From Lawrence Berkeley National Lab: “Mineral Discovery Made Easier: X-Ray Technique Shines a New Light on Tiny, Rare Crystals”

From Lawrence Berkeley National Lab

June 19, 2019

Glenn Roberts Jr.
geroberts@lbl.gov
(510) 486-5582

Berkeley Lab scientists participate in the discovery of ognitite; other candidate new-mineral studies in progress.

Nobumichi Tamura, a staff scientist at Berkeley Lab’s Advanced Light Source (ALS), studies a rare crystal sample at ALS Beamline 12.3.2. An X-ray technique at this beamline was key in a study that helped to confirm the discovery of the mineral ognitite. (Credit: Marilyn Chung/Berkeley Lab)

LBNL ALS

Like a tiny needle in a sprawling hayfield, a single crystal grain measuring just tens of millionths of a meter – found in a borehole sample drilled in Central Siberia – had an unexpected chemical makeup.

And a specialized X-ray technique in use at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) confirmed the sample’s uniqueness and paved the way for its formal recognition as a newly discovered mineral: ognitite.

Based on this success with the technique at Berkeley Lab’s Advanced Light Source (ALS), the research team is employing it to study other tiny samples of promising candidates for new mineral discoveries. The ALS is a synchrotron that produces X-rays and other types of light for dozens of simultaneous experiments.

“The difficulty is that these minerals can be extremely rare and are only available in very small amounts,” said Nobumichi Tamura, a staff scientist at the ALS who helped to customize the experimental technique – known as X-ray Laue microdiffraction (and also micro-Laue X-ray diffraction) – to study tiny crystal samples including minerals. Tamura participated in the ognitite discovery and is now working with the same team to explore other samples.

Taking on the ‘desperate cases’

The ognitite mineral’s structure and other properties are detailed in a study published in May in Mineralogical Magazine and also documented in the European Journal of Mineralogy. The study also describes a new, cobalt-rich mineral variety – described as “cobaltian maucherite” – that Tamura explored using the same technique at the ALS.

“We are looking at cases where no conventional techniques can work,” Tamura said. “These are the desperate cases.”

He added, “I had been interested for years in developing this technique specifically to identify new minerals, because occasionally there are researchers who have an unknown material that they cannot resolve using any of the more conventional techniques.” In the cases of ognitite and the cobaltian maucherite, there are only individual samples of each that have been identified, to date.

This image shows a diffraction pattern for the ognitite sample studied at Berkeley Lab’s Advanced Light Source. The pattern was obtained using a technique known as X-ray Laue microdiffraction. (Image courtesy of Nobumichi Tamura/Berkeley Lab)

The form of X-ray Laue microdiffraction employed at the ALS uses a narrowly focused X-ray beam that spans a range of energies to explore the atomic structure of materials in exquisite detail. The beam is focused to about a hundredth the diameter of a human hair.

Conventional single-crystal X-ray diffraction typically rotates crystal samples in an X-ray beam at a specific energy to help resolve their atomic structure, Tamura noted.

When crystal samples are so precious and small that researchers cannot easily extract them from surrounding materials without damaging the crystals, techniques including electron diffraction, single-crystal X-ray diffraction, and powder X-ray diffraction are typically out of the question.

The ALS technique, meanwhile, scans across the entire sample without the need to rotate the crystal, separate it from its surroundings, or prepare it any other way for study.

The entire scan is completed within a few minutes, though the data analysis for this technique is far more complex than for conventional diffraction and requires substantial computing power. Researchers use computer clusters at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC) and Laboratory Research Computing to process the data from the Laue microdiffraction experiments.

NERSC

NERSC Cray Cori II supercomputer at NERSC at LBNL, named after Gerty Cori, the first American woman to win a Nobel Prize in science

NERSC Hopper Cray XE6 supercomputer

LBL NERSC Cray XC30 Edison supercomputer

The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

NERSC PDSF

PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

Future:

Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supeercomputer

NERSC is a DOE Office of Science User Facility.

Catherine Dejoie, now a beamline scientist at the European Synchrotron Radiation Facility (ESRF), was hired as an ALS postdoctoral researcher in 2009 specifically to develop a method for analyzing the data from the Laue microdiffraction technique to resolve the atomic structure of materials. She worked in close collaboration with Tamura.

Chemical clues in tiny sample

Andrei Barkov, director of the Research Laboratory of Industrial and Ore Mineralogy at Cherepovets State University in Russia, led the international team credited with the ognitite discovery and was the lead author of the ognitite study.

Elise Grenot, a student researcher from ENSTA, an engineering school in France, prepares a mineral sample for study using X-rays at Berkeley Lab’s Advanced Light Source. Nobumichi Tamura, an ALS staff scientist who participated in a study that helped to confirm ognitite as a new mineral, is pictured at right. (Credit: Marilyn Chung/Berkeley Lab)

That team included Tamura and Camelia Stan – Stan was a researcher at the ALS who participated in the ognitite study but has since left Berkeley Lab. Elise Grenot, a student researcher from France’s École Nationale Supérieure de Techniques Avancées (ENSTA), an engineering school, is now assisting Tamura with the latest round of candidate new-mineral experiments at the ALS.

Barkov learned about the technique developed at Berkeley Lab through his connection to Björn Winkler, a professor at Goethe University Frankfurt in Germany who was familiar with the ALS technique.

Barkov had already participated in several other successful mineral discoveries, including studies that led to the formal recognition of tatyanaite, edgarite, laflammeite, and menshikovite as new minerals. But the sample now known as ognitite was challenging to confirm as a new mineral although its chemistry appeared to be unique, Barkov noted.

“This mineral was suspected to be potentially new on the basis of its composition, which is unusually enriched in bismuth,” he said. “We could find just a single specimen, as a tiny grain. The grain is so small – that’s why the micro-Laue contributions from Nobu Tamura were so important.”

It took two attempts, including a follow-up round of experiments at the ALS for the second effort, to receive recognition of ognitite as a unique mineral from the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (IMA). The IMA reported 5,413 recognized minerals as of November 2018, and the list typically grows by 30 or more minerals each year after review and approval by the commission.

Ognitite contains nickel, bismuth, and tellurium. The study notes that its crystal structure is similar to a mineral called melonite, which is also composed of nickel and tellurium but is not associated with a high concentration of bismuth. And ognitite is chemically similar to the mineral tellurohauchecornite, which is composed of nickel, bismuth, tellurium, and sulfur.

New mineral is named for Ognit mineral complex in Siberia

Barkov said the ognitite discovery team’s first choice was to name it “baikalite” after Lake Baikal, which is in the region where the new mineral was discovered, but this name was not approved by the IMA. The commission instead favored “ognitite” as the mineral find was sourced from a place known as the Ognit ultramafic complex in Siberia’s Sayan Mountains region.

This geological formation is known to be rich in metal deposits, including rare platinum-group elements, nickel, and chromium.

The cobaltian maucherite sample was recovered from nickel-rich arsenides in the same Ognit complex, Barkov said, and measured just 20 millionths of a meter across. Because of its size and rarity, “it could only be characterized structurally” using the micro-Laue technique, he said.

These diagrams show the atomic crystal structure of ognitite. At left, atoms in the crystalline structure are represented in red (nickel), white (tellurium), and gray (bismuth). At right, a polyhedral representation of the crystal structure. (Credit: Mineralogical Magazine, May 8, 2019, DOI: 10.1180/mgm.2019.31)

His team is exploring this type of formation in other parts of Russia, and the rock formations of particular interest can vary in size from about a kilometer to tens of kilometers, he said.

“We collect and examine, in detail, thousands of rock specimens and ore samples, and many more mineral grains,” he said. “As a result of these efforts, single grains of potentially new minerals may be found.”

His team typically uses optical microscopes, scanning electron microscopes, a technique known as energy-dispersive X-ray spectroscopy, wavelength-dispersive spectroscopy, and conventional X-ray diffraction to study mineral samples that have been collected over a span of decades.

From Russia to the ALS

Barkov contacted Björn Winkler to find out if he could create a synthetic form of ognitite, and also to synthesize other mineral samples.

“Professor Winkler has a solid background and proper facilities at his lab to synthesize new compounds that are analogous to potentially new minerals,” Barkov said. Winkler had already established a collaboration with Tamura, and Barkov then reached out to Tamura about the possibility of studying the ognitite sample at the ALS.

Dejoie, who helped to develop the data analysis methods to support the use of the ALS technique for studying the structure of tiny crystals, has returned to the ALS nearly every year to conduct experiments using this technique, and to improve upon the data-analysis methods. She said that in her own research she is now using the technique for time-resolved experiments that track how materials transition from one state of matter to another.

While X-ray Laue microdiffraction is not unique among the synchrotron light sources of the world, Dejoie and Tamura noted that its specialized application at the ALS and the maturity of its data-analysis methods are unique.

“We started to look at really small crystals – crystals that you cannot look at with a classic setup,” Dejoie recalled.

Growing interest

She noted that the technique can be used to resolve the timing of processes such as chemical reactions and structural changes in materials.

The Laue microdiffraction technique that she worked on at the ALS “is a really interesting alternative to electron diffraction,” Dejoie said, or at least a complementary tool for studying crystal structure, as it can quickly gather an entire high-precision data set.

She noted that an adaptation of Laue microdiffraction could also be useful for crystal studies at light sources known as X-ray free-electron lasers (XFELs), which have ultrashort, bright pulses.

“It’s funny to see the parallel – we were already using a similar kind of approach” to characterize the structure of crystals in a single pass, and without the need to rotate them or orient them in a particular way, before this was tried in XFEL studies.

In an XFEL technique known as “serial crystallography,” many crystal samples are streamed into the path of narrow-energy X-ray pulses. In these experiments, information is gathered from individual X-ray pulses striking randomly oriented crystals of the same sample type to develop a comprehensive 3D atomic structure.

Dejoie served as the lead author of a 2015 study detailing how the Laue diffraction technique of using a broad-energy X-pulse to strike single or multiple randomly oriented crystals simultaneously could be adapted for use at XFELs as a new “snapshot” approach to conventional serial crystallography.

It is gratifying, she said, to learn that the synchrotron-based technique for Laue microdiffraction she worked to develop at the ALS was helpful in confirming a new mineral. “It’s always good when you see something you’ve been working on getting some interest. It means it’s spreading, and that there may be a bit more development and more people working on it.”

The ALS and NERSC are both DOE Office of Science User Facilities.

The team participating in the ognitite discovery also included researchers from the University off Florence in Italy, Siberian Federal University in Russia, McGill University in Canada, and The Natural History Museum in the U.K. The ALS is supported by the DOE Office of Basic Energy Science. Individuals participating in the study were supported, in part, by the Russian Foundation for Basic Research and the U.K.’s Natural Environment Research Council.

See the full article here .

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Bringing Science Solutions to the World

In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the UC Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

A U.S. Department of Energy National Laboratory Operated by the University of California.

From SLAC National Accelerator Lab: “A quick liquid flip helps explain how morphing materials store information”

From SLAC National Accelerator Lab

June 14, 2019

Experiments at SLAC’s X-ray laser reveal in atomic detail how two distinct liquid phases in these materials enable fast switching between glassy and crystalline states that represent 0s and 1s in memory devices.

In phase-change memory devices, a material switches between glassy and crystalline phases that represent the 0s and 1s used to store information. One pulse of electricity or light heats the material to high temperature, causing it to crystallize, and another pulse melts it into a disordered, glassy state. Experiments at SLAC’s X-ray laser revealed a key part of this switch – a quick transition from one liquid-like state to another – that enables fast and reliable data storage. (Peter Zalden/European XFEL)

Instead of flash drives, the latest generation of smart phones uses materials that change physical states, or phases, to store and retrieve data faster, in less space and with more energy efficiency. When hit with a pulse of electricity or optical light, these materials switch between glassy and crystalline states that represent the 0s and 1s of the binary code used to store information.

Now scientists have discovered how those phase changes occur on an atomic level.

Researchers from European XFEL and the University of Duisburg-Essen in Germany, working in collaboration with researchers at the Department of Energy’s SLAC National Accelerator Laboratory, led X-ray laser experiments at SLAC that collected more than 10,000 snapshots of phase-change materials transforming from a glassy to a crystalline state in real time.

They discovered that just before the material crystallizes, it changes from one liquid-like state to another, a process that could not be clearly seen in prior studies because it was blurred by the rapid motions of the atoms. And they showed that this transition is responsible for the material’s unique ability to store information for long periods of time while also quickly switching between states.

The results, published in Science today, offer a new strategy for designing improved phase-change materials for specialized memory storage.

“Current data storage technology has reached a scaling limit, so that new concepts are required to store the amounts of data that we will produce in the future,” said Peter Zalden, a scientist at European XFEL and lead author of the study. “Our study explains how the switching process in a promising new technology can be fast and reliable at the same time.”

When stable becomes unstable

The experiments took place at SLAC’s Linac Coherent Light Source (LCLS) which produces X-ray laser pulses that are short enough and intense enough to capture snapshots of atomic changes occurring in femtoseconds – millionths of a billionths of a second.

To store information with phase-change materials, they must be cooled quickly to enter a glassy state without crystallizing, and remain in this glassy state as long as the information needs to stay there. This means the crystallization process must be very slow to the point of being almost absent, such as is the case in ordinary glass. But when it comes time to erase the information, which is done by applying high temperatures, the same material has to crystallize very quickly. The fact that a material can form a stable glass but then become very unstable at elevated temperatures has puzzled researchers for decades.

At LCLS, the scientists used an optical laser to rapidly heat amorphous films of phase-change materials, just 50 nanometers thick, atop an equally thin support. The films cooled into a crystalline state as the heat from the laser blast dissipated into the surrounding support structure over billionths of a second.

They used X-ray laser pulses to make images of the material’s structural evolution, collecting each snapshot in the instant before a sample deteriorated.

A tale of two liquids

The researchers found that when the liquid cools far enough below the material’s melting temperature, it undergoes a structural change to form another, lower-temperature liquid that exists for just billionths of a second.

The two liquids not only have very different atomic structures, but they also behave differently: The one at higher temperature has highly mobile atoms that can quickly arrange themselves into the well-ordered structure of a crystal. But in the lower-temperature liquid, some chemical bonds become stronger and more rigid and can hold the disordered atomic structure of the glass in place. It is only the rigid nature of these chemical bonds that keeps the glass from crystallizing and – in the case of phase-change memory devices – secures information in place. The results also help scientists understand how other classes of materials form a glass.

The research team after performing experiments at SLAC’s Linac Coherent Light Source X-ray laser. (Klaus Sokolowski-Tinten/University of Duisburg-Essen)

See the full article here.
See the XFEL press release here .

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SLAC/LCLS

SLAC/LCLS II projected view

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From Lawrence Livermore National Laboratory: “Making metal with the lightness of air”

From Lawrence Livermore National Laboratory

June 3, 2019
Breanna Bishop
bishop33@llnl.gov
925-423-9802

A mosquito standing on cotton fibers carries a sample of ultra-low density gold aerogel. Photos by Joshua DeOtte.

Gold, silver and copper are heavy metals, but LLNL scientists can now make them nearly as light as air — in a form so tiny it can ride on a mosquito’s back.

The groundbreaking science, part of a joint NIF/Physical and Life Sciences (PLS) project supported by the Laboratory Directed Research and Development (LDRD) Program, created these ultra-low density metal foams to give physicists better X-ray sources to employ in experiments that support NIF’s Stockpile Stewardship mission.

The foam is the product of a nearly decade-long research effort by members of the Lab’s NIF and PLS directorates for use on inertial confinement fusion (ICF) experiments at NIF, the world’s most energetic laser system.

“We are looking primarily at fundamental science questions that govern how to synthesize, assemble and shape metal nanowire-based aerogels,” said materials scientist Michael Bagge-Hansen, the LDRD project’s principal investigator.

The material is called foam because that’s historically what these types of materials were named, but it’s not a material made by foaming. It’s a spaghetti-like web of randomly connected nanometer-sized wires, formed into the shape of a miniature marshmallow and containing the same or fewer number of atoms as air.

Physicist Sergei Kucheyev calls it a “porous metal monolith. There’s a lot going on here in terms of both chemistry and physics.”

X-ray sources

Scientists sought different ultra-low density metals that can be used as targets for laser-driven X-ray sources for experiments further probing the properties of various materials placed under the extreme conditions possible when NIF’s 192 high-powered lasers [see below] are directed inside the target chamber, said Tyler Fears, a staff scientist with the LLNL’s Materials Science Division (MSD).

Each element emits a characteristic set of X-rays when heated by lasers into a plasma, Fears explained. Metal foams can mimic gas even though they are made from materials that are not gas at room temperature.

The underlying physics of laser-driven X-ray sources, however, sets the bar high with rigorous specifications for the types, densities, shapes and sizes of metal foams needed for experiments.

“We need heavy metal targets to be around the density of air and a few millimeters in size within well-defined dimensions,” he said. “Our challenge is to try to meet all those goals at the same time.”

The team also had to make sure the techniques they developed could be repeated to consistently produce the foams, even if the size, shape and composition are changed to meet future experimental needs.

An ultra-low density metal foam sample dangles from a single strand of a spider’s web.

“You need to be able to make either the same material or a comparable material every time,” Fears said. “We have to understand when we change something, how is that going to change the product? If you change the density or if you change the shape, you have to know that’s the only thing you’re changing.”

Kucheyev said the research dates back nearly a decade, but “only in the last couple of years did we get foams of this amazing quality.”

Some previous versions aged in air before they could be brought into the target chamber, when they “ended up looking like old stale marshmallows,” he said. Another iteration came out of molds looking distorted, while others fell apart so easily one team member called them “cigarette ash.”

The team also tried using other types of low-density material to create scaffolding that provided a supporting structure for embedded particles of the specific metals. But the scaffolding materials would create unwanted X rays when hit by lasers, which would interfere with the X-ray data scientists wanted from the specific types of foam they were testing.

So, to maintain the purity of the X-ray spectrum, the team had to create the wire structure out of the specific metal itself, which was “the biggest challenge we had,” said materials scientist Fang Qian.

“The dearth of previous literature on creating these types of wires in large amounts meant we had to perform numerous experiments and fundamental studies to understand the synthetic mechanisms,” she said. “We also have leveraged several characterization tools in MSD to evaluate growth models, structure, surface and chemistry of these unique materials. We eventually developed our own unique recipe and protocol.”

Qian added that MSD “can now rapidly perform the on-site research and development of metallic nanomaterials, such as particles and wires, and reproduce feedstocks at the gram-scale using rigorously tested procedures.”

Supercritical drying

The team freezes the nanowire inside a shape-creating mold typically filled with a water-glycerol mix. When it hardens, the nanowire looks like a “randomly interconnected mesh of frozen spaghetti,” Kucheyev said.

The material is then removed from the mold and the frozen water is extracted by replacing it with the solvent acetone, which is then dissolved in a supercritical drying process using liquid carbon dioxide, leaving only the metal and air. Supercritical drying ensures the liquid transforms into a gas phase without creating a meniscus that could damage the fragile ultra-low density metal foam structure.

“You don’t have any capillary pressures and that also allows you to maintain the very small pores without any shrinkage,” Fears said.

The team has produced copper and silver foam, and silver has performed well in NIF shots. The team is able to produce gold foams, which still tend to fall off the mounts that hold them in front of NIF’s lasers. “That’s the challenge we’re trying to overcome now,” Fears said.

The joint PLS/NIF-funded LDRD project is designed to build on the team’s previous work with silver and copper so materials scientists can make ultra-low density metallic foams with other metals “to respond to current and future needs,” Bagge-Hansen said. The team is now working on tin as well as gold.

“Translating these successes into other materials (e.g., gold) raised significant technical challenges that we are navigating in the LDRD,” he said. “I attribute our success to an innovative, diverse team of scientists that share their varied technical backgrounds to solve a highly multi-disciplinary challenge.”

The effort also included Mark May, Brent Blue, Alyssa Troksa, Tom Braun, Thomas Yong-Jin Han, Ted Baumann, Daniel Malone, Corie Horwood, Chantel Aracne-Ruddle, Kelly Youngblood, Michael Stadermann and Suhas Bhandarkar.

The foams were developed specifically for NIF as X-ray sources. The material also could be applied to other uses, however, such as target shells or hohlraum liners. And now that scientists know the material can be made, it could spur creative ideas for future experiments.

The foams were developed specifically for NIF as X-ray sources. The material also could be applied to other uses, however, such as target shells or hohlraum liners. And now that scientists know the material can be made, it could spur creative ideas for future experiments.

“The physicists come up with ideas, but usually they’ll ask what someone can make, and they’ll design an experiment around that,” Fears said. “If we can make a material that they never thought we could make before, they’ll come up with new experiments to fit those capabilities.”

See the full article here .

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Operated by Lawrence Livermore National Security, LLC, for the Department of Energy’s National Nuclear Security Administration
Lawrence Livermore National Laboratory (LLNL) is an American federal research facility in Livermore, California, United States, founded by the University of California, Berkeley in 1952. A Federally Funded Research and Development Center (FFRDC), it is primarily funded by the U.S. Department of Energy (DOE) and managed and operated by Lawrence Livermore National Security, LLC (LLNS), a partnership of the University of California, Bechtel, BWX Technologies, AECOM, and Battelle Memorial Institute in affiliation with the Texas A&M University System. In 2012, the laboratory had the synthetic chemical element livermorium named after it.
LLNL is self-described as “a premier research and development institution for science and technology applied to national security.” Its principal responsibility is ensuring the safety, security and reliability of the nation’s nuclear weapons through the application of advanced science, engineering and technology. The Laboratory also applies its special expertise and multidisciplinary capabilities to preventing the proliferation and use of weapons of mass destruction, bolstering homeland security and solving other nationally important problems, including energy and environmental security, basic science and economic competitiveness.

The Laboratory is located on a one-square-mile (2.6 km2) site at the eastern edge of Livermore. It also operates a 7,000 acres (28 km2) remote experimental test site, called Site 300, situated about 15 miles (24 km) southeast of the main lab site. LLNL has an annual budget of about $1.5 billion and a staff of roughly 5,800 employees.

LLNL was established in 1952 as the University of California Radiation Laboratory at Livermore, an offshoot of the existing UC Radiation Laboratory at Berkeley. It was intended to spur innovation and provide competition to the nuclear weapon design laboratory at Los Alamos in New Mexico, home of the Manhattan Project that developed the first atomic weapons. Edward Teller and Ernest Lawrence,[2] director of the Radiation Laboratory at Berkeley, are regarded as the co-founders of the Livermore facility.

The new laboratory was sited at a former naval air station of World War II. It was already home to several UC Radiation Laboratory projects that were too large for its location in the Berkeley Hills above the UC campus, including one of the first experiments in the magnetic approach to confined thermonuclear reactions (i.e. fusion). About half an hour southeast of Berkeley, the Livermore site provided much greater security for classified projects than an urban university campus.

Lawrence tapped 32-year-old Herbert York, a former graduate student of his, to run Livermore. Under York, the Lab had four main programs: Project Sherwood (the magnetic-fusion program), Project Whitney (the weapons-design program), diagnostic weapon experiments (both for the Los Alamos and Livermore laboratories), and a basic physics program. York and the new lab embraced the Lawrence “big science” approach, tackling challenging projects with physicists, chemists, engineers, and computational scientists working together in multidisciplinary teams. Lawrence died in August 1958 and shortly after, the university’s board of regents named both laboratories for him, as the Lawrence Radiation Laboratory.

Historically, the Berkeley and Livermore laboratories have had very close relationships on research projects, business operations, and staff. The Livermore Lab was established initially as a branch of the Berkeley laboratory. The Livermore lab was not officially severed administratively from the Berkeley lab until 1971. To this day, in official planning documents and records, Lawrence Berkeley National Laboratory is designated as Site 100, Lawrence Livermore National Lab as Site 200, and LLNL’s remote test location as Site 300.[3]

The laboratory was renamed Lawrence Livermore Laboratory (LLL) in 1971. On October 1, 2007 LLNS assumed management of LLNL from the University of California, which had exclusively managed and operated the Laboratory since its inception 55 years before. The laboratory was honored in 2012 by having the synthetic chemical element livermorium named after it. The LLNS takeover of the laboratory has been controversial. In May 2013, an Alameda County jury awarded over $2.7 million to five former laboratory employees who were among 430 employees LLNS laid off during 2008.[4] The jury found that LLNS breached a contractual obligation to terminate the employees only for “reasonable cause.”[5] The five plaintiffs also have pending age discrimination claims against LLNS, which will be heard by a different jury in a separate trial.[6] There are 125 co-plaintiffs awaiting trial on similar claims against LLNS.[7] The May 2008 layoff was the first layoff at the laboratory in nearly 40 years.[6]

On March 14, 2011, the City of Livermore officially expanded the city’s boundaries to annex LLNL and move it within the city limits. The unanimous vote by the Livermore city council expanded Livermore’s southeastern boundaries to cover 15 land parcels covering 1,057 acres (4.28 km2) that comprise the LLNL site. The site was formerly an unincorporated area of Alameda County. The LLNL campus continues to be owned by the federal government.

LLNL/NIF

From Brookhaven National Lab:”Ten Years and Nearly a Billion Dollars: How Project Management Made a Massive X-Ray Light Source Possible”

From Brookhaven National Lab

May 29, 2019
Shannon Brescher Shea, D.O.E.

Aerial view of the construction site of the National Synchrotron Light Source II, taken in 2009, four years after the project started.

Replacing a beloved tool is never easy. Erik Johnson had worked with the National Synchrotron Light Source (NSLS) for nearly 15 years when he and his colleagues began thinking about its replacement. But this switch wasn’t a matter of walking down to the hardware store.

The NSLS, a Department of Energy (DOE) Office of Science (SC) user facility at Brookhaven National Laboratory (BNL), opened in 1982.

BNL NSLS

Over 30 years, scientists — three of whom won Nobel prizes for their work — used its intense beams of light over the course of more than 55,000 visits to study atomic structures and chemical processes. Johnson came to the NSLS in 1985 as a post-doctoral student. By 2000, Johnson and other leaders in the field realized the NSLS would soon be past its glory days.

They began dreaming up its successor: the NSLS-II.

BNL NSLS II

After five years of planning and research, SC approved the project to move forward.
“There was elation in the hallways,” said Johnson.

This was just the beginning. Ahead of Johnson and his co-workers stood a project that would take a decade and almost a billion dollars to build.

SC’s scientists and managers are familiar with this type of challenge. For decades, DOE and its predecessors have been developing federal user facilities for scientists to probe the building blocks of the universe and of life.

Constructing these user facilities requires immense planning and coordination. Good project management keeps projects on-time and on-budget. The $912-million NSLS-II project put SC’s project management skills to the test.

A Big Machine Comes with Big Challenges

With the NSLS reaching its technical limits, scientists needed the next big tool to study incredibly small materials under real-world conditions. To look closer than ever at subjects ranging from batteries’ chemical reactions to viruses’ structures, researchers required an X-ray beam 10,000 times brighter than the original NSLS.

To make the investment worthwhile, the team needed to design NSLS-II to be so advanced that it could stay at the forefront of science for more than three decades. It took more than 20 different scientific workshops to hammer out the requirements. Participants included both scientists who would use the facility and engineers who would design it.

“I had gone from 15, 20 years where I knew everybody by first name and what they did to being surrounded by all new people,” said Johnson. “Which was pretty neat.”

To satisfy as many stakeholders as possible, the team designed the facility to immediately run at full capacity. They then scaled the plans down to what they could build initially. If they finished early or had funding left over, they could add pieces back. To make it possible to adapt the most advanced technologies, the team planned to add more research equipment and capabilities in phases after they finished construction of the main facility.

“[The process] was 90 percent preplanning and 10 percent execution,” said Robert Caradonna, the DOE Brookhaven Site Office deputy federal project director for the NSLS-II project.

All of that planning clarified the challenges that awaited them.

Creating powerful X-rays requires massive machines that accelerate electrons to high energies. These machines use specialized magnets to control the electrons that produce the X-rays. Equipment at experimental stations then harness these X-rays. Most facilities have rings that store the electrons; NSLS-II’s ring needed to be a half-mile around.

The building needed to meet several other specific requirements. Because temperature changes can influence the magnets’ size and position, the inside of the storage ring could never waver from a balmy 78 F. To ensure the beams would never tremble, the team needed to minimize the effect of vibrations from trucks on the nearby Long Island Expressway and waves from the Atlantic Ocean.

The project’s sheer complexity was perhaps the biggest challenge of all. The original schedule projected 5,000 separate activities. At the height of the project, the list expanded to 11,000. At some points, the team was managing a million dollars of work each day.

“We spent so much time with our heads down pushing on this thing that it didn’t really get to be overwhelming,” said Johnson. “We were too damn busy for it to get overwhelming.”

Prepared for Disaster

In project management, being a pessimist can pay off. A huge part of ensuring the project ran smoothly was anticipating and managing risks.

The Office of Science purposely plans for the worst case scenarios. Over the course of the project, the team ran more than 400 separate risk assessments. They also built numerous computer models that pinpointed exactly where every single piece of equipment needed to go.

One of the biggest areas of uncertainty was manufacturing the massive magnets. Buying 900 magnets anywhere is difficult. Buying 900 extremely high-powered, cutting-edge magnets from one supplier wasn’t going to happen.

“It would be nice if we could give it to one guy and he could produce all the magnets,” said Caradonna, but, “we knew that was going to be impossible.”

There are only a handful of places in the world that could produce the magnets and other specialized pieces of equipment. The team developed seven contracts with five different suppliers, several of which were in other countries. The different languages, management cultures, geographic locations, and even measurement units caused conflicts. Some vendors were unresponsive.

To solve these problems, members of the NSLS-II team flew to the suppliers and consulted with them on site. The hands-on assistance improved communications and quality control. It even allowed NSLS-II staff members to get experience with the components before they arrived to BNL. Despite some early delays, the magnet manufacturing didn’t hold up the process as a whole.

The team was able to compensate for these delays because of savvy scheduling. In many projects like this, a delay in one step can cascade down to others, creating multiple delays and scheduling conflicts. In contrast, the NSLS-II team designed the project so they could change the order of the steps. For example, they built five identical pieces of the accelerator ring that fit together like LEGOs®. If the magnets weren’t finished for one piece of the ring, they could still finish the others in time.

This approach also came in handy when the project received $150 million in funding earlier than planned through a special bill to help the country recover from the economic crash in 2008. With this funding and a favorable construction market, they negotiated a lower price with the construction company and finished the laboratory buildings nearly a year ahead of schedule.

“You never know when fortune is going to smile on you, and you never know when you’re going to do something sooner rather than later,” said Johnson. “It’s all about being ready.”

Here a Review, There a Review

Preparation will only get you so far. SC’s regular and strict project reviews by independent experts got the team the rest of the way there. Every step of the process had a review, from the scope and scientific goals to the construction: 54 in total.

Over the course of the project, the review teams gave more than 1,300 recommendations.

As the NSLS-II lessons learned document states: “Project reviews are the most important management tool to ensure the project is staying on track. If you are not required to have them, you should inflict them on yourself.”

NSLS-II is not the only project to benefit from rigorous reviews. The GAO has cited SC’s reviews as a major reason why the majority of SC’s projects are completed on-time and on-budget.

The project teams aren’t the only ones who learn from the experience. The independent experts are often in charge of similar projects at their own agencies, national laboratories, or universities.

10 Years Later

Ten years after DOE approved the idea for NSLS-II, it was finished. SC declared it complete in March 2015, three months before its target date. It opened to users that July.

Owing to sound project management practices, there was enough funding available for the NSLS-II to include $68 million in optional features beyond the basic construction plan. It had an additional beamline to provide X-rays to another experimental station, a larger building that would make it easier to expand, and extra components to increase reliability. In 2016, the team won both the Project Management Institute’s Project of the Year award and the DOE Secretary’s Award of Excellence, the highest honor that DOE awards to a project.

“I was immensely proud,” said Johnson, “but fully cognizant of all of the work that needs to be done still to fully realize the potential of this instrument.”

Since it opened, the team has launched 28 experimental stations, or beamlines, out of a total of 60 stations it can support.

“Everything from the dreaming to the final delivery is going on at the same time,” said Johnson.

Despite all of the new machinery, one day the NSLS-II will become obsolete just like its predecessor. One Friday night, Johnson went home and noted that the old NSLS sign was still up. The next Monday, it was gone, replaced by a sign for the lab’s new Computational Science Initiative. To Johnson, that change reinforced the fact that his mission is about more than equipment.

“Those people who used it, they still have those experiences,” he said. “It’s not the stuff that you build, it’s that what you build that enables other people to do what’s important.”

See the full article here .
Original publication by D.O.E.

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One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

From Brookhaven National Lab: “STAR Detector has a New Inner Core”

From Brookhaven National Lab

May 23, 2019
Karen McNulty Walsh
kmcnulty@bnl.gov

Upgrade to detector sectors tracking particles close to beamline produces stunning images and precision measurements at the Relativistic Heavy Ion Collider.

BNL/RHIC

BNL/RHIC Star Detector

The STAR detector at the Relativistic Heavy Ion Collider (RHIC) is the size of a small house. It captures snapshots of tracks left by thousands of particles created when two gold ions collide. Upgrades to STAR’s inner core now allow the detector to track even more particles, including those with low momentum and those emerging close to the beamline.

For scientists tracking the transformation of protons and neutrons—the components of atomic nuclei that make up everything we see in the universe today—into a soup of fundamental building blocks known quark-gluon plasma, more is better. More particle tracks, that is. Thanks to a newly installed upgrade of the STAR detector at the Relativistic Heavy Ion Collider (RHIC), nuclear physicists now have more particle tracks than ever to gain insight into the crucial matter-building transition that ran this process in reverse nearly 14 billion years ago.

RHIC—a U.S. Department of Energy Office of Science User Facility for nuclear physics research at Brookhaven National Laboratory—collides beams of heavy particles such as the nuclei of gold atoms to recreate the extreme conditions of the early universe, including temperatures more than 250,000 times hotter than the center of the sun. The collisions melt the atoms’ protons and neutrons, momentarily setting free their inner building blocks—quarks and gluons—which last existed as free particles one millionth of a second after the Big Bang. The STAR detector captures tracks of particles emerging from the collisions so nuclear physicists can learn about the quarks and gluons—and the force that binds them into more familiar particles as the hot quark-gluon plasma cools.

Part of the team installing new sectors for the inner Time Projection Chamber (iTPC) at STAR (l to r): Saehanseul Oh, Prashanth Shanmuganathan, Robert Soja, Bill Struble, Peng Liu, and Rahul Sharma.

The STAR detector upgrade of the “inner Time Projection Chamber,” or iTPC, was completed just in time for this year’s run of collisions at RHIC. It increases the detector’s ability to capture particles emerging close to the beamline in the “forward” and “rearward” directions, as well as particles with low momentum.

“With the upgrade of the inner TPC, we can dramatically increase the detector coverage and the total number of particles we can measure in any given event,” said Grazyna Odyniec, group leader of Lawrence Berkeley National Laboratory’s Relativistic Nuclear Collisions group, which was responsible for the construction of original STAR TPC and the mechanical components of the new sectors.

Shrinking electronics, more snapshots

One key element of the upgrade was incorporating advanced readout electronics, which have come a long way since STAR’s original TPC was assembled at Berkeley Lab in the late 1990s.

“Because the readout electronics have gotten much smaller, we now fit many more sensors into the inner sectors,” said Brookhaven Lab physicist Flemming Videbaek, project manager for the upgrade. The electronics also have become much faster. That means the detector can take “snapshots” more frequently to capture more details about individual particles’ paths. More frequent sampling also gives STAR access to particles that were previously lost in the measurements with the detector.

“We are now able to reconstruct tracks that were simply too short for the detector to see,” said Daniel Cebra, a physicist from the University of California, Davis, and a leader of the iTPC effort. “These shorter tracks come from particles that were either emitted at a low angle—meaning close to the beamline in the direction of the colliding ions—or have a low momentum and are thus curled up as they move through the detector’s the magnetic field.”

Capturing these low-angle and low-momentum particles will give STAR scientists much more data to work with as they search for signs of the quark-gluon plasma phase transition—the main goal of RHIC’s Beam Energy Scan II.

Collaborative effort

Building components for the detector enhancement and getting them assembled in time for the low-energy collisions that started in February was a collaborative effort—and a global one.

A team from the Instituto de Física da Universidade de São Paulo in Brazil designed the main chips for the new signal-readout electronics, which were incorporated into the final assembly by the Brookhaven Lab STAR electronics group.

Scientists at Berkeley Lab led by Jim Thomas and Howard Wieman prepared the mechanical parts of the new sectors, including “trimming” the alignment of the aluminum frames to match the design specifications within 50 microns in all dimensions.

And much of the Berkeley team’s wisdom and methods were instrumental in guiding the assembly of the sectors’ wire components by STAR collaborators in China.

A side view of particle tracks (left) and hits (right) from a collision in STAR, as recorded by the new iTPC sectors (top) compared to the old sectors (bottom). Notice how the new sectors record more hits per track, especially close to the beamline, as well as tracks at more forward and rearward angles (more to the left and right in this view).

Each of the iTPC’s 24 particle-tracking sectors contains 1500 thin wires arrayed in three layers that amplify signals, establish a particle-guiding electric field, and control which tracks get recorded at STAR. These wires needed to be mounted with extreme precision to keep the relative distance between the layers the same—within 10 microns, or millionths of a meter.

“We gained experience by building a small prototype even before the design was finalized, and then when it was, we built a full-size version,” said Qinghua Xu, a physicist at Shandong University, who led the Chinese effort. When they completed the first full prototype in 2017, they sent it to Brookhaven for a test run.

“For the 2018 run, we replaced one of the old sectors with the new prototype, and confirmed that it worked as expected,” Videbaek said. “That gave us confidence that we were ready to build and install the 23 other sectors.”

Race against time

The team at Brookhaven started installing sectors in October 2018, using a crane and a precision installation tool designed by Brookhaven Lab engineer Rahul Sharma and fabricated with help from a team lead by Olga Evdokimov at the University of Illinois, Chicago.

“It was a bit of a race with time,” Videbaek said. “We installed the last electronics just before Christmas and then, in January, filled the TPC with its argon/methane gas mixture and started taking cosmic data,” he said.

Mounting 1500 thin wires arrayed in three layers on each of the 24 new iTPC sectors took patience, practice, and precision. (Credit: Shandong University)

The scientists use cosmic rays (charged particles from outer space)—which come through the roof at a rate of about 150 per second—to calibrate the detector and make sure everything is working.

When the first low-energy collisions came in February, the STAR team was ready with a fully functioning newly efficient detector.

“We’re grateful to everyone on the team who helped to make this upgrade a success,” Videbaek said.

Stay tuned for updates about the science the new iTPC will reveal.

The iTPC upgrade was funded by the DOE Office of Science (NP) with significant financial contributions from the National Science Foundation of China, the Chinese Ministry of Science and Technology, and Shandong University for work done at Shandong U., the University of Science and Technology of China, and the Shanghai Institute of Applied Physics.

See the full article here .

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One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

From Brookhaven National Lab: “New Approach for Solving Protein Structures from Tiny Crystals”

From Brookhaven National Lab

May 3, 2019
Karen McNulty Walsh
kmcnulty@bnl.gov
(631) 344-8350

Peter Genzer,
genzer@bnl.gov
(631) 344-3174

Technique opens door for studies of countless hard-to-crystallize proteins involved in health and disease.

Wuxian Shi, Martin Fuchs, Sean McSweeney, Babak Andi, and Qun Liu at the FMX beamline at Brookhaven Lab’s National Synchrotron Light Source II [see below], which was used to determine a protein structure from thousands of tiny crystals.

Using x-rays to reveal the atomic-scale 3-D structures of proteins has led to countless advances in understanding how these molecules work in bacteria, viruses, plants, and humans—and has guided the development of precision drugs to combat diseases such as cancer and AIDS. But many proteins can’t be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structures from tiny crystals.

The method relies on unique sample-handling, signal-extraction, and data-assembly approaches, and a beamline capable of focusing intense x-rays at Brookhaven’s National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science user facility—to a millionth-of-a-meter spot, about one-fiftieth the width of a human hair.

“Our technique really opens the door to dealing with microcrystals that have been previously inaccessible, including difficult-to-crystallize cell-surface receptors and other membrane proteins, flexible proteins, and many complex human proteins,” said Brookhaven Lab scientist Qun Liu, the corresponding author on the study, which was published on May 3 in IUCrJ, a journal of the International Union of Crystallography.

Deciphering protein structures

Protein crystallography has been a dominant method for solving protein structures since 1958, improving over time as x-ray sources have grown more powerful, allowing more precise structure determinations. To determine a protein structure, scientists measure how x-rays like those generated at NSLS-II diffract, or bounce off, the atoms in an ordered crystalline lattice consisting of many copies of the same protein molecule all arrayed the same way. The diffraction pattern conveys information about where the atoms are located. But it’s not sufficient.

A cartoon representing the structure of a well-studied plant protein that served as a test case for the newly developed microcrystallography technique. Magenta mesh patterns surrounding sulfur atoms intrinsic to the protein (yellow spheres) indicate the anomalous signals that were extracted using low-energy x-ray diffraction of thousands of crystals measuring less than 10 millionths of a meter, the size of a bacterium.

“Only the amplitudes of diffracted x-ray ‘waves’ are recorded on the detector, but not their phases (the timing between waves),” said Liu. “Both are required to reconstruct a 3-D structure. This is the so-called crystallographic phase problem.”

Crystallographers have solved this problem by collecting phase data from a different kind of scattering, known as anomalous scattering. Anomalous scattering occurs when atoms heavier than a protein’s main components of carbon, hydrogen, and nitrogen absorb and re-emit some of the x-rays. This happens when the x-ray energy is close to the energy those heavy atoms like to absorb. Scientists sometimes artificially insert heavy atoms such as selenium or platinum into the protein for this purpose. But sulfur atoms, which appear naturally throughout protein molecules, can also produce such signals, albeit weaker. Even though these anomalous signals are weak, a big crystal usually has enough copies of the protein with enough sulfur atoms to make them measurable. That gives scientists the phase information needed to pinpoint the location of the sulfur atoms and translate the diffraction patterns into a full 3-D structure.

“Once you know the sulfur positions, you can calculate the phases for the other protein atoms because the relationship between the sulfur and the other atoms is fixed,” said Liu.

But tiny crystals, by definition, don’t have that many copies of the protein of interest. So instead of looking for diffraction and phase information from repeat copies of a protein in a single large crystal, the Brookhaven/Columbia team developed a way to take measurements from many tiny crystals, and then assemble the collective data.

Tiny crystals, big results

To handle the tiny crystals, the team developed sample grids patterned with micro-sized wells. After pouring solvent containing the microcrystals over these well-mount grids, the scientists removed the solvent and froze the crystals that were trapped on the grids.

Micro-patterned sample grids for manipulation of microcrystals.

“We still have a challenge, though, because we can’t see where the tiny crystals are on our grid,” said Liu. “To find out, we used microdiffraction at NSLS-II’s Frontier Microfocusing Macromolecular Crystallography (FMX) beamline to survey the whole grid. Scanning line by line, we can find where those crystals are hidden.”

As Martin Fuchs, the lead beamline scientist at FMX, explained, “The FMX beamline can focus the full intensity of the x-ray beam down to a size of one micron, or millionth of a meter. We can finely control the beam size to match it to the size of the crystals—five microns in the case of the current experiment. These capabilities are crucial to obtain the best signal,” he said.

Wuxian Shi, another FMX beamline scientist, noted that “the data collected in the grid survey contains information about the crystals’ location. In addition, we can also see how well each crystal diffracts, which allows us to pick only the best crystals for data collection.”

The scientists were then able to maneuver the sample holder to place each mapped out microcrystal of interest back in the center of the precision x-ray beam for data collection.

They used the lowest energy available at the beamline—tuned to approach as closely as possible sulfur atoms’ absorption energy—and collected anomalous scattering data.

“Most crystallographic beamlines could not reach the sulfur absorption edge for optimized anomalous signals,” said co-author Wayne Hendrickson of Columbia University. “Fortunately, NSLS-II is a world-leading synchrotron light source providing bright x-rays covering a broad spectrum of x-ray energy. And even though our energy level was slightly above the ideal absorption energy for sulfur, it generated the anomalous signals we needed.”

But the scientists still had some work to do to extract those important signals and assemble the data from many tiny crystals.

“We are actually getting thousands of pieces of data,” said Liu. “We used about 1400 microcrystals, each with its own data set. We have to put all the data from those microcrystals together.”

Scientists used a five-micron x-ray beam at the FMX beamline at NSLS-II to scan the entire grid and locate the tiny invisible crystals. Then a heat map (green) was used to guide the selection of positions for diffraction data acquisition.

They also had to weed out data from crystals that were damaged by the intense x-rays or had slight variations in atomic arrangements.

“A single microcrystal does not diffract x-rays sufficiently for structure solution prior to being damaged by the x-rays,” said Sean McSweeney, deputy photon division director and program manager of the Structural Biology Program at NSLS-II. “This is particularly true with crystals of only a few microns, the size of about a bacterial cell. We needed a way to account for that damage and crystal structure variability so it wouldn’t skew our results.”

They accomplished these goals with a sophisticated multi-step workflow process that sifted through the data, discarded outliers that might have been caused by radiation damage or incompatible crystals, and ultimately extracted the anomalous scattering signals.

“This is a critical step,” said Liu. “We developed a computing procedure to assure that only compatible data were merged in a way to align the individual microcrystals from diffraction patterns. That gave us the required signal-to-noise ratios for structure determination.”

Applying the technique

This technique can be used to determine the structure of any protein that has proven hard to crystallize to a large size. These include cell-surface receptors that allow cells of advanced lifeforms such as animals and plants to sense and respond to the environment around them by releasing hormones, transmitting nerve signals, or secreting compounds associated with cell growth and immunity.

“To adapt to the environment through evolution, these proteins are malleable and have lots of non-uniform modifications,” said Liu. “It’s hard to get a lot of repeat copies in a crystal because they don’t pack well.”

In humans, receptors are common targets for drugs, so having knowledge of their varied structures could help guide the development of new, more targeted pharmaceuticals.

But the technique is not restricted to just small crystals.

“The method we developed can handle small protein crystals, but it can also be used for any size protein crystals, any time you need to combine data from more than one sample,” Liu said.

This research was supported in part by Brookhaven National Laboratory’s “Laboratory Directed Research and Development” program and the National Institutes of Health (NIH) grant GM107462. The NSLS-II at Brookhaven Lab is a DOE Office of Science user facility (supported by DE-SC0012704), with beamline FMX supported primarily by the National Institute of Health, National Institute of General Medical Sciences (NIGMS) through a Biomedical Technology Research Resource P41 grant (P41GM111244), and by the DOE Office of Science.

See the full article here .

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BNL Center for Functional Nanomaterials

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BNL RHIC PHENIX

One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

From European Space Agency: “Storm in the Teacup quasar”

From European Space Agency

06/05/2019

This image shows a quasar nicknamed the Teacup due to its shape. A quasar is an active galaxy that is powered by material falling into its central supermassive black hole. They are extremely luminous objects located at great distances from Earth. The Teacup is 1.1 billion light years away and was thought to be a dying quasar until recent X-ray observations shed new light on it.

X-ray: NASA/CXC/University of Cambridge/G. Lansbury et al; optical: NASA/STScI/W. Keel et al

ESA/XMM Newton

NASA/Chandra X-ray Telescope

NASA/ESA Hubble Telescope

The Teacup was discovered in 2007 as part of the Galaxy Zoo project, a citizen science project that classified galaxies using data from the Sloan Digital Sky Survey. A powerful eruption of energy and particles from the central black hole created a bubble of material that became the Teacup’s handle, which lies around 30 000 light years from the centre.

Observations revealed ionised atoms in the handle of the Teacup, possibly caused by strong radiation coming from the quasar in the past. This past level of radiation dwarfed the current measurements of the luminosity from the quasar. The radiation seemed to have diminished by 50 to 600 times over the last 40 000 to 100 000 years, leading to the theory that the quasar was rapidly fading.

But new data from ESA’s XMM-Newton telescope and NASA’s Chandra X-ray observatory reveal that X-rays are coming from a heavily obscured central source, which suggests that the quasar is still burning bright beneath its shroud. While the quasar has certainly dimmed over time, it is nowhere near as significant as originally thought, perhaps only fading by a factor of 25 or less over the past 100 000 years.

The Chandra data also showed evidence for hotter gas within the central bubble, and close to the ‘cup’ which surrounds the central black hole. This suggests that a wind of material is blowing away from the black hole, creating the teacup shape.

In the image shown here the X-ray data is coloured in blue and optical observations from the NASA/ESA Hubble Space Telescope are shown in red and green. Another image including radio data also shows a second ‘handle’ on the other side of the ‘cup’.

The research is described in The Astrophysical Journal Letters.

Explore the XMM-Newton data from this study in ESA’s archives.

See the full article here .

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Please help promote STEM in your local schools.

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The European Space Agency (ESA), established in 1975, is an intergovernmental organization dedicated to the exploration of space, currently with 19 member states. Headquartered in Paris, ESA has a staff of more than 2,000. ESA’s space flight program includes human spaceflight, mainly through the participation in the International Space Station program, the launch and operations of unmanned exploration missions to other planets and the Moon, Earth observation, science, telecommunication as well as maintaining a major spaceport, the Guiana Space Centre at Kourou, French Guiana, and designing launch vehicles. ESA science missions are based at ESTEC in Noordwijk, Netherlands, Earth Observation missions at ESRIN in Frascati, Italy, ESA Mission Control (ESOC) is in Darmstadt, Germany, the European Astronaut Centre (EAC) that trains astronauts for future missions is situated in Cologne, Germany, and the European Space Astronomy Centre is located in Villanueva de la Cañada, Spain.

From SLAC National Accelerator Lab: “Researchers create the first maps of two melatonin receptors essential for sleep”

From SLAC National Accelerator Lab

April 24, 2019

Andrew Gordon
agordon@slac.stanford.edu
(650) 926-2282

Written by Ali Sundermier

The behavior of humans and all animals is governed by a variety of natural cycles. The shift of seasons, tides, and day and night influences animal breeding and mating, predator-prey relationships, migration and foraging. Melatonin, depicted as a constellation in the night sky, is the key molecule that allows one of the most stable of these external cycles, a 24-hour day-night rhythm, to be correlated to an internal cycle, with responses at the level of individual cells and the whole animal. High melatonin levels during night time induce sleep-promoting properties by acting through melatonin receptors, depicted in the central reference point of the image composition. (Yekaterina Kadyshevskaya/Bridge Institute of the University of Southern California)

A better understanding of how these receptors work could enable scientists to design better therapeutics for sleep disorders, cancer and Type 2 diabetes.

An international team of researchers used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to create the first detailed maps of two melatonin receptors that tell our bodies when to go to sleep or wake up, and guide other biological processes. A better understanding of how they work could enable researchers to design better drugs to combat sleep disorders, cancer and Type 2 diabetes. Their findings were published in two papers today in Nature: Structural basis of ligand recognition at the human MT1 melatonin receptor; XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity.

The team, led by the University of Southern California, used X-rays from SLAC’s Linac Coherent Light Source (LCLS) to map the receptors, MT1 and MT2, bound to four different compounds that activate them: an insomnia drug, a drug that mixes melatonin with the antidepressant serotonin, and two melatonin analogs.

SLAC/LCLS

They discovered that both melatonin receptors contain narrow channels embedded in the fatty membranes of the cells in our bodies. These channels only allow melatonin – which can exist in both water and fat – to pass through and bind to the receptors, blocking serotonin, which has a similar structure but is only happy in watery environments. They also uncovered how some much larger compounds may only target MT1 and not MT2, despite the structural similarities between the two receptors. This should inform the design of drugs that selectively target MT1, which so far has been challenging.

“These receptors perform immensely important functions in the human body and are major drug targets of high interest to the pharmaceutical industry,” said Linda Johansson, a postdoctoral scholar at USC who led the structural work on MT2. “Through this work we were able to obtain a highly detailed understanding of how melatonin is able to bind to these receptors.”

Time for bed

People do it, birds do it, fish do it. Almost all living beings in the animal kingdom sleep, and for good reason.

“It’s critical for the brain to take rest and process and store memories that we have accumulated during the day,” said co-author Alex Batyuk, a scientist at SLAC. “Melatonin is the hormone that regulates our sleep-wake cycles. When there’s light, the production of melatonin is inhibited, but when darkness comes that’s the signal for our brains to go to sleep.”

Melatonin receptors belong to a group of membrane receptors called G protein-coupled receptors (GPCRs) which regulate almost all the physiological and sensory processes in the human body. MT1 and MT2 are found in many places throughout the body, including the brain, retina, cardiovascular system, liver, kidney, spleen and intestine.

These receptors oversee our clock genes, the timekeepers of the body’s internal clock, or circadian rhythm. In a perfect world, our internal clocks would sync up with the rising and setting of the sun. But when people travel across time zones, work overnight shifts or spend too much time in front of screens or other artificial sources of blue light, these timekeepers are thrown out of whack.

Controlling the rhythm

When our circadian rhythms are disrupted, it can lead to a number of downstream symptoms, increasing the risk of cancer, Type 2 diabetes and mood disorders. MT1 in particular plays an important role in controlling these rhythms but designing drugs that can selectively target this receptor has proven difficult. Many people take over-the-counter melatonin supplements to combat sleep issues or shift their circadian rhythms, but these drugs often wear off within hours and can produce unwanted side effects.

By cracking the blueprints of these receptors and mapping how ligands bind to and activate them, the researchers lit the way for others to design drugs that are safer, more effective and capable of selectively targeting each receptor.

“Since the discovery of melatonin 60 years ago, there have been many landmark discoveries that led to this moment,” said Margarita L. Dubocovich, a State University of New York Distinguished Professor of pharmacology and toxicology at the University at Buffalo who pioneered the identification of functional melatonin receptors in the early 80s and provided an outside perspective on this research. “Despite remarkable progress, discovery of selective MT1 drugs has remained elusive for my team and researchers around the world. The elucidation of the crystal structures for the MT1 and MT2 receptors opens up an exciting new chapter for the development of drugs to treat sleep or circadian rhythm disorders known to cause psychiatric, metabolic, oncological and many other conditions.”

Harvesting crystals

To map biomolecules like proteins, researchers often use a method called X-ray crystallography, scattering X-rays off of crystallized versions of these proteins and using the patterns this creates to obtain a three-dimensional structure. Until now, the challenge with mapping MT1, MT2 and similar receptors was how difficult it was to grow large enough crystals to obtain high-resolution structures.

“With these melatonin receptors, we really had to go the extra mile,” said Benjamin Stauch, a scientist at USC who led the structural work on MT1. “Many people had tried to crystallize them without success, so we had to be a little bit inventive.”

A key piece of this research was the unique method the researchers used to grow their crystals and to collect X-ray diffraction data from them. For this research, the team expressed these receptors in insect cells and extracted them by using detergent. They mutated these receptors to stabilize them, enabling crystallization. After purifying the receptors, they placed them in a membrane-like gel, which supports crystal growth directly from the membrane environment. After obtaining microcrystals suspended in this gel, they used a special injector to create a narrow stream of crystals that they zapped with X-rays from LCLS.

“Because of the tiny crystal size, this work could only be done at LCLS,” said Vadim Cherezov, a USC professor who supervised both studies. “Such small crystals do not diffract well at synchrotron sources as they quickly suffer from radiation damage. X-ray lasers can overcome the radiation damage problem through the ‘diffraction-before-destruction’ principle.”

The researchers collected hundreds of thousands of images of the scattered X-rays to figure out the three-dimensional structure of these receptors. They also tested the effects of dozens of mutations to deepen their understanding of how the receptors work.

The researchers showed that both melatonin receptors contain narrow channels embedded in the cell’s fatty membranes. These channels only allow melatonin, which can exist happily in both water and fat, to pass through, preventing serotonin, which has a similar structure but is only happy in watery environments, from binding to the receptor. They also uncovered how some much larger compounds only target MT1 despite the structural similarities between the two receptors. (Greg Stewart/SLAC National Accelerator Laboratory)

In addition to discovering tiny, gatekeeping melatonin channels in the receptors, the researchers were able to map Type 2 diabetes-associated mutations onto the MT2 receptor, for the first time seeing the exact location of these mutations in the receptor.

Laying the groundwork

In these experiments, the researchers only looked at compounds that activate the receptors, known as agonists. To follow up, they hope to map the receptors bound to antagonists, which block the receptors. They also hope to use their techniques to investigate other GPCR receptors in the body.

“As a structural biologist, it was exciting to see the structure of these receptors for the first time and analyze them to understand how these receptors selectively recognize their signaling molecules,” Cherezov said. “We’ve known about them for decades but until now no one could say how they actually look. Now we can analyze them to understand how they recognize specific molecules, which we hope lays the groundwork for better, more effective drugs.”

The team also included researchers from the University of North Carolina at Chapel Hill; Stanford University; Arizona State University; the University of Lille in France; and the University at Buffalo. LCLS is a DOE Office of Science user facility. This research was largely supported by the National Institutes of Health and the National Science Foundation BioXFEL Science and Technology Center.

See the full article here .

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SLAC/LCLS

SLAC/LCLS II projected view

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From SLAC National Accelerator Lab: “Capturing the behavior of single-atom catalysts on the move”

From SLAC National Accelerator Lab

April 23, 2019
Glennda Chui

A new study precisely controlled the attachment of platinum atoms (white balls) to a titanium dioxide surface (latticework of red and blue balls). It found that their positions varied from being deeply embedded in the surface (lower left) to standing almost free of the surface (upper right). This change in position affected the atoms’ ability to catalyze a chemical reaction that converts carbon monoxide to carbon dioxide (upper right). (Greg Stewart, SLAC National Accelerator Laboratory)

Scientists are excited by the prospect of stripping catalysts down to single atoms. Attached by the millions to a supporting surface, they could offer the ultimate in speed and specificity.

Now researchers have taken an important step toward understanding single-atom catalysts by deliberately tweaking how they’re attached to the surfaces that support them – in this case the surfaces of nanoparticles. They attached one platinum atom to each nanoparticle and observed how changing the chemistry of the particle’s surface and the nature of the attachment affected how keen the atom was to catalyze reactions.

Key experiments for the study took place at the Department of Energy’s SLAC National Accelerator Laboratory, and the results were reported in Nature Materials yesterday.

“We believe this is the first time the reactivity of a metallic single-atom catalyst has been traced to a specific way of attaching it to a particular supporting structure. This study is also unique in systematically controlling that attachment,” said Simon R. Bare, a distinguished staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and a co-author of the study.

SLAC/SSRL

“This is an important scientific breakthrough, and understanding on a fundamental level how the structure relates to the reactivity will ultimately allow us to design catalysts to be much more efficient. There is a huge number of people working on this problem.”

Harsh treatment, good results

Bare and other SLAC scientists were part of a previous study at SSRL [Nature Catalysis] that found that individual iridium atoms could catalyze a particular reaction up to 25 times more efficiently than the iridium nanoparticles used today, which contain 50 to 100 atoms.

This latest study was led by Associate Professor Phillip Christopher of the University of California, Santa Barbara. It looked at individual atoms of platinum that were attached to separate nanoparticles of titanium dioxide in his lab. While this approach would probably not be practical in a chemical plant or in your car’s catalytic converter, it did give the research team exquisitely fine control of where the atoms were placed and of the environment immediately around them, Bare said.

Researchers gave the nanoparticles chemical treatments – either harsh or mild – and used SSRL’s X-rays to observe how those treatments changed where and how the platinum atoms attached to the surface.

Meanwhile, scientists at the University of California, Irvine directly observed the attachments and positions of the platinum atoms with electron microscopes, and researchers at UC-Santa Barbara measured how active the platinum atoms were in catalyzing reactions.

Breaking through the surface

A platinum atom has six binding sites where it can hook up with other atoms. In untreated nanoparticles, the atoms were buried in the surface and firmly bound to six oxygen atoms each; they had no free binding sites that could grab other atoms and start a catalytic reaction.

In mildly treated particles, the platinum atoms emerged from the surface and were bound to just four oxygen atoms apiece, leaving them two free binding sites and the potential for more catalytic activity.

And in harshly treated particles, the atoms clung to the surface by only two bonds, leaving four binding sites free. When the researchers tested the ability of the variously treated nanoparticles to catalyze a reaction where carbon monoxide combines with oxygen to form carbon dioxide – the same reaction that takes place in a car’s catalytic converter – this one came out on top, Bare said, with five times greater activity than the others.

“While this study shows the importance of understanding the dynamic nature of catalysts,” Christopher said, “the next challenge will be to translate the findings to industrially relevant systems.”

SSRL is a DOE Office of Science user facility. The changing positions of the platinum atoms on the particle surfaces were imaged and observed with transmission electron microscopy using state-of-the-art facilities recently established at the Irvine Materials Research Institute (IMRI) at UC-Irvine. Detailed experimental insights obtained in the study were correlated with predictions made by theorists at the University of Milano-Bicocca in Italy.

See the full article here .

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Please help promote STEM in your local schools.

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SLAC/LCLS

SLAC/LCLS II projected view

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From SLAC National Accelerator Lab: “A day in the life of a midnight beam master”

From SLAC National Accelerator Lab

April 16, 2019 [Just today 4.23.19 in social media]
Angela Anderson

In SLAC’s accelerator control room, shift lead Ben Ripman and a team of operators fine-tune X-ray beams for science experiments around the clock.

When is a day not a day? When you work in the central nervous system of the world’s longest linear accelerator, open 24-7.

“There’s a constant cycle of people coming and going,” says Ben Ripman, an operations engineer at the Department of Energy’s SLAC National Accelerator Laboratory.

Ben Ripman, operations engineer at the SLAC accelerator control room (Angela Anderson/SLAC National Accelerator Laboratory)

He might start at 8 a.m., at 4 p.m. or at midnight. But the shift rotations are no barrier to his passion for the job – leading a team of control room operators who deliver brilliant X-ray beams for scientific experiments.

Control room operators spend most of their workdays (or nights) in a room filled with monitors, three deep and crowded with numbers, charts and graphs. Those displays track the status of thousands of devices and systems in the linear accelerator that runs through a tunnel below Highway 280 and feeds SLAC’s X-ray laser, the Linac Coherent Light Source (LCLS).

SLAC/LCLS

The accelerator boosts electrons to almost the speed of light and then wiggles them between magnets to generate X-rays. That X-ray light is formed into pulses and optimized for materials science, biology, chemistry, and physics experiments.

The entire operation is monitored in the control room, which also serves SPEAR3, the accelerator that produces X-rays for the Stanford Synchrotron Radiation Lightsource (SSRL).

SLAC SPEAR3

SLAC/SSRL

Another set of monitors, staffed by SLAC Facilities, tracks water, compressed air and electricity systems that serve the lab campus.

Ripman and his fellow operators are experts in reading these digital vital signs. But they are also some of the most knowledgeable people at the lab when it comes to the entire physical machine.

“We know the accelerator from beginning to end,” he says. “When an operator adjusts something from the control room, they can picture that machine part and what it is doing.”

For LCLS, they measure the amount of energy in individual X-ray pulses being fed to experimental hutches and often spend hours improving the pulses: tweaking magnets, adjusting the undulators, tuning the shape and length of the electron bunches.

Some days the control room is quiet, and the operators focus on training and individual projects. On other, more challenging days when the machine is running in exotic modes, they work elbow to elbow with physicists.

“We love this machine, but the accelerator was built decades ago and can be cantankerous,” Ripman explains. “When things do go wrong, it’s like a game of pickup sticks – one problem triggers another and you need to know how it all fits together.”

An important part of the job is knowing who to call for help. “We wake up a lot of people in the middle of the night,” Ripman says with a smile.

Control room operators also make sure everyone who goes into the accelerator tunnel stays safe.

There are two ways to get into the accelerator. For minor repairs and inspections, people take keys from special key banks that block the accelerator from turning on until all the keys have been returned. On official maintenance days, the doors are thrown open.

“On those days, maintenance crews, engineers and physicists descend into the tunnel and swarm the machine to resolve as many issues as possible before we have to summon them out again,” Ripman says. “We search the machine to make sure everyone is out before it’s turned back on.”

Almost all of the displays in the control room were designed by the operators, he says. “We are known to hide ‘Easter eggs’ in them, but you have to get in our good graces to find out about them.”

New operators take more than a year to get trained and proficient, Ripman says. “People come with a physics degree, but there is not a lot of formal coursework you can take on accelerator operations – it’s a lot of on-the-job training.”

It was that hands-on learning that drew him to the job in 2010.

“I was a nerd in high school,” Ripman admits proudly, “Stephen Hawking was my hero.” After studying physics and astronomy in college, Ripman worked as a contractor for NASA before joining SLAC. On his off hours, he plays board games and travels several times a year for card tournaments. He also loves hiking, skiing and snowboarding, and is a member of the Stanford University Singers.

His favorite thing about the job? “My coworkers,” he says. “I have the privilege of working with smart, fun, quirky people. We all get along quite well, and there’s a great camaraderie.”

Operators leave sticky notes with jokes or short messages for the next shift and share stories about their days and nights in the accelerator’s brain.

Like the one about a ghost calling from an abandoned tunnel. But that’s a tale for another night…

LCLS and SSRL are DOE Office of Science user facilities.

See the full article here .

five-ways-keep-your-child-safe-school-shootings
Please help promote STEM in your local schools.

Stem Education Coalition

SLAC/LCLS

SLAC/LCLS II projected view

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.