Engineering Commons^™

Activity Preservation Of Plasmonic Biosensors With A Metal-Organic Framework, Lu Wang

McKelvey School of Engineering Theses & Dissertations

Antibody-antigen recognition enables antibody-conjugated nanostructures to serve as plasmonic biosensors with tunable specificity. However due to the instability of antibodies, these biosensors are susceptible to changes in the environment such as heat and aridity, leading to constraints on the transportation and handling of these sensors. Here we establish a method using a metal-organic framework crystal to preserve biosensor activity under severe environmental conditions, including exposure to high temperatures, an organic solvent and a proteolytic agent. After zeolitic imidazolate framework-8 (ZIF-8) crystals formed for 12 hours on a biosensor of gold nanorods conjugated with a model antibody, rabbit IgG, 80% of …

On Control Systems Of The Brain: A Study Of Their Connections, Activations, And Interactions, Haoxin Sun

McKelvey School of Engineering Theses & Dissertations

Implementation of daily functions in humans crucially relies on both the bottom-up moment-to- moment processing of relevant input and output information as well as the top-down controls that instantiate and regulate goal-directed strategies. The current dissertation focuses on different systems of brain regions related to task control. We are interested in investigating, in detail, some of the basic activity patterns that different control systems carry during simple tasks, and how differences in activity patterns may shed new insight onto the distinctions among the systems' functional roles. In addition, carefully coordinated interactions between brain regions specialized for control-related activity and regions …

Focusing Light Inside Scattering Media With Optical Phase Conjugation, Yan Liu

McKelvey School of Engineering Theses & Dissertations

In scattering media such as biological tissue, the heterogeneous refractive index distribution causes light to scatter, which makes the media look opaque and prevents us from focusing light beyond ~1 mm deep inside the media to achieve optical imaging and manipulation. Hence, the ability to focus light deep inside scattering media is highly desired, and it could revolutionize biophotonics by enabling deep-tissue non-invasive high-resolution optical microscopy, optical tweezing, optogenetics, micro-surgery, and phototherapy.

To break the optical diffusion limit and focus light deep inside scattering media, optical phase conjugation based wavefront shaping techniques, such as time-reversed ultrasonically encoded (TRUE) optical focusing, …

Novel Contrasts In Photoacoustic Tomography, Ruiying Zhang

McKelvey School of Engineering Theses & Dissertations

Photoacoustic tomography (PAT) combines rich optical contrast and high ultrasonic resolution in optically scattering tissue at depths. Taking advantage of its 100% sensitivity to optical absorption, PAT has been widely applied to structural, functional and molecular imaging, with both endogenous and exogenous contrasts, at superior depths than pure optical methods. This dissertation explores novel absorption contrast mechanisms of PAT based on optical/thermal patterns, endogenous cellular chromophores, nanoparticles, small-molecule dyes and genetically-encoded proteins. With these novel contrasts, the proof-of-concept applications of PAT have been extended to include homogenous flow measurements, targeted angiogenesis imaging and therapy, label-free white blood cell imaging, 3D-whole-organ …

Towards Clinical Photoacoustic Imaging: Developing Next-Generation Endoscopy Systems And Exploring New Contrast Agents, Chiye Li

McKelvey School of Engineering Theses & Dissertations

Photoacoustic imaging holds great clinical promise because it achieves high-resolution tomographic imaging at depths. Moreover, its strong spectroscopic imaging capability provides a wealth of molecular and functional information based on. Still, despite recent advances, existing photoacoustic systems cannot be readily applied in the clinical environment. This dissertation aims to push the frontier of clinical photoacoustic imaging from both technological and applicational perspectives.

The first part of this dissertation describes the development of photoacoustic endoscopy (PAE) systems for imaging human Barrett's esophagus and studying preterm birth. We have developed optical resolution-PAE, which significantly improved lateral resolutions, laparoscopic-PAE, which can guide minimally-invasive …

A Transactional Model And Platform For Designing And Implementing Reactive Systems, Justin Ross Wilson

McKelvey School of Engineering Theses & Dissertations

A reactive program is one that has "ongoing interactions with its environment." Reactive programs include those for embedded systems, operating systems, network clients and servers, databases, and smart phone apps. Reactive programs are already a core part of our computational and physical infrastructure and will continue to proliferate within our society as new form factors, e.g. wireless sensors, and inexpensive (wireless) networking are applied to new problems.

Asynchronous concurrency is a fundamental characteristic of reactive systems that makes them difficult to develop. Threads are commonly used for implementing reactive systems, but they may magnify problems associated with asynchronous concurrency, as …

Applications Of Aerosol Technologies In The Silicon Industry, Miguel Vazquez Pufleau

McKelvey School of Engineering Theses & Dissertations

In this dissertation, the focus was on two unit operations that have the potential to significantly lower the cost and energy required for refining silicon. First, the removal of carbon from silicon kerf (sawing dust from wafering) was examined to enable its recycling. Second, silane pyrolysis was studied to better understand the dynamics of the initial stages of silicon aerosol formation and growth.

Fluorescence Imaging Of Cortical Calcium Dynamics: A Tool For Visualizing Mouse Brain Functions, Connections, And Networks, Patrick William Wright

McKelvey School of Engineering Theses & Dissertations

Hemodynamic-based markers of cortical activity (e.g. functional magnetic resonance imaging (fMRI) and optical intrinsic signal imaging) are an indirect and relatively slow report of neural activity driven by electrical and metabolic activity through neurovascular coupling, which presents significant limiting factors in deducing underlying brain network dynamics. As application of resting state functional connectivity (FC) measures is extended further into topics such as brain development, aging, and disease, the importance of understanding the fundamental basis for FC will grow.

In this dissertation, we extend functional analysis from hemodynamic- to calcium-based imaging. Transgenic mice expressing a fluorescent calcium indicator (GCaMP6) driven by …

Characterizing Nonmodel Microorganisms And Reconstructing Catabolic Pathways For Bio-Productions, Whitney Hollinshead

McKelvey School of Engineering Theses & Dissertations

In the 1970s, spikes in oil prices sparked early interests into first-generation biofuels (i.e., the production of ethanol from corn). Four decades later, biofuel manufacturing has under-performed as developed industrial strains suffer from poor performance and high costs of feedstocks. While the advancement in molecular biology has greatly benefited pathway engineering, synthetic biology hosts still cannot overcome the obstacles for profitable microbial bio-production. One approach may be to study non-model organisms and employ their metabolic features towards an improved bio-production pipeline. Here, this thesis aims to develop 13C-metabolism analysis tools to characterize novel organisms and re-program cell metabolism using novel …

Development And Characterization Of Genetic Sensors And Regulators For The Construction Of Environmentally-Responsive Genetic Circuits, Allison Hoynes-O'Connor

McKelvey School of Engineering Theses & Dissertations

Genetic circuits enable engineers to program complex logical behaviors into living organisms. Organisms can be programmed to optimize the production of fuels and chemicals, diagnose and treat diseases, or remediate environmental pollutants. A well-characterized toolbox of genetic sensors and regulators is needed to construct these circuits. Genetic sensors that respond to environmentally-relevant signals allow circuits to evaluate the cell's conditions, and versatile and designable regulators translate information about the cell's environment into the desired response. In this work, we demonstrate the de novo design of RNA thermosensors in Escherichia coli, and integrate these sensors into complex genetic circuits. Next, we …

Understanding The Role Of Dynamics In Brain Networks: Methods, Theory And Application, Mohammadmehdi Kafashan

McKelvey School of Engineering Theses & Dissertations

The brain is inherently a dynamical system whose networks interact at multiple spatial and temporal scales. Understanding the functional role of these dynamic interactions is a fundamental question in neuroscience. In this research, we approach this question through the development of new methods for characterizing brain dynamics from real data and new theories for linking dynamics to function. We perform our study at two scales: macro (at the level of brain regions) and micro (at the level of individual neurons).

In the first part of this dissertation, we develop methods to identify the underlying dynamics at macro-scale that govern brain …

Developing High Purity Embryonic Stem Cell-Derived V2a Interneurons For In Vitro Investigation And Transplantation Following Spinal Cord Injury, Nisha Iyer

McKelvey School of Engineering Theses & Dissertations

Functional recovery following spinal cord injury has been attributed to plasticity in local interneuron populations, which are able to create novel circuits that bypass the inhibitory lesion to activate pre-existing motor pathways. Cell replacement strategies and growth factor delivery platforms often attempt to enhance these natural mechanisms of regeneration. The work of this thesis sought to overcome the major obstacle to manipulating specific interneurons for therapy: an inability to obtain large, enriched interneuron subpopulations for drug screening and transplantation. We focused on the generation of V2a interneurons, which normally coordinate a wide range of locomotor tasks in both the spinal …

Genetic Circuits For Transcriptional Regulation In Synechocystis Sp. Pcc 6803, Cheryl M. Immethun

McKelvey School of Engineering Theses & Dissertations

Microbial biosynthesis has produced a variety of complex compounds using processes that are more environmentally-friendly than many conventional methods. The most common hosts are heterotrophs, which require the addition of an organic carbon source; while cyanobacteria possess many traits that make them a more sustainable biotechnology platform. As phototrophs, cyanobacteria can employ sunlight and carbon dioxide to create many value-added compounds. A wealth of tools has been developed to engineer the commonly used heterotrophs for higher yields and titers; yet, few synthetic biology tools have been designed for cyanobacteria. Furthermore, many of the tools created for heterotrophs do not function …

Guided Medical Data Segmentation Using Structure-Aligned Planar Contours, Michelle Vaughan Holloway

McKelvey School of Engineering Theses & Dissertations

Segmentation of 3D/4D biological images is a critical step for a wide range of applications such as treatment planning, quantitative analysis, virtual simulations, and rendering visualizations. Automatic segmentation methods are becoming more reliable, but many experts still rely on manual intervention which makes segmentation a time and resource intensive bottleneck. Marking boundary contours in 3D images can be difficult when images are often noisy or the delineation of biological tissue is unclear. Non-parallel contours can be more accurate and reduce the amount of marking necessary, but require extra effort to ensure boundary consistency and maintain spatial orientation. This dissertation focuses …

Development Of A One-Equation Eddy Viscosity Turbulence Model For Application To Complex Turbulent Flows, Timothy Wray

McKelvey School of Engineering Theses & Dissertations

Computational fluid dynamics (CFD) is routinely used in performance prediction and design of aircraft, turbomachinery, automobiles, and in many other industrial applications. Despite its wide range of use, deficiencies in its prediction accuracy still exist. One critical weakness is the accurate simulation of complex turbulent flows using the Reynolds-Averaged Navier-Stokes equations in conjunction with a turbulence model. The goal of this research has been to develop an eddy viscosity type turbulence model to increase the accuracy of flow simulations for mildly separated flows, flows with rotation and curvature effects, and flows with surface roughness. It is accomplished by developing a …

High-Throughput Exploration Of Glass Formation Via Laser Deposition And The Study Of Heterogeneous Microstructure In A Bulk Metallic Glass Alloy, Peter Te-Chuan Tsai

McKelvey School of Engineering Theses & Dissertations

Bulk metallic glasses are a relatively novel class of engineering alloys characterized by a "disordered" atomic structure devoid of long-range translational symmetry. Compared to crystalline alloys, the confluence of metallic bonding and amorphous structure imbues bulk metallic glasses with a unique set of properties that makes them particularly attractive for a wide variety of structural applications. Such properties include exceptional yield strengths, high elastic resilience, resistance to corrosion, and in particular, the unparalleled ability among metals to be thermoplastically formed across a wide range of length scales when heated above the glass transition temperature. Formation of metallic glass from a …

Indoor Scene Localization To Fight Sex Trafficking In Hotels, Abigail Stylianou

McKelvey School of Engineering Theses & Dissertations

Images are key to fighting sex trafficking. They are: (a) used to advertise for sex services,(b) shared among criminal networks, and (c) connect a person in an image to the place where the image was taken. This work explores the ability to link images to indoor places in order to support the investigation and prosecution of sex trafficking. We propose and develop a framework that includes a database of open-source information available on the Internet, a crowd-sourcing approach to gathering additional images, and explore a variety of matching approaches based both on hand-tuned features such as SIFT and learned features …

A Traders Guide To The Predictive Universe- A Model For Predicting Oil Price Targets And Trading On Them, Jimmie Harold Lenz

Doctor of Business Administration Dissertations

At heart every trader loves volatility; this is where return on investment comes from, this is what drives the proverbial “positive alpha.” As a trader, understanding the probabilities related to the volatility of prices is key, however if you could also predict future prices with reliability the world would be your oyster. To this end, I have achieved three goals with this dissertation, to develop a model to predict future short term prices (direction and magnitude), to effectively test this by generating consistent profits utilizing a trading model developed for this purpose, and to write a paper that anyone with …

Development And Evaluation Of A Near-Infrared (1047 Nm) Photoacoustic-Nephelometer Spectrometer For Detection And Optical Characterization Of Black Carbon Aerosol, Yang Yu

McKelvey School of Engineering Theses & Dissertations

Black carbon (BC) aerosol are aggregates of small carbon spherules of <10 nm to approximately 50 nm in diameter. They are characterized by their strong visible light absorption property with a mass absorption cross-section (MAC) value above 5 m² g ⁻¹ at a wavelength λ = 550 nm, which increases inversely with wavelengths from near-infrared (≈1 µm) to ultraviolet with a power law of one. The absorbing nature of BC aerosol has been implicated in regional atmospheric warming, changing of monsoon patterns, and accelerated melting of the glaciers. The BC radiative effects over earth is currently estimated within a factor of four, resulting in one of the largest uncertainties in climate modeling. This uncertainty results from our inadequate knowledge about regional BC emission rates, and associated aerosol …

Nanostructured Thin Film Synthesis By Aerosol Chemical Vapor Deposition For Energy Storage Applications, Tandeep Singh Chadha

McKelvey School of Engineering Theses & Dissertations

Renewable energy sources offer a viable solution to the growing energy demand while mitigating concerns for greenhouse gas emissions and climate change. This has led to a tremendous momentum towards solar and wind-based energy harvesting technologies driving efficiencies higher and costs lower. However, the intermittent nature of these energy sources necessitates energy storage technologies, which remain the Achilles heel in meeting the renewable energy goals. This dissertation focusses on two approaches for addressing the needs of energy storage: first, targeting direct solar to fuel conversion via photoelectrochemical water-splitting and second, improving the performance of current rechargeable batteries by developing new …

Crumpled Graphene Oxide: Aerosol Synthesis And Environmental Applications, Yi Jiang

McKelvey School of Engineering Theses & Dissertations

Environmental technologies, such as for water treatment, have advanced significantly due to the rapid expansion and application of nanoscale material science and engineering. In particular, two-dimensional graphene oxide (GO), has demonstrated considerable potential for advancing and even revolutionizing some of these technologies, such as engineered photocatalysts and membranes. To realize such potential, an industrially scalable process is needed to produce monomeric and aggregation-resistant GO nanostructures/composites, in addition to new knowledge of material properties, behavior, and performance within an environmental context.

Research presented in this thesis addresses both scientific and engineering gaps through the development of a simple, yet robust aerosol-based …

State Space Analysis Of Dominant Structures In Dynamic Social Systems, Jeremy B. Sato

McKelvey School of Engineering Theses & Dissertations

Many systems involving human relationships are modeled as dynamic systems, as diverse as urban population growth, diffusion of innovations, spread of viruses, and supply chain management. A fundamental assumption is that these systems contain variables which accumulate and deplete over time (people, innovation adoptions, infections, and orders), and whose dynamics are determined by societal rules and human decision making processes. These assumptions allow the system to be formally expressed by ordinary differential equations which are often nonlinear and contain multiple state variables and feedback loops. Analytical methods have been developed to identify the dominant feedback loops which primarily influence the …

Computational Fluid Dynamics Modeling And Simulations Of Fluidized Bed Reactors For Chemical Looping Combustion, Subhodeep Banerjee

McKelvey School of Engineering Theses & Dissertations

Chemical looping combustion (CLC) is a next generation combustion technology that shows great promise as a solution for the need of high-efficiency low-cost carbon capture from fossil fueled power plants. To realize this technology on an industrial scale, the development of high-fidelity simulations is a necessary step to develop a thorough understanding of the CLC process. Although there have been a number of experimental studies on CLC in recent years, CFD simulations have been limited in the literature.

In this dissertation, reacting flow simulations of a CLC reactor are developed using the Eulerian approach based on a laboratory-scale experiment of …

New Tools For Viscoelastic Spectral Analysis, With Application To The Mechanics Of Cells And Collagen Across Hierarchies, Behzad Babaei

McKelvey School of Engineering Theses & Dissertations

Viscoelastic relaxation spectra are essential for predicting and interpreting the mechanical responses of materials and structures. For biological tissues, these spectra must usually be estimated from viscoelastic relaxation tests. Interpreting viscoelastic relaxation tests is challenging because the inverse problem is expensive computationally. We present here (1) an efficient algorithm and (2) a quasi-linear model that enable rapid identification of the viscoelastic relaxation spectra of both linear and nonlinear materials. We then apply these methods to develop fundamental insight into the mechanics of collagenous and fibrotic tissues.

The first algorithm, which we term the discrete spectral approach, is fast enough to …

Nanoparticle Formation In The Flame Synthesis Of Multicomponent Nanostructured Materials For Clean Energy Applications, Jiaxi Fang

McKelvey School of Engineering Theses & Dissertations

This dissertation studies the initial stages of particle formation during the combustion synthesis of multicomponent nanomaterials. Combustion is commonly used for the production of nanomaterials at industrial scales and has advantages of high production rates, low waste generation, and scalability. However, there are limitations in being able to apply this synthesis approach to more advanced multicomponent systems. Gas to particle conversion in flames occurs through precursor decomposition, collisional growth, coagulation, condensation, and sintering. There is a fundamental gap in knowledge on the initial stages of particle formation in flames below 2nm due to measurement difficulties and instrumentation limitations. Using a …

Calcium Carbonate Formation In Energy-Related Subsurface Environments And Engineered Systems, Qingyun Li

McKelvey School of Engineering Theses & Dissertations

Geologic CO2 sequestration (GCS) in subsurface saline aquifers is a promising strategy to mitigate climate change caused by increasing anthropogenic CO2 emissions from energy production. At GCS sites, interactions between fluids and geomedia are important because they can affect CO2 trapping efficiency and the safety of CO2 storage. These interactions include the dissolution and precipitation of minerals. One of the most important minerals is calcium carbonate, because it can permanently trap CO2.

In this work, Portland cement was used as a model geomedium to investigate the chemical reactions, mechanical alterations, transport of reactive fluids, and the interplay of all these …

Silk As A Biomaterial Paste For Biomimetic Composite, Sang Hyun Park

McKelvey School of Engineering Theses & Dissertations

Silk is a highly promising biomaterial with unique bio-physicochemical properties, such as excellent mechanical and optical properties, biocompatibility and programmable biodegradability. Among many different types, silk from domesticated silkworm, bombyx mori has received wide attention owing to its availability in virtually unlimited quantities and ease of extraction. In this study, we investigated silkworm silk as a protein glue to realize nacre-like composites. We have employed spin assisted layer-by-layer technique to fabricate ultrathin free-standing biocomposite films. Two different composites have been studied: (i) graphene oxide (GO)/silk and (ii) chitin/silk. From our prior work, it is known that the adsorption of amphiphilic …

Neural Representation Of Vocalizations In Noise In The Primary Auditory Cortex Of Marmoset Monkeys, Ruiye Ni

McKelvey School of Engineering Theses & Dissertations

Robust auditory perception plays a pivotal function in processing behaviorally relevant sounds, particularly when there are auditory distractions from the environment. The neuronal coding enabling this ability, however, is still not well understood. In this study we recorded single-unit activity from the primary auditory cortex of alert common marmoset monkeys (Callithrix jacchus) while delivering conspecific vocalizations degraded by two different background noises: broadband white noise (WGN) and vocalization babble (Babble).

Noise effects on single-unit neural representation of target vocalizations were quantified by measuring the response similarity elicited by natural vocalizations as a function of signal-to-noise ratio (SNR). Four consistent response …

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

McKelvey School of Engineering Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess …

Shape Optimization Of Supersonic Bodies To Reduce Sonic Boom Signature, Junhui Li

McKelvey School of Engineering Theses & Dissertations

In recent years there has been resurgence of interest by aerospace industry and NASA in supersonic transport aircraft. In recent studies, the emphasis has been on shape optimization of supersonic plane to reduce the acoustic signature of sonic boom resulting from the supersonic aircraft at high altitude in cruise flight. Because of the limitations of in-flight testing and cost of laboratory scale testing, CFD technology provides an attractive alternative to aid in the design and optimization of supersonic vehicles. In last decade, the predictive capability of CFD technology has significantly improved because of substantial increase in computational power, which allows …