IMPACT March 2013
What's New in XSEDE
"What's New in XSEDE" is a monthly e-newsletter providing information on scientific discoveries made possible by the Extreme Science and Engineering Discovery Environment, as well as the people, places, and programs involved. XSEDE is a five-year high-performance computing project supported by the National Science Foundation.
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The Ties That Bind
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| Representative structures of PTEN protein after 300ns of simulation in solution (A) and on the membrane (B). Simulations show the C-terminal tail of PTEN (end of the amino acid chain) (red) can wrap around the core of the protein (grey) and block the primary membrane-binding region (yellow). On the membrane, however, the flexible tail remains distal from the membrane surface. |
Proteins can play either pernicious or positive roles in the dynamics of disease. XSEDE is aiding researchers in determining why some proteins that anchor to cell membranes promote the development of HIV (human immunodeficiency virus), while some proteins thwart the growth of cancer. Hirsh Nanda of the National Institute of Standards and Technology (NIST) is leading the multi-institution research team using XSEDE-allocated Kraken supercomputer at the National Institute for Computational Sciences (NICS) to find answers to this question.
The team has found that combining experimental neutron-scattering methods with molecular simulations can tell them a lot about the conformational changes in proteins and how they bind to cell membranes. Successes in their quest are essential to the advancement of biomedical research, including understanding the conformational, or structural, changes proteins undergo when they move from the cell fluid and anchor to the cell membranes.
Read more about play a role in the dynamics of disease
The Origins of Evolutionary Innovation
Using XSEDE-allocated resources, researchers compared 40 genomes from a population of E. colito trace the key changes that led to the emergence of a new evolutionary innovation. E. colibacteria multiplied in their Erlenmeyer flasks, evolving slowly over more than 50,000 generations. Throughout that time, scientists at Michigan State University kept records of each successive generation, waiting for the telltale signs of evolution to show themselves. The most dramatic sign first appeared after approximately 33,000 generations in the form of a cloudy bloom of bacteria in one flask.
To make this discovery, Jeffrey Barrick, a former researcher in the Michigan State lab and now professor of chemistry and biochemistry at The University of Texas at Austin, used a host of technologies that have made DNA sequencing cheaper, faster, and more accurate in recent years. He also developed tools, including breseq, which are capable of finding more, and more difficult-to-locate, mutations. Advanced computing is enabling researchers to analyze DNA sequences, develop and test synthetic organisms, experiment with artificial populations, and explore evolution as never before; that is precisely why Barrick turned to the XSEDE-allocated Ranger and Lonestar supercomputers at the Texas Advanced Computing Center.
Read more about research on the emergence of a new evolution of E. coli
Energy Models of the Future
Researchers have turned to XSEDE to realize their vision of a world in which an energy model can attain cost savings, security, and sustainability in buildings. A team of researchers at Oak Ridge National Laboratory are leading a project known as Autotune, working to develop a methodology which places the bargain of energy efficiency within reach for more commercial and residential buildings. Compute time on the XSEDE-allocated Nautilus supercomputer is helping the team create a more accurate energy model than exists today.
This advanced analytical and optimization methodology leverages terabytes of HPC-generated simulation data and data mining with multiple-machine learning algorithms for quickly calibrating a building energy model to measured (utility or sensor) data. The Autotune project has clocked approximately 300,000 compute hours on Nautilus -- completing about 1.6 million parametric simulations of the eventual 8 million and generating more than 50 terabytes of data of the planned 270 terabytes, so far.
Read more about XSEDE-allocated resources helping create a more accurate energy model
Pocket Full of Promise
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| Stictic acid (highlighted in green) docked in the open p53 pocket. |
Researchers from the University of California (UC) are using XSEDE advanced computing resources to discover new target docking site for cancer drugs. Tumor protein 53 (p53) regulates the body's cell cycle and suppresses tumors. Rommie Amaro, a professor of chemistry and biochemistry at UC, and her team of UC Irvine biologists, chemists, and computer scientists discovered a pocket for reactivating the mutant p53 gene in human cells through simulations run on the XSEDE-allocated Ranger supercomputer at the Texas Advanced Computing Center.
The discovery might herald new and better-targeted therapies for cancer treatment. "What's very exciting about the reactivation of the p53 would be that it could ideally lead to therapies that will not kill all cells," Amaro explains. "It would be a drug that would react only when interacting with a cancer cell. This means less aggressive, more effective treatments, with the patient having to bear very little cytotoxic danger."
Read more about the open p53 pocket and how it could lead to new cancer treatments
Two sponsors commit to XSEDE13
Two corporate sponsors—Cray Inc. and Intel—have committed to supporting XSEDE13, the annual conference focused on science, education, outreach, software, and technology related to XSEDE. The conference will bring together hundreds of scientists, technology experts, educators, and students July 22-25, 2013, at the Marriott Marquis & Marina in San Diego. Cray was the first company to commit as an XSEDE13 sponsor. A silver sponsor of last year's conference, Cray increased its commitment to become a Gold sponsor of XSEDE13. Intel also increased its support this year and has agreed to support XSEDE13 at the highest sponsorship level, Platinum. Sponsorship opportunities are still available for corporations and non-profit organizations.
Read more about Cray and Intel's corporate sponsorship of the XSEDE13 conference
XSEDE in a nutshell
Following are events, deadlines and opportunities related to XSEDE.
Registration for the XSEDE13 conference opens April 5. XSEDE13, July 22-25 in San Diego
Extreme Scaling Workshop 2013 Call for Presentations due May 15. Workshop Aug. 15-16 in Boulder, CO
Students invited to get involved with XSEDE in multiple ways