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Clemson University

2010

Articles 1 - 30 of 209

Full-Text Articles in Physical Sciences and Mathematics

In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov Dec 2010

In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov

Publications

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity …

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A Reasoning Framework For Dependability In Software Architectures, Tacksoo Im Dec 2010

A Reasoning Framework For Dependability In Software Architectures, Tacksoo Im

All Dissertations

The degree to which a software system possesses specified levels of software quality attributes, such as performance and modifiability, often have more influence on the success and failure of those systems than the functional requirements. One method of improving the level of a software quality that a product possesses is to reason about the structure of the software architecture in terms of how well the structure supports the quality. This is accomplished by reasoning through software quality attribute scenarios while designing the software architecture of the system.
As society relies more heavily on software systems, the dependability of those systems …

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Debugging Techniques For Locating Defects In Software Architectures, Kyungsoo Im Dec 2010

Debugging Techniques For Locating Defects In Software Architectures, Kyungsoo Im

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The explicit design of the architecture for a software product is a well established part of development projects. As the software architecture descriptions are becoming larger and more complex, there is more likelihood of defects being present in the software architecture. Studies have shown that a defect in the software architecture that has propagated to the development phase is very expensive to fix. To prevent such propagation of defects, this research proposes to provide debugging support for software architecture design.
Debugging is commonly used in programming languages to effectively find the cause of a failure and locate the error to …

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Design And Regioselective Synthesis Of Two And Three-Pronged C60 Fullerene Derivatives And Their Applications In Molecular Electronics, Angy Ortiz-Hernandez Dec 2010

Design And Regioselective Synthesis Of Two And Three-Pronged C60 Fullerene Derivatives And Their Applications In Molecular Electronics, Angy Ortiz-Hernandez

All Dissertations

Since the introduction of semiconductors in the second half of the 20th century, advancements in electronics and technology have been tremendous. In particular, the rapid development of silicon-based computer chip technology and miniaturization of electronic components has been tremendous. Since silicon-based materials have a limit in terms of size, scientists proposed that individual molecules could behave as single electronic components for high degree of miniaturization.
Given that the molecules of interest must have dimensions on the nanometer scale, be able to bind to the electrode surface and have electron donor-acceptor properties, C60 fullerene has been a prime candidate for …

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Novel Neomycin Conjugates For Multi-Recognition Of Nucleic Acids, Albert Willis Dec 2010

Novel Neomycin Conjugates For Multi-Recognition Of Nucleic Acids, Albert Willis

All Dissertations

Neomycin is an aminoglycoside antibiotic known for its high affinity for RNA duplex structures. Recent developments from our labs have indicated that aminoglycoside binding is not limited to RNA, but to nucleic acids that, like RNA, adopt conformations similar to A-form. Our group sought to further expand the utility of aminoglycoside binding to B-DNA structures by conjugating neomycin, an aminoglycoside antibiotic, with the B-DNA minor groove binding ligand Hoechst 33258. Envisioning a dual groove-binding mode, we have extended the potential recognition process to include a third, intercalative moiety. Furthermore, we observe remarkable recognition of such conjugates with RNA duplex. Spectroscopic …

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A Framework For Virtual Device Driver Development And Virtual Device-Based Performance Modeling, Zachary Jones Dec 2010

A Framework For Virtual Device Driver Development And Virtual Device-Based Performance Modeling, Zachary Jones

All Dissertations

Operating system virtualization tools such as VMWare, XEN, and Linux KVM export only minimally capable SVGA graphics adapters. This paper describes the design and implementation of system
that virtualizes high-performance graphics cards of arbitrary design to support the construction of authentic device drivers. Drivers written for the virtual cards can be used verbatim, without special function calls or kernel modifications, as drivers for real cards, should real cards of the same design exist. While this allows for arbitrary design, it is not able to model performance characteristics. We describe a new kernel system that allows for arbitrarily changing the performance …

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Modeling The Galactic 511 Kev Positron Annihilation Emission, Production, And Propagation, Bethany Johns Dec 2010

Modeling The Galactic 511 Kev Positron Annihilation Emission, Production, And Propagation, Bethany Johns

All Dissertations

The Galactic 511 keV positron annihilation emission has a strong bulge component to the emission and a weak disk component. The bulge emission is about 1.4 -- 6 times as the disk emission. The bulge emission is defined to be a diffuse emission centered at the Galactic center and extends to about a FWHM of 8 degrees in Galactic longitude and latitude. An asymmetry has also been observed in the disk emission, where the negative longitudes are brighter than the positive longitudes by a factor of 1.8.
This research examines the morphology of the Galactic 511 keV positron annihilation emission …

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Synthesis And Optical Properties Of Silver Nanostructures, John Heckel Dec 2010

Synthesis And Optical Properties Of Silver Nanostructures, John Heckel

All Dissertations

Silver nanoparticles interact with light via the excitation of plasmon resonances that are the collective oscillations of the free electron density. This excitation represents the most efficient mechanism for the interaction of light with matter and therefore the nanoparticles are of great interest for both fundamental and practical points of view. In the following dissertation, silver nanoparticles, core-shell nanoparticles, and silver nanoparticle clusters were synthesized and there optical properties were investigated.
Chapter 1 contains general background information about the optical properties of bulk and silver nanoparticles. It also contains a concise description of two of my collaborative projects that did …

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A Study Of African American Forest Landowners In South Carolina: Implications For Land Ethic And Forest Stewardship, Keenan Adams Dec 2010

A Study Of African American Forest Landowners In South Carolina: Implications For Land Ethic And Forest Stewardship, Keenan Adams

All Dissertations

African Americans account for a significant proportion of South Carolina`s
population but reportedly own a disproportionally smaller amount of land. Research indicates that landowners who hold significant sources of sustainable wealth and power can dramatically increase their quality of life and ultimately that of their communities. Current land loss trends for African Americans are increasing at an alarming rate, which may have larger social implications for this traditionally underserved population. The remaining African American landowners are a rapidly declining group, due to an assortment of factors (e.g., age, heirs property). Understanding the experiences of the residual African American forest landowners …

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Synthesis Of Trimetallic Nitride Endohedral Metallofullerene Derivatives For Enhanced Solar Energy Conversion, Julio Pinzon Joya Dec 2010

Synthesis Of Trimetallic Nitride Endohedral Metallofullerene Derivatives For Enhanced Solar Energy Conversion, Julio Pinzon Joya

All Dissertations

The preparation and electrochemical properties of donor - acceptor systems based on trimetallic nitride endohedral metallofullerenes (TNT-EMFs) for enhanced solar energy conversion is described. It was found that TNT-EMFs have an enhanced ability to stabilize charge separated states formed upon light irradiation when compared to empty cage fullerene analogues. The influence of the linker connecting the donor and acceptor moieties was studied in two different systems. Optimal conditions for preparing cyclopropanated Bingel-Hirsch derivaties of the most common TNT-EMFs were found; this functionalization approach is a very useful alternative to the 1,3-dipolar cycloaddition reactions that yield pyrrolidine derivatives, because the latter …

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Evolutionary Strategies For Data Mining, Rose Lowe Dec 2010

Evolutionary Strategies For Data Mining, Rose Lowe

All Dissertations

Learning classifier systems (LCS) have been successful in generating rules for solving classification problems in data mining. The rules are of the form IF condition THEN action. The condition encodes the features of the input space and the action encodes the class label. What is lacking in those systems is the ability to express each feature using a function that is appropriate for that feature. The genetic algorithm is capable of doing this but cannot because only one type of membership function
is provided. Thus, the genetic algorithm learns only the shape and placement of the membership function, and in …

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Using Nestling Bald Eagles To Assess Spatial And Temporal Trends Of Environmental Contaminants, Voyageurs National Park, Minnesota, Henry Pittman Dec 2010

Using Nestling Bald Eagles To Assess Spatial And Temporal Trends Of Environmental Contaminants, Voyageurs National Park, Minnesota, Henry Pittman

All Theses

Bald eagles (Haliaeetus leucocephalus) are a avian species used to monitor environmental contaminants such as mercury (Hg), methylmercury (MeHg), polychlorinated biphenyls (PCBs), and organochlorine pesticides (OCs) in North America. Populations of bald eagles nesting along the Great Lakes were very slow to recover after the ban of PCBs and OCs because these compounds were very persistent. Bald eagles at Voyageurs National Park (VNP) have been monitored since 1973 and provide an opportunity to assess temporal and spatial trends of persistent environmental contaminants. Nestling bald eagle feathers were analyzed for Hg concentrations for the past 12 years. Nestling bald …

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Preparation And Studies Of Fluorescent Carbon Nanomaterials, Xin Wang Dec 2010

Preparation And Studies Of Fluorescent Carbon Nanomaterials, Xin Wang

All Dissertations

There have been rapid advances in the development and applications of semiconductor quantum dots (QDs) represented by CdSe/ZnS. However, a serious limitation of these QDs is the necessary use of toxic heavy metals. Fluorescent 'carbon dots' (surface passivated carbon nanoparticles) are developed as alternative to classical semiconductor QDs.
The carbon dots could be made to be highly fluorescence, with emission quantum yields close to 60%. Their optical properties resemble bandgap transitions found in nanoscale semiconductors, suggesting that carbon particles at the nanoscale acquire essentially semiconductor-like characteristics.
The fluorescence in carbon dots could be quenched efficiently by electron acceptor or donor …

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Uncertainty Of Dimensional Measurments Obtained From Self-Initialized Instruments, Vincent Lee Dec 2010

Uncertainty Of Dimensional Measurments Obtained From Self-Initialized Instruments, Vincent Lee

All Dissertations

Precision dimensional measurement instruments often contain sensors that can only measure displacement of a moving body from some reference position. In order to measure the length of an object they often require a calibrated artifact to initialize their measurement sensors so that they may provide an absolute measurement instead of displacement. Instruments which can realize a null value, i.e. zero length, don't require one; however instruments which can't need to reference an object of known size. These calibration artifacts also serve as part of the chain of metrological traceability.
The group of instruments presented in this dissertation can self-initialize by …

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Poly (Acrylonitrile-Co-1-Vinylimidazole): A New Melt Processable Carbon Fiber Precursor, Wenjin Deng Dec 2010

Poly (Acrylonitrile-Co-1-Vinylimidazole): A New Melt Processable Carbon Fiber Precursor, Wenjin Deng

All Dissertations

Carbon fiber polymer composites have attracted worldwide interest in sporting goods and aerospace industries due to their excellent specific strength, stiffness and lightweight. The replacement of solution-spinning process by melt-spinning process is one of the major approaches to make cost effective carbon fiber. In recent years, researchers have explored the possibilities to synthesize melt processable carbon fiber precursors, but their thermal stabilization is still a challenge. The goal for this research project is to prepare melt processable carbon fiber precursors which have the capability of thermal stabilization. Acrylonitrile/1-vinylimidazole (AN/VIM) copolymers containing various mol% of VIM were synthesized by free radical …

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Fuor And Exor Variables: A Nir High-Resolution Spectroscopic Survey, Joseph Liskowsky Dec 2010

Fuor And Exor Variables: A Nir High-Resolution Spectroscopic Survey, Joseph Liskowsky

All Theses

To better understand the labyrinth of heating and cooling processes in YSOs (young stellar objects), we study systems where there exists a large variability in the heating of this gas due to accretion. This research project focuses on several classes of early young eruptable T-Tauri stars, namely the FUors, the EXors and the so-called FU Ori-like, which all have the property of large amplitude oscillations in accretion rate. Each of these categories may well represent specific stages in early low-mass stellar evolution. While these objects have specific spectroscopic and circumstellar diagnostics (as means of identification) our research suggests that there …

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Libstatmech And Applications To Astrophysics, Tianhong Yu Dec 2010

Libstatmech And Applications To Astrophysics, Tianhong Yu

All Theses

In this work an introduction to Libstatmech is presented and applications especially to astrophysics are discussed. Libstatmech is a C toolkit for computing the statistical mechanics of fermions and bosons, written on top of libxml and gsl (GNU Scientific Library). Calculations of Thomas-Fermi Screening model and Bose-Einstein Condensate based on libstatmech demonstrate the expected results. For astrophysics application, a simple Type Ia Supernovae model is established to run the network calculation with weak reactions, in which libstatmech contributes to compute the electron chemical potential and allows the weak reverse rates to be calculated from detailed balance. Starting with pure 12C …

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Identification Of Patterns And Controls Of The Distribution Of Groundwater Discharge To Streams, Curtis Gebhard Dec 2010

Identification Of Patterns And Controls Of The Distribution Of Groundwater Discharge To Streams, Curtis Gebhard

All Theses

Groundwater discharge is a key component in understanding the interaction between groundwater and surface water. It provides baseflow to streams and can transport nutrients and contaminants to related aquatic ecosystems. It can also influence fish behaviour, spawning, migration and provide areas of refuge during summer and winter months. There are a variety of techniques that are used to characterize the magnitude of groundwater discharge including seepage meters, field permeameters, and piezometers and manometers, however the controls for the magnitude and distribution of discharge remain poorly understood. The purpose of this study was to conduct field investigations complimented with numerical analysis …

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Use Of Sub-Saharan Vultures In Traditional Medicine And Conservation And Policy Issues For The African Grey Parrot (Psittacus Erithacus), Kristina Dunn Dec 2010

Use Of Sub-Saharan Vultures In Traditional Medicine And Conservation And Policy Issues For The African Grey Parrot (Psittacus Erithacus), Kristina Dunn

All Theses

ABSTRACT
Wildlife populations worldwide are being negatively affected by the illegal wildlife trade. The severity of the impact to both Sub-Saharan vultures and African Grey Parrot (Psittacus erithacus) (AGP) populations are explored in this thesis. Many species of Sub-Saharan vultures are used in the traditional medicinal trade. Previous studies have found that vultures have mystical powers attributed to them due to their keen
ability to find food. AGP's are sought after for international trade due to their ability to mimic human vocabularies and for their aesthetic beauty.
Due to the illegal, secret, and illusive nature of this trade, the monetary …

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Home Range, Habitat Selection, And Migratory Pathways Of Canada Geese Wintering At The Santee National Wildlife Refuge, Molly Giles Dec 2010

Home Range, Habitat Selection, And Migratory Pathways Of Canada Geese Wintering At The Santee National Wildlife Refuge, Molly Giles

All Theses

Information on local and flyway-scale space use is lacking for the cohort of migrant geese (Branta canadensis interior) that winter in and adjacent to the Santee National Wildlife Refuge in Summerton, South Carolina. I examined home range and habitat selection of Canada geese in this region. I deployed transmitters on 17 geese (9 VHF and 8 PTT) on wintering grounds at Santee NWR during the winter of 2009-2010. Estimates of fixed kernel home range size ranged from 214.2 to 263.6 ha for VHF-marked geese and 1190.2 to 1915.6 ha for PTT-marked geese. Home ranges of all birds were compact and …

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Sysml-Based Domain-Specific Executable Workflows, Vikas Patel Dec 2010

Sysml-Based Domain-Specific Executable Workflows, Vikas Patel

All Theses

The Systems Modeling Language (SysML) is a general-purpose graphical modeling language for specifying, analyzing, designing, and verifying complex systems. This thesis presents a tool called SysFlow Workflow Engine (SWE) that is being developed to execute a domain workflow defined using SysML's Activity Diagram. The thesis also describes extensions added to the SysML semantics to make them SWE executable. SWE focuses on grid computing, cyberinfrastructure and related domains; however, support for other domains can be easily added. SWE aims to provide a common interface to grid, cyberinfrastructure and other domain-specific software by abstracting their complexity and idiosyncrasies. To create a workflow, …

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The Synthesis, Characterization, And Electrochemical Study Of Tris(Pyrazolyl)-Type Iron(Ii) Complexes, Iron(Ii) Sulfur- And Selenium-Containing Complexes, And Tris(Pyrazolyl)-Type Ruthenium(Ii) Complexes, Christopher Underwood Dec 2010

The Synthesis, Characterization, And Electrochemical Study Of Tris(Pyrazolyl)-Type Iron(Ii) Complexes, Iron(Ii) Sulfur- And Selenium-Containing Complexes, And Tris(Pyrazolyl)-Type Ruthenium(Ii) Complexes, Christopher Underwood

All Theses

Highly reactive radical species such as hydroxyl radical cause oxidative stress, resulting in chronic or degenerative diseases. In the biological Fenton reaction, iron(II) generates hydroxyl radical, OH, but only within a specific electrochemical potential window (-324 mV to 640 mV). Selenium and sulfur compounds have been extensively studied for their antioxidant properties, and they may exert their effects by binding iron(II) and shifting its electrochemical potential out of this window. This work has investigated the synthesis and electrochemical characterization of iron(II) chalcogenate complexes and iron(II) chalcogenone complexes. Cyclic voltammetry (CV) of [Fe(EPh)4][(PPh4)2] (E = S, Se) complexes shows Fe2+/3+ redox …

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Approximation Algorithms For Network Interdiction And Fortification Problems, Adam Whitley Dec 2010

Approximation Algorithms For Network Interdiction And Fortification Problems, Adam Whitley

All Dissertations

This dissertation discusses algorithms and results on several NP–hard graph problems which can all be classified as network interdiction and network fortification problems.
The first problem studied, the multiway cut problem, is a generalization of the well–studied s–t min–cut problem, in which we must remove a minimum–cost subset of edges from a graph so that r > 2 designated terminals become disconnected from each other. We investigate an approximation algorithm for general r with a relatively simple analysis guaranteeing an approximation ratio ≤ 1.4647 − epsilonr, where epsilonr is a small constant related to the number of terminals …

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Gamma Ray Bursts As Probes Of Dust In The Evolving Universe, Adria Updike Dec 2010

Gamma Ray Bursts As Probes Of Dust In The Evolving Universe, Adria Updike

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Dust is ubiquitous in the universe. Understanding where it comes from and where we observe it can have major implications to all astronomical observations. In this study, we investigate how gamma ray bursts (GRBs) can be used as probes of dust in the evolving universe. Making the simplification that silicate dust comes from core collapse supernovae and that graphite dust is produced in the winds of low- to intermediate-mass stars, we present numerical simulations of the resulting dust evolution in GRB hosts and show how the SEDs evolve. Dust extinction laws are re-derived from scattering theory of small particles and …

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Batch Testing, Adaptive Algorithms, And Heuristic Applications For Stable Marriage Problems, John Dabney Dec 2010

Batch Testing, Adaptive Algorithms, And Heuristic Applications For Stable Marriage Problems, John Dabney

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In this dissertation we focus on different variations of the stable matching (marriage) problem, initially posed by Gale and Shapley in 1962. In this problem, preference lists are used to match n men with n women in such a way that no (man, woman) pair exists that would both prefer each other over their current partners. These two would be considered a blocking pair, preventing a matching from being considered stable. In our research, we study three different versions of this problem.
First, we consider batch testing of stable marriage solutions. Gusfield and Irving presented an open problem in their …

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Conceptual Model Testing And Development For Neptunium And Radium Sorption To Srs Sediments, Todd Miller Dec 2010

Conceptual Model Testing And Development For Neptunium And Radium Sorption To Srs Sediments, Todd Miller

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Models which can estimate environmental transport of contaminants are required to ensure minimal risk to the public. These models require accurate transport parameters in order to correctly predict how these contaminants will move in the subsurface. This work aimed to determine more accurately the distribution coefficients for neptunium, strontium, and radium for the Savannah River Site (SRS) Performance Assessment (PA). All neptunium sorption studies were performed at a pH value of 5.50 and an ionic strength of 0.01M as NaCl with neptunium concentrations ranging from 0.01 to 50 ppb. Two different sediments were examined, SRS Subsurface Clayey and SRS Subsurface …

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A Ptas For The Uncertain Capacity Knapsack Problem, Matthew Dabney Dec 2010

A Ptas For The Uncertain Capacity Knapsack Problem, Matthew Dabney

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The standard NP-hard knapsack problem can be interpreted as a scheduling problem with n jobs with weights w1 . . .wn and processing times p1 . . . pn, where our goal is to order the jobs on a single machine so as to maximize the weight of all jobs completing prior to a known common deadline d. In this paper, we study the uncertain capacity knapsack problem (UCKP), a generalization of this problem in which the deadline d is not known with certainty, but rather is provided as a probability distribution, and our goal …

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Explicit Level Lowering Of 2-Dimensional Modular Galois Representations, Rodney Keaton Dec 2010

Explicit Level Lowering Of 2-Dimensional Modular Galois Representations, Rodney Keaton

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Let f be a normalized eigenform of level Npα for some positive integer α and some odd prime p satisfying gcd(p,N)=1. A construction of Deligne, Shimura, et. al., attaches a p-adic continuous two-dimensional Galois representation to f. The Refined Conjecture of Serre states that such a representation should in fact arise from a normalized eigenform of level prime to p.
In this presentation we present a proof of Ribet which allows us to 'strip' these powers of p from the level while still retaining the original Galois representation, i.e., the residual of our new representation arising from level N will …

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The Dependence Of Electrical Resistivity, Saturation And Saturation Exponent On Multi-Phase Flow Instability, Zuolin Liu Dec 2010

The Dependence Of Electrical Resistivity, Saturation And Saturation Exponent On Multi-Phase Flow Instability, Zuolin Liu

All Theses

Multiphase flow channeling in oil reservoirs during water floods reduces oil recovery. Electrical methods may be used to monitor reservoirs and detect the onset of channeling, but the dependence of electrical resistivity on reservoir flow conditions is complex. The present study is directed toward understanding how the parameters of Archie's law, a commonly assumed relationship between electrical resistivity and water saturation in a porous medium, depends on multiphase flow instability leading to flow channeling. In this research a series of 34 flow experiments were conducted in a thin, two-dimensional tank (55cm x 55cm x 3.75cm) packed with 2mm glass beads …

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A Synthetic Analysis Of Integrated Data Fusion: Combining Hydrologic And Geophysical Data Collected During A Tracer Test To Estimate Aquifer Flow And Transport Parameters, Dylan Fowler Dec 2010

A Synthetic Analysis Of Integrated Data Fusion: Combining Hydrologic And Geophysical Data Collected During A Tracer Test To Estimate Aquifer Flow And Transport Parameters, Dylan Fowler

All Theses

Integrated data fusion (IDF), also known as coupled inversion, is becoming a more widely used method for estimating hydrologic parameters from geophysical data. IDF is being used in this research as an approach to inversion that couples mathematical models of groundwater flow, solute transport, and electrical resistivity for the direct estimation of hydraulic conductivity, porosity, and dispersivity from transient resistivity data collected during a tracer test. In this work, synthetic field resistivity data are generated using only a single current electrode pair and many potential electrodes. This data is then used within the IDF framework to a) estimate hydraulic conductivity …

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