Science News
Protein Dynamics Hit the Big Screen
Scientists from Berkeley Lab and UC Berkeley are using one the world's most powerful computers to simulate how protein molecules move, rotate, and fold as they carry out life's most fundamental tasks.Although they only approximate real-life phenomena, the increasingly realistic movies are becoming useful complements to real-world experiments in helping scientists determine how proteins function. Using them, biologists can gain a better understanding of how incorrectly folded proteins lead to a… Read More »
Climate Models Show That Sea Level Rise from Thermal Expansion Is Inevitable
Even if all greenhouse gases had been stabilized in the year 2000, we would still be committed to a warmer Earth and greater sea level rise in the present century according to a new study by a team of climate modelers at the National Center for Atmospheric Research (NCAR). The models were run on supercomputers at NCAR and several DOE labs, including NERSC, and on the Earth Simulator in Japan. The findings were published in the March 18, 2005 issue of the journal Science. The modeling study… Read More »
Fusion Researchers Use 4,096 Processors to Study Electron Collisions
As NERSC moves to allocate more resources to larger jobs, researchers are making greater use of the opportunity to run on more processors and combine this with NERSC's well-established reliability. In March, Connor Ballance, of Rollins College, a research scientist within a collaborative research effort between Rollins College, Auburn University, and Oak Ridge National Laboratory, undertook a large R-matrix scattering calculation on this iron ion. He used 4,096 processors for a twelve-hour… Read More »
Simulating a Map of the Cosmic Microwave Background: What the Planck Satellite Will See
In the year 2007 the European Space Agency, with substantial NASA participation, will launch the Planck satellite on a mission to map the cosmic microwave background (CMB), the remnant radiation believed to be an echo of the Big Bang that started the universe.Planck is designed to map CMB temperature and polarization fluctuations with unprecedented resolution and sensitivity, but the enormous volume of data this will generate poses a major computational challenge. Can such a mountain of data be… Read More »
Magnetic Fusion Simulations at NERSC Advance SSPX Research at LLNL
In pursuing the potential of fusion energy, experimentalists try to understand precisely what is going on inside the fusion plasma so they can tune the system to improve the conditions that would lead to a sustained reaction within the heated plasma. If the temperature can be kept high enough and the energy contained, net power can be produced. A major problem is that determining exactly what is happening inside a fusion plasma is very difficult experimentally. A conventional probe inserted… Read More »
Laser Wakefield Acceleration: Channeling the Best Beams Ever
BERKELEY, CA -- Researchers at the U.S. Department of Energy's Lawrence Berkeley National Laboratory have taken a giant step toward realizing the promise of laser wakefield acceleration, by guiding and controlling extremely intense laser beams over greater distances than ever before to produce high-quality, energetic electron beams. The experimental results were then analyzed by running the VORPAL plasma simulation code on supercomputers at DOE's National Energy Research Scientific Computing… Read More »
Laser Wakefield Acceleration: Channeling the Best Beams Ever
Researchers at the Department of Energy's Lawrence Berkeley National Laboratory have taken a giant step toward realizing the promise of laser wakefield acceleration, by guiding and controlling extremely intense laser beams over greater distances than ever before to produce high-quality, energetic electron beams. Read More »
NERSC Helps Climate Researchers Get Results Faster to Meet Deadline
When experts on the Earth’s environment join forces with experts on the high performance computing environment, the future of our global climate comes into focus faster — at least in the results of model simulations. That’s what happened this summer when researchers from the National Center for Atmospheric Research (NCAR) asked NERSC consultants to help them improve the throughput of their simulations so that they could present the results at an upcoming meeting of the Intergovernmental… Read More »
LLNL Scientists Use NERSC to Advance “Aerosol Initiative
While “greenhouse gases” have been the focus of climate change research for a number of years, DOE’s “Aerosol Initiative” is now focusing on how aerosol emissions affect the climate on both a global and regional scale. Scientists in the Atmospheric Science Division at Lawrence Livermore National Laboratory are using NERSC’s IBM supercomputer to create simulations showing the historic effects of aerosol emissions at a finer spatial resolution than ever done before. Simulations were… Read More »
Climate Model Developed on NERSC System Shows Faster CO2 Emissions Will Overwhelm Capacity of Land and Ocean to Absorb Carbon
One in a new generation of computer climate models that include the effects of Earth's carbon cycle indicates there are limits to the planet's ability to absorb increased emissions of carbon dioxide. If current production of carbon from fossil fuels continues unabated, by the end of the century the land and oceans will be less able to take up carbon than they are today, the model indicates, according to Inez Y. Fung, a professor at UC Berkeley, director of the Berkeley Atmospheric Sciences… Read More »
Tuning the Nanoworld
Scientists at Lawrence Berkeley National Laboratory have found new ways of combining quantum dots and segmented nanorods into multiply branching forms and have applied new ways to calculate the electronic properties of these nanostructures, whose dimensions are measured in billionths of a meter. Read More »
Heidelberg Talk Tells How to "Fool the Masses"
David Bailey, chief technologist for the Computational Research and NERSC Center divisions, delivered a tongue-in-cheek yet still serious presentation here on June 25, reminding attendees at the 2004 International Supercomputer Conference that hype and exaggeration still loom large in the field. As an invited speaker, Bailey drew one of the largest and most enthusiastic audiences of the conference to his talk on "12 Ways to Fool the Masses." Read More »
NERSC’s Spinning Cube of Doom Takes a Turn in the Spotlight
When Stephen Lau of NERSC’s networking and security created a graphical display to highlight the many malicious scans and threats lurking in cyberspace, he christened it the “Spinning Cube of Potential Doom.” Developed to increase awareness of the level of malicious traffic on the Internet, the Cube is a visual display of network traffic collected using the Bro Intrusion Detection System developed by LBNL’s Vern Paxson. Bro monitors network links, searching for traffic that… Read More »
INCITE Project Reports Unprecedented Full-Star Simulations
One of three computationally intensive large-scale research projects selected under DOE’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program has achieved unprecedented simulations of stars and supernovae using NERSC’s computing resources. Called “Thermonuclear Supernovae: Stellar Explosions in Three Dimensions,” the project is led by Tomasz Plewa of the Center for Astrophysical Thermonuclear Flashes at the University of Chicago and is a collaboration… Read More »
Combustion Researcher Outlines Advances Due to SciDAC
The U.S. Department of Energy’s Scientific Discovery through Advanced Computing (SciDAC) program is making important contributions to combustion research, according to Arnaud Trouvé, a professor of engineering at the University of Maryland and a NERSC user. Trouvé, who has extensive experience in the field of multi-dimensional numerical modeling for turbulent combustion applications, is a leader of SciDAC’s Terascale High-Fidelity Simulations of Turbulent Combustion with Detailed… Read More »
NERSC Helps Nearby Supernova Factory Discover Supernovae at a Rate of 8 per Month
The Nearby Supernova Factory based at Berkeley Lab has discovered 34 supernovae during its first year of operation and 99 to date — the best performance ever for a "rookie" supernova search. This remarkable discovery rate of eight per month is made possible by a high-speed data link, custom data pipeline software, and NERSC's ability to store and process 50 gigabytes of data every night. Read More »
Improved Algorithm Speeds Up Fusion Code by a Factor of 5
Developers of the NIMROD code, which is used to simulate fusion reactor plasmas, collaborated with members of the SciDAC Terascale Optimal PDE Simulations Center to implement the SuperLU linear solver software within NIMROD. As a result, NIMROD runs four to five times faster for cutting-edge simulations of nonlinear macroscopic electromagnetic dynamics — with a corresponding increase in scientific productivity. Read More »
Scientists Find "Fingerprint" of Human Activities in Recent Tropopause Height Changes
A team of scientists, including Michael Wehner of LBNL's Computational Research Division, has determined that human-induced changes in ozone and well-mixed greenhouse gases are the primary drivers of recent changes in the height of the tropopause. The team is led by Ben Santer of LLNL and their work is described in a paper entitled, "Contributions of Anthropogenic and Natural Forcing to Recent Tropopause Height Changes," which appears in the July 25, 2003 edition of Science. Read More »
Simulation Computed at NERSC Matches Historic Gamma-Ray Burst
After three decades of scientific head-scratching, the origins of at least some gamma-ray bursts (GRBs) are being revealed, thanks to a new generation of orbiting detectors, fast responses from ground-based robotic telescopes, and a new generation of computers and astrophysics software. Read More »
New Computational and Scientific Results at NERSC: Science-of-Scale Applications Achieve Significant Results and up to 68% of Peak Performance on 10 Tflop/s IBM SP (3-10-03)
Initial results from NERSC’s 10 teraflop/s IBM SP supercomputer, which became available for general use in early March 2003, show scientific applications running at up to 68% of the system’s theoretical peak speed, compared with the 5–10% of peak performance typical for scientific applications running on massively parallel or cluster architectures. Read More »
NERSC Helps Get the Physics out of KamLAND Data
The Standard Model of Particle Physics, which has successfully explained fundamental physics since the 1970s, predicts that neutrinos have no mass and come in three types or "flavors," electron, muon, and tau. But for the past four years, solar neutrino experiments at the Super-Kamiokande Observatory (Super-K) in Japan and the Sudbury Neutrino Observatory (SNO) in Canada have offered compelling evidence that neutrinos do have nonzero mass and oscillate between the three flavors Read More »
NERSC Helps Climate Scientists Complete First Ever 1,000-Year Run of Nation's Leading Climate Change Modeling Application
Scientists from the National Center for Atmospheric Research (NCAR) have just completed a 1,000-year run of a powerful new climate system model on a supercomputer at the U.S. Department of Energy's National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Accurately predicting global climate change demands complex and comprehensive computer simulation codes, the fastest supercomputers available and the ability to run those simulations long enough to model century after century of the global climate. Read More »
Are the Digits of Pi Random?
David H. Bailey, chief technologist of the Department of Energy's National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, and his colleague Richard Crandall, director of the Center for Advanced Computation at Reed College, Portland, Oregon, have taken a major step toward answering the age-old question of whether the digits of pi and other math constants are "random." Their results are reported in the Summer 2001 issue of Experimental Mathematics. Read More »
A Lucky Catch: The Oldest, Most Distant Type Ia Supernova Confirmed by Supercomputer Analysis at NERSC
An exploding star dubbed SN 1997ff, caught once on purpose and twice by accident by NASA's Hubble Space Telescope, is the oldest and most distant Type Ia supernova ever seen, according to a recent analysis by the Department of Energy's National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Read More »
BOOMERANG Antarctic Balloon Flight Sees a Flat Universe
On April 26, 2000, the international BOOMERANG consortium led by Andrew Lange of the California Institute of Technology and Paolo de Bernardis of Università de Roma, "La Sapienza," announced results of the most detailed measurement yet made of the cosmic microwave background radiation (CMB). Read More »
An Algorithm for the Ages
Among the top 10 "Algorithms of the Century" announced in the January/February, 2000, issue of Computing in Science and Engineering magazine is the integer-relation algorithm dubbed PSLQ, discovered by mathematician and sculptor Helaman Ferguson of Maryland's Center for Computing Sciences, and implemented in practical computer software by David Bailey, chief technologist of the National Energy Research Scientific Computing Center (NERSC) at the Department of Energy's Lawrence Berkeley National… Read More »
Solved at Last: A Fundamental Problem of Quantum Physics
For over half a century, theorists have tried and failed to provide a complete solution to scattering in a quantum system of three charged particles, one of the most fundamental phenomena in atomic physics. Such interactions are everywhere; ionization by electron impact, for example, is responsible for the glow of fluorescent lights and for the ion beams that engrave silicon chips. Read More »
BOOMERanG Analysis Finds Flat Universe
Newly released data from the 1997 North American test flight of BOOMERanG, which mapped anisotropies in the cosmic microwave background radiation (CMB) in a narrow strip of sky, show a pronounced peak in the CMB "power spectrum" at an angular scale of about one degree, strong evidence that the universe is flat. Analyzed at the Department of Energy's National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, the new… Read More »
New Biological Database Seeks Out Products of Alternative Gene Splicing
In its first half year of operation, a new database that identifies clusters of proteins arising from alternative gene splicing has received more than 35,000 requests from researchers in genetics and cell and developmental biology around the world. Read More »
NERSC and the Fate of the Universe
When the National Energy Research Scientific Computing Center (NERSC) moved to Berkeley Lab in 1996, a computational science program was created to encourage collaborations between physical and computer scientists. The Supernova Cosmology Project's work was one of the first projects funded; it demonstrates how high-performance computing can accelerate scientific discovery. Read More »
A Flaw in the Law
Turbulence is a primal force that can be seen all around us, from the scudding of clouds to the frothing of the sea, from the wrinkling of flames to the swirling of leaves. It is especially important to the study of aerodynamics, in which correctly calculating the effects of turbulence can determine whether or not an airplane remains aloft. Since 1938, the standard equation presented in aerodynamics and engineering textbooks for calculating the forces exerted on a solid object by turbulence has… Read More »
Powerful Computers Advance Fusion Research at the Princeton Plasma Physics Laboratory
Scientists at the U.S. Department of Energy's (DOE) Princeton Plasma Physics Laboratory (PPPL) report a major advance in the computer modeling of fusion plasmas in the September 18 edition of Science magazine. The new results were obtained utilizing the massively parallel processing (MPP) capabilities of the DOE's National Energy Research Scientific Computing Center (NERSC) at the Lawrence Berkeley National Laboratory in Berkeley, California. Read More »
Did the Big Bang Come With Strings Attached?
The power of supercomputers at the National Energy Research Scientific Computing Center (NERSC) has enabled Julian Borrill of the Department of Energy’s Lawrence Berkeley National Laboratory to model, in striking detail, a possible state of the universe only a hundred billionth of a trillionth of a trillionth of a second after the Big Bang. Read More »
Quantum Dot Simulations From T3E Make Journal Cover
Results of million-atom Quantum Dot simulations performed on the Cray T3E at NERSC by Alex Zunger's group at the National Renewable Energy Laboratory in Golden, Colo., will appear on the cover of the February issue of the Materials Research Society Bulletin. Read More »
Berkeley Researchers Eliminate One Theory in Mystery of Missing Xenon, but Find New Clues About Element's Behavior
Scientists at Ernest Orlando Lawrence Berkeley National Laboratory and the University of California, Berkeley, looking into the "mystery of the missing xenon" have found strong evidence against one leading theory and, along the way, discovered new information about the behavior of the element. Read More »
Protein Dynamics and Biocatalysis
Investigators: P. A. Bash, Northwestern University Medical School and M. Karplus, Harvard University Research Objectives A guiding principle of molecular biology is that the structure of a biomolecule defines its function. This principle is especially true in the case of the protein molecules known as enzymes, which serve as highly specific and extraordinarily efficient catalysts of biochemical reactions. Despite the growing availability of the atomic structures of enzymes, details of the… Read More »
Theoretical Study on Catalysis by Protein Enzymes and Ribozyme
Principal Investigator: Martin Karplus, Harvard University Research Objectives The goal of this project is to develop a greater understanding of the mechanisms involved in enzyme catalysis and related protein functions. We are studying two types of enzymes: proteins and a nucleic acid (hammerhead ribozyme). Computational Approach For active-site models in the gas phase, ab initio or density functional (DFT) calculations are used. A few calculations with continuum dieletric models are… Read More »
QM/MM Studies of the Triosephosphate Isomerase-Catalyzed Reaction
Triosephosphate isomerase (TIM) is a dimeric enzyme that catalyzes the conversion between dihydroxyacetone phosphate (DHAP) and R-glyceraldehyde 3-phosphate (GAP), which is an important step in glycolysis (the enzymatic breakdown of carbohydrates). TIM increases the reaction rate by more than109 times, and has thus been referred to as a “perfect” enzyme. Many experimental techniques have been used to study the enzyme, supplemented by a number of theoretical calculations, but the complex… Read More »
Theoretical Study on Catalysis by Protein Enzymes, Ribosome, and Molecular Motors
Principal Investigator: Martin Karplus, Harvard University Research Objectives This project's goal is to develop a greater understanding of the mechanisms involved in enzyme catalysis and related protein functions. We are studying the protein enzymes chorismate mutase, flavoxireductase, and aminopeptidase, and a nucleic acid enzyme, the hammerhead ribosome. We are also studying another class of enzymes known as molecular motors, which play important roles in bioenergy transduction and gene… Read More »
