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DEAC Cluster

 

Academic Year 2010-2011

Fall 2011

Physics of Biological Macromolecules (PHY 320/620)
Students in the course cover a wide-ranging interdisciplinary set of topics, including nucleic acid/protein biochemistry, statistical thermodynamics, polymer physics, and chemical association kinetics. These subjects are applied to protein folding and aggregation processes, which are widely thought to be directly involved in diseases such as HIV, mad cow disease, and cancer. The following are protein structures rendered on university-issued Lenovo IBM laptops using the VMD visualization suite.

Gallery of Protein Structures
(click to enlarge)
by Don Nguyendac, Luke Schwartz, and Randy Conrad

To apply their knowledge to practical problems that are currently studied in the field, the students used the WFU DEAC high-performance computing cluster to perform molecular dynamics (MD) simulations of a hexaglycine in explicit water using the NAMD simulation suite with the CHARMM force field.

MD Simulation Movie
by Brandon Turner

Academic Year 2009-2010

Spring 2010

Parallel Algorithms (CSC726)
Students in this course learn how to develop parallel versions of their favorite serial algorithms that are scalable and efficient. To enhance their design efforts, they are required to implement their algorithms on the cluster in half of the assignments.
http://menehune.opt.wfu.edu/CSC726/index.html

Introductory Drug Discovery Virtual Laboratory (BICM 745)
"Interactive laboratory course complements "Seminars in Drug Discovery: Concept to Clinic" by providing students with hands-on experience with state-of-the-art software used by the pharmaceutical industry to discover new drugs and refine their target interactions in silico. Following an introduction to structure-based drug design principles, students will complete tutorials; guided by WFU faculty from both the Reynolda and Bowman Gray campuses, they will develop and present exercises that examine how structure-based drug design has contributed to recently approved pharmaceuticals." (WFU Graduate School Bulletin, 2009)

Academic Year 2007-2008

Fall 2007

Parallel Computation (CSC346/646)
This Computer Science course directed at students in the major or minor program provides students with an overview "of hardware and software issues in parallel computing. Topics include a comparison of parallel architectures and network topologies, and an introduction to parallel algorithms, languages, programming, and applications." (WFU Student Handbook, 2009). Specifically, students used the cluster to explore distributed computing concepts at the core of cluster computing.

Academic Year 2006-2007

Fall 2006

Computational Biophysics Laboratory (PHY 323/623)
Students in this course will be performing dynamics simulations (NAMD), trajectory analysis (CHARMM) and molecular visualization (VMD) of Eglin C mutants. The Computational Biophysics Lab uses a research-based learning format, in which students are taught methods and theory, but then apply the methods and theory to a problem for which the answer is not known. Student observations, analyses of the results, and critical comparison of to the results produced by other students thus become a critical part of the learning process. Each student will submit a research paper on their work at the end of the semester.
http://www.wfu.edu/~fetrowjs/Courses/CompMolBiophysFal06/

Academic Year 2005-2006

Spring 2006

Computational Physics Lab (PHY 346)
Required for all Physics BS majors, PHY 346 introduces students to several types of research areas. The purpose of the computational physics segment was to introduce some of the basic concepts of computation and to provide several examples of computation on the DEAC cluster. One exercise involved calculating the electronic structure of an atom another exercise involved a simple molecular dynamics simulation. In both cases, the results could be visualized with graphics software. For the first exercise the students could construct radial plots of the electron densities and wavefunctions using a gnuplot script. For the second exercise, students could visualize a movie of their simulation using a public domain software package -- xcrysden.
http://www.wfu.edu/~natalie/s06phy346/

Fall 2005

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715)
Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.
http://www.cs.wfu.edu/~djj/CSC685/

Academic Year 2004-2005

Fall 2004

Parallel Algorithms (CSC726)
Students in this course learn how to develop parallel versions of their favorite serial algorithms that are scalable and efficient. To enhance their design efforts, they are required to implement their algorithms on the cluster in half of the assignments.
http://www.cs.wfu.edu/~djj/CSC726
http://www.wfu.edu/~millerte/courses/CSC726

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715)
Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.
http://www.wfu.edu/~fetrowjs/Courses/BioinformaticsFal04

Computational Biophysics Laboratory (PHY 323/623)
Students in this course will be performing dynamics simulations (NAMD) and electrostatic calculations (MEAD) of peroxiredoxin monomer units, trajectory analysis (CHARMM), and molecular visualizations (VMD). The Computational Biophysics Lab uses a research-based learning format, in which students are taught methods and theory, but then apply the methods and theory to a problem for which the answer is not known. Student observations, analyses of the results, and critical comparison of to the results produced by other students thus become a critical part of the learning process.

In the Fall 2004, semester, each student will be assigned one peroxiredoxin protein structure to analyze during the course. They will apply each method to their own peroxiredoxin structure and submit a research paper on their work at the end of the semester.
http://www.wfu.edu/~fetrowjs/Courses/CompMolBiophysFal04

Academic Year 2003-2004

Spring 2004

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715)
Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.

Fall 2003

Parallel Computation (CSC346/646)
Students in this course learned how to create distributed and multiprocessor programs. Their efforts in the distributed programming material helped produce the software components used in "Fibonacci and Phi".
http://www.cs.wfu.edu/~burg/Courses/Fall03/CSC346-646/
http://www.wfu.edu/~millerte/courses/CSC346/
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Winston-Salem, NC 27105
E-mail:
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Last Updated: 2011-Mar-09, 17:25 EST Website templates and general design
by the WFU Physics Department