As members of the
Bioinformatics Research Center
and the Department
Dr. Alison Motsinger-Reif and her group develop methods for
finding predictive models in high-throughput genomic data. She aims to
develop analytic strategies to identify complexes of genetic and environmental
factors. In particular, Dr. Motsinger's computational
methods aim to detect genetic risk factors of common complex disease
and drug response outcomes in human, canine, and porcine populations.
Distributed and shared memory computations on the blade center have
been key to her research, both in methodological development and real
Spring 2011: Maize Diversity
Dr. James Holland with the USDA-ARS maize breeding and genetics
program at NCSU aims to understand and exploit the vast diversity
of maize found world-wide. By studying the genetic variation
of maize and how it relates to phenotypic variation for
important agricultural traits, this research aims
to enhance the genetic base of the U.S. corn crop.
In collaboration with other NCSU faculty, Major Goodman, Peter Balint-Kurti, Gary
Payne and others, Dr.
identifying new sources of improved productivity, stress resistance,
and disease resistance in tropical maize. To understand the genetic basis of
complex traits in maize, Holland and other USDA collaborators created the maize
Nested Association Mapping population, a collection of 5000 lines representing much
of the variability in maize. They conducted the single largest genetic mapping
experiment ever in plants, involving evaluating these 5000 in 11 environments for
diverse quantitative traits. Analyzing this huge experiment requires significant
high performance computing resources. Dr. Holland uses the HPC blade center to
perform statistical analysis of this trait data, which has enabled high resolution
genetic mapping of important complex traits in maize. The HPC staff provided support
to enable the use of specialized software on the blade center.
Ocean Observing and Modeling Group -- Modeling Gulf Currents
The Ocean Observing and Modeling Group is headed by
Dr. Ruoying He , with the team currently including Dr. Kyung Hoon Hyun, Dr. Zuo Xue, Ke Chen, Yizhen Li,
Joseph Zambon, Hui Qian, Zhigan Yao, Yanlin Gong, Jill Nelson, Andrew
Stieneke, and Yao Zhao. The group performs research in coastal and estuarine
circulation, bio-physical interactions, numerical modeling, data
simulation, and design and implementation of a coastal ocean observing
system. Their research is supported by NSF, NOAA, ONR, NASA,
USGS, and DOE, and uses the NCSU Blade Center to model ocean circulation.
The graphic is generated using the South Atlantic Bight and Gulf of Mexico (so-called
NC State SABGOM )
model. This model (along with weather prediction) is run daily on a
myrinet equipped subcluster of the NCSU Blade Center, predicting
present and future (84 hour) "ocean weather".
NOAA emergency response division has been using the SABGOM ocean current
nowcast and forecast (along with 3 other ocean models)
to generate an official oil trajectory prediction, used to
guide responses of the local, state, and federal governments.
and today's oil trajectory prediction.
Linear/Nonlinear Equations and Multilevel Methods
Dr. Tim Kelley
and his team of mathematicians (left to right, Anne Costolanski, Kai Fan, Corey Winton, Dave Mokrauer, Tim Kelley, Anna Meade, and Deena Hannoun) explore algorithms for solving systems of linear and
nonlinear equations, multievel methods for integral equations, radiative transfer
problems, optimal control, large scale optimization, optimization of noisy functions,
and flow in porous media. Dr. Kelley has recently been selected as
Society of Industrial and Applied Mathematics Fellow for his work in porous
Dr. Kelley supports Matlab software for Linear Equations, Nonlinear Equations, and
Optimization. His group supports Matlab codes for optimization
of noisy functions. They use the blade center to solve large distributed
problems using the DOE ACTS software Trilinos, as well as smaller
problems using many copies of matlab and the chemistry software Gaussian. Dr.
Kelley's work is partly supported by the Army Research Office, which has purchased
several hundred of the processors currently in use on the Blade Center.
RNA in Biopolymer Nanostructures
Dr. Yara Yingling
and her group in materials science explore biopolymeric
and composite nanoassembly processes.
The NCSU Blade Center enables Dr. Yingling to perform
complex simulations to guide
efforts in synthesis and to analyze properties of biopolymers.
For example, RNA based biopolymers can be used
as nanoarrays and nanocircuits. Dr. Yingling proposes to use
protein-free RNA nanoparticles as efficient
minimally toxic drug delivery devices.
Dr. Yingling and her team
designed an RNA hexagonal nanoring formed from
six simple building blocks held together via loop-loop
contacts. Drugs or therapeutic agents can be incorporated
within or attached to the ends of building blocks. Moreover,
the 3' and 5' sequence can be engineered to facilitate a
self-assembly of these rings into a nanotube.
Dr. Blondin's work
was featured in a recent
Astrophysics professor John Blondin recalls staring into the nighttime Wisconsin skies when he was growing up and marveling at the stars. Even as a kid, I can remember being fascinated by the fact that our world here on Earth is such a small piece of the universe, he says. Now, he exudes the same boyish enthusiasm as he marvels at some of the
world's most powerful computers, which are helping him solve a vexing problem of the
universe: How does a supernova explode?
Summer 2006 Featured Research
Dr. Frank Mueller and his research team in the Department
of Computer Science are developing software tools
to tune and scale applications in the
high performance computing area.
The tools detect and alleviate sources of scalability problems and
use runtime/operating system synergy to exploit shared-memory
multi-processors and simultaneous
multithreading for shared memory computing. As multi-core
architectures spread to the desktop (and the laptop),
so does the applicability of their work in shared memory computation.
Spring 2006 Featured Research
Dr. Marco Buongiorno Nardelli in the Department of Physics and
his research group are using first principles
simulations to study the application of carbon nanotubes as
a potential method to produce hydrogen by dissociation of
water. Defects in the carbon lattice structure provide pathways
that significantly reduce the energy required for the dissociation
of water. An economical and
environmentally friendly source of hydrogen could provide
an important future energy source.
Fall 2005 Featured Research
Dr. Yang Zhang's Air Quality Forecasting Laboratory applies state-of-the-science numerical models
to simulate human-induced air pollution and its impact on human
health, climate, the environment, and society. By using
university HPC resources, the AQF Lab is able to focus on constructing,
improving, and implementing atmospheric modeling systems.
Spring 2005 Featured Research
The Genome Research Laboratory
transitioned the computationally
intensive processing of sequencer output from an internal cluster
to the university Linux center. By utilizing the university resource
for the computationally intensive work the GRL has been able to
focus their resources on the sequence generation services the
Winter 2005 Featured Research
NC State researchers are simulating the death of a massive
star leading to a supernova explosion. Of particular interest
is the dynamics of the shock wave generated by the initial
implosion of the star which ultimately destroys the star
as a highly energetic supernova.
Dr. John Blondin and his research group work with
models of supernova as part of the Department of Energy
TeraScale Supernova Initiative. In addition to
NC State HPC resources, the group also uses the
computational resources at Oak Ridge National Laboratory
and, for visualization of model results, their own 22-node Linux cluster.
Fall 2004 Featured Research