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Supercomputers help ORNL researchers identify molecular switch that controls cell behavior

Posted at 12:39 am December 18, 2013
By Oak Ridge National Laboratory Leave a Comment

E. coli Chemoreceptor Switch

Red and blue molecules represent a conformational switch essential to the signaling mechanism of an E. coli chemoreceptor that researchers discovered using computational molecular dynamics simulations. (Image credit: Davi Ortega)

If scientists can control cellular functions such as movement and development, they can cripple cells and pathogens that are causing disease in the body.

Supported by National Institutes of Health grants, researchers at Oak Ridge National Laboratory, the University of Tennessee, and the UT-ORNL Joint Institute for Computational Sciences discovered a molecular “switch” in a receptor that controls cell behavior using detailed molecular dynamics simulations on a computer called Anton built by D.E. Shaw Research in New York City. To study an even larger signaling complex surrounding the switch, the team is expanding these simulations on Titan—the nation’s most powerful supercomputer, managed by the Oak Ridge Leadership Computing Facility at ORNL.

Researchers identified the molecular switch on Anton (which was designed to perform speedy molecular dynamics simulations) by simulating 140,000 atoms that make up the signaling part of the Tsr chemoreceptor that controls motility in E. coli. Like other receptors, Tsr spans the cell membrane, communicating to proteins inside the cell in order to respond to threats or opportunities in the environment. [Read more…]

Filed Under: Front Page News, Oak Ridge National Laboratory, Science Tagged With: Anton, cell behavior, chemoreceptor, D.E. Shaw Research, Davi Ortega, dimer, E. coli, Igor Zhulin, Jerome Baudry, JICS, John Parkinson, molecular switch, National Institutes of Health, Nature Communications, Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, ORNL, ORNL Computer Science and Mathematics Division, Phe396, phenylalanine amino acids, phenylalanine pairs, receptor, signaling, supercomputer, Titan, Tsr, University of Tennessee, University of Utah, UT Biochemistry and Cellular and Molecular Biology Department, UT Department of Microbiology, UT-ORNL Center for Molecular Biophysics, UT-ORNL Joint Institute for Computational Sciences

Intel funding for UT will develop codes, open computing center at joint UT-ORNL institute

Posted at 6:10 pm October 31, 2013
By University of Tennessee Leave a Comment

Joint Institute for Computational Sciences

The Joint Institute for Computational Sciences at Oak Ridge National Laboratory is pictured above. (Photo courtesy of ORNL)

KNOXVILLE—Imagine going to the doctor and the doctor peering into your genetic code to determine the best medicine to treat what ails you.

The University of Tennessee in Knoxville has received funding from computer chip maker Intel to develop computer codes to make personalized medicine like this and other transformative scientific discoveries possible.

The funding will open an Intel Parallel Computing Center at the Joint Institute for Computational Sciences, or JICS, at UT and Oak Ridge National Laboratory. Parallel computing, used in supercomputers, is a form of computation in which many calculations are carried out simultaneously. The focus of the center will be to take supercomputing to the next level to meet scientific computing demands. Today’s research faces limitations due to the amount of data, time, and energy it takes to run calculations. [Read more…]

Filed Under: College, Education, Oak Ridge National Laboratory, Science, Top Stories Tagged With: Bhanu Rekepalli, biochemical molecules, biotechnology, BLAST, CINECA, computer codes, drug discovery, genomics, Glenn Brook, GROMACS, Intel, Intel Parallel Computing Center, Jeremy Smith, JICS, Jimmy G. Cheek, John Eblen, Joint Institute for Computational Sciences, medicine, National Institute for Computational Sciences, National Science Foundation, Oak Ridge National Laboratory, parallel computing, Purdue University, Roland Schulz, Shane Sawyer, supercomputers, Texas Advanced Computing Center, Tony Mezzacappa, Travis Thompson, University of Tennessee, University of Texas, UT, UT-ORNL Governor's Chair for Molecular Biophysics, Zuse Institut Berlin

New leader named to UT-ORNL Supercomputer Center

Posted at 11:11 am December 12, 2012
By University of Tennessee Leave a Comment

Tony Mezzacappa

Tony Mezzacappa

Tony Mezzacappa, a leader in the field of astrophysics and supernova science, has been named director of the Joint Institute for Computational Sciences at the University of Tennessee and Oak Ridge National Laboratory.

Mezzacappa is a world leader in computational astrophysics and a pioneer in the field of supernova science. He is a UT-Battelle Corporate Fellow and group leader for theoretical physics in the Physics Division at ORNL.

He is also a joint professor in the UT Department of Physics and Astronomy. With this new position, Mezzacappa will become the department’s Newton W. and Wilma C. Thomas Endowed Chair in Theoretical and Computational Astrophysics.

[Read more…]

Filed Under: Education, Science, Top Stories Tagged With: computational astrophysics, JICS, Joint Institute for Computational Sciences, National Institute for Computational Sciences, Oak Ridge National Laboratory, ORNL, Physics Division, supernova science, Tony Mezzacappa, U.S. Department of Energy, University of Tennessee, UT, UT Department of Physics and Astronomy, UT-Battelle Corporate Fellow

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Classifieds

Public Notice: NNSA announces no significant impact of Y-12 Development Organization operations at Horizon Center

AVAILABILITY OF THE FINAL ENVIRONMENTAL ASSESSMENT FOR THE OFFSITE HOUSING OF THE Y-12 DEVELOPMENT … [Read More...]

ADFAC seeks contractors for five homes

Aid to Distressed Families of Appalachian Counties (ADFAC) is a non-profit community based agency, … [Read More...]

Public notice: Draft environmental assessment for Y-12 Development Organization at Horizon Center

AVAILABILITY OF THE DRAFT ENVIRONMENTAL ASSESSMENT FOR THE OFFSITE HOUSING OF THE Y-12 DEVELOPMENT … [Read More...]

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