Computational Science Graduate Fellowships
By Jon Bashor
Four graduate students who are part of a DOE fellowship program
took a detour from their main areas of research this summer to spend
three months honing their computational science skills with scientists
at Berkeley Lab.
As participants in DOE’s Computational Science Graduate
Fellowship program, Catherine Grasso, Ben Keen, Heather Netzloff
and Catherine Norman are required to do a practicum at a national
laboratory. They all chose Berkeley Lab, though for different reasons.
For example, Ben Keen attended a talk by Phil Colella, leader
of NERSC’s Applied Numerical Algorithms Group, at the University
of Michigan, where he is studying mathematics and scientific computation.
Keen looked at both Lawrence Berkeley and Lawrence Livermore as
candidate sites for his practicum, and settled on Berkeley Lab.
He has spent the summer working with Colella’s group working
on the Chombo library, an adaptive mesh refinement (AMR) program
developed by the group.
AMR uses grid boxes of varying sizes to focus a computer’s
power on the most interesting part of a problem, such as a moving
flame front or mixing of gases. Keen’s interested in expanding
the capability of AMR codes to efficiently handle embedded boundaries,
so that problems with fixed objects, such as air flowing over an
aircraft wing, can be addressed. This summer, he implemented an
algorithm using the new EBChombo framework for embedded boundaries
and AMR, and then testing the application. His code was one of the
first flow calculation using the EBChombo extension to the Chombo
“It’s been very useful,” Keen said. “I’m
definitely going to take away the EB Chombo package. There are a
lot of AMR codes out there, but having a chance to sit down and
work with the developer of this code is a great opportunity.
“It’s educational to work in this environment because
you acquire a point of view on what’s important and how to
address a problem,” said Keen, whose university research is
in the area of developing tools to study moving boundaries.
Catherine Norman, who is studying applied math at Northwestern
University, also spent the summer here working on AMR with Ann Almgren
of the Center for Computational Sciences and Engineering. Her worked
involved adding level set methods to an existing AMR library for
studying fluid dynamics problems. Berkeley Lab’s Mathematics
Department is a leader in level sets research and that reputation
attracted Norman’s attention.
“It’s been a very good experience at the Lab, seeing
that there are communities doing research outside the universities,”
she said, adding that she expects to continue working with her newfound
colleagues her after she returns to school.. Here you have people
of all different backgrounds working together – bringing people
together like that is something that makes the Lab unique.”
One of the high points of her summer was helping a friend who
lives here and is a certified pyrotechnician set up the fireworks
for the Fourth of July celebration in Yountville.
Heather Netzloff, who was born in North Dakota and studies physical
chemistry at the Iowa State University, said she found the East
Bay quite a change of scenery. "Berkeley is definitely not
Netzloff's advisor, Mark Gordon, is a collaborator of Teresa Head-Gordon
in the Physical Biosciences Division, and Netzloff spent the summer
in Head-Gordon's lab. She parallelized several methods of the Ewald
summation technique to treat long-range forces when doing molecular
"It was very useful. Even though it was not exactly my thesis
work, it is related in many ways. The practicum also gave me a chance
to meet more people that I can talk to about my research--networking
is always good," she said. "I will also bring some good
ideas back to Iowa from Berkeley."
Her research in Iowa covers a variety of problems in quantum/computational
chemistry. She is currently coupling the effective fragment potential
method for solvation with molecular dynamics in GAMESS, a quantum
chemistry calculation program supported by her group, to study the
condensed phase and effects of solvation in chemical reactions.
Another project looks at the the theoretical study of high energy
density materials, a topic of interest to NASA.
Catherine Grasso's practicum brought her west from Cornell University,
where she studies computational biology, and landed her in Stephen
Holbrook's lab, where she helped look for RNA genes in yeast. Unlike
other genes, RNA genes have no start or stop delimiters, which makes
them hard to find. But RNA genes are of great interest because many
scientists now believe that the most basic forms of life started
as RNA, with proteins and DNA evolving from them. Because life evolves
through reappropriation of proteins and RNAs, rather than through
building them from scratch, Grasso said, RNAs have continued to
play a significant role in cell function.
"We're just starting to get a picture of how extensively RNA
is involved in all living things. Recent attempts to find RNA genes,
such as those undertaken in the Holbrook Lab, suggest that there
are many more than previously imagined." she said.
Grasso's work focuses on using what is known about RNA folding
to develop machine learning techniques to search for patterns in
the Yeast Genome which have characteristics of patterns found in
known RNA genes. By developing general computer codes to search
for those patterns, scientists can search for RNA genes in various
organisms. "It's a cool problem from a computational biology
perspective, because it combines the problem of searching for meaningful
motifs in a very large genome, with the problem of accurately modeling
the process by which RNA folds." Grasso said.
About the Computational Science Graduate
The Department of Energy established its Computational Science
Graduate Fellowship program 10 years ago to recruit and support
graduate students pursuing studies in areas important to DOE’s
Students are selected through a very competitive process and are
supported for four years in graduate school. As part of the program,
they are required to spend a three-month practicum at a national
laboratory. The Lab’s Computing Sciences organization is looking
to increase the number of students who do their practicum here and
staff have been actively recruiting them. Lab scientists interested
in learning more about the participants can view summaries
of their research areas or contact Jon Bashor at JBashor@lbl.gov.
The Computational Science Graduate Fellowship program is administered
for DOE by the Krell Institute in Ames, Iowa. For more information,
go to the Web site.
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