority of worker dimensions. Couplings at the arm, shoulders, and hip comfortably secure the frame to the body in a familiar manner that is easy to use while glenohumeral, scapulothoracic, and spinal degrees of freedom allow for relatively unrestricted mobility. A modular approach to combining the shoulder supporting exoskeleton to neck, trunk, and leg assisting devices is discussed to accommodate tasks with risk of injury to multiple joints. A combination of two, three, and four devices is presented for commonly occurring tasks, comprising what is probably the most sophisticated workplace exoskeletons that has been designed to date. A controlled study has been conducted to assess the shoulder supporting exoskeleton’s effects on effort and usability for a common set of workplace tasks and tools. Results show a substantial and desirable decrease in muscle activation for all conditions.

Advisor: Kazerooni, Homayoon