Advanced Light Source (ALS) – Page 9

ALS passes the 7000-protein milestone

2018/05/302018/06/11

The eight structural biology beamlines at the ALS have now collectively deposited over 7000 proteins into the Protein Data Bank (PDB), a worldwide, open-access repository of protein structures. The 7000th ALS protein structure (entry no. 6C7C) is an enzyme from Mycobacterium ulcerans (strain Agy99), solved with data from Beamline 5.0.2. This bacterium produces a toxin that eats away at skin tissue, causing what’s known as Buruli ulcers (Google at your own risk!). The bacterium is antibiotic-resistant, and treatment involves the surgical removal of infected tissues, including amputation.

The enzyme structure was solved by a group from the Seattle Structural Genomics Center for Infectious Disease (SSGID), whose mission is to obtain crystal structures of potential drug targets on the priority pathogen list of the National Institute of Allergy and Infectious Diseases (NIAID). As of May 2018, SSGCID has deposited 1090 structures in the PDB, with data for more than a quarter of those collected at ALS beamlines.

Image: PDB 6C7C: Enoyl-CoA hydratase, an enzyme from M. ulcerans (strain Agy99).

Rational optimization of organic solar-cell materials

2018/05/222018/06/07

The work suggests a way to quickly identify ideal material mixtures and processing methods, bypassing trial-and-error strategies and minimizing labor-intensive synthesis.

To generate electricity from light, the photoactive layer of an organic solar cell (OSC) must allow the photoexcitation and separation of charges, something that can happen in blends of electron-donating and electron-accepting organic materials. Not surprisingly, such blends have been created in steady succession with the goal of improving device efficiency.

However, there are over a thousand combinations of electron donors and acceptors available for use in OSCs and countless processing variations. The reliance on trial and error to identify the best materials and methods is a serious limitation. A way to predict device efficiency based on easily measurable or derivable parameters would go a long way toward streamlining the process.

Image: (extract) Artistic interpretation of an organic solar-cell mixture containing a blend of polymers and fullerenes. Interactions between these molecules (represented by the interaction parameter, χ) affect the degree of mixing that occurs, which in turn is key to device performance.

Respiratory virus study points to likely vaccine target

2018/05/142018/05/21

The work provides a promising route for designing a vaccine effective against a broad range of RSV strains, which cause serious respiratory disease in infants and older adults.

Respiratory syncytial virus (RSV) causes 118,000 deaths in young children each year worldwide and 57,000 hospitalizations of children each year in the United States alone. Attempts to develop a vaccine—at first based on inoculations with inactivated virus, and then targeting a key viral surface protein (RSV F)—have failed. Recent studies, however, suggest that a second viral surface protein (RSV G) is a promising target.

In one earlier study, elevated concentrations of antibodies targeting both RSV F and RSV G were associated with lower clinical disease severity scores, despite a substantially lower absolute abundance of anti-G antibodies. Another study found that higher levels of maternal anti-G antibodies correlated with less severe disease in infants (up to 4-6 months of age), even though anti-G antibodies were again found in lower concentrations.

While the RSV F surface protein allows the virus to enter a host cell, RSV G is what allows the virus to stick to lung cells and distort immune responses. This disruption of the immune response by RSV G might explain why vaccines based on RSV F have failed. Thus, a protective antibody response that blocks RSV G activity could be more effective, but scientists didn’t know how antibodies target RSV G at the molecular level.

>Read more on the ALS website.

Image: Stanislav Fedechkin and Rebecca DuBois.
Credit: C. Lagattuta/UC Santa Cruz

Monovalent Manganese for High-Performance Batteries

2018/04/192018/04/30

The discovery enables the design of a high-performance, low-cost battery that, according to its developers, outperforms Department of Energy goals on cost and cycle life for grid-scale energy storage.

The widespread deployment of renewable energy sources such as solar and wind power destabilizes the electric grid because conventional power-generation systems cannot ramp quickly enough to balance the power variations from these intermittent sources. Storing energy in batteries could help to even things out, but the cost of most existing technologies—including lithium-ion batteries—is significant, hindering grid-scale applications.

Emerging storage technologies such as aqueous sodium (Na) systems offer low costs for long-duration storage, but they do not have the charge/discharge rates needed to balance volatile power generation. In particular, it remains a critical challenge to develop a stable negative electrode (anode) for high-rate Na-ion battery systems.

A battery breakthrough

Compared with the relatively mature designs of anodes used in Li-ion batteries, anodes for Na-ion batteries remain an active focus of research and development. Natron Energy (formerly Alveo Energy), a battery-technology company based in Santa Clara, California, developed an unconventional anode design using a blend of elements chemically similar to the paint pigment known as Prussian blue.

Image: Atomic structure of an electrode material, manganese hexacyanomanganate (MnHCMn), that achieved high performance in a sodium-ion battery. The open framework contains large interstices and channels that allow sodium (Na) ions to move in and out with near-zero strain. Manganese (Mn) ions form the corners of the cage: Mn(N) has six nitrogen nearest neighbors and Mn(C) has six carbon nearest neighbors.

Toward control of spin states for molecular electronics

2018/04/172018/04/19

The results represent a major step toward the goal of programmable, nanoscale molecular electronics for high-speed, low-power, logic and memory applications.

To squeeze more information into smaller spaces, we will need to downsize from microchips to the nanoscale: the molecular level. Compared to bulk silicon, organic molecules have many advantages when used as building blocks for memory and logic components. They can be implemented as flexible thin films, they can be easily printed, and their potential switching speed is high, while their power requirements are low. But the field of molecular spintronics is still very young, and before its promise can be realized, scientists need a fuller understanding of the fundamental physics in play.

A molecule with crossover appeal

In the molecule studied here—[Fe{H₂B(pz)₂}₂(bipy)]—the spin state is determined by the configuration of the central metal’s outer electrons (i.e., the Fe d-orbital electrons). The presence of the surrounding organic ligands splits the Fe d orbitals. If the splitting is large, the electrons will pair up in the lower orbitals (a low-spin state). If the splitting is small, the electrons can spread out over both levels (a high-spin state). For some classes of molecules, transitions from low- to high-spin states (and vice versa) can be triggered. This “spin crossover” phenomenon is a promising functionality that may be suitable for application in molecular spintronic devices.

>Read more on the ALS website

Image: The molecule studied in this work is a metal–organic coordination complex, i.e., a molecule with a transition metal (iron) at the center, surrounded by organic compounds (“ligands”). The molecular formula is [Fe{H₂B(pz)₂}₂(bipy)], where pz = pyrazol-1-yl and bipy = 2,2′-bipyridine. This picture shows a ball-and-stick model (see more here)

Scientists develop sugar-coated nanosheets to target pathogens

2018/03/292018/04/12

Molecular Foundry-designed 2-D sheets mimic the surface of cells

Researchers have developed a process for creating ultrathin, self-assembling sheets of synthetic materials that can function like designer flypaper in selectively binding with viruses, bacteria, and other pathogens.
In this way the new platform, developed by a team led by scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), could potentially be used to inactivate or detect pathogens.

The team, which also included researchers from New York University, created the synthesized nanosheets at Berkeley Lab’s Molecular Foundry, a nanoscale science center, out of self-assembling, bio-inspired polymers known as peptoids. The study was published earlier this month in the journal ACS Nano.
The sheets were designed to present simple sugars in a patterned way along their surfaces, and these sugars, in turn, were demonstrated to selectively bind with several proteins, including one associated with the Shiga toxin, which causes dysentery. Because the outside of our cells are flat and covered with sugars, these 2-D nanosheets can effectively mimic cell surfaces.

Image: A molecular model of a peptoid nanosheet shows loop structures in sugars (orange) that bind to the Shiga toxin (shown as a five-color bound structure at upper right).
Credit: Berkeley Lab

Secretary of Energy visits Berkeley Lab

2018/03/272018/04/16

Secretary of Energy Rick Perry visited Berkeley Lab on March 27, stopping at the Advanced Light Source, Molecular Foundry, NERSC, and ESnet.

Secretary of Energy Rick Perry visited the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) today, getting a firsthand view of how Berkeley Lab combines team science with world-class facilities to develop solutions for the scientific, energy, and technological challenges facing the nation.

As the top official at the Department of Energy, Perry oversees Berkeley Lab and the 16 other DOE national laboratories that form the backbone of the nation’s scientific infrastructure.

His visit began with a welcome and brief introduction to Berkeley Lab, followed by tours of several of the Lab’s DOE Office of Science user facilities, which provide state-of-the-art resources for scientists across the nation and around the world. After the tour, Perry addressed the Berkeley Lab community in a town hall meeting that was livestreamed to Lab staff.

“One of the things that I enjoy as much about this job as anything, is going and telling the uninitiated about what’s happening at the national labs in this country. Your engagement in the future of the sciences, in innovation and knowledge, is invaluable,” said Secretary Perry at the town hall.

Image: The Advanced Light Source, synchrotron facility the Secretary of Energy Rick Perry visited on March 274th 2018.

Phase diagram leads the way to tailored metamaterial responses

2018/03/262018/04/12

This unique combination of material, methods, and results could lead to a paradigm shift in the design of metamaterial devices that manipulate light.

A metamaterial is an artificial material with repeating elements that enable it to reflect, transmit, or scatter waves (typically light) in ways that natural materials cannot. For example, a hypothetical “cloaking device” might be based on a metamaterial that can adaptively bend a wide spectrum of light waves around an object, making it invisible to an observer.

More pragmatically, metamaterials can be used to make lots of things—antennas, computers, batteries, solar cells—smaller and/or more efficient. The more we know about how electrons move in a material, the easier it is to engineer it into a metamaterial, where interactions between light (electromagnetic waves) and plasmons (collective electron waves) can be manipulated to produce a desired result.

Image: In one part of the study, SINS data was obtained at three locations on the SmS surface: (1) the region of maximum local strain, (2) a transition region adjacent to the maximum strain, and (3) an unstrained region.

COSMIC impact: next-gen X-ray microscopy platform now operational

2018/03/21

A next-generation X-ray beamline now operating at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) brings together a unique set of capabilities to measure the properties of materials at the nanoscale.

Called COSMIC, for Coherent Scattering and Microscopy, this X-ray beamline at Berkeley Lab’s Berkeley Lab’s Advanced Light Source (ALS) allows scientists to probe working batteries and other active chemical reactions, and to reveal new details about magnetism and correlated electronic materials.
COSMIC has two branches that focus on different types of X-ray experiments: one for X-ray imaging experiments and one for scattering experiments. In both cases, X-rays interact with a sample and are measured in a way that provides, structural, chemical, electronic, or magnetic information about samples.

The beamline is also intended as an important technological bridge toward the planned ALS upgrade, dubbed ALS-U, that would maximize its capabilities.

Image: X-rays strike a scintillator material at the COSMIC beamline, causing it to glow.
Credit: Simon Morton/Berkeley Lab

Tuning the electronic structure of a 2D material

2018/03/162018/03/23

Stacked 2D materials possess an array of tunable properties that are expected to be important for future applications in electronics and optics.

When some atomically thin—or 2D—materials are stacked like Lego bricks in different combinations with other ultrathin materials, new properties often emerge that are potentially useful for next-generation device applications. For example, tungsten disulfide (WS₂) is a semiconductor that belongs to a family of 2D materials (transition-metal dichalcogenides, or TMDs) that have received an enormous amount of interest due to their many advantageous properties that can be tuned by mixing and matching them in stacks with other 2D materials.

In this work, single-layer WS₂ was stacked on a thin flake of hexagonal boron nitride (h-BN), all on a base of titanium dioxide (TiO₂). This heterostructure provided a stable, non-interacting platform that enabled a team of researchers to directly and accurately probe the WS₂ electronic states and excitations, including the effects of interactions between the electrons themselves (many-body effects), at a level of detail not previously possible.

MAESTRO’s exquisite sensitivity

MAESTRO (Microscopic and Electronic Structure Observatory), a facility at ALS Beamline 7.0.2 that opened to scientists in 2016, can handle very small sample sizes, on the order of tens of microns, which is key to studying 2D materials. Scientists are continuing to push MAESTRO’s capabilities to study even smaller features—down to the nanoscale. The endstation also features the ability to fabricate and manipulate samples for x-ray studies while maintaining pristine conditions that protect them from contamination.

Image: Rendering of the atomic structure of a 2D layer of tungsten disulfide, or WS₂ (blue and yellow), on top of layers of 2D boron nitride (silver and gold). Above that is a representation of the WS₂ conduction band (pink-edged metallic surface) and valence bands (green- and blue-edged metallic surfaces). The results of this experiment suggest that the observed increase in valence-band splitting could be due to the presence of “trions,” exotic three-particle combinations of holes and electrons (red circles), in the conduction and valence bands. The background shows the raw WS₂ electronic-structure data, as measured in the experiment.
Credit: Chris Jozwiak/Berkeley Lab

Study suggests water may exist in Earth’s lower mantle

2018/03/162018/03/16

Water on Earth runs deep – very deep. The oceans have been measured to a maximum depth of 7 miles, though water is known to exist well below the oceans. Just how deep this hidden water reaches, and how much of it exists, are the subjects of ongoing research.

Now a new study suggests that water may be more common than expected at extreme depths approaching 400 miles and possibly beyond – within Earth’s lower mantle. The study, which appeared March 8 in the journal Science, explored microscopic pockets of a trapped form of crystallized water molecules in a sampling of diamonds from around the world.

Diamond samples from locations in Africa and China were studied through a variety of techniques, including a method using infrared light at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). Researchers used Berkeley Lab’s Advanced Light Source (ALS), and Argonne National Laboratory’s Advanced Photon Source, which are research centers known as synchrotron facilities.

Photo: Oliver Tschauner, professor of research in the Department of Geoscience at the University of Nevada, Las Vegas, holds a diamond sample during a recent round of experiments at Berkeley Lab’s Advanced Light Source.
Credit: Marilyn Chung/Berkeley Lab

Possible Path to the Formation of Life’s Building Blocks in Space

2018/03/052018/03/08

Experiments at Berkeley Lab’s Advanced Light Source reveal how a hydrocarbon called pyrene could form near stars

Scientists have used lab experiments to retrace the chemical steps leading to the creation of complex hydrocarbons in space, showing pathways to forming 2-D carbon-based nanostructures in a mix of heated gases.

The latest study, which featured experiments at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), could help explain the presence of pyrene, which is a chemical compound known as a polycyclic aromatic hydrocarbon, and similar compounds in some meteorites.

A team of scientists, including researchers from Berkeley Lab and UC Berkeley, participated in the study, published March 5 in the Nature Astronomy journal. The study was led by scientists at the University of Hawaii at Manoa and also involved theoretical chemists at Florida International University.

Image: A researcher handles a fragment and a test tube sample of the Murchison meteorite, which has been shown to contain a a variety of hydrocarbons and amino acids, in this photo from a previous, unrelated study at Argonne National Laboratory. Experiments at Berkeley Lab are helping to retrace the chemical steps by which complex hydrocarbons like pyrene could form in the Murchison meteorite and other meteorites.
Credit: Argonne National Laboratory

Scientists confirm speculation on the chemistry of a high-performance battery

2018/02/282018/03/05

X-ray experiments at Berkeley Lab reveal what’s at work in an unconventional electrode.

Scientists have discovered a novel chemical state of the element manganese. This chemical state, first proposed about 90 years ago, enables a high-performance, low-cost sodium-ion battery that could quickly and efficiently store and distribute energy produced by solar panels and wind turbines across the electrical grid.

This direct proof of a previously unconfirmed charge state in a manganese-containing battery component could inspire new avenues of exploration for battery innovations.

X-ray experiments at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) were key in the discovery. The study results were published Feb. 28 in the journal Nature Communications.

Scientists at Berkeley Lab and New York University participated in the study, which was led by researchers at Natron Energy, formerly Alveo Energy, a Santa Clara, California-based battery technology company.

The battery that Natron Energy supplied for the study features an unconventional design for an anode, which is one of its two electrodes. Compared with the relatively mature designs of anodes used in lithium-ion batteries, anodes for sodium-ion batteries remain an active focus of R&D.

Photo: An array of solar panels and windmills.
Credit: PxHere

Unraveling the Complexities of Auto-Oxidation

2018/02/232018/03/07

A better understanding of auto-oxidation reaction mechanisms could lead to better engines, less air pollution, and improved climate models.

Oxygen plays a key role in chemical reactions that produce pollutants in the atmosphere and that fuel combustion engines. In these reactions, auto-oxidation (spontaneous oxidation in air or in the presence of oxygen) produces highly oxygenated molecules.

For example, volatile organic compounds (VOCs)—gas molecules emitted from vehicles, factories, and power plants (as well as living plants)—undergo a sequence of auto-oxidation reactions with the surrounding air, forming highly oxygenated molecules that contribute to air pollution, affecting health and climate. The same highly oxygenated molecules are also produced during the ignition of fuels in advanced combustion engines; controlling their formation and destruction processes can help to develop higher-efficiency engines.

However, because these highly oxygenated molecules are very reactive and decompose quickly, determining their identities has been difficult.

>Read more on the ALS website

Image: Illustration of the jet-stirred reactor used in this experiment. Jet nozzles in the reaction chamber (center) generate turbulence for mixing the incoming fuel molecules with oxidizer (lower right). After the fuels react, the products exit the apparatus (upper left) to be analyzed by advanced mass spectrometry.
Credit: Ahmed Najjar

Tuning magnetic frustration in a dipolar trident lattice

2018/02/212018/02/22

Frustrated interactions are key to a wide range of phenomena, from protein folding and magnetic memory to fundamental studies of emergent exotic states.

Geometrical frustration and “spin ice”

When bar magnets are brought together, opposite poles will attract and like poles will repel, and the magnets will arrange themselves accordingly, to minimize energy. However, if the magnets are constrained to a lattice structure where each one has just two possible orientations, some magnets could end up geometrically “frustrated,” with neither orientation being lower in energy than the other. The system becomes what’s known as a “spin ice,” analogous to water ice, which retains intrinsic randomness (residual entropy) even at absolute zero.

Systems incorporating geometrical frustration are fascinating because their hard-to-predict behavior is key to a wide range of phenomena, from protein folding and magnetic memory to the emergence of exotic states of matter. For example, the emergence of magnetic monopole–like excitations in spin ice raises the intriguing possibility of “magnetic-charge” circuitry based on currents of magnetic monopole excitations.

Image: (extract, entire image here) Magnetic scattering patterns calculated from XMCD data for various lattice parameters. While relatively sharp peaks indicative of long-range order are seen in (a) and (c), the diffuse patterns in (b) indicate highly disordered configurations.

The microstructure of a parrotfish tooth contributes to its toughness

2018/02/082018/02/15

During a 2012 visit to the Great Barrier Reef off the coast of Australia, ALS staff scientist Matthew Marcus became intrigued with parrotfish. “I was reminded that this is a fish that crunches up coral all day and is responsible for much of the white sand on beaches,” Marcus said. “But how can this fish eat coral and not lose its teeth?” So Marcus teamed up with Pupa Gilbert, a biophysicist at the University of Wisconsin–Madison, and an international team of researchers she assembled, to understand how parrotfish teeth work.

Because conventional microscopes can overlook the unique orientation of crystals in tooth enamel, the team used the technique called polarization-dependent imaging contrast (PIC) mapping that Gilbert invented, which uses the photoemission electron microscopy (PEEM) Beamline 11.0.1 at the ALS. The PIC maps allowed them to visualize the orientation of individual crystals of fluorapatite, the main mineral component of parrotfish teeth.

Separate experiments used tomography (Beamline 8.3.2) and microdiffraction (Beamline 12.3.2) to further analyze the crystal orientations and strains in the teeth.

>Read more on the ALS website

Image: (extract) PIC maps acquired at the tips of four different parrotfish teeth show that they consist of 100-nm-wide, microns-long crystals, bundled into “fibers” interwoven like warp and weft fibers in fabric. These fibers gradually decrease in average diameter from 5 μm at the back of a tooth to 2 μm at the tip. Intriguingly, this decrease in size is spatially correlated with an increase in hardness and stiffness. The orientation angle of the crystals is color-coded (chart at bottom).