Digital Commons Network^™

Link/Loop/Node Networks, Mark E. Gilbert

Honors Theses

This document is really two separate documents that have been appended together. The first is Link/Loop/Node Networks. This document describes the theory behind link/loop/node networks (LLN), as well as the basic operating instructions for the LLN Simulator (LLNS). The second document is LLN Simulator Technical Reference. This second document describes how the LLNS was constructed using Microsoft Access 2.0, as well as how the LLNS simulates LLN.

The Effect Of Protein Environment And Ring Substitution On The Electrostatic Charges, Dipole Moment, And Ultraviolet Spectra Of Flavin, Jared Berger

Honors Theses

Old Yellow Enzyme is an interesting protein clue to its involvement in many biochemical systems, such as bioluminescence and degradation of variety of substrates. The flavin mononucleotide (FMN) is the active site of the protein. The FMN is an isoalloxazine ring with a phospholipid tail, which attaches to the protein through a phosphate group and hydrogen bonding in the hydrophilic section of the ring system. My research is a theoretical, computational calculation, which uses Spartan, a quantum mechanical calculation program, to determine how the dipole moment and electrostatic charges change upon the substitution of the FMN and within the protein …

Molecular Recognition Of Blunt-Ended Dna, Michael D. Farwell

Honors Theses

Many important enzymatic and physical processes occur specifically at the ends of DNA molecules. The goal of this project was to develop a molecule that would be an effective probe of the chemistry a. the ends of DNA. To do this, ethidium bromide, a well-known intercalation (a molecule that binds between DNA base pairs), was blocked to intercalation with bulky t-butyl groups. We proposed that this new molecule would preferentially bind to blunt-ended DNA, where there is much less steric hindrance. The synthesized molecule was characterized by NMR, Fluorescence, UV/Vis, and Mass Spectroscopy. Supporting data were acquired through fluorescence lifetime …

Methylene Blue Doped Sol-Gels Preparation And Application As Fiber-Optic Fluorescence Sensors, Dawn M. Landry

Honors Theses

The goal of this thesis project was to create a Methylene Blue (MB) doped sol-gel fiber-optic fluorescence sensor. Ideally this sensor would be capable of detecting changes in sulfite concentration in solution continuously and reversibly. In aqueous solution, MB, a redox indicator, is converted from a bright blue color to the colorless leuco-MB species upon exposure to sulfite or other reducing agents. This reaction is reversible in the presence of an oxidizing agent Therefore, if MB can be immobilized properly, it would make a suitable reversible indicator for the sulfite anion in solution. The method of MB immobilization employed in …

Comparison Of Outgassing And Surface Reactivity Of Graphic Substrates, Philip Ross Tavernier

Honors Theses

Materials constructed of carbon are widely used in applications requiring high emissivity at temperatures above 1300°C. The ability to transmit heat efficiently makes these materials an excellent choice for use with x-ray tubes. However, heating carbon substrates to high temperatures also leads to thermal desorption of surface bound species. The release of these species increases the total vapor pressure inside sealed x-ray tubes. Our present study considers the outgassing of these carbon substrates as a function of temperature, as a result of their reactivity towards oxygen, carbon monoxide, carbon dioxide, and water vapor. By modeling the factors that influence outgassing …

Design, Synthesis, And Characterization Of Short Salt And Non-Salt Bridged Peptides, Clark K.N. Choi

Honors Theses

Peptides with secondary characteristics such as α-helices are among the most important structures in nature. Previous studies from Baldwin and coworkers have shown that short alanine-based peptides with specific salt spacing adopt helical conformations. In the study of helix formation, we have synthesized our versions of alanine- and glutamine-based peptides with (i, i + 4) and (i, i + 5) salt spacing. The design of the salt bridge is most suitable when it contains (i, i + 4) salt spacing. The rational is that the (i, i + 4) salt spacing yields a value close to 3.6, the number of …

Kinetics And Mechanism Of Chromium Hexacarbonyl Photochemistry Using Flash By Photolysis, Marina Zaydman

Honors Theses

Chromium hexacarbonyl, Cr(CO)6, has been shown to be a very effective photochemical catalyst for many reactions, such as the 1,4- hydrogenation and 1 ,4-hydrosilation of conjugated 1 ,3-dienes resulting in the formation of a cis alkene product in greater than 99% yield. Although much research has been done on the reactions which Cr(CO)6 catalyzes, not much data exists on the reactions of photochemically created fragments of Cr(CO)6 , such as Cr(CO)6. This study focuses on the reactivity of organotransition metal intermediates with the goal of contributing to the growing database of the reactions involving the photochemistry of Cr(CO)6. Particular emphasis …

A Computational Study Of The Inclusion Processes Of Cyclodextrins And Cyclodextrin Polymers, James A. Best

Honors Theses

Cyclodextrins (CDs) are molecules that are composed of glucopyranose rings. Cyclodextrins can be formed from either 6, 7, or 8 glucopyranose units yielding, α-, β-, or y-Cyclodextrins respectively. Cyclodextrin polymers (COPs) can occur when glyceryl linkers are added to the previously mentioned cyclodextrins. CDs and COPs are hydrophilic, yet contain a hydrophobic cavity. This cavity allows for the binding of numerous guest molecules. Some practical purposes resulting from the host-guest interactions can be seen in cosmetology, food science, and pharmacy. Using the MacroModel Interactive Molecular Modeling System Version 5.0 we studied the binding of guest molecules to α-, β-, and …

The Crystallation Of Estrogen-Binding Protein From Candida Albicans, Chia-En Chen

Honors Theses

In the past decade scientists have discovered that the pathogenic fungus Candida albicans contains a highly specific estrogen-binding protein (EBP). Since it is known that the use of estrogen-containing compounds causes one to be more prone to infection by this organism, it is hypothesized that this estrogen system may have a role in infection. Understanding the structure and function of EBP would be helpful in developing treatments for infection by C. albicans. One way to approach the structure and function question of any protein is to crystallize the protein and solve its structure using X-ray diffraction. In the past few …

A Binding Investigation Of Fluorescence\Probes And Cyclodextrin Derivatives, Sara L. Mcintosh

Honors Theses

Cyclodextrins (CDs) are cyclical carbohydrates composed of repeating glucopyranose units. The three most common CDs, α-, β-, or y-, contain 6, 7 and 8 glucopyranose units, respectively, and have hydrophilic exteriors, which makes them water soluble. CD polymers (CDPs) have been synthesized, containing glyceryl link, between CD units. These polymers are more water soluble than their monomer counterparts. CDs and CDPs, because of their hydrophobic interior cavities, form inclusion complexes with various molecules, including aromatics. This latter property is one we have investigated using fluorophores, including naphthalenes and pyrene. We have shown, through absorption spectral and fluorescence lifetime data, that …

Signal Transduction Pathways In Volvox Carteri, Heide Girardin

Honors Theses

The green alga Volvox carteri exhibits a virtual absence of protein synthesis in the dark, but begins synthesizing proteins necessary for growth and development almost immediately after exposure to the light. The regulation of protein synthesis in this system is known to be translational since extracts prepared in the dark have identical pools and quantities of mRNA as extracts prepared in the light (Kirk and Kirk, 1983). Exploration of the mechanism of translational regulation has led us to consider the importance of signal transduction pathways. By using a variety of commercially available drugs that affect specific components of known signaling …

Celluloid Blackness : Race, Modernity, And The Conflicted Roots Of American Cinema (1915-1939), Lincoln Farr

Honors Theses

Introduction: "The Problem of the Twentieth Century" In a full page interview in the New York Times on May 29, 1912, the Swiss psychiatrist Dr. Carl G. Jung told the American people, "It seems to me that you are about to discover yourselves. You have discovered everything else-all the land of this continent; all the resources, all the hidden things of nature."Jung used the interview to address the American people, at a moment which he somehow recognized as crucial in the development of human civilization. America, the "tragic" country which he struggled to comprehend, would soon become the harbinger of …

On Some New Constructions Of Difference Sets, Sarah Agnes Spence

Honors Theses

Difference sets are mathematical structures which arise in algebra and combinatorics, with applications in coding theory. The fundamental question is when and how one can construct difference sets. This largely expository paper looks at standard construction methods and describes recent findings that resulted in new families of difference sets. This paper provides explicit examples of difference sets that arise from the recent constructions. By gaining a thorough understanding of these new techniques, it may be possible to generalize the results to find additional new families of difference sets. The paper also introduces partial and relative difference sets and discusses how …

Bioremediation Of Creosote Contaminated Soils In An Old Wood Preserving Facility, Claudia Rush

Honors Theses

No abstract provided.

Effects Of Acid Mine Drainage On Stream Fish Assemblages In The North Chickamauga Creek Watershed, Tennessee, Kristie J. Jenkins

Honors Theses

Approximately 18 miles of the NCC system, Tennessee is polluted by acid mine drainage (AMD). The effects of AMD upon the North Chickamauga Creek (NCC) system were evaluated from water quality measurements, habitat assessments, and fish collections. Sampling surveys were conducted at three AMO-impacted (pH < 5.5) and two reference sites (pH> 6.2) in the NCC system. Stream fish were collected using backpack electroshockers and hoop nets. A total of seven species were collected at the reference sites, whereas three species were collected at the AMO-impacted sites. Fish abundance was significantly greater (P < 0.1) at the reference sites than at the AMO-impacted sites, regardless of the sampling technique. No fish were collected at one of the AMO-impacted streams where the pH was <5 and the concentration of dissolved aluminum was > 700 mg/L. Results of my study indicate that fish populations were affected more by …

Synthesis Of 1-Alloc-Piperidine-4-Fmoc-Amino-4-Carboxylic Acid: A Novel, Protected ?,?- Disubstituted Amino Acid, Muna K. Thalji

Honors Theses

No abstract provided.

Angle-Resolved Study Of Ar 2p₁/₂,₃/₂⁻1Ns,D Resonant Auger Decay, Marc Andrew Humphrey

Honors Theses

Angle-resolved measurements of the Ar 2p_1/2,3/2^-14s,3d,4d and 2p_3/2^-14s,3d,4d resonant Auger transitions have been carried out using photons from an undulator beamline at the Advanced Light Source of Lawrence Berkeley National Laboratory. The intensity distributions and angular distribution anisotropy (β) parameters have been reported for nearly all of the possible 3p⁴nl final ionic states. These results further verify the predictions of the spectator model for the 2p_1/2,3/2^-14s resonances and the subsequent breakdown of this model for the 2p_1/2,3/2^-13d and 2p_1/2,3/2^-14d relative intensities. This work …

On The Automatic Generation Of Network Protocol Simulators, Andrew Chen

Honors Theses

Computers communicate with each other over various communication networks via a language known as a protocol. The design of the protocol can have a significant impact on the efficiency (and effectiveness) of the network. Because building an actual network to test the performance (and reliability) of a new protocol is rather expensive and time consuming, there is an interest in simulating network protocols in order to determine how efficient the communication network is. We are therefore interested in automatically generating simulators that could measure the performance of the new protocols. There are two main parts to this project. The first …

Parallel Programming, Peter Dailey

Honors Theses

The speed of technology is always increasing, especially in the field of computing. Unfortunately, the size of the problems needing to be solved are also growing in many areas. In order to keep up with this, parallel computing has become an important research area. The term parallel computing essentially refers to using multiple processors cooperating to solve a problem. For certain problems this can speed up the solution by a factor ofN, the number of processors being used. There are algorithms, for which there is no speed increase due to certain dependencies.

Temporal Flocking And Cacophony Simulating Agent Communication In A Noisy Environment, Jessica R. Crawford

Honors Theses

Realistic communication is one of the most difficult aspects of simulating group behavior because the patterns produced by group communication are complex and not easily definable. In this paper, we present a model, developed using artificial life methodology, for creating simulations of group communication. Our model employs autonomous, artificial agents to produce emergent group behavior that resembles the communication patterns of a group, specifically, a flock of birds. Each agent collects information about its environment and its neighbors and follows a set of rules designed to meet both group goals and individual agent goals. Because we seek to establish emergent …

Acid Mine Drainage And Its Effects On Salamander Assemblages In Cumberland Plateau Streams Of The North Chickamauga Creek Watershed, Tennessee, Melissa Combs

Honors Theses

In Appalachia's coal mining regions, acid mine drainage (AMD) has contributed to the widespread degradation of stream ecosystems. Salamanders are common inhabitants of healthy headwater streams and because of their permeable skins are excellent indicators of ecosystem intergrity. Hence, we investigated the potential effects of AMD on the species richness and relative abundance of aquatic salamanders in selected stream reaches (sites) of the North Chickamauga Creek (NCC) system, Tennessee. Specimens were collected by kick-net sampling with a 500um mesh dip net and/or electroshocking at four AMD-impacted sites (pH< 5.6) and two reference sites pH> 6.2), May-July 1996. Species richness was similarly low at reference sites, 2 …

Computational Studies Of Hydroboration: Remote Functional Groups And Ring Size Effects, Sarah Liberty Olbrich

Honors Theses

This study is a preliminary computational study of the energies of complex molecules. We are looking at the roles of remote heteroatoms in the hydroboration of propellane systems and ring size effects in the solvolysis of cyclic alkyl halides was examined using computational methods. Geometry and transition state optimizations were done using semi empirical (MNDO. AMI) and ab initio (STO-3G, 3-2IG, and 6-31G*) methods. Attempts to correlate computational results with previously reported data will be presented.

An Introduction To The Standard Model And The Electroweak Force With A Numerical Analysis Of The Yang-Mills-Higgs Equation, Zine Smith

Honors Theses

Particle physics is a relatively new field in science that has made amazing discoveries in the last few years. Particle physics seeks to know the most basic structure of mass and force which makes up our uni verse. This search has made tremendous leaps forward in the last part of this century with the use of particle accelerators and theoretical advances. The work of particle physics has begun to accumulate to the formation of what is known as the standard model.

This is a model of the universe which includes all basic forces and matter. Though this model is not …

Irreducible K-To-1 Maps Onto Grids, Susan M. Parker

Honors Theses

In this paper we explore the existence of exactly k-to-1 continuous functions between graphs, and more specifically 2-to-1 continuous function between graphs that are irreducibly 2-to-1, meaning that no restriction of the function to a subgraph is 2-to-l. We show how to construct such functions in some general cases, and then more specifically onto rectangular grids. We have in mind an application to distributed networks and signal verification.

Calcium Metabolismn In Volvox Carteri, Bridget Anne Neville

Honors Theses

Calcium metabolism is involved in many ways in the cellular activities of the colonial green alga, Volvox carteri. Various drugs that are known in other systems to cause specific changes in calcium metabolism, gave rise to various visible metabolic effects in this study. These effects provide evidence for calcium's role in Volvox growth and development and in its cytoskeleton. Another way that calcium exerts its effect on Volvox is by acting as a second messenger in a G-protein/inositol phosphate signal transduction pathway.

This study also supports the fact that cytoskeletal components are important for development in Volvox. Both microtubules and …

Suspended Particulate Matter And Sediment Of Penobscot Estuary, Craig M. Pochini

Honors Theses

An automated scanning electron microscope with an energy dispersive spectrometer was used to gather morphological and chemical information on individual particles from the suspended particulate matter of the Penobscot Estuary and the sediment of Goose Cove/Pond. The goals of the Penobscot Estuary study were to investigate the transport of particles into and through an estuary, the speciation of elements, the abundance of heavy metals, and the background levels of heavy metals. The majority of particles were aluminosilicates originating from a riverine source. Heavy metals were not abundant in the Penobscot Estuary. The objectives of the Goose Cove/Pond study were to …