Maya GokhaleLLNL’s Maya Gokhale creates computational sleuthing tools

Computer scientist Maya Gokhale of DOE's Lawrence Livermore National Laboratory enjoys reading mysteries in her leisure time, which is not surprising given her aptitude for computational sleuthing, notably finding the proverbial ‘needle in the haystack,’ the key nugget of information buried in the avalanche of data today’s supercomputers produce.

“Not only is the amount of data being generated growing exponentially,” Gokhale told LLNL’s Science & Technology Review in 2012, “but when the raw data are analyzed, more data — called ‘metadata’ — are generated as well. It’s truly an issue of ‘drowning in data.’”

Recently named a Distinguished Member of Technical Staff by Lab Director Parney Albright, Gokhale leads a group developing data-intensive computing architectures and techniques for addressing the “data overload” problem. This involves the synergy of multiple disciplines including computer science, applied mathematics, and statistics.

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NREL scientists Michael Crowley and Antti-Pekka Hynninen have developed algorithms that speed calculations done by the software tool CHARMM (Chemistry at Harvard Molecular Mechanics) by several orders of magnitude, using code such as the one pictured. Using the new petascale high performance computer housed in NREL's Energy Systems Integration Facility, scientists will be able to simulate the motions of thousands of atoms, leading to greater understanding of how molecular models work. Credit: Dennis SchroederMakeover Puts CHARMM Back in Business

Biofuels scientists are asking more complex questions about how molecules spin, bond, and break when enzymes attack plants — all in the name of quickening the process of turning biomass into fuels for the sake of cleaner air and better energy security.

They're the kinds of questions that require trillions of mathematical operations each second on supercomputers. But, software engineers hadn't been able to keep up with the ever-increasing demands of the scientists and the growing capabilities of modern supercomputers. That is, until unique work at DOE’s National Renewable Energy Laboratory (NREL) supercharged an essential decades-old software program to run on a single high performance computer such as the new petascale computer at NREL's Energy Systems Integration Facility.

Software engineers at NREL have reworked codes and algorithms on the CHARMM (Chemistry at Harvard Molecular Mechanics) program to allow it to simulate molecular motion with millions to billions of steps of computation. It does so by simulating nanoseconds to microseconds of molecular motion, which takes days of computing time.

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See also…

DOE Pulse
  • Number 388  |
  • May 13, 2013
  • New battery design could help solar and wind energy power the grid

    Professor Yi Cui holds a lab demonstration of his group's new lithium-polysulfide flow battery contained in a simple flask. Researchers from DOE's SLAC National Accelerator Laboratory and Stanford University have designed a low-cost, long-life battery that could enable solar and wind energy to become major suppliers to the electrical grid.

    "For solar and wind power to be used in a significant way, we need a battery made of economical materials that are easy to scale and still efficient," said Yi Cui, a Stanford associate professor of materials science and engineering and a member of the Stanford Institute for Materials and Energy Sciences, a SLAC/Stanford joint institute. "We believe our new battery may be the best yet designed to regulate the natural fluctuations of these alternative energies."

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  • Fertilizer that fizzles in a homemade bomb could save lives around the world

    Sandia National Laboratories chemical engineer Vicki Chavez worked with Kevin Fleming to prove that iron sulfate mixed with ammonium nitrate could produce a non-detonable fertilizer. (Photo by Randy Montoya) An engineer at DOE's Sandia National Laboratories who trained U.S. soldiers to avoid improvised explosive devices (IEDs) has developed a fertilizer that helps plants grow but can’t detonate a bomb. It’s an alternative to ammonium nitrate, an agricultural staple that is also the raw ingredient in most of the IEDs in Afghanistan.

    Sandia has decided not to patent or license the formula, but to make it freely available in hopes of saving lives.

    Ammonium nitrate fertilizer is illegal in Afghanistan but legal in neighboring Pakistan, where a quarter of the gross domestic product and half the workforce depend on agriculture. When mixed with a fuel such as diesel, ammonium nitrate is highly explosive. It was used in about 65 percent of the 16,300 homemade bombs in Afghanistan in 2012, according to government reports. There were 9,300 IED events in the country in 2009. 

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  • GrayQbTM: A new tool for contamination mapping

    GrayQbTM device is approximately the size of a soccer ball and can be controlled remotely.Nuclear facilities in the midst of cleanup due to normal routine or unexpected incident face a remarkable challenge – how to safely determine the exact location of radioactive contamination.  Such determinations are typically performed with portable count rate instruments operated by personnel wearing protective gear, which can consume many man-hours and expose personnel to radiation or contamination.  Some areas may be too small or confined or have limited entry for personnel access.  Some areas may be too large, perhaps encompassing a city street, or problematic in another way, such as a fluctuating area of storm water runoff.

    Scientists at DOE's Savannah River National Laboratory have developed an innovative new technology named GrayQbTM.  This device is approximately the size of a soccer ball and can locate, identify, and generate a map of radioactive contamination within an enclosed area or outdoor environment or near water sources such as storm drains.  SRNL Environmental Science and Biotechnology Principal Engineer Dr. Eduardo B. Farfan, and SRNL Applied Computational Engineering and Statistics Senior Engineer J. Rusty Coleman developed this cutting-edge technology.

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  • Combining chromatography, proteomics and database searching identifies hard-to-find heme proteins

    Detection of heme c peptides (red) and all peptides (black) by LC-MS before (top) and after (bottom) HAC. Iron is a critical part of many biological processes; however, it is often not biologically available or it can be toxic in high quantities. So, biological systems have developed intricate methods for its use and storage. Scientists at DOE's Pacific Northwest National Laboratory combined chromatography, proteomics and a database search strategy to find higher numbers of modified iron-containing protein fragments (called peptides) that play an important role in respiration, metal reduction and nitrogen fixation by environmental microbes. The microbes containing these proteins are being studied because of their potential use in microbial fuel cells and electrosynthesis of valuable biomaterials.

    The modifying group of atoms, called heme c, is an important iron-containing post-translational modification found in many proteins. Until recently, it was hard to find. The PNNL scientists combined a heme c protein affinity purification strategy called histidine affinity chromatography (HAC) with enhanced database searching. This combination confidently identified heme c peptides in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments by as much as 100-fold in some cases. They used proteomics capabilities housed at DOE’s EMSL, located at PNNL.

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