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.

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.

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.

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.

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.

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".