Digital Commons Network^™

Probing Mechanical Forces In Flagella By Manipulation Of Media Viscosity And Axonemal Structure, Kate Wilson

McKelvey School of Engineering Theses & Dissertations

Cilia and flagella are subcellular organelles used to generate fluid flow or propel the cell. These long cylindrical structures are composed of cytoskeletal elements activated by the unidirectional motor protein dynein. Cilia and flagella are crucial to a number of physiological functions, yet the specific mechanisms of dynein activation and coordination remain unclear. This work investigates the response of the flagellum of Chlamydomonas reinhardtii to increased mechanical loading achieved by variation of media viscosity, and to structural changes achieved by genetic manipulation. Effects of these perturbations are quantified using high spatiotemporal resolution recordings; the results demonstrate mutation-specific changes to the …

Development Of 13c Fingerprint Tool And Its Application For Exploring Carbon And Energy Metabolism In Cyanobacterium Synechocystis Sp. Pcc 6803, Le You

McKelvey School of Engineering Theses & Dissertations

Cyanobacteria are important microbial cell factories that are widely used in the biotechnology filed nowadays. They can use light as the sole energy source to fix CO2, accumulate biomass, and produce various valuable bio-products. Engineered cyanobacterial species can uptake nutrients from wastes to further reduce the cost. Recently, it is reported that cyanobacteria will provide much higher carbon yield than heterotrophs by co-utilizing organic carbons and CO2. However, the quantitative information of such `photo-fermentation' process is still limited. Decoding the carbon metabolism of cyanobacteria during the photo-fermentation process can reveal the functional pathways, carbon distribution, and the energy requirement, all …

Effects Of Biomass Moisture Content On Volatile Flame Length During Cofiring With Coal, Matthew Pollard

McKelvey School of Engineering Theses & Dissertations

Cofiring biomass with coal can contribute to meeting Renewable Portfolio Standards (RPS) and reduce pollutant emissions. The physical characteristics and composition of biomass can vary significantly, which can affect the combustion characteristics. When cofiring biomass with coal, these differences can impact the structure of the volatile flame, the region where combustion of volatiles dominates. The length and location of the volatile flame is important to flame stability and determines the location and extent of volatile release. This has an effect on pollutant emissions, such as NOx (nitrogen oxides). Previously, the effects of parameters such as cofiring ratio, particle size, and …

Numerical Simulation And Optimization Of Carbon Dioxide Utilization For Enhanced Oil Recovery From Depleted Reservoirs, Razi Safi

McKelvey School of Engineering Theses & Dissertations

Due to concerns about rising CO₂ emissions from fossil fuel power plants, there has been a strong emphasis on the development of a safe and economical method for Carbon Capture Utilization and Storage (CCUS). One area of current interest in CO₂ utilization is the Enhanced Oil Recovery (EOR) from depleted reservoirs. In an Enhanced Oil Recovery system, a depleted or depleting oil reservoir is re-energized by injecting high-pressure CO₂ to increase the recovery factor of the oil from the reservoir. An additional benefit beyond oil recovery is that the reservoir could also serve as a long-term storage …

Interfacial Chemistry Of Trace Elements At Mineral Surfaces In Engineered Water Systems, Lin Wang

McKelvey School of Engineering Theses & Dissertations

This thesis research consists of two independent research projects that both studied interfacial chemical processes affecting trace elements at mineral surfaces.

The objectives of Project 1 were to 1) quantify the impact of water chemistry on As(III) adsorption on lepidocrocite, 2) develop a surface complexation model to describe equilibrium As(III) and As(V) adsorption to lepidocrocite and 3) elucidate the mechanism of Fe(II)-mediated As(III) oxidation at the lepidocrocite-water interface. Arsenic is a regulated element that can be found at high concentrations in groundwater resources that are used as drinking water sources. Iron (oxyhydr)oxides are one of the most abundant groups of …

Gold Nanostructures For Sensing And Functional Bioimaging, Maximilian Y. Fei

McKelvey School of Engineering Theses & Dissertations

Gold nanostructures offer an extremely promising path forward in the fields of imaging and sensing because of their unique optical and chemical properties. Here, we demonstrate that plasmonic nanostructures can be employed as nanoscale transducers to monitor the growth and phase transitions in ultrathin polymer films. In particular, gold nanorods with high refractive index sensitivity (~150 nm / refractive index unit (RIU)) were employed to probe the growth and swelling of polyelectrolyte multilayers (PEM). By comparing the wavelength shift and extinction intensity of the localized surface plasmon resonance (LSPR) of the gold nanorods coated with PEM in air and water, …

Genetic Algorithm Based Optimization Of Baffle Positions In A Forward Osmosis Draw Channel, James Koch

McKelvey School of Engineering Theses & Dissertations

Forward Osmosis (FO) driven asymmetric membrane filtration is a developing technology which shows promise for seawater desalination and wastewater treatment. Due to the fact that asymmetric membranes are widely used in conjunction with this technology, internal concentration polarization (ICP), a flow-entrainment effect occurring within such membranes, is a significant if not dominant source of overall osmotic pressure loss across the membrane. Accurate modeling of ICP effects is therefore very critical for accurate Computational Fluid Dynamic (CFD) modeling of asymmetric membranes. A related, dilutive effect known as external concentration polarization (ECP) also develops on both the rejection and draw sides of …

Strategies For Increasing The Applicability Of Biological Network Inference, Ezekiel John Maier

McKelvey School of Engineering Theses & Dissertations

The manipulation of cellular state has many promising applications, including stem cell biology and regenerative medicine, biofuel production, and stress resistant crop development. The construction of interaction maps promises to enhance our ability to engineer cellular behavior. Within the last 15 years, many methods have been developed to infer the structure of the gene regulatory interaction map from gene abundance snapshots provided by high-throughput experimental data. However, relatively little research has focused on using gene regulatory network models for the prediction and manipulation of cellular behavior. This dissertation examines and applies strategies to utilize the predictive power of gene network …

Integration Of Alignment And Phylogeny In The Whole-Genome Era, Hongtao Sun

McKelvey School of Engineering Theses & Dissertations

With the development of new sequencing techniques, whole genomes of many species have become available. This huge amount of data gives rise to new opportunities and challenges. These new sequences provide valuable information on relationships among species, e.g. genome recombination and conservation. One of the principal ways to investigate such information is multiple sequence alignment (MSA). Currently, there is large amount of MSA data on the internet, such as the UCSC genome database, but how to effectively use this information to solve classical and new problems is still an area lacking of exploration. In this thesis, we explored how to …

Potential-Flow Inflow Model Including Wake Distortion And Contraction, Jianzhe Huang

McKelvey School of Engineering Theses & Dissertations

Dynamic wake models have been used in real-time flight simulations for over thirty years. The models have evolved from the earliest, three-degree-of-freedom models (derived from momentum theory) to full finite-state models derived from potential flow theory by a formal Galerkin method. These models are widely used in industry, but still have some drawbacks that need to be remedied. These drawbacks include: 1.) lack of good convergence both on the disk and off the disk (one can use one or the other but not both), 2.) poor results downstream in the limit of shallow skew angles, 3.) poor convergence inside of …

Utilizing Magnetic Tunnel Junction Devices In Digital Systems, Michael James Hall

McKelvey School of Engineering Theses & Dissertations

The research described in this dissertation is motivated by the desire to effectively utilize magnetic tunnel junctions (MTJs) in digital systems. We explore two aspects of this: (1) a read circuit useful for global clocking and magnetologic, and (2) hardware virtualization that utilizes the deeply-pipelined nature of magnetologic.

In the first aspect, a read circuit is used to sense the state of an MTJ (low or high resistance) and produce a logic output that represents this state. With global clocking, an external magnetic field combined with on-chip MTJs is used as an alternative mechanism for distributing the clock signal across …

Polarization Sensor Design For Biomedical Applications, Timothy York

McKelvey School of Engineering Theses & Dissertations

Advances in fabrication technology have enabled the development of compact, rigid polarization image sensors by integrating pixelated polarization filters with standard image sensing arrays. These compact sensors have the capability for allowing new applications across a variety of disciplines, however their design and use may be influenced by many factors. The underlying image sensor, the pixelated polarization filters, and the incident lighting conditions all directly impact how the sensor performs.

In this research endeavor, I illustrate how a complete understanding of these factors can lead to both new technologies and applications in polarization sensing. To investigate the performance of the …

Application-Specific Memory Subsystems, Joseph George Wingbermuehle

McKelvey School of Engineering Theses & Dissertations

The disparity in performance between processors and main memories has

led computer architects to incorporate large cache hierarchies in

modern computers. These cache hierarchies are designed to be

general-purpose in that they strive to provide the best possible

performance across a wide range of applications. However, such a memory

subsystem does not necessarily provide the best possible performance for

a particular application.

Although general-purpose memory subsystems are desirable when the

work-load is unknown and the memory subsystem must remain fixed,

when this is not the case a custom memory subsystem may be beneficial.

For example, in an application-specific integrated circuit …

Real-Time And Energy-Efficient Routing For Industrial Wireless Sensor-Actuator Networks, Chengjie Wu

McKelvey School of Engineering Theses & Dissertations

With the emergence of industrial standards such as WirelessHART, process industries are adopting Wireless Sensor-Actuator Networks (WSANs) that enable sensors and actuators to communicate through low-power wireless mesh networks. Industrial monitoring and control applications require real-time communication among sensors, controllers and actuators within end-to-end deadlines. Deadline misses may lead to production inefficiency, equipment destruction to irreparable financial and environmental impacts. Moreover, due to the large geographic area and harsh conditions of many industrial plants, it is labor-intensive or dan- gerous to change batteries of field devices. It is therefore important to achieve long network lifetime with battery-powered devices.

This dissertation …

Metabolic Engineering Of Cyanobacteria For Photosynthetic Production Of Drop-In Liquid Fuels, Bertram Michael Berla

McKelvey School of Engineering Theses & Dissertations

Cyanobacteria are oxygenic phototrophs with great potential as hosts for renewable fuel and chemical production. They grow very quickly (compared with plants) and can use sunlight for energy and CO2 as a carbon source (unlike yeast or E. coli). While cyanobacteria have been engineered to make many chemicals that are native and non-native parts of their metabolism, this work is concerned with the production of heptadecane in Synechocystis sp. PCC 6803. Heptadecane is in a class of natural products produced by all cyanobacteria, but in quantities insufficient for industrialization. Towards this future goal, we have built enabling systems for the …

Toward Improved Computational Tools For Electronic Transport Analysis And Their Use In The Development Of Materials For Energy Applications, Maria Stoica

McKelvey School of Engineering Theses & Dissertations

With the rapid rise in computational speed and capacity of massively parallel computing clusters in recent years, theoretical screening of large, previously unexplored sets of complex compounds to find materials with a given set of desired properties is quickly becoming a reality. In order to maximize the predictive ability of these large-scale computations, it is desirable to develop accurate post-processing algorithms that can efficiently manipulate electronic structure data to produce theoretical predictions of experimentally observable quantities. To address this need, the work of this dissertation has been to expand existing \textit{ab initio} methods for determining electronic properties of bulk complex …

Joint Representation Of Translational And Rotational Components Of Self-Motion In The Parietal Cortex, Adhira Sunkara

McKelvey School of Engineering Theses & Dissertations

Navigating through the world involves processing complex visual inputs to extract information about self-motion relative to one's surroundings. When translations (T) and rotations (R) are present together, the velocity patterns projected onto the retina (optic flow) are a combination of the two. Since navigational tasks can be extremely varied, such as deciphering heading or tracking moving prey or estimating one's motion trajectory, it is imperative that the visual system represent both the T and R components. Despite the importance of such joint representations, most previous studies have only focused on the representation of translations. Moreover, these studies emphasized the role …

Contextualized Robot Navigation, David Vincent Lu

McKelvey School of Engineering Theses & Dissertations

In order to improve the interaction between humans and robots, robots need to be able to move about in a way that is appropriate to the complex environments around them. One way to investigate how the robots should move is through the lens of theatre, which provides us with ways to analyze the robot's movements and the motivations for moving in particular ways. In particular, this has proven useful for improving robot navigation. By altering the costmaps used for path planning, robots can navigate around their environment in ways that incorporate additional contexts. Experimental results with user studies have shown …

A Reinforcement-Learning Framework For Interpreting Trial-By-Trial Motor Adaptation To Novel Haptic Environments, Ranjan Patrick Khan

McKelvey School of Engineering Theses & Dissertations

Motor adaptation is often considered to occur under the influence of sensory signals, which is usually readily available for humans performing most motor tasks. However, humans can also use reward or other qualitative feedback to reinforce previous actions and perform adaptation. In these experiments, we introduce reward feedback to a traditional motor adaptation experiment: reach adaptation to a velocity-dependent force field. Drawing from the literature of computer science and machine learning, we use a reinforcement-learning framework to interpret the pattern of force generation and reward-prediction errors and observe the effects of concurrent and isolated reward and sensory feedback.

It is …

A Four-Dimensional Image Reconstruction Framework For Pet Under Arbitrary Geometries, Aswin John Mathews

McKelvey School of Engineering Theses & Dissertations

Positron Emission Tomography (PET) is a functional imaging modality with applications ranging from the treatment of cancer, studying neurological diseases and disease models. Virtual-Pinhole PET technology improves the image quality in terms of resolution and contrast recovery. The technology calls for having a detector with smaller crystals placed near a region of interest in a conventional whole-body PET scanner. The improvement is from the higher spatial sampling of the imaging area near the detector. A prototype half-ring PET insert built to study head-and-neck cancer imaging was extended to breast cancer imaging. We have built a prototype half-ring PET insert for …

Novel Mobile Computation Offloading Framework For Android Devices, Meng Wang

McKelvey School of Engineering Theses & Dissertations

The thesis implements an offloading framework for GoogleTM AndroidTM based on mobile devices. Today, the full potential for smartphones may be constrained by certain technical limits such as battery endurance and computational performance. Modern mobile applications own more powerful functions but need larger computation and faster frame rate, which consume more battery energy. Using the proposed offloading framework, mobile devices can offload computational intensive workload to servers to save battery energy consumption and reduce the execution time. The framework can also enable software developers to easily build and deploy services on the servers to support mobile devices to run computationally …

Real-Time Temperature Imaging Using Ultrasonic Change In Backscattered Energy, Weiyuan Zhao

McKelvey School of Engineering Theses & Dissertations

Thermal therapy from low-temperature cryosurgery to high-temperature ablation of tumors and unwanted electrical pathways has gained increased attention. Temperature imaging (TI) from magnetic resonance studies is the de facto standard for volumetric estimation of temperature. Ultrasound has the advantages of being cheap, portable, non-invasive and non-ionizing. Our group showed in predictions for single scatterers, simulations of scatterer populations and measurements in 1D, 2D and 3D, that CBE changed monotonically with temperature with 1^oC accuracy. An obstacle to clinical application of CBE TI is estimation of temperature in real time, which is limited by time for motion compensation (MC). …

Ultrasound-Mediated Optical Imaging And Focusing In Scattering Media, Yuta Suzuki

McKelvey School of Engineering Theses & Dissertations

Because of its non-ionizing and molecular sensing nature, light has been an attractive tool in biomedicine. Scanning an optical focus allows not only high-resolution imaging but also manipulation and therapy. However, due to multiple photon scattering events, conventional optical focusing using an ordinary lens is limited to shallow depths of one transport mean free path (lt'), which corresponds to approximately 1 mm in human tissue.

To overcome this limitation, ultrasonic modulation (or encoding) of diffuse light inside scattering media has enabled us to develop both deep-tissue optical imaging and focusing techniques, namely, ultrasound-modulated optical tomography (UOT) and time-reversed ultrasonically encoded …

Approximation And Relaxation Approaches For Parallel And Distributed Machine Learning, Stephen Tyree

McKelvey School of Engineering Theses & Dissertations

Large scale machine learning requires tradeoffs. Commonly this tradeoff has led practitioners to choose simpler, less powerful models, e.g. linear models, in order to process more training examples in a limited time. In this work, we introduce parallelism to the training of non-linear models by leveraging a different tradeoff--approximation. We demonstrate various techniques by which non-linear models can be made amenable to larger data sets and significantly more training parallelism by strategically introducing approximation in certain optimization steps.

For gradient boosted regression tree ensembles, we replace precise selection of tree splits with a coarse-grained, approximate split selection, yielding both faster …

Accelerating Heuristic Search For Ai Planning, You Xu

McKelvey School of Engineering Theses & Dissertations

AI Planning is an important research field. Heuristic search is the most commonly used method in solving planning problems. Despite recent advances in improving the quality of heuristics and devising better search strategies, the high computational cost of heuristic search remains a barrier that severely limits its application to real world problems. In this dissertation, we propose theories, algorithms and systems to accelerate heuristic search for AI planning.

We make four major contributions in this dissertation. First, we propose a state-space reduction method called Stratified Planning to accelerate heuristic search. Stratified Planning can be combined with any heuristic search to …

Aerosol Techniques For Deposition And Characterization Of Biological And Biomimetic Sensitizers For Solar Devices, Vivek B. Shah

McKelvey School of Engineering Theses & Dissertations

Nano-structured columnar films synthesized by the aerosol chemical vapor deposition (ACVD) system are unique, and have proved to be useful for fabricating solar cells and in other applications. The film formation by ACVD process involves three main phenomenon - aerosol formation and growth, deposition, and restructuring. In this work, thin film formation by the ACVD process is simulated by combining three models - (A) particle formation in gas phase by atrimodal model, (B) particle deposition onto heated substrate by a Brownian dynamics model and (C) sintering on the heated substrate by a multi-particle geometric sintering model (MPGSM). Modelling and simulation …

The Effects Of Gamifying Optional Lessons On Motivation, Aaron Zemach

McKelvey School of Engineering Theses & Dissertations

Adding video-game elements to non-video-game interfaces (“gamification”) has become a common engagement strategy over the past several years in the domain of education. While prior studies have found that adding game elements to mandatory educational materials can increase students’ motivation to complete the materials, there has yet to be a study to investigate if game elements can make users more likely to engage with optional educational materials. In this study, we investigate whether users of a gamified educational interface are more motivated than users of a non-gamified interface to voluntarily complete educational materials. We found users of a gamified interface …

The Synchronized Filtering Dataflow, Peng Li

McKelvey School of Engineering Theses & Dissertations

In the past decade, the world has seen the rise of big data, which calls for a paradigm shift in data processing. Streaming processing, where data are processed in their spatial or temporal order, is increasingly common. Meanwhile, parallel computing has become a household term in the computing world. The combination of streaming processing and parallel computing, streaming computing, has been playing an important role in data processing.

A streaming computing system is a network of nodes connected by unidirectional first-in first-out (FIFO) data channels. When a node has multiple input channels, to ensure the deterministic behavior of the whole …

Modeling Algorithm Performance On Highly-Threaded Many-Core Architectures, Lin Ma

McKelvey School of Engineering Theses & Dissertations

The rapid growth of data processing required in various arenas of computation over the past decades necessitates extensive use of parallel computing engines. Among those, highly-threaded many-core machines, such as GPUs have become increasingly popular for accelerating a diverse range of data-intensive applications. They feature a large number of hardware threads with low-overhead context switches to hide the memory access latencies and therefore provide high computational throughput. However, understanding and harnessing such machines places great challenges on algorithm designers and performance tuners due to the complex interaction of threads and hierarchical memory subsystems of these machines. The achieved performance jointly …

Shape Optimization Of Airfoils Without And With Ground Effect Using A Multi-Objective Genetic Algorithm, Yilei He

McKelvey School of Engineering Theses & Dissertations

The focus of this thesis is on shape optimization using a genetic algorithm. A multi-objective genetic algorithm (MOGA) is employed to optimize the shape of an airfoil to improve its lift and drag characteristics, in particular to achieve two objectives simultaneously that is to increase its lift as well as its lift to drag ratio. The commercially available software FLUENT is employed to calculate the flow field on an adaptive structured mesh, which is generated by the commercial mesh generating software ICEM. The flow field is calculated using the Reynolds-Averaged Navier-Stokes (RANS) equations in conjunction with a two equation k-ω …