VictorJuiz/thesis huggingface dataset:
Developing and testing a reconstitution model for RNA folding [electronic resource]
Keywords: Biochemistry.

One of the most fascinating phenomena in biology is the folding of macromolecules into complex three-dimensional shapes that carry out all biological functions. Critical to the efficacy of these molecules is their capacity to fold on timescales relevant to biology and form specific and stable (but not too stable) structures. For decades, scientists have been studying how the physical properties of each macromolecule are utilized to combat the entropy of countless alternative conformations to form a native state. The function of structured RNAs is critical at every level of gene-expression regulation, thus developing a predictive model for how these molecules fold is of fundamental importance as it holds the promise of therapeutic design and control. Previous studies of RNA structure have determined that the architecture of RNA is structurally modular, therefore we posit that we can harness this feature of RNA to simplify the folding process into separate energetic contributions that are additive to predict the kinetic and thermodynamic behavior of structure RNA, i.e. energetic "Reconstitution". These energetic contributions are the conformational entropy due to the dynamics of the helices and junctions that connect them, the electrostatic penalty for bringing these RNA elements together, and the free energy of formation of tertiary contacts. Using, smFRET I provide support for energetic independence of these contributions from comparisons of measurements of rate and equilibrium constants for the effects of mutations in the tertiary contacts of the P4-P6 RNA, which found these energetics were the same over a range of conditions and structural contexts. To further test this reconstitution hypothesis and determine other simplifying and predictive rules for RNA building blocks, we utilized a simple RNA tertiary system, the tectoRNA, in concert with RNA-array technology to assess variations in ~ 100,000 variants. The number of variants provided by this approach and the simplicity of this system allowed us to address multiple open questions in the field of RNA folding regarding the conformational preferences of RNA helical sequences, junctions, and tertiary contacts. This thesis represents a step towards testing and developing a quantitative and predictive model for RNA folding.
Developing code [electronic resource] : aspiration and exclusion in the making of 'Silicon Savannah'
Keywords: Anthropology.

On a 2013 tour across Africa, Google's Executive Chairman Eric Schmidt proclaimed that Kenya's capital city of Nairobi "has emerged as a serious tech hub and may become the African leader." Echoing this statement, local and international press outlets have dubbed Nairobi "Silicon Savannah." They celebrate its burgeoning technology sector for spurring democracy and development, and for precipitating Africa's political and economic "rise." Based on twenty-five months of ethnographic fieldwork in Nairobi, my research addresses both these grandiose claims and the disparate places in which they find empirical traction: the elite spaces of software's production and the impoverished informal settlements in which such software is implemented and used. By putting into conversation theoretical approaches from anthropology, science and technology studies, African studies, and urban geography, this dissertation examines how diverse political and ethical claims become enmeshed in and expressed through digital technologies, which in turn shape understandings and experiences of development, citizenship, and governance in Nairobi.
Developing gold-based electrocatalysts for the production of fuels from CO2 and water [electronic resource]
Keywords: Mechanical Engineering.

Carbon dioxide electroreduction is presented as a way to convert CO2 into commodity chemicals. This thesis starts with an overview of CO2 electroreduction, the methods used to study CO2 electroreduction catalysts and analysis of a specific application of CO2RR: the conversion of CO2 emissions from the fermentation of corn. Subsequently, a thorough analysis of gold as a catalyst for CO2 electroreduction is presented, followed by analysis of four novel gold-based materials for CO2 electroreduction. For these materials, electrochemical analysis and characterization is discussed as well as some mechanistic implications. The thesis is concluded with a combination of theory and experimental hydrogen partial current densities to generate a relationship between surface CO-binding and HER during CO2 electroreduction.
Developing maximum-efficiency architectures for steady-flow chemical engines [electronic resource]
Keywords: Mechanical Engineering.

Improving the efficiency of natural gas-based power plants is essential for significantly curtailing future greenhouse gas emissions. Historically, improvements to power plant thermodynamics have been implemented as incremental changes from existing systems. Only recently has work been done to systematically develop optimally-efficient combustion engines using existing technologies without artificial constraints on the system's size, components, or shape. This systematic process was used to optimize steady-flow combustion engines for work and heat transfer. This dissertation builds off of this recent work by additionally optimizing systems for matter transfer. The best flow paths for air and fuel are determined, as well as the flow path for an additional environmental (non-exergetic) fluid: water. As an alternative to the highly-entropic combustion process, a solid-oxide fuel cell is also incorporated into the design scope. Both numerical and analytical approaches to optimizing these architectures are examined. Through a systematic expansion in the scope of candidate systems, this thesis develops optimal thermodynamic schematics that achieve efficiencies more than 15 percentage points better than those for the most efficient existing power plants.
Developing subtype-specific stochastic simulation models of breast cancer incidence and mortality [electronic resource]
Keywords: Biomedical Informatics.

Breast cancer is the second leading cause of death among women in the United States. Several advances have been made in early detection and treatment of breast cancer in the last few decades, in particular with the widespread adoption of screening mammography and the identification of molecular targets that have enabled the development of therapies for specific subtypes. In light of the changing landscape of available interventions, there is an urgent need to develop approaches that integrate molecular and population-level data to evaluate the efficacy of current and emerging screening and treatment technologies in order to support the development of clinical guidelines that reduce the burden of breast cancer. Population modeling is a comparative effectiveness paradigm capable of linking the complex dynamics of adopting new interventions and their net effects on breast cancer incidence and mortality. Although several population-level models of breast cancer have been constructed, there are several challenges that must be addressed in order to construct estrogen receptor (ER) and human growth epidermal factor 2 (HER2) subtype-specific models. In this dissertation, I present several methodologies developed to enable the construction of molecular-specific population models of breast cancer progression, screening and treatment. I propose to achieve this goal through the following specific aims: 1) develop a framework to model breast cancer incidence in the U.S from 1975 to 2010, explicitly accounting for the effects of screening and menopausal hormonal therapy (MHT), 2) develop an approach to estimate parameters that characterize progression and baseline survival by estrogen receptor (ER) and human epidermal growth factor 2 (HER2) status in the absence of any intervention, and 3) use these results to construct an ER and HER2-specific breast cancer population model to evaluate the effects of screening and treatment on breast cancer incidence and mortality trends. Finally, I will also discuss an implementation of our model to characterize breast and ovarian cancer among women with a BRCA1 or BRCA2 mutation, and how it was used to quantify the benefits of risk-reducing interventions, such as prophylactic surgery and screening, to support women choosing to undergo these procedures at different ages.
Development and evaluation of two novel instruments for X-ray imaging [electronic resource]
Keywords: Mechanical Engineering.

The evolution of x-ray equipment has been stagnant because of its demanding design requirements, but clinical need for an advanced imaging technique has been continually growing. To contribute to hardware advances in the x-ray imaging devices, we designed and implemented innovative instruments by applying both mechanical and electrical principles. Herein, we explore two essential novel instruments for x-ray imaging: (1) a new electric motor for an MR-compatible x-ray tube and (2) a testing system for a high-energy x-ray detector. Because each imaging modality has different strengths and limitations, we are able to obtain more accurate medical images by combining at least two modalities. A hybrid x-ray/MR imaging system, leveraging the complementary advantages of both x-ray and MR imaging, is ideal for image guidance of catheters, guide wires, and prosthetic devices in real time. However, the performance of conventional x-ray tube motors is degraded when exposed to an external magnetic field, thus we developed and evaluated a new x-ray tube motor that can operate in the presence of the strong magnetic fields of an MRI machine. We further explored simulation models to improve the performance and dynamic characteristics of the new motor. High-energy x-ray imaging used in concert with low-energy x-ray imaging creates clearer and more accurate images. It is necessary to have a thicker scintillating phosphor layer to improve quantum efficiency for high-energy x-rays, but the spreading becomes more severe in that case. To resolve this issue, we can use a thick scintillating layer segmented by other thin layers (a.k.a. pixelated detector). Even though the pixelated detector prototype based on Sawant's design demonstrates relatively high detective quantum efficiency (DQE), both measured DQE and spatial resolution differ from corresponding expectations from theory and simulations. In order for the Monte Carlo method to accurately simulate the imaging performances, the characteristics of the basic pixelated unit must be understood. Therefore, we developed a new instrument to measure both light reflection and transmission distribution within the basic detector unit as a function of material, surface, and angle of incidence. Based on manufacturing procedures and the light distributions of the candidate samples, we also made valuable suggestions for a better, more profitable detector. We expect that our instruments will lead the next generation of diagnostic and therapeutic equipment to produce accurate diagnoses and efficient treatments for various disease states.
The device physics of organic solar cells [electronic resource]
Keywords: Materials Science and Engineering.

Organic solar cells are photovoltaic devices that use semiconducting plastics as the active layer rather than traditional inorganic materials such as Silicon. Like any solar cell, their efficiency at producing electricity from sunlight is characterized by three parameters: their short-circuit current (Jsc), open-circuit voltage (Voc) and fill factor (FF). While the factors that determine each of these parameters are well-understood for established solar technologies, this is not the case for organic solar cells. The short-circuit current is much higher than we would expect given the strong attraction between electrons and holes in organic semiconductors that should lead to fast recombination, preventing the carriers from being collected as current. In contrast, the open-circuit voltage is much lower than we would expect based on the traditional relationship between optical absorption and voltage in inorganic semiconductors. Finally, the fill factor is highly variable from device to device and typically gets much worse as the cells are made thicker. In this work we develop a novel and general framework for understanding the short-circuit current, open-circuit voltage and fill factor of organic solar cells. The concept that turns out to unify all three aspects of device operation is the idea that electrons and holes move rapidly enough relative to their lifetimes to equilibrate with each other in the statistical mechanics sense before recombining. Previously, it had been thought that such equilibration was impossible because of the low macroscopic mobilities of charge carriers in organic solar cells. We first show using Kinetic Monte Carlo simulations that the charge carrier mobility is 3-5 orders of magnitude higher on short length scales and immediately after light absorption by comparing simulated results to experimental terahertz spectroscopy data. Combining this high mobility with experimental lifetime data fully rationalizes high charge carrier generation efficiency and also explains how carriers can live long enough to be affected by strong inhomogeneities in the energetic landscape of the solar cell, which also improves charge generation. Turning to Voc, we use the same concept of fast carrier motion relative to the recombination rate to show that recombination proceeds from an equilibrated population of Charge Transfer states. This simplification permits us to develop an analytical understanding of the open-circuit voltage and explain numerous puzzling Voc trends that have been observed over the years. Finally, we generalize our equilibrium result from open-circuit to explain the entire IV curve and use it to show how the low fill-factor of organic solar cells is not caused, as is often thought, by a voltage dependent carrier generation process but instead by low macroscopic charge carrier mobilities and the presence of dark charge carriers injected during device fabrication. Taken together, these results represent the first complete theory of organic solar cell operation.
Diffraction of elastic waves by edges [electronic resource]
Keywords: Mathematics.

The purpose of this thesis is to investigate the diffraction of singularities of solutions to the linear elastic equation on manifolds with edge singularities. Such manifolds are modeled on the product of a smooth manifold and a cone over a compact fiber. For the fundamental solution, the initial pole generates a pressure wave (p-wave), and a secondary, slower shear wave (s-wave). If the initial pole is appropriately situated near the edge, we show that when a p-wave strikes the edge, the diffracted p-waves and s-waves (i.e. loosely speaking, are not limits of p-rays which just miss the edge) generated from such an interaction are weaker in a Sobolev sense than the incident p-wave. More generally, we show that subject to a "coinvolutivity" hypothesis, if a p-singularity (or s-singularity) of any solution strikes the edge, the diffracted p and s wavefronts are smoother that the incident singularity.
Diffusion of designerly finite element analysis [electronic resource]
Keywords: Mechanical Engineering.

To address a variety of difficulties surrounding the use of finite element analysis (FEA) in product development at Sandia National Laboratories, this research explored a 'designerly' insertion of FEA into the design-build-test product development cycle. Designerly FEA is characterized by the use of simplified FEA models, designer-friendly FEA software, an FEA analyst embedded in the product design team, relative comparisons of design options, and a deliberate leveraging of routine prototype testing to collect model validation data. Two case study projects were used to explore the impact of this approach on the product development teams' thinking and perceptions of FEA. The case study data was collected using a variety of methods and analyzed using a theory-building approach. The results were synthesized into a framework that describes how the use of FEA to build confidence in a product design is related to the process by which product development teams gain or lose confidence in FEA itself. The implications may extend to other organizations that desire to increase the impact of FEA or other simulation technologies in their product development process.
Directed self-assembly for nanofabrication and device integration [electronic resource]
Keywords: Electrical Engineering.

For more than 50 years, the size of the semiconductor devices has been scaling by approximately a factor of two every 1.5-2 years. This has brought tremendous benefits for the industry including lower cost per transistor, more computing power and higher speed. However, it has been recently observed that the scaling of devices is approaching fundamental (i.e. atomic scale) and economic (i.e. cost per fabrication facility) limits, in large part because traditional lithography is facing substantial challenges for printing the shrinking features while maintaining a reasonable cost. In response to this urgent need, researchers are actively searching for alternative patterning approaches as the next generation lithography. Potential solutions such as extreme ultraviolet lithography, electron beam lithography, and multiple patterning lithography have attracted much attention from the lithography community. However, each one of these solutions has its own drawbacks, such as extremely high cost or low throughput. Among these solutions, block copolymer directed self-assembly (DSA) stands out due to its low cost, high throughput, well-controlled sub-20 nm features, and experimentally demonstrated potential to scale below 14 nm. Block copolymers are unique soft materials that can self-assemble through microphase separation into various periodic nanostructures such as cylinders, spheres and lamellas, driven by the incompatibility between the different blocks. The feature size of these nanostructures is dependent on the molecular weight of the block copolymers and therefore not limited by the same factors that limit optical lithography such as ultraviolet light wavelength. In addition, the self-assembly could be controlled by a simple thermal annealing process, which significantly reduces the cost and improves the throughput. Among all the varieties of nanostructures, the cylindrical self-assembled patterns are especially suitable for patterning contacts and vias in integrated circuits (ICs). This dissertation focuses on the application of block copolymer DSA for contact hole patterning in ICs. This work first demonstrates the flexible control of aperiodic DSA patterns using small physical guiding templates, using both experiments and computational simulations. This is followed by the first patterning example of memory and random logic circuit contacts using DSA. To enable practical technology adoption, I introduce an alphabet approach that uses a minimal set of small physical templates to pattern all contact configurations on integrated circuits. This work also illustrates, through experiments, a general and scalable template design strategy that links the DSA material properties to the technology node requirements. Last but not least, the dissertation introduces a method to reduce DSA defectivity by using sub-DSA-resolution Assist Features (SDRAFs).
Discovering entrepreneurial opportunities [electronic resource] : individual, team and organizational capabilities
Keywords: Management Science and Engineering.

The discovery of profitable entrepreneurial opportunities is a challenging endeavor. Even for expert entrepreneurs and investors. Particularly in high-growth, dynamic and uncertain environments. I begin by analyzing empirical literature in the fields of entrepreneurship, strategy and institutions to explain where opportunities emerge in time and space, and which unique behaviors help to discover them. Next, I empirically explore how individuals, teams and organizations can develop the capabilities to discover high-value opportunities. My first empirical study shows how entrepreneurs can acquire these capabilities by interacting with the right peers. The second study shows how team composition aids the necessary cognitive flexibility during the discovery process. My final study shows how organizations can use rational heuristics to discover and accurately predict high-potential ventures. I explore these questions by studying two novel entrepreneurship policies: Start-Up Chile and I-Corps.
Dissociating cognitive and behavioral functions of the human striatum [electronic resource]
Keywords: Psychology.

The striatum, initially identified as a primarily motoric structure, is now known to facilitate many cognitive functions, including learning, motivation, and the experience of reward. Although the striatum's involvement with these functions is well established, uncertainty remains regarding the structural and functional neural pathways that give rise to these capacities. Here, we present results from functional imaging experiments on human participants that were designed to dissociate the processes supported by striatal subregions. Across two studies, we show that the dorsal and ventral striatum contribute to distinct aspects of behavior and cognition: whereas the ventral striatum is associated with reward processing and model-free learning, the dorsal striatum is more involved in the initiation of motivated actions and learning abstract behavioral rules.
Divided Intentions: Iraqi Nuclear Weapons Policy Between the First and Second Gulf Wars
Keywords:  Program in International Relations
Iraq
Nuclear Weapons
Weapons of Mass Destruction
Gulf War
Deception
UNSCOM
Inspections
Disarmament
International Security
Center for International Security and Cooperation
International Security Honors
International Relations
Thesis

Contrary to common belief, Saddam Hussein did not intend to deceive UN inspectors and the international community concerning his nuclear weapons program between the First and Second Gulf Wars; rather, internal discussions between Hussein and his ministers indicate that they desired cooperation with inspections so that sanctions would be removed. However, it is also clear that the overriding belief held by the Iraqi government was that the United States was a nearly omnipotent threat that was completely controlling the UN Security Council and the UN inspections teams. They believed that the United States was intentionally prolonging inspections to keep sanctions on Iraq as a means to weaken the state in preparation for a future invasion aimed at regime change. This belief was present at every stage of inspections after the First Gulf War, but did not significantly alter Hussein’s strategic intent to cooperate. Nevertheless, it is clear that elements in the Iraqi government did deceive UN inspectors by intentionally hiding information about the nuclear weapons program and failing to cooperate with inspectors when they arrived in Iraq. However, deception appears to have been carried out by members of the Iraqi government subordinate to Hussein and his cabinet without their knowledge. The case of Iraqi nuclear weapons policy from 1991-2003 demonstrates the difficulty in understanding the strategic intent of foreign governments, especially when a seemingly centralized government actually allows a high level of autonomy to the non-cabinet level officials that actually carry out the regime’s policy.