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Primeur weekly 2017-05-15

Special

NVIDIA ushers in new era of robotics, with breakthroughs making It easier to build and train intelligent machines ...

NVIDIA and Toyota collaborate to accelerate market introduction of autonomous cars ...

NVIDIA launches GPU Cloud platform to simplify AI development ...

NVIDIA advances AI computing revolution with new Volta-based DGX systems ...

NVIDIA launches revolutionary Volta GPU platform, fueling next era of AI and high performance computing ...

NVIDIA to train 100,000 developers on deep learning in 2017 ...

NVIDIA paves path to AI cities with Metropolis Edge-to-Cloud platform for video analytics ...

NVIDIA Tesla accelerators on IBM Cloud demonstrate advanced performance for training deep learning models ...

BSC and NVIDIA a step forward to the interactive simulation of humans ...

Quantum computing

Refrigerator for quantum computers discovered ...

Focus on Europe

EoCoE service page open for PRACE user community ...

Spring 2017 edition of the e-IRG newsletter available ...

PRACE to issue Annual Report 2016 ...

Middleware

Bright Computing announces 8.0 release - Setting new standard for automation and ease-of-use for Linux-based clusters and public, private and hybrid Clouds ...

CETIAT France chooses Bright Cluster Manager for aerodynamics and fluid mechanics HPC environment ...

2016 National Research Infrastructure Roadmap for Australia is now available ...

Hardware

Cray delivers production-ready AI with new Cray CS-Storm accelerated cluster supercomputers ...

Inspur to unveil 2U 8-GPU AI supercomputer at GTC 2017 ...

Inspur unveiled AIStation, AI deep learning training cluster management software at GTC 2017 ...

Supermicro systems deliver 170 Tflop/s FP16 of peak performance for artificial intelligence, and deep learning at GTC 2017 ...

NCSA's Blue Waters project provides $1.08 billion direct return to Illinois' economy ...

Applications

SDSC's Comet helps replicate brain circuitry to direct a realistic prosthetic arm ...

University of Wyoming graduate student one of 36 selected for CyberGIS Summer School ...

Supercomputing mimics berkelium experiments to validate new find ...

'Inverse designing' spontaneously self-assembling materials ...

Story of silver birch from genomic Big Data ...

Targeted, high-energy cancer treatments get a supercomputing boost ...

Computer accurately identifies and delineates breast cancers on digital tissue slides ...

Sound over silicon: Computing's wave of the future ...

USC Viterbi School of Engineering faculty awarded multiple MURI grants ...

New funding announced for Digital Earth Australia ...

NCSA releases annual report highlighting scientific exploration and breakthroughs enabled by the Blue Waters Project ...

Supercomputer can disprove the theory of sunspot formation ...

The Cloud

Inspur to release InCloud OS 5.0 "F.A.S.T" at the 2017 OpenStack Summit ...

IBM extends data science collaborative workspace to the private Cloud ...

Pointwise and Envenio Join Forces on Demand ...

Supercomputing mimics berkelium experiments to validate new find

The structure of berkelium in oxidation state +IV is pictured here. First observed in experiment, the Titan supercomputer at the Oak Ridge Leadership Computing Facility has enabled scientists to explore this unexpected oxidation state in the rare, radioactive element. Image credit: Bert de Jong, Lawrence Berkeley National Laboratory.9 May 2017 Oak Ridge - The Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) has enabled scientists to explore an unexpected oxidation state in the rare, radioactive element berkelium that was first observed in experiment. The OLCF is a U.S. Department of Energy (DOE) Office of Science User Facility.

An atom's oxidation state is characterized by the number of electrons it exchanges to form a compound and provides information on how an element interacts with the surrounding environment. Published in April inNature Chemistry, the study is helping to fill in gaps in the fundamental understanding of berkelium and could have future applications for low-toxicity separation in nuclear waste management.

Scientists from Lawrence Berkeley National Laboratory acquired a minute sample of the most common berkelium isotope, Bk-249, from DOE's Oak Ridge National Laboratory (ORNL) through the DOE Isotope Programme. Incidentally, the element and Berkeley Lab are namesakes of Berkeley, California where the element was discovered in 1949.

At ORNL, radioactive isotopes for research, including Bk-249, are produced and purified with support from the DOE Isotope Program, which recently contributed to a separate and highly publicized study - the discovery of element 117. The new element was officially named "Tennessine" thanks, in part, to ORNL's role in synthesizing the berkelium required for its creation.

Although berkelium was first synthesized over 60 years ago, its isotope is produced in such small amounts and remains stable for such a short time - less than a year - that its fundamental structure and properties are rarely studied. Producing Bk-249 is also a lengthy undertaking that includes many precise steps and the expertise of an entire staff of scientists and engineers, said Julie Ezold of ORNL's Nuclear Materials Processing Group.

However, scientists do know many properties of berkelium. With an atomic number of 97, it occurs in a class of elements known as the actinides, which are metallic, radioactive elements with atomic numbers between 89 and 103. Uranium and plutonium are also actinides, yet most of their respective isotopes have much longer half-lives than Bk-249 and emit high-energy alpha particles, whereas Bk-249 emits lower energy beta particles. Researchers at Berkeley Lab are using high-powered X-ray crystallography and mass spectrometry to study the chemical structure of Bk-249 and how it may interact with the environment.

"We've been investigating the spectroscopic properties of the heavier actinides to gain a more fundamental understanding of these elements, which have applications in the nuclear fuel cycle and waste management", stated Rebecca Abergel, research scientist and principal investigator at Berkeley Lab and a 2014 winner of a DOE Office of Science Early Career Research Programme award.

Rebecca Abergel's team of actinide chemists, including Gauthier Deblonde, worked closely with protein crystallographers from Roland Strong’s laboratory at the Fred Hutchinson Cancer Research Center.

In the course of their experimental work, Rebecca Abergel's team noticed something strange. Previous research has shown all trans-plutonium actinides - those with atomic numbers greater than plutonium, or 94 - to stabilize in a +III oxidation state - a property that describes how the element makes chemical bonds. To explore its chemical boundaries, scientists have tried to push berkelium into the +IV oxidation state using highly acidic chemicals, but the effect, though possible, is fleeting.

In this study, Rebecca Abergel's team bound the Bk-249 to a synthesized organic ligand, which is a molecule that binds to a central metal ion - in this case Bk-249 - to form a compound. The team has previously used this ligand on actinides for its ability to bind with that class of elements. By capturing the structure of the Bk-249 while bound to the ligand, researchers expected to learn more about berkelium's structural and chemical properties, including its +III oxidation state.

"We use natural molecules, or ligands, made from bacteria to bind to actinides. A couple of those molecules are bound by proteins, so you end up with a system including a protein, ligand, and metal - the actinide - bound together", Rebecca Abergel stated. "In this case, the protein did not bind to the metal-ligand complex, indicating a +IV oxidation state."

Unlike acidic chemicals, an organic ligand could offer a more natural and easier alternative for waste management applications.

To help shed more light on the interesting experimental results, Rebecca Abergel's team turned to computational scientist Wibe (Bert) de Jong, Computational Chemistry, Materials and Climate group leader at Berkeley Lab. As part of a large-scale Innovative and Novel Computational Impact on Theory and Experiment project focused on fundamental actinide chemistry led by David Dixon at the University of Alabama, de Jong used the 27-petaflop Titan system at the OLCF to simulate Bk-249 binding to the ligand then generated corresponding spectroscopy data.

"Actinide chemistry is a difficult field in general with very little experimental data available", Bert de Jong stated. "Computing is helping a lot by verifying experimental results, informing the design of new experiments, or serving as a replacement for experiments so researchers don't have to deal with the radioactivity."

Simulations on Titan and the OLCF's 736-node Cray XC30 Eos included about 100 atoms, capturing how Bk-249 binds to the ligand in both +III and +IV oxidation states. The computational study used NWChem, a scalable computational chemistry code that can run efficiently on thousands of computer processors. To compute the large number of excited states present in molecular systems like the metal and ligand compound in this study, the team relied on significant advances in NWChem that were developed as part of a Scientific Discovery through Advanced Computing (SciDAC) project led by Chris Cramer at the University of Minnesota, for which Bert de Jong is a co-principal investigator.

"After we did the calculations, we generated spectra that we could directly compare to those generated by Abergel’s experiments", Bert de Jong stated.

By translating the computational data into what it would look like as experimental data, researchers were able to confirm that they had indeed observed a +IV oxidation state in experiment.

"The ligand actually allows the berkelium to oxidize from +III to +IV, so this tells us a lot about how environments can change the physics and chemistry of actinide elements", Bert de Jong stated.

Researchers are planning to use more computational modeling and simulations in extensions of this study.

"We've been extending it to the whole series of actinides to understand the systemic trend for bonding in this series", Rebecca Abergel stated. "We're just at the beginning of this, but it means we're getting a better understanding of how chemistry affects how the element interacts with the environment."

Gauthier J.P. Deblonde, Manuel Sturzbecher-Hoehne, Peter B. Rupert, Dahlia D. An, Marie-Claire Illy, Corie Y. Ralston, Jiri Brabec, Wibe A. de Jong, Roland K. Strong, and Rebecca J. Abergel are the authors of the paper titled " Chelation and Stabilization of berkelium in oxidation state +IV ". The paper appeared inNature Chemistryonline on April 10, 2017 - doi:10.1038/nchem.2759.

The work received support from DOE's Office of Science and the National Institutes of Health.

Source: Oak Ridge Leadership Computing Facility - OLCF

Back to Table of contents

Primeur weekly 2017-05-15

Special

NVIDIA ushers in new era of robotics, with breakthroughs making It easier to build and train intelligent machines ...

NVIDIA and Toyota collaborate to accelerate market introduction of autonomous cars ...

NVIDIA launches GPU Cloud platform to simplify AI development ...

NVIDIA advances AI computing revolution with new Volta-based DGX systems ...

NVIDIA launches revolutionary Volta GPU platform, fueling next era of AI and high performance computing ...

NVIDIA to train 100,000 developers on deep learning in 2017 ...

NVIDIA paves path to AI cities with Metropolis Edge-to-Cloud platform for video analytics ...

NVIDIA Tesla accelerators on IBM Cloud demonstrate advanced performance for training deep learning models ...

BSC and NVIDIA a step forward to the interactive simulation of humans ...

Quantum computing

Refrigerator for quantum computers discovered ...

Focus on Europe

EoCoE service page open for PRACE user community ...

Spring 2017 edition of the e-IRG newsletter available ...

PRACE to issue Annual Report 2016 ...

Middleware

Bright Computing announces 8.0 release - Setting new standard for automation and ease-of-use for Linux-based clusters and public, private and hybrid Clouds ...

CETIAT France chooses Bright Cluster Manager for aerodynamics and fluid mechanics HPC environment ...

2016 National Research Infrastructure Roadmap for Australia is now available ...

Hardware

Cray delivers production-ready AI with new Cray CS-Storm accelerated cluster supercomputers ...

Inspur to unveil 2U 8-GPU AI supercomputer at GTC 2017 ...

Inspur unveiled AIStation, AI deep learning training cluster management software at GTC 2017 ...

Supermicro systems deliver 170 Tflop/s FP16 of peak performance for artificial intelligence, and deep learning at GTC 2017 ...

NCSA's Blue Waters project provides $1.08 billion direct return to Illinois' economy ...

Applications

SDSC's Comet helps replicate brain circuitry to direct a realistic prosthetic arm ...

University of Wyoming graduate student one of 36 selected for CyberGIS Summer School ...

Supercomputing mimics berkelium experiments to validate new find ...

'Inverse designing' spontaneously self-assembling materials ...

Story of silver birch from genomic Big Data ...

Targeted, high-energy cancer treatments get a supercomputing boost ...

Computer accurately identifies and delineates breast cancers on digital tissue slides ...

Sound over silicon: Computing's wave of the future ...

USC Viterbi School of Engineering faculty awarded multiple MURI grants ...

New funding announced for Digital Earth Australia ...

NCSA releases annual report highlighting scientific exploration and breakthroughs enabled by the Blue Waters Project ...

Supercomputer can disprove the theory of sunspot formation ...

The Cloud

Inspur to release InCloud OS 5.0 "F.A.S.T" at the 2017 OpenStack Summit ...

IBM extends data science collaborative workspace to the private Cloud ...

Pointwise and Envenio Join Forces on Demand ...