VictorJuiz/thesis huggingface dataset:
Submodular optimization for risk-aware coordination of multi-robot systems

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.

Keywords: Electrical Engineering.
Advisor: Pavone Marco
Schwager Mac
Van Roy Benjamin 
Vondrak Ján (Mathematician)
Subthreshold analog circuit design for large-scale, low-power, spiking neuromorphic systems

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.

Keywords: Electrical Engineering.
Advisor: Boahen Kwabena (Kwabena Adu) 
Murmann Boris 
Wong Hon-Sum Philip
Sustainable sourcing in agricultural supply chains : an analysis across scales

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.

Keywords: Environment and Resources.
Advisor: Lambin Eric F. 
Naylor Rosamond 
Clark William
Hainmueller Jens
Symbiotic encounters between performers and media in two large-scale compositions

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.

Keywords: Music.
Advisor: Kapuscinski Jaroslaw
Applebaum Mark
Ferneyhough Brian
Ulman Erik
Syntheses, applications, and transformations of 2D and 3D lead halide perovskites for photovoltaics and other energy technologies [electronic resource]

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.

Keywords: Chemistry.
Advisor: Karunadasa Hemamala
Solomon Edward I. advisor. Thesis advisor
Stack T. (T. Daniel P.)
Syntheses of non-linear polymers and anti-aromatic conjugated molecules

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.

Keywords: Chemistry.
Advisor: Xia Yan
Kool Eric T. 
Waymouth Robert M.
The synthesis and utilization of geometrically defined olefins

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.

Keywords: Chemistry.
Advisor: Trost Barry M. 
Burns Noah
Waymouth Robert M.
Synthesis of the ladderane lipids

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.

Keywords: Chemistry.
Advisor: Burns Noah
Du Bois Justin 
Kanan Matthew William
Synthesizing decision analysis : a pattern language approach

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.

Keywords: Management Science and Engineering.
Advisor: Howard Ronald A. (Ronald Arthur)
Raha Somik
Shachter Ross D.
A synthetic batrachotoxin derivative as a novel molecular probe to study slow inactivation in voltage-gated sodium channels

Voltage-gated sodium channels (NaVs) are obligatory transmembrane proteins responsible for electrical signaling in biology. By transitioning between different conformational states, NaVs initiate the rising phase of the action potential. A large array of neurotoxins target specific conformational states of the channel or disrupt transitions between them. Among the most powerful of these pharmacological tools is batrachotoxin (BTX), the active ingredient in poison-tipped darts used by the indigenous people of Colombia. Every measurable aspect of channel function is disrupted when this potent small molecule binds in the NaV central pore. Using de novo synthesis, we sought to perform structure-activity relationship (SAR) studies to uncover the molecular underpinnings of the action of this potent toxin. SAR studies focused on derivatizing the C20-ester of BTX. Synthetic toxin analogues were characterized using whole-cell voltage clamp electrophysiology. Using this technique, the efficacy of BTX against a recombinantly expressed single channel isoform was measured for the first time. The ester derivatives show comparable ability to the natural product in their ability to hyperpolarize NaV activation potential, indicating changes to this region of the molecule are tolerated. A BTX derivative having a conformationally flexible ester, BTX-yne, uniquely alters NaV inactivation. With the exception of BTX-yne, BTX and all synthetic ester derivatives completely eliminate both fast and slow inactivation, distinct mechanisms that regulate NaV availability. In contrast, BTX-yne selectively eliminates fast inactivation while allowing channels to undergo slow inactivation. Electrophysiology experiments with rNaV1.4 and a prokaryotic sodium channel, NaVAe, were performed to fully characterize the behavior of this novel pharmacological tool compound. A novel sodium channel mutant, rNaV1.4 A438K, that is incapable of fast inactivation was characterized. The behavior of unmodified A438K resembles that of wild-type channels modified by BTX-yne, demonstrating that slow inactivation can be studied without the influence of fast inactivation with small molecules and mutant NaVs. The experiments in this thesis lay the groundwork for future work to understand the molecular elements underlying the dynamic conformational rearrangements that underlie channel gating.

Keywords: Chemistry.
Advisor: Du Bois Justin 
Boxer Steven G. (Steven George)
Wender Paul A.
Systematic perturbation of retroviral long terminal repeats reveals widespread long-range effects on human gene regulation

Recent work suggests the extensive adaptation of transposable elements (TEs) for host gene regulation. However, the high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made the systematic interrogation of the regulatory contributions of TEs quite challenging. I employed chimeric arrays of gRNA oligos (CARGO), our recently developed method for CRISPR guide RNA (gRNA) multiplexing, to facilitate the targeting of LTR5HS, an ape-specific class of HERVK (HML-2) long terminal repeats (LTRs) that is transcriptionally active during early human development and present in ~700 copies throughout the human genome. I combined CARGO with CRISPR activation (CRISPRa) to induce or CRISPR interference (CRISPRi) to silence LTR5HS en masse in human embryonal carcinoma cells, enabling strong control of RNA levels of LTR5HS, and both RNA and protein levels of HERVK proviral genes. This system robustly and specifically targeted the vast majority of LTR5HS insertions, while critically excluding non-HERVK (HML-2) TE sequences. CRISPRa and CRISPRi also affected the chromatin state at LTR5HS insertions by manipulating histone tail modifications, with CRISPRa causing the deposition of active chromatin marks, and CRISPRi triggering the removal of active chromatin marks and the addition of repressive marks instead. Remarkably, activation and silencing of LTR5HS were associated with massive changes in the transcriptional profile of these cells, with thousands of genes affected. Most importantly, CRISPRa and CRISPRi reciprocally up- and down-regulated a set of 275 genes, termed LTR5HS-regulated genes, including many genes that are expressed in the developing human blastocyst concurrently with the LTR5HS insertions themselves. Interestingly, genes controlled by LTR5HS are more highly expressed in the developing blastocyst of humans compared to rhesus, an old-world monkey that predates the infection by HERVK (HML-2) LTR5HS. Expression of LTR5HS-regulated genes in human cells was strongly dependent on the presence of specific LTR5HS retroviral sequences located up to hundreds of kilobases away, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in apes.

Advisor: Wysocka Joanna
Fuller Margaret T.
Jarosz Daniel 
Wernig Marius
System-driven circuit design for ADC-based wireline data links

In the era of connectivity, wireline I/O has been a key technology underpinning the aggressive performance improvements of computer and communication systems. All standards, ranging from electrical to optical, long haul to short reach interconnects, have increased their aggregate bandwidth at a rate of about 2x every 4 years. This trend drives the usage of multi-level modulation schemes, such as PAM4. As a result, ADC-DSP based links are gaining more attention and are now heavily investigated. ADC links also take advantage of the intrinsic bandwidth and area improvements from process technology scaling. It is becoming very difficult for conventional mixed-signal links to meet the bandwidth and performance requirements of next-gen systems. As equalization is moved into the digital domain for ADC-based links, the ADC needs to be very fast, have reasonably high resolution and yet be very power efficient. Consequently, these stringent requirements pose significant challenges in both ADC links' architecture and circuit design. In this thesis, we focus on a statistical framework for understanding ADC nonidealities, including quantization and nonlinearity, and their impact in a link context. We will then present studies on equalization locations along the link's signal path, motivating the need of pre-equalization before the ADC. With the importance as well as the implementation challenges of pre-equalizers in mind, we present the first inverterbased analog front-end (AFE) for 56Gb/s transceivers for both PAM2 and PAM4 vapplications. Such AFEs include continuous time linear equalizers (CTLE), programmable gain amplifiers (PGA) and the ADC's track and hold circuits (T/H). The inverter-based AFE is process scaling friendly, consumes smaller power and achieves significant area reduction over prior art. Finally, system identification (SID) methodologies are used with silicon measurements to show validity of the before-mentioned analysis. SID-based bit error rate (BER) estimation method is also presented to compare measured and predicted link performance for different ADC resolutions.

Keywords: Electrical Engineering.
Advisor: Murmann Boris 
Arbabian Amin 
Horowitz Mark (Mark Alan)