Design of Biomimetic Antimicrobial Polymers
The SDSC Storage Resource Broker (SRB)
Simulating Emulsion Behavior Using NCSA's SGI Origin2000 Supercomputer
SDSC Science Interest Group
EOT-PACI
Design of Biomimetic Antimicrobial Polymers
Michael Klein, Robert Doerksen in collaboration with William
DeGrado et al.
In this study, reported in Proc. Natl. Acad. Sci, 99, 5110 (April
16, 2002), Michael Klein's group at University of Pennsylvania collaborated
with experimentalists at the University of Pennsylvania School of
Medicine led by William DeGrado. This team has synthesized a novel
family of 'arylamide' polymers that are antibacterial
and could eventually be used to treat surfaces to be antibacterial
on contact. Potential applications include treated fabrics, in effect
an antimicrobial suit. The researchers have applied for patent protection
of the technology.
The polymers mimic the structure and function of a class of endogenous
defense proteins. These natural peptides have facially 'amphiphilic'
structure -- postively charged hydrophilic and uncharged hydrophobic
aminogroups segregate on opposite faces of the structure. It's believed
thatthis 'amphilicity' accounts for the peptides ability
to kill bacteria by attaching to and piercing the bacterial cell
membrane.
The Univ. of Penn group and other groups (including Ghadiri of Scripps)
have synthesized related peptides. A key advance of the University
of Pennsylvania work, however, is that arylamide polymers appear
to offer the same antibacterial properties but are much less expensive
to produce.
Klein & post-doc Robert Doerksen used the TCS to carry out density-functional
calculations to develop accurate torsional potentialsfor the arylamide
polymers. The potentials available with packages such as CHARMM
proved to be unsuited for these structures, giving inaccurate results
in preliminary molecular dynamics runs. With
extensive computations -- 60,000 SUs to generate 14 torsional potentials
during the
friendly user period, with efficient runs on 128 processors of Lemieux
--
the researchers generated torsional potentials to describe the backbone
unit of a
particular arylamide polymer, a potential which they then used to
modify the CHARMM torsional potential.
The SDSC Storage Resource Broker (SRB)
Reagan Moore et al.
The data-intensive computing thrust group at SDSC, led by Reagan
Moore, is building an integrated national digital library that accelerates
the publication of scientific data. This requires the integration
of distributed persistent digital archives, hierarchical storage
systems, databases, data-handling systems, and digital libraries
into integrated scientific information repositories.
One the their most important enabling technologies deployed to
date is called Storage Resource Broker (SRB). SRB is client-server
middleware that provides a uniform interface for
connecting to heterogeneous data resources over a network and accessing
replicated data sets.
SRB, when used in conjunction with the Metadata Catalog (MCAT),
provides a way to access data sets and resources from a user's workstation
based on their attributes rather than their names or physical locations.
SRB provides a uniform programmer interface that can be used to
connect to heterogeneous resources that may be distributed and access
data sets that may be replicated. SRB is available for several platforms
including UNIX and Windows NT Workstations.
Meta data Catalog (MCAT) is a meta data repository system implemented
at SDSC to provide a mechanism for storing and querying system-level
and domain-dependent meta data using a uniform interface. MCAT provides
a resource and data set discovery mechanism that can be effectively
used to identify and discover resources and data sets of interest
using a combination of their characteristic attributes instead of
their physical names and/or locations.
Simulating Emulsion Behavior Using NCSA's SGI Origin2000 Supercomputer
Yuriko Renardy and Michael Renardy et al.
From household products to life-saving medical applications, emulsions
improve our daily
activities in countless ways. We coat our hardwood floors with emulsions
that add shine and prevent scratches. We keep cream cheese and margarine
sealed against bacteria in plastic tubs made from emulsions. We
mold emulsions to form intravenous tubes with glasslike clarity
through which doctors can spot fluid blockages. Emulsions, stable
suspensions of one liquid in another unmixable liquid, are some
of the most versatile resources available.
'The experimental study of emulsions dates back to the ancient
Egyptians and Babylonians, who mixed oil and vinegar to season their
salads. However, the numerical simulation of that process is a more
recent event,' explains Yuriko Renardy of Virginia Tech. Renardy,
a math professor at the university, leads a group of scientists
at Virginia Tech devoted to providing the expertise needed to making
production of state-of-the-art emulsions a science.
For instance, the mayonnaise in your refrigerator is an emulsion
of vegetable oil in lemon
juice, stabilized by a molecule found in egg yolks. When you put
mayonnaise on bread with a knife, the spreading motion causes a
process that scientists call shearing. During shearing, lipid globules
in the mayonnaise deform, break up, and then coalesce. This drop
deformation process resembles a simple version of emulsions mixed
on a large scale for industrial use. Industries that use and produce
emulsions want to know, if they feed a mixture of liquids with different
sized drops into a mixer, how will it look when it comes out? The
outcome is what scientists call drop-size distribution.
Imagine you want to make an IV tube. To do so, you must blend
two unmixable liquids, each of which has a valuable characteristic,
such as transparency and flexibility. After the liquids are blended,
poured in molds, and cooled to a solid, the tube formed must espouse
both characteristics. In order to accomplish this, you want the
drop sizes of each liquid to be small and evenly dispersed. Smaller
drops approximate mixing better than large drops because they provide
more surface area in contact between the two liquids. They will
still be unmixable liquids, but the separate drops will hold together
much more securely. A secure emulsion will make the original liquids
in the IV tube less likely to separate over time.
Renardy's team which includes another math professor, Michael Renardy,
Jie Li, a postdoc, Damir Khismatullin, a research assistant professor,
and Mary Ann Clarke, a PhD student, is numerically modeling the
drop-size distribution of emulsion drops using NCSA's SGI Origin2000
supercomputer. So far they have used about 200,000 hours on the
Origin2000 since the project's inception. The simulations required
32 to 64 processors for the most intense runs.
SDSC Science Interest Group
Girl Scout Science Interest Group 3908 is an ongoing program for
7th to 12th grade girls in San Diego County who have an interest
in science. There are no prerequisites to be part of this program
and no cost besides a small Girl Scout registration fee. The program
consists of girl-planned science activities (including computer
science), trips, and speakers in addition to normal Girl Scout activities.
Mentoring by a scientist is available to interested girls.
The group is sponsored by the San Diego Supercomputer Center and
under the supervision of Rozeanne Steckler and Michael Bailey.
The girls in the Science Interest Group offer a Computer Badge
Day once or twice a year for Junior Girl Scouts (grades 4-6). Attendees
spend most of a Saturday at the San Diego Supercomputer Center.
They complete various exercises to familiarize themselves with the
uses of computers in today's world.
They get hands-on experience on desktop computers (Macintoshes)
and 3D UNIX-based graphics workstations (Silicon Graphics). They
complete various exercises to familiarize themselves with the uses
of computers in today's world. At the end of the day, each girl
will have earned the Junior Girl Scout Computer badge and will receive
the patch.
For more information see http://sciencegroup.sdsc.edu/
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