Digital Commons Network^™

Cs 4810: Algorithms For Bioinformatics, Michael L. Raymer

Computer Science & Engineering Syllabi

No abstract provided.

Aspect-Dependent Radiated Noise Analysis Of An Underway Autonomous Underwater Vehicle, John Gebbie, Martin Siderius, John S. Allen Iii

Electrical and Computer Engineering Faculty Publications and Presentations

This paper presents an analysis of the acoustic emissions emitted by an underway REMUS-100 autonomous underwater vehicle(AUV) that were obtained near Honolulu Harbor, HI using a fixed, bottom-mounted horizontal line array (HLA). Spectral analysis,beamforming, and cross-correlation facilitate identification of independent sources of noise originating from the AUV. Fusion of navigational records from the AUV with acoustic data from the HLA allows for an aspect-dependent presentation of calculated source levels of the strongest propulsion tone.

Lateral-Mode Vibration Of Microcantilever-Based Sensors In Viscous Fluids Using Timoshenko Beam Theory, Joshua Schultz

Dissertations (1934 -)

Dynamic-mode microcantilever-based devices are well suited to biological and chemical sensing applications. However, these applications often necessitate liquid-phase sensing, introducing significant fluid-induced dissipative forces and reducing device quality factors (Q). Recent experimental and analytical research has shown that higher in- fluidQis achieved by exciting microcantilevers in the lateral flexural mode. However, the experimental results show that, for microcantilevers having larger width-to-length (b/L) ratios, the behaviors predicted by current analytical models differ from measurements.

To more accurately model microcantilever resonant behavior in viscous fluids and to improve understanding of lateral-mode sensor performance, a new analytical model is developed, incorporating both viscous …

Stem Cell Based Tissue Engineering And Regenerative Medicine: A Review Focusing On Adult Stem Cells, Jordan Greenberg, Veronica R. Fortino, Daniel Pelaez, Herman S. Cheung

Biology Faculty Articles

Tissue engineering has emerged as a field that attempts to harness the bodies' own developmental and repair features to treat diseases and illnesses. Many of these illnesses are caused by necrosis or loss of functionality of complete organs or specific cell types. Early discoveries in embryonic stem cells fueled a wave of research that led to claims about possibly regenerating nonfunctioning organs. Although we are still far away from being able to grow functional organs in a Petri dish, the field continues to progress forward, and new clinical trials have been approved for using both embryonic and adult stem cell …

Electroluminescence From Zno Nanostructure Synthesizes Between Nanogap, Cheng Jiang

Master's Theses (2009 -)

This thesis presents the investigation of a nanoscale light-emitting diode (LED) device. The nanoscale LED has a great potential to be used as a light source for biomedical screening and fluorescence lifetime spectroscopy. It can also be developed to a single photon emitter for the application of quantum computing. The nano-LED has the electrical structure of a metal-semiconductor-metal (MSM) junction. The MSM junction has been formed on the nanogap device that is fabricated on a SOI wafer by optical lithography and KOH solution silicon etching. The Ni evaporated on the surface of the nanogap device performs the metal contact for …

2012 (Fall) Ensi Informer Magazine, Morehead State University. Engineering Sciences Department

ENSI Informer Magazine Archive

The ENSI Informer Magazine published in the fall of 2012.

Level Of Agreement In The Mental Models Of Human Factors Practitioners And Systems Engineers Working In Collaborative Teams, Jerry A. Gordon

Doctoral Dissertations and Master's Theses

Emerging research in complexity science recognizes traditional techniques for engineering systems do not always work for complex systems. Designing complex systems requires individuals to have knowledge of engineering as well as human performance. To this end, design efforts rely often on multi-disciplinary teams. While any two members of a design team may view the system design problem in vastly different manners, this study sought to identify a possible systemic effect on approach by the differing education and experience obtained by social practitioners, represented by human factors, and technical practitioners, represented by systems engineers. It further examined the impact of the …

Development Of A Supervisory Control Unit For A Series Plug-In Hybrid Electric Vehicle, Brian Neal Harries

Doctoral Dissertations and Master's Theses

A Series PHEV was chosen, as ERAU's entry into EcoCAR2 through a multidisciplinary architecture selection process. The series architecture was chosen for its mechanical feasibility, consumer acceptability and its performance on energy consumption simulations. The Series PHEV architecture was modeled using Matlab, Simulink, and dSPACE ASM tools, to create a plant model for controller development. A supervisory controller was developed to safely control the interactions between powertrain components. The supervisory control unit was tested using SIL and HIL methodologies. The supervisory controller was developed with an emphasis on fault detection and mitigation for safety critical systems. A power management control …

Fabrication Of Ph- Or Temperature-Responsive Single Wall Carbon Nanotubes Via A Graft From Photopolymerization, Pu Zhang, David B. Henthorn

Chemical and Biochemical Engineering Faculty Research & Creative Works

An ultraviolet light initiated "graft from" polymerization method to fabricate polymer-functionalized single wall carbon nanotubes (SWNTs) with pendant pH- and temperature-responsive polymer chains is utilized. the attached polymer chains, formed from methacrylic acid and poly (ethylene glycol) methyl ether methacrylate monomers, are well established for its pH-responsive swelling/deswelling behavior. This special property was utilized here to control the aqueous dispersibility of the carbon nanotubes. Furthermore, poly(N-isopropylacrylamide), a temperature-responsive polymer, was utilized in the fabrication of SWNTs whose dispersibility was dependent on solution temperature. the morphology of the polymer-functionalized carbon nanotubes was characterized by scanning electron microscopy (SEM) before and after …

Analysis Of The Detection Of Organophosphate Pesticides In Aqueous Solutions Using Polymer-Coated Sh-Saw Sensor Arrays, Tian Newman

Master's Theses (2009 -)

The shear horizontal surface acoustic wave (SH-SAW) device was investigated as a micro-chemical sensor for the direct, rapid and in-situ monitoring of chemical contaminants in groundwater and wastewater. The chemical contaminants of interest are organo-phosphate-based compounds (parathion, parathion-methyl, and paraoxon). The polymers used as partially chemically selective coatings are 2,2’-diallylbisphenol A - 1,1,3,3,5,5-hexamethyltrisiloxane (BPA-HMTS), and 2,2’-diallylbisphenol A- polydimethylsiloxane (BPA-PDMS), polyepichlorohydrin (PECH). The experimental results indicate that the analyte/polymer interaction is a result of mass loading and viscoelastic changes in the polymer. BPA-HMTS, BPA-PDMS, and PECH have the highest to lowest sensitivity towards parathion, parathion-methyl, and paraoxon respectively. The polymers tested …

Development And Performance Of A Sparsity-Exploiting Algorithm For Few-View Single Photon Emission Computed Tomogrpahy (Spect) Reconstruction, Paul Arthur Wolf

Master's Theses (2009 -)

Single Photon Emission Computed Tomography (SPECT) provides noninvasive images of the distribution of radiotracer molecules. Dynamic Single Photon Emission Computed Tomography provides information about tracer uptake and washout from a series of time-sequence images. Stationary ring-like multi-camera systems are being developed to provide rapid dynamic acquisitions with high temporal sampling. Reducing the number of cameras reduces the cost of such systems but also reduces the number of views acquired, limiting the angular sampling of the system. Novel few-view image reconstruction methods may be beneficial and are being investigated for the application of dynamic SPECT. A sparsity-exploiting algorithm intended for few-view …

Modeling Martian Planetary Entry Descent And Landing Using Monte Carlo Driven Response Surface Methodology, Narcrisha S. Norman

Mechanical & Aerospace Engineering Theses & Dissertations

Response surface methodology (RSM) is a statistical method that explores the relationships between several descriptive variables and one or more response variables. For over sixty years, among other areas, it has been utilized in quality engineering, process engineering, aircraft engineering, economics, chemical engineering, automotive engineering and design/technique optimization. In this dissertation, RSM is utilized to produce regression models that represent the planetary entry, descent and landing (EDL) process. A complete understanding of EDL process is an essential component of any planetary exploration. Research in this area is ongoing and confidence in the ability to explore known celestial bodies is growing. …

Nonthermal Plasma Jet Efficacy On Candida Kefyr, Amber Marie Mattson Jackson

Electrical & Computer Engineering Theses & Dissertations

The inactivation abilities of a nonthermal plasma jet were investigated with the yeast C. kefyr, a pathogen with increasing importance in healthcare. The plasma is generated using a microhollow cathode discharge (MHCD) geometry operated with a DC voltage of 2 kV and a current of 30 mA using air as the operating gas at an airflow rate of 8 SLM. The plasma discharge approaches room temperature at a few mm away from the plasma jet allowing for the use on heat sensitive surfaces. Dry air and humid air were used as the operating gas to see if humidity plays …

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 …

Configuration Studies Of Electrostatic And Magnetostatic Active Space Radiation Shielding, Trac K. Nguyen

Electrical & Computer Engineering Theses & Dissertations

Developing successful and optimal solutions for mitigating the hazards of radiation in deep space is critical for the success of deep-space long duration explorations, including mission to the Moon, Mars and beyond. A recent report (Tripathi et al., 2008) had explored the feasibility of using electrostatic shielding in conjunction with state-of-the-art materials shielding technologies.

In this thesis research, we study the active electrostatic shielding strategy and examine a hybrid configuration that utilizes both electrostatic and magnetostatic fields. The main advantages of this system are shown to be: (i) much lower magnetic fields that could be below the thresholds set for …

Characterization Of Xylan Utilization And Discovery Of A New Endoxylanase In Thermoanaerobacterium Saccharolyticum Through Targeted Gene Deletions, Kara K. Podkaminer, Adam M. Guss, Heather L. Trajano, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C5 and C6 sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of …

Educating Undergraduate Space Science Students With Real Space Missions: Nanosatellite And Nanolab Missions In Kentucky, Robert J. Twiggs

Robert "Bob" Twiggs STEM Education Collection

A PowerPoint presentation created by Professor Bob Twiggs titled "Educating Undergraduate Space Science Students with Real Space Missions: NanoSatellite and NanoLab Missions in Kentucky" from September 27, 2012.

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 …

Application Of Seawinds Scatterometer Data To The Study Of Antarctic Icebergs, Keith Mitchell Stuart

Theses and Dissertations

Knowledge of iceberg location and size is important for safety reasons as well as for understanding many geophysical and biological processes. This dissertation analyzes large tabular icebergs in the Southern Ocean using the SeaWinds scatterometer. SeaWinds is a spaceborne radar designed to measure the microwave backscatter from the Earth's surface. Using resolution-enhancement techniques, backscatter measurements are processed into backscatter images in which icebergs can be observed. An iceberg detection methodology is formalized using daily scatterometer images. Radar profiles from common Antarctic scatterers are quantified and an iceberg detection methodology is formalized using daily scatterometer images. Iceberg positions are determined in …

Efficient Algorithms For Improving The Accuracy In Motifs Prediction, Jerlin C. Merlin

Master's Theses

Analysis of sequence homology has always played a major role in the understanding of biological factors such as protein domain identification, gene product relationships, and gene function determination. Short contiguous protein sequences that are conserved across proteins provide important information about such factors, and are of at most 15 residues in length. These segments of proteins are known as minimotifs. Identifying minimotifs has been of much use in the formulation of the hypothesis about the biological functions that otherwise might be uncharacterized. Mechanisms of motif predictions such as Minimotif Miner are widely used for predicting minimotifs. However, due to the …

The Bench Scientist's Guide To Statistical Analysis Of Rna-Seq Data, Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram

Cyber Center Publications

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression.

Serpentine Low Loss Trapezoidal Silica Waveguides On Silicon, Xiaomin Zhang, Mark Harrison, Audrey Harker, Andrea M. Armani

Engineering Faculty Articles and Research

We report the fabrication and characterization of straight and serpentine low loss trapezoidal silica waveguides integrated on a silicon substrate. The waveguide channel was defined using a dual photo-lithography and buffered HF etching and isolated from the silicon substrate using an isotropic silicon etchant. The waveguide is air-clad and thus has a core-cladding effective index contrast of approximately 25%. Measured at 658, 980 and 1550nm, the propagation loss was found to be 0.69, 0.59, and 0.41dB/cm respectively, with a critical bending radius less than 375μm. The waveguide’s polarization behavior was investigated both theoretically and experimentally. Additionally, the output power shows …

Novel Discretization Schemes For The Numerical Simulation Of Membrane Dynamics, Kyle F. Kolsti

Theses and Dissertations

Motivated by the demands of simulating flapping wings of Micro Air Vehicles, novel numerical methods were developed and evaluated for the dynamic simulation of membranes. For linear membranes, a mixed-form time-continuous Galerkin method was employed using trilinear space-time elements, and the entire space-time domain was discretized and solved simultaneously. For geometrically nonlinear membranes, the model incorporated two new schemes that were independently developed and evaluated. Time marching was performed using quintic Hermite polynomials uniquely determined by end-point jerk constraints. The single-step, implicit scheme was significantly more accurate than the most common Newmark schemes. For a simple harmonic oscillator, the scheme …

The Characterization Of Material Properties And Structural Dynamics Of The Manduca Sexta Forewing For Application To Flapping Wing Micro Air Vehicle Design, Ryan P. O'Hara

Theses and Dissertations

The Manduca Sexta species of moth serves as a source of biological inspiration for the future of micro air vehicle flapping flight. The ability of this species to hover in flapping flight has warranted investigation into the critical material, structural, and geometric properties of the forewing of this biological specimen. A rigorous morphological study of the Manduca Sexta forewing was conducted to characterize the physical and material properties of the biological forewing for the purpose of developing an advanced parametric three dimensional model finite element analysis (FEA) model. This FEA model was tuned to match the experimentally determined structural dynamics …

Increasing Pt Oxygen Reduction Reaction Activity And Durability With A Carbon-Doped Tio 2 Nanocoating Catalyst Support, Kan Huang, Kotaro Sasaki, Radoslav R. Adzic, Yangchuan Xing

Chemical and Biochemical Engineering Faculty Research & Creative Works

We report a conductive TiO2 nanocoating on carbon nanotubes (CNTs) as a Pt electrocatalyst support that shows a significant enhancement in Pt catalyst activity and durability for the oxygen reduction reaction. by using CNTs as the substrate for TiO2 nanocoating, the nanoscale morphology of the oxide was retained during heat treatment. after carbon doping of the TiO2 nanocoating, X-ray photoelectron spectroscopy suggests a shift in the binding energy of Ti 2p, implying a suboxide formation. the X-ray absorption near-edge structure showed the mid-edge and post-edge up to 5010 eV, which are attributed to a 1s → 4p transition and promotion …

Proposed Msu Matchbooksat For Iss Launch 2014, Robert J. Twiggs

Robert "Bob" Twiggs STEM Education Collection

A PowerPoint presentation created by Professor Bob Twiggs titled "Proposed MSU MatchBookSat for ISS Launch 2014" from September 6, 2012.

Image-Based Quantification Of Benzoporphyrin Derivative Uptake, Localization, And Photobleaching In 3d Tumor Models, For Optimization Of Pdt Parameters, Michael D. Glidden, Jonathan P. Celli, Iqbal Massodi, Imran Rizvi, Brian Pogue, Tayyaba Hasan

Dartmouth Scholarship

Photodynamic therapy (PDT) is a light-based treatment modality in which wavelength specific activation of a photosensitizer (PS) generates cytotoxic response in the irradiated region. PDT response is critically dependent on several parameters including light dose, PS dose, uptake time, fluence rate, and the mode of light delivery. While the systematic optimization of these treatment parameters can be complex, it also provides multiple avenues for en- hancement of PDT efficacy under diverse treatment conditions, provided that a rational framework is established to quantify the impact of parameter selection upon treatment re- sponse. Here we present a theranostic technique, combining the inherent …

Dendrochemistry Of Multiple Releases Of Chlorinated Solvents At A Former Industrial Site, Jean Christophe Balouet, Joel Gerard Burken, Frank Karg, Don Vroblesky, Kevin T. Smith, Håkan Grudd, Anders Rindby, François Beaujard, Michel Chalot

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Trees Can Take Up and Assimilate Contaminants from the Soil, Subsurface, and Groundwater. Contaminants in the Transpiration Stream Can Become Bound or Incorporated into the Annual Rings Formed in Trees of the Temperate Zones. the Chemical Analysis of Precisely Dated Tree Rings, Called Dendrochemistry, Can Be Used to Interpret Past Plant Interactions with Contaminants. This Investigation Demonstrates that Dendrochemistry Can Be Used to Generate Historical Scenarios of Past Contamination of Groundwater by Chlorinated Solvents at a Site in Verl, Germany. Increment Cores from Trees at the Verl Site Were Collected and Analyzed by Energy-Dispersive X-Ray Fluorescence (EDXRF) Line Scanning. the …

Defining The Role Of Ultrasound In Drug Delivery, William G. Pitt

Faculty Publications

Ultrasound is a very effective modality for drug delivery because energy that is noninvasively transmitted through the skin can be focused on a specific location and employed to release drug at that site. Most of the drug delivery techniques employ one or both of the results of ultrasonic insonation – the generation of thermal energy, called hyperthermia, or the oscillation of gas bubbles, called acoustic cavitation. Cavitation perturbs cell membrane structures via several modes and increases the permeability to drugs or other solutes. Microconvection, caused by stable cavitation, shears cell membranes. The shock waves and fluid jets of inertial cavitation …

Characterizing Physical Properties Of Gas-Phase Biofilter Media, Guilherme Del Nero Maia, G. Tatiana Sales, George B. Day V, Richard S. Gates, Joseph L. Taraba

Biosystems and Agricultural Engineering Faculty Publications

Gas-phase biofiltration is an effective technology for reduction of odors and trace-gas contaminants. Significant contributions to the technical literature regarding the characterization of biofilter media have been generated in the past two decades. Nevertheless, the information produced has not been systematically organized. The objective of this study is to demonstrate and document methods for physical characterization of gas-phase compost biofilters (GPCB). The inclusion of moisture content, compaction, and particle size effects in the determination of media bulk density and porosity, field capacity, drying rate analysis, water sorption isotherms, and resistance to airflow is demonstrated. Results indicated that: (1) higher moisture …