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Computer Cluster
In addition to computers located in individual laboratories, the Department
has a dedicated Computer Cluster consisting of 16 Pentium computers
and 2 laserprinters that are available for use by both undergraduate and
graduate students, as part of their instructional and research activities.
Use of these computers is integrated into the entire undergraduate curriculum,
beginning with the "Principles of Chemistry" course taken by freshman,
through the senior "Seminar" course.
Each computer is equipped with high-speed internet connectivity and appropriate
software needed for classroom and/or research needs, including applications
such as
- Microsoft Office
- Corel WordPerfect
- Sigma Plot
- Bio-Rad Laboratories ChemWindow Suite
- Molecular Visualization Programs
- Internet Explorer
West Center for Computational Chemistry
and Drug Design
The West Center for Computational Chemistry
and Drug Design was established by an initial gift to the University from the
West Foundation in 1999 for the support of Computational Chemistry,
especially as applied to Drug Discovery, or as it is also referred,
Drug Design.
The original gift, plus a second gift in 2002, in combination with
support from the University, has allowed us to renovate a classroom
and purchase a variety of computer systems dedicated to computational
chemistry, including stand alone PC's, i-Macs, Mac G4's and G5's,
servers, Silicon Graphics Workstations and Beowulf Supercomputer
Clusters (see below). Most of the original computers have
since been replaced with newer, more powerful computers (picture
is of the West Center as it existed in 2002).
A variety of sophisticated software packages are also available in the West Center,
including Oracle, Gaussian 98 and AMBER, which allow database management of
both chemical and genetic databases, as well as greatly improved computer
modeling capabilities.
Drs. Moore (West Center Director),
Li,
Moyna,
Pophristic and
Zauhar, are all heavily involved in the
continued improvements to, and operation of the West Center.
Beowulf "Supercomputer" Clusters - What do they do?
The Department currently has four Beowulf Supercomputer Clusters
in operation, including the original 20-processor cluster (now upgraded
wtih new and faster processors), along with a 32-processor and two 128-processor
clusters which are located in a separate machine room. These Beowulf Clusters
are configured with the individual processors operating in parallel, so that
simultaneious operations can take place. Parallel-processing computer clusters
are designed for problems that can be broken up into small tasks,
each of which can be accomplished on the single processor of an ordinary
PC. By then combining the completed tasks of all the individual processors
in the cluster, very large, complex computations can be completed
in a relatively short time. Additional detail is provided below, but if you would
like more information about these kind of computers and how they are used in research, please
contact either Dr. Preston Moore,
the West Center Director, or Dr.
Guillermo Moyna.
The original 20-processor cluster (upgraded with newer, and faster processors)
and one of the newer 128-processor clusters are shown above (with Dr. Ed Birnbaum, the
Department Chair sandwiched in between). Both Beowulf clusters occupy
about the same amount of space, but with greatly different computational
power.
These powerful computers are used by computational chemists to model and display all
different kinds of chemical systems; anything from the structure of a very small
molecule such as aspirin, to a very large molecule such as the protein HIV protease.
The software packages available in the West Center allow faculty and students to carry
out complex calculations which simulate the charge attractions and repulsions that exist
between the atoms that make up molecules, as well as the stretching and bending of the
chemical bonds within a molecule. Complex molecular systems can be modeled in the gas phase,
or in solution, where interactions between solvent molecules must also be incorporated,
or in the solid state.
 In addition to
modeling a specific molecular structure, these computational methods
can also be used to evaluate how two molecules, such as a potential
drug and it's receptor protein, are likely to interact. This is a
powerful tool for the design of new drugs. In the picture to the right,
Dr. Liu is reviewing the results of her calculation, which was carried
out on one of the West Center's 128-processor Beowulf clusters.
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