Digital Commons Network^™

Information Architecture For A Chemical Modeling Knowledge Graph, Adam R. Luxon

Theses and Dissertations

Machine learning models for chemical property predictions are high dimension design challenges spanning multiple disciplines. Free and open-source software libraries have streamlined the model implementation process, but the design complexity remains. In order better navigate and understand the machine learning design space, model information needs to be organized and contextualized. In this work, instances of chemical property models and their associated parameters were stored in a Neo4j property graph database. Machine learning model instances were created with permutations of dataset, learning algorithm, molecular featurization, data scaling, data splitting, hyperparameters, and hyperparameter optimization techniques. The resulting graph contains over 83,000 nodes …

A Mechanism Behind The Mechanotransduction Of Surface Characteristics In Osteoblasts, Otto J. Juhl Iv

Theses and Dissertations

Biomaterials for use in bone regeneration and healing range from metal and metal alloy implants to hydrogel-based solutions. These materials can be optimized to increase bone healing and integration by improving the mechanical and biological properties. Regardless of the material itself, the cell-substrate interaction is key to the success of the biomaterial once implanted. Substrate surface characteristics such as roughness, wettability, and particle density are well-known contributors to a substrate’s overall osteogenic potential, and therefore the substrate's overall success. Unfortunately, it is still unknown how these substrate surface characteristics are transduced into intracellular signals by cells, preventing specific tailoring of …

Computational Analysis And Prediction Of Intrinsic Disorder And Intrinsic Disorder Functions In Proteins, Akila I. Katuwawala

Theses and Dissertations

COMPUTATIONAL ANALYSIS AND PREDICTION OF INTRINSIC DISORDER AND INTRINSIC DISORDER FUNCTIONS IN PROTEINS

By Akila Imesha Katuwawala

A dissertation submitted in partial fulfillment of the requirements for the degree of Engineering, Doctor of Philosophy with a concentration in Computer Science at Virginia Commonwealth University.

Virginia Commonwealth University, 2021

Director: Lukasz Kurgan, Professor, Department of Computer Science

Proteins, as a fundamental class of biomolecules, have been studied from various perspectives over the past two centuries. The traditional notion is that proteins require fixed and stable three-dimensional structures to carry out biological functions. However, there is mounting evidence regarding a “special” class …

Nature-Inspired Material Strategies Towards Functional Devices, Sayantan Pradhan

Theses and Dissertations

Naturally sourced, renewable biomaterials possess outstanding advantages for a multitude of biomedical applications owing to their biodegradability, biocompatibility, and excellent mechanical properties. Of interest in this dissertation are silk (protein) and chitin (polysaccharide) biopolymers for the fabrication of functional biodevices. One of the major challenges restricting these materials beyond their traditional usage as passive substrate materials is the ability to combine them with high-resolution fabrication techniques. Initial research work is directed towards the fabrication of micropatterned, flexible 2D substrates of silk fibroin and chitin using bench-top photolithographic techniques. Research is focused on imparting electrochemical properties to silk proteins using conducting …

Improving Patient-Specific Assessments Of Regional Aortic Mechanics Via Quantitative Magnetic Resonance Imaging With Early Applications In Patients At Elevated Risk For Thoracic Aortopathy, Patrick A. Jones

Theses and Dissertations

Unstable aortic aneurysms and dissections are serious cardiovascular conditions associated with high mortality. The current gold standards for assessment of stability, however, rely on simple geometric measurements, like cross-sectional area or increased diameter between follow-up scans, and fail to incorporate information about underlying aortic mechanics. Displacement encoding with stimulated echoes (DENSE) magnetic resonance imaging (MRI) has been used previously to determine heterogeneous circumferential strain patterns in the aortas of healthy volunteers. Here, I introduce technical improvements to DENSE aortic analysis and early pilot application in patients at higher risk for the development of aortopathies. Modifications to the DENSE aortic postprocessing …

Learning-Based Predictive Control Approach For Real-Time Management Of Cyber-Physical Systems, Roja Eini

Theses and Dissertations

Cyber-physical systems (CPSs) are composed of heterogeneous, and networked hardware and software components tightly integrated with physical elements [72]. Large-scale CPSs are composed of complex components, subject to uncertainties [89], as though their design and development is a challenging task. Achieving reliability and real-time adaptation to changing environments are some of the challenges involved in large-scale CPSs development [51]. Addressing these challenges requires deep insights into control theory and machine learning. This research presents a learning-based control approach for CPSs management, considering their requirements, specifications, and constraints. Model-based control approaches, such as model predictive control (MPC), are proven to be …

Continuous Preparation And Application Of Novel Heterogeneous Catalysis, Michael B. Burkholder

Theses and Dissertations

Transition metal heterogeneous catalysts are widely used across many chemical industries to reduce waste and emissions and reduce production time while increasing rate. The prevalence of these materials results from the complex relationship between metal nanoparticles and supports affecting final catalytic performance. Rational catalyst synthesis describes the ability to precisely engineer structures through controlled preparation. Novel materials and continuous processing represent a promising approach for rational catalyst synthesis.

The application of these catalysts in continuous, multiphase processes, such as cross-coupling reactions, oxidation chemistry, and nitroreduction processes, are paramount to developing new commercial routes for high-value products. Pd/G catalysts synthesized by …

Applied Machine Learning In Extrusion-Based Bioprinting, Shuyu Tian

Theses and Dissertations

Optimization of extrusion-based bioprinting (EBB) parameters have been systematically conducted through experimentation. However, the process is time and resource-intensive and not easily translatable across different laboratories. A machine learning (ML) approach to EBB parameter optimization can accelerate this process for laboratories across the field through training using data collected from published literature. In this work, regression-based and classification-based ML models were investigated for their abilities to predict printing outcomes of cell viability and filament diameter for cell-containing alginate and gelatin composite hydrogels. Regression-based models were investigated for their ability to predict suitable extrusion pressure given desired cell viability when keeping …

Design And Development Of Soft Earthworm Robot Driven By Fibrous Artificial Muscles, Beau Ragland

College of Graduate Studies: Theses & Dissertations

Earthworm robots have proven their viability in the fields of medicine, reconnaissance, search and rescue, and infrastructure inspection. These robots are traditionally typically hard-shelled and must be tethered to whatever drives their locomotion. For this reason, truly autonomous capabilities are not yet feasible. The goal of this thesis is to introduce a robot that not only sets the groundwork for autonomous locomotion, but also is safe for human-robot interaction. This was done by ensuring that the actuation principle utilized by the robot is safe around humans and can work in an untethered design. Artificial muscle actuation allowed for these prerequisites …

Development Of A Mathematical Model For Galvanic Cells, Joshua C. Johnson

College of Graduate Studies: Theses & Dissertations

It is possible to utilize principles of equilibrium thermodynamics to model the voltage a battery renders as it powers a load in time and discharges. Similarly, consideration of the internal chemistry inside a battery, or galvanic cell, enables modeling thereof. This paper builds upon these principles and presents a derivation of the Nernst equation that utilizes this result to model discharge curves in time for different types of batteries. The Nernst equation relates chemical activity of the reagents inside a battery to the open circuit voltage rendered by the system. By combining the Nernst equation with Faraday's laws of electrolysis, …

Nanomaterials In The Environment, Human Exposure Pathway, And Health Effects: A Review, Arindam Malakar, Sushil R. Kanel, Chittaranjan Ray, Daniel D. Snow, Mallikarjuna N. Nadagouda

Daugherty Water for Food Global Institute: Faculty Publications

Nanomaterials (NMs), both natural and synthetic, are produced, transformed, and exported into our environment daily. Natural NMs annual flux to the environment is around 97% of the total and is significantly higher than synthetic NMs. However, synthetic NMs are considered to have a detrimental effect on the environment. The extensive usage of synthetic NMs in different fields, including chemical, engineering, electronics, and medicine, makes them susceptible to be discharged into the atmosphere, various water sources, soil, and landfill waste. As ever-larger quantities of NMs end up in our environment and start interacting with the biota, it is crucial to understand …

Baseflow Nitrate Dynamics Within Nested Watersheds Of An Agricultural Stream In Nebraska, Usa, Galen Richards, Troy E. Gilmore, Aaron R. Mittelstet, Tiffany Messer, Daniel D. Snow

Daugherty Water for Food Global Institute: Faculty Publications

There is a need to evaluate high surface nitrate concentrations across agricultural watersheds, both spatially and temporally, to increase understanding of source and timing of nitrogen loads in streams and rivers. Bazile Creek is a high-nitrate stream originating in the agriculturally intensive Bazile Groundwater Management Area of Eastern Nebraska, USA. It is a gaining stream that receives groundwater with high nitrate concentrations originating from nonpoint sources. The objective of this study was to determine spatial and temporal variability of baseflow nitrate concentrations in Bazile Creek and its tributaries and to relate this variability to watershed characteristics. Surface-water nitrate samples were …

Surveillance Of Plasticizers, Bisphenol A, Steroids And Caffeine In Surface Water Of River Ganga And Sundarban Wetland Along The Bay Of Bengal: Occurrence, Sources, Estrogenicity Screening And Ecotoxicological Risk Assessment, Paromita Chakraborty, Nancy W. Shappell, Moitraiyee Mukhopadhyay, Sathaporn Onanong, Daniel D. Snow

Daugherty Water for Food Global Institute: Faculty Publications

The transboundary River Ganga serves as a conduit for meltwater from the Himalayas and is a major freshwater source for two thirds of Indian population before emptying into the Sundarban Delta, the largest estuary in the Bay of Bengal. Endocrine disrupting compounds (EDCs) such as phthalic acid esters (PAEs) and bisphenol A (BPA) used as organic plastic additives can pollute the aquatic environment receiving plastic litter. Hence, we have investigated these EDCs in water samples from Ganga and Sundarban wetland of India. Since these compounds exhibit estrogenic potential, we have further measured steroids and evaluated the estrogenic activity (estradiol equivalents, …

Transmission Routes Of The Microbiome And Resistome From Manure To Soil And Lettuce, Yuepeng Sun, Daniel D. Snow, Harkamal Walia, Xu Li

Daugherty Water for Food Global Institute: Faculty Publications

The land application of animal manure can introduce manure microbiome and resistome to croplands where food crops are grown. The objective of this study was to characterize the microbiome and resistome on and in the leaves of lettuce grown in manured soil and identify the main transmission routes of microbes and antibiotic resistance genes (ARGs) from soil to the episphere and endosphere of lettuce. Shotgun metagenomic results show that manure application significantly altered the composition of the microbiome and resistome of surface soil. SourceTracker analyses indicate that manure and original soil were the main source of the microbiome and resistome …

Low-Level Groundwater Atrazine In High Atrazine Usage Nebraska Counties: Likely Effects Of Excessive Groundwater Abstraction, Moses New-Aaron, Olufemi Abimbola, Raheleh Mohammadi, Oluwaseun Famojuro, Zaeema Naveed, Azar Abadi, Jesse E. Bell, Shannon Bartelt-Hunt, Eleanor G. Rogan

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Recent studies observed a correlation between estrogen-related cancers and groundwater atrazine in eastern Nebraska counties. However, the mechanisms of human exposure to atrazine are unclear because low groundwater atrazine concentration was observed in counties with high cancer incidence despite having the highest atrazine usage. We studied groundwater atrazine fate in high atrazine usage Nebraska counties. Data were collected from Quality Assessed Agrichemical Contaminant Nebraska Groundwater, Parameter–Elevation Regressions on Independent Slopes Model (PRISM), and water use databases. Descriptive statistics and cluster analysis were performed. Domestic wells (59%) were the predominant well type. Groundwater atrazine was affected by well depth. Clusters consisting …

Improvements In Sub-Catchment Fractional Snowpack And Snowmelt Parameterizations And Hydrologic Modeling For Climate Change Assessments In The Western Himalayas, Vishal Singh, Francisco Muñoz-Arriola

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work proposes to improve estimates of snowpack and snowmelt and their assessment in the steep Himalayan ranges at the sub-catchment scale. Temporal variability of streamflow and the associated distribution of accumulated snow in catchments with glacier presence in the Himalayas illustrates how changes in snowpack and snowmelt can affect the water supply for local water management. The primary objective of this study is to assess the role of elevation, temperature lapse rate (TLR), and precipitation lapse rate (PLR) in the computation of snowpack (or snowfall) and snowmelt in sub-catchments of the Satluj River basin. Modeling of snowpack and …

Simultaneous Wound Border Segmentation And Tissue Classification Using A Conditional Generative Adversarial Network, Salih Sarp, Murat Kuzlu, Manisa Pipattanasomporn, Ozgur Guler

Engineering Technology Faculty Publications

Generative adversarial network (GAN) applications on medical image synthesis have the potential to assist caregivers in deciding a proper chronic wound treatment plan by understanding the border segmentation and the wound tissue classification visually. This study proposes a hybrid wound border segmentation and tissue classification method utilising conditional GAN, which can mimic real data without expert knowledge. We trained the network on chronic wound datasets with different sizes. The performance of the GAN algorithm is evaluated through the mean squared error, Dice coefficient metrics and visual inspection of generated images. This study also analyses the optimum number of training images …

Biocybersecurity: A Converging Threat As An Auxiliary To War, Lucas Potter, Orlando Ayala, Xavier-Lewis Palmer

Engineering Technology Faculty Publications

Biodefense is the discipline of ensuring biosecurity with respect to select groups of organisms and limiting their spread. This field has increasingly been challenged by novel threats from nature that have been weaponized such as SARS, Anthrax, and similar pathogens, but has emerged victorious through collaboration of national and world health groups. However, it may come under additional stress in the 21st century as the field intersects with the cyberworld-- a world where governments have already been struggling to keep up with cyber attacks from small to state-level actors as cyberthreats have been relied on to level the playing field …

Osteocyte Activity And Skeletal Muscle Relative Gene Expression Profiling After Short-Term Muscle Paralysis, Michelle Gelbs

Dissertations and Theses

Mechanical loading is essential for maintaining bone tissue. Reduced mechanical loading has been shown to have a negative effect on bone, and can result in the development of disuse osteoporosis. Disuse models of muscle inactivity and immobilization, like the Botox model used in this study, result in changes in the bone microarchitecture, the mechanisms behind which are not fully understood. In a previous four-week Botox disuse study, skeletally mature 20- week-old rats experienced degradation of intracortical bone, increased vascular porosity, and decreased osteocyte lacunar density in the tibiae. The focus of this study was to explicate a potential source of …

Development Of An Injectable Methylcellulose Hydrogel System For Nucleus Pulposus Repair And Regeneration, Nada A. Haq-Siddiqi

Dissertations and Theses

Low back pain is the most common cause of disability in the world and is often caused by degeneration or injury of the intervertebral disc (IVD). The IVD is a complex, fibrocartilaginous tissue that allows for the wide range of spinal mobility. Disc degeneration is a progressive condition believed to begin in the central, gelatinous nucleus pulposus (NP) region of the tissue, for which there are few preventative therapies. Current therapeutic strategies include pain management and exercise, or surgical intervention such as spinal fusion, none of which address the underlying cause of degeneration. With an increasingly aging population, the socioeconomic …

Development Of Light Actuated Chemical Delivery Platform On A 2-D Array Of Micropore Structure, Hojjat Rostami Azmand, Hojjat Rostami Azmand

Dissertations and Theses

Localized chemical delivery plays an essential role in the fundamental information transfers within biological systems. Thus, the ability to mimic the natural chemical signal modulation would provide significant contributions to understand the functional signaling pathway of biological cells and develop new prosthetic devices for neurological disorders. In this paper, we demonstrate a light-controlled hydrogel platform that can be used for localized chemical delivery in a high spatial resolution. By utilizing the photothermal behavior of graphene-hydrogel composites confined within micron-sized fluidic channels, patterned light illumination creates the parallel and independent actuation of chemical release in a group of fluidic ports. The …

Restoration Of Bone Material And Microstructural Properties After Long-Term Remodeling Suppression, Abigail A. Coffman

Dissertations and Theses

Anti-resorptive drugs, principally bisphosphonates (BPs), are the mainstay of osteoporosis treatment. They work by inhibiting bone resorption/remodeling, thus preventing bone loss. However, long-term suppression of bone resorption adversely affects bone tissue mechanical properties, even while conserving bone mass. Lack of remodeling leads to accumulation of fatigue-induced microdamage, altered matrix mineralization and reduction in normal bone tissue heterogeneity, causing impaired strength and fracture toughness. The most severe consequence to patients, while rare, is Atypical Femur Fractures (i.e., complete fatigue fractures of the femoral shaft). To counteract the effects of long-term remodeling suppression, a temporary break in BP treatment (a "drug holiday) …

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

Dynamics Of Simultaneous Nitrite Ion And Ammonia Chlorination In Complex Water Quality Matrices And Their Impact On Chlorine Residual Speciation During Disinfection, Shirin Estahbanati

Dissertations and Theses

Although chlorination of ammonia and nitrite ions have been studied comprehensively, the kinetics of chlorination in water matrices containing ammonia in the presence of nitrite ion have not been fully understood. The coexistence of the two nitrogen compounds is a phenomenon most often encountered during biological nitrification of municipal wastewaters. The spatial variation of the nitrogen species generates unpredictable complications in the effectiveness of chlorination as the disinfection process. The focus of the research study was the examination of chlorine residual speciation and the fate of ionic nitrogen species, i.e. nitrite and nitrate ions, under various experimental conditions. The experimental …

Understanding The Effect Of Climate And Hydrometeorological Extremes On Natural And Human-Induced Hydrosystems, Jeongwoo Hwang

Dissertations and Theses

The contemporary hydrosystems of the United States involve a complex combination of natural and modified basins in the presence of changing climate and anthropogenic impacts. An enhanced understanding of the interdependence between climate forcings, human-induced interventions, and water balance in both natural and modified basins are essential for developing reliable and resilient hydrosystems and for better water resources management. In response, this dissertation focuses on investigating the hydroclimatology of natural and modified basins across the contiguous United States. It has three research objectives: (1) to explain flow alterations due to anthropogenic activities, especially dam operations, in modified basins and understand …

Investigating The Effect Of Electrolyte Concentration And Charging Protocol On Materials Utilization In Rechargeable Zinc Manganese Dioxide Batteries, Snehal H. Kolhekar

Dissertations and Theses

Achieving a highly cyclable, high energy density battery with MnO₂ cathodes encounters many obstacles. Chief among these is the inability of the widely-used γ-MnO₂ polymorph to retain its structural integrity when cycled to near full one-electron discharge capacity, which is about 280mAh/g for commercially available electrolytic manganese dioxide (EMD). In this one-electron range, discharge occurs by proton insertion producing Mn⁺³ which then reverts to γ-MnO₂ on charging. In the first part of the thesis, we investigate the root cause of failure of MnO₂ cathodes under deep cycling in the one-electron discharge range and establish a …

Development Of A Biaxial Testing System For Research Of Soft Tissue Biomechanics Using Laboratory Models, Tariq Shameen

Dissertations and Theses

The rupture of the cap tissue layer of a fibroatheroma in human coronary vessels is considered the key event leading to the formation of a thrombus and myocardial infarction, resulting in more than half a million deaths in the US every year. In this study, we are interested in investigating the biomechanics of different elastomer materials that can be used as laboratory models to replicate coronary arteries’ ultimate tensile stress (0.2 - 2.08 MPa). To this end, we developed a biomechanical testing system that allows us to characterize the material properties of small samples with high accuracy and precision. We …

An Experimental Study Investigating The Impact Of Miscible And Immiscible Nitrogen Injection On Asphaltene Instability In Nano Shale Pore Structure, Mukhtar Elturki, Abdulmohsin Imqam

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Miscible gas injection has become the most used enhanced oil recovery (EOR) method in the oil and gas industry. The deposition and precipitation of asphaltene during the gas injection process is one of the problems during the oil production process. The asphaltene can deposit and plug the pores, which reduces the permeability in a reservoir; thus, decreasing the oil recovery and increasing the production costs. This research investigates the nitrogen (N2) miscible and immiscible pressure injections on asphaltene instability in shale pore structures. First, a slim tube was used to determine the minimum miscibility pressure (MMP) of N2 to ensure …

Optimization Of Gelatin-Based Cellular Coating Of Msc For Myocardial Infarction Therapy, Kara Amelle Davis

Theses and Dissertations--Chemical and Materials Engineering

Cardiovascular disease remains the number one threat to American lives. During an acute myocardial infarction (AMI), blood flow is blocked and results in the formation of scar tissue. As the body’s immune system responds, inflammatory signaling causes an increase in both scar tissue size and the patient’s risk for further chronic heart failure. In order to reduce the risk of continued heart disease inflammatory signaling must be reduced. Stem cell therapies have the ability to alter the immune system’s pro-inflammatory signal. However, stem cell retention is limited due to blood flow shear. Gelatin methacrylate (GelMA) based coatings have been shown …

Electrochemical Performance Of Biomass-Derived Activated Carbon Supercapacitor Under Compression, Yulin Zhang

Theses and Dissertations--Chemical and Materials Engineering

Supercapacitors are important energy storage device of high-power density, fast charge/discharge rate, environmental friendliness and long service life. Currently, flexible supercapacitors have attracted widespread interest in academia and industry. Supercapacitors under the action of external force will inevitably cause structural changes, performance degradation and even loss of energy storage and supply functionalities. As the most abundant renewable resource so far, biomass is an important energy source for human survival and development. Most electrode materials for supercapacitors are porous activated carbons, which can be derived from abundant renewable biomass, contributing to the sustainable development of society and environmental protection. This thesis …