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On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov

Publications

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine …

Teaching Hdfs/Mapreduce Systems Concepts To Undergraduates, Linh B. Ngo, Amy W. Apon, Edward B. Duffy

Publications

This paper presents the development of a Hadoop MapReduce module that has been taught in a course in distributed computing to upper undergraduate computer science students at Clemson University. The paper describes our teaching experiences and the feedback from the students over several semesters that have helped to shape the course. We provide suggested best practices for lecture materials, the computing platform, and the teaching methods. In addition, the computing platform and teaching methods can be extended to accommodate emerging technologies and modules for related courses.

On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li

Publications

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily …

Chronic Beryllium Disease: Revealing The Role Of Beryllium Ion And Small Peptides Binding To Hla-Dp2, Marharyta Petukh, Bohua Wu, Shannon Stefl, Nick Smith, David Hyde-Volpe, Li Wang, Emil Alexov

Publications

Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within …

Computational And Experimental Approaches To Reveal The Effects Of Single Nucleotide Polymorphisms With Respect To Disease Diagnostics, Tugba G. Kucukkal, Ye Yang, Susan C. Chapman, Weiguo Cao, Emil Alexov

Publications

DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and …

Empirical Modeling Of Residual Stress Profile In Machining Nickel-Based Superalloys Using The Sinusoidal Decay Function, D. Ulutan, Y. M. Arisoy, T. Ozel, Laine Mears

Publications

After machining nickel-based superalloys, tensile surface residual stresses can cause end-product issues such as fatigue failure. Modeling the residual stress profile is currently tedious and inaccurate. This study introduces a new method of understanding the residual stress profile in terms of quantifiable key measures: peak tensile stress at the surface, magnitude and depth of peak compressive stress, and depth at which residual stress becomes near-zero. Experiments in turning IN-100 and milling GTD-111 have been conducted and subsequent X-ray Diffraction measurements have been utilized to obtain residual stress profiles. Using a sinusoidal decay function fitted to measured residual stress profiles, these …

Examining The Effects Of School-Level Variables On Elementary School Students' Academic Achievement: The Use Of Structural Equation Modeling, Matthew Robert Della Sala

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School finance scholars have called for the alignment of accountability policies with state finance formulae to allocate resources toward student learning goals (Adams, 2008; Ryan, 2008; Superfine, 2009; Verstegen, 2002). With the presence of accountability policies that focus on improving students’ academic achievement, state finance systems must be repurposed to allocate educational resources to schools based on research-based practices that are linked to student achievement. The purpose of this study is to test the sufficiency of a new conceptual model of the effects of educational resources on student achievement using structural equation modeling. The goal of this study is to …

Assessing College Students' Understanding Of Acid Base Chemistry Concepts, Yanjun Wan

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Typically most college curricula include three acid base models: Arrhenius', Bronsted-Lowry's, and Lewis'. Although Lewis' acid base model is generally thought to be the most sophisticated among these three models, and can be further applied in reaction mechanisms, most general chemistry curricula either do not include Lewis' acid base model, or quickly mention it at the end of the acid base chapter, because of the concern that Lewis' model may confuse general chemistry students (Shaffer 2006). While such a disconnection in curriculum might put students to disadvantage as they try to construct solid and coherent acid base mental models, there …

Monte Carlo Modeling Based Patient Dose Optimization In Diagnostic Radiology, Wenjun He

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Radiation doses are caused by the energy deposited in unit mass of matter from ionizing radiation. In the US, radiation doses from medical imaging increased six-fold in the past generation. Among medical exposures to patients, computed tomography (CT) composes about half of the collective doses, and interventional fluoroscopy composes 14%. Radiation exposure to patients undergoing diagnostic radiological procedures causes increased lifetime carcinogenic risks, especially for pediatric patients who are more radiosensitive than adults. The correlation between procedural x-ray techniques and the radiation doses to patients, as well as the resultant image quality, is not well understood, and therefore the focus …

Miniaturization Of Chemical Analysis Tools: Micro-Solid Phase Extraction Tips For Protein Extractions And Development Of A Miniaturized Glow Discharge Source For Elemental Analysis, Benjamin Manard

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An increased interest has been placed on the miniaturization of chemical processes. Focus is placed on rapid chemical analysis, decreased operation cost, minimal generation of chemical waste, and reduced sample size. Presented here is an approached the goal of 'miniaturization' through two distinct areas of analytical chemistry: 1) employing capillary-channeled polymer (C-CP) fibers as a stationary phase in micro-SPE (solid phase extraction) tips for the extraction of proteins from buffered solutions (i.e. biofluids) with analysis by mass spectrometry (MS) and 2) the development of the liquid sampling-atmospheric pressure glow discharge (LS-APGD) as an excitation source for elemental analysis. Determination of …

Nonparametric And Semiparametric Group Testing Regression Models, Dewei Wang

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This dissertation consists of three projects in the area of group testing. The method of group testing, through the use of pooling, has proven to be an efficient method of reducing the time and cost associated with screening for a binary characteristic of interest, such as infection status. The salient feature of group testing that provides for these gains in efficiency is that testing is performed on pooled specimens, rather than testing specimens one-by-one. In Chapter 1, we present a general introduction of group testing. Typically, the statistical literature surrounding group testing has investigated the implementation of pooled testing for …

Multidimensional Simulations Of Non-Linear Cosmic Ray Production In Supernova Remnant Evolution, Joshua Wood

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When a high-mass star (& 4Msun) explodes at the end of its life, a supernova occurs, leaving its degenerate core and a fast-moving shell of matter, known as a supernova remnant (SNR). The SNR shell lasts for many thousands of years, generating emissions from low-frequency radio (~ 10-7 eV) up to γ-ray regime (~ 1015 eV). It is also believed that SNRs are the predominant source of galactic cosmic rays, accelerating a population of thermal ions, primarily protons, up to relativistic energies by means of the diffusive shock acceleration (DSA) mechanism. The small population of thermal (Boltzmann) particles, p ~ …

A Study Of The Effects Of Manufacturing Complexity On Product Quality In Mixed-Model Automotive Assembly, Kavit Ravindra Antani

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The objective of this research is to test the hypothesis that manufacturing complexity can reliably predict product quality in mixed-model automotive assembly.

Originally, assembly lines were developed for cost efficient mass-production of standardized products. Today, in order to respond to diversified customer needs, companies have to allow for an individualization of their products, leading to the development of the Flexible Manufacturing Systems (FMS). Assembly line balancing problems (ALBP) consist of assigning the total workload for manufacturing a product to stations of an assembly line as typically applied in the automotive industry. Precedence relationships among tasks are required to conduct partly …

Isolated And Ephemeral Wetlands Of Southern Appalachia: Biotic Communities And Environmental Drivers Across Multiple Temporal And Spatial Scales, Joanna Hawley

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Throughout the world, wetlands are known to support a wide variety of taxa as well as high levels of biodiversity and species richness. Although the ecological significance of wetlands is well documented in the scientific literature, efforts to map and assess wetlands on regional or national scales (e.g., National Wetlands Inventory (NWI)) often overlook wetlands which are either very small (< 1 ha) or have ephemeral hydroperiods. While the vast majority of wetland research in the southeastern United States has focused on wetlands distributed across the coastal plain ecoregion, very little information exists on small and/or ephemeral wetlands in areas of southern Appalachia, although there are several notable exceptions. Despite the paucity of small wetland data in this region, the southeastern US is known as a hotspot for both aquatic biodiversity and species endemism. My goal with this project was to examine the biotic communities inhabiting small, ephemeral and geographically-isolated wetlands to identify the major environmental drivers that contribute to observed community patterns and species' distributions. I studied a set of small, mostly-ephemeral, mostly-isolated wetlands (N = 41) in the upper Piedmont and lower Blue Ridge ecoregions of South Carolina from January-June of 2010 and 2011 and focused my efforts on describing the structure, biotic communities and surrounding habitat characteristics of my study wetlands. I observed high levels of species richness and biodiversity in this previously-undocumented wetland system, despite the small size and ephemeral nature of study wetlands. My results indicated that the amphibian and benthic invertebrate communities of small, ephemeral wetlands responded to different environmental drivers (e.g., wetland depth, area, hydroperiod, canopy cover, surrounding land use types) occurring across multiple spatial and temporal scales. Additionally, the amphibian community was significantly influenced by a number of environmental variables occurring at both the within-pond scale and larger spatial scales (250 m, 500 m and 1 km surrounding land cover variables). By contrast, the benthic invertebrate community was significantly influenced primarily by variables occurring at the within-pond scale. This wetland system also served as both breeding and overwintering habitat for a variety of species such as wood frogs (Lithobates sylvatica), spotted salamanders (Ambystoma maculatum), bullfrogs (Lithobates catesbeiana), cricket frogs (Acris crepitans). This study highlights the ecological importance of small, ephemeral aquatic habitats in a region where little research exists regarding such systems; these often-unnoticed ecosystems are likely the result of a combination of historical anthropogenic and natural environmental process. These legacy wetlands (i.e., wetlands that are the unintended result of some human-induced environmental change in either the recent or long-term past) are found ubiquitously across the landscape and are often missed by coarse-filter mapping approaches (e.g., National Wetlands Inventory). I observed many study wetlands to be extremely small in size (< 0.05 ha) and that many wetlands were habitats of circumstance and opportunity rather than of permanence and predictability. The ephemerality of the majority of study wetlands demonstrates the biological significance of small, temporary habitats for many species requiring these habitats for breeding activity. Despite the small size and ephemeral nature of my study wetlands, I found that these wetlands represented a large proportion of amphibian biodiversity in the regional species pool and thus, are an important conservation feature at the local, landscape and regional scales. My study demonstrates that small, semi-isolated, mostly-ephemeral wetlands in southern Appalachia support high levels of biodiversity and are an important asset deserving of further study and conservation recognition.

Numerical Analysis Of The Extrusion Of Fiber Optic And Photonic Crystal Fiber Preforms Near The Glass Transition Temperature, Mohamed Trabelssi

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Conventional clad core fiber optic technology has relied on a concentric structure of glass of different refraction indices. These conventional fibers suffer from constraints and limitations related to thermal expansion compatibility between the core and the glass. The new fiber technology broadly characterized as Microstructured Optic Fibers (MOFs) is intended to lift the limitations of conventional clad core fibers and also extend the range of application of fiber optics. Photonic Cristal Fibers(PCFs) are a special family of Microstructured Optic Fibers characterized by the presence of holes in the cross section of the fiber that are organized in a hexagonal pattern. …

Drug Delivery With Feedback Control In Bioresponsive Hydrogels, Andrew Wilson

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Bioresponsive hydrogels are emerging with technological significance in targeted drug delivery, biosensors and regenerative medicine. The design challenge is to effectively link the conferred biospecificity with an engineered response tailored to the needs of a particular application. Moreover, the fundamental phenomena governing the response must support an appropriate dynamic range, limit of detection and the potential for feedback control. The design of these systems is inherently complicated due to the high interdependency of the governing phenomena that guide sensing, transduction and actuation of the hydrogel. The objective of the dissertation is to review the current state of bioresponsive hydrogel technology …

Identifying Codes And Domination In The Product Of Graphs, Kirsti Wash

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An identifying code in a graph is a dominating set that also has the property that the closed neighborhood of each vertex in the graph has a distinct intersection with the set. The minimum cardinality of an identifying code in a graph $G$ is denoted $\gid(G)$. We consider identifying codes of the direct product $K_n \times K_m$. In particular, we answer a question of Klav\v{z}ar and show the exact value of $\gid(K_n \times K_m)$. It was recently shown by Gravier, Moncel and Semri that for the Cartesian product of two same-sized cliques $\gid(K_n \Box K_n) = \lfloor{\frac{3n}{2}\rfloor}$. Letting $m \ge …

Towards The Development Of Performance Based Guidelines For Using Phase Change Materials In Lightweight Buildings, Niraj Poudel

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Incorporating Phase Change Materials (PCMs) in construction materials can increase the thermal mass of a building. With this increase in thermal mass, PCMs are known to reduce the heating and cooling loads of a building significantly. During the past 10 years, studies have estimated potential reduction of energy consumption of buildings between 10 and 30 percent. This wide range is due to the large number of parameters that effect energy consumption and make the process of selecting the optimal type and amount of PCM challenging. In fact, extensive engineering studies are generally necessary to determine the practicality of PCM in …

The Development Of Empirical Models To Evaluate Energy Use And Energy Cost In Wastewater Collection, David Young

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This research introduces a unique data analysis method and develops empirical models to evaluate energy use and energy cost in wastewater collection systems using operational variables. From these models, several Best Management Processes (BMPs) are identified that should benefit utilities and positively impact the operation of existing infrastructure as well as the design of new infrastructure. Further, the conclusions generated herein display high transferability to certain manufacturing processes. Therefore, it is anticipated that these findings will also benefit pumping applications outside of the water sector. Wastewater treatment is often the single largest expense at the local government level. Not surprisingly, …

Processes Utilized By High School Students Reading Scientific Text, Alicia Clinger

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In response to an increased emphasis on disciplinary literacy in the secondary science classroom, an investigation of the literacy processes utilized by high school students while reading scientific text was undertaken. A think-aloud protocol was implemented to collect data on the processes students used when not prompted while reading a magazine article and a selection from a textbook. Following the think-aloud, participants provided an oral summary that was analyzed for content and quality to assess the effectiveness of the strategies. The data showed that familiarity with text structure and prior knowledge of the content affected the processes utilized. Differences between …

New Synthetic Methodologies For Chemo-, Stereo-, And Regioselective 1,4-Conjugate Additions Of Organometallic Reagents To Michael And Extended Michael Substrates And Alkene Halofunctionalization Reactions, Ramesh Dhakal

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The research discussed in this dissertation is focused on developing new synthetic methodologies for the construction of carbon-carbon and carbon-heteroatom bonds present in several natural products and synthetic intermediates employing organometallic reagents and/or organocatalytic procedure. The presence of rich functionality in the reactive synthons under study provides opportunities for studying a variety of reactions. Effecting a reaction in a regio- and stereoselective fashion is highly attractive as the resulting synthons can be used for the syntheses of larger molecules. We have explored unprecedented variation of Michael Initiated Ring Closure (MIRC) reactions for the syntheses of 1,2,3-trisubstituted cyclopropane derivatives, owing to …

A Memento Of Complexity: The Rhetorics Of Memory, Ambience, And Emergence, Glen Southergill

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Drawing from complexity theory, this dissertation develops a schema of rhetorical memory that exhibits extended characteristics. Scholars traditionally conceptualize memory, the fourth canon in classical rhetoric, as place (loci) or image (phantasm). However, memory rhetoric resists the traditional loci-phantasm framework and instead emerges from enmeshments of interiority, collectivity, and technology. Emergence considers the dynamics of fundamental parts that generate complex systems and offers a methodological lens to theorizing memory. The resulting construct informs everyday life, which includes interfacing with pervasive computing or sensing familiarity. Further, congruently with a neurological turn that contradicts simplification, this dissertation resituates rhetorical memory as generative …

A Computational Model Of Memetic Evolution: Optimizing Collective Intelligence, Noah Welsh

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The purpose of this study was to create an adaptive agent based simulation modeling the processes of creative collaboration. This model aided in the development of a new evolutionary based framework through which education scholars, academics, and professionals in all disciplines and industries can work to optimize their collective ability to find creative solutions to complex problems. The basic premise follows that the process of idea exchange, parallels the role sexual reproduction in biological evolution and is essential to society's collective ability to solve complex problems. The study outlined a set of assumptions used to develop a new theory of …

Building Chemistry One Atom At A Time: An Investigation Of The Effects Of Two Curricula In Students' Understanding Of Covalent Bonding And Atomic Size, Barbara Bull

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Chemists have to rely on models to aid in the explanation of phenomena they experience. Instruction of atomic theory has been used as the introduction and primary model for many concepts in chemistry. Therefore, it is important for students to have a robust understanding of the different atomic models, their relationships and their limitations. Previous research has shown that students have alternative conceptions concerning their interpretation of atomic models, but there is less exploration into how students apply their understanding of atomic structure to other chemical concepts. Therefore, this research concentrated on the development of three Model Eliciting Activities to …

Growing Pains: Exploring The Transition From A Community College Into A Four-Year Comprehensive College, Edna Martinez

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The highest degree awarded by the community college has generally been the associate in arts or the associate in science degree (Cohen & Brawer, 2008); however, an increasing number of community colleges have expanded their missions to award baccalaureate degrees (Levin, 2004; Russell, 2010; Walker, 2005). Although some community colleges have adopted the four-year degree function while maintaining their community college mission, others have become full baccalaureate degree granting colleges. In fact, this trend contributed to a 70% increase in the number of baccalaureate colleges from 1995-2006 (Longanecker, 2008). Nevertheless, little research exists on what this process looks like (Longanecker, …

Adaptive And Robust Braking-Traction Control Systems, John Adcox

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The designs of commercial Anti-Lock Braking Systems often rely on assumptions of a torsionally rigid tire-wheel system and heavily rely on hub-mounted wheel speed sensors to manage tire-road slip conditions. However, advancements in high-bandwidth braking systems, in-wheel motors, variations in tire/wheel designs, and loss of inflation pressure, have produced scenarios where the tire's torsional dynamics could be easily excited by the braking system actuator. In these scenarios, the slip conditions for the tire-belt/ring will be dynamically different from what can be inferred from the wheel speed sensors. This dissertation investigates the interaction of tire torsional dynamics with ABS & traction …

Strategies To Improve The Efficiency Of Emergency Medical Service (Ems) Systems Under More Realistic Conditions, Kanchala Sudtachat

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Emergency medical service (EMS) systems provide medical care to pre-hospital patients who need rapid response and transportation. This dissertation proposes a new realistic approach for EMS systems in two major focuses: multiple unit dispatching and relocation strategies. This work makes recommendations for multiple-unit dispatch to multiple call priorities based on simulation optimization and heuristics. The objective is to maximize the expected survival rate. Simulation models are proposed to determine the optimization. A heuristic algorithm is developed for large-scale problems. Numerical results show that dispatching while considering call priorities, rather than always dispatching the closest medical units, could improve the effectiveness …

Involutive Translation Surfaces And Panov Planes, Charles Johnson

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This dissertation is concerned with the study of Panov planes and involutive translation surfaces, motivated by questions encountered in trying to understand certain self-similar billiard trajectories in the periodic variant of the Ehrenfest wind-tree model. In particular, we outline a new approach for studying billiard trajectories in certain types of infinite billiard tables by using Panov planes. After describing how this is done in the special case of the wind-tree model, we generalize our construction to show that there are typically several Panov planes that may be associated to an involutive translation surface. The first three chapters of the dissertation …

Demonstrating Reflection: A Content Analysis Of Reflection That English Teacher Candidates Demonstrate In Writing, William Kerns

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This study is an analysis of the depth of reflection exhibited in written documents produced by English teacher candidates. Description and insights were drawn into the reflective thinking of the undergraduate teacher candidates in the context of teacher research essays that they produced. Reflection is widely viewed as enabling teacher candidates to make connections between actions and consequences as well as between theory and practice. Teacher education programs are encouraged by accreditation agencies to adopt a framework that helps teacher candidates to reflect on practice. However, there is no broadly accepted protocol in place for determining depth of reflection that …

Numerical Investigation Of One-Dimensional Shallow Water Flow And Sediment Transport Model Using Discontinouous Galerkin Method, Farzam Safarzadeh Maleki

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A one-dimensional shallow water flow and sediment transport model is developed using a discontinuous Galerkin finite element scheme. As a first step, four different time marching schemes as well as three different slope limiters have been investigated to find the optimum modeling combination. The efficiency and accuracy of the time marching schemes and slope limiters are quantitatively examined using CPU runtime and comparison between the simulated results and theoretical/experimental data. It is found that using the second order Adam-Bashforth time marching scheme and Monotonized Central method leads to most efficient and accurate results. As the second part of this research, …