VictorJuiz/thesis huggingface dataset:
Micro-patterned polymeric surfaces as directional and selective adhesives [electronic resource]
Keywords: Mechanical Engineering

Nature has recently become a great source of inspiration for researchers in the fields of adhesion and adhesives. A number of biological specimen have inspired impressive advancements as evolution has produced interesting solutions to the problems researchers are looking to solve. This work focuses on a particular type of adhesive, the manufacturing methods used to produce it, and the viability of such adhesives in standard and radiological environments. A novel type of micro-structure based adhesive, the selective adhesive, is introduced. This adhesive utilizes polymer micro-structures to selectively adhere to particles within a desired size range. Two iterations of the micro-structure design are presented and the performance of these adhesives is described. The second generation of the adhesive proves to be effective at sorting large numbers of particles based on their size in a passive manner, without the requirement of gravity or electrical input energy common to other particle sorting methods used in industrial or laboratory settings. Previous production methods used to manufacture the adhesive micro-structures have proven to have a number of limitations that would make the production of the desired micro-structure geometry difficult. To address this, a novel manufacturing method has been presented. This method, called micro-wedge machining, allows for significantly improved control over a number of micro-structure parameters. This improved control has allowed for the production of not only better selective adhesives, but also directional adhesives used for climbing applications, allowing for an improvement in maximum normal adhesion of approximately 100% over adhesives produced via older manufacturing methods. The biologically inspired adhesives discussed previously could foreseeably be used in a large number of environments. In most cases, the polymers that make up the adhesives can be assumed to be mechanically and chemically stable for the usable lifetime of the adhesive. However, this is not the case for a small number of environments. In the case of nuclear facilities or space applications, ionizing radiation fields can be present and have the capability to cause significant changes in the bulk polymer making up the adhesives. Because these effects can be significant, the effects of gamma and alpha radiation on the adhesives has been investigated. The adhesives prove to be quite robust, maintaining their performance out to very high absorbed radiation doses.
A millimeter-sized wirelessly powered and remotely controlled locomotive implant [electronic resource]
Keywords: Electrical Engineering

A wirelessly powered and controlled implantable device capable of locomotion in a fluid medium is presented. Two scalable low-power propulsion methods are described that achieve roughly an order of magnitude better performance than existing methods in terms of thrust conversion efficiency. The wireless prototype occupies 0.6mm x 1mm in 65 nm CMOS with an external 2mm x 2mm receive antenna . The IC consists of a matching network, a rectifier, a bandgap reference, a regulator, a demodulator, a digital controller, and high-current drivers that interface directly with the propulsion system. It receives 500 uW from a 2 W 1.86 GHz power signal at a distance of 5 cm. Asynchronous pulse-width modulation on the carrier allows for data rates from 2.5-25 Mbps with energy efficiency of 0.5 pJ/b at 10 Mbps. The received data configures the propulsion system drivers, which are capable of driving up to 2 mA at 0.2 V and can achieve a speed of 0.53 cm/sec in a 60 mT magnetic field.
Mixing time of Markov chains on finite and compact lie groups [electronic resource]
Keywords: Mathematics

This thesis studies the mixing time of three Markov chains on non-abelian groups. The first is a Metropolis Markov chain on the symmetric groups, initially introduced by Hanlon and Diaconis, and the last two are random walks on the special orthogonal groups, known as Rosenthal's walk and Kac's walk respectively. Using input from representation theory and symmetric function theory, it is shown that cut-off phenomena occur under total variation distance for the Hanlon-Diaconis chain and Rosenthal's walk. For the Kac random walk, a combination of functional-analytic and probabilistic techniques are used to establish the first polynomial order upper bound for its mixing time.
A model diffractive boundary value problem on an asymptotically anti-de Sitter space [electronic resource]
Keywords: Mathematics

We study the propagation of singularities (in the sense of smooth wave front set) of the solution of a model case initial-boundary value problem with glancing rays for a concave domain on an asymptotically anti-de Sitter manifold. The main result addresses the diffractive problem and establishes that there is no propagation of singularities into the shadow for the solution, i.e. the diffractive result for codimension-1 smooth boundary holds in this setting. The approach adopted is motivated by the work done for a conformally related diffractive model problem by Friedlander, in which an explicit solution was constructed using the Airy function. This work was later generalized by Melrose and by Taylor, via the method of parametrix construction. Our setting is a simple case of asympotically anti-de Sitter spaces, which are Lorentzian manifolds modeled on anti-de Sitter space at infinity but whose boundary are not totally geodesic (unlike the exact anti-de Sitter space). Most technical difficulties of the problem reduce to studying and constructing a global resolvent for a semiclassical ODE on the real half line, which at one end is a b-operator (in the sense of Melrose) while having a scattering behavior at infinity. We use different techniques near zero and infinity to analyze the local problems: near infinity we use local resolvent bounds and near zero we build a local semiclassical parametrix. After this step, the `gluing' method by Datchev-Vasy serves to combine these local estimates to get the norm bound for the global resolvent.
Model validation of mixed-signal systems [electronic resource]
Keywords: Electrical Engineering

Today it is difficult to validate a mixed-signal System-on-Chip, i.e., one which contains analog and digital components. The problem is that the analog and digital subsystems are usually strongly intertwined so they must be validated together as a system, but the validation approach for analog and digital blocks are completely different. We address this problem by creating high-level functional models of the analog components that are compatible with top-level digital system validation, and then providing a method of formal checking to ensure that these functional models match the operation of the transistor level implementations of these blocks. The formal checking of the functional analog models is enabled by observing that the result surface of an analog block is a smooth function of its analog inputs -- that is what makes it an analog block. This smooth result surface means it is not difficult to "explore" the design space of an analog block. We use this insight to create an equivalence checker between two analog descriptions: a SPICE netlist and its Verilog model. This checker exploits the fact that most analog circuits have a linear intent. Lastly we use this same insight to simplify statistical analysis of large mixed-signal systems to ensure that the system is robust to process variations. We describe a way to characterize the statistical behavior of circuits and to map the results to the functional model so one can estimate the parametric yield of the system by running system-level Monte Carlo simulations with analog models instead of circuit netlists.
Modeling Gas Production from Shales and Coal-Beds
Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis

Development of shale gas has transformed the energy outlook of US in the past decade. Identification of massive global resources and development of technology for economically producing gas from such sources is making a huge impact on the energy picture. According to EIA (EIA, 2011) the total gas resources of the world are estimated to be about 22,600 TCF of which 40% is now contributed by shale plays. Shales have complex pore networks and distinct scales for fluid flow. There are at least four types of porosities present in shales — Inorganic porosity, nano-porosity within organic Kerogen and porosity associated with both natural and artificially created fractures. Also, significant gas is assumed to be adsorbed in the Kerogen. Naturally occurring shales have little matrix permeability though. Horizontal drilling assisted by multi-stage hydraulic fracturing make gas production from shales viable. This increases near well-bore conductivity and also stimulates the network of natural fractures. Modeling fluid transport in shales is challenging. This is due to the combination of multiple porosities, gas desorption and slippage effects. We present two numerical schemes to simulate gas production from such systems. In the Single Porosity Model, we assume that there is only one distinct pore network and the gas desorbs instantaneously from the shale matrix as the reservoir depletes. In the Dual Porosity Model we consider two coupled porous networks with desorption in the organic nano-pores. Langmuir Adsorption Isotherm (Langmuir’s 1916) is used to model the desorption process. Slippage of gas molecules within nano-pores is incorporated using Klinkenberg’s Effect, (Klinkenberg 1941). Single Porosity Model is observed to be less consistent with both pore networks and desorption process in shales. In Dual Porosity Model, natural fractures permeability (kf) significantly affects early stage of gas production and matrix-fracture flux coefficient (Dmf) controls the slow desorbed flux in later half of production. Also, high Langmuir’s Volume (VL) increase production and delay pressure depletion within the reservoir. We also present a scheme to simulate gas recovery from naturally occurring coal seams. Single porosity, two phase gas-water code with instantaneous desorption is developed to model initial-dewatering and depletion phase of a typical Coal-bed Methane well.
Modeling scalar dispersion in urban environments [electronic resource]
Keywords: Mechanical Engineering

The expansion of High Performance Computing (HPC) capabilities is allowing Computational Fluid Dynamics (CFD) methods to be applied to model dispersion in urban areas. The problem of dispersion in such environments is of growing concern to governmental organizations and first responders interested in mitigating the effects of a terrorist attack or intentional release of a harmful substance. The fundamental physical phenomena underlying the dispersion processes to be modeled is that of turbulent mixing and transport. The processes are inherently of a multi-scale nature as releases proceed from localized sources to envelop larger areas. Adding to the modeling challenge within an urban environment is that complex geometries create strong anisotropies which traditional reduced-order modeling approaches fail to capture. In the first portion of this work, the computational infrastructure is assembled to enable simulations of dispersion in real urban environments. An Oklahoma City validation case is presented and compared with available experimental tracer data. Next, high-fidelity Direct Numerical Simulations (DNS) and Large-Eddy Simulations (LES) of dispersion in "building block" geometries are performed. The results are used to study dispersion flow physics within an urban-like canopy from the building to neighborhood scales. Additionally, the high-fidelity datasets are used to evaluate and drive improvements in the Reynolds-Averaged Navier-Stokes (RANS) modeling approach. Algebraic models are shown to yield an improved representation of the turbulent scalar flux as compared to the standard Schmidt number approach. It is shown that these scalar flux models can be combined with eddy-viscosity type turbulence closures when a better representation of normal Reynolds stress anisotropy is provided. The v2-f model is adapted to provide such a representation and improvement is demonstrated in predicting the scalar field from a point source release.
Modular scalable techniques for advanced magnetic resonance systems and radio-frequency instrumentation [electronic resource]
Keywords: Electrical Engineering

Magnetic resonance imaging (MRI) is unique among imaging modalities in providing exceptional versatility for examining a wide spectrum of anatomy and physiological functions. Modern MRI systems are moving toward higher magnetic field strengths for increased signal, and depend on rising receiver and transmitter channel counts to enhance speed, image quality, specificity, and safety. This has left researchers in a predicament. Commercial MRI scanners are becoming ever more capable and complex, yet by their nature inevitably lag the leading edge of science, failing to anticipate new research directions. Moreover, their closed proprietary hardware, software, and interfaces frustrate any expansion or adaptation to new techniques and experiments. Developed to address these challenges, the Medusa MRI console is a modular scalable open platform for advanced MRI research and development. Medusa enables MR methods and applications that would have been challenging or impossible using only commercial hardware, and does so with an efficient flexible architecture designed to grow to meet future needs. The Medusa MRI console delivers the complete set of functionality required for MRI including multi-channel radio-frequency (RF) excitation and reception, gradient waveform generation, coil and amplifier gating, and an open software platform for pulse sequencing and experimental development. Key features of Medusa include the use of direct-conversion digital RF components, distributed processing and memory for modularity and flexibility, and USB 2.0 High-Speed (480Mb/s) interfaces to the host PC. Medusa was first tested with the novel Stanford University Pre-Polarized MRI scanner, and is now used regularly for experiments on a diverse range of commercial and custom-built imaging systems. A significant application of Medusa has been the investigation and development of MRI Parallel Transmit techniques (PTx), which hold promise for improving MR safety and high-field image quality. Yet PTx methods demand high-fidelity delivery of RF pulses at kilowatt power levels across multiple channels into an unknown load. Vector Iterative Predistortion (VIP) was developed to address this challenge, using Medusa to encode the non-ideal response from RF amplifiers using sensors and iteratively pre-distort the input to achieve desired output. Even when used with cost-efficient low-fidelity RF power amps, VIP drives errors to below 0.1~dB and +/-1~degree phase, and is capable of correcting time-dynamic memory effects where traditional look-up table methods fail. Accurate RF sensing is essential in any RF control system, and on-coil and in-line vector RF sensing approaches were developed to enable real-time current, power, and impedance measurements. Notably, this monitoring permits not only the hardware characterization and control needed for VIP, but can also detect patient motion, cardiac and respiratory rhythms, and has the potential to assess and improve MR safety for patients with implanted devices.
Modulation of hepatitis C virus RNA abundance by the liver-specific microRNA miR-122 [electronic resource]
Keywords: Microbiology and Immunology.

Hepatitis C virus (HCV) is a global health problem, infecting approximately 2% of the world's population. The virus is hepatotropic, replicating in liver cells, and its only known hosts are humans and chimpanzees. HCV is an unusual virus in that it requires the liver-specific host microRNA (miRNA) miR-122 for HCV RNA accumulation. Though the precise mechanism by which miR-122 upregulates HCV RNA is still under investigation, it is known that miR-122 must bind to two adjacent sites in the 5' end of the HCV genome. In this dissertation, a stepwise mutational analysis of the entire sequence of miR-122 was performed to identify residues important for HCV RNA accumulation. All mutant miRNAs were tested in canonical miRNA reporter assays and in HCV RNA accumulation assays. The identities of two nucleotides within miR-122, at positions 15 and 16, were shown to be dispensable for canonical miRNA and siRNA activity but required for HCV RNA accumulation. Compensatory mutations in the HCV genome upstream of the original binding sites uncovered supplementary binding sites for nucleotides 15 and 16 of miR-122. This analysis led to a new model for miR-122-HCV RNA interactions. To further define the requirements of HCV for miR-122, we investigated whether the predecessor of mature miR-122, a long hairpin precursor designated pre-miR-122, was also able to mediate HCV RNA accumulation. The function of pre-miR-122 was tested in miRNA, siRNA, and HCV RNA accumulation assays. Inhibition of pre-miR-122 processing was achieved by substituting deoxyribonucleotides into the loop of pre-miR-122 to prevent Dicer-mediated cleavage. Full-length pre-miR-122 was demonstrated to be functional in miRNA and siRNA assays and to be sufficient for HCV RNA accumulation. Pre-miR-122 also required traditional components of the RNA-induced silencing complex (RISC) for activity. Taken together, this research has uncovered novel requirements of miR-122 for HCV RNA accumulation. Components shown to be dispensable for canonical miRNA interactions were necessary for this unusual microRNA-target RNA interaction. Uncovering hepatitis C virus's stringent requirements for the mature and precursor forms of miR-122 will pave the way for new antiviral therapies targeting a host factor.
Molecular mechanisms in neonatal naive CD4+ T cells contributing to the reduced Th1 immune response in human neonates [electronic resource]
Keywords: Immunology.

Human neonates are highly susceptible to infection by intracellular pathogens compared to adults, due in large part to a reduction in CD4+ T cell-mediated T helper type 1 (Th1) immunity. We have investigated the molecular mechanisms in the neonatal naive CD4+ T cell response that contribute to this reduction in neonatal Th1 immunity, and have identified differences in gene expression, epigenetic regulation, and T cell receptor signaling between neonatal an adult naive CD4+ T cells. Significantly, neonatal naive CD4+ T cells flux calcium to a higher degree than do adult naive CD4+ T cells in response to CD3 engagement. This enhanced calcium signaling is mediated by higher levels of the microRNA miR-181a, and is not accompanied by an increase in response to CD28-mediated costimulation. In neonatal cells, an increase in calcium signaling relative to a lack of induction of the AP-1 transcription factor indicates that neonatal naive CD4+ T cells may be prone to an anergic response. Neonatal naive CD4+ T cells share an enhanced calcium response with adult CD4+ recent thymic emigrants, a less mature peripheral CD4+ T cell population. We have also confirmed decreased capacity of neonatal naive CD4+ T cells to produce the prototypic Th1 cytokine interferon-gamma (IFN-[gamma]), and have obtained evidence that epigenetic modifications mediated by de novo methyltransferase 3a (Dnmt3a) are responsible for impaired cytokine production. Comprehensive profiling of gene expression and microRNA expression have uncovered further support for our functional observations of increased calcium flux and reduced Th1 function in neonatal naive CD4+ T cells. We have found that neonatal naive CD4+ T cells have reduced Th1 function and have enhanced T cell receptor proximal signaling in the absence of an enhanced response to costimulation, constituting a unique T cell phenotype.
Molecular packing in organic solar cells [electronic resource]
Keywords: Materials Science and Engineering

Organic solar cells based on blends of a conjugated polymer (donor) with a fullerene derivative (acceptor) offer promise as an inexpensive, printable, and flexible source of renewable energy. It is often assumed that polymer:fullerene blends used in organic solar cells phase separate into pure polymer and pure fullerene phases. However, my research has demonstrated the existence and importance of molecularly mixed polymer:fullerene bimolecular crystals, which form due to fullerene intercalation between the polymer side chains. I will demonstrate methods to control the presence of bimolecular crystals by tuning the fullerene size and the spacing and branching of the polymer side chains. This ability to control fullerene intercalation is used to make solar cells with and without bimolecular crystals so that their properties can be compared. I find that the presence of bimolecular crystals can significantly affect important properties such as absorption, exciton splitting, and charge transport due to the intimate mixing of the donor and acceptor. I will also discuss the determination and significance of the molecular packing in a polymer:fullerene bimolecular crystal using x-ray diffraction techniques, solid-state nuclear magnetic resonance, and molecular mechanics simulations.
Molecular recognition of phosphatases [electronic resource] : insights into specificity and the destabilizing influence of an enzyme active site
Keywords: Chemical and Systems Biology.

Chemical transfer of the phosphoryl group is perhaps the most critical and pervasive reaction in biology, and the enzymes that catalyze these reactions provide some of the largest reaction rate enhancements known. Phosphoryl transfer enzymes have evolved active sites with a remarkable ability to recognize and distinguish similar substrates and transient species along the reaction pathway. A full understanding of the physical features and recognition strategies used by these active sites is lacking and remains as a critical obstacle to the design of novel enzymes for applications in health and industry. All enzymes must provide preferential stabilization to reaction transition states while limiting binding to ground state substrates and products. Alkaline Phosphatase (AP) is one of Nature's most impressive examples, as it prefers stabilizing the phosphoryl group transition state by 10^22-fold compared to its modest binding of the phosphate monoester substrate in the ground state. Binding studies were carried out with a set of highly similar ground state molecules to probe this tremendous molecular discrimination. The results showed that despite the similarities of these molecules, AP has a very strong preference for binding inorganic phosphate (Pi). A vibrational spectroscopy approach was used to dissect the atomic details of Pi binding to AP. These measurements in addition to pH-dependent binding studies suggest that a proton from Pi is transferred to AP upon binding allowing it to bind more strongly than related molecules that lack a transferrable proton. It was proposed that the proton transfer neutralizes electrostatic repulsion between the anionic active site nucleophile of AP and the negatively charged oxygen atoms of the bound ligand. This model implicated a role for anionic active site nucleophiles, when left deprotonated, in destabilizing ground state binding and contributing to the enzyme's enormous preferential stabilization of the transition state. This previously unknown role for anionic nucleophiles was tested further using mutagenesis studies and binding affinity comparisons in AP and another phosphatase. The results provide new insights into how anionic nucleophiles of phosphoryl transfer enzymes contribute to catalysis.