VictorJuiz/thesis huggingface dataset:
Electronic and vibrational dynamics of photo-excited A7 structures [electronic resource]
Keywords: Applied Physics.

The interaction of intense femtosecond laser pulses with matter leads to highly excited transient states far from equilibrium. The dynamics of these excited states relate to many applications from laser machining to energy conversion. Ultrafast optical and x-ray light-scattering has emerged as a powerful experimental method to study material dynamics on the time-scale of atomic and even electronic motion. Here I report results of ultrafast coherent and squeezed phonon scattering experiments in bismuth and antimony. In response to laser-generated coherent phonons, I find dynamics of the coherent A1g vibrational mode greatly dependent on non-thermal electronic band-occupation. And in response to laser generated squeezed phonons, I find anisotropic changes in dynamical forces evidenced by differentiated high wavevector acoustic mode softening. These results advance our understanding of microscopic electron-electron and electron-phonon interactions in transient systems.
Elucidation of Topographical Design Principles for Electrospun Matrices
Keywords: Benitez, Patrick
Bioengineering.
Bioengineering
Materials Science and Engineering
electrospinning
vascular grafts
topography
VE-cadherin
mechanotransduction
YAP
endothelial cell
endothelium
matrix
fabric
cytoskeleton
nuclear actin
epigenetic regulation
Firestone Medal for Excellence in Undergraduate Research
Thesis

Synthetic vascular grafts are characterized by poor long-term patency as low as 50% for small-diameter applications. Thrombosis is a major cause of failure and is attributed to the inability of the neighboring, quiescent endothelium to migrate and proliferate across the graft luminal surface. Hence, there is a large clinical need for implantable biomaterials that promote endothelial migration and proliferation. Recent strategies for engineering implantable biomaterials in the vasculature have leveraged well-defined mechanical and biochemical design principles to achieve such cellular phenotypes. However, despite the clear influence of native extracellular matrix topography on endothelial cell physiology and morphology in vivo, well-defined design principles regarding fibrous matrix topography are lacking. Here, we engineer and characterize an electrospun elastin-like protein platform with mean fiber diameter varied from 0.8 to 2.0 μm, independently of biochemical and mechanical properties. We then demonstrate that an increase in topographical size scale from the submicron to micron level drives an increase in endothelial cell migration and proliferation, specifically through the disruption of VE-cadherin cell junctions. The resulting loss of contact inhibition via VE-cadherin and upsurge in cytoskeletal contractility-induced mechanotransduction signaling is associated with a monolayer-wide shift in intracellular signaling (ERK1/2 phosphorylation, YAP localization), transcriptional activity (nuclear actin accumulation, interleukin 8 expression) and even epigenetic regulation (heterochromatin fraction) in response to more undulant fibrous topography. Finally, we propose and assess a mechanism linking undulant fibrous topography to endothelial cell junction disruption, wherein increased membrane curvature around larger diameter fibers imparts local tensile forces via the cytoskeleton to physically disrupt junction integrity. Results here have implications not only for the design of next generation vascular grafts that maintain long term patency by supporting migratory and proliferative endothelial phenotypes, but also for current understanding of how topographical features of the native vascular extracellular matrix drive cellular organization and organogenesis.
Emergent symmetries in quantum impurity experiments [electronic resource]
Keywords: Physics.

In systems involving a continuum of energy scales, one can imagine that under renormalization an effective Hamiltonian valid at low energies could possess a symmetry that the bare Hamiltonian does not. We are interested in the extent to which measurements of a physical system may reflect such emergent symmetries. Localized spins coupled to reservoirs of electrons are a natural domain to study these phenomena. Such "quantum impurity" systems can be realized using quantum dots. We report transport measurements of two lithographically patterned quantum dot systems in GaAs/AlGaAs heterostructures: 1. In a capacitively-coupled double quantum dot, gate voltage can be used to tune the system so that it is equally favorable for either dot to hold one electron. The effective Kondo Hamiltonian valid at low energies has been predicted to have an emergent SU(4)-symmetric exchange interaction based on the spin and orbital degrees of freedom. We provide evidence for emergent SU(4) symmetry by carefully comparing temperature-dependent conductance with numerical renormalization group calculations. In our device, conductance may be measured through each dot individually, uniquely enabling orbital state-resolved spectroscopy of the Kondo state. 2. A quantum dot tunnel-coupled to a metallic grain can host a non-Fermi liquid two-channel Kondo state, where a spin-1/2 impurity is exchange-coupled to two independent electron reservoirs. It occurs at the critical point of a second-order quantum phase transition, which surprisingly has exact theoretical descriptions both at and away from the critical point, even at finite temperature. We confirm transport signatures of quantum criticality as first reported by Potok, et al. (Nature 446, 167 (2007)), and then go further by quantitatively validating a universal theory for the crossover to a Fermi liquid. The universality of this crossover in the presence of arbitrary symmetry-breaking perturbations is a consequence of emergent symmetry at the non-Fermi liquid fixed point.
Empirical studies of expert behavior [electronic resource]
Keywords: Business.

"The Foreclosed Option Fallacy." Foreclosed options influence behavior even when they have no bearing on future outcomes. This paper documents a foreclosed option fallacy in NFL kickoff returns. I compare returns from just behind the goal line, for which the returner declined an option to achieve the 20-yard line with certainty, to returns from just in front of the goal line, for which no such option was available. Consistent with loss aversion around the certain outcome of the declined option, returners are 56% more likely to be tackled at the 20-yard line after the touchback option is foreclosed than when it was never available. "Expertise in the Field Fades in the Lab" (with Justin M. Rao and David Rothschild). We conduct field and laboratory experiments on the same panel of experts, measuring the internal consistency of their predictions 1) in the field, in their domain of expertise, and 2) on a conceptually identical laboratory exercise. Experts make internally consistent predictions in the field, both in absolute terms and relative to a panel of novices, but they exhibit markedly less consistency on the isomorphic lab exercise. Possible explanations for this fading expertise include low motivation in the lab and a failure to transfer skills learned implicitly in the field to the more abstract lab setting. "Impact Aversion in Arbitrator Decisions" (with David P. Daniels). An aversion to salient mistakes leads arbitrators to make mistakes more often, even where directives are clear, incentives strong, and post-hoc evaluation perfect. We study the choices of Major League Baseball umpires, who are directed to make binary decisions according to a single, objective criterion: pitch location. Using state-of-the-art pitch location technology, we examine over one million such decisions and find that every umpire in our sample distorts his directive by avoiding the option that would more strongly change the expected outcome of the game. This impact aversion is consistent with an avoidance of public scrutiny. Umpires face criticism from the public for mistakes that disrupt the course of the game; impact-averse umpires avoid scrutiny by avoiding game-changing options that could be mistaken.
Energy-efficient coarse-grain out-of-order execution [electronic resource]
Keywords: Electrical Engineering.

Throughout the past decade, energy efficient computing has been a major problem in the computer system space from device technologies, to chip design, to computer architecture and software systems. Today, we have more smartphone devices in the hands of consumers than ever before, and we generate more data on the internet than ever before. This trend implies that moving forward, building energy efficient systems remains an increasingly significant challenge both in the mobile industry and in the server industry. Building energy efficient processors is at the forefront of solving these technological challenges. This doctoral dissertation describes the Coarse-Grain Out-of-Order (CG-OoO) processor architecture. Block-level code processing is at the heart of the CG-OoO architecture; CG-OoO speculates, fetches, schedules, and commits code at block-level granularity. CG-OoO eliminates unnecessary accesses to energy consuming tables, and turns large tables into smaller and distributed tables that are cheaper to access. CG-OoO leverages compiler-level code optimizations to deliver more efficient static code. It exploits instruction-level parallelism and block-level parallelism. CG-OoO introduces the Skipahead model which is a complexity effective, limited out-of-order instruction issue model. It is an energy-performance proportional design that can scale according to the program load. Through the energy efficiency techniques applied to the compiler and processor pipeline stages, CG-OoO delivers over 50% energy reduction at the performance of the baseline out-of-order processor.
Energy-efficient optical access/in-building networks [electronic resource]
Keywords: Electrical Engineering.

This dissertation focuses on the design of energy-efficient optical access/in-building networks and their protocols. We introduce the Cascaded Bit-interleaved optical network protocol, an energy-efficient solution aiming to achieve low power consumption in converged optical access/in-building networks while providing high data rates to end-users, and propose a novel network architecture for optical access/in-building networks. In the proposed network architecture, optical-electrical-optical (OEO) regeneration is employed at the interface between access and in-building networks. The downstream frames are generated in the central office using a two-stage bit-interleaving scheme. In the downstream direction, the network nodes only process the data destined for them at a lower clock rate than that of the aggregate passive optical network (PON). In the upstream direction, no word alignment or decoding is performed in the intermediate nodes. We present detailed simulation and experimental results we obtained and show that a significant reduction in the power consumption of access/in-building networks can be achieved when the proposed Cascaded Bit-interleaved Protocol is employed in conjunction with the proposed network architecture.
Engaging Children in Discussions of Disfigurement and Disability: The Wonder of Palacio’s Wonder
Keywords:  Program in Human Biology
Graduate School of Education
disfigurement
disability
children's literature
Thesis

This study examined children's engagement with Wonder by RJ Palacio and explored the ways in which the children's literature could be used to promote critical, reflective and broad discussions of complex themes, such as disfigurement and disability, among young children. Eight students between the ages of 9 and 12 were assigned the reading of Wonder. They participated in an individual interview followed by a group interview. Interviews were coded with the objective of classifying each participant by type of engagement and examining references to specific themes of appearance, bullying, disability and disfigurement. Results indicated that children differentially engage with Wonder: four were engaged with both the novel and discussion, two were engaged with only the novel, one was engaged with only the discussion, and one was engaged with neither. Some children are capable of using Wonder to inform their own real-life experiences of and encounters with bullying, disfigurement and disability and/or discuss these social issues beyond the scope of the novel. Furthermore, some children are not only capable of discussing Wonder through critical lenses such as disfigurement and disability studies, but doing so adds crucial nuance to their simplistic initial interpretations of the novel and its themes.
Engineering cell access using nanostraws [electronic resource]
Keywords: Materials Science and Engineering.

The study of biology is driven by our ability to perturb biological systems and observe the outcomes. At the cellular level, by predicting the presence of a biological interaction and perturbing elements of that interaction, we increase our understanding of how a cell functions. Interactions between biomolecules consist of binding events, enzymatic breakdown, metabolic synthesis, and many others, but one valuable distinction between interactions is the locale, which can be extracellular or intracellular. Extracellular signals allow cells to interface with their environments including other cells and soluble signals, but the majority of signaling events occur intracellularly. To protect the integrity of the cell, the cell membrane tightly regulates the passage of molecules, which provides a robust barrier between the extracellular and intracellular space. Therefore, perturbing intracellular elements of the cell effectively requires a method for accessing the cell without disruption. One strategy for passing material through the cell membrane is to use the cell's natural uptake mechanisms, thereby limiting the disruption to the cell. Unfortunately, methods which leverage endocytosis or other uptake mechanisms can do little to protect the cargo from the cell's inherent defense mechanisms. An alternative strategy is to physically deliver material into the cell by creating gaps in the cell membrane. Until recently, this was difficult because small nanometer scale gaps could not be reliably formed in cells. However, advances in fabrication have allowed nanometer scale objects to be reliably produced, which have demonstrated promise as a pathway to cell access. This thesis describes the development of a technique based on high aspect ratio hollow nanowires, called nanostraws, which we use to deliver material into cells. Compared to other nanowire techniques, nanostraws are capable of timed delivery, which provides a powerful, unique lever in engineering cell access. Beginning with fabrication, we discuss the types of nanostraw devices used for delivery and we characterize cell behavior on the nanostraws. Later, we apply the nanostraw devices to study a point of controversy in the field of nanowire delivery, the question of whether or not nanowires penetrate into cells. This study is complemented with studies of cell behavior or adhesion and their effects on delivery. We then use the nanostraws to observe the effects of perturbing the cell cytoskeleton on delivery and penetration. This thesis concludes with a discussion of the field of nanowire delivery at large, and future directions for nanowires and nanostraws in particular.
Engineering electron metabolism in cyanobacteria [electronic resource]
Keywords: Bioengineering.

Photosynthesis offers tremendous promise for driving sustainable production of the chemicals our society requires. Recent years have seen many inspiring demonstrations of an array of biochemical pathways in photosynthetic hosts, but progress has been limited by a lack of foundational engineering capabilities. We have made advances along two avenues towards using photosynthesis for sustainable chemical production: metabolic engineering of a cyanobacterium to produce hydrogen from sunlight, and new procedures to make cyanobacteria easier to engineer. As a metabolite, hydrogen is unique. The pathway is rather simple, just one reaction away from a major product of photosynthetic electron transport. What is complex is the enzyme that catalyzes the hydrogen production reaction. We describe two projects to prepare a cyanobacterial host to express a complex foreign hydrogenase: upregulating the synthesis of iron-sulfur clusters required for electron transfer, and developing the ability to express proteins anaerobically. Both are ultimately connected to electron metabolism. Our work and that of others has been hindered by the relatively limited state-of-the-art of cyanobacterial engineering. Thus, we made parallel efforts to improve two fundamental operations in the strain engineering cycle: transformation with foreign DNA and cell lysis for intracellular analysis. This resulted in a simple procedure to reliably lyse cyanobacteria for high-throughput and small-sample applications.
Engineering fluorescent proteins for improved FRET performance and four-color biosensing [electronic resource]
Keywords: Bioengineering.

Engineered fluorescent proteins (FPs) have been widely used as biosensor components and protein tags. Improved and diversified variants continue to expand the FP toolbox, allowing us to re-design existing biosensors and develop new ones. In my thesis work, I present three new FPs and demonstrate the relevance of their improved properties in two applications. In the first example, I show that Clover and mRuby2, new green and red FPs engineered as a FRET (Förster Resonance Energy Transfer) pair, improve the performance of FRET-based reporters when substituted for traditional cyan FP (CFP) and yellow FP (YFP) pairs. Clover and mRuby2 improved photostability, FRET dynamic range, and emission ratio changes; and these improvements enhanced detection of transient biochemical events such as neuronal action potential firing and RhoA activation in growth cones. In the second example, I show that an engineered red FP, Maroon1, possessing a uniquely red-shifted excitation, enables the use of genetically encoded reporters in a fourth wavelength channel beyond the three common blue-cyan, green-yellow, and orange-red channels. In conjunction with the Fucci cell cycle reporter system, I used Maroon1 and the cyan FP, mTurquoise2, to label histone H1.0 and PCNA, respectively. Using this system, Fucci4, all four cell cycle stages can be visualized during live-cell imaging.
Engineering in vitro photobiological hydrogen production [electronic resource]
Keywords: Bioengineering.

Hydrogen is an important industrial chemical and attractive next-generation fuel. Current methods for its production rely on steam reformation of fossil fuels which liberates greater than 1% of the annual global carbon dioxide emissions; therefore, there is a need for sustainable hydrogen production processes. Nature has provided a biological catalyst for hydrogen production in [FeFe] hydrogenases. These complex enzymes catalyze the reaction which combines electrons and protons to generate hydrogen. Our long term goal is to integrate a non-native [FeFe] hydrogenase into the photosynthetic electron transport chain of a cyanobacterium to couple photosynthetic water-splitting with hydrogen production. One challenge to implementing this pathway is that heterologous hydrogenases interact inefficiently with the photosynthetic machinery and electrons will be lost to native, competing pathways in the cyanobacteria. Engineering the hydrogenase and other pathway components in vivo is challenging due to the limited tools available for genetic engineering these photosynthetic organisms. We developed an improved in vitro pathway using Photosystem I complexes isolated from a cyanobacterium to mimic in vivo electron flow to the hydrogenase or the main competing pathway, the production of NADPH. This system provides fine-tuned control over the reaction components and environment including concentrations of proteins in the pathways to study and control electron flux. We demonstrate the use of a non-native ferredoxin to facilitate electron transfer between the photosystem and hydrogenase. Finally, we will describe coupling our photosystem-pathway with a high-throughput hydrogen sensor to assess hydrogen production rates in microtiter plates. This approach can be extended to the high-throughput screening of in vitro synthesized enzyme or electron carrier libraries to develop components that support high photobiological hydrogen production rates.
Engineering new capabilities into optical microscopes [electronic resource] : toward measuring the three-dimensional position and orientation of single molecules in living cells
Keywords: Electrical Engineering.

The labeling of specific biological structures with single fluorescent molecules has ushered in a new era of imaging technology: super-resolution optical microscopy with resolution far beyond the diffraction limit down to some tens of nm. With the features of these exquisite tools in mind, this Dissertation discusses optical strategies for measuring the three-dimensional (3D) position and orientation of single molecules with nanoscale precision and several super-resolution imaging studies of structures in living cells. The concepts of single-molecule imaging, super-resolution microscopy, the engineering of optical point spread functions (PSFs), and quantitative analysis of single-molecule fluorescence images are introduced. The various computational methods and experimental apparatuses developed during the course of my graduate work are also discussed. Next, a new engineered point spread function, called the Corkscrew PSF, is shown for 3D imaging of point-like emitters. This PSF has been demonstrated to measure the location of nanoscale objects with 2-6 nm precision in 3D throughout a 3.2-micrometer depth range. Characterization and application of the Double-Helix (DH) PSF for super-resolution imaging of structures within mammalian and bacterial cells is discussed. The DH-PSF enables 3D single-molecule imaging within living cells with precisions of tens of nanometers throughout a ~2-micrometer depth range. Finally, the impact of single-molecule emission patterns and molecular orientation on optical imaging is treated, with particular emphasis on multiple strategies for improving the accuracy of super-resolution imaging. The DH microscope is shown to be well-suited for accurately and simultaneously measuring the 3D position and orientation of single molecules.