Project Director Dave Robin announces ALS-U project beamlines

Over the past year, a process involving ALS and ALS-U staff, the ALS user community, and external advisory committees has been ongoing to select the insertion-device beamlines that will be built and upgraded within the scope of the ALS-U Project. These beamlines will join existing ALS beamlines to form the full complement of capabilities that will be available at the upgraded ALS in several years. I am delighted to inform you that the selection process is now complete and to announce the result.

The ALS-U Project will build two new beamlines

  • a soft x-ray beamline in Sector 10, dubbed “FLEXON,” whose high-brightness coherent flux and multiple complementary techniques will probe the roles of multiscale heterogeneity in quantum materials; and
  • a tender x-ray beamline in Sector 8, whose coherent scattering and scanning spectromicroscopy capabilities will address challenges at the frontiers of diverse scientific areas, ranging from soft condensed matter and biomaterials to energy science and Earth and environmental sciences.

>Read more on the Advanced Light Source website

Image: ALS-U Project Director Dave Robin.

Award for a pioneer in synchrotron techniques and tools

Zahid Hussain is honored with the Secretary’s Distinguished Service Award during a surprise ceremony.

Zahid Hussain, a longtime scientist at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), has always been more focused on achievements than accolades, though his lists run long in both categories.

His fingerprints are on many of the instruments and scientific milestones at Berkeley Lab’s Advanced Light Source (ALS), which produces many types of light, from infrared to X-rays, for a range of experiments carried out by visiting scientists from around the world. He has pioneered soft X-ray techniques and instrumentation at the ALS that have been widely adopted by the global scientific community.

>Read more on the Advanced Light Source (ALS) at Berkeley Lab

A two-pronged defense against bacterial self-intoxication

Researchers solved the structure of a bacterial toxin bound to a neutralizing protein, revealing two distinct mechanisms for how the toxin-producing bacteria avoid poisoning themselves.

Microbial communities are of fundamental importance to virtually all natural ecosystems, from the ocean floor to the gastrointestinal tract. Although the term “communities” implies cooperation, scientists now realize that bacterial colonies compete with each other for life-sustaining resources, availing themselves of a variety of strategies to reduce overcrowding. In some cases, they secrete toxins in their fight for survival. Here, researchers studied one such toxin from the bacterium Serratia proteamaculans, various strains of which live inside tree roots or inhabit the digestive tracts of insects and other animals.

Toxin targets cell division

The researchers showed that the toxin, Tre1, targets a bacterial protein, FtsZ, which is analogous to tubulin in human cells. Tubulin molecules are the building blocks of microtubules—long polymers that provide structure and shape to our cells and play an important role in cell division. In bacteria, FtsZ loses the ability to polymerize when attacked by the Tre1 toxin. Instead of dividing, the intoxicated cells grow longer and longer until they eventually split open and die (cellular elongation and lysis).

>Read more on the Advanced Light Source website

Image: Healthy bacteria (left) and bacteria (right) whose cell-division machinery has been disrupted by a toxin newly discovered in some bacterial arsenals.
Credit: Mougous Lab

Topological matters: toward a new kind of transistor

X-ray experiments at Berkeley Lab provide first demonstration of room temperature switching in ultrathin material that could serve as a ‘topological transistor’

Billions of tiny transistors supply the processing power in modern smartphones, controlling the flow of electrons with rapid on-and-off switching. But continual progress in packing more transistors into smaller devices is pushing toward the physical limits of conventional materials. Common inefficiencies in transistor materials cause energy loss that results in heat buildup and shorter battery life, so researchers are in hot pursuit of alternative materials that allow devices to operate more efficiently at lower power.
Now, an experiment conducted at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has demonstrated, for the first time, electronic switching in an exotic, ultrathin material that can carry a charge with nearly zero loss at room temperature. Researchers demonstrated this switching when subjecting the material to a low-current electric field.

>Read more on Advanced Light Source (ALS) at LBNL website

Image: James Collins, a researcher at Monash University in Australia, works on an experiment at Beamline 10.0.1, part of Berkeley Lab’s Advanced Light Source.
Credit: Marilyn Chung/Berkeley Lab

Toward a blueprint for anti-influenza drugs

The structures provide an atomic-level blueprint from which to design more effective anti-influenza drugs that can overcome growing drug resistance.

Influenza virus infection is a perennial problem. According to the Centers for Disease Control and Prevention, the 2017-18 flu season saw high levels of emergency-department visits for influenza-like illness, high influenza-related hospitalization rates, and elevated and geographically widespread influenza activity for an extended period.

Although yearly vaccinations can reduce the number of flu infections, these vaccines are able to target only a subset of viral strains—there is, as yet, no “universal vaccine.” As a result, there is still a need for antiviral drugs to treat the illness after infection has occurred. This is especially important for groups of people who can experience serious complications from the flu, such as those with respiratory diseases or immune disorders. In recent years, however, resistance to certain classes of antiviral drugs has become a problem.

>Read more on the Advanced Light Source website

Image: Molecular dynamics simulation of a drug molecule, amantadine (cyan sticks), in the M2 proton channel. The drug’s ammonium group (blue tip) mimics hydronium, stabilizing the drug molecule in a position to block the channel.

Tunable ferromagnetism in a 2D material at room temperature

Breakthroughs in next-generation spintronic logic and memory devices could hinge on our ability to control spin behavior in two-dimensional materials—stacks of ultrathin layers held together by relatively weak electrostatic (van der Waals) forces. The reduced dimensionality of these so-called “van der Waals materials” often leads to tunable electronic and magnetic properties, including intrinsic ferromagnetism. However, it remains a challenge to tune this ferromagnetism (e.g. spin orientation, magnetic domain phase, and magnetic long-range order) at ambient temperatures.

In this work, researchers performed a study of Fe3GeTe2, a van der Waals material that consists of Fe3Ge layers alternating with two Te layers. The material’s magnetic properties were characterized using a variety of techniques, including x-ray absorption spectroscopy (XAS) with x-ray magnetic circular dichroism (XMCD) contrast at Beamline 6.3.1 and photoemission electron microscopy (PEEM) at Beamline 11.0.1.

>Read more on the Advanced Light Source (ALS) at LBNL website

Image: PEEM images for unpatterned and patterned Fe3GeTe2 samples at 110 K and 300 K. The unpatterned samples formed stripe domains at 110 K, which disappeared at 300 K. The patterned samples formed out-of-plane stripe domains at 110 K and transitioned to in-plane vortex states at 300 K, demonstrating control over magnetism at room temperature and beyond.

Researchers create most complete high-res atomic movie of photosynthesis to date

In a major step forward, SLAC’s X-ray laser captures all four stable states of the process that produces the oxygen we breathe, as well as fleeting steps in between. The work opens doors to understanding the past and creating a greener future.

Despite its role in shaping life as we know it, many aspects of photosynthesis remain a mystery. An international collaboration between scientists at SLAC National Accelerator Laboratory, Lawrence Berkeley National Laboratory and several other institutions is working to change that. The researchers used SLAC’s Linac Coherent Light Source (LCLS) X-ray laser to capture the most complete and highest-resolution picture to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe. The results were published in Nature today.

Explosion of life

When Earth formed about 4.5 billion years ago, the planet’s landscape was almost nothing like what it is today. Junko Yano, one of the authors of the study and a senior scientist at Berkeley Lab, describes it as “hellish.” Meteors sizzled through a carbon dioxide-rich atmosphere and volcanoes flooded the surface with magmatic seas.
Over the next 2.5 billion years, water vapor accumulating in the air started to rain down and form oceans where the very first life appeared in the form of single-celled organisms. But it wasn’t until one of those specks of life mutated and developed the ability to harness light from the sun and turn it into energy, releasing oxygen molecules from water in the process, that Earth started to evolve into the planet it is today. This process, oxygenic photosynthesis, is considered one of nature’s crown jewels and has remained relatively unchanged in the more than 2 billion years since it emerged.

>Read more on the SLAC website (for LCLS)
>Read also the article on the Berkeley website (for ALS)

Image: Using SLAC’s X-ray laser, researchers have captured the most complete high-res atomic movie to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe.
Credit: Gregory Stewart, SLAC National Accelerator Laboratory)

Expanding the infrared nanospectroscopy window

The ability to investigate heterogeneous materials at nanometer scales and far-infrared energies will benefit a wide range of fields, from condensed matter physics to biology.

Scientific studies require tools that match the natural length and energy scales of the phenomena under investigation. For many questions in biology, quantum materials, and electronics, this means nanometer spatial resolution combined with far-infrared energies. For example, scientists might want to study collective electron oscillations in quantum materials for optoelectronic circuits, or the characteristic vibration modes of protein molecules in biological systems.

A recently developed infrared technique—synchrotron infrared nanospectroscopy (SINS)—combines broadband synchrotron light with atomic-force microscopes to enable infrared imaging and spectroscopy at the nanoscale. However, the technique could only be used in a narrow range of the electromagnetic spectrum that excluded far-infrared wavelengths, due to a scarcity of suitable light sources and detectors for that range. In this work, researchers extended SINS to far-infrared wavelengths, opening up a whole new experimental regime.

> Read more on the Advanced Lightsource at Berkeley Lab website

Image: Left: Nanoscale images of SiO2 hole array, obtained using atomic-force microscopy (AFM, top) and synchrotron infrared nanospectroscopy (SINS, bottom), demonstrating SINS contrast between patterned SiO2 and underlying Si substrate with ~30 nm spatial resolution (inset). Scale bar = 200 nm. Right: SINS broadband spectroscopic data for SiO2, taken along dotted line in images at left, showing amplitude (top) and phase (bottom) information from asymmetric  Si–O stretching (1200 cm–1) and bending (460 cm–1) modes. The lower-energy bending mode had previously been inaccessible with this technique.

Targeting bacteria that cause meningitis and sepsis

The work provides molecular-level information about how the antibody confers broad immunity against a variable target and suggests strategies for further improvement of available vaccines.

Our central nervous systems (brain and spinal cord) are surrounded by three membranes called “meninges.” Meningitis is caused by the swelling of these membranes, resulting in headache, fever, and neck stiffness. Most cases of meningitis in the United States are the result of viral infections and are relatively mild. However, meningitis caused by bacterial infection, if left untreated, can be deadly or lead to serious complications, including hearing loss and neurologic damage.

The bacterium responsible for meningitis (Neisseria meningitidis) can also infect the bloodstream, causing another life-threatening condition known as sepsis. N. meningitidis is spread through close contact (coughing or kissing) or lengthy contact (e.g. in dorm rooms or military barracks). In this work, researchers were interested in understanding how humans develop immunity to bacterial meningitis and sepsis, collectively known as meningococcal disease, by vaccination with a new protein-based vaccine.

>Read more on the Advanced Light Source website

Image: The work provides molecular-level information about how the antibody confers broad immunity against a variable target and suggests strategies for further improvement of available vaccines.

2018 ALS User Meeting Highlights

Past, present, and future converged at the ALS User Meeting, held October 2–4, 2018. About 480 registrants helped celebrate the 25th anniversary of first light at the ALS and the announcement of CD-1 approval for the ALS Upgrade project (ALS-U), a major federal milestone. Users’ Executive Committee (UEC) Chair Will Chueh kicked things off by acknowledging the organizers—UEC members Jennifer Ciezak-Jenkins, Alex Frañó, and Michael Jacobs—and thanking the ALS for its support. He also explained the organizing principle behind the program: to engage student and young-scientist users and strengthen interactions between users in general. Jeff Neaton, Berkeley Lab’s Associate Laboratory Director for Energy Sciences, then extended an official welcome to attendees. He noted that it’s been an exciting year for the ALS, which gained a new director, Steve Kevan, in addition to CD-1 approval for ALS-U.

>Read more on the Advanced Light Source website

Image: Plenary session, Day 1.
Credit: Peter DaSilva/Berkeley Lab

New clues to cut through the mystery of Titan’s atmospheric haze

A team including Berkeley Lab scientists homes in on a ‘missing link’ in Titan’s one-of-a-kind chemistry.

Saturn’s largest moon, Titan, is unique among all moons in our solar system for its dense and nitrogen-rich atmosphere that also contains hydrocarbons and other compounds, and the story behind the formation of this rich chemical mix has been the source of some scientific debate.
Now, a research collaboration involving scientists in the Chemical Sciences Division at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has zeroed in on a low-temperature chemical mechanism that may have driven the formation of multiple-ringed molecules – the precursors to more complex chemistry now found in the moon’s brown-orange haze layer.
The study, co-led by Ralf Kaiser at the University of Hawaii at Manoa and published in the Oct. 8 edition of the journal Nature Astronomy, runs counter to theories that high-temperature reaction mechanisms are required to produce the chemical makeup that satellite missions have observed in Titan’s atmosphere.

>Read more on the Advanced Light Source/Berkeley Lab website

Image: The atmospheric haze of Titan, Saturn’s largest moon (pictured here along Saturn’s midsection), is captured in this natural-color image (box at left). A study that involved experiments at Berkeley Lab’s Advanced Light Source has provided new clues about the chemical steps that may have produced this haze.
Credits: NASA Jet Propulsion Laboratory, Space Science Institute, Caltech

Advanced Light Source upgrade project moves forward

An upgrade of Berkeley Lab’s X-ray facility clears next stage in federal approval process.

The Advanced Light Source (ALS), a scientific user facility at the Department of Energy’s (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab), has received federal approval to proceed with preliminary design, planning and R&D work for a major upgrade project that will boost the brightness of its X-ray beams at least a hundredfold.

The upgrade will give the ALS, which this year celebrates its 25th anniversary, brighter beams with a more ordered structure – like evenly spaced ripples in a pond – that will better reveal nanoscale details in complex chemical reactions and in new materials, expanding the envelope for scientific exploration.
“This upgrade will make it possible for Berkeley Lab to be the leader in soft X-ray research for another 25 years, and for the ALS to remain at the center of this Laboratory for that time,” said Berkeley Lab Director Mike Witherell.

Steve Kevan, ALS Director, added, “The upgrade will transform the ALS. It will expand our scientific frontiers, enabling studies of materials and phenomena that are at the edge of our understanding today. And it will renew the ALS’s innovative spirit, attracting the best researchers from around the world to our facility to conduct their experiments in collaboration with our scientists.”

>Read more on the Advanced Light Source website

Image: A computer rendering providing a top view of the ALS and shows equipment that will be installed during the ALS-U project.
Credit: Berkeley Lab

X-rays uncover a hidden property that leads to failure in a lithium-ion battery material

Experiments at SLAC and Berkeley Lab uproot long-held assumptions and will inform future battery design.

Over the past three decades, lithium-ion batteries, rechargeable batteries that move lithium ions back and forth to charge and discharge, have enabled smaller devices that juice up faster and last longer.
Now, X-ray experiments at the Department of Energy’s SLAC National Accelerator Laboratory and Lawrence Berkeley National Laboratory have revealed that the pathways lithium ions take through a common battery material are more complex than previously thought. The results correct more than two decades worth of assumptions about the material and will help improve battery design, potentially leading to a new generation of lithium-ion batteries.

An international team of researchers, led by William Chueh, a faculty scientist at SLAC’s Stanford Institute for Materials & Energy Sciences and a Stanford materials science professor, published these findings today in Nature Materials.
“Before, it was kind of like a black box,” said Martin Bazant, a professor at the Massachusetts Institute of Technology and another leader of the study. “You could see that the material worked pretty well and certain additives seemed to help, but you couldn’t tell exactly where the lithium ions go in every step of the process. You could only try to develop a theory and work backwards from measurements. With new instruments and measurement techniques, we’re starting to have a more rigorous scientific understanding of how these things actually work.”

>Read more on the SLAC website

Image: When lithium ions flow into the battery’s solid electrode – illustrated here in hexagonal slices – the lithium can rearrange itself, causing the ions to clump together into hot spots that end up shortening the battery lifetime.
Credit: Stanford University/3Dgraphic

Structure reveals mechanism behind periodic paralysis

The results suggest possible drug designs that could provide relief to patients with a genetic disorder that causes them to be overcome suddenly with profound muscle weakness.

A rare genetic disorder called hypokalemic periodic paralysis (hypoPP) causes sudden, profound muscle weakness in people who occasionally exhibit low levels of potassium in their blood, or hypokalemia. When a patient is hypokalemic, hypoPP affects the function of the muscles responsible for skeletal movement. The disease has been known to stem from mutations in certain membrane proteins that channel and regulate the flow of sodium into cells. Exactly how the mutation affects the proteins’ function, however, was not known.

In earlier work, researchers from the Catterall Lab at the University of Washington had solved the structure of a sodium channel called NavAb from a prokaryote (single-celled organism). As a next step, the group decided to see if NavAb could serve as a model for studying the mutations that cause hypoPP in humans (eukaryotes), with the goal of finding a way to prevent or treat this disorder.

A leak in the pipe?

In a resting state, muscle-cell membranes keep potassium ions and sodium ions separated, inside and outside the cell, respectively, creating a voltage across the membrane. A chemical signal from a nerve cell sets off a cascade of events that results in sodium ions flowing into the cell, changing the membrane potential and and ultimately triggering muscle contraction.

>Read more on the Advanced Light Source website

Image: Three states of the voltage-sensing domain (VSD) of a membrane-channel protein. In the normal state, the water-accessible space (magenta) does not extend through the channel, preventing sodium (gray spheres) from passing through. In the disease state, a clear passage allows sodium to leak through, resulting in muscle paralysis. In the “rescued” state, the binding of guanidinium (blue and yellow spheres) effectively closes the channel and blocks sodium leakage. The red sphere represents the location of the disease-causing mutation. The side-chain sticks represent the voltage sensors of the sodium channel.

Infrared beams show cell types in a different light

Berkeley Lab scientists developing new system to identify cell differences.

By shining highly focused infrared light on living cells, scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) hope to unmask individual cell identities, and to diagnose whether the cells are diseased or healthy.
They will use their technique to produce detailed, color-based maps of individual cells and collections of cells – in microscopic and eventually nanoscale detail – that will be analyzed using machine-learning techniques to automatically sort out cell characteristics.

Using microscopic color maps to unlock cell identity

Their focus is on developing a rapid way to easily identify cell types, and features within cells, to aid in biological and medical research by providing a way to probe living cells in their native environment without harming the cells or requiring obtrusive cell-labeling techniques.
“This is totally noninvasive,” said Cynthia McMurray, a biochemist and senior scientist in Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) Division who is leading this new imaging effort with Michael Martin, a physicist and senior staff scientist at Berkeley Lab’s Advanced Light Source (ALS).
The ALS has dozens of beamlines that produce beams of intensely focused light, from infrared to X-rays, for a broad range of experiments.

>Read more on the Advanced Light Source website

Image: From left to right: Aris Polyzos, Edward Barnard, and Lila Lovergne, pictured here at Berkeley Lab’s Advanced Light Source, are part of a research team that is developing a cell-identification technique based on infrared imaging and machine learning.
Credit: Marilyn Chung/Berkeley Lab

Graphene-Based Catalyst Improves Peroxide Production

Hydrogen peroxide is an important commodity chemical with a growing demand in many areas, including the electronics industry, wastewater treatment, and paper recycling.

Hydrogen peroxide (H2O2) is a common household chemical, well known for its effectiveness at whitening and disinfecting. It’s also a valuable commodity chemical used to etch circuit boards, treat wastewater, and bleach paper and pulp—a market expected to grow as demand for recycled paper products increases.

Compared to chlorine-based bleaches, hydrogen peroxide is more environmentally benign: the only degradation product of its use is water. However, it’s currently produced through a multistep chemical reaction that consumes significant amounts of energy, generates substantial waste, and requires a catalyst of palladium—a rare and expensive metal. Furthermore, the transport and storage of bulk hydrogen peroxide can be hazardous, making local, on-demand production highly desirable.

Better living through electrochemistry

Scientists seek a way to generate hydrogen peroxide electrochemically—by a much simpler process called the oxygen reduction reaction (ORR). This reaction takes oxygen from the air and combines it with water and two electrons to produce H2O2. If this reaction could be efficiently catalyzed, it could enable the disinfection of water at remote locations, or during disaster recovery, using hydrogen peroxide made from local air and water. For this work, the researchers focused on hydrogen peroxide synthesis in alkaline environments, where the reaction bath can be used directly, such as for bleaching or the treatment of acidic waste streams.

>Read more on the Advanced Light Source website

Image: The production of hydrogen peroxide (H2O2) from oxygen (O2) was efficiently catalyzed by graphene oxide, a form of graphene characterized by various oxygen defects that act as centers for catalytic activity. Depicted are two types of defects: one in which an oxygen atom bridges two carbon atoms above the graphene plane, and one where oxygen atoms replace carbon atoms within the graphene plane.