VictorJuiz/thesis huggingface dataset:
Ultra-Low Latency NIC-CPU Interface Design and Realization

This thesis builds off an ultra-low latency network interface device, known as the Lightning NIC (or L-NIC) [7], that opts to bypass the entire processor memory system and cache hierarchy in favor of delivering network data directly into the processor's register file. L-NIC is itself inspired by the J-machine [4], an earlier experimental parallel computer that investigated register-based, rather than memory-based, interactions with data. We expect a particular class of self-contained, granular, cache-resident, sub-microsecond applications, known as nanoservices, to enjoy a substantial performance benefit from the lower latency this approach provides. In turn, nanoservices, by allowing for much finer-grained parallelism than has been previously possible, can be used to significantly accelerate many existing distributed applications.
In "The nanoPU: From Microservices to Nanoservices" [6], our group presents a modified RISC-V processor, known as a nanoPU, that supports this L-NIC approach to network data and is optimized for running nanoservices. We also present a set of candidate nanoservice applications, demonstrate an order of magnitude performance improvement over a baseline NIC, and discuss how other distributed applications with a high degree of parallelism might stand to benefit from a nanoservice-focused refactor and a network of nanoPUs.
Here, I expand upon several complete components of this larger effort, focusing specifically on the design and development of the nanoPU's hardware-software interface — that is, on the particular instructions and registers relevant to the integration of the L-NIC into the processor. This is itself a novel undertaking. The challenge, at its core, is to design a system that supports easily usable software interfaces in an environment where each individual instruction constitutes a noticeable latency increase and a single DRAM access in an executing nanoservice introduces an unacceptably high delay.

Keywords:  Department of Electrical Engineering
electrical engineering
networking
computer architecture
low latency
NIC
RISC-V
Thesis
Advisor: McKeown Nick
Hennessy John
Ultraviolet light-induced genome instabilities

Exposure to the ultraviolet (UV) radiation in sunlight creates DNA lesions, which if left unrepaired can induce mutations and contribute to skin cancer. The two most common UV-induced DNA lesions are the cis-syn cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4PP), both of which can initiate mutations. Interestingly, mutation frequency across the genomes of many cancers is heterogenous with significant increases in heterochromatin. Corresponding increases in UV lesion susceptibility and decreases in repair are observed in heterochromatin versus euchromatin. However, the individual contributions of CPDs and 6-4PPs has not been systematically examined in specific genomic and epigenomic regions. In this study, we generated a genome-wide map of 6-4PP lesion abundance in primary cells and conducted a comprehensive analysis to determine the genetic and epigenetic features associated with 6-4PP susceptibility. We found high degree of similarity between 6-4PP and CPD formation, with enrichment of both in heterochromatin regions. However, when examining the relative levels of the two UV lesions, we found that bivalent and Polycomb repressed chromatin states were uniquely more susceptible to 6-4PPs. Interestingly, when comparing UV susceptibility and repair with melanoma mutation frequency in these regions, disparate patterns were observed in that susceptibility was not always inversely associated with repair and mutation frequency. Functional enrichment analysis hint at mechanisms of negative selection for these regions that are essential for cell viability and immune function and induce cell death when mutated. Ultimately, these results reveal both the similarities and differences between UV-induced lesions that contribute to skin carcinogenesis

Keywords: Biology.
Advisor: Morrison Ashby J.
Dixon Scott James
Gozani Or Pinchas
Sage Julien
The uncensored man : Leonid Tsypkin, Russian writer and Soviet jew (1926-1982)

This dissertation introduces the reader to the uncensored Russian writer Leonid Tsypkin (1926-1982) and his unique mode of creation. A doctor by profession, Tsypkin was too afraid of the possible ramifications on his career to publish and instead "wrote for the drawer." It was not until he was denied an exit visa and became a "refusenik, " that he decided to finally seek publication in earnest. Tsypkin carried with him a consciousness of his marginal position in Russian literature, as well as the peripheral position of Jews in Russian culture and in contemporary Soviet society. I argue that not only do his texts' orientation toward the drawer endow them with a unique orientation toward history, but the lack of an obvious interlocutor contributes to what I have termed Tsypkin's act of "co-creation." Through a series of encounters with material objects, photographs, or literary texts, Tsypkin is able to forge his texts in dialogue with other voices and perspectives, thus gaining a new understanding of himself at the same time. The four chapters of this dissertation move chronologically through Tsypkin's work, offering close readings and analysis of three major prose works and one collection of photographs. They trace Tsypkin's search for material which reflects him and can thus provide a view on the self from the outside. To this end he uses photography, autobiographical fiction, and the travel narrative. His most successful attempt at achieving that view on the self from the outside comes from the act of reading -- and, in particular, reading the Dostoevskys, both Fyodor Mikhailovich and Anna Grigorievna (née Snitkina). Identifying with these writers and their characters during the act of reading gives Tsypkin the means to fashion himself into what I call an "uncensored man, " in the vein of Dostoevsky's "Underground Man, " who also wrote as if he had no reader. When Susan Sontag eventually discovered Tsypkin's novel in translation and helped to bring it to attention, she was drawn to the "Tsypkin sentence" that can extend for pages and unite a multitude of characters, places, and epochs. Tsypkin's unique form encapsulates an understanding of history as non-linear. I argue that his texts' mode of existence as unpublished literature, their distinctive sentence structure, and their transgressive content allow readers to feel as if they are in two places at once - a feat of escapism and a necessary skill for the new type of "underground man, " the "internal emigre, " or the Jew in the late Soviet Union

Keywords: Ilchuk, Yuliya degree committee member.
Slavic Languages and Literatures.
Advisor: Safran Gabriella
Greenleaf Monika
Zipperstein Steven J.
Unconventional shale gas field development under price uncertainty

We present an optimization framework for unconventional shale gas resource development under price uncertainty. Shale gas developers must balance the ability to implement price-reactive actions with the operational and financial constraints of long-term service agreements. Both can improve project NPV, but they typically act in opposition to one another. We represent gas price uncertainty with a Ornstein-Uhlenbeck stochastic natural gas price model. We develop a mixed-integer linear program (MILP) framework to define optimal month-to-month field development decisions based on current gas prices and future expectations. Our workflow then provides the optimal set of long-term upstream and midstream agreements based on NPV and NPV-risk preferences. Using two case studies, we illustrate both how a field developer can leverage flexible on-demand services, as well as the restrictive effect of long-term agreements on price-reactive actions. For the financial parameters and natural gas price uncertainty used in one of our case studies, a stochastic solution that utilizes on-demand services is, on an NPV basis, equivalent to a 3.1% reduction in the field development costs associated with long-term agreements. Larger cost savings would be achieved in cases with greater price volatility, weaker reversion speeds, and increased availability of on-demand services

Keywords: Energy Resources Engineering.
Advisor: Brandt Adam (Adam R.) 
Durlofsky Louis
Uncovering natural variation in root system architecture dynamics

The plant kingdom contains an immense array of complex morphologies that provide adaptive advantages for life on Earth. While we can easily observe the stunning diversity of plant form in the above-ground portions of plants, it is much more difficult below ground. As the interface between the soil environment and the shoot system, roots play a key role in plant anchorage and resource uptake. The distribution of roots, termed root system architecture (RSA), is determined by root growth and branching and is influenced by the surrounding environment. GLO-Roots (Growth and Luminescence Observatory for Roots) is a new soil-based root imaging technology, which enables detailed observations of Arabidopsis thaliana root system growth in soil. Expanding upon this system using automation, we developed GLO-Bot, a linear-rail robot designed to accurately manipulate the position of plants, which enables automated watering and treatment of plants, and time-lapse imaging of root luminescence reporters. To take advantage of this technological improvement in plant growth and imaging, I improved and further developed a data analysis pipeline to extract root traits from these images in order to quantitatively describe changes in RSA. I examined architectural diversity amongst six diverse accessions and observed differences in how the spatial distribution of roots within the soil changed over time. I then characterized a larger diverse population of 93 Arabidopsis accessions and found root angle to be a major driving force in determining RSA diversity. I uncovered correlations between traits and climate variables which suggested that roots with shallow angles are found in climates with larger diurnal changes in temperature. Finally, I performed multiple genome wide association (GWA) analyses, which identified putative alleles involved in controlling RSA. Future experiments simulating stressful environmental conditions could elucidate how these factors aid in plant fitness

Keywords: Biology.
Advisor: Dinneny José R.
Bergmann Dominique 
Exposito-Alonso Moises 
Long Sharon R.
Uncovering the role of biochemical ligands in modulating stem cell mechanotransduction and differentiation : a biomaterials-based approach

The extracellular matrix (ECM) is comprised of different types of proteins and adhesive ligands, which change in composition and ratios during morphogenesis and disease progression. ECM proteins provide cell adhesion and impart mechanical cues to the cells. Increasing substrate stiffness has been shown to trigger Yes-associated protein (YAP) translocation from the cytoplasm to the nucleus, yet the role of ligand parameters in modulating mechanotransduction and stem cell fate remains largely unexplored. Studies of stem cell mechanotransduction and fate have widely used polyacrylamide hydrogels. However, conventional methods of conjugating biochemical ligands to polyacrylamide hydrogels suffer from low efficiency and heterogeneous protein incorporation, making studies of ligand effects on cellular mechanotransduction difficult. Here we report a method that enhances the conjugation of biochemical ligands to polyacrylamide hydrogels, enabling a greater incorporation and tunability of the amount incorporated. Using this method, we studied the effect of ligand density, ligand type, and ligand solvent on modulating cellular mechanotransduction. We showed stiffness-induced YAP translocation occurs only at intermediate ligand densities, whereas at low or high ligand densities, YAP localization is dominated by ligand density independent of substrate stiffness, mediated by cytoskeleton tension and integrin binding. We further showed that, comparing four major ECM proteins: fibronectin, collagen I, collagen IV, and laminin, the density required for such biochemical ligand-induced YAP translocation differs across ECM types. While stiffness-dependent YAP translocation can be induced by all four ECM types, each ECM requires a different optimized ligand density for this to occur. Finally, we assessed the effect of ligand solvent on modulating collagen coatings and downstream cell response. We found that collagen I coatings are highly dependent on solvent pH and composition, with solvents of pH from 3.4 to 8.5 leading to different conjugation efficiencies and distributions. We found that acetic acid of pH 3.4 led to the highest conjugation efficiency and most homogeneous coating, and induced robust MSC spreading and nuclear YAP localization across the broadest range of densities and stiffnesses, as compared to coating solvents such as PBS. The hydrogel platform with enhanced conjugation efficiency of biochemical cues provides a powerful tool for uncovering the role of biochemical cues in regulating mechanotransduction of various stem cell types. Together, results from this work highlight the important role of ligand density, ligand type, and type of ligand solvent as important parameters in studies of mechanotransduction and differentiation, and call for future mechanistic studies to further elucidate the role of changes in ECM compositions in mediating mechanotransduction during morphogenesis and disease progression

Keywords: Bioengineering.
Advisor: Yang Fan
Chaudhuri Ovijit 
Fordyce Polly
Understanding and manipulating charges surrounding carbon nanotubes : a step towards high-performance computing with carbone nanotube transistors

The biggest obstacle in introducing new nanomaterials is that innovative techniques and solutions are required to overcome the various challenges. In particular, conventional understandings based on bulk channel materials (i.e. Si) are often not applicable to carbon nanotubes (CNTs) due to their ultrathin (1~2 nm) one-dimensional structure. Additionally, the large surface-to-volume ratio from the one-dimensional structure makes CNTs greatly susceptible to nearby charges. In this dissertation, I will document the new knowledge obtained for understanding the physics behind -- and even utilize -- the charges surrounding the CNT with a view toward high-performance computing using carbon nanotube field effect transistors (CNFETs). In particular, this thesis presents a study on the following topics in CNFETs: Hysteresis -- A pulse-based measurement technique combined with a physics-based model is developed to characterize traps which affect hysteresis in CNFETs. With the insight gained from this work, hysteresis-free CNFETs are fabricated by minimizing the effect of traps onto the CNTs. Subthreshold Swing -- Hysteresis-free curves are an important, but often neglected, prerequisite to measuring the subthreshold swing (SS). By continuing our studies using hysteresis-free CNFETs, the source of large SS is identified. Doping -- Through a charge transfer doping mechanism, molybdenum oxide (MoOx) heavily dopes the CNTs, but the effect is unstable over time. The gradual change in material properties of MoOx and a method to stabilize the doping strength are investigated

Keywords: Electrical Engineering.
Advisor: Wong Hon-Sum Philip
Mitra Subhasish 
Saraswat Krishna
Understanding natural plastic biodegradation : case study of tenebrio molitor

We live in the "Age of Plastics, " an era in which plastic's versatility, strength, and low production costs have led to its ubiquity and accumulation in the environment. One potential solution to this problem is plastic biodegradation, but current approaches are slow and plastic-specific, limiting their use as a scalable solution. This dissertation explores the rapid biodegradation of plastics in an unexpected natural system: the gut of mealworms (Tenebrio molitor). I discovered that mealworms can degrade chemically dissimilar plastics (polystyrene and polyethylene), rapidly degrading nearly 50% to CO2 within 15 -- 20 hours. These results provide the first evidence of a non-specific degradation mechanism within the mealworm gut and highlight the need for additional research to elucidate this mechanism. I performed the first investigation into the fate of chemical additives during plastic biodegradation and found that mealworms do not bioaccumulate toxic chemical additives within plastics, highlighting their potential use as a feedstock. Finally, I explored the role of the mealworm and its gut microbiome in degrading plastic, discovering novel mechanisms such as the secretion of factors by the mealworm that promote the bioavailability of plastic for microbial attack. This work provides new insights into insect-mediated mechanisms of plastic degradation and opens the door for the cultivation of plastic-degrading microorganisms in future investigations and scale-up. Novel approaches to plastic degradation together with the development of sustainable bioplastics will hopefully enable us to retain the utility of these revolutionary materials while mitigating their harmful environmental effects

Advisor: Criddle Craig 
Luthy Richard G.
Wu Weimin (Environmental engineer)
Understanding the limits of hybrid optoelectronic semiconductors : photothermal techniques and beyond

Some of our earliest artisans were pioneers of nanoengineering, building the stained-glass windows of Notre-Dame before anyone knew to define the length scale. But, today, there are fewer nano-artisans than scientists studying life at the sub 10nm scale. In this dissertation, we leverage and develop sensitive characterization techniques to further push the limits of functional devices at the nanoscale and hopefully walk away with new and exciting materials. We begin with the history and fundamental chemical developments of nanoscience, from the early days of extracting metal and semiconductive crystals from sintered glass. Followed by the vital Brus equation for quantum confinement and its optical properties. We then explore the kinetics and surface chemistry that makes up 20 yrs of scientific advancement in semiconductive nanocrystals chemistry. There is an overview of some of the standard techniques used in this work to characterize and study nanocrystals. We introduce transverse photothermal deflection spectroscopy, a very sensitive photothermal absorption spectrometer, invented by Warren Jackson at LBNL in the 1980's to study thin film single crystals, polycrystals and amorphous glasses. Photothermal deflection spectroscopy measures the photothermal heat-wave propagating into a deflection fluid and can indirectly measure optical absorptivities over the range of (0.1 -10000.0 1/cm). We review the fundamental principles and limitations of a modern-day photothermal deflection spectrometer, and how to use one of the world's most sensitive optical thermometers. Then we look at how photothermal deflection spectroscopy (PDS) can be used to study modern-day thin films and solution process materials. We show new ways to apply ultra-sensitive absorption techniques towards making better optoelectronic materials. In doing so, we introduce our first look at semiconductive nanocrystals in the form of lead sulfide. I aim to use PDS as a new tool to overcome some of the fundamental limitations still hindering the development of better near-IR materials for solar-cell and transistors. Finally, we take what we learned about studying photothermal absorption and lensing at the nanoscale to push the fundamental limits of solid-state luminescence in core-shell nanocrystals. We run into the significant challenges associated with the upper limit of the uncertainty in absolute integrating sphere techniques, based on Richard Friend's photons in and photons out approach. By borrowing inspiration from the solid-state optical refrigeration community, we develop a new calorimetric quantum yield technique that uses a heat out/ light out increasing accuracy 100x when measuring highly luminescent systems. Finally, we take advantage of this increased accuracy to synthetically build and benchmark the world's brightest quantum dot emitters. All of this builds on the hope of pushing for better and more advanced nanomachines through chemistry and spectroscopy

Keywords: Chemistry.
Advisor: Salleo Alberto
Pecora Robert
Waymouth Robert M.
UNESCO and the global responsibility for heritage preservation

Under the aegis of the 1972 UNESCO World Heritage Convention, heritage preservation has gained considerable public visibility, but it has also become gridlocked in multilateral diplomacy. This thesis examines the history and challenges, of implementing, within UNESCO, the ideal of international fiscal responsibility for the preservation of the world's heritage. With the popular success of the World Heritage List and a growing global economy of international tourism, the original aims of the Convention have been misplaced. Conceived as a program of international collaboration for the protection of heritage of significance to humanity, World Heritage has been transformed into an international certification scheme, subject to the selfish ambitions of UNESCO's Member States. I expose the divide between the goals of the Convention and the national politics that rule the decisions of its governing body, the World Heritage Committee. My archival and ethnographic analysis goes beyond snapshots of the current political and financial challenges confronting World Heritage, instead tracing their development over time. Adopting a diachronic view and following the money, I deconstruct the idea of sudden crisis and show how that theme is a tactic used to mask recurring missed opportunities and repetitive patterns. My work shows the gradual unfolding of bureaucratic decisions, buried in documents, that pretend to take action but result in maintenance of the status quo. I reveal how inertia, more than natural disasters or conflicts, threatens the lofty ideals of the World Heritage Convention. The current political and financial difficulties within UNESCO also indicate the faltering of post-WWII ideals, integral to the UN and its specialized agencies, of an intergovernmental responsibility for rebuilding and rehabilitation . The events described in my study may serve as an object lesson for the multilateral agencies seeking to enforce collective responsibility for issues of global significance

Keywords: Anthropology.
Advisor: Meskell Lynn 
Hodder Ian 
Inoue Miyako