NERSC Science Highlights of 2017
December 25, 2017 by Richard Gerber and Kathy Kincade
As the mission High Performance Computing and Data center for the DOE Office of Science, NERSC provides services and systems that enable its 7,000 users to produce world-class science results that are published in 2,000+ peer-reviewed research papers per year. It would impossible to highlight them all, but here are some of our favorites for 2017 (in no particular order).
Understanding the Function of Biomolecules
cryo-EM for Better Control of Diseases
Former NERSC user and Principal Investigator Joachim Frank shared the 2017 Nobel Prize in Chemistry for the development of software used to reconstruct three-dimensional structure of in situ biological molecules from transmission electron microscopy images. Frank's work continues at NERSC today, prominently by Berkeley Lab's Eva Nogales. In a recent paper in the journal Science ("The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion", J. Tenthorey, et al, Science Nov. 17 2017, Vol. 358, Issue 6365 doi:10.1126/science.aao1140) Nogales and her team used cryo-EM to capture a high-resolution image of a protein ring called an “inflammasome” as it was bound to flagellin, a protein from the whiplike tail used by bacteria to propel themselves forward. This insight holds great promise for developing strategies for protection from diseases. NERSC project PI: Eva Nogales, UC Berkeley.
How Bacteria Adapt to Environmental Stress
Researchers at the University of California San Diego have developed a technique that can accurately predict how E. coli bacteria respond to temperature changes and genetic mutations and then reallocate their resources to stabilize proteins. Writing in the Proceedings of the National Academy of Sciences ("Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation", K. Chen, et al, PNAS, vol. 114 no. 43, 11548–11553, doi: 10.1073/pnas.1705524114) the researchers describe how they ran large-scale simulations at NERSC to gain insight into a systems-level understanding of how cells adapt under environmental stress. The model could aid in designing engineered organisms for biofuel production and patient-specific treatments for bacterial infections. NERSC Project PI: Bernhard Palsson, UC San Diego.
The Era of Gravitational Wave Astronomy Begins
Kilonova GW170817: A Merger of Two Neutron Stars Produces Heavy Elements
With the first detection of gravitational waves in 2015, a new era of astronomy was born – one which was recognized by the 2017 Nobel Prize in Physics. On August 17 of this year (2017), gravitational waves with a distinct signature were recorded from a source known as GW170817. Quickly afterward it was also detected in gamma rays by the Fermi satellite and followup observations were able to pinpoint the source in the optical and infrared wavelengths. In a pair of papers in the journal Nature, NERSC PI Daniel Kasen of UC Berkeley and his team showed that detailed simulations of neutron star mergers led to a "kilonova" that were consistent with observations of GW170817. The team also showed that such events are able to synthesize heavy elements that exist in the universe today but were not produced in the big bang. ("Origin of the heavy elements in binary neutron-star mergers from a gravitational-wave event," Kasen et al, Nature, 551:80+; Nov. 2 2017, 10.1038/nature24453; "Optical emission from a kilonova following a gravitational-wave-detected neutron-star merger," Arcavi et al., Nature, 551:64+; Nov. 2 2017, 10.1038/nature24291) NERSC PI: Daniel Kasen, UC Berkeley and Berkeley Lab
Determining the Signature of a Neutron Star Merger with a Black Hole
A team of scientists from UC Berkeley and Berkeley Lab, led by Francois Foucart and Daniel Kasen, used NERSC supercomputers to make detailed simulations of a merger between a black hole and a neutron star. As in the case of a merger of two neutron stars (see above) a black hole-neutron star collision produces a kilonova, but with its own distinctive signature. The simulations done at NERSC showed how heavy elements are formed in a tidal tail and disk. The results will be important for identifying such a merger when seen by gravitational wave detectors. The results appear in the journal Classical and Quantum Gravity ("Dynamics, nucleosynthesis, and kilonova signature of black hole-neutron star merger ejecta," Fernandez et al., Classical and Quantum Gravity, 34 Aug. 3 2017, 10.1088/1361-6382/aa7a77) NERSC PI: Francois Foucart, UC Berkeley and Berkeley Lab.
The New Energy Economy
Energy runs our lives. We depend on it for lighting and heating our buildings, cooking our food, transportation, powering technology and industry. As the energy sources and production methods of the 19th and 20th century decline, the new energy economy is being driven by efficient and sustainable energy technologies like those being developed by thousands of scientists using NERSC today.
Converting Carbon Dioxide into Methanol
Carbon Dioxide and Hydrogen can react to produce methanol, which is used as a fuel, antifreeze, solvent, and for producing biodiesel. But the reaction will not take place on its own; catalysts made from copper (Cu) and zinc oxide (ZnO) on alumina supports are often used to drive the conversion, but the process and sites of the reaction were not understood. A team of Brookhaven scientists combined experiment and calculations performed at NERSC to show how the process proceeds in detail, an important step to improving the manufacturing process. The results are reported in the journal Science ("Active sites for CO2 hydrogenation to methanol on Cu/ZnO catalysts," S. Kattel, et al, Science, 2017; 355 (6331): 1296 doi:10.1126/science.aal3573). NERSC PI: Ping Liu, Brookhaven National Laboratory.
Producing Fuel with Power Supplied by the Sun
Scientists have been trying to develop low-cost, efficient materials, known as photoanodes, that can act as a solar-powered catalyst to transform water into a hydrogen fuel. But there are a limited number of materials with the necessary properties and they have limited efficiency and/or high cost. By combining ab initio calculations run at NERSC with experiments, researchers from Caltech and Berkeley Lab used data produced by the Materials Project hosted at NERSC to identify 12 new promising materials for photoanodes, nearly doubling the number of viable candidates. This study promises to greatly accelerate the discovery and production of commercially viable materials, a process that otherwise can take more than a decade. The results appears in the Proceedings of the National Academy of Sciences ("Solar fuels photoanode materials discovery by integrating high-throughput theory and experiment"; PNAS, 114:3040-3043; Mar. 21 2017, 10.1073/pnas.1619940114) NERSC PI: Jeffrey Neaton, UC Berkeley and Berkeley Lab.
Cheap and Efficient Catalysts for Electrically Converting Water into Hydrogen and Oxygen
Scientists at Rice and the University of Houston have developed a new catalyst—an electrolytic film comprising nickel, graphene and a compound of iron, manganese and phosphorus—that can split water into hydrogen and oxygen to produce clean energy. Exiting catalysts are often made of expensive materials like platinum and palladium; cheaper and more efficient catalysts are key to the commercial production of clean energy. Writing in the journal Nano Energy, the researchers describe running a series of density functional theory calculations at NERSC to identify the atomic structure of active catalytic sites and how to control the catalytic material for better selectivity. ("Bifunctional metal phosphide FeMnP films from single source metal organic chemical vapor deposition for efficient overall water splitting"; Nano Energy, 39:444-453; SEP 2017, 10.1016/j.nanoen.2017.07.027). NERSC PI: Lars Grabow, University of Houston.
Avoiding Defects in Solar Cell Nanomaterials
Heterogeneous nanostructured materials are used in various optoelectronic devices, including solar cells. But the interfaces contain structural defects that can affect device performance. Using calculations run at NERSC, researchers from Argonne National Lab and the University of Chicago found the root cause of the defects in two materials and provided design rules to avoid them. In an article in the journal Nano Letters the team used computations performed at NERSC to identify certain atomic “trap states.” They then used the model to predict a new material that does not have these trap states and should perform better in solar cells. ("Design of Heterogeneous Chalcogenide Nanostructures with Pressure-Tunable Gaps and without Electronic Trap States"; Giberti et al., Nano Letters, 17:2547-2553; April 2017, 10.1021/acs.nanolett.7b00283) NERSC PI: Martin Voros, Argonne National Laboratory.
Earth Systems Science
Few natural phenomena effect our lives more directly than the day-to-day weather and the longer term climate phenomena.
More Dust, Better Air Quality
Researchers from Pacific Northwest National Lab, Scripps Institution of Oceanography and UC San Diego used simulations performed at NERSC to arrive at the surprising conclusion that when less dust blows in over eastern China, air pollution gets worse. Writing in the journal Nature Communications the team showed that dust plays an important role in controlling air temperature differences and thereby promoting winds to blow away man-made pollution. Less dust means air stagnates, with pollution becoming more concentrated and sticking around longer. The results match observational data from dozen of sites in eastern China. The team found that two to three days after winds had brought dust into the region from western China, the air was cleaner than before the dust arrived. ( "Dust-wind interactions can intensify aerosol pollution over eastern China," Yang et al., Nature Communications, 8 May 11 2017, 10.1038/ncomms15333) NERSC PI: Steven Ghan, Pacific Northwest National Laboratory.
Hindcasting Extreme Weather Events
Researchers have been able to “hindcast” the conditions that led to the Sept. 9-16, 2013 flooding around Boulder, CO and found that climate change made the storm much more severe. By running simulations using various climate scenarios, researchers wrote in the journal Weather and Climate Extremes ("Diagnosing conditional anthropogenic contributions to heavy Colorado rainfall in September 2013"; Pall et al., Weather and Climate Extremes, 17:1-6; 2017, https://doi.org/10.1016/j.wace.2017.03.004) that the storm was more severe in today’s climate than it would have been in one without climate change. Even today’s largest supercomputers couldn’t resolve critical features features of the storm using global climate models so researchers used the “WRF” regional model to “hindcast” conditions that led to the flooding, allowing them to study the problem in greater detail, breaking the area into 12-km squares. They used NERSC supercomputers to run 101 hindcasts. NERSC PI: Michael Wehner, Berkeley Lab.
Fundamental Interactions of Particles and Fields
New Analysis Shows that the Earth Absorbs Ghostly Neutrinos
The IceCube Collaboration researchers showed for the first time that high-energy neutrinos are absorbed by Earth as predicted by the Standard Model of particle physics. Neutrinos interact rarely with normal matter, but the Earth is large enough to stop some of them, and IceCube was able to measure that effect, as reported in the journal Nature. The results not only support the Standard Model, but are inconsistent with some more speculative theories. A detailed understanding of how high-energy neutrinos interact with Earth’s matter will also allow researchers to probe the composition of Earth’s core and mantel. The analysis was run at NERSC using historical Ice Cube data repository hosted by NERSC. ("Measurement of the multi-TeV neutrino interaction cross-section with IceCube using Earth absorption"; Nature, 551:596+; Nov. 30, 2017, 10.1038/nature24459) NERSC PI: T. Palczewski, Berkeley Lab.
First Complex Calculations of the Sigma Particle
An international team of researchers, representing the Hadron Spectrum Collaboration, achieved the first complex calculations of a subatomic particle called the Sigma. After decades of catching only brief glimpses of the Sigma’s existence from experimental data that showed its effects on other subatomic particles, this calculation gives scientists a new way to study the sigma and gain new insights about the “strong force” that exists inside all matter. This study is part of a larger effort to investigate quantum chromodynamics (QCD), the fundamental theory of strong interactions. Understanding QCD is important to gain a deeper understanding of the fundamental laws of physics. Calculations were carried out at NERSC, Oak Ridge National Lab, and the University of Illinois at Urbana-Champaign. Results were published in the journal Physical Review Letters. ("Isoscalar pi pi Scattering and the sigma Meson Resonance from QCD"; Briceno et al., Physical Review Letters, 118 Jan. 9, 2017, 10.1103/PhysRevLett.118.022002) NERSC PI: Robert Edwards, Thomas Jefferson National Accelerator Laboratory.
Technology and Computer Science
The World's Smallest Diamond Nanowires
Scientists at Stanford University and SLAC have discovered a way to use diamondoids – the smallest bits of diamond – to assemble atoms into the thinnest possible electrical wires, just 3 atoms wide. By grabbing various types of atoms and putting them together LEGO-style, the new technique could potentially be used to build tiny wires for a wide range of applications, including fabrics that generate electricity, optoelectronic devices that employ both electricity and light, and superconducting materials that conduct electricity without any loss. Using supercomputers at NERSC, the research team modeled and predicted the electronic properties of the nanowires, which were examined with X-rays at SLAC’s Stanford Synchrotron Radiation Light Source to determine their structure and other characteristics. The results are reported in the journal Nature Materials ("Hybrid metal-organic chalcogenide nanowires with electrically conductive inorganic core through diamondoid-directed assembly"; Yan et al, Nature Materials, 16:349+; Mar. 2017, 10.1038/NMAT4823). NERSC PI: Thomas Devereaux, Stanford University.
A Better Way to Grow Graphene for Electronic Devices
Researchers from Oak Ridge National Laboratory found a new way to grow narrow ribbons of graphene, a lightweight and strong structure of single-atom-thick carbon atoms linked into hexagons, that may address a shortcoming that has prevented the material from achieving its full potential in electronic applications. Through experiments and first-principle quantum simulations done at NERSC and Oak Ridge National Lab, the researchers established how the bottom-up synthesis of a graphene nanoribbon can be controlled by charge injections from a scanning tunneling microscopy tip. At selected sites, this new technique can create interfaces between materials with different electronic properties. Such interfaces are the basis of many semiconductor electronic devices, including integrated circuits, transistors, LEDs and solar cells. The results are published in the journal Nature Communications. ("Controllable conversion of quasi-freestanding polymer chains to graphene nanoribbons"; Ma et al., Nature Communications, 8 Mar. 13 2017, 10.1038/ncomms14815) NERSC PI: Paul Kent, Oak Ridge National Laboratory.
Improved Memristors for Future Memory Devices
In a recent Nature Materials article researchers describe a new robust “memristor” device and theoretical insights into why it has the size, stability, reproducibility, and endurance to supplant flash memory technologies in future generations of digital devices. The team performed calculations at NERSC to gain an understanding of why their device, based on a spin-coated active layer of a transition metal complex, performs so well. The insight may accelerate the deployment of organic resistive memory devices and the findings have wider applicability for other semiconductor materials, particularly those used in neuromorphic and logic circuits. ("Robust resistive memory devices using solution-processable metal-coordinated azo aromatics"; Nature Materials, 16:1216+; Dec. 2017, doi: 10.1038/NMAT5009) NERSC PI: Victor Batista, Yale University.
A Record Quantum Qubit Simulation
Researchers from the Swiss Federal Institute of Technology (ETH Zurich) used NERSC’s 30-petaflop supercomputer, Cori, to successfully simulate a 45-qubit (quantum bit) quantum circuit, the largest simulation of a quantum computer achieved to date. The simulation used 8,192 of Cori's Intel Xeon Phi nodes (557,056 compute cores). The current consensus is that a quantum computer capable of handling 49 qubits will offer the computing power of the most powerful supercomputers in the world. This new simulation is an important step in achieving “quantum supremacy”— the point at which quantum computers finally become more powerful than ordinary computers. ("0.5 Petabyte Simulation of a 45-Qubit Quantum Circuit," Thomas Häner, Damian S. Steiger, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. SC 2017. Article No. 33, doi: 10.1145/3126908.3126947) NERSC PI: Thomas Haner, ETH Zurich.
Fusion Energy Sciences
Shedding Light on Mysterious Plasma Flows in Fusion Reactors
Researchers at Princeton Plasma Physics Laboratory and General Atomics used NERSC supercomputers to simulate a mysterious self-organized flow of the superhot plasma that drives fusion reactions. The findings show that pumping more heat into the core of the plasma can drive instabilities that create plasma rotation inside the doughnut-shaped tokamak reactor. The findings could lead to improved control of fusion reactions in ITER, the international experiment under construction in France to demonstrate the feasibility of fusion power, and other fusion devices. The findings were published in Physical Review Letters. ("Main-Ion Intrinsic Toroidal Rotation Profile Driven by Residual Stress Torque from Ion Temperature Gradient Turbulence in the DIII-D Tokamak"; Grierson et al., Physical Review Letters, 118 Jan. 6, 2017 10.1103/PhysRevLett.118.015002)
Predicting Electron Energy Transport in Tokamaks
Multiscale fusion plasma simulations run at NERSC provide the first evidence that electron transport in tokamak plasmas such as those in ITER likely has a strong multiscale nature. Accurately understanding electron transport in a fusion reactor is critical for predicting performance in future reactors like ITER. This study provides significant new evidence that electron energy transport in burning plasmas occurs over many scales and illustrates that simulations are vital for identifying phenomena in future reactors. ("Gyrokinetic predictions of multiscale transport in a DIII-D ITER baseline discharge"; Nuclear Fusion, 57 JUN 2017, 10.1088/1741-4326/aa6c16) NERSC PI: Christopher Holland UC San Diego.