SC08 Education Program Poster Session

The Education Program Poster Reception will be Saturday, November 15, 7:00 pm – 9:00 pm in the Oaks Room at the Omni Southpark Hotel. Hors d'oeuvres will be served.

View the room layout of the poster session

Poster Abstracts

P01 - SC09 Education Program

Join us in Portland, OR next year for the SC09 Education program (November 13-17, 2009). The SC09 Education program goals are to

  • provide continuity and broader, sustained impact in education
  • increase participation of larger, more diverse communities in the SC Conference
  • and integrate HPC into undergraduate science, technology, engineering and mathematics classrooms

The on-site SC09 Education program begins Saturday, November 13th, and includes educational workshops, an expanded student program, student team competitions, and presentations of prestigious awards for students, undergraduate faculty, and K-12 educators.

P02 - SC Education Award Opportunities

The SC Education Program is pleased to announce that three categories of awards will be presented at the SC Education Conferences.

  • The Dr. Mary Ellen Verona Computational Science Teacher Leader Award is open to those who demonstrate computational science leadership and education, either in a formal classroom setting or in an after school program.
  • The Dr. Robert M. Panoff Student Award for Explorations in Science Through Computation is open to high school, undergraduate, and graduate students exploring science made possible through computation.
  • The Undergraduate Computational Engineering and Sciences (UCES) Award, hosted by the Krell Institute, is open for undergraduate faculty who have developed computational science curricula.

P03 - A Survey of Computational Physics
Introductory Computational Science

Rubin H Landau
Oregon State University

Princeton University Press has published two new textbooks in the last three years based on courses that are part of the Computational Physics curriculum at Oregon State University. Together they form a bridge through an undergraduate curriculum in computational science, with only the more advanced parts specialized to physics. The paper text is accompanied by video lectures, codes in Java, Fortran90, C and VPython, visualizations, animations, and tutorials.

P04 - Grid Computing at UHD

Hong Lin
University of Houston

In the trend of moving from traditional parallel computing to multi-disciplinary scientific computing, grid computing has provided a framework for more efficient use of computing resources and therefore served as a platform for inter-disciplinary collaboration for solving large-scale computation-intense problems. To position UHD in an active role in this trend, we started to establish a grid computing lab, which supports high performance computing with computing clusters. This poster will present a historic review of the work we have done and show applications that have been developed on the clusters and therefore demonstrate the support that the grid computing can bring to the research and education in various fields.

P05 - Dense Linear System Solver Templates for Distributed Memory Architectures Using MPI

S.V. Providence
Hampton University

Dense linear system solvers are important in many applications, such as: fluid flow around dynamic and static objects, solid body diffusion into a liquid, and noise reduction. When migrating from a sharedmemory system to more available scalable distributed memory systems, alternatives for scalable parallel software libraries include: traditional function libraries, to protect legacy code; reactive servers on a network, that can respond to users special computational needs; general interactive environments, such as Mathematica; domain specific problem solving environments; or reusable templates, a description of a general algorithm rather than executable object code that offers whatever degree of customization the user may require. This paper explains how our O(n log3 n) algorithms based on an algebra of scaling and displacement generators which describe dense general matrices, will be used with the message passing interface through templates to perform dense linear system solver computations.

P06 - Graphics Processor Based Implementation of Bioinformatics Codes

Andrew Bellenir , Christian Trefftz, and Greg Wolffe
Grand Valley State University

We created a powerful computing platform based on video cards with the goal of accelerating the performance of bioinformatics codes. To satisfy the demands of the video gaming industry, modern graphics processing units (GPUs) have become very advanced computational devices, using a large set of stream processors to render multiple pixels in parallel. Recently, computer scientists have taken interest in a GPU's ability to execute a single instruction on multiple data (SIMD computation) for general applications, as opposed to graphics processing only. This is known as general purpose computation on a graphics processing unit, or GPGPU.

Our project was comprised of three stages. First, we researched and constructed a computer containing GPGPU capable hardware including two high-end graphics cards. Second, we explored the hardware and software characteristics of the GPU cards to fully understand both how they function and how to program them. Third, we developed and wrote bioinformatics software; specifically a massively parallelized version of the Smith-Waterman algorithm, which is used for performing DNA or protein sequence alignment. We are currently in the final optimization and performance analysis stage of development.

P07 - PS: A Portable Secure Peer-To-Peer Protocol for Wireless Sensor Networks

Graciela Perera
Youngstown State University

Unstructured Peer-to-Peer (P2P) networks for content distribution are decentralized and robust. Searching for content in the network is based on the Gnutella protocol which does not provide security. As more wireless and mobile communication devices are used to share information anywhere, anytime on any device, there is a need for secure and robust decentralized P2P protocols that enable users to search and distribute content. For example, soldiers can use wireless sensor networks for battlefield surveillance and enemy tracking.

We propose to investigate a likely secure P2P protocol based on the Diffie-Hellman key agreement protocol (DH) over a wireless sensor network. The challenge is how to deploy DH in a decentralized manner over a wireless sensor network with limited processing, energy, and memory capabilities? DH is a simple solution to establish a shared session key that can provide confidentiality and integrity. The computation of the shared session key requires considerable processing capability that can drain the energy available in a wireless sensor node. Thus, we propose to experimentally evaluate a new power efficient DH protocol called PDH (Portable Diffie-Hellman). In PDH each sensor node uses a set of previously calculated primes to compute the shared session key that expires. Experimental results show that although replicated shared session key are more than likely because shared session key expire and are recalculated, it is improbable that an intruder for a given moment of time determine the shared session key of a sensor node.

P08 - Microwulf: Personal, Portable, High-Performance Computing

Joel C. Adams and Timothy H. Brom
Calvin College

Microwulf is a 4-node 8-core Beowulf cluster whose measured performance is 26.25 Gflops (Rmax, measured via HP Linpack). It cost less than $2500 to build in 2007, giving it a cost-efficiency of $94/Gflop, making it the first cluster to break the $100/Gflop barrier. Today it can be built for less than $1000, improving its cost-efficiency to $38/Gflop.

Microwulf’s theoretical maximum performance (Rpeak) is 32 Gflops, giving it a computational efficiency (Rmax / Rpeak) of 82%.

Microwulf measures just 11” x 12” x 17”, making it small enough to sit on one’s desk or fit into a checkedluggage suitcase. It plugs into a normal 120V wall outlet, runs at room temperature, and draws just 450W under load, giving it a power efficiency of just 17W/Gflop.

P09 - Material Point Method Investigations of Trauma to Fluids and Elastic Solids Due to Finite Barriers

J.L. Dean
Iowa State University
M.W. Roth and Paul A. Gray
University of Northern Iowa

A Material Point Method (MPM) algorithm is developed and utilized to investigate how the dynamics of (Langrangian) Navier-Stokes fluids as well as that of elastic solids are affected by trauma due to finite barriers. For fluid simulations, material point particles are placed in a two dimensional pipe with various initial and boundary conditions and stationary perturbations to fluid flow. Results show that eddy currents are present not only in the wake of the perturbing object but are also responsible for disruption of laminar flow upstream from the barrier. However, unphysical simulated conditions arise due to failures for the fluid medium to enclose the region. An unfortunately relevant application for sudden finite trauma to an elastic solid involves simulations of an aircraft striking a large building under varying system conditions. The work presented here is introductory in nature; the ramification and importance of continued study is discussed and emphasized.

P10 - The North Polk CSD Computational Science Curriculum and Outreach Program

Bruce Bennett, Rosalie Eimers, and Steve Latimer
North Polk Jr-Sr High School, Alleman, IA
Marian Houseman, Carol Peterson, and Jennifer Raes
St Pius X Middle School, Des Moines, IA

Computational Science is offered as an introductory class in our computer science program. In addition to learning beginning Fortran90, students in this class learn to use SketchUp, a 3-D program that uses visualization and modeling. Students design structures such as dream homes, schools, and sports stadiums and then compete in a spring regional technology fair.

Computational science is introduced to our middle school students in an exploratory technology class. Students in this class learn to use Jaroo - a free program that stimulates problem solving and experimentation and engages the students with story telling and animation.

During the 2007-08 school year, plans were made to extend the use of computational science into other curricular areas (TAG, science, math, social studies and vocational classes) within our district and to develop an outreach program with a small private school in the area. Those plans will be solidified and developed during the 2008-09 school year.

P11 - Virginia STEM initiative: STEM summit, student projects and Teacher Professional Development

Bonnie Bracey Sutton, Mano Talaiver, and Bill Wilson

In this poster session, we will share details on our STEM initiatives with the participants.

  • STEM summit: We conducted a two-day STEM summit for rural teachers and guidance counselors. Academic experts from Pittsburgh Supercomputing Center, Longwood University, George Mason University, the College of William & Mary, and Shodor Foundation addressed the need for developing 21st century skills to prepare STEM work force. Speakers from Technology and Utility companies addressed the STEM work force needs
  • Student project: As part of the NSF grant: Developing interactive game design and programming skills, our activities included workshop on climate changes and robotics.
  • Expanding STEM Career and Technical Education (ESTEMCaTE): As result of our networking in SC 07, Talaiver developed a professional development program for teams of math, science, and CTE teachers.
  • STEM Learning for ALL (summit planned for January 2009)

P12 - Integrating Computational Chemistry into the Undergraduate Chemistry Curriculum

Roxanna Delgado, Nicole Massanet, Yashira Negrón, Camila Ramírez and Carlos M. Torres Díaz
University of Puerto Rico, Río Piedras Campus, San Juan, PR

The objective of this project is to integrate Computational Chemistry as a formal area along the Chemistry Curriculum at University of Puerto Rico in Río Piedras. Last year we already installed WebMO facilities integrating through this graphic inter-phase the programs Gaussian, MOPAC, Tinker and Gamess. Hosted by SC08 the Workshop of Computational Chemistry for Chemistry Educators was offered in our campus. Of the 28 participants, 10 professors and 4 undergraduate students come from our campus. Since August 2008 we are offering a special topic course of Computational Chemistry with an enrollment of 22 undergraduate students, most of them in their second year of bachelor. Topics in Computational Chemistry are introduced in the General Chemistry and Physical Chemistry courses. Looking for new learning activities in this field, an educational research is being developed beginning with learning-research activities as interstellar chemistry modeling of several organic compounds found in comets, photophysics of the nucleic acid bases and the study of the boron-nitrogen bond in aromatic compounds. In these works ab-initio and semi-empirical calculations are being performed to calculate: ionization energies in aqueous solutions and in vacuum of the nucleic acid bases, modeling different addition reactions that leads to simple molecules observed in comets and the strength of the B-N bond in aromatic rings upon changing their bonded H for other substituent.

P13 - On the Integration of High Performance Computing into 4-year CS Curriculum

Weidong Liao
Shepherd University

With the emergence of cluster and grid computing, High Performance Computing has become a more and more important subject to undergraduate students in the 4-year CS programs. Nevertheless, several challenges exist for 4 year colleges to offer high performance computing in their curriculum. Among these challenges are lacking of lab resource, motivation and interest from students, and qualified faculty members. Herein we describe several attempts we have made to integrate high performance computing in our CS courses.

P14 - Theoretical Studies of Some Donor-π-Donor Heterocyclic Systems for Molecular Electronics

Courtney E. Dula and Edmund Moses N. Ndip
Hampton University

It is well known that organic molecular systems with large multi-photon absorption, MPA, in particular, 2PA cross sections have a broad spectrum of technological applications (optical power limiting, frequency up converted lasing, three dimensional optical data storage, three dimensional microfabrication, three dimensional fluorescence imaging, and photodynamic therapy, etc.). The ease with which organic molecules can be modified (tunability) coupled with molecular-level optimization of various nonlinear optical properties (NLO) has resulted in a large number of both experimental and theoretical studies aimed at broadening the pool of materials with large MPA cross sections. Factors that influence the MPA cross section include: strength of the donor/acceptor, the extent of conjugation (π-conjugation length), molecular polarization, molecular dimensionality, and aggregation.

The present study focuses on the design and computational characterization of a series of D-π-D / A heterocyclic systems. The linear absorption spectra, energy gaps, intensities and / or oscillator strengths, dipole moments, and other molecular properties have been computed for these systems at both the semi empirical and ab initio levels of theory. Optimized geometries, linear absorption (uv-vis) spectra, and HOMO-LUMO energies have been determined at the DFT/B3LYP level with 6-31G (d,p) basis set using Titan and Spartan06 programs. The ZINDO-CI method in Arguslab was used to calculate the uv-vis spectra, the corresponding oscillator strengths, and the groundexcited transition dipole moments.

Optimized geometries, the HOMOs, the LUMOs, and uv-vis spectra were visualized with Arguslab, Jamberoo, ORCA, and Spartan06.

P15 - Evolution of Earth Science Education

Kathleen Affholter1, Peggy Bertrand2, Marie Westfall3, Audrey Williams1
1. Pellissippi State Technical Community College
2. Oak Ridge High School
3. Oak Ridge Institute for Science and Education

From giving 200 question pencil and paper exams and one and one half hour lectures, to developing a mashup of the Smoky Mountains, plotting real-time wave data from the National Data Buoy center, and participation in S'COOL (a NASA cloud project), earth science education for pre-service teachers at a community college has changed. Exposure to CSERD (Computational Science Education Reference Desk), mashup instruction, TeraGrid resources, and visualization has inspired educators to rethink teaching methods. The new methods inspire students to be creative, develop teamwork and make earth science a more personal experience.

P16 - Development of a Multiagent System Platform for the Study of Social Cognition

Alvaro de la Ossa and Andrés Segura
National Collaboratory for Advanced Computing
National Center for Advanced Technology Studies
San José, Costa Rica

We are currently developing a multiagent platform to study social interaction. First, we extend current multiagent system (MAS) architectures with Theory-of- Mind, or ToM features in the agent's model. Second, we incorporate data mining (DM) methods to support the analysis of social interactions within an instance of the MAS. Both components together provide a unique tool for cognitive scientists and social psychologists to study cognitive aspects of social interaction and the emergence of social cognition.

Adding the above mentioned ToM features, however, poses some interesting computational problems related to the size complexity of the agent's model and the time complexity of the decision making task during social interaction. Complexity arises from the possible number of ToM features within an agent's model and the distributed nature of social memory.

We are currently evaluating various MAS platforms to pick one for the proposed extensions. Simultaneously, a set of mining methods is being developed that will comprise the social interaction analysis component.

Next steps include the development of the interaction protocol language extensions to the selected MAS architecture and the design of the underlying knowledge representation language and the structure of the agent's and shared memories, and putting the resulting environment to test with a pilot sample social group.

P17 - Using MATLAB and Simulink in Introductory Computational Science

Robert J. Olsen
Richard Stockton College of New Jersey

A high priority of the Computational Science program at Stockton is that graduating students have a thorough working knowledge of MATLAB. MATLAB is not widely used in mathematics and other science courses at Stockton as yet, so its use in the Computational Science curriculum must be pervasive if we are to reach our goal. It is therefore essential that students begin using MATLAB as early as possible. I report on the incorporation of MATLAB and Simulink in CPLS 2110 (Introduction to Computational Science) this semester primarily through presentation of student projects modeling dynamics of competing populations, meteor trajectories, rocket flight, and star formation in Simulink.

P18 - Center for Computational Biology at the University of California, Merced

Mike Colvin, Arnold Kim, and Masa Watanabe
School of Natural Science
University of California at Merced

Since its establishment in fall, 2004, UC Merced Center for Computational Biology (UCM-CCB) has been a crucial part of this university by creating its academic and research programs for building towards its longterm goal of life sciences researchers who possess advanced knowledge in mathematics and computational sciences.

The center’s educational contribution to the university’s academic program is also indisputable: its involvement is exemplified by 1) creation of courseware bridge between biology and computer application and 2) establishment of the undergraduate summer research internship program. This has a sixweek intense program to experience and learn computational biology and its practical applications. The center is also facilitating the development and dissemination of undergraduate and graduate course materials based on the latest research in computational biology. This project is a multi-institutional collaboration including the new University of California campus at Merced, Rice University, Rensselaer Polytechnic Institute, and Lawrence Livermore National Laboratory, as well as individual collaborators at other sites.

All course materials are being released under an open public license. The electronic, modular course materials produced by the UCM-CCB are also facilitating linkages to feeder schools at the state university, community college, and high school levels.

P19 - An Inexpensive Self-Contained Field-Deployable Water Parameter Measuring Device

Nhlanhla Maduna, Mikio Takizawa, Dylan Parkhurst, Bryan Purcell, and Charlie Peck
Earlham College
Richmond, IN

Typical field-deployable water parameter measurement devices with the capability to store and transmit readings via the public switched telephone network are very expensive and almost always use proprietary software. Here we present a simple, inexpensive design based on commodity off-the-shelf hardware, open source software, and an industry standard water sonde.

Each unit is powered by a small solar panel which charges a battery which is housed in a waterproof case with a single board computer and charge controller. The unit communicates data via an embedded cell phone. All of this makes it possible to deploy the unit in remote locations without power or wireline/wireless data service.

The units measure, record, and transmit the water's temperature, conductivity, oxidation-reduction potential, salinity, total dissolved solids, dissolved oxygen, and pH. To analyze the reported parameters we built a simple mashup with Google Earth which visualizes the data.

P20 - LittleFe + BCCD + CSERD = Acme; Computational Science Education on the Move

Paul Gray1, Kevin Hunter2, David Joiner3, Alex Lemann2, Tom Murphy4, Skylar Thompson5, Charlie Peck5, and Kristina Wanous1
1. University of Northern Iowa
2. CAKTUS
3. Kean University
4. Contra Costa College
5. Earlham College

The overwhelming majority of the High Performance Computing (HPC) resources currently deployed are dedicated to research rather than education -- yet the nation faces a shortage of HPC expertise, due largely to the lack of faculty trained in HPC pedagogy. To address a part of this situation our group designs and implements hardware, software, and curriculum to support teaching parallel and distributed computing, computational science, and Grid technologies to a range of 9-16 STEM students and faculty. Acme is the sum of LittleFe, a complete multi-node Beowulf-style portable computational cluster, the Bootable Cluster CD (BCCD), a complete Linux distribution designed for HPC and computational science education, and the Computational Science Education Reference Desk (CSERD), a source of verified and validated curriculum modules.

P21 - Institute for Chemistry Literacy through Computational Science (ICLC)

Edee Norman Wiziecki and Thom Dunning
The National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign

The Institute for Chemistry Literacy Through Computational Science (ICLCS) is a National Science Foundation-funded 5-year program to increase the chemistry literacy and chemistry-related pedagogical skills of rural Illinois high school teachers. We will immerse these “ICLCS Fellows” and their students in new models of instruction, especially focusing on computers and their instructional uses, that will improve student achievement and prepare students for 21st Century careers through an intensive, multi-year Summer Institute for teachers built upon existing, successful curricula and methods, enhanced with stateof- the-art science research data and applications. The use of computational tools for 21st Century science will be the context for the delivery of the curriculum that includes particular focuses on medicinal chemistry (biomedicine), materials science, including nanotechnology, agricultural chemistry and the computational aspects of molecular-level chemistry. The Institute is designed to build teachers' competence and confidence in teaching chemistry, to use computational tools and methods in their curriculum, and to create a community of practice among research faculty and high school teachers working together as colleagues to improve student achievement.

One goal of the program is to increase teachers' use of, and comfort with, computational and visualization tools.

The Summer Institutes, key to the professional development program, are two-week, intensive residential experiences that build in content-level each year over three years. Additional real and virtual presentations over the course of the year provide 340 hours of continuous professional development, mentoring, and support to ICLCS participants.

P22 - Supporting High Performance Computing Research: DOE Computational Science Graduate Fellowship Program

Mary Ann Leung
The Krell Institute

This poster will provide an overview of the Department of Energy Computational Science Graduate Fellowship (DOE CSGF) program, its benefits, requirements, and unique approach to supporting Ph.D. students. This program provides a stipend renewal for up to four years, full tuition reimbursement, an academic allowance, an annual conference, and other benefits to students pursuing full-time study towards a Ph.D. in a variety of computational science and engineering disciplines. We will also be available to share information about current fellows, alumni, and the application process.

P23 - TeraGrid Campus Champions

Scott A. Lathrop
Blue Waters Technical Program Manager for Education
TeraGrid Area Director for Education

The Campus Champions program supports campus representatives as the local source of knowledge about high-performance computing opportunities and resources. This knowledge and assistance will empower campus researchers, educators, and students to advance scientific discovery. Your campus will benefit by having direct access to the TeraGrid and input to its staff, resource allocations awarded for their use, and assistance in using those resources.

The Campus Champion Program will serve as a:

  • Source of local, regional and national highperformance computing and cyberinfrastructure information on your campus,
  • Source of information regarding TeraGrid resources and services that will benefit research and education on your campus,
  • Source of start-up accounts on your campus to quickly get researchers and educators using their allocations of time on TeraGrid resources, and
  • Conduit for the campus high-performance computing needs, requirements and challenges, with direct access to TeraGrid staff.

http://www.teragrid.org/eot/campuschamps.html

P24 - Impact of the Copyright Limitation for Sensory Disabilities on Assistive Technology

Raja Kushalnagar
University of Houston

The copyright act grants authors exclusive rights to display, distribute, or prepare derivative works. However, people with sensory disabilities cannot fully access and enjoy multimedia works. Assistive technology solutions such as speech production and recognition transfer information carried in the nonfunctioning sense to the functioning sense, therefore creating a derivative work. Under the copyright act, derivative works may not be reproduced or distributed without the author's consent, absent a limitation. A limitation to the copyright statutes, section 121, permits derivative works to be reproduced or distributed in Braille, audio or digital text only, along with specified added disclaimers for the blind. There is no limitation on copyright for works partially or wholly inaccessible to the deaf.

The copyright limitation boundary is examined for the various assistive technology reader approaches for sensory disabilities in commerce and research labs. Research and development guidelines on avoidance of breaching the copyright limitation privileges for assistive devices for sensory disabilities are discussed.

P25 - Computer Modules in Science Teaching (CMIST) - a program of the National Resource for Biomedical Supercomputing (NRBSC) at Pittsburgh Supercomputing Center (PSC)

Karen Runtich
Pittsburgh Supercomputing Center

Being a part of CMIST, I was able to incorporate these modules into virtual lab experiences that paralled concept discussions from my students. Here they were able to apply critical analysis of a variety of sophisticated visualizations of molecular transport illustrating many science concepts that are difficult to convey with only textbook photos and discussion.

The goal of CMIST is to bring innovative science tutorials to secondary classrooms, focusing on the integration of computational science skills to various branch science courses. These lessons will inspire and improve student learning and understanding of a variety of topics. Ultimately, this encourages application of critical thinking analysis to prepare our students for cutting edge career paths and the opportunities of tomorrow.

Careers in the Biosciences

Karen Runtich
Pittsburgh Supercomputing Center

Being a part of the Better Educators of Science for Tomorrow (BEST) High School Teachers (2007 – 2008), I was exposed to the undergraduate Bioinformatics curriculum and shown integrative techniques to incorporate these concepts across the various disciplines. We developed and aligned to state standards a semester draft for a high school bioinformatics curriculum.

I plan to present at SC08 one of the lessons developed that my Advanced Chemistry students just completed as a research topic which had introduced this new unit module. More lessons will continue to follow in my class. The presentation will include some of my students brochures on "Careers in the Biosciences" . Today, the multidisciplinary nature of the Human Genome Project (HGP) impacts many different career fields such as: engineering, computer science, math, law, agriculture, education, pharmaceuticals, instrumentation, medicine, forensics, biofuels and journalism. My students were overwhelmed and excited to learn through this project how these future programs would be so influenced by the HGP to be dubbed the "biology century" since it is implemented in biological research, practice of medicine and also agriculture. This project has opened many doors and windows of opportunity that await them in the world of science for tomorrow.