Digital Commons Network^™

2013 Budget Document, Clemson University

Budget Documents

No abstract provided.

Common Data Set 2012-2013, Clemson University

Common Data Sets

No abstract provided.

Faculty Senate Minutes, 2013 Meetings, Clemson University

Faculty Senate Minutes

No abstract provided.

Obstacles To Developing Digital Literacy On The Internet In Middle School Science Instruction, Jamie Colwell, Sarah Hunt-Barron, David Reinking

Publications

Obstacles, and instructional responses to them, that emerged in two middle school science classes during a formative experiment investigating Internet Reciprocal Teaching (IRT), an instructional intervention aimed at increasing digital literacy on the Internet, are reported in this manuscript. Analysis of qualitative data revealed that IRT enabled students to explain and demonstrate appropriate strategies for locating and evaluating information on the Internet when they were asked to do so. However, students did not use these strategies or they quickly abandoned them when working independently or in small groups during inquiry projects. Data revealed three obstacles that inhibited efforts to promote …

Center For Career And Professional Development Annual Report, 2012-2013, Clemson University

Annual Report

Our annual reports provide an overview of the services, events, and programs provided to undergraduate, graduate students, and first-year alumni. Our data reporting cycle runs from August 15 – August 14 to follow the academic year.

Design Of A Professional Practice Simulator For Educating And Motivating First-Year Engineering Students, Naomi C. Chesler, Golnaz Arastoopour Irgens, Cynthia M. D'Angelo, Elizabeth A. Bagley, David Williamson Shaffer

Publications

Increasingly, first-year engineering curricula incorporate design projects. However, the faculty and staff effort and physical resources required for the number of students enrolled can be daunting and affect the quality of instruction. To reduce these costs, ensure a high quality educational experience, and reduce variability in student outcomes that occur with individual design projects, we developed a simulation of engineering professional practice, NephroTex, in which teams of students are guided through multiple design-build-test cycles by a mentor in a virtual internship. Here we report on the design process for the virtual internship and results of testing with first-year engineering students …

Predictive Modeling Of The Virtual Hemi-Fontan Operation For Second Stage Single Ventricle Palliation: Two Patient-Specific Cases, Ethan Kung, Alessia Baretta, Catriona Baker, Gregory Arbia, Giovanni Biglino, Chiara Corsini, Silvia Schievano, Irene E. Vignon-Clementel, Gabriele Dubini, Giancarlo Pennati, Andrew Taylor, Adam Dorfman, Anthony M. Hlavacek, Alison L. Marsden, Tain-Yen Hsia, Francesco Migliavacca

Publications

Single ventricle hearts are congenital cardiovascular defects in which the heart has only one functional pumping chamber. The treatment for these conditions typically requires a three-staged operative process where Stage 1 is typically achieved by a shunt between the systemic and pulmonary arteries, and Stage 2 by connecting the superior venous return to the pulmonary circulation. Surgically, the Stage 2 circulation can be achieved through a procedure called the Hemi-Fontan, which reconstructs the right atrium and pulmonary artery to allow for an enlarged confluence with the superior vena cava.

Based on pre-operative data obtained from two patients prior to Stage …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Teacher's Toolkit: Differentiating Inquiry, Brooke A. Whitworth, Jennifer L. Maeng, Randy L. Bell

Publications

Differentiated instruction and teaching science as inquiry are two pedagogical approaches frequently discussed among science teachers. Teachers know these approaches are important but often have difficulty translating them into their classroom science instruction. This article describes how to differentiate a density investigation for variations in student readiness by varying the level of inquiry using an approach that is easily translated to experiments in any science content area.

Analytic Approximation Of Carbon Condensation Issues In Type Ii Supernovae, Donald D. Clayton

Publications

I present analytic approximations for some issues related to condensation of graphite, TiC, and silicon carbide in oxygen-rich cores of supernovae of Type II. Increased understanding, which mathematical analysis can support, renders researchers more receptive to condensation in O-rich supernova gases. Taking SN 1987A as typical, my first analysis shows why the abundance of CO molecules reaches an early maximum in which free carbon remains more abundant than CO. This analysis clarifies why O-rich gas cannot oxidize C if 56Co radioactivity is as strong as in SN 1987A. My next analysis shows that the CO abundance could be regarded as …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …

Enduring Quests - Daring Visions (Nasa Astrophysics In The Next Three Decades), Dieter H. Hartmann

Publications

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Bright Radio Emission From An Ultraluminous Stellar-Mass Microquasar In M31, Matthew J. Middleton, James C. A. Miller-Jones, Sera Markoff, Rob Fender, Martin Henze, Natasha Hurley-Walker, Anna M. M. Scaife, Timorthy P. Roberts, Dominic Walton, John Carpenter, Jean-Pierre Macquart, Geoffrey C. Bower, Mark Gurwell, Wolfgang Pietsch, Frank Haberl, Jonathan Harris, Michael Daniel, Junayd Miah, Chris Done, John Morgan, Hugh Dickinson, Phil Charles, Vadim Burwitz, Massimo Della Valle, Michael Freyberg, Jochen Greiner, Margarita Hernanz, Dieter H. Hartmann, Despina Hatzidimitriou, Arno Riffeser, Gloria Sala, Stella Seitz, Pablo Reig, Arne Rau, Marina Orio, David Titterington, Keith Grainge

Publications

A subset of ultraluminous X-ray sources (those with luminosities < 10^40 erg s^-1)^1 are thought to be powered by the accretion of gas onto black holes with masses of ~5-20 M⊙, probably via an accretion disc. The X-ray and radio emission are coupled in such Galactic sources, with the radio emission originating in a relativistic jet thought to be launched from the innermost regions near the black hole4,5, with the most powerful emission occurring when the rate of infalling matter approaches a theoretical maximum (the Eddington limit). Only four such maximal sources are known in the Milky Way, and the absorption of soft X-rays in the interstellar medium precludes determining the causal sequence of events that leads to the ejection of the jet. Here we report radio and X-ray observations of a bright new X-ray source whose peak luminosity can exceed 1039 erg s^-1 in the nearby galaxy, M31. The radio luminosity is extremely high and shows variability on a timescale of tens of minutes, arguing that the source is highly compact and powered by accretion close to the Eddington limit onto a stellar mass black hole. Continued radio and X-ray monitoring of such sources should reveal the causal relationship between the accretion flow and the powerful jet emission.

Supersoft X-Rays Reveal A Classical Nova In The M31 Globular Cluster Bol 126, M. Henze, W. Pietsch, F. Haberl, M. Della Valle, A. Riffeser, G. Sala, D. Hatzidimitriou, F. Hofmann, Dieter H. Hartmann, J. Koppenhoefer

Publications

Context. Classical novae (CNe) represent the main class of supersoft X-ray sources (SSSs) in the central region of our neighbouring galaxy M 31. Only three confirmed novae and three SSSs have been discovered in globular clusters (GCs) of any galaxy so far, of which one nova and two SSSs (including the nova) were found in M 31 GCs. Aims. To study the SSS state of CNe we carried out a high-cadence X-ray monitoring of the M 31 central area with XMM-Newton and Chandra. This project is supplemented by regular optical monitoring programmes at various observatories. Methods. We analysed X-ray and …

Clemson Commencement Program, December 2012, Clemson University

Clemson Commencement Programs

No abstract provided.

Application Essays As An Effective Tool For Assessing Instruction In The Basic Communication Course: A Follow-Up Study, Joseph P. Mazer, Cheri J. Simonds, Stephen K. Hunt

Publications

The assessment of student learning in general education courses is of critical importance in higher education. This study examines the utility of a writing assignment (application essays) in a basic communication course as an effective assessment tool. The authors conducted a content analysis of student portfolios to determine the extent to which application essays provide evidence of student learning in the basic course. The present study extends the findings from recent assessment efforts (Jones, Simonds, & Hunt, 2005) to explore types of mass media events students address in application essays and assess the revisions made to the assignment based on …

Multi-Color Observations Of Short Grb Afterglows: 20 Events Observed Between 2007 And 2010, A. Nicuesa Guelbenzu, S. Klose, J. Greiner, D. A. Kann, T. Krühler, A. Rossi, S. Schulze, P. M. J. Afonso, J. Elliott, R Filgas, Dieter H. Hartmann, A Kupcu Yoldas, S Mcbreen, M Nardini, F Olivares E., A Rau, S Schmidl, P Schady, V Sudilovsky, A C. Updike, A Yoldas

Publications

We report on follow-up observations of 20 short-duration gamma-ray bursts (GRBs; T90 <2 >s) performed in g'r'i'z' JHKs with the Gamma-Ray Burst Optical Near-Infrared Detector (GROND) between mid-2007 and the end of 2010. This is one of the most compre-hensive data sets on GRB afterglow observations of short bursts published so far. In three cases, GROND was on target within less than 10 min after the trigger, leading to the discovery of the afterglow of GRB 081226A and its faint underlying host galaxy. In addition, GROND was able to image the optical afterglow and follow the light curve evolution in five …

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

A Process Analysis Of Engineering Problem Solving And Assessment Of Problem Solving Skills, Sarah Grigg

All Dissertations

In the engineering profession, one of the most critical skills to possess is accurate and efficient problem solving. Thus, engineering educators should strive to help students develop skills needed to become competent problem solvers. In order to measure the development of skills, it is necessary to assess student performance, identify any deficiencies present in problem solving attempts, and identify trends in performance over time. Through iterative assessment using standard assessment metrics, researchers/instructors are able to track trends in problem solving performance across time, which can serve as a gauge of students' learning gains.
This research endeavor studies the problem solving …

Sensitivity Analysis In Magnetic Resonance Elastography And A Local Wavelength Reconstruction Based On Wave Direction, Christopher Gillam

All Dissertations

or the detection of early stage cancer. MRE utilizes interior data for its inverse problems, which greatly reduces the ill-posedness from which most traditional inverse problems suffer.
In this thesis, we first establish a sensitivity analysis for viscoelastic scalar medium with complex wave number and compare it with the purely elastic case. Also we estimate the smallest detectable inclusion for breast and liver, which is about twice larger than using the purely elastic model. We also found the existence of optimal frequency (50 Hz) that maximizes the detectability when the Voigt model is used.
Second, we propose a local wavelength …

Conservation Needs Of Nearshore Seabirds In The Southeastern U.S. Addressed Through Habitat Use Surveys And Assessments Of Health And Mercury Concentrations, Lisa Eggert

All Dissertations

Seabirds encounter a range of natural and anthropogenic stressors in the nearshore environment and are ideal candidate species for long-term monitoring of changes to coastal systems. The mitigation of threats to nearshore seabirds requires management of essential coastal habitat and monitoring population health and trends. In this dissertation, I first evaluated intertidal habitat use for a suite of coastal species as it relates to management practices at a seabird nesting island in South Carolina. Specifically, my objectives were (1) to determine intertidal areas of high bird abundance, (2) to examine course-scale habitat characteristics and human use of intertidal areas associated …

Network Target Coordination For Design Optimization Of Decomposed Systems, Wenshan Wang

All Dissertations

A complex engineered system is often decomposed into a number of different subsystems that interact on one another and together produce results not obtainable by the subsystems alone. Effective coordination of the interdependencies shared among these subsystems is critical to fulfill the stakeholder expectations and technical requirements of the original system. The past research has shown that various coordination methods obtain different solution accuracies and exhibit different computational efficiencies when solving a decomposed system. Addressing these coordination decisions may lead to improved complex system design. This dissertation studies coordination methods through two types of decomposition structures, hierarchical, and nonhierarchical.
For …

Planet Formation In Transition Disks: Modeling, Spectroscopy, And Theory, Joseph Liskowsky

All Dissertations

An important field of modern astronomy is the study of planets. Literally for millennia, careful observers of the night sky have tracked these 'wanderers', with their peculiar motions initiating avenues of inquiry not able to elucidated by a study of the stars alone: we have discovered that the planets (as well as Earth) orbit the sun and that the stars are so far away, even their relative positions do not seem to shift perceptibly when Earth's position moves hundreds of millions of miles. With the advent of the telescope, and subsequent improvements upon it over the course of centuries, accelerating …

Asymptotics For The Arc Length Of A Multivariate Time Series And Its Applications As A Measure Of Risk, Tharanga Wickramarachchi

All Dissertations

The necessity of more trustworthy methods for measuring the risk (volatility) of financial assets has come to the surface with the global market downturn This dissertation aims to propose sample arc length of a time series, which provides a measure of the overall magnitude of the one-step-ahead changes over the observation time period, as a new approach for quantifying the risk. The Gaussian functional central limit theorem is proven under finite second moment conditions. Without loss of generality we consider equally spaced time series when first differences of the series follow a variety of popular stationary models including autoregressive moving …

Supply Chain Network Design: Risk-Averse Vs. Risk-Neutral Decision Making, Alireza Madadi

All Dissertations

Recent events, such as the Heparin tragedy, highlight the necessity for designers and planners of supply chain networks to consider the risk of disruptions in spite of their low probability of occurrence. One effective way to hedge against supply chain network disruptions is to have a robustly designed supply chain network. This involves strategic decisions, such as choosing which markets to serve, which suppliers to source from, the location of plants, the types of facilities to use, and tactical decisions, such as production and capacity allocation. In this dissertation, we focus on models for designing supply chain networks that are …

Network Traffic Analysis Using Stochastic Grammars, Chen Lu

All Dissertations

Network traffic analysis is widely used to infer information from Internet
traffic. This is possible even if the traffic is encrypted. Previous work uses
traffic characteristics, such as port numbers, packet sizes, and frequency,
without looking for more subtle patterns in the network traffic. In this work,
we use stochastic grammars, hidden Markov models (HMMs) and probabilistic
context-free grammars (PCFGs), as pattern recognition tools for traffic
analysis.
HMMs are widely used for pattern recognition and detection. We use a HMM
inference approach. With inferred HMMs, we use confidence intervals (CI) to
detect if a data sequence matches the HMM. To …

Managing Elective And Non-Elective Case Assignments For An Operating Room Suite, Narges Hosseini

All Dissertations

The success of operating room management depends on all levels of decision making, from strategic to tactical and operational decisions. One key decision in systems with block booking is to assign sufficient amount of block time to surgeons and surgery groups. While the typical method of block assignment identifies the share of surgery groups from OR times based on average of past usage, this method does not count for the difference between cost of under and overtime. One of the goals of this research is to develop a decision framework for block assignment. This work is presented in chapter two. …

Stochastic Tools For Network Security: Anonymity Protocol Analysis And Network Intrusion Detection, Lu Yu

All Dissertations

With the rapid development of Internet and the sharp increase of network crime, network security has become very important and received a lot of attention.
In this dissertation, we model security issues as stochastic systems. This allows us to find weaknesses in existing security systems and propose new solutions. Exploring the vulnerabilities of existing security tools can prevent cyber-attacks from taking advantages of the system weaknesses. We consider The Onion Router (Tor), which is one of the most popular anonymity systems in use today, and show how to detect a protocol tunnelled through Tor. A hidden Markov model (HMM) is …