Digital Commons Network^™

Parweb: A Front-End Interface For Cluster Computing., Jacob Potter

Honors Theses

The High Performance Computational Science Laboratory at Western Michigan University operates a cluster of systems for use by students, professors, and professional researchers. Currently users that want to access the cluster, known as “Thor”, require knowledge of the Unix/Linux command line. They also require knowledge of operating a piece of software known as TORQUE to correctly achieve results from the High Performance Computing Lab.

The Web User Interface Framework for High Performance Cluster Computing alleviates the need for intimate knowledge of a command line interface, and replaces the current interaction interface with a more user friendly and graphical oriented system. …

Ultrafast Interfacial Electron Transfer Across Molecule-Tio2 Nanocomposites: Towards Solar Cells And Two Photon Absorption, Edwin Mghanga

Dissertations

Interfacial charge transfer (ICT) across the molecule-TiO2 nanoparticle interface has gained enormous research attention for applications in dye sensitized solar cells (DSSC), photo-catalysis, water splitting and nonlinear optics. DSSCs are promising clean alternative energy sources. However, current DSSCs suffer from lower efficiencies and higher cost. Better understanding of the ICT processes in DSSCs can help solve these problems. We have used two strategies to understand ICT in the context of DSSCs. Firstly, we used a computationally validated anchor group, acetylacetonate (acac) to bind molecules to the semiconductor surface and facilitate charge separation. Secondly, we used natural dye sensitizers, …

Probing The Unfolding And The Stability Of The Last Four Metal Binding Domains Of Wilson Disease Protein Using Circular Dichroism And Novel Spectroscopic Techniques, Ibtesam Yaseen Alja’Afreh

Dissertations

Wilson disease protein is a copper-transporting P_1B type ATPase. It has large N-terminal copper binding domain which is composed of six homologous sub-domains. Each of these six domains is ~72 residues and connected to one another by linking regions of various lengths. They all possess similar ferrodoxin fold, and metal-binding motif, MXCXXC.

The need of having six metal binding domains and the manner in which they are communicating with each other is not well understood. To better understand how the last four metal binding domains function, I pursued a detailed biophysical characterization of these domains. Using molecular biology I …

Lnference On Differences In K Means For Data With Excess Zeros And Detection Limits, Haolai Jiang

Dissertations

Many data have excess zeros or unobservable values falling below detection limit. For example, data on hospitalization costs incurred by members of a health insurance plan will have zeros for the percentage who did not get sick. Benzene exposure measurements on petroleum re nery workers have some exposures fall below the limit of detection. Traditional methods of inference like one-way ANOVA are not appropriate to analyze such data since the point mass at zero violates typical distribution assumptions.

For testing for equality of means of k distributions, we will propose a likelihood ratio test that accounts for excess zeros or …

Modular Monochromatic Colorings, Spectra And Frames In Graphs, Chira Lumduanhom

Dissertations

Abstract attached as separate document.

A Remote Sensing Based Early Warning System For Algal Blooms In Kuwait Bay And Coastal Waters, Cameron Manche

Masters Theses

The Kuwait Bay and its coastal waters are being threatened by a perpetual hazard, the proliferation of harmful algal blooms (HABS). The frequency of HAB occurrences is a growing problem that is only reported subsequent to the onset of a HAB event. Little effort has been invested in investigating the spatial and temporal distribution of these events in Kuwait Bay and even less is known about their controlling factors. All previous studies within the Kuwait Bay have focused either on measuring nutrient availability and the biodiversity of algal species.

The overall study objective is four-fold: (1) to monitor the spatial …

Geosciences Newsletter - 2014, Department Of Geosciences

Geological and Environmental Sciences News

Vol. 7, No. 1

• Faculty Updates
• Michigan Geological Survey
• News from MGRRE
• WMU Geosciences Advisory Council
• Meet our Students
• Geology Club
• In Remembrance
• Meet Our New Graduate Students
• CoreKids: our K-12 Outreach Program
• 2014 Geosciences Distinguished Alumni Award Recipient
• Gifts to Geosciences

Comparison Of Hazard, Odds And Risk Ratio In The Two-Sample Survival Problem, Benedict P. Dormitorio

Dissertations

Cox proportional hazards is the standard method for analyzing treatment efficacy when time-to-event data is available. In the absence of time-to-event, investigators may use logistic regression which only requires relative frequencies of events, or Poisson regression which requires only interval-summarized frequency tables of time-to-event. When event frequencies are used instead of time-to-events, does it always result in a loss in power?

We investigate the relative performance of the three methods. In particular, we compare the power of tests based on the respective effect-size estimates (1)hazard ratio (HR), (2)odds ratio (OR), and (3)risk ratio (RR). We use a variety of survival …

The Experiences Of Women In Post Graduate Physics And Astronomy Programs: The Roles Of Support, Career Goals, And Gendered Experiences, Ramón S. Barthelemy

Dissertations

In physics and astronomy the low representation of women is obvious at every stage of the educational pathway from undergraduate students to full professors. These low numbers perpetuate themselves by failing to create new mentors to foster the next generation of women. Women and men also have different experiences as they traverse into physics and astronomy careers. Women often experience chilly climates, discrimination, and challenges coordinating the demands of young families with their careers. In the literature exploring this topic, little focus is put on the experiences of women graduate students in physics and no focus is put on women …

Effects Of Road Salt On Asylum Lake Geochemistry, Davina A. Wyman

Masters Theses

Several studies indicate that seasonal applications of road deicers can lead to saline runoff entering surface water and groundwater, which can in turn change the chemistry, density, and physical mixing patterns of urban lakes. An investigation at Asylum Lake, an urban lake located near three major roadways, was conducted to determine the degree of road salt contamination in the lake, to determine if salt loading disrupts seasonal mixing patterns, and to determine the extent of redox stratification present due to eutrophic conditions. Samples were collected monthly from the deepest point in Asylum Lake over a 19-month period and analyzed for …

Michigan's Clay Bluffs: The Description And Comparison Of An Erosion-Dependent Natural Community, Nathaniel G. Fuller

Masters Theses

The clay bluffs of Michigan are a natural community found along the shores of the Great Lakes. Groundwater is found to be critical to sustaining the alkaline wetlands on the face of the bluff as well as the source of most erosion events. The clay bluffs are unusual in their vegetation, disturbance regime and geographical context. This thesis focuses primarily on describing seeping clay bluffs and exploring the comparison to other natural communities. The purpose of this is twofold, to better understand the ways in which natural communities are described as distinct from one another, and to assess the distinctness …

Gpu-Accelerated Influenza Simulations For Operational Modeling, Peter Holvenstot

Masters Theses

Simulations of influenza spread are useful for decision-making during public-health emergencies. Policy-makers use models to predict disease spread and estimate the effects of various intervention strategies. Effective modeling of targeted intervention strategies requires accurate modeling of individual-level behavior and transmission. However, this greatly increases the computational costs of these agent-based models. In addition, if the models are used as an outbreak progresses, some operational decisions must occur rapidly in order to contain the spread of the disease.

Graphics Processing Units (GPUs) are a type of specialized processor used to drive graphical displays. Many recent devices also allow users to write …

Electron Transfer In Pnicogen Bond, Liangyu Guan

Masters Theses

Abstract is available for download as a separate file.

The Nucleic Acid Binding Properties Of The Pwi Motif, Hamideh Keshavarz-Mohammadian

Masters Theses

The PWI motif is a highly conserved domain that contains a Proline-Tryptophan-Isoleucine (PWI) tripeptide sequence, for which it is named. Proteins that contain a PWI motif are known to be involved in the constitutive and alternative splicing and the 3'-end processing of messenger RNA transcripts. The hypothesized role of the PWI motif is to nonspecifically interact with nucleic acids. The PWI motif is capable of binding both doublestranded and single stranded forms of DNA and RNA. The structure of the highly conserved core of the PWI motif reveals that it adopts a four-helix bundle fold. The structured core domain, however, …

On Eulerian Irregularity And Decompositions In Graphs, Eric Andrews

Dissertations

Abstract attached as separate file.

Studies Of The Quantum Phase Transition In Chromium Using Inelastic X-Ray Scattering And Ab Initio Methods, Chengyang Li

Dissertations

In this project, inelastic x-ray scattering (IXS) was used to measure the phonon dispersion in chromium at high pressure and low temperature, and an ab initio method was used to simulate the phonon dispersion with different lattice constants and magnetic orders. The IXS measurements were carried out in Sector 30 at the Advanced Photon Source at Argonne National Laboratory. Data were taken at room temperature with pressures of 1.29 GPa, 8.15 GPa, 10.6 GPa, and at 5 K with a pressure of 18.36 GPa. The data shows similar phonon behavior in the antiferromagnetism (AFM) and the spin density wave (SDW) …

Biophysical Characterization Of The First Four Metal-Binding Domains Of Human Wilson Disease Protein, Alia V.H. Hinz

Dissertations

Wilson disease protein (WLNP) is a P_1b-type ATPase crucial for maintaining copper homeostasis in humans. Mutations in this protein result in the autosomal recessive disorder Wilson disease, a condition characterized by copper accumulation in the liver and brain. WLNP provides copper for incorporation into cuproproteins and exports excess copper into the bile for excretion. There are six metal-binding domains (MBDs) in WLNP, found within the first 650 amino acids of this 1,465 amino acid protein. Though each MBD has a different amino acid sequence, all MBDs possess a similar ferredoxin fold with a conserved hydrophobic core and a …

Lie Loops Associated With Gl(ℋ), ℋ A Separable Infinite Dimensional Hilbert Space, Alper Bulut

Dissertations

Abstract attached as separate file.

Mathematical Methods Of Analysis For Control And Dynamic Optimization Problems On Manifolds, Robert J. Kipka

Dissertations

Mathematical Methods Of Analysis For Control And Dynamic Optimization Problems On Manifolds Driven by applications in fields such as robotics and satellite attitude control, as well as by a need for the theoretical development of appropriate tools for the analysis of geometric systems, problems of control of dynamical systems on manifolds have been studied intensively during the past three decades. In this dissertation we suggest new mathematical techniques for the study of control and dynamic optimization problems on manifolds. This work has several components including: an extension of the classical Chronological Calculus to control and dynamical systems which are merely …

Connecting The Disciplinary Dots: Faculty Attitudes Toward The Professionalization Of Web Development, Kathleen Mary Kalata

Dissertations

Professionalization offers rewards such as prestige, financial benefits and autonomy. Fields such as nursing and social work have undergone the professionalization process. This exploratory study examined faculty attitudes regarding the professionalization of web development as defined by the Hall model of professionalism. The purpose of the study was to understand how faculty view web development as a profession. Based on the Hall’s Professionalism Scale (1968) and modified survey by Snizek (1972), the Web Development Professionalism Inventory (WDPI) was used to explore faculty attitudes toward professionalization.

This study surveyed faculty about their views on the structural and attitudinal components of web …

Opportunistic Service Differentiation And Cloud Resource Management In Support Of Enhanced Vehicular Applications, Mohammad Ali Salahuddin

Dissertations

An integral part of Intelligent Transportation Systems (ITS) are Vehicular Ad hoc Networks (VANETs), which consist of vehicles with on-board units (OBUs) and fixed road-side units (RSUs). Wireless Access in Vehicular Environment (WAVE) offers QoS via service differentiation by using application defined priorities. However, WAVE has unbounded delay and is oblivious to network load and severity of vehicles with respect to their environment. Our context severity metric innovatively enhances WAVE to be sensitive to vehicle and environment interactions. Our novel Opportunistic Service Differentiation (OSD) technique, dynamically readjusts the WAVE packet priorities to improve utilization of lower latency queues, prioritizing packets …

Chemistry Graduate Teaching Assistants: A Comparison Of The Classroom Discourse Within Expository And Problem-Based Learning Laboratories, Kelley M. Current

Masters Theses

Graduate Teaching Assistants (GTAs) commonly function as instructors within undergraduate chemistry laboratories. This study sought to explore and describe GTA classroom discourse within two distinct instructional modes, using discourse analysis as the theoretical framework. Theclassroom discourse within a series of verification style labs was comparedto the classroom discourse produced within a set of Problem-Based Learning (PBL) labs. The results suggest three primary findings: (1) the apparent relationship between the instructional mode and form of GTA classroom discourse, (2) the patterns in classroom discourse observed within a given instructional mode repeat, irrespective of content, and (3) the classroom discourse observed within …

An Integral Framework For Sustainable Building Design, Bushra Asfari

Masters Theses

Selection of materials for building design is a delicate process hinged of a number of factors which can be cost or environmental related, depending on the objectives of the design. This process becomes more difficult when designers are faced with several material options for each building component. This thesis presents the design and development of a framework that enables designers understand the trade-off between cost and environmental related factors when selecting materials for building design. The framework is based on the integration of Autodesk Revit, Microsoft access, and modeling modified Harmony search multi-objective optimization tool adapted to account for material …

Predictive Modeling In The Search For Vertebrate Fossils: Geographic Object Based Image Analysis (Geobia) In The Eocene Of Wyoming, Bryan Bommersbach

Masters Theses

The development and testing of predictive models for identifying productive fossil localities represents a promising interdisciplinary endeavor among geographic information scientists, paleoanthropologists, and vertebrate paleontologists. This thesis analyzed high resolution (2m spatial resolution) commercial satellite imagery from the Worldview-2 satellite of five areas of the Great Divide Basin using a GEographic Object-Based Image Analysis (GEOBIA) technique, which segments the image into spectrally homogeneous, multi-pixel image objects. In addition to allowing statistical analysis of the spectral characteristics of the image objects, GEOBIA techniques also let analysts incorporate expert knowledge and contextual information to improve classification accuracy. The spectral characteristics of the …

Owning Our Food System: Urban Community Gardening And Local Food Movements, Paige A. Edwards

Masters Theses

Food is a means of examining culture, including identity, autonomy and power. It creates relationships and memories between people via shared connections. Through food, I explore local food movements and urban community gardening.

We both ingest and produce garden-grown foods. This movement is often described as simple nostalgia. I suggest that it is a response against heavily processed foods within a system reliant on mass produced food. This desire for ownership pushes community gardens and other counter-hegemonic spaces forward in their goals of using social practice to challenge the established food industry and take control within their own lives.

Stratigraphic Framework And Landsystem Correlation For Deposits Of The Saginaw Lobe, Michigan, Usa, Ivan R. Guzman

Masters Theses

Since the time of the Last Glacial Maximum (LGM) the south-central portion of the Lower Michigan Peninsula has been subject to several glacial advances and retreats by the Saginaw lobe. As part of the U.S Geological Survey Great Lakes Geological Mapping Coalition projects, several rotosonic borings were drilled between 2006 and 2013 in Barry, Kalamazoo and Calhoun Counties. Gamma ray logs and textural analyses were completed for each core. Five of these borings were selected according to their diamicton (till) content and correlated using water well logs and surficial geology maps. Glacial deposits such as diamicton serve as evidence of …

Increasing Sustainability By Going Paperless: A Wmu Case Study, James Amos, James Kison

Research and Creative Activities Poster Day

This is a study analyzing the use of digital signatures to reduce paper consumption at WMU. The poster demonstrates ways in which technology promotes sustainability by saving time, fuel and paper.

Probing Stability And Unfolding Of The N-Terminal Domains 5-6 Of Wilson Protein, Ibtesam Y. Alja'afreh, Ramakrishna Guda, David L. Huffman

Research and Creative Activities Poster Day

The Wilson protein (ATP7B) is a copper transporting P1b type ATPase found in the liver, brain, and other organs. The N-terminal end consists of six copper binding domains which have a ferrodoxin βαββαβ fold with a CxxC motif. Despite similarities in copper binding affinities they interact differently with the HAH1 metallochaperone. Studying the stability of these domains will help understanding the differences in their functions. The stability of WLN5-6 was probed using several different methods: Dynamic light scattering (DLS), Circular dichroism (CD) and Fluorescence spectroscopy methods.

Previous studies show that WLN5-6 has a spherical shape and CD chemical unfolding studies …

Optical Properties Of Bi-Icosahedral Au25 And Au24 Clusters: Influence Of Central Gold Atom, Viraj Dhanushka Thanthirige, Ekkehard Sinn, Rongchao Jin, Guda Ramakrishna

Research and Creative Activities Poster Day

Temperature-dependent absorption and ultrafast luminescence measurements of [Au₂₄(PPh₃)₁₀(SC₂H₄Ph)₅Cl₂]+(bi-Au₂₄) were studied and compared with [Au₂₅(PPh₃)₁₀(C₆S)₅Cl₂]₂+ (bi-Au₂₅). The investigations are carried out on these two clusters as they are structurally similar except for the absence of central Au atom for bi-Au24. The objective of the work is to probe the influence of the central gold atom on the optical transitions and electron-phonon interactions in bi-icosahedral nanoclusters. The investigations are focused …

Are You Getting What You Paid For? A Case Study In Forensic Geochemistry, Abdelmawgoud Mohammed, R. V . Krishnamurthy

Research and Creative Activities Poster Day

Introduction

Isotopes are atoms of the same element that differ in atomic mass due to different number of neutrons in the nucleus. Some isotopes are stable isotopes and others are unstable, or radioactive, isotopes. Stable isotopes maintain constant concentrations in the environment over time. Unstable isotopes continue to decay into daughter elements. Stable isotopes of oxygen, hydrogen, carbon, sulfur, and nitrogen are the most commonly used in environmental and ecological research.

Forensic geochemistry is a relatively new discipline that uses chemical and isotopic markers to solve problems of forensic interest. These include fingerprinting oil spills, food adulteration and forgery in …