Digital Commons Network^™

Development Of High-Throughput Catalyst Screening For Ammonia Based Selective Catalytic Reduction Of Nitric Oxide With Parallel Analysis Using Fourier Transform Infrared Imaging, Shahriar Salim

Theses and Dissertations

Lean-burn engines, which operate under excess air to fuel ratio offer significant fuel efficiency as well as contribute to the reductions of greenhouse gas emissions. However, lean burn engines produce three main pollutants carbon monoxide (CO), nitrogen oxides (NOx) and unburned or partially burned hydrocarbons (HC), which have detrimental effect on both environment and human life. The conventional three way catalyst (TWC) which was designed to reduce NOx under stoichiometric conditions is not effective under lean-burn engine exhaust condition. Recent studies have shown that copper (Cu) exchanged chabazite (CHA) type zeolites are very promising catalysts for urea or ammonia (NH3) …

Phylogeny And Ancestral Genome Reconstruction From Gene Order Using Maximum Likelihood And Binary Encoding, Fei Hu

Theses and Dissertations

Over the long history of genome evolution, genes get rearranged under events such as rearrangements, losses, insertions and duplications, which in all change the ordering and content along the genome. Recent progress in genome-scale sequencing renews the challenges in the reconstructions of phylogeny and ancestral genomes with gene-order data. Such problems have been proved so interesting that a large number of algorithms have been developed rigorously over the past few years in attempts to tackle these problems following various principles. However, difficulties and limitations in performance and scalability largely prevent us from analyzing emerging modern whole-genome data, our study presented …

Design Of A Running Robot And The Effects Of Foot Placement In The Transverse Plane, Timothy James Sullivan

Open Access Theses

The purpose of this thesis is to make advances in the design of humanoid bipedal running robots. We focus on achieving dynamic running locomotion because it is one metric by which we can measure how far robotic technologies have advanced, in relation to existing benchmarks set by humans and other animals. Designing a running human-inspired robot is challenging because human bodies are exceptionally complex mechanisms to mimic. There are only a few humanoid robots designed specifically for running and the existing robots are either constrained to a plane, do not yet exhibit human-like motion, or are unstable.

One aspect of …

Performance Evaluation Of Data Intensive Computing In The Cloud, Bhagavathi Kaza

UNF Graduate Theses and Dissertations

Big data is a topic of active research in the cloud community. With increasing demand for data storage in the cloud, study of data-intensive applications is becoming a primary focus. Data-intensive applications involve high CPU usage for processing large volumes of data on the scale of terabytes or petabytes. While some research exists for the performance effect of data intensive applications in the cloud, none of the research compares the Amazon Elastic Compute Cloud (Amazon EC2) and Google Compute Engine (GCE) clouds using multiple benchmarks. This study performs extensive research on the Amazon EC2 and GCE clouds using the TeraSort, …

Method Development For A Chemical And Biological Analysis Of Glucocorticoids In Wastewater, Maria Carmen Lozano

Open Access Theses & Dissertations

Glucocorticoids are a class of steroid hormones that can either be produced synthetically or naturally by the adrenal glands. The synthetic glucocorticoids are highly prescribed in the United States for their anti-inflammatory and immunosuppressive properties to treat a variety of ailments and diseases; however, these have been implicated in a number of adverse human conditions such as obesity, metabolic syndrome, immune-suppression, delayed puberty, adrenal insufficiency and Cushing Syndrome, among others. Ongoing research has shown that synthetic and natural hormones are transported to aquatic environments via mammalian excretion or wastewater effluent, and as a result, the release of glucocorticoids into the …

A Novel Microfluidic Enrichment Technique For Carbonylated Proteins, Bryant C. Hollins

Doctoral Dissertations

Proteins are the building blocks of cells in living organisms, and are composed of amino acids. The expression of proteins is regulated by the processes of transcription and translation. Proteins undergo post-translational modifications in order to dictate their role physiologically within a cell.

Not all post-translational modifications are beneficial for the protein or the cell. One type of post-translational modification, called carbonylation, irreversibly places a carbonyl group onto an amino acid residue, most commonly proline, lysine, arginine, and threonine. This modification can have severe consequences physiologically, including loss of solubility, loss of function, and protein aggregation.

Carbonylated proteins have commonly …

Subnanosecond Exposure Systems For Biological Studies, Jongbong Nah

Electrical & Computer Engineering Theses & Dissertations

The research of bioelectrics has expanded to subnanosecond pulse region and entered a new domain of biophysics of cell interaction with ultra-short and intense electric fields. As subnanosecond pulses may be delivered by antennas to the human body and is very attractive to the medical community, the study of subnanosecond pulse effects calls for exposure systems for both cells and tissues. Two systems were designed in the scope of this thesis, used for cells and tissues respectively. The exposure system designed for cell exposure is a cuvette consisting of two parallel aluminum gaps. This cuvette is placed in a coaxial …

Soft Microenvironments Promote The Early Neurogenic Differentiation But Not Self-Renewal Of Human Pluripotent Stem Cells, Albert Keung, Prashanth Asuri, Sanjay Kumar, David Schaffer

Bioengineering

Human pluripotent stem cells (hPSCs) are of great interest in biology and medicine due to their ability to self-renew and differentiate into any adult or fetal cell type. Important efforts have identified biochemical factors, signaling pathways, and transcriptional networks that regulate hPSC biology. However, recent work investigating the effect of biophysical cues on mammalian cells and adult stem cells suggests that the mechanical properties of the microenvironment, such as stiffness, may also regulate hPSC behavior. While several studies have explored this mechanoregulation in mouse embryonic stem cells (mESCs), it has been challenging to extrapolate these findings and thereby explore their …

Hydrodynamic Focused Passive Separation Under Continuous Flow In A Microfluidic Chip, Jad Kanbar

Master's Theses

A continuous flow, passive separation device was designed using an equivalent circuit to create variable flow rates for hydrodynamic focusing to drain channels and collection outlets. By varying the diameter of the sample inlet connection into the reservoir, the particle position was influenced significantly, which enabled desired separations. Additionally it was noted that the relative, horizontal position of the inlet also had a significant influence on particle position within the device. A dimensionless number, the Characteristic Sample Inlet, was developed to relate geometric properties of the inlet reservoir to downstream particle distribution. It was found that a 2:1 ratio between …

High Aspect Ratio Electrodes For High Yield Electroporation Of Cells, Anil B. Shrirao

Dissertations

Electroporation is a widely used process in cell biology studies. It uses an electric field to create pores on the cell membrane in order to either insert exogenous molecules inside the cells or disrupt the cell membrane to kill the cells. Current micro-fluidic electroporation devices use the planar electrodes situated at the bottom of a microchannel. These planar electrodes i) require a high voltage and ii) generate a nonuniform electric field which result in low yield of the electroporation. The standard silicon microfabrication technologies are not suitable to fabricate non-planar electrodes required to increase the yield of electroporation.

In this …

Methods Of Cellular Integration And Techniques For Improving Encapsulated Cell Viability For The Purpose Of Developing Living Materials And Cell Based Bio-Sensing Materials, Travis J. Savage

Chemical and Biological Engineering ETDs

Living materials offer the potential for detection-reporter systems based on living cells that are genetically tailored to sense target analytes with high levels of specificity and accuracy. A biotic or living material would allow the development of simple, hand held devices that could be utilized for many applications including industrial process monitoring, environmental remediation, military and defense applications and drug delivery. Many living materials have been developed and characterized but they still lack heightened and prolonged encapsulated cell viability necessary to make the material a candidate for widespread use. One particular material offers several advantages to increase yeast cell viability …

Nanopillar Based Electrochemical Biosensor For Monitoring Microfluidic Based Cell Culture, Rajan Gangadharan

All Dissertations

In-vitro assays using cultured cells have been widely performed for studying many aspects of cell biology and cell physiology. These assays also form the basis of cell based sensing. Presently, analysis procedures on cell cultures are done using techniques that are not integrated with the cell culture system. This approach makes continuous and real-time in-vitro measurements difficult. It is well known that the availability of continuous online measurements for extended periods of time will help provide a better understanding and will give better insight into cell physiological events.
With this motivation we developed a highly sensitive, selective and stable microfluidic …

Synergistic Effect Of Subnanosecond Pulsed Electric Fields And Temperature On The Viability Of Biological Cells, James Thomas Camp

Electrical & Computer Engineering Theses & Dissertations

Pulsed electric fields have been used to induce a biological response in cells, and at sufficient energy, can cause cell death. By reducing the pulse duration from presently used nanosecond to subnanosecond ranges, the electric field can be delivered to biological tissue non-invasively by the use of an antenna instead of electrodes, such as needles. Studies have previously been completed in which the aim was to determine the energy density (electric field strength, number of pulses) required to induce cell death with 800 ps pulses. Based on this data, it was concluded that for pulse durations of 200 ps, with …

Nonosecond Pulsed Electric Field Induced Changes In Dielectric Properties Of Biological Cells, Jie Zhuang

Electrical & Computer Engineering Theses & Dissertations

Nanosecond pulsed electric field induced biological effects have been a focus of research interests since the new millennium. Promising biomedical applications, e.g. tumor treatment and wound healing, are emerging based on this principle. Although the exact mechanisms behind the nanosecond pulse-cell interactions are not completely understood yet, it is generally believed that charging along the cell membranes (including intracellular membranes) and formation of membrane pores trigger subsequent biological responses, and the number and quality of pores are responsible for the cell fate. The immediate charging response of a biological cell to a nanosecond pulsed electric field exposure relies on the …

Session 1c, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• The Effects of Prescribed Fire on Amphibian and Reptile Diversity in an Oak-Grassland Restoration Area, Robert Knopp and Howard Whiteman, Dept Biological Sciences and Watershed Studies, Murray State University
• Results of a Data Evaluation to Establish Priority Remediation Areas for Dry Weather Fecal Contamination in a Karst Influenced Watershed, Steve Evans and others, Third Rock Consultants, Lexington, KY
• Development of In-House Methods for High-Throughput DNA Extraction, Kimberly L. Cook and LorraBelle Hill, USDA-ARS, Bowling Green, KY
• Validation of the Sanitary Category Value Model (SCV) for the Identification of Leaking Sewer Lines: A Study of the West Hickman …

Proceedings Of 2012 Kentucky Water Resources Annual Symposium, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

This symposium was planned and conducted as a part of the state water resources research institute annual program that is supported by Grant/Cooperative Agreement Number G11AP20081 from the United States Geological Survey. The contents of this proceedings document and the views and conclusions presented at the symposium are solely the responsibility of the individual authors and presenters and do not necessarily represent the official views of the USGS or of the symposium organizers and sponsors. This publication is produced with the understanding that the United States Government is authorized to reproduce and distribute reprints for government purposes.

Biomechanics, Brooke A. Slavens, Gerald F. Harris

Biomedical Engineering Faculty Research and Publications

Biomechanics is a vast discipline within the field of Biomedical Engineering. It explores the underlying mechanics of how biological and physiological systems move. It encompasses important clinical applications to address questions related to medicine using engineering mechanics principles. Biomechanics includes interdisciplinary concepts from engineers, physicians, therapists, biologists, physicists, and mathematicians. Through their collaborative efforts, biomechanics research is ever changing and expanding, explaining new mechanisms and principles for dynamic human systems. Biomechanics is used to describe how the human body moves, walks, and breathes, in addition to how it responds to injury and rehabilitation. Advanced biomechanical modeling methods, such as inverse …

Gaining Insight Into The Physics Of Dynamic Atomic Force Microscopy In Complex Environments Using The Veda Simulator, Daniel Kiracofe, John Melcher, Arvind Raman

Birck and NCN Publications

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In …

Scale Invariant Object Recognition Using Cortical Computational Models And A Robotic Platform, Danny Voils

Dissertations and Theses

This paper proposes an end-to-end, scale invariant, visual object recognition system, composed of computational components that mimic the cortex in the brain. The system uses a two stage process. The first stage is a filter that extracts scale invariant features from the visual field. The second stage uses inference based spacio-temporal analysis of these features to identify objects in the visual field. The proposed model combines Numenta's Hierarchical Temporal Memory (HTM), with HMAX developed by MIT's Brain and Cognitive Science Department. While these two biologically inspired paradigms are based on what is known about the visual cortex, HTM and HMAX …

Effect Of Extracellular Matrix (Ecm) Protein Micropatterns On The Behavior Of Human Neuroblastoma Cells, Ishwari Poudel

Department of Engineering Mechanics: Dissertations, Theses, and Student Research

Recent advances in patterning techniques and emerging surface microtechnologies have allowed cell micropatterning to control spatial location of the cells on a surface as well as cell shape, attachment area, and number of contacting neighbor cells. These parameters play important roles in cell cellular behaviors. Cell micropatterning has thus become one of the most important strategies for biomedical applications, such as, tissue engineering, diagnostic immunoassays, lab-on-chip devices, bio-sensing, etc., and cell biology studies as well. For neuronal cells, there have been attempts to distribute neuronal cells on specific patterns to control cell-to-cell interaction. However, there have been very limited understanding …

Radio Frequency Micro/Nano-Fluidic Devices For Microwave Dielectric Property Characterizations, Chunrong Song

All Dissertations

In this dissertation, a number of different topics in microwave dielectric property measurements have been covered by a systematic approach to the goals of development of dielectric spectroscopy and study of its high electric field effects with integrated on-chip microwave microfluidic / nanofluidic devices.
A method of parasitic effects cancellation for dielectric property measurement is proposed, analyzed, and experimentally evaluated for microwave characterization of small devices and materials that yield low intensity signals. The method dramatically reduces parasitic effects to uncover the otherwise buried signals. A high-sensitive radio frequency (RF) device is then developed and fabricated to detect small dielectric …

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …

Effects Of Non-Planar Distortions In Porphyrin Compounds On Their Properties And Functionality, Raid Haddad

Chemical and Biological Engineering ETDs

Porphyrins and related compounds are ubiquitous in nature, performing diverse functions including solar energy transduction, electron transport, molecular transport and storage, and catalysis. Due to their unique photophysical and chemical properties, they are excellent candidates for application as photosensitizers, catalysts, photocatalysts, molecular electronics and opto-electronics. Several properties of porphyrins are sensitive to small variations in their structure, and this dissertation investigates the effects of out-of-plane distortions of the macrocycle on optical properties, reactivity to axial ligands, and substituent rotation. The structure-functions relationships are examined using molecular simulations, UV-visible absorption spectroscopy, resonance Raman spectroscopy, and normal-coordinate structural decomposition (NSD) analysis of …

Characterization Of A Pdms Microfluidic Reactor For Synthesizing Quantum Dots, Brian Harley

Materials Engineering

A PDMS microfluidic reactor was made in Cal Poly’s class 1000 clean room for the purpose of synthesizing quantum dots.  The device master mold was made from a silicon substrate and SU-8 features 50μm tall.  The PDMS reactor was cast from that mold.  The flow rates of fluid through the channels, heating of the reactor and pressure in the reactor were measured in order to characterize the potential for synthesizing quantum dots.  Flow rates of 20 mL/hr through 4 mL/hr were tested to characterize the consistency of amount of time the fluid remains in the reactor at a constant flow …

A Quantitative, Technology Independent, Fidelity Metric For Evaluating Bioprinted Patterned Co-Cultures, Matthew Pepper

All Theses

The study of cell-cell interactions is crucial in the understanding of cell behaviors such as tumor genesis, proliferation, migration, metastasis, and apoptosis. To break down the complex web of signals in vivo, researchers must replicate some parts of this environment with in vitro tissue test systems, composed of multiple cell types arranged close enough to communicate with their neighbors, i.e. high-resolution co-culture patterns. The field of bioprinting is specifically focused on creating co-culture patterns for the purposes of cell studies, but the sample resolutions of most bioprinting systems are still too coarse to permit cell communication. No way currently exists …

Manipulating Cellular Growth Responses To Patterning, Apoptotic, And Environmental Cues, James N. Mcnamara

Doctoral Dissertations

In this work, various methods of controlling cell growth are examined. Cell-cell interaction, apoptotic cues, three dimensional scaffolds, and non-adherent environments are evaluated for their ability to affect the differentiation, morphology, and growth rate of different cell types. Previous work has shown that cell growth and cell morphology can be influenced by patterns of polymers coated on surfaces in two dimensions, designated here as the x and y dimensions of a standard Cartesian coordinate system. Tissue engineering and regenerative medicine studies have shown limited success in modifying growth in the third, z dimension. This work considers not only the x, …

Direct Current Electrokinetic Particle Transport In Micro/Nano-Fluidics, Ye Ai

Mechanical & Aerospace Engineering Theses & Dissertations

Electrokinetics has been widely used to propel and manipulate particles in micro/nano-fluidics. The first part of this dissertation focuses on numerical and experimental studies of direct current (DC) electrokinetic particle transport in microfluidics, with emphasis on dielectrophoretic (DEP) effect. Especially, the electrokinetic transports of spherical particles in a converging-diverging microchannel and an L-shaped microchannel, and cylindrical algal cells in a straight microchannel have been numerically and experimentally studied. The numerical predictions are in quantitative agreement with our own and other researchers' experimental results. It has been demonstrated that the DC DEP effect, neglected in existing numerical models, plays an important …

Developing Methods To Assess The Potential Effects Of Global Climate Change On Deer Creek Reservoir Using Water Quality Modeling, Reed Earl Chilton

Theses and Dissertations

To evaluate the potential impacts of future climate change on a temperate reservoir, I used a calibrated water quality and hydrodynamic model validated using three years of data (2007-2009) from Deer Creek Reservoir (Utah). I evaluated the changes due to altered air temperatures, inflow rates, and nutrient loads that might occur under Global Climate Change (GCC). I developed methods to study GCC on reservoirs. I produced Average Water Temperature Plots, Stratification Plots, and Total Concentration Plots. Average Water Temperature Plots show the sensitivity of the water temperature to various parameters. Stratification Plots quantify stratification length and strength as well as …

Biological Investigation Of The Stimulated Flapping Motions Of The Moth, Manduca Sexta, Travis B. Tubbs

Theses and Dissertations

No abstract provided.

Optimization And Characterization Of Multifunctional Polymeric-Nanodiamond Electrospun Scaffolds, Amanee Salaam

All ETDs from UAB

Due to the lack of treatment options available for patients suffering from bone abnormalities, current research focuses on developing novel biomaterials for bone tissue engineering. Since a tissue scaffold is implanted in vivo, it could also serve as a substrate for localized, systemic delivery of therapeutics. Particularly in primary bone cancer after removal of a cancerous lesion, there is a need for a system that can support the generation of new tissue while delivering localized chemotherapy. However, a complex molecule is needed to serve as a vehicle for delivering the drug and targeting only cancerous cells. Detonation nanodiamond (DND) is …