Visit additional Tabor Communication Publications
October 04, 2010
OAK RIDGE, Tenn., Oct. 4 -- Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life.
A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms.
Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions -- two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.
"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."
The research team found a theoretical explanation for why the Diels-Alder ribozyme needs magnesium to function. Computational models of the ribozyme's internal motions allowed the researchers to capture and understand the finer details of the fast-paced reaction. The static nature of conventional experimental techniques such as chemical probing and X-ray analysis had not been able to reveal the dynamics of the system.
"Computer simulations can provide insight into biological systems that you can't get any other way," Smith said. "Since these structures are changing so much, the dynamic aspects are difficult to understand, but simulation is a good way of doing it."
Smith explained how their calculations showed that the ribozyme's internal dynamics included an active site, or "mouth," which opens and closes to control the reaction. The concentration of magnesium ions directly impacts the ribozyme's movements.
"When there's no magnesium present, the mouth closes, the substrate can't get in, and the reaction can't take place. We found that magnesium ions bind to a special location on the ribozyme to keep the mouth open," Smith said.
The research was published as "Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme" in the Journal of the American Chemical Society. The research team included Tomasz Berezniak and Mai Zahran, who are Smith's graduate students, and Petra Imhof and Andres Jäschke from the University of Heidelberg.
Smith's research was supported by Laboratory Directed Research and Development program funding. The bulk of the simulations were performed on the Kraken supercomputer at the UT/ORNL National Institute for Computational Sciences, supported by a National Science Foundation Teragrid allocation, and the resulting data were analyzed on the Heidelberg Linux Cluster System at the Interdisciplinary Center for Scientific Computing of the University of Heidelberg.
ORNL is managed by UT-Battelle for the Department of Energy's Office of Science.
Source: Oak Ridge National Laboratory
In quieter times, sounding the bell of funding big science with big systems tends to resonate further than when ears are already burning with sour economic and national security news. For exascale's future, however, the time could be ripe to instill some sense of urgency....
In a recent solicitation, the NSF laid out needs for furthering its scientific and engineering infrastructure with new tools to go beyond top performance, Having already delivered systems like Stampede and Blue Waters, they're turning an eye to solving data-intensive challenges. We spoke with the agency's Irene Qualters and Barry Schneider about..
Large-scale, worldwide scientific initiatives rely on some cloud-based system to both coordinate efforts and manage computational efforts at peak times that cannot be contained within the combined in-house HPC resources. Last week at Google I/O, Brookhaven National Lab’s Sergey Panitkin discussed the role of the Google Compute Engine in providing computational support to ATLAS, a detector of high-energy particles at the Large Hadron Collider (LHC).
May 23, 2013 |
The study of climate change is one of those scientific problems where it is almost essential to model the entire Earth to attain accurate results and make worthwhile predictions. In an attempt to make climate science more accessible to smaller research facilities, NASA introduced what they call ‘Climate in a Box,’ a system they note acts as a desktop supercomputer.
May 22, 2013 |
At some point in the not-too-distant future, building powerful, miniature computing systems will be considered a hobby for high schoolers, just as robotics or even Lego-building are today. That could be made possible through recent advancements made with the Raspberry Pi computers.
May 16, 2013 |
When it comes to cloud, long distances mean unacceptably high latencies. Researchers from the University of Bonn in Germany examined those latency issues of doing CFD modeling in the cloud by utilizing a common CFD and its utilization in HPC instance types including both CPU and GPU cores of Amazon EC2.
May 15, 2013 |
Supercomputers at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) have worked on important computational problems such as collapse of the atomic state, the optimization of chemical catalysts, and now modeling popping bubbles.
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.