Lab Report

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The Lab Report is a weekly compendium of media reports on science and technology achievements at Lawrence Livermore National Laboratory. Though the Laboratory reviews items for overall accuracy, the reporting organizations are responsible for the content in the links below.

Jul. 17, 2015

As part of Lawrence Livermore National Laboratory's Center of Excellence, Sierra will be the next supercomputer to be delivered to the Lab in 2017.

Excelling at supercomputing

IBM will team up with NVIDIA and the Department of Energy to launch two new supercomputer centers of excellence. These efforts primarily revolve around making sure applications can take advantage of supercomputing horsepower and gathering feedback from developers, engineers and scientists.

The centers, housed at Lawrence Livermore National Laboratory and Oak Ridge National Laboratory, will focus on advancing supercomputing and developing code innovation.

Under the partnership, outlined at the International Supercomputing Conference in Frankfurt, Germany, technology from the IBM-led OpenPOWER effort, NVIDIA and Mellanox will be showcased. IBM already has a supercomputing contract with the Department of Energy and is deploying two new supercomputer systems for operation in 2018.

Lawrence Livermore’s Sequoia ranked No. 3 again in the Top500 list of the fastest supercomputers.

Three is the magic number

Lawrence Livermore has retained its No. 3 position in the Top500 list of the fatest supercomputers.

The Tianhe-2 computer, based at the National Super Computer Center in China, has been on the top of the list for more than two years with its maximum achieved performance of 33,863 teraflops per second. The Cray Titan supercomputer, which is at the Oak Ridge National Laboratory, ranked No. 2.

The Top500 list, published twice a year to coincide with supercomputer conferences, is closely watched as an indicator of the status of development and investment in high-performance computing around the world. It also provides insights into what technologies are popular among organizations building these machines.

This simulation depicts a comet hitting the young Earth, generating the amino acids necessary for life. Image courtesy of Matthew Genge/Imperial College London.

Out of this world

According to Lawrence Livermore’s Nir Goldman, life may have come to Earth from outer space onboard icy comets.

Some of those comets contained complex prebiotic materials, such as amino acids and peptides (chains of amino acids), which are some of the most basic building blocks of life.

Goldman’s early research found that the impact of icy comets crashing into Earth billions of years ago could have produced a variety of small prebiotic or life-building compounds. His work using quantum simulations predicted that the simple molecules found in comets (such as water, ammonia, methanol and carbon dioxide) could have supplied the raw materials, and the impact with early Earth would have yielded an abundant supply of energy to drive the synthesis of compounds like protein forming amino acids.

DNA contamination is a large problem when it affects analysis equipment and databases.

Creeping in from the most unlikely places

Here, there and everywhere  — DNA contamination impacts sequence data generation, when DNA from other species finds its way into samples or equipment, and analysis, when DNA sequence data from contamination finds its way into databases.

Bioinformatician Tom Slezak from the Lawrence Livermore National Laboratory noted that even sequencing machines carry their own risks of contamination, as DNA left behind from previous sequencing experiments may persist, “despite however many stringent bleach rinses are employed above and beyond what the manufacturer suggests,” he said.

But the biggest problem in Slezak's view is so‐called "naked DNA": “Once a sample is present in a laboratory, there will be some amount of DNA that wafts around and becomes part of the laboratory environment. Such DNA may eventually contaminate subsequent samples.”

DOE recently funded research to study algae-based biofuels.

Protecting algae

The Department of Energy is providing $18 million for projects to reduce the modeled price of algae-based biofuels to less than $5 per gasoline gallon equivalent (gge) by 2019. This funding supports the development of a bioeconomy that can help create green jobs, spur innovation, improve the environment and achieve national energy security.

Algal biomass can be converted to advanced biofuels that offer promising alternatives to petroleum-based diesel and jet fuels. Additionally, algae can be used to make a range of other valuable bioproducts, such as industrial chemicals, biobased polymers and proteins.

Lawrence Livermore will receive up to $1 million to protect algal crops by developing “probiotic” bacteria to combat pond infestation and increase ecosystem functioning and resilience.