VictorJuiz/thesis huggingface dataset:
Deposition, performance, and stability of halide perovskite solar cells [electronic resource]
Keywords: Materials Science and Engineering.

Halide perovskites have had unprecedented improvements since they first were used as a solar cell absorber in 2009. These materials have the formulation ABX3 and their properties can be tuned by changing the specific stoichiometry, while keeping the same crystal structure. Halide perovskites can be deposited many different ways and despite being polycrystalline they have excellent opto-electronic properties. We performed an in depth study of one of the highest performance deposition methods using lead chloride and three molar equivalents of methylammonium iodide to understand how it formed high quality films. Using x-ray photoelectron spectroscopy and x-ray fluorescence, we determined that the final film contains less than 1% chlorine. We also ascertained that the chlorine and excess methylammonium sublimated during annealing. Finally, using in-situ UV-vis absorption and x-ray diffraction measurements, we examined the kinetics of film formation and discuss possible structures for the crystalline precursor phase. Sensitive optical absorption measurements can help determine what limits solar cell efficiency and identify sub-bandgap trap states. We characterized several perovskite compositions with photothermal deflection spectroscopy and Fourier transform photocurrent spectroscopy. Using these techniques we identify Sn4+ as a trap state in lead tin mixed perovskites. We discuss the challenges of using these techniques as well as those associated with using these measurements to determine the radiatively limitied voltage. Finally, we discuss the stability of the solar cells in reverse bias. In a solar module, a shaded cell is forced to pass the photocurrent of its unshaded neighbors. This forces the cell into reverse bias where it dissipates power which can cause damaging heating. Halide perovskite solar cells breakdown or allow current to pass in reverse bias between -1V and -4V and the breakdown current is passed uniformly across the entire device. Holding a cell in reverse bias causes a significant decrease in efficiency, but this is due to a drop in open-circuit voltage rather than a decrease in shunt resistance seen in other technologies. Additionally, this efficiency degradation is mostly reversible. Our proposed mechanism supported with drift-diffusion modeling is that under reverse bias mobile ions move towards the electrodes causing band bending which allows for tunneling of carriers. The decrease in efficiency appears to be due to some reaction of these ions which causes them to be charge compensated. The degradation that takes longer and longer to recover each time, so there may be permanent damage. We propose two solutions. First, if the degradation reaction could be prevented, we would actually want a lower breakdown voltage to lower the dissipated power and heating. Second, if the degradation cannot be prevented, bypass diodes will need to be used and in that case we would want to increase the breakdown voltage.
Depth perception in holography [electronic resource]
Keywords: Physics.

According to the holographic principle, information about our world can be encoded in a projection of one less dimension, similar to a hologram. This principle has culminated in the discovery of the AdS/CFT duality, an explicit example of holography where, miraculously, the lower-dimensional projection is a theory of familiar local fields. But how is the extra dimension encoded in this holographic theory? The equivalence between a gravitational theory and a lower-dimensional theory implies a radical reorganization of the degrees of freedom: the fundamental building blocks of a gravitational theory are likely extended, not point-like, objects. In this thesis, I describe progress towards formulating both sides of the duality in terms of extended probes -- objects which naturally possess the ability of "holographic depth perception.".
Design and analysis of loyalty reward programs [electronic resource]
Keywords: Management Science and Engineering.

This thesis provides an in-depth analysis of two major components in the design of loyalty reward programs. First, we discuss the design of coalition loyalty programs - schemes where customers can earn and spend reward points across multiple merchant partners. And second, we conduct a model based comparison of a standalone loyalty reward program against traditional pricing - we theoretically characterize the conditions under which it is better to run a reward program within a competitive environment. Coalition loyalty programs are agreements between merchants allowing their customers to exchange reward points from one merchant to another at agreed upon exchange rates. Such exchanges lead to transfer of liabilities between merchant partners, which need to be frequently settled using payments. We first conduct an empirical investigation of existing coalitions, and formulate an analytical model of bargaining for merchant partners to agree upon the exchange rate and payment parameters. We show that our bargaining model produces networks that are close to optimal in terms of social welfare, in addition to cohering with empirical observations. Then, we introduce a novel alternate methodology for settling the transferred liabilities between merchants participating in a coalition. Our model has three interesting properties -- it is decentralized, arbitrage-proof, and fair against market power concentration -- which make it a real alternative to how settlements happen in coalition loyalty programs. Finally, we investigate the design of an optimal reward program for a merchant competing against a traditional pricing merchant, for varying customer populations, where customers measure their utility in rational economic terms. We assume customers are either myopic or strategic, and have a prior loyalty bias toward the reward program merchant, drawn from a known distribution. We show that for the reward program to perform better, it is necessary for a minimum fraction of the customer population to be strategic, and the loyalty bias distribution to be within an optimal range. This thesis is a useful read for marketers building promotional schemes within retail, researchers in the field of marketing and behavioral science, and companies investigating the intersection of customer behavior, loyalty, and virtual currencies.
Design and control of series elastic actuators for disturbance rejection [electronic resource]
Keywords: Mechanical Engineering.

Control abstractions allow robotic control systems to be built up layer upon layer. Each subsystem is considered independent, enforcing modularity, hierarchy, and clarity. At the foundation lie actuators, the source of force and motion. Ideally, actuators produce precisely the force or motion commanded, with no knowledge of the control layer above. But in reality, joints with elasticity couple the robot link dynamics to the actuator dynamics. In this thesis, we present the design and control of series elastic actuators (SEA) for disturbance rejection, in order to better realize uncoupled behavior. This thesis is presented in five parts. First, we introduce the concept of SEA, and show the importance of disturbance rejection for actuator abstraction. Current design and control practices have shortcomings with regard to multi-joint robotic systems. In order to treat actuators as ideal sources of commanded torque, we consider both the force response and disturbance response. Second, we review existing SEA controller design for torque control, and present a modification which simplifies control parameter tuning by reshaping the system's dynamics. The controller is validated on an experimental setup. Third, we describe the relevance and implications of disturbance rejection of SEA under closed-loop control. A new design and control methodology based on disturbance rejection is presented. One application of this methodology is ensuring hybrid actuation design and control synergy. Fourth, we present new mathematical models for reactive SEA dynamics, and an accompanying controller design. Reactive SEAs can produce higher bandwidth torque and can be easier to build. Four configuration of reactive SEA are compared to traditional SEA, in force response, disturbance response, and force measurement. The proposed controller reshapes the dynamics, similar to that proposed for traditional SEA. The methods proposed throughout this thesis for design and control of SEA provide tools for shaping SEA's interaction with external forces, and characterizing each actuators' behavior as an independent subsystem.
Determining rare state populations in nucleic acid ensembles [electronic resource]
Keywords: Chemical Engineering.

Several features of nucleic acid behavior including RNA folding, protein-nucleic acid binding, and assembly of large nucleoprotein complexes (such as the ribosome or splicesosome) are dictated by the dynamic properties of nucleic acid molecules in solution. Understanding the properties of nucleic acids which influence their conformational landscape, and thereby their ability to engage in a multitude of functions, is an important biophysical challenge. While the methods of small angle X-ray scattering, Au-Au X-ray interferometry and nuclear magnetic resonance have enabled a characterization of the nucleic acid energy landscape, they do not allow for the characterization of low-populated states in the energy landscape. Low-populated states in nucleic acid energy landscapes play an important role because they represent intermediates in the molecules' folding pathway, and hence their identification and characterization could enable an understanding of higher order nucleic acid binding or assembly processes. In this work, a crosslinking approach has been employed to derive an understanding of low-populated states in the energy landscape of a nucleic acid. The crosslinking approach relies on using nucleic acid conjugated with a disulfide on one hand and a thiol modification on the other, which upon reaction result in the formation of nucleic acids crosslinked via a disulfide bridge. With this approach, the kinetics of disulfide bridge formation is measured and the populations in low-populated states, inferred. The crosslinking approach was applied to a number of nucleic acid motifs in order to provide a proof-of-principle that it can be employed to resolve differences in dynamics between them. The approach was extended to measure populations of molecules in low-populated states within nucleic acid ensembles, through estimations of an Effective Molarity (EM). The approach applied to a double-stranded DNA duplex showed that a large variation in EM for crosslink tether positions on the dsDNA duplex could be observed. When applied to double-stranded DNA duplexes linked by a polyethylene glycol (PEG) junction, relative populations within different subspaces of the molecule could be determined. The approach was also utilized to determine the dynamic circularization behavior of an RNA motif. The experiments described in this work indicate that the crosslink approach may indeed be useful to probe low-populated state populations in nucleic acid ensembles. It permits us to further our understanding of nucleic acid folding and higher order binding and assembly processes, since it opens us the possibility of isolating and characterizing low-populated states, which serve as intermediates in these processes.
Developing an instrumented mouthguard to study human mild traumatic brain injury [electronic resource]
Keywords: Bioengineering.

Mild traumatic brain injury has been recognized as a silent epidemic, with seemingly transient acute symptoms but potential long-term irreversible brain changes. In more recent years, with increasing awareness of the dangers of concussive and subconcussive trauma, the condition is becoming less and less silent, but still remains invisible. It is known that external forces on the head cause injury, yet their exact effects on the brain are unknown. Although animal studies have helped uncover potential biomechanical mechanisms of injury, there is a lack of human data to confirm any hypotheses. In the current thesis work, an instrumented mouthguard was developed to optimize for kinematic accuracy and impact detection accuracy for the collection of high quality human data in contact sports. It was found that a mouthguard form factor provided tighter skull-coupling than soft tissue-mounted or headgear-mounted sensors. In addition, we identified sensor bandwidth requirements to ensure head impact kinematics are sufficiently captured for computing injury risk criteria. We also designed and validated a head impact detection system in both laboratory and field scenarios to accurately detect helmet contacts from other field activities. Applying the instrumented mouthguard in field studies helped to provide the first evidence of directional dependence of injury from human data, and linked subconcussive head impact exposure with neurological deficit. In the near future, human data gathered using the instrumented mouthguard can help better understand the mechanisms of mild traumatic brain injury, enable on-field real-time injury screening, and aid in the design of better preventative equipment.
Development and application of high-throughput sequencing based methods to explore human variation and disease [electronic resource]
Keywords: Genetics.

In-depth studies of human disease and variation have been greatly enabled by a variety of high-throughput sequencing methods. Efforts that integrate genomic, transcriptomic and protein/nucleic acid binding genome-wide further expand our understanding of the genome and the regulatory information that governs it. In this work we present three efforts centered on the use of integrated high-throughput sequencing methods to unravel questions of human disease and variation. The first describes a novel method for simultaneous DNA and RNA sequencing library preparation (Simul-seq), which provides comprehensive data from small quantities of cells or tissue in a streamlined workflow. Single assay integration provides opportunities for analysis of regulatory variation, RNA editing and allele-specific expression, in addition to genotype and phenotype information. Applying Simul-seq to a laser-capture microdissected esophageal adenocarcinoma, we reveal a highly aneuploid genome with corresponding increases in allele specific expression and both novel and known expressed, nonsynomous mutations. The next work uses ChIP-seq, RNA-seq and Hi-C among other data types to enumerate the effects of genetic variation on chromatin state and RNA levels. Among the findings, we show that long-range interactions govern the effects of QTLs on distal chromatin variation. Finally we profile a diverse panel of 25 cell lines using an improved ChIA-PET method along with RNA-seq to better understand the role chromosomal looping plays in genetic and epigenetic regulation. Enabled by the modified protocol, we find evidence for differential looping between cell types. Taken together we have shown that integration of sequencing methods, or their data provide the best possible foundation for genome interpretation and personalized medicine.
Development and organization of the Drosophila olfactory circuit [electronic resource]
Keywords: Biology.

The formation of complex but highly organized neural circuits requires precise recognition and interactions between cells that constitute the nervous system. A growing body of research has discovered numerous neuro-neuronal interactions underlying neural development, while the important roles played by glia are appreciated only more recently. In this thesis, I utilized the olfactory circuit of Drosophila melanogaster as a model to study the roles of both neurons and glia which together establish the unique structure of the olfactory system. During the assembly of the Drosophila olfactory circuit, ~50 olfactory receptor neuron (ORN) classes and ~50 projection neuron (PN) classes form one-to-one synaptic connections in ~50 glomerular compartments in the antennal lobe, each of which represents a discrete olfactory information processing channel. Several cell surface molecules have been reported to mediate neuro-neuronal interactions and determine the specific connectivity of olfactory neurons. However, we are still far from a complete understanding of this process. In a genetic screen to look for additional wiring molecules in this process, I identified Fish-lips (Fili), a leucine-rich repeat transmembrane protein, to be expressed in a subset of olfactory neurons. Loss- and gain-of-function experiments indicate that Fili can instruct PN dendrites to project to proper glomerular targets. Besides olfactory neurons, the antennal lobe is also permeated by several types of glia. Specifically, each glomerular compartment is separated from the adjacent compartments by membranous processes from the ensheathing glia. In a genetic screen designed to reveal molecular mechanisms underlying glia morphogenesis, I identified that Thisbe, a fibroblast growth factor released from olfactory neurons particularly local interneurons (LNs), controls ensheathing glia to wrap each glomerulus. The FGF receptor, Heartless, acts cell-autonomously in ensheathing glia to regulate process elaboration so as to insulate each neuropil compartment. Overexpressing Thisbe in ORNs or PNs causes over-wrapping of glomeruli to which their axons or dendrites target. Failure to establish the FGF-dependent glia structure disrupts precise ORN axon targeting and discrete glomerular formation. In summary, I have identified two molecular mechanisms underpinning the assembly of the olfactory circuit. Fili, combined with previously identified cell surface cues, can define dendrites from different PN classes and instruct them to target correct glomeruli. After the initial innervation of PN dendrites and ORN axons, ensheathing glia respond to a neuronal cue, Thisbe, to pattern the boundaries of the nascent glomerular compartments; neural compartments in turn require such glial barriers to separate themselves from neighboring compartments, so as to ensure the correct organization of the olfactory circuit. These findings highlight the synergism of neurons and glia in shaping the intricate network of the nervous system.
Development of a Human iPSC-based Model System for Functional Analysis of PPARγ Knockout in Patient-derived Cardiomyocytes Using CRISPR/Cas9
Keywords:  Department of Biology
Biology
CRISPR
Rosiglitazone
Diabetes
PPAR
Gene-editing
Stem-cell
Thesis

Diabetes is a devastating disease that affects over 400 million people worldwide. Most of those affected with diabetes have some degree of insulin resistance. Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulatory receptor often targeted by drugs such as Rosiglitazone to overcome insulin resistance, and plays a major role in cardiovascular health and metabolism regulation. This research aims to elucidate the mechanism underlying PPARγ function by knocking out the gene using CRISRP/Cas9 as well as by assessing the effects of Rosiglitazone treatment on cardiomyocytes. In this study, a human induced pluripotent stem cell (hiPSC) platform was utilized for the first time to successfully induce a PPARγ knock-out (KO) and allow for further study of the KO’s effect on cellular metabolic function in human cardiac cells. A CRISPR-based approach was employed to knockout PPARγ in an iPSC line obtained from healthy individuals. Successful KO was verified via TOPO screening and Sanger sequencing. These cells are currently being differentiated for further analysis. In parallel, cardiomyocytes treated with varying doses of Rosiglitazone were assayed for changes in gene expression and cell viability. These cells were characterized by measuring mRNA expression of PPARγ and related genes implicated in cardiovascular and metabolic regulation. qRT-PCR of these genes, including PPARγ showed a significant increase in mRNA expression in treated cardiomyocytes compared to controls. Importantly, these genes have been suggested to be regulated by PPARγ and to participate in control of cellular metabolic function. Therefore, analysis of their differential expression following Rosiglitazone treatment may provide insight into PPARγ-dependent regulation of cardiovascular health. These results contribute to the molecular and genetic understanding of PPARγ and Rosiglitazone treatment in development of cardiovascular diseases, as they show effects on key metabolic genes and cell function.
Development of X-ray absorption diagnostics for gas-phase reacting flows [electronic resource]
Keywords: Mechanical Engineering.

Accurate experimental measurements are critical to the design and understanding of efficient combustion systems. While new heterogeneous combustion technologies such as Porous Media Burners (PMBs) have demonstrated favorable combustion properties including an extended lean flammability limit, low emissions, and wide dynamic power range, they also pose challenges for traditional experimental techniques. Because combustion occurs within a porous ceramic matrix, physical probes can disturb the combustion environment while engineering optical access becomes difficult. Further, data provided by existing methods is generally of insufficient spatial dimensionality to fully describe complex internal PMB physics. In this context, the development of new diagnostics that can provide measurements of relevant physical quantities non-intrusively, without optical access, and with high spatial resolution becomes a challenge in creating experimental datasets that improve fundamental physical understanding of PMB systems. In this work, a diagnostic for gas-phase reacting flows is developed based on the principles of X-ray computed Tomography (XCT) at clinical energies, and applied to three different systems of interest. Clinical fan-beam XCT is first applied to a turbulent gas-phase krypton jet, and it is shown that X-ray attenuation measurements can resolve krypton mole fraction within the jet in three dimensions with high quantitative accuracy. A cone-beam X-ray system is then used to image a krypton-diluted, premixed Bunsen flame via XCT. Simultaneous data series describing visual emission and X-ray attenuation are performed, and scanner noise trends are evaluated via both experiment and simulation. Comparison of experimental data to an axisymmetric simulation with detailed chemistry is demonstrative of both the utility and phenomenology of the X-ray attenuation signal as a density surrogate in reacting flow measurements. Effects of the krypton contrast agent on important combustion quantities such as flame speed and temperature are also evaluated. Finally, measurements of a porous media burner are performed with cone-beam XCT, and theory is developed to relate X-ray attenuation to gas-phase temperature. Using this method, experiments are performed to demonstrate temperature measurement of a krypton-diluted flame within the optically opaque porous ceramic matrix of the PMB. Temperature measurements in the gas phase are contrasted with direct thermocouple measurements, and the effect of imaging artifacts and experimental uncertainties is analyzed in detail.