VictorJuiz/thesis huggingface dataset:
The structure and maintenance of centromeric chromatin
Keywords: Biochemistry.

When a human cell divides, it pulls its chromosomes into regions that will become new cells. The pull is applied to a single region on each chromosome called the centromere. Centromeres are defined by high concentrations of nucleosomes containing the protein CENP-A instead of the canonical histone H3. CENP-A nucleosomes directly recruit proteins that bridge between the nucleosomes and the forces that pull chromosomes apart. These proteins also affect CENP-A chromatin itself. This thesis examines the role of two proteins that directly interact with CENP-A nucleosomes, CENP-C and CENP-N, in centromere maintenance and structure. It was found that CENP-A nucleosomes have little to no dissociation from centromeric regions. We hypothesized that this lack of dissociation is caused by increased nucleosome stability due to binding to CENP-C and CENP-N. To test this, we generated cell lines where we could induce the degradation of the endogenous proteins. Using these cells, we employed several orthogonal methods to show that CENP-C and CENP-N do not affect CENP-A nucleosome stability at the centromere. Next, we explored the role of these proteins on centromeric chromatin structure. Not much is known about CENP-A chromatin structure due to technical limitations. To overcome this, we instead looked for activities that alter CENP-A chromatin structure. We developed a novel activity-based assay that detects CENP-A nucleosome clustering. Using this assay, we discovered that CENP-C can cluster CENP-A nucleosomes from different strands of DNA. We showed that this activity is specific and depends on CENP-C's ability to bind CENP-A nucleosomes. We identified the minimal domain necessary for the clustering which will serve as the basis for further studies. Lastly, we examined the role of these proteins in disease. We looked at CENP-N mutations associated with familial idiopathic pulmonary fibrosis. We found that one mutation, E46Q, lowered the levels of CENP-T at the centromere. Since CENP-T functions in kinetochore formation, we hypothesize that this leads to impaired kinetochore function and more chromosome segregation errors. Consistent with this, we found that this mutation sensitized the cells to PDMP, a drug that selectively kills aneuploid cells.
Studies in structure and electrochemistry of halide perovskite semiconductors and covalently-functionalized carbon with applications in optoelectronic devices, energy storage, and CO₂ capture
Keywords: Chemistry.

Described here are the results of my efforts to understand and control the structural, electrochemical, and transport properties of materials under development for the field of energy generation and storage. I first give the results of transport and defect chemistry studies in halide perovskite semiconductors. These crystalline solids have risen to the forefront of applied materials science research owing to the high performance demonstrated in optoelectronic devices incorporating them as active layers and their easy synthesis at low temperatures. Despite their favorable electronic properties, defect chemistry can be shown to play a pivotal role in halide perovskite properties, and thus its understanding is crucial to the technology that uses these semiconductors. I have measured electronic and ionic conductivities in multiple perovskite compounds, and have found them to change significantly, even in nominally inert environments. The behavior of ionic and electronic transport has led to the development of defect chemistry models that successfully predict how material properties change with component activity, and point to methods to control doping, defects, and conduction in halide perovskites. I next report a method to modify the physical and electronic structure of two-dimensional halide perovskites, which are of interest for solid-state lighting and other optoelectronic applications. These materials have electronic band-gaps in the visible or near UV region of the spectrum, and typically have high exciton binding energies due to 2D electronic confinement. Zwitterionic alkylammonium molecules reliably modify the structure of 2D perovskites by incorporating additional metallic or nonmetallic ions between the 2D perovskite layers. I show that these ions modify the electronic properties; they lower exciton binding energy and introduce light emission from new photoluminescent defect states. I also give an account of the development of quinone-functionalized carbons, materials whose favorable electrochemical properties lead to potential applications as high-power lithium-ion battery electrodes and as a CO2 capture materials in electrochemical CO2 separation process. Due to the particular nature of halide perovskites and other materials included in this work, nonstandard electrochemical and synthetic methods have often been required. I end by describing the tools and techniques developed with the hope that they will help fellow researchers carry out rigorous measurements simply and effectively.
A study of the dynamic response of plasma filled microwave cavity resonators
Keywords: Aeronautics and Astronautics.

This dissertation details research done to study microwave cavity resonators and their dynamic actuation using laboratory pulsed plasma discharges. The work is encompassed in a broader research effort to study the utility of gaseous plasmonics in controlling the propagation of electromagnetic waves. In support of this effort, I present numerical and experimental findings that together describe with consistency the transient behavior of laboratory pulsed plasma discharges through their interaction with electromagnetic resonant modes. The research contained in this thesis combines the fields of microwave engineering, plasma physics, and photonic crystals in novel ways that enables actively tunable electromagnetic devices at high frequencies. Two devices are presented, the first consisting of a metallic two-post 14 GHz resonator located inside a WR62 waveguide section, and the second consisting of a hexagonal lattice photonic crystal with a defect state at 27 GHz. The microwave transmission through both devices is measured during a 150 ns pulsed plasma discharge and pulsed microwaves are seen of various widths and delays, depending on the transmission frequency. In this way, the resonant cavities are shown to have pulse shaping properties, with the photonic crystal cavity able to generate pulses with widths and delays ranging from tens of microseconds down to hundreds nanoseconds. A fluid plasma simulation was developed to model with high fidelity the transient dynamics of laboratory plasma discharges. The simulated plasma properties are used in conjunction with microwave theory to predict and provide insight into the experimentally measured microwave transmission signals. The results of the modeling efforts are compared with the experimental findings and show good qualitative and quantitative agreement, such as predicting the magnitude and time of the maximum frequency shift within the cavity within ten percent error. Lastly, the nonlinear coupling between high power microwaves and the plasma-cavity system are studied. It is shown that both resonator devices are capable of microwave plasma breakdown, suggesting that they could be used as nonlinear power limiting devices or plasma sources. Additionally, the coupling between high power microwaves and pulsed plasma discharges is also studied. Here, the previously elusive microwave pulses generated due to plasma ionization were finally captured due to the nonlinear behavior of high power microwaves interacting with the plasma ignition process, and pulse widths and delays were measured as low as several hundred nanoseconds.
Submodular optimization for risk-aware coordination of multi-robot systems
Keywords: Electrical Engineering.

Robots are often designed for dangerous environments such as severe storms, but routing algorithms rarely are. This dissertation introduces a new class of routing problems with ``risky traversal'' where a robot may fail when travelling between two sites. Our key insight is that many objectives in the risky traversal model satisfy a diminishing returns property known as submodularity. We develop a set of tools based on submodular optimization which lead to efficient solutions for a wide variety of problems: 1. The "Team Surviving Orienteers" (TSO) problem, where the size of the team is fixed and we seek routes which maximize the expected rewards collected at nodes, subject to survival probability constraints on each robot. 2. The "On-line TSO" problem, where observations are incorporated to update the paths on-line in a parallel fashion (in response to survival events). 3. The "Heterogeneous TSO" problem, which allows robots to have different capabilities such as sensors (affecting rewards collected), actuation (affecting ability to traverse between sites), and robustness (affecting survival probabilities). 4. The "Matroid TSO" problem, where the set of routes must satisfy an `independence' constraint represented by a matroid, for example limits on the number of each type of robot available, traffic through regions of the environment, total risk budgets for the team, or combinations of these limits. 5. The "Risk Sensitive Coverage" problem, which is the dual to the TSO where the team must satisfy a coverage constraint (e.g., ensure that nodes are visited with specified probabilities) while using minimum resources (e.g., number of robots deployed, distance travelled, or expected number of failures). Our algorithms are based on the approximate greedy algorithm, where we iteratively select a path which approximately maximizes the expected incremental rewards subject to some constraints. Due to the submodular structure of the problems considered in this dissertation, we can prove bounds on the suboptimality of our algorithms. The approach developed in this dissertation provides a foundational set of tools for routing large scale teams in dangerous environments while explicitly planning for robot failure.
Subthreshold analog circuit design for large-scale, low-power, spiking neuromorphic systems
Keywords: Electrical Engineering.

Subthreshold current-mode circuits are attractive for low-power, large-scale neuromorphic systems due to their compact design and extremely small operating currents. I first discuss Neurogrid, such a large-scale system that I worked on, and its various components in Part I. One of the major issues that was not completely addressed in Neurogrid's design was these circuits' exponential sensitivity to ambient temperature and threshold-voltage mismatch. The lesson learned from Neurogrid was that, to properly design large-scale systems with such circuits, we need to model their sensitivity as well as the overall system's sensitivity. The former requires a statistical device model and the latter requires a statistical circuit model. While it is possible to study system-level behavior by performing detailed Monte-Carlo SPICE simulations of the analog circuits, this is computationally extremely expensive and difficult to scale. So, in order to ease designing large-scale systems, I developed a compact device model that captures the effect of drain-current mismatch and temperature variations in the subthreshold regime. I applied this device model to study current mirror and Soma circuits, representative examples of linear and nonlinear circuits. Using insights gleaned from these analyses, I designed various circuits for Braindrop, another mixed-analog-digital neuromorphic chip. I discuss the device model, circuit analysis techniques and the various analog circuits used in Braindrop in Part II.
Sustainable sourcing in agricultural supply chains : an analysis across scales
Keywords: Environment and Resources.

This dissertation seeks to understand how and why companies are addressing sustainability in their agricultural supply chains. To do this, I examine corporate approaches to sustainable sourcing across scales, from a global view of hundreds of firms, to a single exemplary environmental supply chain program, to the interactions across industry members within a particular commodity chain. In my first chapter my co-authors and I examine the sustainable sourcing practices of a random sample of 449 companies in the food, apparel and wood products sector. This study provides the first large-scale analysis of how a broad range of companies address social and environmental issues in their supply chains. Our results highlight both the opportunities and limitations of sustainable sourcing practices in contributing to the United Nations' Sustainable Development Goals. My second chapter builds key findings from Chapter One to provide one of the first examinations of the impact of a company-led standard on the adoption of improved environmental farm management practices in the fresh produce sector. Using a critical case approach, my co-authors and I find that the major South African food retailer Woolworths' sustainable fresh produce program is associated with an increased uptake of improved environmental farm management practices. We identify Woolworths' long-term partnership with farmers and the use of highly trained auditors to provide farm-specific recommendations as key design principles that make this program particularly effective in comparison to an existing industry standard. Finally, in my third chapter I look at how different stakeholders influence the evolution of chocolate manufacturers' sustainable sourcing practices over time. Both internal and external stakeholders play an important role in influencing the evolution of sustainable sourcing practices. I find that companies continue to build out their approaches to sustainable sourcing as new stakeholder pressures and threats arise. Together, Tannis Thorlakson's work provides insights into the role companies' sustainable sourcing practices play in addressing the pressing global sustainability challenges we face today.
Symbiotic encounters between performers and media in two large-scale compositions
Keywords: Music.

In my recent works, I have been exploring different ways of engaging performers and media—specifically video—in mutually beneficial interrelations on stage. Whether direct or indirect, literal or metaphorical, the connections between performers and digital entities have both generated and been triggered by musical and narrative structures. In this paper, I talk about such interrelations and their conceptual and formal impact in two large-scale compositions that constitute my DMA Final Project: "Knot an Opera!" (2016) for three sopranos, baritone, pianist, electronics, and three-channel video, and "Chord Optimization in Music Composition: Towards a Machine-Inspired Technique for Human-Based Performance" (2018) for ten performers, composer, electronics, live 360° video, and multichannel video.
Syntheses, applications, and transformations of 2D and 3D lead halide perovskites for photovoltaics and other energy technologies [electronic resource]
Keywords: Chemistry.

Halide perovskites have recently had a precipitous rise in the photovoltaic community because they can be solution-processed from inexpensive materials and produce solar conversion efficiencies that rival mature thin film and Si technologies. Here, I will discuss my own contributions to halide perovskite optoelectronics by discussing two projects. First, I will detail our studies on a subclass of two-dimensional halide perovskites whose structure is analogous to the Ruddlesden--Popper oxide perovskites. These materials are intermediate to the traditional halide perovskite structure-types and therefore they display intermediate optoelectronic properties that can be favorable for photovoltaics. We demonstrated the first example of a layered perovskite acting as a solar cell absorber and also show that these materials have greater stability towards humidity. Second, I present a strategy to manufacture high-quality halide perovskites via post-synthetic modification. Halogen redox chemistry governs that halide ions in the lattice of perovskites can be oxidized and exchanged with external halogens of a higher oxidation state. This reaction is shown to be a single-crystal-to-single-crystal transformation and provides a general strategy for making device-quality halide perovskites where traditional methods are difficult or impossible to use. These findings show how the Chemist's approach is valuable for halide perovskite optoelectronics, where advances have real potential to positively impact the global energy economy.
Syntheses of non-linear polymers and anti-aromatic conjugated molecules
Keywords: Chemistry.

Efficient and versatile catalytic chemistry has continuously stimulated the syntheses of novel materials. This thesis describes the syntheses of non-linear polymers and anti-aromatic conjugated molecules using catalytic arene-norbornene annulation reactions and metathesis polymerizations. Bottlebrush polymers have a very high density of side chains grafted to the backbone, leading to an extended worm-like conformation. Efficient, modular synthesis of brush polymers is the first step for thorough understanding of their solution and assembly behaviors and to enable various applications. In the first part of this thesis, we investigated the limitations of the previous methods used for brush polymer synthesis. We further developed a streamlined one-pot macromonomer synthetic strategy to synthesize well-defined brush (co)polymers via ring-opening metathesis polymerization (ROMP). In the pursuit of facile methods for the synthesis of rigid ladder structures, we have developed Catalytic Arene-Norbornene AnnuLation (CANAL) chemistry to couple aryl bromides with norbornenes (NBEs) to form rigid fused norbornyl benzocyclobutene ladder structures. In the second part of this thesis, we utilized this efficient chemistry to synthesize various polymeric materials and conjugated molecules containing rigid ladder motifs. We first demonstrated the synthesis of polyladders via ROMP of rigid CANAL ladder oligomer to provide porous polymers with high solution processability. We further developed an efficient strategy to prepare star polymers cross-linked via telechelic CANAL ladder using ROMP. The arms of these star polymers can be readily cleaved under acidic conditions to allow isolation of soluble microporous organic nanoparticles. In another manifestation of CANAL chemistry, when oxaNBEs are used in place of NBEs, the CANAL products can be aromatized to form conjugated systems with fused four-membered rings. The conjugated four-membered rings also elicit antiaromaticity arising from cyclobutadienoid (CBD). Non-benzenoid structures with antiaromaticity have been much less explored with limited understanding of their properties due to the challenging synthesis. We developed a modular and streamlined CANAL-aromatization strategy to synthesize a series of polycyclic conjugated hydrocarbons containing CBDs. We further extended this CANAL-aromatization strategy to synthesize a series of regioisomeric CBD-fused phenazines and investigated the effect of bond fusion pattern on local antiaromaticity.
The synthesis and utilization of geometrically defined olefins
Keywords: Chemistry.

The catalytic, and atom economic synthesis of stereodefined olefins remains a major challenge in organic synthesis. Stereodefined olefins are integral in controlling molecular shape and serve as instrumental functional groups for further stereoselective transformations. The following work was focused on the development of more efficient methods towards stereodefined olefins, and on the development of stereoselective functionalizations of these olefin products. Herein we report the first general utilization of 1,1 disubstituted olefins, as well as 1,2-disubstituted olefins in the Ru-catalyzed alkene--alkyne coupling reaction. The products of these reactions were used towards the asymmetric synthesis of aminocyclopentitols, 1,2-amino alcohols, and extended polyketide motifs. Additionally these pursuits led the simultaneous discovery of a general atom economic method for the isomerization of N-allyl amides to form Z-di-, tri-, and tetrasubstituted enamides with exceptional geometric selectivity. Applications of these geometrically defined enamides toward the synthesis of cis vicinal amino alcohols and tetrasubstituted α-borylamido complexes were investigated. Finally we developed new methods towards the synthesis of a particularly interesting class of stereodefined enamides, vinyl nucleotides. Utilization of these building blocks towards the synthesis of nucleotide derivatives led to the discovery of a novel asymmetric Pd catalyzed iodoetherification reaction.
Synthesis of the ladderane lipids
Keywords: Chemistry.

The ladderane phospholipids are perhaps the most structurally unique membrane lipids in the natural world. They are produced exclusively by anaerobic ammonium oxidizing (anammox) bacteria and are theorized to form dense, impermeable bilayers, but the role these lipids play in anammox membranes has not been determined. A synthetic campaign to prepare both ladderane lipid tails and a selection of natural and unnatural ladderane phospholipids comprises the bulk of this dissertation. Expedient, enantioselective routes to both [5]-ladderane and [3]-ladderane lipids have been developed. As part of this campaign, the absolute stereochemical configuration of natural [3]-ladderane lipid tails was established by comparison to natural material. The dissertation also contains two collaborative projects. First, the biophysical properties of our synthetic ladderane phospholipids were thoroughly explored. We established a structure-function relationship for the ladderane lipid tails and provided evidence that the ladderane phospholipids serve to slow proton diffusion across anammox membranes. Second, we developed the synthesis of a poly(ladderene) material comprised of monomers based on the [5]-ladderane scaffold. The polymer undergoes a dramatic structural rearrangement in response to mechanical force, converting from an insulating to a conducting organic material.
Synthesizing decision analysis : a pattern language approach
Keywords: Management Science and Engineering.

A common problem for all applied fields is the practicality gap, which is the disconnect between academia and practice, and decision analysis is no exception. Two qualitative studies conducted with the members of the field led to three main conclusions. First, the practicality gap is there for decision analysis, and the gap is wide. Second, there is no common definition of what decision analysis is. Third, practitioners, despite knowing the art of application, have lost the wisdom of certain parts of the process. This dissertation proposes that a pattern language framework will be able to combine and capture explicit and tacit knowledge in the field in a format that is clear and shareable. To verify this claim, I developed a catalog of patterns and tested them in a case study with students of decision analysis. As part of this case study, a qualitative study was conducted for which interviews with students, materials they submitted as part of the exercise, and notes from and recording of their discussions were used as data sources. There were three findings from the case study. First, students stated that the catalog was a helpful guideline that combined all relevant knowledge and presented it in a package that provided them with how to apply decision analysis. Second, the patterns helped students apply the decision analysis processes in their projects successfully. Third, they were able to conduct a quality decision conversation, which helped decision-makers get to the clarity of action. In summary, this dissertation showed that it is possible for a pattern language for decision analysis to gather the collective wisdom of the practice by reviving the lost wisdom and demystifying the art of application. This language can be shared so that both students of decision analysis can apply what they learn and professionals can enrich their skill set.